Fabricating high-performance, binder-free biomaterials from microalgae grown during wastewater treatment is an opportunity in sustainable materials. However, the impact of strain morphology and mechanical preprocessing on material properties remains largely uncharacterized. This study investigates binder-free biomaterials fabricated from wastewater-grown, filamentous Tribonema minus and food-grade, unicellular Chlorella vulgaris. The impact of three mechanical comminution methods (ball mill, mortar-and-pestle, and speed mixer) on the mechanical properties is evaluated. The results demonstrate that feedstock morphology and processing are critical, interacting factors. Under gentle comminution (mortar-and-pestle), filamentous Tribonema biomaterials exhibit significantly higher flexural modulus and strength than unicellular Chlorella. Conversely, high-shear speed mixing diminishes Tribonema's structural advantage while enhancing Chlorella's particle packing, leading to a convergence in mechanical properties. All final biomaterials exhibit near-hydrophobic surfaces (contact angles > 85°). This research validates that non-food-competing wastewater algae can be transformed into high-performance biomaterials, yielding materials with densities of ≈1.0–1.1 g/cm3 and flexural moduli ranging from ≈0.3 to 1.0 GPa.
\nMarine viruses impact biogeochemical cycles through cell lysis, releasing organic matter and nutrients that fuel ocean productivity. Identifying and quantifying the specific viruses active in these processes remain a priority in the field. Here, we introduce a click-chemistry method to fluorescently label, sort, and sequence the genomes of newly produced viral particles (viral progeny) released from transcriptionally active host microbial cells, alongside the analysis of co-occurring inactive cells and pre-existing viruses in environmental samples. This approach, called viral bioorthogonal noncanonical amino acid tagging (BONCAT)-fluorescence-activated cell sorting (FACS), combines BONCAT with environmental sample incubation, followed by single-virus and single-cell sorting by flow cytometry (FACS). Genomic analysis of translationally active cells and new viral progeny in coastal seawater incubations confirmed BONCAT labeling and successful sorting of diverse marine bacteria, microeukaryotic cells, and virioplankton, with stark differences in the predicted turnover of specific groups of infecting viruses, including pelagiphages, methylophages, a Flavobacteriales-associated novel “Far-T4” clade, noncanonical DNA viruses of Naomiviridae using dU instead of dT, algae-infecting giant NCLDV viruses, and parasitic virophages. Sequenced BONCAT-active cells showed a strong enrichment in viral contigs relative to the inactive cell fraction, suggestive of a large proportion of translationally active virocells. This study illustrates the effectiveness of viral BONCAT-FACS for uncovering genome-resolved virus–host dynamics. By providing a direct approach for tracking active viral infections in natural environments, this method enhances our ability to investigate behavior and interactions of these nanoscale predators, expanding our understanding of their role in ecosystem dynamics.
", "doi": "10.1093/ismeco/ycag048", "issn": "2730-6151", "publisher": "Oxford University Press (OUP)", "publication": "ISME Communications", "publication_date": "2026-03-31", "series_number": "1", "volume": "6", "issue": "1", "pages": "ycag048" }, { "id": "authors:6re17-4gj06", "collection": "authors", "collection_id": "6re17-4gj06", "cite_using_url": "https://authors.library.caltech.edu/records/6re17-4gj06", "type": "article", "title": "Microbially mediated carbon utilization by a cold-water coral inhabiting methane seeps", "author": [ { "family_name": "Stabbins", "given_name": "April" }, { "family_name": "Goffredi", "given_name": "Shana", "orcid": "0000-0002-9110-9591" }, { "family_name": "Gasbarro", "given_name": "Ryan" }, { "family_name": "Dawson", "given_name": "Katherine", "orcid": "0000-0001-8856-4609" }, { "family_name": "Magyar", "given_name": "John", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Glazier", "given_name": "Amanda" }, { "family_name": "Meinert", "given_name": "Kelly" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Cordes", "given_name": "Erik" } ], "abstract": "Deep-sea methane seeps fuel biodiverse habitats sustained by the release of hydrocarbon-rich fluids and associated microbial activity. Here, we describe the ecology of a seep-associated cold-water coral and provide evidence of its associations with chemosynthetic bacteria. High-resolution seafloor surveys revealed that the distribution of this coral was predominantly confined to actively seeping zones, and habitat suitability models confirmed that proximity to active seepage was an important factor influencing the coral’s distribution. Stable carbon-isotope values were consistent with a nutritional strategy incorporating chemosynthetically derived carbon, likely as a supplement to suspension feeding on photosynthetically derived material. Microbial metabarcoding confirmed the presence of both thiotrophic and methanotrophic bacteria, including SUP05 and MMG-2 groups. Incubations with 13C-labelled methane further revealed this species may also be capable of assimilating methane-derived carbon into its biomass. These findings provide new evidence of a previously underrecognized facultative symbiosis between cold-water corals and chemosymbiotic bacteria and suggest that these corals are not restricted to the periphery of seep habitats. Instead, they may exploit microbial associations, including contributions from both thiotrophic and potentially methanotrophic taxa, to persist in actively seeping areas.
\nMarine viruses impact biogeochemical cycles through cell lysis, releasing organic matter and nutrients that fuel ocean productivity. Identifying and quantifying the specific viruses active in these processes remains a priority in the field. Here, we introduce a click-chemistry method to fluorescently label, sort, and sequence the genomes of newly produced viral particles (viral progeny) released from transcriptionally active host microbial cells, alongside the analysis of co-occurring inactive cells and pre-existing viruses in environmental samples. This approach, called viral BONCAT-FACS, combines biorthogonal non-canonical amino acid tagging (BONCAT) with environmental sample incubation, followed by single-virus and single-cell sorting by flow cytometry (FACS). Genomic analysis of translationally-active cells and new viral progeny in coastal seawater incubations confirmed BONCAT labelling and successful sorting of diverse marine bacteria, microeukaryotic cells, and virioplankton, with stark differences in the predicted turnover of specific groups of infecting viruses, including Pelagiphages, Methylophages, a Flavobacteriales-associated novel \"Far-T4\" clade, non-canonical DNA viruses of Naomiviridae using dU instead of dT, algae-infecting giant NCLDV viruses, and parasitic virophages. Sequenced BONCAT-active cells showed a strong enrichment in viral contigs relative to the inactive cell fraction, suggestive of a large proportion of translationally-active virocells. This study illustrates the effectiveness of viral BONCAT-FACS for uncovering genome-resolved virus-host dynamics. By providing a direct approach for tracking active viral infections in natural environments, this method enhances our ability to investigate behavior and interactions of these nanoscale predators, expanding our understanding of their role in ecosystem dynamics.
", "doi": "10.1093/ismeco/ycag048", "issn": "2730-6151", "publisher": "Oxford University Press (OUP)", "publication": "ISME Communications", "publication_date": "2026-03-06", "pages": "ycag048" }, { "id": "authors:mp9ma-sg018", "collection": "authors", "collection_id": "mp9ma-sg018", "cite_using_url": "https://authors.library.caltech.edu/records/mp9ma-sg018", "type": "article", "title": "Microbially mediated carbon utilization by a cold-water coral inhabiting methane seeps", "author": [ { "family_name": "Stabbins", "given_name": "April" }, { "family_name": "Goffredi", "given_name": "Shana", "orcid": "0000-0002-9110-9591" }, { "family_name": "Gasbarro", "given_name": "Ryan" }, { "family_name": "Dawson", "given_name": "Katherine", "orcid": "0000-0001-8856-4609" }, { "family_name": "Magyar", "given_name": "John", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Glazier", "given_name": "Amanda" }, { "family_name": "Meinert", "given_name": "Kelly" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Cordes", "given_name": "Erik" } ], "abstract": "Deep-sea methane seeps fuel biodiverse habitats sustained by the release of hydrocarbon-rich fluids and associated microbial activity. Here, we describe the ecology of a seep-associated cold-water coral and provide evidence of its associations with chemosynthetic bacteria. High-resolution seafloor surveys revealed that the distribution of this coral was predominantly confined to actively seeping zones, and habitat suitability models confirmed that proximity to active seepage was an important factor influencing the coral’s distribution. Stable carbon-isotope values were consistent with a nutritional strategy incorporating chemosynthetically derived carbon, likely as a supplement to suspension feeding on photosynthetically derived material. Microbial metabarcoding confirmed the presence of both thiotrophic and methanotrophic bacteria, including SUP05 and MMG-2 groups. Incubations with 13C-labelled methane further revealed this species may also be capable of assimilating methane-derived carbon into its biomass. These findings provide new evidence of a previously underrecognized facultative symbiosis between cold-water corals and chemosymbiotic bacteria and suggest that these corals are not restricted to the periphery of seep habitats. Instead, they may exploit microbial associations, including contributions from both thiotrophic and potentially methanotrophic taxa, to persist in actively seeping areas.
\nAt methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.
", "doi": "10.1093/ismejo/wraf153", "pmcid": "PMC12422003", "issn": "1751-7362", "publisher": "Oxford University Press (OUP)", "publication": "The ISME Journal", "publication_date": "2025-09-05", "series_number": "1", "volume": "19", "issue": "1", "pages": "wraf153" }, { "id": "authors:meq7v-4kw32", "collection": "authors", "collection_id": "meq7v-4kw32", "cite_using_url": "https://authors.library.caltech.edu/records/meq7v-4kw32", "type": "article", "title": "Spatial evidence of cryptic methane cycling and methylotrophic metabolisms along a land\u2013ocean transect in salt marsh sediment", "author": [ { "family_name": "Krause", "given_name": "Sebastian J.E.", "orcid": "0000-0001-5541-3337" }, { "family_name": "Wipfler", "given_name": "Rebecca", "orcid": "0000-0003-0602-1753", "clpid": "Wipfler-Rebecca" }, { "family_name": "Liu", "given_name": "Jiarui", "orcid": "0000-0003-4878-6578" }, { "family_name": "Yousavich", "given_name": "David J.", "orcid": "0000-0002-3420-9019" }, { "family_name": "Robinson", "given_name": "DeMarcus", "orcid": "0000-0002-0745-1109" }, { "family_name": "Hoyt", "given_name": "David W.", "orcid": "0000-0002-2857-719X" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Treude", "given_name": "Tina", "orcid": "0000-0001-6366-286X" } ], "abstract": "Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane. While direct interspecies electron transport is proposed to enable ANME/SRB symbiosis, its electrochemical properties remain uncharacterized. Here, using sediment-free enrichment cultures, we measured the electron transport capabilities of marine consortia under physiological conditions. Diverse ANME/SRB consortia exhibited high dry conductance close to electrogenic biofilms. This conductance diminished upon exposure to heat or oxygen but was preserved following paraformaldehyde fixation, indicating a biomolecular origin for this electric charge transfer. Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively. Generator-collector measurements further demonstrated that these redox components facilitate electron transport over micrometer-scale distances, sufficient to link archaeal and bacterial partners. Collectively, our results establish that marine ANME/SRB symbiosis uses redox conduction, consistent with multiheme cytochrome c, for direct interspecies electron transport.
", "doi": "10.1126/sciadv.adw4289", "pmcid": "PMC12372872", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2025-08-22", "series_number": "34", "volume": "11", "issue": "34", "pages": "eadw4289" }, { "id": "authors:ez5sy-z9v96", "collection": "authors", "collection_id": "ez5sy-z9v96", "cite_using_url": "https://authors.library.caltech.edu/records/ez5sy-z9v96", "type": "article", "title": "Preparation of Cuvette-Based Sorters for Sorting Submicron Microbial Cells and Viruses from Environmental and Biological Samples", "author": [ { "family_name": "Tijerina", "given_name": "Jamie C.", "orcid": "0009-0007-5089-9332", "clpid": "Tijerina-Jamie-C" }, { "family_name": "Martinez\u2010Hernandez", "given_name": "Francisco", "orcid": "0000-0002-2590-3834", "clpid": "Martinez\u2010Hernandez-Francisco" }, { "family_name": "Beilinson", "given_name": "Vera", "orcid": "0000-0002-1259-733X", "clpid": "Beilinson-Vera" }, { "family_name": "Finney", "given_name": "Olivia", "orcid": "0009-0005-5139-661X", "clpid": "Finney-Olivia" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Diamond", "given_name": "Rochelle A.", "orcid": "0009-0000-8684-8173", "clpid": "Diamond-Rochelle-A" } ], "abstract": "This protocol set focuses on the preparation of the BD FACSAria II/III/Fusion, a cuvette\u2010based cell sorting system commonly found in shared resource settings, to sort submicron samples, including but not limited to virus\u2010like particles (VLPs) and bacteria. This is meant to serve as a proven workflow for staff in general shared resource laboratories (SRL) and individual labs. It is also useful for labs purchasing cuvette\u2010based sorters with similar fluidic paths to the FACSAria Fusion from BD Biosciences, such as the BD FACSSymphony S6 and BD FACSDiscover S8, as well as for specialized SRLs that will need to move away from Influx and MoFlo platforms that are approaching end of life. VLPs and submicron\u2010sized cells (e.g., ultramicrobacteria and archaea) are found at or near the limit of detection of most flow cytometers and cell sorters. With VLPs, the small quantity of DNA recovered requires amplification before downstream sequencing. Thorough cleaning of the fluidic system and careful sample preparation are necessary both to improve detection and to prevent genomic contamination from amplifiable free DNA or microorganisms. These protocols include instructions for the preparation of sheath fluid, decontamination of the cell sorter, and removal from the fluidic system of free DNA and endotoxin that could interfere with the high\u2010throughput amplification and sequencing of the target DNA in downstream processes. To minimize noise when sorting submicron\u2010sized samples, clean PBS filtered with a 0.1\u2010µm\u2010pore\u2010size filter is prepared, minimizing microbubbles and particulates; use of commercially available sheath fluids is not recommended, as they contain preservatives and surfactants that can affect microbial viability and are not filtered at the optimal pore size for this experimentation. In addition, detailed steps are provided for cleaning the instrument, tanks, and related media to prepare the sort, along with guidance for setting up the software, voltages, and gating strategies for successful experiments.
\nBasic Protocol 1: Preparation of the BD FACSAria II/III/Fusion cell sorter fluidics and software to perform sorts for validation by culture or microscopyBasic Protocol 2: Preparation of the BD FACSAria II/III/Fusion cell sorter fluidics and software to perform sorts for high\u2010throughput whole\u2010genome amplification and genomic sequencingSupport Protocol 1: Autoclaving the BD FACSAria II/III/Fusion stainless\u2010steel sheath tankSupport Protocol 2: Chemical decontamination and maintenance of the BD FACSAria II/III/Fusion stainless\u2010steel sheath fluid tankSupport Protocol 3: Preparation of 1 L of 1× PBSSupport Protocol 4: Inspection of the BD FACSAria II/III/Fusion cell sorter for contaminationSupport Protocol 5: Manual aseptic sorting procedure using BD FACSAria II/III/Fusion cell sorterSupport Protocol 6: Chemical decontamination and maintenance of the BD FACSAria II/III/Fusion wet cart containersSupport Protocol 7: Preparation of 1× PBS/0.1% (v/v) Tween 20 (PBST)Support Protocol 8: Preparation of DNA\u2010free liquids and solutionsSupport Protocol 9: Cleaning of the BD FACSAria II/III/Fusion nozzle by sonication.
", "doi": "10.1002/cpz1.70176", "issn": "2691-1299", "publisher": "Wiley", "publication": "Current Protocols", "publication_date": "2025-08", "series_number": "8", "volume": "5", "issue": "8", "pages": "e70176" }, { "id": "authors:4d18s-xm327", "collection": "authors", "collection_id": "4d18s-xm327", "cite_using_url": "https://authors.library.caltech.edu/records/4d18s-xm327", "type": "article", "title": "Targeted genomic analysis of a predominant uncultured marine pelagiphage-host model via microfluidics and semipermeable capsule technology", "author": [ { "family_name": "Martinez-Garcia", "given_name": "Manuel", "orcid": "0000-0001-5056-1525" }, { "family_name": "Lluesma-Gomez", "given_name": "Monica" }, { "family_name": "Perez-Martin", "given_name": "Laura" }, { "family_name": "Rubio-Portillo", "given_name": "Esther", "orcid": "0000-0002-5602-5333" }, { "family_name": "Martin-Cuadrado", "given_name": "Ana Belen", "orcid": "0000-0002-0063-8181" }, { "family_name": "Nadal-Molero", "given_name": "Francisco", "orcid": "0000-0002-9396-2596" }, { "family_name": "Escolano-Vico", "given_name": "Aitana" }, { "family_name": "Sanchez", "given_name": "Fernando Santos" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Ant\u00f3n", "given_name": "Josefa", "orcid": "0000-0002-5823-493X" } ], "abstract": "Microbes and their viruses drive central biogeochemical cycles on a global scale. Understanding the biology and ecology of virus–host interactions and their impact on ecosystems depends on our ability to develop tools that enable high-throughput screening of ecologically relevant, uncultured virus–host pairs. Viruses infecting Pelagibacterales, the predominant bacteria in surface oceans, have been studied through computational analyses and cultivation efforts. Here, we employ an accessible microfluidics and semi-permeable capsule (SPC) technology to investigate the uncultured pelagiphage vSAG 37-F6–host interactions since it is one of the most abundant and ubiquitous viruses in the marine virosphere. First, we validated this technology using cultured virus–host pairs. Then, marine single cells were microfluidically encapsulated in SPCs, lysed, whole-genome amplified, and screened using fluorescent polymerase chain reaction (PCR) for the presence of a hallmark gene of vSAG 37-F6. Data indicate that ~30% of the targeted cell population (cell fraction ≤0.45 μm) contained the virus vSAG 37-F6-like. A total of ~500 putatively infected cells were sorted, combined, and sequenced. Data showed that most reads (~60%) and assembled genome fragments (~85%) were identified as viral, indicating that the sorted host cells were likely in the final stages of infection. Two major viral clusters were detected: one corresponding to vSAG 37-F6 and another mixed viral cluster consisting of cyanophages, pelagiphages, and vibriophages. A significant proportion of total reads (~20%) were assigned to Pelagibacter spp. TMED287, a bacterium reported to be abundant in the Mediterranean Sea. This flexible microfluidic-SPC technology holds enormous potential for exploring uncultured microbial and viral communities across various perspectives and microbiology fields.
", "doi": "10.1093/ismeco/ycaf123", "pmcid": "PMC12404659", "issn": "2730-6151", "publisher": "Oxford University Press (OUP)", "publication": "ISME Communications", "publication_date": "2025-07-17", "series_number": "1", "volume": "5", "issue": "1", "pages": "ycaf123" }, { "id": "authors:evb9f-3a841", "collection": "authors", "collection_id": "evb9f-3a841", "cite_using_url": "https://authors.library.caltech.edu/records/evb9f-3a841", "type": "article", "title": "Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea", "author": [ { "family_name": "Woods", "given_name": "Philip H.", "orcid": "0000-0003-1673-8096", "clpid": "Woods-Philip-H" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Laso-P\u00e9rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865" }, { "family_name": "Utter", "given_name": "Daniel R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Ruff", "given_name": "S. Emil", "orcid": "0000-0002-6872-6188" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, \"\n Candidatus\n Methanovorans\" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of\n hdrA\n homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in\n Methanovorans\n evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple\n Methanovorans\n genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.", "doi": "10.1126/sciadv.adq5232", "pmcid": "PMC12180501", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2025-06-20", "series_number": "25", "volume": "11", "issue": "25", "pages": "eadq5232" }, { "id": "authors:bz6mp-4wh10", "collection": "authors", "collection_id": "bz6mp-4wh10", "cite_using_url": "https://authors.library.caltech.edu/records/bz6mp-4wh10", "type": "article", "title": "Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura", "author": [ { "family_name": "Dal B\u00f3", "given_name": "Bianca", "orcid": "0009-0007-1691-8181" }, { "family_name": "Guo", "given_name": "Yongzhao", "orcid": "0009-0005-3983-8382", "clpid": "Guo-Yongzhao" }, { "family_name": "Mayr", "given_name": "Magdalena J.", "orcid": "0000-0002-3182-1480", "clpid": "Mayr-Magdalena-J" }, { "family_name": "Pereira", "given_name": "Olivia S." }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591" } ], "abstract": "Methane seeps harbor uncharacterized animal–microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane- and methanol-oxidizing bacteria on their exoskeleton. δ13C tissue isotope values of in situ specimens corroborated methane assimilation (−45‰, on average). Live animal incubations with 13C-labeled methane and methanol, followed by nanoscale secondary ion mass spectrometry, confirmed that carbon derived from both compounds was actively incorporated into the tissues within five days. Methano- and methylotrophs of the bacterial families Methylomonadaceae, Methylophagaceae and Methylophilaceae were abundant, based on environmental metagenomics and 16S rRNA sequencing, and fluorescence and electron microscopy confirmed dense epibiont aggregations on the sea spider exoskeleton. Egg sacs carried by the males hosted identical microbes suggesting vertical transmission. We propose that these sea spiders farm and feed on methanotrophic and methylotrophic bacteria, expanding the realm of animals known to harness C1 compounds as a carbon source. These findings advance our understanding of the biology of an understudied animal lineage, unlocking some of the unique nutritional links between the microbial and faunal food webs in the oceans.
", "doi": "10.1073/pnas.2501422122", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-06-16", "series_number": "26", "volume": "122", "issue": "26", "pages": "e2501422122" }, { "id": "authors:9x30e-z5459", "collection": "authors", "collection_id": "9x30e-z5459", "cite_using_url": "https://authors.library.caltech.edu/records/9x30e-z5459", "type": "article", "title": "CABO-16S\u2014a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples", "author": [ { "family_name": "Eitel", "given_name": "Eryn\u00a0M.", "orcid": "0009-0007-2391-9297", "clpid": "Eitel-Eryn-M" }, { "family_name": "Utter", "given_name": "Daniel\u00a0R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Connon", "given_name": "Stephanie\u00a0A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani" } ], "abstract": "Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by \"universal\" primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.
", "doi": "10.1093/nargab/lqaf061", "pmcid": "PMC12086536", "issn": "2631-9268", "publisher": "Oxford University Press (OUP)", "publication": "NAR Genomics and Bioinformatics", "publication_date": "2025-06", "series_number": "2", "volume": "7", "issue": "2", "pages": "lqaf061" }, { "id": "authors:0pyc2-zsz80", "collection": "authors", "collection_id": "0pyc2-zsz80", "cite_using_url": "https://authors.library.caltech.edu/records/0pyc2-zsz80", "type": "article", "title": "Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground", "author": [ { "family_name": "Quinn", "given_name": "Laura", "orcid": "0000-0002-6112-028X", "clpid": "Quinn-Laura" }, { "family_name": "Sharma", "given_name": "Kriti", "clpid": "Sharma-Kriti" }, { "family_name": "Faber", "given_name": "Katherine T", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Orphan", "given_name": "Victoria J", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here we generated microbially-compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex three-dimensional structure of sediments and rocks, by adapting a suspension-based freeze-casting technique commonly used in materials science. Fine-tuning of parameters such as freezing rate and choice of solvent provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity-tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and ¹³C enrichment in microorganisms, highlighting the potential to directly couple D\u2082O or ¹³C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant, using epifluorescence microscopy. The new tool presented here enables highly resolved, spatially explicit, and multi-modal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.
", "doi": "10.1093/pnasnexus/pgaf118", "issn": "2752-6542", "publisher": "National Academy of Sciences", "publication": "PNAS Nexus", "publication_date": "2025-04-16", "series_number": "5", "volume": "4", "issue": "5", "pages": "pgaf118" }, { "id": "authors:1f3ye-d0c36", "collection": "authors", "collection_id": "1f3ye-d0c36", "cite_using_url": "https://authors.library.caltech.edu/records/1f3ye-d0c36", "type": "article", "title": "Microbial Cycling of Sulfur and Other Redox-Sensitive Elements in Porewaters of San Clemente Basin, California, and Cocos Ridge, Costa Rica", "author": [ { "family_name": "Osorio-Rodriguez", "given_name": "Daniela", "orcid": "0000-0001-6676-4124", "clpid": "Osorio-Rodriguez-Daniela" }, { "family_name": "Pavia", "given_name": "Frank J.", "orcid": "0000-0003-3627-0179" }, { "family_name": "Utter", "given_name": "Daniel R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Quinan", "given_name": "Matthew", "orcid": "0000-0002-1158-9020" }, { "family_name": "Landry", "given_name": "Kameko" }, { "family_name": "Gomes", "given_name": "Maya" }, { "family_name": "Dalleska", "given_name": "Nathan D.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-Nathan-D" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re\u2010oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox\u2010sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid\u2010phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors.
", "doi": "10.1111/gbi.70013", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2025-02", "series_number": "1", "volume": "23", "issue": "1", "pages": "e70013" }, { "id": "authors:5y60a-wmb13", "collection": "authors", "collection_id": "5y60a-wmb13", "cite_using_url": "https://authors.library.caltech.edu/records/5y60a-wmb13", "type": "article", "title": "Isotopic evidence of acetate turnover in Precambrian continental fracture fluids", "author": [ { "family_name": "Mueller", "given_name": "Elliott P.", "orcid": "0000-0002-6837-0409", "clpid": "Mueller-Elliott-P" }, { "family_name": "Panehal", "given_name": "Juliann", "clpid": "Panehal-Juliann" }, { "family_name": "Meshoulam", "given_name": "Alexander", "orcid": "0009-0006-0566-0157", "clpid": "Meshoulam-Alexander" }, { "family_name": "Song", "given_name": "Min", "orcid": "0000-0002-3291-0282" }, { "family_name": "Hansen", "given_name": "Christian T." }, { "family_name": "Warr", "given_name": "Oliver", "orcid": "0000-0001-8240-7979" }, { "family_name": "Boettger", "given_name": "Jason", "orcid": "0000-0002-2853-8772" }, { "family_name": "Heuer", "given_name": "Verena B.", "orcid": "0000-0002-1856-116X" }, { "family_name": "Bach", "given_name": "Wolfgang", "orcid": "0000-0002-3099-7142" }, { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Lollar", "given_name": "Barbara Sherwood" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "abstract": "The deep continental crust represents a vast potential habitat for microbial life where its activity remains poorly constrained. Organic acids like acetate are common in these ecosystems, but their role in the subsurface carbon cycle - including the mechanism and rate of their turnover - is still unclear. Here, we develop an isotope-exchange 'clock' based on the abiotic equilibration of H-isotopes between acetate and water, which can be used to define the maximum in situ acetate residence time. We apply this technique to the fracture fluids in Birchtree and Kidd Creek mines within the Canadian Precambrian crust. At both sites, we find that acetate residence times are <1 million years and calculated a rate of turnover that could theoretically support microbial life. However, radiolytic water-rock reactions could also contribute to acetate production and degradation, a process that would have global relevance for the deep biosphere. More broadly, our study demonstrates the utility of isotope-exchange clocks in determining residence times of biomolecules with possible applications to other environments.
", "doi": "10.1038/s41467-024-53438-4", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2024-10-23", "series_number": "1", "volume": "15", "issue": "1", "pages": "9130" }, { "id": "authors:kv1bp-d3g98", "collection": "authors", "collection_id": "kv1bp-d3g98", "cite_using_url": "https://authors.library.caltech.edu/records/kv1bp-d3g98", "type": "article", "title": "Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California", "author": [ { "family_name": "Pe\u00f1a-Salinas", "given_name": "Manet E.", "orcid": "0000-0002-5835-0455" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Utter", "given_name": "Daniel R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Spelz", "given_name": "Ronald M.", "orcid": "0000-0002-9561-355X" }, { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" }, { "family_name": "Zierenberg", "given_name": "Robert", "orcid": "0000-0001-9384-7355" }, { "family_name": "Caress", "given_name": "David W.", "orcid": "0000-0002-6596-9133" }, { "family_name": "N\u00fa\u00f1ez", "given_name": "Patricia G.", "orcid": "0000-0001-9594-559X" }, { "family_name": "V\u00e1zquez", "given_name": "Roberto", "orcid": "0000-0002-3279-9764" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
", "doi": "10.7717/peerj.17724", "pmcid": "PMC11340630", "issn": "2167-8359", "publisher": "PeerJ", "publication": "PeerJ", "publication_date": "2024-08-19", "volume": "12", "pages": "e17724" }, { "id": "authors:8yqhw-jfm43", "collection": "authors", "collection_id": "8yqhw-jfm43", "cite_using_url": "https://authors.library.caltech.edu/records/8yqhw-jfm43", "type": "article", "title": "Editorial: Studies on life at the energetic edge \u2013 from laboratory experiments to field-based investigations, volume II", "author": [ { "family_name": "Hoehler", "given_name": "Tori M." }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776" }, { "family_name": "J\u00f8rgensen", "given_name": "Bo Barker", "orcid": "0000-0001-9398-8027" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Lever", "given_name": "Mark A." } ], "editor": [ { "family_name": "Teske", "given_name": "Andrea" } ], "abstract": "[Opening paragraph] Among the diverse inhabitants of Earth's biosphere, microorganisms reign supreme in their capabilities to occupy an expansive range of ecological niches. We often conceive of the fringes of our biosphere in terms of physicochemical “extremes”, but perhaps the most pervasive environmental challenge to microbial life is that of extreme energy limitation (Hoehler and Jørgensen, 2013; Lever et al., 2015; Bradley et al., 2020). Globally, for example, the marine deep biosphere occupies a volume and hosts a biomass comparable to that of the overlying oceans, yet that deep biosphere is sustained by an energy flux about 1,000 times lower (Hoehler et al., 2023). Both in the sub-seafloor and in the continental subsurface, these energy-starved organisms exist at the interface between the inhabited and uninhabited realms of our planet. To understand their physiology in the face of extreme energy limitation would, therefore, be to understand the capabilities and limitations of the ultimate arbiters of chemical exchange between the biosphere and the geosphere.
", "doi": "10.3389/fmicb.2023.1351761", "issn": "1664-302X", "publisher": "Frontiers Media SA", "publication": "Frontiers in Microbiology", "publication_date": "2024-01-03", "volume": "14" }, { "id": "authors:k1ay9-fht81", "collection": "authors", "collection_id": "k1ay9-fht81", "cite_using_url": "https://authors.library.caltech.edu/records/k1ay9-fht81", "type": "article", "title": "Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation", "author": [ { "family_name": "Osorio-Rodriguez", "given_name": "Daniela", "orcid": "0000-0001-6676-4124", "clpid": "Osorio-Rodriguez-Daniela" }, { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-Shawn-E" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-Anne-E" }, { "family_name": "Ellisman", "given_name": "Mark", "orcid": "0000-0001-8893-8455", "clpid": "Ellisman-Mark" }, { "family_name": "Deerinck", "given_name": "Tom", "clpid": "Deerinck-Tom" }, { "family_name": "Aristilde", "given_name": "Ludmilla", "orcid": "0000-0002-8566-1486", "clpid": "Aristilde-Ludmilla" }, { "family_name": "Grotzinger", "given_name": "John P.", "orcid": "0000-0001-9324-1257", "clpid": "Grotzinger-J-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM\u2014often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)\u2014are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4 , 1\u20139 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88 , e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48 , 862\u2013866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.
", "doi": "10.1073/pnas.2302156120", "pmcid": "PMC10743459", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2023-12-19", "series_number": "51", "volume": "120", "issue": "51", "pages": "e2302156120" }, { "id": "authors:rj6hx-mj965", "collection": "authors", "collection_id": "rj6hx-mj965", "cite_using_url": "https://authors.library.caltech.edu/records/rj6hx-mj965", "type": "article", "title": "Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities", "author": [ { "family_name": "Candry", "given_name": "Pieter", "orcid": "0000-0002-7784-3650", "clpid": "Candry-Pieter" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Caravajal-Arroyo", "given_name": "Jos\u00e9 Maria" }, { "family_name": "Lacoere", "given_name": "Tim", "clpid": "Lacoere-Tim" }, { "family_name": "Winkler", "given_name": "Mari-Karoliina Henriikka", "orcid": "0000-0002-8366-3293", "clpid": "Winkler-Mari-Karoliina-Henriikka" }, { "family_name": "Ganigu\u00e9", "given_name": "Ramon", "orcid": "0000-0002-9564-0195", "clpid": "Ganigu\u00e9-Ramon" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Rabaey", "given_name": "Korneel", "orcid": "0000-0001-8738-7778", "clpid": "Rabaey-Korneel" } ], "abstract": "Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150\u2013500\u2009\u00b5m of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of \u00b9\u2075N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.
", "doi": "10.1038/s41396-023-01508-8", "pmcid": "PMC10579388", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2023-11", "series_number": "11", "volume": "17", "issue": "11", "pages": "2014-2022" }, { "id": "authors:tse8x-ay919", "collection": "authors", "collection_id": "tse8x-ay919", "cite_using_url": "https://authors.library.caltech.edu/records/tse8x-ay919", "type": "article", "title": "Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea", "author": [ { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Laso-P\u00e8rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865", "clpid": "Laso-P\u00e8rez-Rafael" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Woyke", "given_name": "Tanja", "orcid": "0000-0002-9485-5637", "clpid": "Woyke-Tanja" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.", "doi": "10.1371/journal.pbio.3002292", "pmcid": "PMC10553843", "issn": "1545-7885", "publisher": "Public Library of Science", "publication": "PLOS Biology", "publication_date": "2023-09", "series_number": "9", "volume": "21", "issue": "9", "pages": "e3002292" }, { "id": "authors:bddjd-7q556", "collection": "authors", "collection_id": "bddjd-7q556", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230502-987371300.3", "type": "article", "title": "\u00b2H-\u00b2H clumping in molecular hydrogen method and preliminary results", "author": [ { "family_name": "Mangenot", "given_name": "Xavier", "orcid": "0000-0001-8770-6767", "clpid": "Mangenot-Xavier" }, { "family_name": "Xie", "given_name": "Hao", "orcid": "0000-0001-5656-2035", "clpid": "Xie-Hao" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Giunta", "given_name": "Thomas", "clpid": "Giunta-Thomas" }, { "family_name": "Lilley", "given_name": "Marvin", "clpid": "Lilley-Marvin" }, { "family_name": "Sissmann", "given_name": "Olivier", "orcid": "0000-0001-9372-1779", "clpid": "Sissmann-Olivier" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Schimmelmann", "given_name": "Arndt", "orcid": "0000-0003-4648-5253", "clpid": "Schimmelmann-Arndt" }, { "family_name": "Gaucher", "given_name": "Eric C.", "orcid": "0000-0002-7976-8455", "clpid": "Gaucher-Eric-C" }, { "family_name": "Girard", "given_name": "Jean-Pierre", "clpid": "Girard-Jean-Pierre" }, { "family_name": "Eiler", "given_name": "John", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "abstract": "We present a method for measuring the clumped isotope composition of molecular hydrogen (H\u2082) using a high-resolution mass spectrometer, the Thermo 253 Ultra, improved to address subtle artifacts arising from instrument baselines and non-linear responses. We also present methods for purification and concentration of H\u2082 from natural and experimental samples, tailored to this measurement. We document the accuracy of the method through comparison to established methods for the determination of \u03b4D values, and through measurements of H\u2082 gases of widely varying D content that were driven to isotopic equilibrium with respect to their distributions of isotopologues by heating in the presence of a catalyst. Experimental reproducibility of \u03b4D and \u0394DD values over months averages \u00b10.5 and \u00b1 6.9 \u2030, respectively (1\u03c3) \u2014 both small fractions of common natural variations. We explore methods of gas purification and handling, and show that preferred methods result in low (0\u20134 \u2030) changes in \u03b4D and undetectable changes in \u0394DD. Our methods and data processing procedures were further tested by comparing measurements of mixtures of H\u2082 gases that varied widely in \u03b4D and \u2206DD with a model describing proportions of isotopologues in such mixtures. Application of these methods to H\u2082 that is residual to laboratory consumption by cultured methanogens shows that metabolic 'back reaction' (metabolic production of H\u2082 from water-derived protons during net H2 consumption) is responsible for driving the \u0394DD value of residual H\u2082 toward equilibrium at environmental temperatures. Finally, we report the first measurements of the clumped isotope composition of molecular hydrogen in natural geological samples collected from high and low temperature submarine hydrothermal vents (Lost city, Rainbow, Ashadze) and an intracontinental natural reservoir in Mali; initial findings suggest that \u2206DD of H\u2082 generally records temperatures of fluid venting or long-term storage, even in cases where the \u03b4D of H\u2082 has not equilibrated with water at those temperatures. This study establishes the first clumped isotope systematics of molecular hydrogen based on both experimental and natural samples, including key processes in the biogeochemical cycle of H\u2082.", "doi": "10.1016/j.chemgeo.2022.121278", "issn": "0009-2541", "publisher": "Elsevier", "publication": "Chemical Geology", "publication_date": "2023-03-30", "volume": "621", "pages": "Art. No. 121278" }, { "id": "authors:tdxeh-7zh34", "collection": "authors", "collection_id": "tdxeh-7zh34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230215-866986000.1", "type": "article", "title": "Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome", "author": [ { "family_name": "Laso-P\u00e9rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865", "clpid": "Laso-P\u00e9rez-Rafael" }, { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Magyar", "given_name": "John S.", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Zhao", "given_name": "Kehan", "clpid": "Zhao-Kehan" }, { "family_name": "Krupovic", "given_name": "Mart", "orcid": "0000-0001-5486-0098", "clpid": "Krupovic-Mart" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus\u2013host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.", "doi": "10.1038/s41564-022-01297-4", "pmcid": "PMC9894754", "issn": "2058-5276", "publisher": "Nature Publishing Group", "publication": "Nature Microbiology", "publication_date": "2023-02", "series_number": "2", "volume": "8", "issue": "2", "pages": "231-245" }, { "id": "authors:h1gaq-80325", "collection": "authors", "collection_id": "h1gaq-80325", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230420-614686900.8", "type": "article", "title": "Gifts hidden in shadowy genome islands", "author": [ { "family_name": "Utter", "given_name": "D. R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Despite being typically perceived as \"clonal\" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.", "doi": "10.1016/j.cell.2022.12.001", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2023-01-05", "series_number": "1", "volume": "186", "issue": "1", "pages": "5-7" }, { "id": "authors:c9ep7-pzp47", "collection": "authors", "collection_id": "c9ep7-pzp47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221212-796746500.36", "type": "article", "title": "A Cristae-Like Microcompartment in Desulfobacterota", "author": [ { "family_name": "McGlynn", "given_name": "Shawn Erin", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-Shawn-Erin" }, { "family_name": "Perkins", "given_name": "Guy", "orcid": "0000-0002-1834-6646", "clpid": "Perkins-Guy" }, { "family_name": "Sim", "given_name": "Min Sub", "orcid": "0000-0002-3491-9002", "clpid": "Sim-Min-Sub" }, { "family_name": "Mackey", "given_name": "Mason", "clpid": "Mackey-Mason" }, { "family_name": "Deerinck", "given_name": "Thomas J.", "clpid": "Deerinck-Thomas-J" }, { "family_name": "Thor", "given_name": "Andrea", "clpid": "Thor-Andrea" }, { "family_name": "Phan", "given_name": "Sebastien", "orcid": "0000-0003-4261-6973", "clpid": "Phan-Sebastien" }, { "family_name": "Ballard", "given_name": "Daniel", "clpid": "Ballard-Daniel" }, { "family_name": "Ellisman", "given_name": "Mark H.", "orcid": "0000-0001-8893-8455", "clpid": "Ellisman-Mark-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Some Alphaproteobacteria contain intracytoplasmic membranes (ICMs) and proteins homologous to those responsible for the mitochondrial cristae, an observation which has given rise to the hypothesis that the Alphaproteobacteria endosymbiont had already evolved cristae-like structures and functions. However, our knowledge of microbial fine structure is still limited, leaving open the possibility of structurally homologous ICMs outside the Alphaproteobacteria. Here, we report on the detailed characterization of lamellar cristae-like ICMs in environmental sulfate-reducing Desulfobacterota that form syntrophic partnerships with anaerobic methane-oxidizing (ANME) archaea. These structures are junction-bound to the cytoplasmic membrane and resemble the form seen in the lamellar cristae of opisthokont mitochondria. Extending these observations, we also characterized similar structures in Desulfovibrio carbinolicus, a close relative of the magnetotactic D. magneticus, which does not contain magnetosomes. Despite a remarkable structural similarity, the key proteins involved in cristae formation have not yet been identified in Desulfobacterota, suggesting that an analogous, but not a homologous, protein organization system developed during the evolution of some members of Desulfobacterota.", "doi": "10.1128/mbio.01613-22", "pmcid": "PMC9764997", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2022-11-02", "series_number": "6", "volume": "13", "issue": "6", "pages": "Art. No. 01613-22" }, { "id": "authors:5rb33-34b68", "collection": "authors", "collection_id": "5rb33-34b68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220912-80857800", "type": "article", "title": "Anaerobic Degradation of Alkanes by Marine Archaea", "author": [ { "family_name": "Wegener", "given_name": "Gunter", "orcid": "0000-0002-6819-373X", "clpid": "Wegener-Gunter" }, { "family_name": "Laso-P\u00e9rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865", "clpid": "Laso-P\u00e9rez-Rafael" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Boetius", "given_name": "Antje", "orcid": "0000-0003-2117-4176", "clpid": "Boetius-Antje" } ], "abstract": "Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.", "doi": "10.1146/annurev-micro-111021-045911", "issn": "0066-4227", "publisher": "Annual Reviews", "publication": "Annual Review of Microbiology", "publication_date": "2022-09", "series_number": "1", "volume": "76", "issue": "1", "pages": "553-577" }, { "id": "authors:hgz8w-55503", "collection": "authors", "collection_id": "hgz8w-55503", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220728-730554000", "type": "article", "title": "Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA", "author": [ { "family_name": "Aronson", "given_name": "Heidi S.", "orcid": "0000-0002-6777-0304", "clpid": "Aronson-Heidi-S" }, { "family_name": "Monteverde", "given_name": "Danielle R.", "orcid": "0000-0002-0198-8220", "clpid": "Monteverde-Danielle-R" }, { "family_name": "Barnes", "given_name": "Ben Davis", "clpid": "Barnes-Ben-Davis" }, { "family_name": "Johnson", "given_name": "Brooke R.", "clpid": "Johnson-Brooke-R" }, { "family_name": "Zawaski", "given_name": "Mike J.", "clpid": "Zawaski-Mike-J" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Wang", "given_name": "Xingchen Tony", "orcid": "0000-0001-5316-789X", "clpid": "Wang-Xingchen-Tony" }, { "family_name": "Wu", "given_name": "Fenfang", "orcid": "0000-0003-1134-280X", "clpid": "Wu-Fenfang" }, { "family_name": "Webb", "given_name": "Samuel M.", "orcid": "0000-0003-1188-0464", "clpid": "Webb-Samuel-M" }, { "family_name": "Trower", "given_name": "Elizabeth J.", "orcid": "0000-0001-9898-5589", "clpid": "Trower-Elizabeth-J" }, { "family_name": "Magyar", "given_name": "John S.", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "literal": "Geobiology Course 2017" }, { "literal": "Geobiology Course 2018" } ], "abstract": "Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O2 concentrations were lower and sulfide was more prevalent in Earth surface environments. We identified a new site at Santa Paula Creek (SPC) in Ventura County, CA\u2014a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.", "doi": "10.1111/gbi.12512", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2022-09", "series_number": "5", "volume": "20", "issue": "5", "pages": "707-725" }, { "id": "authors:jkr11-te807", "collection": "authors", "collection_id": "jkr11-te807", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211103-160314501", "type": "article", "title": "Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles", "author": [ { "family_name": "Schwartzman", "given_name": "Julia A.", "orcid": "0000-0003-4563-4835", "clpid": "Schwartzman-Julia-A" }, { "family_name": "Ebrahimi", "given_name": "Ali", "orcid": "0000-0003-4472-867X", "clpid": "Ebrahimi-Aliakbar" }, { "family_name": "Chadwick", "given_name": "Grayson", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Sato", "given_name": "Yuya", "clpid": "Sato-Yuya" }, { "family_name": "Roller", "given_name": "Benjamin R. K.", "orcid": "0000-0003-4458-8267", "clpid": "Roller-Benjamin-R-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Cordero", "given_name": "Otto X.", "orcid": "0000-0002-2695-270X", "clpid": "Cordero-Otto-X" } ], "abstract": "Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static \"shell\" surrounding a motile, carbon-storing \"core.\" Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.", "doi": "10.1016/j.cub.2022.06.011", "pmcid": "PMC9496226", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2022-07-25", "series_number": "14", "volume": "32", "issue": "14", "pages": "3059-3069.e7" }, { "id": "authors:d3xr8-fst55", "collection": "authors", "collection_id": "d3xr8-fst55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220715-744227000", "type": "article", "title": "A Reduced F\u2084\u2082\u2080-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon", "author": [ { "family_name": "Heryakusuma", "given_name": "Christian", "clpid": "Heryakusuma-Christian" }, { "family_name": "Susanti", "given_name": "Dwi", "clpid": "Susanti-Dwi" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang-ENV" }, { "family_name": "Li", "given_name": "Zhou", "clpid": "Li-Zhou" }, { "family_name": "Purwantini", "given_name": "Endang", "clpid": "Purwantini-Endang" }, { "family_name": "Hettich", "given_name": "Robert L.", "clpid": "Hettich-Robert-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Mukhopadhyay", "given_name": "Biswarup", "clpid": "Mukhopadhyay-Biswarup" } ], "abstract": "Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F\u2084\u2082\u2080-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F\u2084\u2082\u2080 (F\u2084\u2082\u2080H\u2082), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F\u2084\u2082\u2080H\u2082. Instead, it acted as an F\u2084\u2082\u2080H\u2082-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 \u03bcM; F\u2084\u2082\u2080H\u2082, 14\u2009\u03bcM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F\u2084\u2082\u2080H\u2082-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E\u2070\u2032 [standard potential], +440\u2009mV) but not sulfite (E\u2070\u2032, \u2212116\u2009mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies.", "doi": "10.1128/jb.00078-22", "pmcid": "PMC9295563", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2022-07", "series_number": "7", "volume": "204", "issue": "7", "pages": "Art. No. e00078-22" }, { "id": "authors:cee4z-fzt63", "collection": "authors", "collection_id": "cee4z-fzt63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220405-464784300", "type": "article", "title": "Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily", "author": [ { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Yu", "given_name": "Feiqiao B.", "orcid": "0000-0003-3416-3046", "clpid": "Yu-Feiqiao-B" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" }, { "family_name": "Magyar", "given_name": "John S.", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Pe\u00f1a-Salinas", "given_name": "Manet E.", "orcid": "0000-0002-5835-0455", "clpid": "Pe\u00f1a-Salinas-Manet-E" }, { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-Stephen-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400\u2009km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.", "doi": "10.1038/s41396-022-01222-x", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2022-07", "volume": "16", "pages": "1750-1764" }, { "id": "authors:bza61-q9r11", "collection": "authors", "collection_id": "bza61-q9r11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220721-8119000", "type": "article", "title": "Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep", "author": [ { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang-ENV" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Woyke", "given_name": "Tanja", "orcid": "0000-0002-9485-5637", "clpid": "Woyke-Tanja" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (\"Candidatus Methanocomedenaceae\") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses.", "doi": "10.1128/aem.02109-21", "pmcid": "PMC9195934", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2022-06-14", "series_number": "11", "volume": "88", "issue": "11", "pages": "Art. No. e0210921" }, { "id": "authors:1bk5d-84e83", "collection": "authors", "collection_id": "1bk5d-84e83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220304-60741000", "type": "article", "title": "Exploring Space via Astromycology: A Report on the CIFAR Programs Earth 4D and Fungal Kingdom Inaugural Joint Meeting", "author": [ { "family_name": "Case", "given_name": "Nicola T.", "orcid": "0000-0001-7692-3424", "clpid": "Case-Nicola-T" }, { "family_name": "Song", "given_name": "Min", "orcid": "0000-0002-3291-0282", "clpid": "Song-Min" }, { "family_name": "Fulford", "given_name": "Avery H.", "orcid": "0000-0001-8011-3360", "clpid": "Fulford-Avery-H" }, { "family_name": "Graham", "given_name": "Heather V.", "clpid": "Graham-Heather-V" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Stajich", "given_name": "Jason E.", "orcid": "0000-0002-7591-0020", "clpid": "Stajich-Jason-E" }, { "family_name": "Casadevall", "given_name": "Arturo", "orcid": "0000-0002-9402-9167", "clpid": "Casadevall-Arturo" }, { "family_name": "Mustard", "given_name": "John", "orcid": "0000-0003-2509-0287", "clpid": "Mustard-John-F" }, { "family_name": "Heitman", "given_name": "Joseph", "orcid": "0000-0001-6369-5995", "clpid": "Heitman-Joseph" }, { "family_name": "Sherwood Lollar", "given_name": "Barbara", "orcid": "0000-0001-9758-7095", "clpid": "Sherwood-Lollar-Barbara" }, { "family_name": "Cowen", "given_name": "Leah E.", "orcid": "0000-0001-5797-0110", "clpid": "Cowen-Leah-E" } ], "abstract": "\"Fungi on Mars!\": a popular news heading that piques public interest and makes scientists' blood boil. While such a statement is laden with misinformation and light on evidence, the search for past and present extraterrestrial life is an ongoing scientific effort. Moreover, it is one that is increasingly gaining momentum with the recent collection of martian rock cores from Jezero Crater by NASA's Perseverance rover. Despite the increasingly sophisticated approaches guiding the search for microbial life on other planets, fungi remain relatively underexplored compared to their bacterial counterparts, highlighting a gap between the astrobiological and fungal research communities. Through a meeting in April 2021, the CIFAR Earth 4D and Fungal Kingdom research programs worked to bridge this divide by uniting experts in each field. CIFAR is a Canadian-based global research organization that convenes researchers across disciplines to address important questions facing science and humanity. The CIFAR Earth 4D: Subsurface Science & Exploration and Fungal Kingdom: Threats & Opportunities research programs were launched by CIFAR in July 2019, each made up of approximately two dozen international researchers who are experts in their fields. The Earth 4D program, led by co-directors John Mustard (Brown University, USA) and Barbara Sherwood Lollar (University of Toronto, Canada), aims to understand the complex chemical, physical, and biological interactions that occur within and between Earth's surface and subsurface to explore questions on the evolution of planets and life. The Fungal Kingdom program, led by co-directors Leah Cowen (University of Toronto, Canada) and Joseph Heitman (Duke University, USA), seeks to tackle the most pressing threats fungi pose to human health, agriculture, and biodiversity and to harness their extraordinary potential. The programs met to explore areas for synergy within four major themes: (1) the origins of life; (2) the evolution and diversification of life; (3) life in diverse and extreme environments; and (4) extinction: lessons learned and threats. This report covers the research discussed during the meeting across these four themes.", "doi": "10.1089/ast.2021.0186", "pmcid": "PMC9233531", "issn": "1531-1074", "publisher": "Mary Ann Liebert", "publication": "Astrobiology", "publication_date": "2022-06", "series_number": "6", "volume": "22", "issue": "6", "pages": "637-640" }, { "id": "authors:msgbj-8nm49", "collection": "authors", "collection_id": "msgbj-8nm49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220601-258002000", "type": "article", "title": "Early impacts of climate change on a coastal marine microbial mat ecosystem", "author": [ { "family_name": "Lingappa", "given_name": "Usha F.", "orcid": "0000-0001-5691-6788", "clpid": "Lingappa-Usha-F" }, { "family_name": "Stein", "given_name": "Nathaniel T.", "orcid": "0000-0003-2199-6751", "clpid": "Stein-Nathaniel-T" }, { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "Present", "given_name": "Theodore M.", "orcid": "0000-0002-4747-2174", "clpid": "Present-Theodore-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Grotzinger", "given_name": "John P.", "orcid": "0000-0001-9324-1257", "clpid": "Grotzinger-J-P" }, { "family_name": "Knoll", "given_name": "Andrew H.", "orcid": "0000-0003-1308-8585", "clpid": "Knoll-Andrew-H" }, { "family_name": "Trower", "given_name": "Elizabeth J.", "orcid": "0000-0001-9898-5589", "clpid": "Trower-Elizabeth-J" }, { "family_name": "Gomes", "given_name": "Maya L.", "orcid": "0000-0002-9707-350X", "clpid": "Gomes-Maya-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" } ], "abstract": "Among the earliest consequences of climate change are extreme weather and rising sea levels\u2014two challenges to which coastal environments are particularly vulnerable. Often found in coastal settings are microbial mats\u2014complex, stratified microbial ecosystems that drive massive nutrient fluxes through biogeochemical cycles and have been important constituents of Earth's biosphere for eons. Little Ambergris Cay, in the Turks and Caicos Islands, supports extensive mats that vary sharply with relative water level. We characterized the microbial communities across this variation to understand better the emerging threat of sea level rise. In September 2017, the eyewall of category 5 Hurricane Irma transited the island. We monitored the impact and recovery from this devastating storm event. New mat growth proceeded rapidly, with patterns suggesting that storm perturbation may facilitate the adaptation of these ecosystems to changing sea level. Sulfur cycling, however, displayed hysteresis, stalling for >10 months after the hurricane and likely altering carbon storage potential.", "doi": "10.1126/sciadv.abm7826", "pmcid": "PMC9140962", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2022-05-27", "series_number": "21", "volume": "8", "issue": "21", "pages": "Art. No. eabm7826" }, { "id": "authors:x56p4-nq432", "collection": "authors", "collection_id": "x56p4-nq432", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211201-180908972", "type": "article", "title": "Putative fossils of chemotrophic microbes preserved in seep carbonates from Vestnesa Ridge, off northwest Svalbard, Norway", "author": [ { "family_name": "Himmler", "given_name": "Tobias", "orcid": "0000-0001-8847-0266", "clpid": "Himmler-Tobias" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Birgel", "given_name": "Daniel", "clpid": "Birgel-Daniel" }, { "family_name": "Wirth", "given_name": "Richard", "clpid": "Wirth-Richard" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Kirsim\u00e4e", "given_name": "Kalle", "orcid": "0000-0002-1221-3623", "clpid": "Kirsim\u00e4e-Kalle" }, { "family_name": "Knies", "given_name": "Jochen", "orcid": "0000-0002-0114-5629", "clpid": "Knies-Jochen" }, { "family_name": "Peckmann", "given_name": "J\u00f6rn", "orcid": "0000-0002-8572-0060", "clpid": "Peckmann-J\u00f6rn" }, { "family_name": "Lepland", "given_name": "Aivo", "clpid": "Lepland-Aivo" } ], "abstract": "The microbial key players at methane seeps are methanotrophic archaea and sulfate-reducing bacteria. They form spherical aggregates and jointly mediate the sulfate-dependent anaerobic oxidation of methane (SD\u2013AOM: CH\u2084 + SO\u2084\u00b2\u207b \u2192 HCO\u2083\u207b + HS\u207b + H\u2082O), thereby inducing the precipitation of authigenic seep carbonates. While seep carbonates constitute valuable archives for molecular fossils of SD\u2013AOM-mediating microbes, no microfossils have been identified as AOM aggregates to date. We report clustered spherical microstructures engulfed in \u00b9\u00b3C-depleted aragonite cement (\u03b4\u00b9\u00b3C values as low as \u201333\u2030) of Pleistocene seep carbonates. The clusters comprise Mg-calcite spheres between ~5 \u03bcm (single spheres) and ~30 \u03bcm (clusters) in diameter. Scanning and transmission electron microscopy revealed a porous nanocrystalline fabric in the core area of the spheres surrounded by one or two concentric layers of Mg-calcite crystals. In situ measured sphere \u03b4\u00b9\u00b3C values as low as \u201342\u2030 indicate that methane-derived carbon is the dominant carbon source. The size and concentric layering of the spheres resembles mineralized aggregates of natural anaerobic methanotrophic archaea (ANME) of the ANME-2 group surrounded by one or two layers of sulfate-reducing bacteria. Abundant carbonate-bound \u00b9\u00b3C-depleted lipid biomarkers of archaea and bacteria indicative of the ANME-2-Desulfosarcina/Desulfococcus consortium agree with SD\u2013AOM-mediating microbes as critical agents of carbonate precipitation. Given the morphological resemblance, in concert with negative in situ \u03b4\u00b9\u00b3C values and abundant SD\u2013AOM-diagnostic biomarkers, the clustered spheres likely represent fossils of SD\u2013AOM-mediating microbes.", "doi": "10.1130/g49620.1", "issn": "0091-7613", "publisher": "Geological Society of America", "publication": "Geology", "publication_date": "2022-02-01", "series_number": "2", "volume": "50", "issue": "2", "pages": "169-173" }, { "id": "authors:z8b1y-75771", "collection": "authors", "collection_id": "z8b1y-75771", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220118-973186300", "type": "article", "title": "Unique mobile elements and scalable gene flow at the prokaryote\u2013eukaryote boundary revealed by circularized Asgard archaea genomes", "author": [ { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Philosof", "given_name": "Alon", "orcid": "0000-0003-2684-8678", "clpid": "Philosof-Alon" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Narayanan", "given_name": "Aditi", "clpid": "Narayanan-Aditi" }, { "family_name": "Barco", "given_name": "Roman A.", "clpid": "Barco-Roman-A" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-Jan-P" }, { "family_name": "Antoshechkin", "given_name": "Igor A.", "orcid": "0000-0002-9934-3040", "clpid": "Antoshechkin-Igor-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation\u2013decentralized innovation\u2013hierarchical import model that accounts for the emergence of eukaryotic complexity.", "doi": "10.1038/s41564-021-01039-y", "issn": "2058-5276", "publisher": "Nature Publishing Group", "publication": "Nature Microbiology", "publication_date": "2022-02", "series_number": "2", "volume": "7", "issue": "2", "pages": "200-212" }, { "id": "authors:5pnpk-fhp48", "collection": "authors", "collection_id": "5pnpk-fhp48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-145417503", "type": "article", "title": "Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea", "author": [ { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-Connor-T" }, { "family_name": "Laso-P\u00e9rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865", "clpid": "Laso-P\u00e9rez-Rafael" }, { "family_name": "Leu", "given_name": "Andy O.", "orcid": "0000-0002-9882-9364", "clpid": "Leu-Andy-Owen" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang-ENV" }, { "family_name": "Morgan-Lang", "given_name": "Connor", "orcid": "0000-0002-6714-0898", "clpid": "Morgan-Lang-Connor" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Malmstrom", "given_name": "Rex", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Brazelton", "given_name": "William J.", "orcid": "0000-0003-0933-0148", "clpid": "Brazelton-William-J" }, { "family_name": "Woyke", "given_name": "Tanja", "orcid": "0000-0002-9485-5637", "clpid": "Woyke-Tanja" }, { "family_name": "Hallam", "given_name": "Steven J.", "orcid": "0000-0002-4889-6876", "clpid": "Hallam-Steven-J" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-Gene-W" }, { "family_name": "Wegener", "given_name": "Gunter", "orcid": "0000-0002-6819-373X", "clpid": "Wegener-Gunter" }, { "family_name": "Boetius", "given_name": "Antje", "orcid": "0000-0003-2117-4176", "clpid": "Boetius-Antje" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.", "doi": "10.1371/journal.pbio.3001508", "pmcid": "PMC9012536", "issn": "1544-9173", "publisher": "Public Library of Science", "publication": "PLoS Biology", "publication_date": "2022-01-05", "series_number": "1", "volume": "20", "issue": "1", "pages": "Art. No. e3001508" }, { "id": "authors:y1x7w-p8m97", "collection": "authors", "collection_id": "y1x7w-p8m97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210726-170837328", "type": "article", "title": "Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea", "author": [ { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-Connor-T" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Leu", "given_name": "Andy O.", "orcid": "0000-0002-9882-9364", "clpid": "Leu-Andy-Owen" }, { "family_name": "Aoki", "given_name": "Masataka", "orcid": "0000-0002-9352-2072", "clpid": "Aoki-Masataka" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-Gene-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100\u2009\u00b5M increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.", "doi": "10.1038/s41396-021-01047-0", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2022-01", "series_number": "1", "volume": "16", "issue": "1", "pages": "168-177" }, { "id": "authors:012te-b6851", "collection": "authors", "collection_id": "012te-b6851", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211111-215750456", "type": "article", "title": "Methoxyl stable isotopic constraints on the origins and limits of coal-bed methane", "author": [ { "family_name": "Lloyd", "given_name": "M. K.", "orcid": "0000-0001-9367-2698", "clpid": "Lloyd-Max-K" }, { "family_name": "Trembath-Reichert", "given_name": "E.", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-Elizabeth" }, { "family_name": "Dawson", "given_name": "K. S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Feakins", "given_name": "S. J.", "orcid": "0000-0003-3434-2423", "clpid": "Feakins-Sarah-J" }, { "family_name": "Mastalerz", "given_name": "M.", "orcid": "0000-0002-9890-6788", "clpid": "Mastalerz-Maria" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Sessions", "given_name": "A. L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "J. M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "abstract": "Microbial coal-bed methane is an important economic resource and source of a potent greenhouse gas, but controls on its formation are poorly understood. To test whether the microbial degradability of coal limits microbial methane, we monitored methoxyl group demethylation\u2014a reaction that feeds methanogenesis\u2014in a global sample suite ranging in maturity from wood to bituminous coal. Carbon isotopic compositions of residual methoxyl groups were inconsistent with a thermal reaction, instead implying a substrate-limited biologic process. This suggests that deep biosphere communities participated in transforming plant matter to coal on geologic time scales and that methoxyl abundance influences coal-bed methane yield. Carbon isotopic enrichments resulting from microbial methylotrophy also explain an enigmatic offset in the carbon-13 content of microbial methane from coals and conventional hydrocarbon deposits.", "doi": "10.1126/science.abg0241", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2021-11-12", "series_number": "6569", "volume": "374", "issue": "6569", "pages": "894-897" }, { "id": "authors:k1wex-qd335", "collection": "authors", "collection_id": "k1wex-qd335", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210817-204334443", "type": "article", "title": "Sulfur isotope fractionations constrain the biological cycling of dimethylsulfoniopropionate in the upper ocean", "author": [ { "family_name": "Osorio\u2010Rodriguez", "given_name": "Daniela", "orcid": "0000-0001-6676-4124", "clpid": "Osorio\u2010Rodriguez-Daniela" }, { "family_name": "Razo-Mejia", "given_name": "Manuel", "orcid": "0000-0002-9510-0527", "clpid": "Razo-Mejia-Manuel" }, { "family_name": "Dalleska", "given_name": "Nathan F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-Nathan-F" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "The rapid turnover of dimethylsulfoniopropionate (DMSP), likely the most relevant dissolved organic sulfur compound in the surface ocean, makes it pivotal to understand the cycling of organic sulfur. Dimethylsulfoniopropionate is mainly synthesized by phytoplankton, and it can be utilized as carbon and sulfur sources by marine bacteria or cleaved by bacteria or algae to produce the volatile compound dimethylsulfide (DMS), involved in the formation of sulfate aerosols. The fluxes between the consumption (i.e., demethylation) and cleavage pathways are thought to depend on community interactions and their sulfur demand. However, a quantitative assessment of the sulfur partitioning between each of these pathways is still missing. Here, we report for the first time the sulfur isotope fractionations by enzymes involved in DMSP degradation with different catalytic mechanisms, expressed heterologously in Escherichia coli. We show that the residual DMSP from the demethylation pathway is 2.7\u2030 enriched in \u03b4 \u00b3\u2074S relative to the initial DMSP, and that the fractionation factor (\u00b3\u2074\u03b5) of the cleavage pathways varies between \u22121 and \u22129\u2030. The incorporation of these fractionation factors into mass balance calculations constrains the biological fates of DMSP in seawater, supports the notion that demethylation dominates over cleavage in marine environments, and could be used as a proxy for the dominant pathways of degradation of DMSP by marine microbial communities.", "doi": "10.1002/lno.11901", "issn": "0024-3590", "publisher": "American Society of Limnology and Oceanography", "publication": "Limnology and Oceanography", "publication_date": "2021-10", "series_number": "10", "volume": "66", "issue": "10", "pages": "3607-3618" }, { "id": "authors:p2tdc-5gy21", "collection": "authors", "collection_id": "p2tdc-5gy21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210714-151655967", "type": "article", "title": "Evidence of a Streamlined Extracellular Electron Transfer Pathway from Biofilm Structure, Metabolic Stratification, and Long-Range Electron Transfer Parameters", "author": [ { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-Fernanda" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Mickol", "given_name": "Rebecca L.", "orcid": "0000-0002-4493-7263", "clpid": "Mickol-Rebecca-L" }, { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Glaven", "given_name": "Sarah M.", "orcid": "0000-0003-0857-3391", "clpid": "Glaven-Sarah-M" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-Jeffrey-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Bond", "given_name": "Daniel R.", "orcid": "0000-0001-8083-7107", "clpid": "Bond-Daniel-R" } ], "abstract": "A strain of Geobacter sulfurreducens, an organism capable of respiring solid extracellular substrates, lacking four of five outer membrane cytochrome complexes (extABCD\u207a strain) grows faster and produces greater current density than the wild type grown under identical conditions. To understand cellular and biofilm modifications in the extABCD\u207a strain responsible for this increased performance, biofilms grown using electrodes as terminal electron acceptors were sectioned and imaged using electron microscopy to determine changes in thickness and cell density, while parallel biofilms incubated in the presence of nitrogen and carbon isotopes were analyzed using NanoSIMS (nanoscale secondary ion mass spectrometry) to quantify and localize anabolic activity. Long-distance electron transfer parameters were measured for wild-type and extABCD\u207a biofilms spanning 5-\u03bcm gaps. Our results reveal that extABCD\u207a biofilms achieved higher current densities through the additive effects of denser cell packing close to the electrode (based on electron microscopy), combined with higher metabolic rates per cell compared to the wild type (based on increased rates of \u00b9\u2075N incorporation). We also observed an increased rate of electron transfer through extABCD\u207a versus wild-type biofilms, suggesting that denser biofilms resulting from the deletion of unnecessary multiheme cytochromes streamline electron transfer to electrodes. The combination of imaging, physiological, and electrochemical data confirms that engineered electrogenic bacteria are capable of producing more current per cell and, in combination with higher biofilm density and electron diffusion rates, can produce a higher final current density than the wild type.", "doi": "10.1128/aem.00706-21", "pmcid": "PMC8357294", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2021-08", "series_number": "17", "volume": "87", "issue": "17", "pages": "Art. No. AEM.00706-21" }, { "id": "authors:s4kxf-xh613", "collection": "authors", "collection_id": "s4kxf-xh613", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210225-154113785", "type": "article", "title": "Microbial succession and dynamics in meromictic Mono Lake, California", "author": [ { "family_name": "Phillips", "given_name": "Alexandra A.", "orcid": "0000-0001-5959-5238", "clpid": "Phillips-Alexandra-A" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Miller", "given_name": "Laurence G.", "orcid": "0000-0002-7807-3475", "clpid": "Miller-Laurence-G" }, { "family_name": "Wang", "given_name": "Xingchen T.", "orcid": "0000-0001-5316-789X", "clpid": "Wang-Xingchen-Tony" }, { "family_name": "Wu", "given_name": "Fenfang", "orcid": "0000-0003-1134-280X", "clpid": "Wu-Fenfang" }, { "family_name": "Medeiros", "given_name": "Patricia M.", "orcid": "0000-0001-6818-2603", "clpid": "Medeiros-Patricia-M" }, { "family_name": "Monteverde", "given_name": "Danielle R.", "orcid": "0000-0002-0198-8220", "clpid": "Monteverde-Danielle-R" }, { "family_name": "Osburn", "given_name": "Magdalena R.", "orcid": "0000-0001-9180-559X", "clpid": "Osburn-Magdalena-R" }, { "family_name": "Berelson", "given_name": "William M.", "orcid": "0000-0002-1526-3802", "clpid": "Berelson-William-M" }, { "family_name": "Betts", "given_name": "Hannah L.", "clpid": "Betts-Hannah-L" }, { "family_name": "Wijker", "given_name": "Reto S.", "orcid": "0000-0001-5104-9849", "clpid": "Wijker-Reto-S" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-W" }, { "family_name": "Johnson", "given_name": "Hope A.", "orcid": "0000-0001-6721-3340", "clpid": "Johnson-Hope-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "literal": "Geobiology Course 2017" }, { "literal": "Geobiology Course 2018" } ], "abstract": "Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017\u20132018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 \u00b5M, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment \"seed bank\" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.", "doi": "10.1111/gbi.12437", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2021-07", "series_number": "4", "volume": "19", "issue": "4", "pages": "376-393" }, { "id": "authors:kt01k-zan98", "collection": "authors", "collection_id": "kt01k-zan98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210621-144751286", "type": "article", "title": "Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey J.", "orcid": "0000-0003-2858-8806", "clpid": "Marlow-Jeffrey-J" }, { "family_name": "Hoer", "given_name": "Daniel", "orcid": "0000-0002-0644-760X", "clpid": "Hoer-Daniel" }, { "family_name": "Jungbluth", "given_name": "Sean P.", "orcid": "0000-0001-9265-8341", "clpid": "Jungbluth-Sean-P" }, { "family_name": "Reynard", "given_name": "Linda M.", "orcid": "0000-0001-5732-1532", "clpid": "Reynard-Linda-M" }, { "family_name": "Gartman", "given_name": "Amy", "orcid": "0000-0001-9307-3062", "clpid": "Gartman-Amy" }, { "family_name": "Chavez", "given_name": "Marko S.", "clpid": "Chavez-Marko-S" }, { "family_name": "El-Naggar", "given_name": "Mohamed Y.", "clpid": "El-Naggar-Mohamed-Y" }, { "family_name": "Tuross", "given_name": "Noreen", "orcid": "0000-0002-3080-4005", "clpid": "Tuross-Noreen" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Girguis", "given_name": "Peter R.", "orcid": "0000-0002-3599-8160", "clpid": "Girguis-Peter-R" } ], "abstract": "At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated V_(max), and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.", "doi": "10.1073/pnas.2006857118", "pmcid": "PMC8237665", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2021-06-22", "series_number": "25", "volume": "118", "issue": "25", "pages": "Art. No. e2006857118" }, { "id": "authors:ftvzk-9fy26", "collection": "authors", "collection_id": "ftvzk-9fy26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210517-093742807", "type": "article", "title": "Controls on Interspecies Electron Transport and Size Limitation of Anaerobically Methane-Oxidizing Microbial Consortia", "author": [ { "family_name": "He", "given_name": "Xiaojia", "orcid": "0000-0001-8274-5564", "clpid": "He-Xiaojia" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Kempes", "given_name": "Christopher P.", "clpid": "Kempes-Christopher-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Meile", "given_name": "Christof", "orcid": "0000-0002-0825-4596", "clpid": "Meile-Christof-D" } ], "abstract": "About 382 Tg\u2009yr\u207b\u00b9 of methane rising through the seafloor is oxidized anaerobically (W. S. Reeburgh, Chem Rev 107:486\u2013513, 2007, https://doi.org/10.1021/cr050362v), preventing it from reaching the atmosphere, where it acts as a strong greenhouse gas. Microbial consortia composed of anaerobic methanotrophic archaea and sulfate-reducing bacteria couple the oxidation of methane to the reduction of sulfate under anaerobic conditions via a syntrophic process. Recent experimental studies and modeling efforts indicate that direct interspecies electron transfer (DIET) is involved in this syntrophy. Here, we explore a fluorescent in situ hybridization-nanoscale secondary ion mass spectrometry data set of large, segregated anaerobic oxidation of methane (AOM) consortia that reveal a decline in metabolic activity away from the archaeal-bacterial interface and use a process-based model to identify the physiological controls on rates of AOM. Simulations reproducing the observational data reveal that ohmic resistance and activation loss are the two main factors causing the declining metabolic activity, where activation loss dominated at a distance of <8\u2009\u03bcm. These voltage losses limit the maximum spatial distance between syntrophic partners with model simulations, indicating that sulfate-reducing bacterial cells can remain metabolically active up to \u223c30\u2009\u03bcm away from the archaeal-bacterial interface. Model simulations further predict that a hybrid metabolism that combines DIET with a small contribution of diffusive exchange of electron donors can offer energetic advantages for syntrophic consortia.", "doi": "10.1128/mBio.03620-20", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2021-05-12", "series_number": "3", "volume": "12", "issue": "3", "pages": "Art. No. e03620-20" }, { "id": "authors:zhjyh-k7539", "collection": "authors", "collection_id": "zhjyh-k7539", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210224-105659368", "type": "article", "title": "Spatially Resolved Electron Transport through Anode\u2010Respiring Geobacter sulfurreducens Biofilms: Controls and Constraints", "author": [ { "family_name": "He", "given_name": "Xiaojia", "orcid": "0000-0001-8274-5564", "clpid": "He-Xiaojia" }, { "family_name": "Chadwick", "given_name": "Grayson", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-Fernanda" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Meile", "given_name": "Christof", "orcid": "0000-0002-0825-4596", "clpid": "Meile-Christof-D" } ], "abstract": "Microbial fuel cells (MFCs) with Geobacter sulfurreducens have been shown to produce high current densities; however, electron transport in G. sulfurreducens biofilms is not fully understood. Here, we utilize a spatially resolved numerical model describing this electron transfer to constrain mechanisms and controls on metabolic activity. Our model reproduces the metabolic activity profile obtained using nanoSIMS under positive (+0.24\u2005V SHE) and negative (\u22120.1\u2005V SHE) anode potentials. The simulations indicate that the distribution of the electric potential and pH both control cellular metabolism. Model simulations reproducing the experimentally determined activity patterns also support the presence of two activity modes in G. sulfurreducens biofilms, with a shift from a redox mid\u2010potential of \u22120.07\u2005V SHE to \u22120.15\u2005V SHE. Our model provides valuable insights into the fundamental mechanisms of electron transfer at Micron\u2010scale in conductive biofilms which can inform MFCs designs that maximize current production by minimizing the impact of inhibitory factors.", "doi": "10.1002/celc.202100111", "issn": "2196-0216", "publisher": "Wiley", "publication": "ChemElectroChem", "publication_date": "2021-05-11", "series_number": "10", "volume": "8", "issue": "10", "pages": "1747-1758" }, { "id": "authors:12j95-cp943", "collection": "authors", "collection_id": "12j95-cp943", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210430-123641944", "type": "article", "title": "A chemosynthetic ecotone\u2014\"chemotone\"\u2014in the sediments surrounding deep-sea methane seeps", "author": [ { "family_name": "Ashford", "given_name": "Oliver S.", "orcid": "0000-0001-5473-7057", "clpid": "Ashford-Oliver-S" }, { "family_name": "Guan", "given_name": "Shuzhe", "clpid": "Guan-Shuzhe" }, { "family_name": "Capone", "given_name": "Dante", "clpid": "Capone-Dante" }, { "family_name": "Rigney", "given_name": "Katherine", "clpid": "Rigney-Katherine" }, { "family_name": "Rowley", "given_name": "Katelynn", "clpid": "Rowley-Katelynn" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-W" }, { "family_name": "Dawson", "given_name": "Kat S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Kat-S" }, { "family_name": "Cort\u00e9s", "given_name": "Jorge", "orcid": "0000-0001-7004-8649", "clpid": "Cort\u00e9s-Jorge" }, { "family_name": "Rouse", "given_name": "Greg W.", "orcid": "0000-0001-9036-9263", "clpid": "Rouse-Greg-W" }, { "family_name": "Mendoza", "given_name": "Guillermo F.", "clpid": "Mendoza-Guillermo-F" }, { "family_name": "Lee", "given_name": "Raymond W.", "clpid": "Lee-Raymond-W" }, { "family_name": "Cordes", "given_name": "Erik E.", "clpid": "Cordes-Erik-E" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-Lisa-A" } ], "abstract": "Ecotones have been described as \"biodiversity hotspots\" from myriad environments, yet have not been studied extensively in the deep ocean. While physiologically challenging, deep-water methane seeps host highly productive communities fueled predominantly by chemosynthetic pathways. We hypothesized that the biological and geochemical influence of methane seeps extends into background habitats, resulting in the formation of a \"chemotone\" where chemosynthesis-based and photosynthesis-based communities overlap. To investigate this, we analyzed the macrofaunal assemblages and geochemical properties of sediments collected from \"active,\" \"transition\" (potential chemotone), and \"background\" habitats surrounding five Costa Rican methane seeps (depth range 377\u20131908\u2009m). Sediment geochemistry demonstrated a clear distinction between active and transition habitats, but not between transition and background habitats. In contrast, biological variables confirmed the presence of a chemotone, characterized by intermediate biomass, a distinct species composition (including habitat endemics and species from both active and background habitats), and enhanced variability in species composition among samples. However, chemotone assemblages were not distinct from active and/or background assemblages in terms of faunal density, biological trait composition, or diversity. Biomass and faunal stable isotope data suggest that chemotones are driven by a gradient in food delivery, receiving supplements from chemosynthetic production in addition to available photosynthetic-based resources. Sediment geochemistry suggests that chemosynthetic food supplements are delivered across the chemotone at least in part through the water column, as opposed to reflecting exclusively in situ chemosynthetic production in sediments. Management efforts should be cognisant of the ecological attributes and spatial extent of the chemotone that surrounds deep-sea chemosynthetic environments.", "doi": "10.1002/lno.11713", "issn": "0024-3590", "publisher": "American Society of Limnology and Oceanography", "publication": "Limnology and Oceanography", "publication_date": "2021-05", "series_number": "5", "volume": "66", "issue": "5", "pages": "1687-1702" }, { "id": "authors:vbj9s-6jr73", "collection": "authors", "collection_id": "vbj9s-6jr73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200413-101943907", "type": "article", "title": "Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy", "author": [ { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani-S" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-W" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Archaeal anaerobic methanotrophs (\"ANME\") and sulfate-reducing Deltaproteobacteria (\"SRB\") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b\u2014SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b\u2014SEEP-SRB1g consortia incubated with a headspace containing CH\u2084 and \u00b9\u2075N\u2082 revealed differences in cellular \u00b9\u2075N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in \u00b9\u2075N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.", "doi": "10.1038/s41396-020-00757-1", "pmcid": "PMC8027057", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2021-02", "series_number": "2", "volume": "15", "issue": "2", "pages": "377-396" }, { "id": "authors:gw123-twg59", "collection": "authors", "collection_id": "gw123-twg59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210115-120616827", "type": "article", "title": "Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus", "author": [ { "family_name": "Sim", "given_name": "Min Sub", "orcid": "0000-0002-3491-9002", "clpid": "Sim-Min-Sub" }, { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-Connor-T" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.", "doi": "10.1371/journal.pone.0245069", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2021-01-14", "series_number": "1", "volume": "16", "issue": "1", "pages": "Art. No. e0245069" }, { "id": "authors:kdrrd-ax492", "collection": "authors", "collection_id": "kdrrd-ax492", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201224-085808375", "type": "article", "title": "Patterns of in situ Mineral Colonization by Microorganisms in a ~60\u00b0C Deep Continental Subsurface Aquifer", "author": [ { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-W" }, { "family_name": "Wanger", "given_name": "Greg", "clpid": "Wanger-Greg" }, { "family_name": "Kruger", "given_name": "Brittany R.", "clpid": "Kruger-Brittany-R" }, { "family_name": "Sackett", "given_name": "Joshua D.", "clpid": "Sackett-Joshua-D" }, { "family_name": "Hamilton-Brehm", "given_name": "Scott D.", "orcid": "0000-0002-7474-207X", "clpid": "Hamilton-Brehm-Scott-D" }, { "family_name": "Bhartia", "given_name": "Rohit", "orcid": "0000-0002-1434-7481", "clpid": "Bhartia-Rohit" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-Jan-P" }, { "family_name": "Moser", "given_name": "Duane P.", "orcid": "0000-0003-2825-5753", "clpid": "Moser-Duane-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57\u00b0C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.", "doi": "10.3389/fmicb.2020.536535", "pmcid": "PMC7711152", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2020-11-19", "volume": "11", "pages": "Art. No. 536535" }, { "id": "authors:qnczx-gt881", "collection": "authors", "collection_id": "qnczx-gt881", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200506-150820782", "type": "article", "title": "Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions", "author": [ { "family_name": "Fincker", "given_name": "Maeva", "clpid": "Fincker-Maeva" }, { "family_name": "Huber", "given_name": "Julie A.", "orcid": "0000-0002-4790-7633", "clpid": "Huber-Julie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Rapp\u00e9", "given_name": "Michael S.", "orcid": "0000-0002-9829-251X", "clpid": "Rapp\u00e9-Michael-S" }, { "family_name": "Teske", "given_name": "Andreas", "orcid": "0000-0001-8702-3800", "clpid": "Teske-Andreas" }, { "family_name": "Spormann", "given_name": "Alfred M.", "orcid": "0000-0001-5103-9704", "clpid": "Spormann-Alfred-M" } ], "abstract": "Uncultured members of the Chloroflexi phylum are highly enriched in numerous subseafloor environments. Their metabolic potential was evaluated by reconstructing 31 Chloroflexi genomes from six different subseafloor habitats. The near ubiquitous presence of enzymes of the Wood\u2013Ljungdahl pathway, electron bifurcation, and ferredoxin\u2010dependent transport\u2010coupled phosphorylation indicated anaerobic acetogenesis was central to their catabolism. Most of the genomes simultaneously contained multiple degradation pathways for complex carbohydrates, detrital protein, aromatic compounds, and hydrogen, indicating the coupling of oxidation of chemically diverse organic substrates to ubiquitous CO\u2082 reduction. Such pathway combinations may confer a fitness advantage in subseafloor environments by enabling these Chloroflexi to act as primary fermenters and acetogens in one microorganism without the need for syntrophic H\u2082 consumption. While evidence for catabolic oxygen respiration was limited to two phylogenetic clusters, the presence of genes encoding putative reductive dehalogenases throughout the phylum expanded the phylogenetic boundary for potential organohalide respiration past the Dehalococcoidia class.", "doi": "10.1111/1462-2920.15061", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2020-08", "series_number": "8", "volume": "22", "issue": "8", "pages": "3188-3204" }, { "id": "authors:wn78w-rxn20", "collection": "authors", "collection_id": "wn78w-rxn20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200429-124352121", "type": "article", "title": "Resolving micron-scale heterogeneity in porewater \u03b4\u00b3\u2074S_(H\u2082S) by combining films for in-situ sulfide capture and secondary ion mass spectrometry", "author": [ { "family_name": "Houghton", "given_name": "J. L.", "clpid": "Houghton-J-L" }, { "family_name": "Jones", "given_name": "C.", "clpid": "Jones-C" }, { "family_name": "Dawson", "given_name": "K. S.", "clpid": "Dawson-K-S" }, { "family_name": "Orphan", "given_name": "V.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Gomes", "given_name": "M. L.", "clpid": "Gomes-M-L" }, { "family_name": "Fike", "given_name": "D. A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" } ], "abstract": "Sulfur cycling is ubiquitous in marine sedimentary environments and is influenced by microbial and abiotic processes that alter both the abundance and isotopic composition of sulfur species that can ultimately be captured as sedimentary minerals. Microbial metabolisms that generate sulfur isotopic (\u03b4\u00b3\u2074S) signatures in hydrogen sulfide have a spatial distribution that varies on the micron scale, yet porewater hydrogen sulfide is most often measured in bulk samples representing much larger volumes. This mismatch of scales can lead to erroneous or non-unique interpretations of biogeochemical processes and environmental conditions. Recently, an in-situ film-based technique was described that captures dissolved sulfide (H\u2082S) in porewaters and which can be subsectioned to reconstruct the \u03b4\u00b3\u2074S_(H\u2082S) profiles on the sub-cm scale within sediments. Here, we investigate the use of a Cameca 7f-GEO secondary ion mass spectrometer (SIMS) to analyze the \u03b4\u00b3\u2074S_(H\u2082S) captured from porewaters on these films on even smaller spatial scales and particularly in films with low sulfide abundance that could not otherwise be processed with bulk extraction techniques. We present a best-practice method for film analysis that minimizes analytical artifacts from varying sulfide abundance and interactions with silver halide nanocrystals imbedded in the organic-based film amalgam. This method was tested on several films from field deployments, including examples with heterogeneities on small (~100\u202f\u03bcm) scales, steep isotopic gradients, and very low sulfide abundance across the sediment-water interface. The results demonstrate that analysis using SIMS can accurately measure \u03b4\u00b3\u2074S of in-situ sulfide captured by film with high precision (1\u03c3\u202f~\u202f0.3\u2030) in both spot and image modes and that the film itself can accurately record \u03b4\u00b3\u2074S variability down to 25\u202f\u03bcm spatial resolution, below which physical limitations of the film can create artifacts.", "doi": "10.1016/j.marchem.2020.103810", "issn": "0304-4203", "publisher": "Elsevier", "publication": "Marine Chemistry", "publication_date": "2020-06-20", "volume": "223", "pages": "Art. No. 103810" }, { "id": "authors:6hmnc-7a013", "collection": "authors", "collection_id": "6hmnc-7a013", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200207-102104518", "type": "article", "title": "Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae", "author": [ { "family_name": "Leu", "given_name": "Andy O.", "orcid": "0000-0002-9882-9364", "clpid": "Leu-Andy-Owen" }, { "family_name": "McIlroy", "given_name": "Simon J.", "orcid": "0000-0003-3749-8730", "clpid": "McIlroy-Simon-J" }, { "family_name": "Ye", "given_name": "Jun", "clpid": "Ye-Jun-MICROBIO" }, { "family_name": "Parks", "given_name": "Donovan H.", "orcid": "0000-0001-6662-9010", "clpid": "Parks-Donovan-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-Gene-W" } ], "abstract": "Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceace metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate, and the reduction of arsenate, selenate and elemental sulfur. Numerous membrane-bound multi-heme c type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humics and syntrophic partners.", "doi": "10.1128/mBio.01325-20", "pmcid": "PMC7327174", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2020-05", "series_number": "3", "volume": "11", "issue": "3", "pages": "Art. No. e01325-20" }, { "id": "authors:k0ns4-ysj93", "collection": "authors", "collection_id": "k0ns4-ysj93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200102-085056769", "type": "article", "title": "Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage", "author": [ { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Tilic", "given_name": "Ekin", "clpid": "Tilic-E" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-S-W" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Keller", "given_name": "Abigail", "clpid": "Keller-Abogail" }, { "family_name": "Lee", "given_name": "Raymond W.", "clpid": "Lee-Raymond-W" }, { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Rouse", "given_name": "Greg W.", "clpid": "Rouse-G-W" }, { "family_name": "Cordes", "given_name": "Erik E.", "clpid": "Cordes-E-E" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Deep-sea cold seeps are dynamic sources of methane release and unique habitats supporting ocean biodiversity and productivity. Here, we describe newly discovered animal-bacterial symbioses fueled by methane, between two species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct aerobic methane-oxidizing bacteria belonging to the Methylococcales, localized to the host respiratory crown. Worm tissue \u03b4\u00b9\u00b3C of \u221244 to \u221258\u2030 are consistent with methane-fueled nutrition for both species, and shipboard stable isotope labeling experiments revealed active assimilation of \u00b9\u00b3C-labeled methane into animal biomass, which occurs via the engulfment of methanotrophic bacteria across the crown epidermal surface. These worms represent a new addition to the few animals known to intimately associate with methane-oxidizing bacteria and may further explain their enigmatic mass occurrence at 150\u2013million year\u2013old fossil seeps. High-resolution seafloor surveys document significant coverage by these symbioses, beyond typical obligate seep fauna. These findings uncover novel consumers of methane in the deep sea and, by expanding the known spatial extent of methane seeps, may have important implications for deep-sea conservation.", "doi": "10.1126/sciadv.aay8562", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2020-04-03", "series_number": "14", "volume": "6", "issue": "14", "pages": "Art. No. eaay8562" }, { "id": "authors:2msg1-50b70", "collection": "authors", "collection_id": "2msg1-50b70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200203-085914271", "type": "article", "title": "Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae", "author": [ { "family_name": "Leu", "given_name": "Andy O.", "orcid": "0000-0002-9882-9364", "clpid": "Leu-Andy-Owen" }, { "family_name": "Cai", "given_name": "Chen", "orcid": "0000-0002-0167-1397", "clpid": "Cai-Chen" }, { "family_name": "McIlroy", "given_name": "Simon J.", "orcid": "0000-0003-3749-8730", "clpid": "McIlroy-S-J" }, { "family_name": "Southam", "given_name": "Gordon", "clpid": "Southam-G" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Yuan", "given_name": "Zhiguo", "orcid": "0000-0002-7566-1482", "clpid": "Yuan-Zhiguo" }, { "family_name": "Hu", "given_name": "Shihu", "clpid": "Hu-Shihu" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-G-W" } ], "abstract": "Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names \"Candidatus Methanoperedens manganicus\" and \"Candidatus Methanoperedens manganireducens\" for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.", "doi": "10.1038/s41396-020-0590-x", "pmcid": "PMC7082337", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2020-04", "series_number": "4", "volume": "14", "issue": "4", "pages": "1030-1041" }, { "id": "authors:ct2d4-cx655", "collection": "authors", "collection_id": "ct2d4-cx655", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190731-105709287", "type": "article", "title": "Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane\u2010oxidizing archaea", "author": [ { "family_name": "Bird", "given_name": "Laurence R.", "orcid": "0000-0002-6034-9533", "clpid": "Bird-L-R" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Fulton", "given_name": "James M.", "orcid": "0000-0001-7213-8015", "clpid": "Fulton-J-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Freeman", "given_name": "Katherine H.", "orcid": "0000-0002-3350-7671", "clpid": "Freeman-K-H" } ], "abstract": "Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy\u2010archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH_3\u2010tetrahydromethanopterin (H_4MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in ^(13)C (mean \u03b4^(13)C = \u221227\u2030 for Hydrate Ridge and \u221280\u2030 for the Santa Monica Basin) compared to the archaeal lipids (mean \u03b4^(13)C = \u221297\u2030 for Hydrate Ridge and \u2212122\u2030 for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl\u2010CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of \u2212 73\u2030 to \u2212 77\u2030 for F430 and \u2212 105\u2030 for archaeal lipids, values close to those for Santa Monica Basin. The F430 \u03b4^(13)C value for Hydrate Ridge was 13C\u2010enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.", "doi": "10.1111/gbi.12354", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2019-11", "series_number": "6", "volume": "17", "issue": "6", "pages": "611-627" }, { "id": "authors:58hcy-96g59", "collection": "authors", "collection_id": "58hcy-96g59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191003-113812895", "type": "article", "title": "Peptidoglycan Production by an Insect-Bacterial Mosaic", "author": [ { "family_name": "Bublitz", "given_name": "DeAnna C.", "orcid": "0000-0003-3419-2103", "clpid": "Bublitz-DeAnna-C" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Magyar", "given_name": "John S.", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Sandoz", "given_name": "Kelsi M.", "orcid": "0000-0002-6960-0560", "clpid": "Sandoz-Kelsi-M" }, { "family_name": "Brooks", "given_name": "Diane M.", "clpid": "Brooks-Diane-M" }, { "family_name": "Mesnage", "given_name": "St\u00e9phane", "orcid": "0000-0003-1648-4890", "clpid": "Mesnage-St\u00e9phane" }, { "family_name": "Ladinsky", "given_name": "Mark S.", "orcid": "0000-0002-1036-3513", "clpid": "Ladinsky-Mark-S" }, { "family_name": "Garber", "given_name": "Arkadiy I.", "orcid": "0000-0001-7935-0246", "clpid": "Garber-Arkadiy-I" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "McCutcheon", "given_name": "John P.", "orcid": "0000-0002-5489-6039", "clpid": "McCutcheon-John-P" } ], "abstract": "Peptidoglycan (PG) is a defining feature of bacteria, involved in cell division, shape, and integrity. We previously reported that several genes related to PG biosynthesis were horizontally transferred from bacteria to the nuclear genome of mealybugs. Mealybugs are notable for containing a nested bacteria-within-bacterium endosymbiotic structure in specialized insect cells, where one bacterium, Moranella, lives in the cytoplasm of another bacterium, Tremblaya. Here we show that horizontally transferred genes on the mealybug genome work together with genes retained on the Moranella genome to produce a PG layer exclusively at the Moranella cell periphery. Furthermore, we show that an insect protein encoded by a horizontally transferred gene of bacterial origin is transported into the Moranella cytoplasm. These results provide a striking parallel to the genetic and biochemical mosaicism found in organelles, and prove that multiple horizontally transferred genes can become integrated into a functional pathway distributed between animal and bacterial endosymbiont genomes.", "doi": "10.1016/j.cell.2019.08.054", "pmcid": "PMC6838666", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2019-10-17", "series_number": "3", "volume": "179", "issue": "3", "pages": "703-712" }, { "id": "authors:dt13g-z9e19", "collection": "authors", "collection_id": "dt13g-z9e19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190923-160449911", "type": "article", "title": "NanoSIMS imaging reveals metabolic stratification within current-producing biofilms", "author": [ { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Jim\u00e9nez-Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-F" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Bond", "given_name": "Daniel R.", "orcid": "0000-0001-8083-7107", "clpid": "Bond-D-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Metal-reducing bacteria direct electrons to their outer surfaces, where insoluble metal oxides or electrodes act as terminal electron acceptors, generating electrical current from anaerobic respiration. Geobacter sulfurreducens is a commonly enriched electricity-producing organism, forming thick conductive biofilms that magnify total activity by supporting respiration of cells not in direct contact with electrodes. Hypotheses explaining why these biofilms fail to produce higher current densities suggest inhibition by formation of pH, nutrient, or redox potential gradients; but these explanations are often contradictory, and a lack of direct measurements of cellular growth within biofilms prevents discrimination between these models. To address this fundamental question, we measured the anabolic activity of G. sulfurreducens biofilms using stable isotope probing coupled to nanoscale secondary ion mass spectrometry (nanoSIMS). Our results demonstrate that the most active cells are at the anode surface, and that this activity decreases with distance, reaching a minimum 10 \u00b5m from the electrode. Cells nearest the electrode continue to grow at their maximum rate in weeks-old biofilms 80-\u00b5m-thick, indicating nutrient or buffer diffusion into the biofilm is not rate-limiting. This pattern, where highest activity occurs at the electrode and declines with each cell layer, is present in thin biofilms (<5 \u00b5m) and fully grown biofilms (>20 \u00b5m), and at different anode redox potentials. These results suggest a growth penalty is associated with respiring insoluble electron acceptors at micron distances, which has important implications for improving microbial electrochemical devices as well as our understanding of syntrophic associations harnessing the phenomenon of microbial conductivity.", "doi": "10.1073/pnas.1912498116", "pmcid": "PMC6789570", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2019-10-08", "series_number": "41", "volume": "116", "issue": "41", "pages": "20716-20724" }, { "id": "authors:q7p6w-6zz84", "collection": "authors", "collection_id": "q7p6w-6zz84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190624-093344374", "type": "article", "title": "Scientists' warning to humanity: microorganisms and climate change", "author": [ { "family_name": "Cavicchioli", "given_name": "Ricardo", "orcid": "0000-0001-8989-6402", "clpid": "Cavicchioli-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.", "doi": "10.1038/s41579-019-0222-5", "pmcid": "PMC7136171", "issn": "1740-1526", "publisher": "Nature Publishing Group", "publication": "Nature Reviews Microbiology", "publication_date": "2019-09", "series_number": "9", "volume": "17", "issue": "9", "pages": "569-586" }, { "id": "authors:hs12n-r2252", "collection": "authors", "collection_id": "hs12n-r2252", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190607-131617878", "type": "article", "title": "Age Mosaicism across Multiple Scales in Adult Tissues", "author": [ { "family_name": "Arrojo e Drigo", "given_name": "Rafael", "orcid": "0000-0001-7712-013X", "clpid": "Arrojo-e-Drigo-R" }, { "family_name": "Lev-Ram", "given_name": "Varda", "orcid": "0000-0001-7649-0550", "clpid": "Lev-Ram-V" }, { "family_name": "Tyagi", "given_name": "Swati", "clpid": "Tyagi-S" }, { "family_name": "Ramachandra", "given_name": "Ranjan", "clpid": "Ramachandra-R" }, { "family_name": "Deerinck", "given_name": "Thomas", "clpid": "Deerinck-T-J" }, { "family_name": "Bushong", "given_name": "Eric", "orcid": "0000-0001-6195-2433", "clpid": "Bushong-E" }, { "family_name": "Phan", "given_name": "Sebastien", "orcid": "0000-0003-4261-6973", "clpid": "Phan-Sebastien" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Lechene", "given_name": "Claude", "clpid": "Lechene-C" }, { "family_name": "Ellisman", "given_name": "Mark H.", "orcid": "0000-0001-8893-8455", "clpid": "Ellisman-M-H" }, { "family_name": "Hetzer", "given_name": "Martin W.", "orcid": "0000-0002-2111-992X", "clpid": "Hetzer-M-W" } ], "abstract": "Most neurons are not replaced during an animal's lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using ^(15)N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.", "doi": "10.1016/j.cmet.2019.05.010", "issn": "1550-4131", "publisher": "Elsevier", "publication": "Cell Metabolism", "publication_date": "2019-08-06", "series_number": "2", "volume": "30", "issue": "2", "pages": "343-351" }, { "id": "authors:dezhr-bwb82", "collection": "authors", "collection_id": "dezhr-bwb82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190530-074324675", "type": "article", "title": "The Cell and the Sum of Its Parts: Patterns of Complexity in Biosignatures as Revealed by Deep UV Raman Spectroscopy", "author": [ { "family_name": "Sapers", "given_name": "Haley M.", "orcid": "0000-0002-1797-1722", "clpid": "Sapers-H-M" }, { "family_name": "Razzell Hollis", "given_name": "Joseph", "orcid": "0000-0002-6239-694X", "clpid": "Razzell-Hollis-J" }, { "family_name": "Bhartia", "given_name": "Rohit", "clpid": "Bhartia-R" }, { "family_name": "Beegle", "given_name": "Luther W.", "orcid": "0000-0002-4944-4353", "clpid": "Beegle-L-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-J-P" } ], "abstract": "The next NASA-led Mars mission (Mars 2020) will carry a suite of instrumentation dedicated to investigating Martian history and the in situ detection of potential biosignatures. SHERLOC, a deep UV Raman/Fluorescence spectrometer has the ability to detect and map the distribution of many organic compounds, including the aromatic molecules that are fundamental building blocks of life on Earth, at concentrations down to 1 ppm. The mere presence of organic compounds is not a biosignature: there is widespread distribution of reduced organic molecules in the Solar System. Life utilizes a select few of these molecules creating conspicuous enrichments of specific molecules that deviate from the distribution expected from purely abiotic processes. The detection of far from equilibrium concentrations of a specific subset of organic molecules, such as those uniquely enriched by biological processes, would comprise a universal biosignature independent of specific terrestrial biochemistry. The detectability and suitability of a small subset of organic molecules to adequately describe a living system is explored using the bacterium Escherichia coli as a model organism. The DUV Raman spectra of E. coli cells are dominated by the vibrational modes of the nucleobases adenine, guanine, cytosine, and thymine, and the aromatic amino acids tyrosine, tryptophan, and phenylalanine. We demonstrate that not only does the deep ultraviolet (DUV) Raman spectrum of E. coli reflect a distinct concentration of specific organic molecules, but that a sufficient molecular complexity is required to deconvolute the cellular spectrum. Furthermore, a linear combination of the DUV resonant compounds is insufficient to fully describe the cellular spectrum. The residual in the cellular spectrum indicates that DUV Raman spectroscopy enables differentiating between the presence of biomolecules and the complex uniquely biological organization and arrangements of these molecules in living systems. This study demonstrates the ability of DUV Raman spectroscopy to interrogate a complex biological system represented in a living cell, and differentiate between organic detection and a series of Raman features that derive from the molecular complexity inherent to life constituting a biosignature.", "doi": "10.3389/fmicb.2019.00679", "pmcid": "PMC6527968", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2019-05-14", "volume": "10", "pages": "Art. No. 679" }, { "id": "authors:67208-78k28", "collection": "authors", "collection_id": "67208-78k28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114223337", "type": "article", "title": "Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi", "author": [ { "family_name": "Boyd", "given_name": "Joel A.", "clpid": "Boyd-J-A" }, { "family_name": "Jungbluth", "given_name": "Sean P.", "orcid": "0000-0001-9265-8341", "clpid": "Jungbluth-S-P" }, { "family_name": "Leu", "given_name": "Andy O.", "orcid": "0000-0002-9882-9364", "clpid": "Leu-Andy-Owen" }, { "family_name": "Evans", "given_name": "Paul N.", "clpid": "Evans-P-N" }, { "family_name": "Woodcroft", "given_name": "Ben J.", "orcid": "0000-0003-0670-7480", "clpid": "Woodcroft-B-J" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-J-P" }, { "family_name": "Rapp\u00e9", "given_name": "Michael S.", "orcid": "0000-0002-9829-251X", "clpid": "Rapp\u00e9-M-S" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-G-W" } ], "abstract": "The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for \u03b2-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.", "doi": "10.1038/s41396-018-0343-2", "pmcid": "PMC6474303", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2019-05", "series_number": "5", "volume": "13", "issue": "5", "pages": "1269-1279" }, { "id": "authors:0ctcx-rxw62", "collection": "authors", "collection_id": "0ctcx-rxw62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190114-132114245", "type": "article", "title": "Precise determination of equilibrium sulfur isotope effects during volatilization and deprotonation of dissolved H_2S", "author": [ { "family_name": "Sim", "given_name": "Min Sub", "orcid": "0000-0002-3491-9002", "clpid": "Sim-Min-Sub" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "abstract": "Sulfide (H_2S, HS^\u2212, and S^(2\u2212)) is ubiquitous in marine porewaters as a result of microbial sulfate reduction, constituting the reductive end of the biogeochemical sulfur cycle. Stable isotopes have been widely used to constrain the sulfur cycle, because the redox transformations of sulfur compounds, such as microbial sulfate reduction, often exhibit sizable kinetic isotope effects. In contrast to sulfate ion (SO_4^(2\u2212)), the most abundant form of dissolved sulfur in seawater, H2S is volatile and also deprotonated at near neutral pH. Equilibrium isotope partitioning between sulfide species can therefore overlap with kinetic isotope effects during reactions involving sulfide as either reactant or intermediate. Previous experimental attempts to measure equilibrium fractionation between H_2S and HS\u2212 have reached differing results, likely due to solutions of widely varying ionic strength. In this study, we measured the sulfur isotope fractionation between total dissolved sulfide and gaseous H2S at 20.6\u202f\u00b1\u202f0.5\u202f\u00b0C over the pH range from 2 to 8, and calculated the equilibrium isotope effects associated with deprotonation of dissolved H_2S. By using dilute solutions of Na2S, made possible by the improved sensitivity of mass spectrometric techniques, uncertainty in the first dissociation constant of H2S due to ionic strength could be better controlled. This in turn allowed us to close sulfur isotope mass balance for our experiments and increase the accuracy of the estimated fractionation factor. At equilibrium, aqueous H2S was enriched in ^(34)S by 0.7\u2030 and 3.1\u2030 relative to gaseous H_2S and aqueous HS\u2212, respectively. The estimated fractionation between aqueous H_2S and HS^\u2212 lies between two earlier experimental reports, but agrees within the uncertainty of the measurements with a recent theoretical calculation.", "doi": "10.1016/j.gca.2019.01.016", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2019-03-01", "volume": "248", "pages": "242-251" }, { "id": "authors:y79e1-3d457", "collection": "authors", "collection_id": "y79e1-3d457", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190114-133208101", "type": "article", "title": "The next frontier for planetary and human exploration", "author": [ { "family_name": "Stamenkovi\u0107", "given_name": "V.", "orcid": "0000-0003-2416-3683", "clpid": "Stamenkovi\u0107-V" }, { "family_name": "Fischer", "given_name": "W. W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Kirschvink", "given_name": "J. L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The surface of Mars has been well mapped and characterized, yet the subsurface \u2014 the most likely place to find signs of extant or extinct life and a repository of useful resources for human exploration \u2014 remains unexplored. In the near future this is set to change.", "doi": "10.1038/s41550-018-0676-9", "issn": "2397-3366", "publisher": "Nature Publishing Group", "publication": "Nature Astronomy", "publication_date": "2019-02", "series_number": "2", "volume": "3", "issue": "2", "pages": "116-120" }, { "id": "authors:5vy87-34626", "collection": "authors", "collection_id": "5vy87-34626", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190102-135257356", "type": "article", "title": "Microbial interactions in the anaerobic oxidation of methane: Model simulations constrained by process rates and activity patterns", "author": [ { "family_name": "He", "given_name": "Xiaojia", "orcid": "0000-0001-8274-5564", "clpid": "He-Xiaojia" }, { "family_name": "Chadwick", "given_name": "Grayson", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Kempes", "given_name": "Christopher", "orcid": "0000-0002-1622-9761", "clpid": "Kempes-C-P" }, { "family_name": "Shi", "given_name": "Yimeng", "clpid": "Shi-Yimeng" }, { "family_name": "McGlynn", "given_name": "Shawn", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Meile", "given_name": "Christof", "orcid": "0000-0002-0825-4596", "clpid": "Meile-C-D" } ], "abstract": "Proposed syntrophic interactions between the archaeal and bacterial cells mediating anaerobic oxidation of methane coupled with sulfate reduction include electron transfer through (1) the exchange of H2 or small organic molecules between methane\u2010oxidizing archaea and sulfate\u2010reducing bacteria, (2) the delivery of disulfide from methane\u2010oxidizing archaea to bacteria for disproportionation and (3) direct interspecies electron transfer. Each of these mechanisms was implemented in a reactive transport model. The simulated activities across different arrangements of archaeal and bacterial cells and aggregate sizes were compared to empirical data for AOM rates and intra\u2010aggregate spatial patterns of cell\u2010specific anabolic activity determined by FISH\u2010nanoSIMS. Simulation results showed that rates for chemical diffusion by mechanism (1) were limited by the build\u2010up of metabolites, while mechanisms (2) and (3) yielded cell specific rates and archaeal activity distributions that were consistent with observations from single cell resolved FISH\u2010nanoSIMS analyses. The novel integration of both intra\u2010aggregate and environmental data provided powerful constraints on the model results, but the similarities in model outcomes for mechanisms (2) and (3) highlight the need for additional observational data (e.g. genomic or physiological) on electron transfer and metabolic functioning of these globally important methanotrophic consortia.", "doi": "10.1111/1462-2920.14507", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2019-02", "series_number": "2", "volume": "21", "issue": "2", "pages": "631-647" }, { "id": "authors:0z9mw-2np97", "collection": "authors", "collection_id": "0z9mw-2np97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190114-083925177", "type": "article", "title": "Role of APS reductase in biogeochemical sulfur isotope fractionation", "author": [ { "family_name": "Sim", "given_name": "Min Sub", "orcid": "0000-0002-3491-9002", "clpid": "Sim-Min-Sub" }, { "family_name": "Ogata", "given_name": "Hideaki", "orcid": "0000-0002-2894-2417", "clpid": "Ogata-Hideaki" }, { "family_name": "Lubitz", "given_name": "Wolfgang", "orcid": "0000-0001-7059-5327", "clpid": "Lubitz-Wolfgang" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-Shawn-E" } ], "abstract": "Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20\u2030, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.", "doi": "10.1038/s41467-018-07878-4", "pmcid": "PMC6327049", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2019-01-09", "volume": "10", "pages": "Art. No. 44" }, { "id": "authors:3rqv8-h2t22", "collection": "authors", "collection_id": "3rqv8-h2t22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181212-151637497", "type": "article", "title": "Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea", "author": [ { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Susanti", "given_name": "Dwi", "clpid": "Susanti-D" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-C-T" }, { "family_name": "Chourey", "given_name": "Karuna", "clpid": "Chourey-K" }, { "family_name": "Iyer", "given_name": "Ramsunder", "clpid": "Iyer-R" }, { "family_name": "Scheller", "given_name": "Silvan", "orcid": "0000-0002-0667-9224", "clpid": "Scheller-S" }, { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Hettich", "given_name": "Robert L.", "clpid": "Hettich-R-L" }, { "family_name": "Mukhopadhyay", "given_name": "Biswarup", "clpid": "Mukhopadhyay-B" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F_(420)-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.", "doi": "10.3389/fmicb.2018.02917", "pmcid": "PMC6286981", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2018-12-03", "volume": "9", "pages": "Art. No. 2917" }, { "id": "authors:n1g8e-75659", "collection": "authors", "collection_id": "n1g8e-75659", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180703-145300132", "type": "article", "title": "Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading", "author": [ { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Fike", "given_name": "David A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Green-Saxena", "given_name": "Abigail", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Fortney", "given_name": "Julian", "clpid": "Fortney-Julian" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-S-A" }, { "family_name": "Dawson", "given_name": "Katherine", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Nitrogen fixation, the biological conversion of N_2 to NH_3, is critical to alleviating nitrogen limitation in many marine ecosystems. To date, few measurements exist of N_2 fixation in deep\u2010sea sediments. Here, we conducted > 400 bottle incubations with sediments from methane seeps, whale falls and background sites off the western coast of the United States from 600 to 2893 m water depth to investigate the potential rates, spatial distribution and biological mediators of benthic N_2 fixation. We found that N2 fixation was widespread, yet heterogeneously distributed with sediment depth at all sites. In some locations, rates exceeded previous measurements by > 10\u00d7, and provided up to 30% of the community anabolic growth requirement for nitrogen. Diazotrophic activity appeared to be inhibited by pore water ammonium: N_2 fixation was only observed if incubation ammonium concentrations were \u2264 25 \u03bcM, and experimental additions of ammonium reduced diazotrophy. In seep sediments, N_2 fixation was dependent on CH_4 and coincident with sulphate reduction, consistent with previous work showing diazotrophy by microorganisms mediating sulphate\u2010coupled methane oxidation. However, the pattern of diazotrophy was different in whale\u2010fall and associated reference sediments, where it was largely unaffected by CH_4, suggesting catabolically different diazotrophs at these sites.", "doi": "10.1111/1462-2920.14342", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2018-12", "series_number": "12", "volume": "20", "issue": "12", "pages": "4281-4296" }, { "id": "authors:by34v-pmx17", "collection": "authors", "collection_id": "by34v-pmx17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180711-165717508", "type": "article", "title": "Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications", "author": [ { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Hemp", "given_name": "James", "orcid": "0000-0001-7193-0553", "clpid": "Hemp-J" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Respiratory complex I is part of a large family of homologous enzymes that carry out the transfer of electrons between soluble cytoplasmic electron carriers and membrane-bound electron carriers. These complexes are vital bioenergetic enzymes that serve as the entry points into electron transport chains for a wide variety of microbial metabolisms, and electron transfer is coupled to proton translocation. The core complex of this enzyme is made up of 11 protein subunits, with three major proton pumping subunits. Here, we document a large number of modified complex I gene cassettes found in genome sequences from diverse cultured bacteria, shotgun metagenomics, and environmentally derived archaeal fosmids all of which encode a fourth proton pumping subunit. The incorporation of this extra subunit into a functional protein complex is supported by large amino acid insertions in the amphipathic helix that runs the length of the protein complex. Phylogenetic analyses reveal that these modified complexes appear to have arisen independently multiple times in a remarkable case of convergent molecular evolution. From an energetic perspective, we hypothesize that this modification on the canonical complex I architecture allows for the translocation of a fifth proton per reaction cycle\u2014the physiological utility of this modified complex is discussed.", "doi": "10.1038/s41396-018-0210-1", "pmcid": "PMC6194058", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2018-11", "series_number": "11", "volume": "12", "issue": "11", "pages": "2668-2680" }, { "id": "authors:6d6dk-78554", "collection": "authors", "collection_id": "6d6dk-78554", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180925-073151228", "type": "article", "title": "Methane on Mars and Habitability: Challenges and Responses", "author": [ { "family_name": "Yung", "given_name": "Yuk L.", "orcid": "0000-0002-4263-2562", "clpid": "Yung-Y-L" }, { "family_name": "Chen", "given_name": "Pin", "clpid": "Chen-Pin" }, { "family_name": "Nealson", "given_name": "Kenneth", "orcid": "0000-0001-5189-3732", "clpid": "Nealson-K-H" }, { "family_name": "Atreya", "given_name": "Sushil", "orcid": "0000-0002-1972-1815", "clpid": "Atreya-S-K" }, { "family_name": "Beckett", "given_name": "Patrick", "clpid": "Beckett-P" }, { "family_name": "Blank", "given_name": "Jennifer G.", "clpid": "Blank-J-G" }, { "family_name": "Ehlmann", "given_name": "Bethany", "orcid": "0000-0002-2745-3240", "clpid": "Ehlmann-B-L" }, { "family_name": "Eiler", "given_name": "John", "clpid": "Eiler-J-M" }, { "family_name": "Etiope", "given_name": "Giuseppe", "clpid": "Etiope-G" }, { "family_name": "Ferry", "given_name": "James G.", "clpid": "Ferry-J-G" }, { "family_name": "Forget", "given_name": "Fran\u00e7ois", "clpid": "Forget-F" }, { "family_name": "Gao", "given_name": "Peter", "orcid": "0000-0002-8518-9601", "clpid": "Gao-Peter" }, { "family_name": "Hu", "given_name": "Renyu", "orcid": "0000-0003-2215-8485", "clpid": "Hu-Renyu" }, { "family_name": "Kleinb\u00f6hl", "given_name": "Armin", "clpid": "Kleinb\u00f6hl-A" }, { "family_name": "Klusman", "given_name": "Ronald", "clpid": "Klusman-" }, { "family_name": "Lef\u00e8vre", "given_name": "Franck", "clpid": "Lef\u00e8vre-F" }, { "family_name": "Miller", "given_name": "Charles", "orcid": "0000-0002-9380-4838", "clpid": "Miller-C-E" }, { "family_name": "Mischna", "given_name": "Michael", "orcid": "0000-0002-8022-5319", "clpid": "Mischna-M-A" }, { "family_name": "Mumma", "given_name": "Michael", "clpid": "Mumma-M-J" }, { "family_name": "Newman", "given_name": "Sally", "orcid": "0000-0003-0710-995X", "clpid": "Newman-S" }, { "family_name": "Oehler", "given_name": "Dorothy", "clpid": "Oehler-D-Z" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Oremland", "given_name": "Ronald", "clpid": "Oremland-R-S" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Popa", "given_name": "Radu", "clpid": "Popa-R" }, { "family_name": "Russell", "given_name": "Michael", "clpid": "Russell-M-J" }, { "family_name": "Shen", "given_name": "Linhan", "orcid": "0000-0003-3871-655X", "clpid": "Shen-Linhan" }, { "family_name": "Sherwood Lollar", "given_name": "Barbara", "clpid": "Sherwood-Lollar-B" }, { "family_name": "Staehle", "given_name": "Robert", "clpid": "Staehle-R-L" }, { "family_name": "Stamenkovi\u0107", "given_name": "Vlada", "orcid": "0000-0003-2416-3683", "clpid": "Stamenkovi\u0107-V" }, { "family_name": "Stolper", "given_name": "Daniel", "orcid": "0000-0003-3299-3177", "clpid": "Stolper-D-A" }, { "family_name": "Templeton", "given_name": "Alexis", "clpid": "Templeton-A" }, { "family_name": "Vandaele", "given_name": "Ann C.", "clpid": "Vandaele-A-C" }, { "family_name": "Viscardy", "given_name": "S\u00e9bastien", "clpid": "Viscardy-S" }, { "family_name": "Webster", "given_name": "Christopher R.", "clpid": "Webster-C-R" }, { "family_name": "Wennberg", "given_name": "Paul O.", "orcid": "0000-0002-6126-3854", "clpid": "Wennberg-P-O" }, { "family_name": "Wong", "given_name": "Michael L.", "clpid": "Wong-Michael-L" }, { "family_name": "Worden", "given_name": "John", "orcid": "0000-0003-0257-9549", "clpid": "Worden-J-R" } ], "abstract": "Recent measurements of methane (CH_4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH_4 (\u223c0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH_4 with peak abundances of \u223c7\u2009ppbv. What do these CH_4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH_4 a biosignature? Discerning how CH_4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH_4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH_4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, \"Where can we find redox gradients as energy sources for life on Mars?\" Hence, regardless of the pathway that generates CH_4 on Mars, the presence of CH_4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH_4. To discriminate between abiotic and biotic sources of CH_4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH_4 isotopes, methane/ethane ratios, H_2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH_4.", "doi": "10.1089/ast.2018.1917", "pmcid": "PMC6205098", "issn": "1557-8070", "publisher": "Mary Ann Liebert", "publication": "Astrobiology", "publication_date": "2018-10", "series_number": "10", "volume": "18", "issue": "10", "pages": "1221-1242" }, { "id": "authors:ge6w8-r9t97", "collection": "authors", "collection_id": "ge6w8-r9t97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180919-102939169", "type": "article", "title": "The gut of the finch: uniqueness of the gut microbiome of the Gal\u00e1pagos vampire finch", "author": [ { "family_name": "Michel", "given_name": "Alice J.", "orcid": "0000-0002-0273-4097", "clpid": "Michel-Alice-J" }, { "family_name": "Ward", "given_name": "Lewis M.", "orcid": "0000-0002-9290-2567", "clpid": "Ward-L-M" }, { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Baldassarre", "given_name": "Daniel T.", "clpid": "Baldassarre-D-T" }, { "family_name": "Brenner", "given_name": "Alec", "clpid": "Brenner-A" }, { "family_name": "Gotanda", "given_name": "Kiyoko M.", "clpid": "Gotanda-Kiyoko-M" }, { "family_name": "McCormack", "given_name": "John E.", "clpid": "McCormack-J-E" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-S-W" }, { "family_name": "O'Neill", "given_name": "Ariel", "clpid": "O'Neill-A" }, { "family_name": "Tender", "given_name": "Gabrielle S.", "clpid": "Tender-G-S" }, { "family_name": "Uy", "given_name": "J. Albert C.", "clpid": "Uy-J-Albert-C" }, { "family_name": "Yu", "given_name": "Kristie", "orcid": "0000-0001-6735-3968", "clpid": "Yu-Kristie" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Chaves", "given_name": "Jaime A.", "clpid": "Chaves-J-A" } ], "abstract": "Background: Darwin's finches are a clade of 19 species of passerine birds native to the Gal\u00e1pagos Islands, whose biogeography, specialized beak morphologies, and dietary choices\u2014ranging from seeds to blood\u2014make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. \n\nResults: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception\u2014the vampire finch\u2014which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia\u2014bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high \u03b415N isotope values in the vampire finch, resembling top marine predators. The Gal\u00e1pagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons. \n\nConclusions: This study demonstrates the overall conservatism of the finch gut microbiome over short (<\u20091 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.", "doi": "10.1186/s40168-018-0555-8", "pmcid": "PMC6146768", "issn": "2049-2618", "publisher": "BioMed Central", "publication": "Microbiome", "publication_date": "2018-09-19", "volume": "6", "pages": "Art. No. 167" }, { "id": "authors:qq53c-deh68", "collection": "authors", "collection_id": "qq53c-deh68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180926-133207423", "type": "article", "title": "Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales", "author": [ { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-D-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the 'Lake Pavin cluster', an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the 'Lake Pavin cluster' draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.", "doi": "10.7717/peerj.5614", "pmcid": "PMC6147122", "issn": "2167-8359", "publisher": "PeerJ", "publication": "PeerJ", "publication_date": "2018-09-17", "series_number": "6", "volume": "2018", "issue": "6", "pages": "Art. No. e5614" }, { "id": "authors:xq66k-gpc36", "collection": "authors", "collection_id": "xq66k-gpc36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180411-080037971", "type": "article", "title": "Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy", "author": [ { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "O'Neill", "given_name": "Ariel", "clpid": "O'Neill-A" }, { "family_name": "Mackey", "given_name": "Mason", "clpid": "Mackey-M" }, { "family_name": "Thor", "given_name": "Andrea", "clpid": "Thor-A" }, { "family_name": "Deerinck", "given_name": "Thomas J.", "clpid": "Deerinck-T-J" }, { "family_name": "Ellisman", "given_name": "Mark H.", "orcid": "0000-0001-8893-8455", "clpid": "Ellisman-M-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescence in situ hybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.", "doi": "10.1128/AEM.00399-18", "pmcid": "PMC5960974", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2018-06", "series_number": "11", "volume": "84", "issue": "11", "pages": "Art. No. e00399-18" }, { "id": "authors:k753y-v6d34", "collection": "authors", "collection_id": "k753y-v6d34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180613-160656492", "type": "article", "title": "Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex", "author": [ { "family_name": "Ijiri", "given_name": "Akira", "clpid": "Ijiri-Akira" }, { "family_name": "Case", "given_name": "David H.", "clpid": "Case-David-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microbial life inhabiting subseafloor sediments plays an important role in Earth's carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16\u00b0 to 30\u00b0C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (10^2 to 10^3 cells cm^(\u22123)) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated.", "doi": "10.1126/sciadv.aao4631", "pmcid": "PMC6007163", "issn": "2375-2548", "publisher": "American Association for the Advancement of Science", "publication": "Science Advances", "publication_date": "2018-06", "series_number": "6", "volume": "4", "issue": "6", "pages": "Art. No. eaao4631" }, { "id": "authors:322yd-cme50", "collection": "authors", "collection_id": "322yd-cme50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170901-140533444", "type": "article", "title": "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples", "author": [ { "family_name": "Zhu", "given_name": "Ying", "clpid": "Zhu-Ying" }, { "family_name": "Zhao", "given_name": "Rui", "clpid": "Zhao-Rui" }, { "family_name": "Piehowski", "given_name": "Paul D.", "clpid": "Piehowski-Paul-D" }, { "family_name": "Moore", "given_name": "Ronald J.", "clpid": "Moore-Ronald-J" }, { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Pa\u0161a-Toli\u0107", "given_name": "Ljiljana", "clpid": "Pa\u0161a-Toli\u0107-Ljiljana" }, { "family_name": "Qian", "given_name": "Wei-Jun", "clpid": "Qian-Wei-Jun" }, { "family_name": "Smith", "given_name": "Richard D.", "clpid": "Smith-Richard-D" }, { "family_name": "Kelly", "given_name": "Ryan T.", "clpid": "Kelly-Ryan-T" } ], "abstract": "One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-\u03bcm-i.d. columns increase signal intensity by >3-fold relative to those using 75-\u03bcm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos MS significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a \u223c3-fold increase in peptide identifications and 1.7-fold increase in identified protein groups for 2 ng tryptic digests of the bacterium S. oneidensis. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by \u223c 95% for 0.5 ng samples and by \u223c42% for 2 ng samples. Using the best combination of the above variables, we were able to identify >3,000 proteins from 10 ng tryptic digests from both HeLa and THP-1 mammalian cell lines. We also identified >950 proteins from subnanogram archaeal/bacterial cocultures. The present ultrasensitive LC-MS platform achieves a level of proteome coverage not previously realized for ultra-small sample loadings, and is expected to facilitate the analysis of subnanogram samples, including single mammalian cells.", "doi": "10.1016/j.ijms.2017.08.016", "pmcid": "PMC5863755", "issn": "1387-3806", "publisher": "Elsevier", "publication": "International Journal of Mass Spectrometry", "publication_date": "2018-04", "volume": "427", "pages": "4-10" }, { "id": "authors:bmec6-p6p93", "collection": "authors", "collection_id": "bmec6-p6p93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171127-134624207", "type": "article", "title": "Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods", "author": [ { "family_name": "Pasulka", "given_name": "Alexis L.", "clpid": "Pasulka-A-L" }, { "family_name": "Thamatrakoln", "given_name": "Kimberlee", "clpid": "Thamatrakoln-K" }, { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Guan", "given_name": "Yunbin", "orcid": "0000-0002-7636-3735", "clpid": "Guan-Yunbin" }, { "family_name": "Poulos", "given_name": "Bonnie", "clpid": "Poulos-B" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Sullivan", "given_name": "Mathew B.", "clpid": "Sullivan-M-B" }, { "family_name": "Bidle", "given_name": "Kay D.", "clpid": "Bidle-K-D" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus-host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single-virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1, and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.", "doi": "10.1111/1462-2920.13996", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2018-02", "series_number": "2", "volume": "20", "issue": "2", "pages": "671-692" }, { "id": "authors:ty0ky-bbj58", "collection": "authors", "collection_id": "ty0ky-bbj58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171023-152816244", "type": "article", "title": "Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis", "author": [ { "family_name": "Fike", "given_name": "D. A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Houghton", "given_name": "J. L.", "clpid": "Houghton-J-L" }, { "family_name": "Moore", "given_name": "S. E.", "clpid": "Moore-S-E" }, { "family_name": "Gilhooly", "given_name": "W. P.", "clpid": "Gilhooly-W-P-III" }, { "family_name": "Dawson", "given_name": "K. S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Druschel", "given_name": "G. K.", "clpid": "Druschel-G-K" }, { "family_name": "Amend", "given_name": "J. P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-J-P" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Sulfur cycling is ubiquitous in sedimentary environments, where it plays a major role in mediating carbon remineralization and impacts both local and global redox budgets. Microbial sulfur cycling is dominated by metabolic activity that either produces (e.g., sulfate reduction, disproportionation) or consumes (sulfide oxidation) hydrogen sulfide (H_2S). As such, improved constraints on the production, distribution, and consumption of H_2S in the natural environment will increase our understanding of microbial sulfur cycling. These different microbial sulfur metabolisms are additionally associated with particular stable isotopic fractionations. Coupling measurements of the isotopic composition of the sulfide with its distribution can provide additional information about environmental conditions and microbial ecology. Here we investigate the kinetics of sulfide capture on photographic films as a way to document the spatial distribution of sulfide in complex natural environments as well as for in situ capture of H_2S for subsequent stable isotopic analysis. Laboratory experiments and timed field deployments demonstrate the ability to infer ambient sulfide abundances from the yield of sulfide on the films. This captured sulfide preserves the isotopic composition of the ambient sulfide, offset to slightly lower \u03b4^(34)S values by ~ 1.2 \u00b1 0.5\u2030 associated with the diffusion of sulfide into the film and subsequent reaction with silver to form Ag_2S precipitates. The resulting data enable the exploration of cm-scale lateral heterogeneity that complement most geochemical profiles using traditional techniques in natural environments. Because these films can easily be deployed over a large spatial area, they are also ideal for real-time assessment of the spatial and temporal dynamics of a site during initial reconnaissance and for integration over long timescales to capture ephemeral processes.", "doi": "10.1016/j.marchem.2017.10.004", "issn": "0304-4203", "publisher": "Elsevier", "publication": "Marine Chemistry", "publication_date": "2017-12-20", "volume": "197", "pages": "26-37" }, { "id": "authors:6xkm8-vsw65", "collection": "authors", "collection_id": "6xkm8-vsw65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180105-082606163", "type": "article", "title": "Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment", "author": [ { "family_name": "Case", "given_name": "David H.", "clpid": "Case-D-H" }, { "family_name": "Ijiri", "given_name": "Akira", "clpid": "Ijiri-Akira" }, { "family_name": "Morono", "given_name": "Yuki", "orcid": "0000-0001-8928-4254", "clpid": "Morono-Yuki" }, { "family_name": "Tavormina", "given_name": "Patricia", "clpid": "Tavormina-P-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Inagaki", "given_name": "Fumio", "clpid": "Inagaki-Fumio" } ], "abstract": "High-pressure (HP) environments represent the largest volumetric majority of habitable space for microorganisms on the planet, including the deep-sea and subsurface biosphere. However, the importance of pressure as an environmental variable affecting deep microbial life and their biogeochemical functions in carbon cycling still remains poorly understood. Here, we designed a new high-volume HP-sediment core sampler that is deployable on the payload of a remotely operated vehicle and can maintain in situ HP conditions throughout multi-month enrichment incubations including daily amendments with liquid media and gases and daily effluent sampling for geochemical or microbiological analysis. Using the HP core device, we incubated sediment and overlying water associated with methane hydrate-exposed on the seafloor of the Joetsu Knoll, Japan, at 10 MPa and 4\u00b0C for 45 days in the laboratory. Diversity analyses based on 16S rRNA and methane-related functional genes, as well as carbon isotopic analysis of methane and bicarbonate, indicated the stimulation of both aerobic and anaerobic methanotrophy driven by members of the Methylococcales, and ANME, respectively: i.e., aerobic methanotrophy was observed upon addition of oxygen whereas anaerobic processes subsequently occurred after oxygen consumption. These laboratory-measured rates at 10 MPa were generally in agreement with previously reported rates of methane oxidation in other oceanographic locations.", "doi": "10.3389/fmicb.2017.02569", "pmcid": "PMC5742206", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2017-12-19", "volume": "8", "pages": "Art. No. 2569" }, { "id": "authors:d9taj-wmq73", "collection": "authors", "collection_id": "d9taj-wmq73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171005-093343465", "type": "article", "title": "Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds", "author": [ { "family_name": "Trembath-Reichert", "given_name": "Elizabeth", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-Elizabeth" }, { "family_name": "Morono", "given_name": "Yuki", "orcid": "0000-0001-8928-4254", "clpid": "Morono-Yuki" }, { "family_name": "Ijiri", "given_name": "Akira", "orcid": "0000-0001-7140-1491", "clpid": "Ijiri-Akira" }, { "family_name": "Hoshino", "given_name": "Tatsuhiko", "clpid": "Hoshino-Tatsuhiko" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Inagaki", "given_name": "Fumio", "orcid": "0000-0003-2887-6525", "clpid": "Inagaki-Fumio" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be \"hot spots\" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 \u00b0C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ^(13)C- or ^(15)N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50\u20132,000 cells per cubic centimeter), bulk geochemical measurements and single-cell\u2013targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.", "doi": "10.1073/pnas.1707525114", "pmcid": "PMC5676895", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2017-10-31", "series_number": "44", "volume": "114", "issue": "44", "pages": "E9206-E9215" }, { "id": "authors:rsbg3-jhx25", "collection": "authors", "collection_id": "rsbg3-jhx25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170522-080446020", "type": "article", "title": "Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis", "author": [ { "family_name": "Terrado", "given_name": "Ramon", "clpid": "Terrado-R" }, { "family_name": "Pasulka", "given_name": "Alexis L.", "clpid": "Pasulka-A-L" }, { "family_name": "Lie", "given_name": "Alle A.-Y.", "clpid": "Lie-Alle-A-Y" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Heidelberg", "given_name": "Karla B.", "clpid": "Heidelberg-K-B" }, { "family_name": "Caron", "given_name": "David A.", "clpid": "Caron-D-A" } ], "abstract": "Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing. An axenic culture was grown in the presence of either heat-killed bacteria enriched with ^(15)N and ^(13)C, or unlabeled heat-killed bacteria and labeled inorganic substrates (^(13)C-bicarbonate and ^(15)N-ammonium). The alga exhibited high growth rates (up to 2 divisions per day) only until heat-killed bacteria were depleted. NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84\u201399% of its carbon and 88\u201395% of its nitrogen from consumed bacteria. The chrysophyte assimilated inorganic ^(13)C-carbon and ^(15)N-nitrogen when bacterial abundances were very low, but autotrophic (photosynthetic) activity was insufficient to support net population growth of the alga. Our use of nanoSIMS represents its first application towards the study of a mixotrophic alga, enabling a better understanding and quantitative assessment of carbon and nutrient acquisition by this species.", "doi": "10.1038/ismej.2017.68", "pmcid": "PMC5563956", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2017-09", "series_number": "9", "volume": "11", "issue": "9", "pages": "2022-2034" }, { "id": "authors:tg3vp-hna45", "collection": "authors", "collection_id": "tg3vp-hna45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170807-095231730", "type": "article", "title": "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea", "author": [ { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-C-T" }, { "family_name": "Chourey", "given_name": "Karuna", "clpid": "Chourey-K" }, { "family_name": "Iyer", "given_name": "Ramsunder", "clpid": "Iyer-R" }, { "family_name": "Hettich", "given_name": "Robert L.", "clpid": "Hettich-R-L" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-G-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Dubilier", "given_name": "Nicole", "orcid": "0000-0002-9394-825X", "clpid": "Dubilier-N" } ], "abstract": "The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.", "doi": "10.1128/mBio.00530-17", "pmcid": "PMC5539420", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2017-08-01", "series_number": "4", "volume": "8", "issue": "4", "pages": "Art. No. e00530-17" }, { "id": "authors:fbdzt-0y458", "collection": "authors", "collection_id": "fbdzt-0y458", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170914-133025440", "type": "article", "title": "Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Steele", "given_name": "Joshua A.", "clpid": "Steele-J-A" }, { "family_name": "Ziebis", "given_name": "Wiebke", "clpid": "Ziebis-W" }, { "family_name": "Scheller", "given_name": "Silvan", "orcid": "0000-0002-0667-9224", "clpid": "Scheller-S" }, { "family_name": "Case", "given_name": "David", "clpid": "Case-D-H" }, { "family_name": "Reynard", "given_name": "Linda M.", "clpid": "Reynard-L-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH_3D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH_3D procedure and the well-established ^(14)CH_4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH_3D method were directly and consistently proportional to ^(14)C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method.", "doi": "10.1128/mSphereDirect.00309-17", "pmcid": "PMC5566838", "issn": "2379-5042", "publisher": "American Society for Microbiology", "publication": "mSphere", "publication_date": "2017-07", "series_number": "4", "volume": "2", "issue": "4", "pages": "Art. No. e00309" }, { "id": "authors:kaxjq-tkr54", "collection": "authors", "collection_id": "kaxjq-tkr54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170227-143517457", "type": "article", "title": "Quantification and isotopic analysis of intracellular sulfur metabolites in the dissimilatory sulfate reduction pathway", "author": [ { "family_name": "Sim", "given_name": "Min Sub", "orcid": "0000-0002-3491-9002", "clpid": "Sim-Min-Sub" }, { "family_name": "Paris", "given_name": "Guillaume", "orcid": "0000-0001-8368-1224", "clpid": "Paris-G" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "abstract": "Microbial sulfate reduction exhibits a normal isotope effect, leaving unreacted sulfate enriched in ^(34)S and producing sulfide that is depleted in ^(34)S. However, the magnitude of sulfur isotope fractionation is quite variable. The resulting changes in sulfur isotope abundance have been used to trace microbial sulfate reduction in modern and ancient ecosystems, but the intracellular mechanism(s) underlying the wide range of fractionations remains unclear. Here we report the concentrations and isotopic ratios of sulfur metabolites in the dissimilatory sulfate reduction pathway of Desulfovibrio alaskensis. Intracellular sulfate and APS levels change depending on the growth phase, peaking at the end of exponential phase, while sulfite accumulates in the cell during stationary phase. During exponential growth, intracellular sulfate and APS are strongly enriched in ^(34)S. The fractionation between internal and external sulfate is up to 49\u2030, while at the same time that between external sulfate and sulfide is just a few permil. We interpret this pattern to indicate that enzymatic fractionations remain large but the net fractionation between sulfate and sulfide is muted by the closed-system limitation of intracellular sulfate. This 'reservoir effect' diminishes upon cessation of exponential phase growth, allowing the expression of larger net sulfur isotope fractionations. Thus, the relative rates of sulfate exchange across the membrane versus intracellular sulfate reduction should govern the overall (net) fractionation that is expressed. A strong reservoir effect due to vigorous sulfate reduction might be responsible for the well-established inverse correlation between sulfur isotope fractionation and the cell-specific rate of sulfate reduction, while at the same time intraspecies differences in sulfate uptake and/or exchange rates could account for the significant scatter in this relationship. Our approach, together with ongoing investigations of the kinetic isotope fractionation by key enzymes in the sulfate reduction pathway, should provide an empirical basis for a quantitative model relating the magnitude of microbial isotope fractionation to their environmental and physiological controls.", "doi": "10.1016/j.gca.2017.02.024", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2017-06-01", "volume": "206", "pages": "57-72" }, { "id": "authors:ek2hy-sf917", "collection": "authors", "collection_id": "ek2hy-sf917", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180411-113723264", "type": "article", "title": "Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging", "author": [ { "family_name": "Glass", "given_name": "Jennifer B.", "orcid": "0000-0003-0775-2486", "clpid": "Glass-J-B" }, { "family_name": "Chen", "given_name": "Si", "orcid": "0000-0001-6619-2699", "clpid": "Chen-Si" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Horton", "given_name": "Damian R.", "clpid": "Horton-D-R" }, { "family_name": "Vogt", "given_name": "Stefan", "orcid": "0000-0002-8034-5513", "clpid": "Vogt-S" }, { "family_name": "Ingall", "given_name": "Ellery D.", "orcid": "0000-0003-1954-0317", "clpid": "Ingall-E-D" }, { "family_name": "Twining", "given_name": "Benjamin S.", "orcid": "0000-0002-1365-9192", "clpid": "Twining-B-S" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Metal cofactors are required for many enzymes in anaerobic microbial respiration. This study examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron X-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. For both species, zinc and iron were consistently the most abundant cellular metals. M. acetivorans contained higher nickel and cobalt content than D. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper sulfides.", "doi": "10.1080/01490451.2017.1321068", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "2017-05-19", "series_number": "1", "volume": "35", "issue": "1", "pages": "81-89" }, { "id": "authors:jj2kc-5mv06", "collection": "authors", "collection_id": "jj2kc-5mv06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170306-080715333", "type": "article", "title": "Rapid Quantification and Isotopic Analysis of Dissolved Sulfur Species", "author": [ { "family_name": "Smith", "given_name": "Derek A.", "clpid": "Smith-D-A" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Dalleska", "given_name": "Nathan", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Rationale: Dissolved sulfur species are of significant interest, both as important substrates for microbial activities and as key intermediaries in biogeochemical cycles. Species of intermediate oxidation state such as sulfite, thiosulfate, and thiols are of particular interest but are notoriously difficult to analyze, because of low concentrations and rapid oxidation during storage and analysis. \n\nMethods: Dissolved sulfur species are reacted with monobromobimane which yields a fluorescent bimane derivative that is stable to oxidation. Separation by Ultra-Performance Liquid Chromatography (UPLC) on a C18 column yields baseline resolution of analytes in under 5 minutes. Fluorescence detection (380 nm excitation, 480 nm emission) provides highly selective and sensitive quantitation, and Time of Flight Mass Spectrometry (TOF-MS) is used to quantify isotopic abundance, providing the ability to detect stable isotope tracers (either ^(33)S or ^(34)S). \n\nResults: Sulfite, thiosulfate, methanethiol, and bisulfide were quantified with on-column detection limits of picomoles (\u03bcM concentrations). Other sulfur species with unshared electrons are also amenable to analysis. TOF-MS detection of ^(34)S enrichment was accurate and precise to within 0.6% (relative) when sample and standard had similar isotope ratios, and was able to detect enrichments as small as 0.01 atom%. Accuracy was validated by comparison to isotope-ratio mass spectrometry. Four example applications are provided to demonstrate the utility of this method. \n\nConclusions: Derivatization of aqueous sulfur species with bromobimane is easily accomplished in the field, and protects analytes from oxidation during storage. UPLC separation with fluorescence detection provides low \u03bcM detection limits. Using a high-resolution TOF-MS, accurate detection of as little as 0.01% ^(34)S label incorporation into multiple species is feasible. This provides a useful new analytical window into microbial sulfur cycling.", "doi": "10.1002/rcm.7846", "issn": "0951-4198", "publisher": "Wiley", "publication": "Rapid Communications in Mass Spectrometry", "publication_date": "2017-05-15", "series_number": "9", "volume": "31", "issue": "9", "pages": "791-803" }, { "id": "authors:c7wa0-j6j26", "collection": "authors", "collection_id": "c7wa0-j6j26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161017-155437081", "type": "article", "title": "Starvation and recovery in the deep-sea methanotroph Methyloprofundus sedimenti", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Kellermann", "given_name": "Matthias Y.", "clpid": "Kellermann-M-Y" }, { "family_name": "Antony", "given_name": "Chakkiath Paul", "clpid": "Antony-C-P" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Dalleska", "given_name": "Nathan F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" }, { "family_name": "Jensen", "given_name": "Ashley J.", "clpid": "Jensen-A-J" }, { "family_name": "Valentine", "given_name": "David L.", "clpid": "Valentine-D-L" }, { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Dubilier", "given_name": "Nicole", "orcid": "0000-0002-9394-825X", "clpid": "Dubilier-N" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "In the deep ocean, the conversion of methane into derived carbon and energy drives the establishment of diverse faunal communities. Yet specific biological mechanisms underlying the introduction of methane-derived carbon into the food web remain poorly described, due to a lack of cultured representative deep-sea methanotrophic prokaryotes. Here, the response of the deep-sea aerobic methanotroph Methyloprofundus sedimenti to methane starvation and recovery was characterized. By combining lipid analysis, RNA analysis, and electron cryotomography, it was shown that M. sedimenti undergoes discrete cellular shifts in response to methane starvation, including changes in headgroup-specific fatty acid saturation levels, and reductions in cytoplasmic storage granules. Methane starvation is associated with a significant increase in the abundance of gene transcripts pertinent to methane oxidation. Methane reintroduction to starved cells stimulates a rapid, transient extracellular accumulation of methanol, revealing a way in which methane-derived carbon may be routed to community members. This study provides new understanding of methanotrophic responses to methane starvation and recovery, and lays the initial groundwork to develop Methyloprofundus as a model chemosynthesizing bacterium from the deep sea.", "doi": "10.1111/mmi.13553", "issn": "0950-382X", "publisher": "Blackwell", "publication": "Molecular Microbiology", "publication_date": "2017-01", "series_number": "2", "volume": "103", "issue": "2", "pages": "242-252" }, { "id": "authors:y5wta-5nf96", "collection": "authors", "collection_id": "y5wta-5nf96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160418-080655842", "type": "article", "title": "Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps", "author": [ { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-Connor-T" }, { "family_name": "Haroon", "given_name": "Mohamed F.", "clpid": "Haroon-Mohamed-F" }, { "family_name": "Briegel", "given_name": "Ariane", "orcid": "0000-0003-3733-3725", "clpid": "Briegel-Ariane" }, { "family_name": "Shi", "given_name": "Jian", "orcid": "0000-0003-3810-5302", "clpid": "Shi-Jian" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-Gene-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as 'NB1-n' (SILVA taxonomy) or 'RF3' (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these 'NB1-n' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10\u2009\u00b0C, resulting in a mixed culture where these organisms represented ~60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus 'Izimaplasma sp. HR1' and Candidatus 'Izimaplasma sp. HR2' for the two genome representatives.", "doi": "10.1038/ismej.2016.55", "pmcid": "PMC5113845", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2016-11", "series_number": "11", "volume": "10", "issue": "11", "pages": "2679-2692" }, { "id": "authors:a6c91-x2a19", "collection": "authors", "collection_id": "a6c91-x2a19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160808-234129625", "type": "article", "title": "Measurement of rare isotopologues of nitrous oxide by high-resolution multi-collector mass spectrometry", "author": [ { "family_name": "Magyar", "given_name": "Paul M.", "clpid": "Magyar-P-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "abstract": "Rationale: Bulk and position-specific stable isotope characterization of nitrous oxide represents one of the most powerful tools for identifying its environmental sources and sinks. Constraining ^(14)N^(15)N^(18)O and ^(15)N^(14)N^(18)O will add two new dimensions to our ability to uniquely fingerprint N_2O sources. \n\nMethods: We describe a technique to measure six singly and doubly substituted isotopic variants of N2O, constraining the values of \u03b4^(15)N, \u03b4^(18)O, \u2206^(17)O, ^(15)N site preference, and the clumped isotopomers ^(14)N^(15)N^(18)O and ^(15)N^(14)N^(18)O. The technique uses a Thermo MAT 253 Ultra, a high-resolution multi-collector gas source isotope ratio mass spectrometer. It requires 8\u201310 hours per sample and ~10 micromoles or more of pure N_2O. \n\nResults: We demonstrate the precision and accuracy of these measurements by analyzing N_2O brought to equilibrium in its position-specific and clumped isotopic composition by heating in the presence of a catalyst. Finally, an illustrative analysis of biogenic N_2O from a denitrifying bacterium suggests that its clumped isotopic composition is controlled by kinetic isotope effects in N_2O production. \n\nConclusions: We developed a method for measuring six isotopic variants of N_2O and tested it with analyses of biogenic N_2O. The added isotopic constraints provided by these measurements will enhance our ability to apportion N_2O sources.", "doi": "10.1002/rcm.7671", "issn": "0951-4198", "publisher": "Wiley", "publication": "Rapid Communications in Mass Spectrometry", "publication_date": "2016-09-15", "series_number": "17", "volume": "30", "issue": "17", "pages": "1923-1940" }, { "id": "authors:qgtgg-myb60", "collection": "authors", "collection_id": "qgtgg-myb60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151221-150217687", "type": "article", "title": "Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem", "author": [ { "family_name": "Pasulka", "given_name": "Alexis L.", "clpid": "Pasulka-A-L" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Steele", "given_name": "Josh A.", "clpid": "Steele-J-A" }, { "family_name": "Case", "given_name": "David H.", "clpid": "Case-D-H" }, { "family_name": "Landry", "given_name": "Michael R.", "clpid": "Landry-M-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.", "doi": "10.1111/1462-2920.13185", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2016-09", "series_number": "9", "volume": "18", "issue": "9", "pages": "3022-3043" }, { "id": "authors:0v5ac-ffr92", "collection": "authors", "collection_id": "0v5ac-ffr92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160815-131417667", "type": "article", "title": "Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA", "author": [ { "family_name": "Miranda", "given_name": "Priscilla J.", "clpid": "Miranda-P-J" }, { "family_name": "McLain", "given_name": "Nathan K.", "clpid": "McLain-N-K" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Dillon", "given_name": "Jesse G.", "clpid": "Dillon-J-G" } ], "abstract": "The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities.", "doi": "10.3389/fmicb.2016.01163", "pmcid": "PMC4961709", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2016-07-27", "volume": "7", "pages": "Art. No. 1163" }, { "id": "authors:9gq6z-05s57", "collection": "authors", "collection_id": "9gq6z-05s57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160628-092522305", "type": "article", "title": "Visualizing in situ translational activity for identifying and sorting slow-growing archaeal\u2212bacterial consortia", "author": [ { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Woykeb", "given_name": "Tanja", "clpid": "Woykeb-Tanja" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.", "doi": "10.1073/pnas.1603757113", "pmcid": "PMC4948357", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-07-12", "series_number": "28", "volume": "113", "issue": "28", "pages": "E4069-E4078" }, { "id": "authors:hyaec-4vq74", "collection": "authors", "collection_id": "hyaec-4vq74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160811-151334696", "type": "article", "title": "Members of the methanotrophic genus Methylomarinum inhabit inland mud pots", "author": [ { "family_name": "Fradet", "given_name": "Danielle T.", "clpid": "Fradet-D-T" }, { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling.", "doi": "10.7717/peerj.2116", "pmcid": "PMC4950536", "issn": "2167-8359", "publisher": "PeerJ", "publication": "PeerJ", "publication_date": "2016-07-12", "volume": "4", "pages": "Art. No. e2116" }, { "id": "authors:sqzhk-v7j78", "collection": "authors", "collection_id": "sqzhk-v7j78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160620-104423818", "type": "article", "title": "Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment", "author": [ { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Scheller", "given_name": "Silvan", "orcid": "0000-0002-0667-9224", "clpid": "Scheller-S" }, { "family_name": "Dillon", "given_name": "Jesse G.", "clpid": "Dillon-J-G" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with ^(13)C-acetate, ^(15)N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (^(13)C/^(12)C, ^(15)N/^(14)N, and ^(33)S/^(32)S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.", "doi": "10.3389/fmicb.2016.00774", "pmcid": "PMC4881376", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2016-05-26", "volume": "7", "pages": "Art. No. 774" }, { "id": "authors:vq0n5-vd548", "collection": "authors", "collection_id": "vq0n5-vd548", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160601-152032127", "type": "article", "title": "Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-C-T" }, { "family_name": "Li", "given_name": "Zhou", "clpid": "Li-Zhou" }, { "family_name": "Chourey", "given_name": "Karuna", "clpid": "Chourey-K" }, { "family_name": "Hettich", "given_name": "Robert L.", "clpid": "Hettich-R-L" }, { "family_name": "Pan", "given_name": "Chongle", "clpid": "Pan-Chongle" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to ^(15)NH_4^+ and CH_4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were ^(15)N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis\u2014including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)\u2014were all observed to be actively synthesized (^(15)N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of ^(15)N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system.", "doi": "10.3389/fmicb.2016.00563", "pmcid": "PMC4850331", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2016-04-29", "volume": "7", "pages": "Art. No. 563" }, { "id": "authors:xzdvs-b6w75", "collection": "authors", "collection_id": "xzdvs-b6w75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160502-081644901", "type": "article", "title": "Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments", "author": [ { "family_name": "Trembath-Reichert", "given_name": "Elizabeth", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-E" }, { "family_name": "Case", "given_name": "David H.", "clpid": "Case-D-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.", "doi": "10.7717/peerj.1913", "pmcid": "PMC4841229", "issn": "2167-8359", "publisher": "PeerJ", "publication": "PeerJ", "publication_date": "2016-04-18", "volume": "4", "pages": "Art. No. e1913" }, { "id": "authors:wz0yx-1z206", "collection": "authors", "collection_id": "wz0yx-1z206", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150928-110118499", "type": "article", "title": "Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses", "author": [ { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-S-A" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Trembath-Reichert", "given_name": "Elizabeth", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-E" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5\u2032-phosphosulfate reductase \u03b1-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no ^(15)NH^+_4 assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active 'free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N_2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. ^(15)N_2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, ^(15)N_2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced ^(15)N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.", "doi": "10.1038/ismej.2015.145", "pmcid": "PMC4817681", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2016-03", "series_number": "3", "volume": "10", "issue": "3", "pages": "678-692" }, { "id": "authors:6m92v-45022", "collection": "authors", "collection_id": "6m92v-45022", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160216-090201597", "type": "article", "title": "Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction", "author": [ { "family_name": "Scheller", "given_name": "Silvan", "orcid": "0000-0002-0667-9224", "clpid": "Scheller-S" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane.", "doi": "10.1126/science.aad7154", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2016-02-12", "series_number": "6274", "volume": "351", "issue": "6274", "pages": "703-707" }, { "id": "authors:f77p5-wfy55", "collection": "authors", "collection_id": "f77p5-wfy55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160104-065151473", "type": "article", "title": "Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum", "author": [ { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-Sebastian-H" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Cowley", "given_name": "Elise S.", "clpid": "Cowley-Elise-S" }, { "family_name": "Reyes", "given_name": "Carmen", "clpid": "Reyes-Carmen" }, { "family_name": "Van Sambeek", "given_name": "Lindsey", "orcid": "0000-0002-7206-7410", "clpid": "Van-Sambeek-Lindsey" }, { "family_name": "Hu", "given_name": "Yang", "clpid": "Hu-Yang" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Kato", "given_name": "Roberta M.", "clpid": "Kato-Roberta-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Effective treatment for chronic infections is undermined by a significant gap in understanding of the physiological state of pathogens at the site of infection. Chronic pulmonary infections are responsible for the morbidity and mortality of millions of immunocompromised individuals worldwide, yet drugs that are successful in laboratory culture are far less effective against pathogen populations persisting in vivo. Laboratory models, upon which preclinical development of new drugs is based, can only replicate host conditions when we understand the metabolic state of the pathogens and the degree of heterogeneity within the population. In this study, we measured the anabolic activity of the pathogen Staphylococcus aureus directly in the sputum of pediatric patients with cystic fibrosis (CF), by combining the high sensitivity of isotope ratio mass spectrometry with a heavy water labeling approach to capture the full range of in situ growth rates. Our results reveal S. aureus generation times with a median of 2.1 d, with extensive growth rate heterogeneity at the single-cell level. These growth rates are far below the detection limit of previous estimates of CF pathogen growth rates, and the rates are slowest in acutely sick patients undergoing pulmonary exacerbations; nevertheless, they are accessible to experimental replication within laboratory models. Treatment regimens that include specific antibiotics (vancomycin, piperacillin/tazobactam, tobramycin) further appear to correlate with slow growth of S. aureus on average, but follow-up longitudinal studies must be performed to determine whether this effect holds for individual patients.", "doi": "10.1073/pnas.1512057112", "pmcid": "PMC4720290", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-01-12", "series_number": "2", "volume": "113", "issue": "2", "pages": "E110-E116" }, { "id": "authors:yx9xd-rk111", "collection": "authors", "collection_id": "yx9xd-rk111", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160108-103050704", "type": "article", "title": "Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation", "author": [ { "family_name": "Skennerton", "given_name": "Connor T.", "orcid": "0000-0003-1320-4873", "clpid": "Skennerton-C-T" }, { "family_name": "Ward", "given_name": "Lewis M.", "orcid": "0000-0002-9290-2567", "clpid": "Ward-L-M" }, { "family_name": "Michel", "given_name": "Alice", "orcid": "0000-0002-0273-4097", "clpid": "Michel-Alice-J" }, { "family_name": "Metcalfe", "given_name": "Kyle", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-K-S" }, { "family_name": "Valiente", "given_name": "Chanel", "clpid": "Valiente-C" }, { "family_name": "Mullin", "given_name": "Sean", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-S-W" }, { "family_name": "Chan", "given_name": "Ken Y.", "orcid": "0000-0002-8853-5186", "clpid": "Chan-Ken-Y" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at \u223c80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x\u201312x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other Proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.", "doi": "10.3389/fmicb.2015.01425", "pmcid": "PMC4688376", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2015-12-23", "volume": "6", "pages": "Art. No. 1425" }, { "id": "authors:hzdq0-zya89", "collection": "authors", "collection_id": "hzdq0-zya89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160104-131039931", "type": "article", "title": "Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages", "author": [ { "family_name": "Case", "given_name": "David H.", "clpid": "Case-D-H" }, { "family_name": "Pasulka", "given_name": "Alexis L.", "clpid": "Pasulka-A-L" }, { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Grupe", "given_name": "Benjamin M.", "orcid": "0000-0002-5421-7278", "clpid": "Grupe-B-M" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages.", "doi": "10.1128/mBio.01348-15", "pmcid": "PMC4701829", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2015-12", "series_number": "6", "volume": "6", "issue": "6", "pages": "Art. No. e01348-15" }, { "id": "authors:p73rn-8f443", "collection": "authors", "collection_id": "p73rn-8f443", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160104-070726621", "type": "article", "title": "A unified initiative to harness Earth's microbiomes", "author": [ { "family_name": "Alivisatos", "given_name": "A. P.", "orcid": "0000-0001-6895-9048", "clpid": "Alivisatos-A-P" }, { "family_name": "Blaser", "given_name": "M. J.", "clpid": "Blaser-M-J" }, { "family_name": "Brodie", "given_name": "E. L.", "clpid": "Brodie-E-L" }, { "family_name": "Chun", "given_name": "M.", "clpid": "Chun-Miyoung" }, { "family_name": "Dangl", "given_name": "J. L.", "clpid": "Dangl-J-L" }, { "family_name": "Donohue", "given_name": "T. J.", "clpid": "Donohue-T-J" }, { "family_name": "Dorrestein", "given_name": "P. C.", "clpid": "Dorrestein-P-C" }, { "family_name": "Gilbert", "given_name": "J. A.", "clpid": "Gilbert-J-A" }, { "family_name": "Green", "given_name": "J. L.", "clpid": "Green-J-L" }, { "family_name": "Jansson", "given_name": "J. K.", "orcid": "0000-0002-5487-4315", "clpid": "Jansson-J-K" }, { "family_name": "Knight", "given_name": "R.", "orcid": "0000-0002-0975-9019", "clpid": "Knight-R" }, { "family_name": "Maxon", "given_name": "M. E.", "clpid": "Maxon-M-E" }, { "family_name": "McFall-Ngai", "given_name": "M. J.", "orcid": "0000-0002-6046-6238", "clpid": "McFall-Ngai-Margaret-J" }, { "family_name": "Miller", "given_name": "J. F.", "clpid": "Miller-J-F" }, { "family_name": "Pollard", "given_name": "K. S.", "clpid": "Pollard-K-S" }, { "family_name": "Ruby", "given_name": "E. G.", "clpid": "Ruby-E-G" }, { "family_name": "Taha", "given_name": "S. A.", "clpid": "Taha-S-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "literal": "Unified Microbiome Initiative Consortium" } ], "abstract": "Despite their centrality to life on Earth, we know little about how microbes (1) interact with each other, their hosts, or their environment. Although DNA sequencing technologies have enabled a new view of the ubiquity and diversity of microorganisms, this has mainly yielded snapshots that shed limited light on microbial functions or community dynamics. Given that nearly every habitat and organism hosts a diverse constellation of microorganisms\u2014its \"microbiome\"\u2014such knowledge could transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more (see the photo). We propose an interdisciplinary Unified Microbiome Initiative (UMI) to discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems. The impacts of oceans and soil microbes on atmospheric CO_2 are critical for understanding climate change (2). By manipulating interactions at the root-soil-microbe interface, we may reduce agricultural pesticide, fertilizer, and water use enrich marginal land and rehabilitate degraded soils. Microbes can degrade plant cell walls (for biofuels), and synthesize myriad small molecules for new bioproducts, including antibiotics (3). Restoring normal human microbial ecosystems can save lives [e.g., fecal microbiome transplantation for Clostridium difficile infections (4)]. Rational management of microbial communities in and around us has implications for asthma, diabetes, obesity, infectious diseases, psychiatric illnesses, and other afflictions (5, 6). The human microbiome is a target and a source for new drugs (7) and an essential tool for precision medicine (8).", "doi": "10.1126/science.aac8480", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2015-10-30", "series_number": "6260", "volume": "350", "issue": "6260", "pages": "507-508" }, { "id": "authors:585f3-jft03", "collection": "authors", "collection_id": "585f3-jft03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151103-081330300", "type": "article", "title": "Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics", "author": [ { "family_name": "Evans", "given_name": "Paul N.", "clpid": "Evans-P-N" }, { "family_name": "Parks", "given_name": "Donovan H.", "clpid": "Parks-D-H" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Robbins", "given_name": "Steven J.", "clpid": "Robbins-S-J" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Golding", "given_name": "Suzanne D.", "clpid": "Golding-S-D" }, { "family_name": "Tyson", "given_name": "Gene W.", "orcid": "0000-0001-8559-9427", "clpid": "Tyson-G-W" } ], "abstract": "Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl\u2013coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.", "doi": "10.1126/science.aac7745", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2015-10-23", "series_number": "6259", "volume": "350", "issue": "6259", "pages": "434-438" }, { "id": "authors:s1vn4-6z659", "collection": "authors", "collection_id": "s1vn4-6z659", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150729-141906854", "type": "article", "title": "Single cell activity reveals direct electron transfer in methanotrophic consortia", "author": [ { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Kempes", "given_name": "Christopher P.", "orcid": "0000-0002-1622-9761", "clpid": "Kempes-C-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.", "doi": "10.1038/nature15512", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2015-10-22", "series_number": "7574", "volume": "526", "issue": "7574", "pages": "531-535" }, { "id": "authors:9dnqt-02129", "collection": "authors", "collection_id": "9dnqt-02129", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151112-154353069", "type": "article", "title": "A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments", "author": [ { "family_name": "Bryson", "given_name": "Samuel Joseph", "clpid": "Bryson-S-J" }, { "family_name": "Thurber", "given_name": "Andrew R.", "clpid": "Thurber-A-R" }, { "family_name": "Correa", "given_name": "Adrienne M. S.", "clpid": "Correa-A-M-S" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Thurber", "given_name": "Rebecca Vega", "clpid": "Thurber-R-V" } ], "abstract": "Methane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major-capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Peque\u00f1ovirus.", "doi": "10.1111/1462-2920.12758", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2015-10", "series_number": "10", "volume": "17", "issue": "10", "pages": "3708-3721" }, { "id": "authors:fdhmq-5t379", "collection": "authors", "collection_id": "fdhmq-5t379", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151023-073758726", "type": "article", "title": "Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA", "author": [ { "family_name": "Mason", "given_name": "Olivia U.", "clpid": "Mason-O-U" }, { "family_name": "Case", "given_name": "David H.", "clpid": "Case-D-H" }, { "family_name": "Naehr", "given_name": "Thomas H.", "clpid": "Naehr-T-H" }, { "family_name": "Lee", "given_name": "Raymond W.", "clpid": "Lee-Raymond-W" }, { "family_name": "Thomas", "given_name": "Randal B.", "clpid": "Thomas-R-B" }, { "family_name": "Bailey", "given_name": "Jake V.", "clpid": "Bailey-J-V" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Anaerobic oxidation of methane (AOM) impacts carbon cycling by acting as a methane sink and by sequestering inorganic carbon via AOM-induced carbonate precipitation. These precipitates commonly take the form of carbonate nodules that form within methane seep sediments. The timing and sequence of nodule formation within methane seep sediments are not well understood. Further, the microbial diversity associated with sediment-hosted nodules has not been well characterized and the degree to which nodules reflect the microbial assemblage in surrounding sediments is unknown. Here, we conducted a comparative study of microbial assemblages in methane-derived authigenic carbonate nodules and their host sediments using molecular, mineralogical, and geochemical methods. Analysis of 16S rRNA gene diversity from paired carbonate nodules and sediments revealed that both sample types contained methanotrophic archaea (ANME-1 and ANME-2) and syntrophic sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae), as well as other microbial community members. The combination of geochemical and molecular data from Eel River Basin and Hydrate Ridge suggested that some nodules formed in situ and captured the local sediment-hosted microbial community, while other nodules may have been translocated or may represent a record of conditions prior to the contemporary environment. Taken together, this comparative analysis offers clues to the formation regimes and mechanisms of sediment-hosted carbonate nodules.", "doi": "10.1007/s00248-015-0615-6", "issn": "0095-3628", "publisher": "Springer Verlag", "publication": "Microbial Ecology", "publication_date": "2015-10", "series_number": "3", "volume": "70", "issue": "3", "pages": "766-784" }, { "id": "authors:9zqqt-kvn93", "collection": "authors", "collection_id": "9zqqt-kvn93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150505-105030332", "type": "article", "title": "Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps", "author": [ { "family_name": "Dawson", "given_name": "K. S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Osburn", "given_name": "M. R.", "orcid": "0000-0001-9180-559X", "clpid": "Osburn-M-R" }, { "family_name": "Sessions", "given_name": "A. L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro-organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate-reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing Deltaproteobacteria (SRB) recovered from deep-sea methane seeps. Consistent with previously reported trends, we observed a ~80\u2030 range in hydrogen isotope fractionation (\u03b5_(lipid\u2013water)) for D. multivorans grown under different carbon assimilation conditions, with more D-enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of \u03b5_(lipid\u2013water) values (~36\u2030) across substrates with shifts of up to 61\u2030 compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D-enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in \u03b5_(lipid\u2013water) values.", "doi": "10.1111/gbi.12140", "issn": "1472-4677", "publisher": "Wiley-Blackwell", "publication": "Geobiology", "publication_date": "2015-09", "series_number": "5", "volume": "13", "issue": "5", "pages": "462-477" }, { "id": "authors:7v4s2-d5h36", "collection": "authors", "collection_id": "7v4s2-d5h36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150220-131055817", "type": "article", "title": "Heavy water and \u00b9\u2075N labeling with NanoSIMS analysis reveals growth-rate dependent metabolic heterogeneity in chemostats", "author": [ { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Green-Saxena", "given_name": "Abigail", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Guan", "given_name": "Yunbin", "orcid": "0000-0002-7636-3735", "clpid": "Guan-Yunbin" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "To measure single cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labeling of microbial populations with heavy water (a passive tracer) and \u00b9\u2075N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (~0.1 atom % \u00b2H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (~6 hours, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium vs. amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.", "doi": "10.1111/1462-2920.12752", "pmcid": "PMC4587896", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2015-07", "series_number": "7", "volume": "17", "issue": "7", "pages": "2542-2556" }, { "id": "authors:vtzvb-47s30", "collection": "authors", "collection_id": "vtzvb-47s30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150420-090013681", "type": "article", "title": "Autoendoliths: a distinct type of rock-hosted microbial life", "author": [ { "family_name": "Marlow", "given_name": "J.", "clpid": "Marlow-J" }, { "family_name": "Peckmann", "given_name": "J.", "clpid": "Peckmann-J" }, { "family_name": "Orphan", "given_name": "V.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The continued exploration of Earth's biological potential\nhas revealed a range of unexpected microbial habitats. The\ndiscovery of organisms inhabiting rock interiors, known as\nendoliths, was one such revelation that has altered our perspective\nof habitability, bioenergetics, and the relationship\nbetween biology and geology (Walker & Pace, 2007).", "doi": "10.1111/gbi.12131", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2015-07", "series_number": "4", "volume": "13", "issue": "4", "pages": "303-307" }, { "id": "authors:fr4a3-3bm16", "collection": "authors", "collection_id": "fr4a3-3bm16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141111-104738855", "type": "article", "title": "Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-Patricia-L" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-Shawn-E" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1, \"whale fall 1\" that shares 98% 16S rRNA identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep sea mussels, 94.6% 16S rRNA identity with Methylobacter species, and 93.6% 16S rRNA identity with Methylomonas and Methylosarcina species. Strain WF1 represents the first cultivar from the 'Deep Sea 1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. WF1 cells were elongated cocci approximately 1.5 \u00b5m in diameter, and occurred singly, in pairs and clumps. The cell wall was Gram negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic GC content of WF1 was 40.5%, significantly lower than currently described cultivars, and the major fatty acids were 16:0, 16:1 \u03c99c, 16:1 \u03c99t, 16:1 \u03c98c and 16:2 \u03c99, 14. Growth occurred in liquid media at an optimal temperature of 23oC, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1, a capacity that had not been functionally demonstrated in members of Methylobacter. On the basis of unique morphological, physiological, and phylogenetic properties this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti (type strain WF1 = BCCM LMG 28393 = ATCC BAA-2619).", "doi": "10.1099/ijs.0.062927-0", "issn": "1466-5026", "publisher": "International Union of Microbiological Societies", "publication": "International Journal of Systematic and Evolutionary Microbiology", "publication_date": "2015-01", "series_number": "1", "volume": "65", "issue": "1", "pages": "251-259" }, { "id": "authors:jm9wh-8tv60", "collection": "authors", "collection_id": "jm9wh-8tv60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150107-070238329", "type": "article", "title": "Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh", "author": [ { "family_name": "Wilbanks", "given_name": "Elizabeth G.", "clpid": "Wilbanks-E-G" }, { "family_name": "Jaekel", "given_name": "Ulrike", "clpid": "Jaekel-U" }, { "family_name": "Salman", "given_name": "Verena", "clpid": "Salman-V" }, { "family_name": "Humphrey", "given_name": "Parris T.", "clpid": "Humphrey-P-T" }, { "family_name": "Elsen", "given_name": "Jonathan A.", "clpid": "Elsen-J-A" }, { "family_name": "Facciotti", "given_name": "Marc T.", "clpid": "Facciotti-M-T" }, { "family_name": "Buckley", "given_name": "Daniel H.", "clpid": "Buckley-D-H" }, { "family_name": "Zinder", "given_name": "Stephen H.", "clpid": "Zinder-S-H" }, { "family_name": "Druschel", "given_name": "Gregory K.", "clpid": "Druschel-G-K" }, { "family_name": "Fike", "given_name": "David A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and ^(34)S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0\u2013500\u2009\u03bcm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while \u03b4^(34)S-sulfide decreased from 6\u2030 to \u221231\u2030 from the exterior to interior of the berry. These values correspond to sulfate\u2013sulfide isotopic fractionations (15\u201353\u2030) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.", "doi": "10.1111/1462-2920.12388", "pmcid": "PMC4262008", "issn": "1462-2912", "publisher": "Wiley Blackwell", "publication": "Environmental Microbiology", "publication_date": "2014-11", "series_number": "11", "volume": "16", "issue": "11", "pages": "3398-3415" }, { "id": "authors:pwwjq-qxg49", "collection": "authors", "collection_id": "pwwjq-qxg49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141201-092909674", "type": "article", "title": "Spatial variability in photosynthetic and heterotrophic activity drives localized \u03b4^(13)C_(org) fluctuations and carbonate precipitation in hypersaline microbial mats", "author": [ { "family_name": "Houghton", "given_name": "J.", "clpid": "Houghton-J-T" }, { "family_name": "Fike", "given_name": "D.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Druschel", "given_name": "G.", "clpid": "Druschel-G-K" }, { "family_name": "Orphan", "given_name": "V.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Hoehler", "given_name": "T. M.", "clpid": "Hoehler-T-M" }, { "family_name": "Des Marais", "given_name": "D. J.", "clpid": "Des-Marais-D-J" } ], "abstract": "Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for \u03b4^(13)C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on \u03b4^(13)C signatures. In the photic zone, the \u03b4^(13)C_(org) signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO_2 limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits \u03b4^(13)C signatures similar to DIC in the overlying water column (\u22122.0\u2030), with small but variable decreases consistent with localized heterotrophic activity from sulfate-reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and HCO_3^-\nconcentrations to create both phototrophic CO_2 limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter-scale variability in the \u03b4^(13)C_(org) signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on \u03b4^(13)C_(org) signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling.", "doi": "10.1111/gbi.12113", "issn": "1472-4677", "publisher": "Wiley Blackwell", "publication": "Geobiology", "publication_date": "2014-11", "series_number": "6", "volume": "12", "issue": "6", "pages": "557-574" }, { "id": "authors:vc0x8-jxv41", "collection": "authors", "collection_id": "vc0x8-jxv41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140923-111251974", "type": "article", "title": "Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps", "author": [ { "family_name": "Sivan", "given_name": "Orit", "clpid": "Sivan-O" }, { "family_name": "Antler", "given_name": "Gilad", "clpid": "Antler-G" }, { "family_name": "Turchyn", "given_name": "Alexandra V.", "orcid": "0000-0002-9298-2173", "clpid": "Turchyn-A-V" }, { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Seep sediments are dominated by intensive microbial sulfate reduction coupled to the anaerobic oxidation of methane (AOM). Through geochemical measurements of incubation experiments with methane seep sediments collected from Hydrate Ridge, we provide insight into the role of iron oxides in sulfate-driven AOM. Seep sediments incubated with ^(13)C-labeled methane showed co-occurring sulfate reduction, AOM, and methanogenesis. The isotope fractionation factors for sulfur and oxygen isotopes in sulfate were about 40\u2030 and 22\u2030, respectively, reinforcing the difference between microbial sulfate reduction in methane seeps versus other sedimentary environments (for example, sulfur isotope fractionation above 60\u2030 in sulfate reduction coupled to organic carbon oxidation or in diffusive sedimentary sulfate\u2013methane transition zone). The addition of hematite to these microcosm experiments resulted in significant microbial iron reduction as well as enhancing sulfate-driven AOM. The magnitude of the isotope fractionation of sulfur and oxygen isotopes in sulfate from these incubations was lowered by about 50%, indicating the involvement of iron oxides during sulfate reduction in methane seeps. The similar relative change between the oxygen versus sulfur isotopes of sulfate in all experiments (with and without hematite addition) suggests that oxidized forms of iron, naturally present in the sediment incubations, were involved in sulfate reduction, with hematite addition increasing the sulfate recycling or the activity of sulfur-cycling microorganisms by about 40%. These results highlight a role for natural iron oxides during bacterial sulfate reduction in methane seeps not only as nutrient but also as stimulator of sulfur recycling.", "doi": "10.1073/pnas.1412269111", "pmcid": "PMC4209987", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2014-10-07", "series_number": "40", "volume": "111", "issue": "40", "pages": "E4139-E4147" }, { "id": "authors:9evf2-ek834", "collection": "authors", "collection_id": "9evf2-ek834", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141201-133733752", "type": "article", "title": "Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea", "author": [ { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Bowles", "given_name": "Marshall W.", "orcid": "0000-0002-0464-5880", "clpid": "Bowles-M-W" }, { "family_name": "Joye", "given_name": "Samantha B.", "orcid": "0000-0003-1610-451X", "clpid": "Joye-S-B" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Nitrogen (N_2) fixation was investigated at Mound 12, Costa Rica, to determine its spatial distribution and biogeochemical controls in deep-sea methane seep sediment. Using ^(15)N_2 tracer experiments and isotope ratio mass spectrometry analysis, we observed that seep N_2 fixation is methane-dependent, and that N_2 fixation rates peak in a narrow sediment depth horizon corresponding to increased abundance of aggregates of anaerobic methanotrophic archaea (ANME-2) and sulfate-reducing bacteria (SRB). Using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS), we directly measured ^(15)N_2 uptake by ANME-2/SRB aggregates (n\u2009=\u200926) and observed maximum ^(15)N incorporation within ANME-2-dominated areas of the aggregates, consistent with previous analyses. NanoSIMS analysis of single cells (n\u2009=\u200934) from the same microcosm experiment revealed no ^(15)N_2 uptake. Together, these observations suggest that ANME-2, and possibly physically associated SRB, mediate the majority of new nitrogen production within the seep ecosystem. ANME-2 diazotrophy was observed while in association with members of two distinct orders of SRB: Desulfobacteraceae and Desulfobulbaceae. The rate of N_2 fixation per unit volume biomass was independent of the identity of the associated SRB, aggregate size and morphology. Our results show that the distribution of seep N_2 fixation is heterogeneous, laterally and with depth in the sediment, and is likely influenced by chemical gradients affecting the abundance and activity of ANME-2/SRB aggregates.", "doi": "10.1111/1462-2920.12247", "issn": "1462-2912", "publisher": "Wiley Blackwell", "publication": "Environmental Microbiology", "publication_date": "2014-10", "series_number": "10", "volume": "16", "issue": "10", "pages": "3012-3029" }, { "id": "authors:qq4hw-7vy68", "collection": "authors", "collection_id": "qq4hw-7vy68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141002-104139439", "type": "article", "title": "Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Steele", "given_name": "Joshua A.", "clpid": "Steele-J-A" }, { "family_name": "Ziebis", "given_name": "Wiebke", "clpid": "Ziebis-W" }, { "family_name": "Thurber", "given_name": "Andrew R.", "clpid": "Thurber-A-R" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The atmospheric flux of methane from the oceans is largely mitigated through microbially mediated sulphate-coupled methane oxidation, resulting in the precipitation of authigenic carbonates. Deep-sea carbonates are common around active and palaeo-methane seepage, and have primarily been viewed as passive recorders of methane oxidation; their role as active and unique microbial habitats capable of continued methane consumption has not been examined. Here we show that seep-associated carbonates harbour active microbial communities, serving as dynamic methane sinks. Microbial aggregate abundance within the carbonate interior exceeds that of seep sediments, and molecular diversity surveys reveal methanotrophic communities within protolithic nodules and well-lithified carbonate pavements. Aggregations of microbial cells within the carbonate matrix actively oxidize methane as indicated by stable isotope FISH\u2013nanoSIMS experiments and ^(14)CH_4 radiotracer rate measurements. Carbonate-hosted methanotrophy extends the known ecological niche of these important methane consumers and represents a previously unrecognized methane sink that warrants consideration in global methane budgets.", "doi": "10.1038/ncomms6094", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2014-10", "series_number": "10", "volume": "5", "issue": "10", "pages": "Art. No. 6094" }, { "id": "authors:vfq0r-7c398", "collection": "authors", "collection_id": "vfq0r-7c398", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140303-103306009", "type": "article", "title": "In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry", "author": [ { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-R" }, { "family_name": "Scheller", "given_name": "Silvan", "orcid": "0000-0002-0667-9224", "clpid": "Scheller-S" }, { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Babin", "given_name": "Brett M.", "orcid": "0000-0002-4133-6665", "clpid": "Babin-B-M" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for L-methionine, followed by fluorescent labeling of AHA containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater, and anoxic sediment. We also developed combined assays that couple BONCAT with rRNA-targeted FISH, enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labeling by nanoSIMS (^(15)NH_4^+ assimilation) for individual cells within a sediment sourced enrichment culture showed concordance between AHA positive cells and ^(15)N enrichment. BONCAT-FISH offers a fast, inexpensive, and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single cell level.", "doi": "10.1111/1462-2920.12436", "pmcid": "PMC4122687", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2014-08", "series_number": "8", "volume": "16", "issue": "8", "pages": "2568-2590" }, { "id": "authors:v17gj-1ek53", "collection": "authors", "collection_id": "v17gj-1ek53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140717-091139174", "type": "article", "title": "Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments", "author": [ { "family_name": "Glass", "given_name": "Jennifer B.", "orcid": "0000-0003-0775-2486", "clpid": "Glass-J-B" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Steele", "given_name": "Joshua A.", "clpid": "Steele-J-A" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Sun", "given_name": "Shulei", "clpid": "Sun-Shulei" }, { "family_name": "Chourey", "given_name": "Karuna", "clpid": "Chourey-K" }, { "family_name": "Pan", "given_name": "Chongle", "clpid": "Pan-Chongle" }, { "family_name": "Hettich", "given_name": "Robert L.", "clpid": "Hettich-R-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (\u2264\u200910\u00b0C) and sulphidic (>\u20091\u2009mM \u03a3H_(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5\u2013270\u2009nM), cobalt (0.5\u20136\u2009nM), molybdenum (10\u20135600\u2009nM) and tungsten (0.3\u20138\u2009nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B_(12) biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.", "doi": "10.1111/1462-2920.12314", "issn": "1462-2912", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology", "publication_date": "2014-06", "series_number": "6", "volume": "16", "issue": "6", "pages": "1592-1633" }, { "id": "authors:40ae3-cvj72", "collection": "authors", "collection_id": "40ae3-cvj72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140326-130213946", "type": "article", "title": "The rise and fall of methanotrophy following a deepwater oil-well blowout", "author": [ { "family_name": "Crespo-Medina", "given_name": "M.", "clpid": "Crespo-Medina-M" }, { "family_name": "Meile", "given_name": "C. D.", "orcid": "0000-0002-0825-4596", "clpid": "Meile-C-D" }, { "family_name": "Hunter", "given_name": "K. S.", "clpid": "Hunter-K-S" }, { "family_name": "Diercks", "given_name": "A. R.", "clpid": "Diercks-A-R" }, { "family_name": "Asper", "given_name": "V.", "clpid": "Asper-V" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Tavormina", "given_name": "P. L.", "clpid": "Tavormina-P-L" }, { "family_name": "Nigro", "given_name": "L. M.", "clpid": "Nigro-L-M" }, { "family_name": "Battles", "given_name": "J. J.", "clpid": "Battles-J-J" }, { "family_name": "Chanton", "given_name": "J. P.", "clpid": "Chanton-J-P" }, { "family_name": "Shiller", "given_name": "A. M.", "clpid": "Shiller-A-M" }, { "family_name": "Joung", "given_name": "D-J.", "clpid": "Joung-D-J" }, { "family_name": "Amon", "given_name": "R. M. W.", "clpid": "Amon-R-M-W" }, { "family_name": "Bracco", "given_name": "A.", "clpid": "Bracco-A" }, { "family_name": "Montoya", "given_name": "J. P.", "clpid": "Montoya-J-P" }, { "family_name": "Villareal", "given_name": "T. A.", "clpid": "Villareal-T-A" }, { "family_name": "Wood", "given_name": "A. M.", "clpid": "Wood-A-M" }, { "family_name": "Joye", "given_name": "S. B.", "orcid": "0000-0003-1610-451X", "clpid": "Joye-S-B" } ], "abstract": "The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea1. Most of the methane released was thought to have been consumed by marine microbes between July and August 20102, 3. Here, we report spatially extensive measurements of methane concentrations and oxidation rates in the nine months following the spill. We show that although gas-rich deepwater plumes were a short-lived feature, water column concentrations of methane remained above background levels throughout the rest of the year. Rates of microbial methane oxidation peaked in the deepwater plumes in May and early June, coincident with a rapid rise in the abundance of known and new methane-oxidizing microbes. At this time, rates of methane oxidation reached up to 5,900 nmol l\u22121 d\u22121\u2014the highest rates documented in the global pelagic ocean before the blowout4. Rates of methane oxidation fell to less than 50 nmol l\u22121 d\u22121 in late June, and continued to decline throughout the remainder of the year. We suggest the precipitous drop in methane consumption in late June, despite the persistence of methane in the water column, underscores the important role that physiological and environmental factors play in constraining the activity of methane-oxidizing bacteria in the Gulf of Mexico.", "doi": "10.1038/ngeo2156", "issn": "1752-0894", "publisher": "Nature Publishing Group", "publication": "Nature Geoscience", "publication_date": "2014-06", "series_number": "6", "volume": "7", "issue": "6", "pages": "423-427" }, { "id": "authors:x40dj-tn892", "collection": "authors", "collection_id": "x40dj-tn892", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140408-093723442", "type": "article", "title": "The Potential for Biologically Catalyzed Anaerobic Methane Oxidation on Ancient Mars", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "LaRowe", "given_name": "Douglas E.", "clpid": "LaRowe-D-E" }, { "family_name": "Ehlmann", "given_name": "Bethany L.", "orcid": "0000-0002-2745-3240", "clpid": "Ehlmann-B-L" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-J-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO_2 partial pressures. In all scenarios, AOM is exergonic, ranging from \u221231 to \u2212135\u2009kJ/mol CH_4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.", "doi": "10.1089/ast.2013.1078", "issn": "1557-8070", "publisher": "Mary Ann Liebert", "publication": "Astrobiology", "publication_date": "2014-04", "series_number": "4", "volume": "14", "issue": "4", "pages": "292-307" }, { "id": "authors:sybzw-cvw76", "collection": "authors", "collection_id": "sybzw-cvw76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140310-102130554", "type": "article", "title": "Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea", "author": [ { "family_name": "Sapir", "given_name": "Amir", "orcid": "0000-0001-9888-1800", "clpid": "Sapir-A" }, { "family_name": "Dillman", "given_name": "Adler R.", "orcid": "0000-0001-7171-4332", "clpid": "Dillman-A-R" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-S-A" }, { "family_name": "Grupe", "given_name": "Benjamin M.", "orcid": "0000-0002-5421-7278", "clpid": "Grupe-B-M" }, { "family_name": "Ingels", "given_name": "Jeroen", "orcid": "0000-0001-8342-2222", "clpid": "Ingels-J" }, { "family_name": "Mundo-Ocampo", "given_name": "Manuel", "clpid": "Mundo-Ocampo-M" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Baldwin", "given_name": "James G.", "orcid": "0000-0001-6468-0285", "clpid": "Baldwin-J-G" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "The deep sea is Earth's largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over 2 years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes' intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the host's body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep-sea biosphere.", "doi": "10.3389/fmicb.2014.00043", "pmcid": "PMC3918590", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2014-02-10", "volume": "5", "pages": "Art. No. 43" }, { "id": "authors:2ndyf-67w03", "collection": "authors", "collection_id": "2ndyf-67w03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140116-093516040", "type": "article", "title": "Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane", "author": [ { "family_name": "Green-Saxena", "given_name": "A.", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Dekas", "given_name": "A. E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Dalleska", "given_name": "N. F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher 15N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS.", "doi": "10.1038/ismej.2013.147", "pmcid": "PMC3869021", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2014-01", "series_number": "1", "volume": "8", "issue": "1", "pages": "150-163" }, { "id": "authors:fdvjn-ypx09", "collection": "authors", "collection_id": "fdvjn-ypx09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130917-101809185", "type": "article", "title": "Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis", "author": [ { "family_name": "Bailey", "given_name": "J. V.", "clpid": "Bailey-J-V" }, { "family_name": "Corsetti", "given_name": "F. A.", "clpid": "Corsetti-F-A" }, { "family_name": "Greene", "given_name": "S. E.", "clpid": "Greene-S-E" }, { "family_name": "Crosby", "given_name": "C. H.", "clpid": "Crosby-C-H" }, { "family_name": "Liu", "given_name": "P.", "clpid": "Liu-P" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Marine phosphate-rich sedimentary deposits (phosphorites) are important geological reservoirs for the biologically essential nutrient phosphorous. Phosphorites first appear in abundance approximately 600 million years ago, but their proliferation at that time is poorly understood. Recent marine phosphorites spatially correlate with the habitats of vacuolated sulfide-oxidizing bacteria that store polyphosphates under oxic conditions to be utilized under sulfidic conditions. Hydrolysis of the stored polyphosphate results in the rapid precipitation of the phosphate-rich mineral apatite\u2014providing a mechanism to explain the association between modern phosphorites and these bacteria. Whether sulfur bacteria were important to the formation of ancient phosphorites has been unresolved. Here, we present the remains of modern sulfide-oxidizing bacteria that are partially encrusted in apatite, providing evidence that bacterially mediated phosphogenesis can rapidly permineralize sulfide-oxidizing bacteria and perhaps other types of organic remains. We also describe filamentous microfossils that resemble modern sulfide-oxidizing bacteria from two major phosphogenic episodes in the geologic record. These microfossils contain sulfur-rich inclusions that may represent relict sulfur globules, a diagnostic feature of modern sulfide-oxidizing bacteria. These findings suggest that sulfur bacteria, which are known to mediate the precipitation of apatite in modern sediments, were also present in certain phosphogenic settings for at least the last 600 million years. If polyphosphate-utilizing sulfide-oxidizing bacteria also played a role in the formation of ancient phosphorites, their requirements for oxygen, or oxygen-requiring metabolites such as nitrate, might explain the temporal correlation between the first appearance of globally distributed marine phosphorites and increasing oxygenation of Neoproterozoic oceans.", "doi": "10.1111/gbi.12046", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2013-09", "series_number": "5", "volume": "11", "issue": "5", "pages": "397-405" }, { "id": "authors:hdd3w-prt06", "collection": "authors", "collection_id": "hdd3w-prt06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130909-141442695", "type": "article", "title": "Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum", "author": [ { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-E-I" }, { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Morris", "given_name": "Dylan", "clpid": "Morris-D-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "abstract": "Using electron cryotomography, we show that the Gram-negative sporulating bacterium Acetonema longum synthesizes high-density storage granules at the leading edges of engulfing membranes. The granules appear in the prespore and increase in size and number as engulfment proceeds. Typically, a cluster of 8 to 12 storage granules closely associates with the inner spore membrane and ultimately accounts for \u223c7% of the total volume in mature spores. Energy-dispersive X-ray spectroscopy (EDX) analyses show that the granules contain high levels of phosphorus, oxygen, and magnesium and therefore are likely composed of polyphosphate (poly-P). Unlike the Gram-positive Bacilli and Clostridia, A. longum spores retain their outer spore membrane upon germination. To explore the possibility that the granules in A. longum may be involved in this unique process, we imaged purified Bacillus cereus, Bacillus thuringiensis, Bacillus subtilis, and Clostridium sporogenes spores. Even though B. cereus and B. thuringiensis contain the ppk and ppx genes, none of the spores from Gram-positive bacteria had granules. We speculate that poly-P in A. longum may provide either the energy or phosphate metabolites needed for outgrowth while retaining an outer membrane.", "doi": "10.1128/JB.00712-13", "pmcid": "PMC3754598", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2013-09", "series_number": "17", "volume": "195", "issue": "17", "pages": "3940-3946" }, { "id": "authors:qy8k3-d3k57", "collection": "authors", "collection_id": "qy8k3-d3k57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327897", "type": "article", "title": "Autonomous Application of Quantitative PCR in the Deep Sea: In Situ Surveys of Aerobic Methanotrophs Using the Deep-Sea Environmental Sample Processor", "author": [ { "family_name": "Ussler", "given_name": "William, III", "clpid": "Ussler-W-III" }, { "family_name": "Preston", "given_name": "Christina", "clpid": "Preston-C" }, { "family_name": "Tavormina", "given_name": "Patricia", "clpid": "Tavormina-P-L" }, { "family_name": "Pargett", "given_name": "Doug", "clpid": "Pargett-D" }, { "family_name": "Jensen", "given_name": "Scott", "clpid": "Jensen-S" }, { "family_name": "Roman", "given_name": "Brent", "clpid": "Roman-B" }, { "family_name": "Marin", "given_name": "Roman, III", "clpid": "Marin-R-III" }, { "family_name": "Shah", "given_name": "Sunita R.", "clpid": "Sunita-S-R" }, { "family_name": "Girguis", "given_name": "Peter R.", "clpid": "Girguis-P-R" }, { "family_name": "Birch", "given_name": "James M.", "clpid": "Birch-J-M" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Scholin", "given_name": "Christopher", "clpid": "Scholin-C" } ], "abstract": "Recent advances in ocean observing systems and genomic technologies have led to the development of the deep-sea environmental sample processor (D-ESP). The DESP filters particulates from seawater at depths up to 4000 m and applies a variety of molecular assays to the particulates, including quantitative PCR (qPCR), to identify particular organisms and genes in situ. Preserved samples enable laboratory-based validation of in situ results and expanded studies of genomic diversity and gene expression. Tests of the D-ESP at a methane-rich mound in the Santa Monica Basin centered on detection of 16S rRNA and particulate methane monooxygenase (pmoA) genes for two putative aerobic methanotrophs. Comparison of in situ qPCR results with laboratory-based assays of preserved samples demonstrates the D-ESP generated high-quality qPCR data while operating autonomously on the seafloor. Levels of 16S rRNA and pmoA cDNA detected in preserved samples are consistent with an active community of aerobic methanotrophs near the methane-rich mound. These findings are substantiated at low methane sites off Point Conception and in Monterey Bay where target genes are at or below detection limits. Successful deployment of the D-ESP is a major step toward developing autonomous systems to facilitate a wide range of marine microbiological investigations.", "doi": "10.1021/es4023199", "issn": "0013-936X", "publisher": "American Chemical Society", "publication": "Environmental Science and Technology", "publication_date": "2013-08-20", "series_number": "16", "volume": "47", "issue": "16", "pages": "9339-9346" }, { "id": "authors:n6jz3-3nf78", "collection": "authors", "collection_id": "n6jz3-3nf78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130619-100723976", "type": "article", "title": "Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Ussler", "given_name": "William, III", "clpid": "Ussler-W-III" }, { "family_name": "Steele", "given_name": "Joshua A.", "clpid": "Steele-J-A" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-S-A" }, { "family_name": "Klotz", "given_name": "Martin G.", "clpid": "Klotz-M-G" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Diverse copper-containing membrane-bound monooxygenase-encoding sequences (Cu-MMOs) have recently been described from the marine environment, suggesting widespread potential for oxidation of reduced substrates. Here, we used the well-defined oxygen and methane gradients associated with the Costa Rican oxygen minimum zone (OMZ) to gain insight into the physico-chemical parameters influencing the distribution and abundance of Cu-MMO-encoding marine microorganisms. Two Methylococcales-related Cu-MMO-encoding lineages, termed groups OPU1 and OPU3, demonstrated differences in their relative abundance, with both pmoA and candidate 16S rRNA genes correlating significantly with reduced environmental oxygen concentrations and depth. In contrast, a newly identified Cu-MMO-encoding lineage, Group C, was primarily associated with the oxygenated euphotic zone. An updated phylogenetic analysis including these sequences, a marine pxmABC gene cluster, ethylene-utilizing Cu-MMO-encoding lineages and previously reported planktonic Cu-MMOs (Groups W, X, Z and O) demonstrates the breadth of diversity of Cu-MMO-encoding marine microorganisms. Groups C and X affiliated phylogenetically with ethane- and ethylene-oxidizing Cu-MMOs, Groups W and O affiliated phylogenetically with the recently described Cu-MMO 'pXMO', and Group Z clustered with Cu-MMOs recovered from soils. Collectively, these data demonstrate widespread genetic potential in ocean waters for the oxidation of small, reduced molecules and advance our understanding of the microorganisms involved in methane cycling in the OMZ environment.", "doi": "10.1111/1758-2229.12025", "issn": "1758-2229", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology Reports", "publication_date": "2013-06", "series_number": "3", "volume": "5", "issue": "3", "pages": "414-423" }, { "id": "authors:vhx6s-0bd15", "collection": "authors", "collection_id": "vhx6s-0bd15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140310-084832957", "type": "article", "title": "Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study", "author": [ { "family_name": "Yang", "given_name": "Song", "clpid": "Yang-Song" }, { "family_name": "Matsen", "given_name": "Janet B.", "clpid": "Matsen-J-B" }, { "family_name": "Kunopka", "given_name": "Michael", "clpid": "Konopka-M" }, { "family_name": "Green-Saxena", "given_name": "Abigail", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Clubb", "given_name": "Justin", "clpid": "Clubb-J" }, { "family_name": "Sadilek", "given_name": "Martin", "clpid": "Sadilek-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Beck", "given_name": "David", "clpid": "Beck-D" }, { "family_name": "Kalyuzhnaya", "given_name": "Marina G.", "orcid": "0000-0002-9058-7794", "clpid": "Kalyuzhnaya-M-G" } ], "abstract": "In this work we use metabolomics and ^(13)C-labeling data to refine central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is represented by several tightly connected metabolic cycles, such as the serine pathway, the ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle. Both in silico estimations and stable isotope labeling experiments combined with single cell (NanoSIMS) and bulk biomass analyses indicate that a significantly larger portion of the cell carbon (over 60%) is derived from CO_2 in this methanotroph. Our ^(13) C-labeling studies revealed an unusual topology of the assimilatory network in which phosph(enol) pyruvate/pyruvate interconversions are key metabolic switches. A set of additional pathways for carbon fixation are identified and discussed.", "doi": "10.3389/fmicb.2013.00070", "pmcid": "PMC3615224", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2013-04-03", "volume": "4", "pages": "Art. No. 70" }, { "id": "authors:zw79j-mjn87", "collection": "authors", "collection_id": "zw79j-mjn87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130320-133744148", "type": "article", "title": "Classifying the metal dependence of uncharacterized nitrogenases", "author": [ { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Boyd", "given_name": "Eric S.", "clpid": "Boyd-E-S" }, { "family_name": "Peters", "given_name": "John W.", "clpid": "Peters-J-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Nitrogenase enzymes have evolved complex iron\u2013sulfur (Fe\u2013S) containing cofactors that most commonly contain molybdenum (MoFe, Nif) as a heterometal but also exist as vanadium (VFe, Vnf) and heterometal-independent (Fe-only, Anf) forms. All three varieties are capable of the reduction of dinitrogen (N_2) to ammonia (NH_3) but exhibit differences in catalytic rates and substrate specificity unique to metal type. Recently, N_2 reduction activity was observed in archaeal methanotrophs and methanogens that encode for nitrogenase homologs which do not cluster phylogenetically with previously characterized nitrogenases. To gain insight into the metal cofactors of these uncharacterized nitrogenase homologs, predicted three-dimensional structures of the nitrogenase active site metal-cofactor binding subunits NifD, VnfD, and AnfD were generated and compared. Dendrograms based on structural similarity indicate nitrogenase homologs cluster based on heterometal content and that uncharacterized nitrogenase D homologs cluster with NifD, providing evidence that the structure of the enzyme has evolved in response to metal utilization. Characterization of the structural environment of the nitrogenase active site revealed amino acid variations that are unique to each class of nitrogenase as defined by heterometal cofactor content; uncharacterized nitrogenases contain amino acids near the active site most similar to NifD. Together, these results suggest that uncharacterized nitrogenase homologs present in numerous anaerobic methanogens, archaeal methanotrophs, and firmicutes bind FeMo-co in their active site, and add to growing evidence that diversification of metal utilization likely occurred in an anoxic habitat.", "doi": "10.3389/fmicb.2012.00419", "pmcid": "PMC3578447", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2013-01-30", "volume": "3", "pages": "Art. No. 419" }, { "id": "authors:wtw56-d1f95", "collection": "authors", "collection_id": "wtw56-d1f95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130108-135620155", "type": "article", "title": "Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan", "author": [ { "family_name": "Green-Saxena", "given_name": "A.", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Feyzullayev", "given_name": "A.", "clpid": "Feyzullayev-A" }, { "family_name": "Hubert", "given_name": "C. R. J.", "clpid": "Hubert-C-R-J" }, { "family_name": "Kallmeyer", "given_name": "J.", "clpid": "Kallmeyer-J" }, { "family_name": "Krueger", "given_name": "M.", "clpid": "Krueger-M" }, { "family_name": "Sauer", "given_name": "P. U.", "clpid": "Sauer-P-U" }, { "family_name": "Schulz", "given_name": "H.-M.", "clpid": "Schulz-H-M" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Terrestrial mud volcanoes (TMVs) represent geochemically diverse habitats with varying sulfur sources and yet sulfur cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in four TMVs in Azerbaijan. A combination of geochemical analyses, biological rate measurements and molecular diversity surveys (targeting metabolic genes aprA and dsrA and SSU ribosomal RNA) supported the presence of active sulfur-oxidizing and sulfate-reducing guilds in all four TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. The TMVs varied in potential sulfate reduction rates (SRR) by up to four orders of magnitude with highest SRR observed in sediments where in situ sulfate concentrations were highest. Maximum temperatures at which SRR were measured was 60\u00b0C in two TMVs. Corresponding with these trends in SRR, members of the potentially thermophilic, spore-forming, Desulfotomaculum were detected in these TMVs by targeted 16S rRNA analysis. Additional sulfate-reducing bacterial lineages included members of the Desulfobacteraceae and Desulfobulbaceae detected by aprA and dsrA analyses and likely contributing to the mesophilic SRR measured. Phylotypes affiliated with sulfide-oxidizing Gamma- and Betaproteobacteria were abundant in aprA libraries from low sulfate TMVs, while the highest sulfate TMV harboured 16S rRNA phylotypes associated with sulfur-oxidizing Epsilonproteobacteria. Altogether, the biogeochemical and microbiological data indicate these unique terrestrial habitats support diverse active sulfur-cycling microorganisms reflecting the in situ geochemical environment.", "doi": "10.1111/1462-2920.12015", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2012-12", "series_number": "12", "volume": "14", "issue": "12", "pages": "3271-3286" }, { "id": "authors:a43t8-mep20", "collection": "authors", "collection_id": "a43t8-mep20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130807-132330822", "type": "article", "title": "Measurement of nitrous oxide isotopologues and isotopomers by the MAT 253 Ultra", "author": [ { "family_name": "Magyar", "given_name": "Paul", "clpid": "Magyar-P" }, { "family_name": "Kopf", "given_name": "Sebastian", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Eiler", "given_name": "John", "clpid": "Eiler-J-M" } ], "abstract": "The global budget of nitrous oxide is dominated by terrestrial and marine biological sources and atmospheric sinks. Details of the\nbudget remain unclear, including the cause of increasing atmospheric N_2O concentrations. Marine sources of N_2O include\ndenitrification and nitrification. Our understanding of the major microbial players in the nitrogen cycle has changed in recent years\n(for example, the nitrifying Archaea), and the overall contributions of these organisms to N_2O production and their isotopic signatures\nare poorly constrained [1].", "issn": "0026-461X", "publisher": "Mineralogical Society", "publication": "Mineralogical Magazine", "publication_date": "2012-11", "series_number": "6", "volume": "76", "issue": "6", "pages": "2054-2054" }, { "id": "authors:n4tm5-86723", "collection": "authors", "collection_id": "n4tm5-86723", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327760", "type": "article", "title": "Environmental Microbiology: evolution of your premier journal", "author": [ { "family_name": "Polz", "given_name": "Martin", "clpid": "Polz-M-F" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Bonfante", "given_name": "Paola", "clpid": "Bonfante-P" } ], "abstract": "[no abstract]", "doi": "10.1111/j.1462-2920.2012.02869.x", "issn": "1462-2912", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology", "publication_date": "2012-10", "series_number": "10", "volume": "14", "issue": "10", "pages": "2617-2619" }, { "id": "authors:wx5rm-9b195", "collection": "authors", "collection_id": "wx5rm-9b195", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120817-140759648", "type": "article", "title": "Archaea in metazoan diets: implications for food webs and biogeochemical cycling", "author": [ { "family_name": "Thurber", "given_name": "Andrew R.", "clpid": "Thurber-A-R" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" } ], "abstract": "Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk \u03b4^(13)C=\u221292\u00b14\u2030; polar lipids \u2212116\u2030) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'.", "doi": "10.1038/ismej.2012.16", "pmcid": "PMC3400411", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2012-08", "series_number": "8", "volume": "6", "issue": "8", "pages": "1602-1612" }, { "id": "authors:vmfax-psb17", "collection": "authors", "collection_id": "vmfax-psb17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120622-114155202", "type": "article", "title": "A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems", "author": [ { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Rouse", "given_name": "Greg W.", "clpid": "Rouse-G-W" }, { "family_name": "Rathburn", "given_name": "Anthony E.", "clpid": "Rathburn-A-E" }, { "family_name": "Ussler", "given_name": "William, III", "clpid": "Ussler-W-III" }, { "family_name": "Cook", "given_name": "Geoffrey S.", "clpid": "Cook-G-S" }, { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Perez", "given_name": "Elena M.", "clpid": "Perez-E-M" }, { "family_name": "Waren", "given_name": "Anders", "clpid": "Waren-A" }, { "family_name": "Grupe", "given_name": "Benjamin M.", "orcid": "0000-0002-5421-7278", "clpid": "Grupe-B-M" }, { "family_name": "Chadwick", "given_name": "Grayson", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-G-L" }, { "family_name": "Strickrott", "given_name": "Bruce", "clpid": "Strickrott-B" } ], "abstract": "Upon their initial discovery, hydrothermal vents and methane seeps were considered to be related but distinct ecosystems, with different distributions, geomorphology, temperatures, geochemical properties and mostly different species. However, subsequently discovered vents and seep systems have blurred this distinction. Here, we report on a composite, hydrothermal seep ecosystem at a subducting seamount on the convergent Costa Rica margin that represents an intermediate between vent and seep ecosystems. Diffuse flow of shimmering, warm fluids with high methane concentrations supports a mixture of microbes, animal species, assemblages and trophic pathways with vent and seep affinities. Their coexistence reinforces the continuity of reducing environments and exemplifies a setting conducive to interactive evolution of vent and seep biota.", "doi": "10.1098/rspb.2012.0205", "pmcid": "PMC3350710", "issn": "0962-8452", "publisher": "Royal Society", "publication": "Proceedings of the Royal Society of London. Series B, Biological Sciences", "publication_date": "2012-07-07", "series_number": "1738", "volume": "279", "issue": "1738", "pages": "2580-2588" }, { "id": "authors:70w5n-rhy05", "collection": "authors", "collection_id": "70w5n-rhy05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120518-133946986", "type": "article", "title": "Method for Assessing Mineral Composition-Dependent Patterns in Microbial Diversity Using Magnetic and Density Separation", "author": [ { "family_name": "Harrison", "given_name": "Benjamin K.", "clpid": "Harrison-B-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "This study introduces a new method for characterizing mineral-associated microbial diversity in sedimentary environments, a habitat that has been intrinsically challenging to study in regard to microbe-mineral interactions. Mineral components were enriched from bulk environmental samples by magnetic susceptibility or density separation techniques and used in subsequent molecular and microscopic analyses. Testing and optimization of the method was performed on geochemically-distinct sediment horizons from Eel River Basin methane seeps and pyrite and sphalerite-rich hydrothermal vent samples from the Lau Basin. Initial results show reproducible variations in microbial diversity between mineral fractions from marine sedimentary environments enriched in authigenic pyrite and/or transition metal-bearing clay minerals. Specifically, different archaeal clades associated with the anaerobic oxidation of methane and putative sulfate-reducing deltaproteobbacteria show preferential colonization patterns, suggesting potential ecophysiological differences between closely-related taxa. These results indicate that mineral colonization may influence the extent and distribution of microbial diversity throughout unconsolidated sediments of the marine subsurface. The combination of mineral separation and molecular analyses introduced here provide a new approach for revealing previously concealed patterns of mineral-associated microbial diversity across a wide range of environments, from hard rock habitats to fine-grained lithologies.", "doi": "10.1080/01490451.2011.581327", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "2012-03-05", "series_number": "5", "volume": "29", "issue": "5", "pages": "435-449" }, { "id": "authors:afdfv-nwz40", "collection": "authors", "collection_id": "afdfv-nwz40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120312-095005613", "type": "article", "title": "Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide", "author": [ { "family_name": "Glass", "given_name": "Jennifer B.", "orcid": "0000-0003-0775-2486", "clpid": "Glass-J-B" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO_2 cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH_4), and nitrous oxide (N_2O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH_4 and N_2O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH_4 oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N_2O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N_2O reductase, the only known enzyme capable of microbial N_2O conversion to N_2, have only been found in classical denitrifiers. Accumulation of N_2O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N_2O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal scavenging.", "doi": "10.3389/fmicb.2012.00061", "pmcid": "PMC3282944", "issn": "1664-302X", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Microbiology", "publication_date": "2012-02-21", "volume": "3", "pages": "Art. No. 61" }, { "id": "authors:bn69e-qz555", "collection": "authors", "collection_id": "bn69e-qz555", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120206-101449345", "type": "article", "title": "Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria", "author": [ { "family_name": "Bailey", "given_name": "Jake V.", "clpid": "Bailey-J-V" }, { "family_name": "Salman", "given_name": "Verena", "clpid": "Salman-V" }, { "family_name": "Rouse", "given_name": "Gregory W.", "clpid": "Rouse-G-W" }, { "family_name": "Schulz-Vogt", "given_name": "Heide N.", "clpid": "Schulz-Vogt-H-N" }, { "family_name": "Levin", "given_name": "Lisa A.", "orcid": "0000-0002-2858-8622", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.", "doi": "10.1038/ismej.2011.66", "pmcid": "PMC3223306", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2011-12", "series_number": "12", "volume": "5", "issue": "12", "pages": "1926-1935" }, { "id": "authors:jfgwh-6xc96", "collection": "authors", "collection_id": "jfgwh-6xc96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141113-095602878", "type": "article", "title": "The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy", "author": [ { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Beal", "given_name": "Emily J.", "clpid": "Beal-E-J" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "On Earth, marine anaerobic methane oxidation (AOM) can be driven by the\nmicrobial reduction of sulfate, iron, and manganese. Here, we have further characterized\nmarine sediment incubations to determine if the mineral dependent methane oxidation\ninvolves similar microorganisms to those found for sulfate-dependent methane oxidation.\nThrough FISH and FISH-SIMS analyses using ^(13)C and ^(15)N labeled substrates, we find that\nthe most active cells during manganese dependent AOM are primarily mixed and\nmixed-cluster aggregates of archaea and bacteria. Overall, our control experiment using\nsulfate showed two active bacterial clusters, two active shell aggregates, one active mixed\naggregate, and an active archaeal sarcina, the last of which appeared to take up methane in\nthe absence of a closely-associated bacterial partner. A single example of a shell aggregate\nappeared to be active in the manganese incubation, along with three mixed aggregates and\nan archaeal sarcina. These results suggest that the microorganisms (e.g., ANME-2) found\nactive in the manganese-dependent incubations are likely capable of sulfate-dependent\nAOM. Similar metabolic flexibility for Martian methanotrophs would mean that the same\nmicrobial groups could inhabit a diverse set of Martian mineralogical crustal environments.\nThe recently discovered seasonal Martian plumes of methane outgassing could be coupled\nto the reduction of abundant surface sulfates and extensive metal oxides, providing a feasible metabolism for present and past Mars. In an optimistic scenario Martian\nmethanotrophy consumes much of the periodic methane released supporting on the order\nof 10,000 microbial cells per cm2 of Martian surface. Alternatively, most of the methane\nreleased each year could be oxidized through an abiotic process requiring biological\nmethane oxidation to be more limited. If under this scenario, 1% of this methane flux were\noxidized by biology in surface soils or in subsurface aquifers (prior to release), a total of\nabout 10^(20) microbial cells could be supported through methanotrophy with the cells\nconcentrated in regions of methane release.", "doi": "10.3390/life1010019", "pmcid": "PMC4187123", "issn": "2075-1729", "publisher": "MDPI", "publication": "Life", "publication_date": "2011-11-18", "series_number": "1", "volume": "1", "issue": "1", "pages": "19-33" }, { "id": "authors:zfzgx-sxq17", "collection": "authors", "collection_id": "zfzgx-sxq17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110826-090605868", "type": "article", "title": "Microbiology: Hydrogen for dinner", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Hoehler", "given_name": "Tori M.", "clpid": "Hoehler-T-M" } ], "abstract": "The vast array of bacterium\u2013animal symbioses at deep-sea hydrothermal vents was thought to be fuelled by just two chemicals. A study of one such symbiosis in its environmental context reveals a third energy source.", "doi": "10.1038/476154a", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2011-08-11", "series_number": "7359", "volume": "476", "issue": "7359", "pages": "154-155" }, { "id": "authors:n7h9k-g9s55", "collection": "authors", "collection_id": "n7h9k-g9s55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110404-113053920", "type": "article", "title": "Multicellular photo-magnetotactic bacteria", "author": [ { "family_name": "Shapiro", "given_name": "Orr H.", "clpid": "Shapiro-O-H" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-R" }, { "family_name": "Buckley", "given_name": "Daniel H.", "clpid": "Buckley-D-H" }, { "family_name": "Zinder", "given_name": "Stephen H.", "clpid": "Zinder-S-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Multicellular magnetotactic bacteria (MMB) are unique microorganisms typically comprised of 10\u201340 bacterial cells arranged around a central acellular compartment. Their life cycle has no known unicellular stage and division occurs by separation of a single MMB aggregate into two identical offspring. In this study, South-seeking multicellular magnetotactic bacteria (ssMMB) were enriched from a New England salt marsh. When exposed to light, ssMMB reversed their magnetotactic behaviour to become North-seeking. The exposure time needed to generate the reversal response varied with light wavelength and intensity. Extensive exposure to light appeared to be lethal. This is the first report of a Northern hemisphere MMB displaying South-seeking behaviour and the first time a MMB is found to exhibit photo-magnetotaxis. We suggest that this mechanism enables ssMMB to optimize their location with regard to chemical gradients and light intensities, and propose a model to explain the peculiar balance between photo- and magnetotaxis.", "doi": "10.1111/j.1758-2229.2010.00215.x", "issn": "1758-2229", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology Reports", "publication_date": "2011-04", "series_number": "2", "volume": "3", "issue": "2", "pages": "233-238" }, { "id": "authors:5befr-qbj07", "collection": "authors", "collection_id": "5befr-qbj07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327659", "type": "article", "title": "Fish-Sims: Characterizing the Metabolic Potential and Interspecies Interactions between Uncultured Environmental Microorganisms", "author": [ { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The ability to link phylogenetic identity with metabolic function is one of the longstanding goals in the field of microbial ecology. With greater than 99% of the global microbial diversity missing from culture collections, there is a critical need for alternative, culture-independent approaches that can extend beyond diversity surveys and directly illuminate the ecological and biogeochemical roles of microorganisms in nature. To this end, research incorporating the use of secondary ion mass spectrometry (SIMS and nanoSIMS) combined with stable isotope tracers and molecular methodologies such as fluorescence in situ hybridization (FISH) have opened new and exciting avenues of research to study the metabolic potential of individual microorganisms, microbial consortia, and symbiotic associations. Here, we will highlight the application of FISH combined with nanoSIMS ion imaging to unravel complex microbial associations and trophic relationships in marine ecosystems fueled by methane.", "doi": "10.1016/j.bpj.2010.12.406", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2011-02-02", "series_number": "3, S1", "volume": "100", "issue": "3, S1", "pages": "37a" }, { "id": "authors:a7zn4-mvy45", "collection": "authors", "collection_id": "a7zn4-mvy45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110307-110634731", "type": "article", "title": "Getting cozy: hidden microbial interactions in nature", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Understanding microbial interactions is integral to microbial\necology and yet this fundamental component has\nproven to be one of the most challenging to define and\nstudy in nature. While trophic structure, competition and\nfitness are often discussed in the context of microbial\ncommunities, the description of microbe-microbe symbiotic\nassociations are rare (Overmann and Schubert,\n2002), and if identified, are often poorly characterized.\nBroadly defined, symbiosis covers a wide spectrum of\ninteractions, ranging from beneficial associations (syntrophy\nand mutualism) to deleterious relationships (parasitism).\nSyntrophic associations, for example, have long\nbeen recognized as a fundamental component of organic\ncarbon mineralization in anaerobic environments (Schink,\n2002). Parasitic interactions between microorganisms,\nhowever, are far less frequently described and perhaps\nmore difficult to define. In most cases, symbiotic microbial\nassociations involve close physical coupling between\npartners, and through these intimate interspecies interactions,\ncan lead to metabolic innovation and niche expansion.\nRegardless of the nature of the symbiosis, it is\nbecoming clear that these intimate microbial associations\nare likely prevalent in nature, and await the proper tools\nfor discovery.", "doi": "10.1111/j.1758-2229.2010.00236.x", "issn": "1758-2229", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology Reports", "publication_date": "2011-02", "series_number": "1", "volume": "3", "issue": "1", "pages": "16-18" }, { "id": "authors:v2s3a-nc365", "collection": "authors", "collection_id": "v2s3a-nc365", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110308-093513808", "type": "article", "title": "A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Kalyuzhnaya", "given_name": "Marina G.", "orcid": "0000-0002-9058-7794", "clpid": "Kalyuzhnaya-M-G" }, { "family_name": "Jetten", "given_name": "Mike S. M.", "orcid": "0000-0002-4691-7039", "clpid": "Jetten-M-S-M" }, { "family_name": "Klotz", "given_name": "Martin G.", "clpid": "Klotz-M-G" } ], "abstract": "Genomes of alphaproteobacterial and verrucomicrobial methane-oxidizing bacteria (MOB) encode sequence-divergent copies of particulate methane monooxygenase [pMMO = (PmoABC); pmoCAB]. In contrast, sequenced gammaproteobacterial MOB (Gamma-MOB) genomes contain single or multiple near-identical copies of pmoCAB operons. In betaproteobacterial ammonia-oxidizing bacteria (Beta-AOB), near-identical amoCAB operons encode ammonia monooxygenase (AMO), a homologue of pMMO. Here, we report that Gamma-MOB in the genera Methylomonas, Methylobacter and Methylomicrobium also encode a sequence-divergent particulate monooxygenase (pXMO). Whereas all known genes encoding pMMO or AMO cluster in the order 'CAB', the genes encoding pXMO are uniquely organized in the non-canonical form 'pxmABC.' Steady state pxm mRNA was detected in cultures of Methylomonas sp. as well as in freshwater creek sediment samples, demonstrating that pxm genes are expressed in culture and in situ. Inclusion of PxmA and PxmB proteins in phylogenetic analyses of the Pmo/Amo protein superfamilies created trifurcated trees with three major clades: (i) Pmo of Alpha- and Gamma-MOB and Amo of Gamma-AOB; (ii) Amo of Beta-AOB, Pmo of putative ethane-oxidizing Gamma-MOB and Pxm of Gamma-MOB; and (iii) verrucomicrobial Pmo and Amo of ammonia-oxidizing Archaea. These data support but do not prove the hypothesis that oxygen-dependent methane and ammonia monooxygenases evolved from a substrate-promiscuous ancestor after horizontal transfer while being integrated into the catabolic contexts of their extant hosts.", "doi": "10.1111/j.1758-2229.2010.00192.x", "issn": "1758-2229", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology Reports", "publication_date": "2011-02", "series_number": "1", "volume": "3", "issue": "1", "pages": "91-100" }, { "id": "authors:s8m3m-2xk52", "collection": "authors", "collection_id": "s8m3m-2xk52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100611-084926449", "type": "article", "title": "Distributions of putative aerobic methanotrophs in diverse pelagic marine environments", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-P-L" }, { "family_name": "Ussler", "given_name": "William, III", "clpid": "Ussler-W-III" }, { "family_name": "Joye", "given_name": "Samantha B.", "orcid": "0000-0003-1610-451X", "clpid": "Joye-S-B" }, { "family_name": "Harrison", "given_name": "Benjamin K.", "clpid": "Harrison-B-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Aerobic methane oxidization in the pelagic ocean serves an important role in limiting methane release to the atmosphere, yet little is known about the identity and distribution of bacteria that mediate this process. The distribution of putative methane-oxidizing marine groups, OPU1, OPU3 and Group X, was assessed in different ocean provinces using a newly developed fingerprinting method (monooxygenase intergenic spacer analysis (MISA)) in combination with pmoA clone library analysis and quantitative PCR (qPCR). The distribution of these three distinct monooxygenase groups, previously reported from pelagic marine environments, was examined in 39 samples including active methane seeps in the Gulf of Mexico and Santa Monica Bay, submarine canyon heads along the California continental margin, an oligotrophic subtropical gyre and areas proximal to a hydrothermal vent in the North Fiji back-arc basin. OPU1 and OPU3 were widely and similarly distributed within the meso-and bathypelagic zone (110 to similar to 2000 m water depth) and showed a >50-fold greater abundance near methane seeps relative to non-seep sites. In contrast, Group X was predominantly recovered from samples along the California margin, at both seep and non-seep sites. All three phylotypes were below detection in the epipelagic zone to depths of 100 m. Several additional deeply branching monooxygenase sequences were also identified in this study, indicating the presence of uncharacterized groups of microorganisms potentially involved in the cycling of methane or ammonium.", "doi": "10.1038/ismej.2009.155", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2010-05", "series_number": "5", "volume": "4", "issue": "5", "pages": "700-710" }, { "id": "authors:kb2wh-9me37", "collection": "authors", "collection_id": "kb2wh-9me37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100304-142423277", "type": "article", "title": "Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea", "author": [ { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The deep sea is a unique and extreme environment characterized by low concentrations of highly recalcitrant carbon. As a consequence, large organic inputs have potential to cause significant perturbation. To assess the impact of organic enrichment on deep sea microbial communities, we investigated bacterial diversity in sediments underlying two whale falls at 1820 and 2893 m depth in Monterey Canyon, as compared with surrounding reference sediment 10\u201320 m away. Bacteroidetes, Epsilonproteobacteria and Firmicutes were recovered primarily from whale fall-associated sediments, while Gammaproteobacteria and Planctomycetes were found primarily within reference sediments. Abundant Deltaproteobacteria were recovered from both sediment types, but the Desulfobacteraceae and Desulfobulbaceae families were observed primarily beneath the whale falls. UniFrac analysis revealed that bacterial communities from the two whale falls (~30 km apart) clustered to the exclusion of corresponding reference sediment communities, suggesting that deposition of whale fall biomass is more influential on deep sea microbial communities than specific seafloor location. The bacterial population at whale-1820 at 7 months post deposition was less diverse than reference sediments, with Delta- and Epsilonproteobacteria and Bacteroidetes making up 89% of the community. At 70 months, bacterial diversity in reference sediments near whale-2893 had decreased as well. Over this time, there was a convergence of each community's membership at the phyla level, although lower-taxonomic-level composition remained distinct. Long-term impact of organic carbon loading from the whale falls was also evident by elevated total organic carbon and enhanced proteolytic activity for at least 17\u201370 months. The response of the sedimentary microbial community to large pulses of organic carbon is complex, likely affected by increased animal bioturbation, and may be sustained over time periods that span years to perhaps even decades.", "doi": "10.1111/j.1462-2920.2009.02072.x", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2010-02", "series_number": "2", "volume": "12", "issue": "2", "pages": "344-363" }, { "id": "authors:g0pea-w1973", "collection": "authors", "collection_id": "g0pea-w1973", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100302-113604574", "type": "article", "title": "Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia", "author": [ { "family_name": "Bailey", "given_name": "Jake V.", "clpid": "Bailey-J-V" }, { "family_name": "Raub", "given_name": "Timothy D.", "orcid": "0000-0002-7471-0246", "clpid": "Raub-T-D" }, { "family_name": "Meckler", "given_name": "A. Nele", "clpid": "Meckler-A-N" }, { "family_name": "Harrison", "given_name": "Benjamin K.", "clpid": "Harrison-B-K" }, { "family_name": "Raub", "given_name": "Theresa M. D.", "clpid": "Raub-T-M-D" }, { "family_name": "Green", "given_name": "Abigail M.", "clpid": "Green-A-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Pleistocene-age methane seep carbonates from the Eel River Basin, California contain aggregate-like structures composed of tightly-packed hollow spheres that morphologically resemble syntrophic archaeal\u2013bacterial consortia known to catalyze the anaerobic oxidation of methane (AOM). Tetragonal microstructures also present in the carbonates resemble seep-endemic Methanosarcinales cell clusters. Despite morphological similarities to the seep-endemic microbes that likely mediated the authigenesis of Eel River Basin carbonates and sulfides, detailed petrographic, SEM, and magnetic microscopic imaging, remanence rock magnetism, laser Raman, and energy dispersive X-ray spectroscopy, suggest that these microstructures are not microfossils, but rather mineral structures that result from the diagenetic alteration of euhedral Fe-sulfide framboids. Electron microscopy shows that during diagenesis, reaction rims composed of Fe oxide form around framboid microcrystalites. Subsequent dissolution of greigite or pyrite crystals leaves behind hollow cell-like casings (external molds) \u2014 a transformation that occurs on timescales of ~100 kyr or less. Despite their superficial resemblance to morphologically-distinctive extant microbes in local sediments, the presence of acellular precursor grains, as well as of partially-altered transitional forms, complicate the interpretation of these and other framboidal microstructures that have been reported from the rock record.", "doi": "10.1016/j.palaeo.2009.11.002", "issn": "0031-0182", "publisher": "Elsevier", "publication": "Palaeogeography, Palaeoclimatology, Palaeoecology", "publication_date": "2010-01-01", "series_number": "1-2", "volume": "285", "issue": "1-2", "pages": "131-142" }, { "id": "authors:rmm44-f7q77", "collection": "authors", "collection_id": "rmm44-f7q77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100105-130209242", "type": "article", "title": "Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record", "author": [ { "family_name": "Bailey", "given_name": "Jake V.", "clpid": "Bailey-J-V" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Joye", "given_name": "Samantha B.", "orcid": "0000-0003-1610-451X", "clpid": "Joye-S-B" }, { "family_name": "Corsetti", "given_name": "Frank A.", "clpid": "Corsetti-F-A" } ], "abstract": "Putative microbialites are commonly regarded to have formed in association with photosynthetic microorganisms, such as cyanobacteria. However, many modern microbial mat ecosystems are dominated by chemotrophic bacteria and archaea. Like phototrophs, filamentous sulfur-oxidizing bacteria form large mats at the sediment/water interface that can act to stabilize sediments, and their metabolic activities may mediate the formation of marine phosphorites. Similarly, bacteria and archaea associated with the anaerobic oxidation of methane (AOM) catalyze the precipitation of seafloor authigenic carbonates. When preserved, lipid biomarkers, isotopic signatures, body fossils, and lithological indicators of the local depositional environment may be used to identify chemotrophic mats in the rock record. The recognition of chemotrophic communities in the rock record has the potential to transform our understanding of ancient microbial ecologies, evolution, and geochemical conditions. Chemotrophic microbes on Earth occupy naturally occurring interfaces between oxidized and reduced chemical species and thus may provide a new set of search criteria to target life-detection efforts on other planets.", "doi": "10.1089/ast.2008.0314", "issn": "1557-8070", "publisher": "Mary Ann Liebert", "publication": "Astrobiology", "publication_date": "2009-11", "series_number": "9", "volume": "9", "issue": "9", "pages": "843-859" }, { "id": "authors:6ny61-zm519", "collection": "authors", "collection_id": "6ny61-zm519", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091125-115957263", "type": "article", "title": "Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia", "author": [ { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Poretsky", "given_name": "Rachel S.", "clpid": "Poretsky-R-S" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell\u2013resolution nanometer secondary ion mass spectrometry images of ^(15)N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N_2, as well as structurally similar CN^\u2013, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N_2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N_2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.", "doi": "10.1126/science.1178223", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2009-10-16", "series_number": "5951", "volume": "326", "issue": "5951", "pages": "422-426" }, { "id": "authors:y0t0f-29y97", "collection": "authors", "collection_id": "y0t0f-29y97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100127-153113402", "type": "article", "title": "The effect of sulfate concentration on (sub)millimeter-scale sulfide \u03b4^(34)S in hypersaline cyanobacterial mats over the diurnal cycle", "author": [ { "family_name": "Fike", "given_name": "David A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Finke", "given_name": "Niko", "clpid": "Finke-N" }, { "family_name": "Zha", "given_name": "Jessica", "clpid": "Zha-Jessica" }, { "family_name": "Blake", "given_name": "Garrett", "clpid": "Blake-Garrett" }, { "family_name": "Hoehler", "given_name": "Tori M.", "clpid": "Hoehler-T-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Substantial isotopic fractionations are associated with many microbial sulfur metabolisms and measurements of the bulk \u03b4^(34)S isotopic composition of sulfur species (predominantly sulfates and/or sulfides) have been a key component in developing our understanding of both modern and ancient biogeochemical cycling. However, the interpretations of bulk \u03b4^(34)S measurements are often non-unique, making reconstructions of paleoenvironmental conditions or microbial ecology challenging. In particular, the link between the \u03bcm-scale microbial activity that generates isotopic signatures and their eventual preservation as a bulk rock value in the geologic record has remained elusive, in large part because of the difficulty of extracting sufficient material at small scales. Here we investigate the potential for small-scale (~100 \u03bcm\u20131 cm) \u03b4^(34)S variability to provide additional constraints for environmental and/or ecological reconstructions. We have investigated the impact of sulfate concentrations (0.2, 1, and 80 mM SO_4) on the \u03b4^(34)S composition of hydrogen sulfide produced over the diurnal (day/night) cycle in cyanobacterial mats from Guerrero Negro, Baja California Sur, Mexico. Sulfide was captured as silver sulfide on the surface of a 2.5 cm metallic silver disk partially submerged beneath the mat surface. Subsequent analyses were conducted on a Cameca 7f-GEO secondary ion mass spectrometer (SIMS) to record spatial \u03b4^(34)S variability within the mats under different environmental conditions. Isotope measurements were made in a 2-dimensional grid for each incubation, documenting both lateral and vertical isotopic variation within the mats. Typical grids consisted of ~400\u2013800 individual measurements covering a lateral distance of ~1 mm and a vertical depth of ~5\u201315 mm. There is a large isotopic enrichment (10\u201320\u2030) in the uppermost mm of sulfide in those mats where [SO_4] was non-limiting (field and lab incubations at 80 mM). This is attributed to rapid recycling of sulfur (elevated sulfate reduction rates and extensive sulfide oxidation) at and above the chemocline. This isotopic gradient is observed in both day and night enrichments and suggests that, despite the close physical association between cyanobacteria and select sulfate-reducing bacteria, photosynthetic forcing has no substantive impact on \u03b4^(34)S in these cyanobacterial mats. Perhaps equally surprising, large, spatially-coherent \u03b4^(34)S oscillations (~20\u201330\u2030 over 1 mm) occurred at depths up to ~1.5 cm below the mat surface. These gradients must arise in situ from differential microbial metabolic activity and fractionation during sulfide production at depth. Sulfate concentrations were the dominant control on the spatial variability of sulfide \u03b4^(34)S. Decreased sulfate concentrations diminished both vertical and lateral \u03b4^(34)S variability, suggesting that small-scale variations of \u03b4^(34)S can be diagnostic for reconstructing past sulfate concentrations, even when original sulfate \u03b4^(34)S is unknown.", "doi": "10.1016/j.gca.2009.07.006", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2009-10-15", "series_number": "20", "volume": "73", "issue": "20", "pages": "6187-6204" }, { "id": "authors:d8kp3-zge96", "collection": "authors", "collection_id": "d8kp3-zge96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090923-143137088", "type": "article", "title": "Extensive carbon isotopic heterogeneity among methane seep microbiota", "author": [ { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Turk", "given_name": "Kendra A.", "clpid": "Turk-K-A" }, { "family_name": "Thomas", "given_name": "Burt", "clpid": "Thomas-B" }, { "family_name": "Pernthaler", "given_name": "Annelie", "clpid": "Pernthaler-A" }, { "family_name": "Vrentas", "given_name": "Jennifer M.", "clpid": "Vrentas-J-M" }, { "family_name": "Joye", "given_name": "Samantha B.", "orcid": "0000-0003-1610-451X", "clpid": "Joye-S-B" } ], "abstract": "To assess and study the heterogeneity of \u03b4^(13)C values for seep microorganisms of the Eel River Basin, we studied two principally different sample sets: sediments from push cores and artificial surfaces colonized over a 14 month in situ incubation. In a single sediment core, the \u03b4^(13)C compositions of methane seep-associated microorganisms were measured and the relative activity of several metabolisms was determined using radiotracers. We observed a large range of archaeal \u03b4^(13)C values (> 50\u2030) in this microbial community. The \u03b4^(13)C of ANME-1 rods ranged from \u221224\u2030 to \u221287\u2030. The \u03b4^(13)C of ANME-2 sarcina ranged from \u221218\u2030 to \u221275\u2030. Initial measurements of shell aggregates were as heavy as \u221219.5\u2030 with none observed to be lighter than \u221257\u2030. Subsequent measurements on shell aggregates trended lighter reaching values as ^(13)C-depleted as \u221273\u2030. The observed isotopic trends found for mixed aggregates were similar to those found for shell aggregates in that the initial measurements were often enriched and the subsequent analyses were more ^(13)C-depleted (with values as light as \u221256\u2030). The isotopic heterogeneity and trends observed within taxonomic groups suggest that ANME-1 and ANME-2 sarcina are capable of both methanogenesis and methanotrophy. In situ microbial growth was investigated by incubating a series of slides and silicon (Si) wafers for 14 months in seep sediment. The experiment showed ubiquitous growth of bacterial filaments (mean \u03b4^(13)C = \u221238 \u00b1 3\u2030), suggesting that this bacterial morphotype was capable of rapid colonization and growth.", "doi": "10.1111/j.1462-2920.2009.01934.x", "issn": "1462-2912", "publisher": "Blackwell", "publication": "Environmental Microbiology", "publication_date": "2009-09", "series_number": "9", "volume": "11", "issue": "9", "pages": "2207-2215" }, { "id": "authors:99p2g-4s229", "collection": "authors", "collection_id": "99p2g-4s229", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090804-142607950", "type": "article", "title": "Manganese- and iron-dependent marine methane oxidation", "author": [ { "family_name": "Beal", "given_name": "Emily J.", "clpid": "Beal-E-J" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Anaerobic methanotrophs help regulate Earth's climate and may have been an important part of the microbial ecosystem on the early Earth. The anaerobic oxidation of methane (AOM) is often thought of as a sulfate-dependent process, despite the fact that other electron acceptors are more energetically favorable. Here, we show that microorganisms from marine methane-seep sediment in the Eel River Basin in California are capable of using manganese (birnessite) and iron (ferrihydrite) to oxidize methane, revealing that marine AOM is coupled, either directly or indirectly, to a larger variety of oxidants than previously thought. Large amounts of manganese and iron are provided to oceans from rivers, indicating that manganese- and iron-dependent AOM have the potential to be globally important.", "doi": "10.1126/science.1169984", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2009-07-10", "series_number": "5937", "volume": "325", "issue": "5937", "pages": "184-187" }, { "id": "authors:fxgda-pw796", "collection": "authors", "collection_id": "fxgda-pw796", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090909-123033461", "type": "article", "title": "Patterns of ^(15)N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Turk", "given_name": "Kendra A.", "clpid": "Turk-K-A" }, { "family_name": "Green", "given_name": "Abigail M.", "clpid": "Green-A-M" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" } ], "abstract": "Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking ^(15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of 15N distribution within individual aggregates showed enhanced ^(15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 \u03bcm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME\u22122/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater ^(15)N uptake and doubling times ranging from 3 to 5 months. The combination of ^(15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.", "doi": "10.1111/j.1462-2920.2009.01903.x", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2009-07", "series_number": "7", "volume": "11", "issue": "7", "pages": "1777-1791" }, { "id": "authors:tbg63-b8p20", "collection": "authors", "collection_id": "tbg63-b8p20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090909-131707316", "type": "article", "title": "Methods for unveiling cryptic microbial partnerships in nature", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet our ability to recognize these partnerships in nature or to effectively study their behavior in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in new methodologies. These include: comparative metagenomics and transcriptomics; discovery-based methods such as Magneto-FISH; and metabolic substrate tracking using stable isotopes coupled either with density gradient separation (SIP) or with FISH-SIMS. These novel approaches are redefining the way we study microbial mutualism and are making intimate microbial associations accessible to both identification and characterization in their native habitats.", "doi": "10.1016/j.mib.2009.04.003", "issn": "1369-5274", "publisher": "Elsevier", "publication": "Current Opinion in Microbiology", "publication_date": "2009-06", "series_number": "3", "volume": "12", "issue": "3", "pages": "231-237" }, { "id": "authors:nqq04-jjz48", "collection": "authors", "collection_id": "nqq04-jjz48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090909-130537989", "type": "article", "title": "Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "House", "given_name": "C. H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" } ], "abstract": "The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.", "doi": "10.1111/j.1472-4669.2009.00201.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2009-06", "series_number": "3", "volume": "7", "issue": "3", "pages": "360-372" }, { "id": "authors:7z6av-vs724", "collection": "authors", "collection_id": "7z6av-vs724", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327430", "type": "article", "title": "High resolution SIMS-based sulfide \u03b4^(34)S: A new tool for characterizing microbial activity in a variety of depositional environments", "author": [ { "family_name": "Fike", "given_name": "David A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The sulfur isotopic compositions of sedimentary sulfates\nand sulfides are useful for understanding modern microbial\necology and for reconstructing paleoenvironmental conditions\nassociated with the deposition of ancient sediments. In many\nmodern microbially-dominated sedimentary environments,\nsuch as microbial mats, or methane seeps, the redox gradients\ncan be steep with the transition from oxic to sulfidic condition\nover the space of mm to cm. In these environments, it is\nfrequently difficult (either for logistical reasons or sample\nvolume requirements) to sample at a sufficiently high\nresolution to capture the geochemical and microbiological\ndetails associated with these redox transitions. We build upon\nearlier work [1] to demonstrate the ability to capture aqueous\nsulfide as silver sulfide, which can then be analyzed using a\nCameca NanoSIMS 50L or 7F/Geo for its isotopic\ncomposition at a spatial resolution down to ~ 1 - 50 um. This\nallows for the construction of 2D isotopic datasets that\ndocument vertical isotope gradients as well as lateral\nheterogeneity [2]. Here we present the application of this\nsulfide capture technique to three different modern\nenvironments: (1) microbial mats from Guerrero Negro, Baja\nCalifornia Sur, Mexico; (2) the chemocline of meromictic\nLake Mahoney, British Columbia, Canada; and (3) methane\nseep-associated marine sediments offshore Costa Rica.\nCoherent variations up to 20 permil in \u03b434S are observed over\nranges as small as 1 mm at all depths examined. These data\nhighlight the additional ecological information that can be\nextracted from high resolution isotopic data, which may\nimprove our understanding of the activity of the microbial\necosystems driving biogeochemical cycling in these systems.", "doi": "10.1016/j.gca.2009.05.005", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2009-06", "series_number": "13, S", "volume": "73", "issue": "13, S", "pages": "A375" }, { "id": "authors:ag539-0j585", "collection": "authors", "collection_id": "ag539-0j585", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090706-143447493", "type": "article", "title": "Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California)", "author": [ { "family_name": "Harrison", "given_name": "Benjamin K.", "clpid": "Harrison-B-K" }, { "family_name": "Zhang", "given_name": "Husen", "clpid": "Zhang-Husen" }, { "family_name": "Berelson", "given_name": "Will", "clpid": "Berelson-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The sulfate-methane transition zone (SMTZ) is a widespread feature of continental margins, representing a diffusion-controlled interface where there is enhanced microbial activity. SMTZ microbial activity is commonly associated with the anaerobic oxidation of methane (AOM), which is carried out by syntrophic associations between sulfate-reducing bacteria and methane-oxidizing archaea. While our understanding of the microorganisms catalyzing AOM has advanced, the diversity and ecological role of the greater microbial assemblage associated with the SMTZ have not been well characterized. In this study, the microbial diversity above, within, and beneath the Santa Barbara Basin SMTZ was described. ANME-1-related archaeal phylotypes appear to be the primary methane oxidizers in the Santa Barbara Basin SMTZ, which was independently supported by exclusive recovery of related methyl coenzyme M reductase genes (mcrA). Sulfate-reducing Deltaproteobacteria phylotypes affiliated with the Desulfobacterales and Desulfosarcina-Desulfococcus clades were also enriched in the SMTZ, as confirmed by analysis of dissimilatory sulfite reductase (dsr) gene diversity. Statistical methods demonstrated that there was a close relationship between the microbial assemblages recovered from the two horizons associated with the geochemically defined SMTZ, which could be distinguished from microbial diversity recovered from the sulfate-replete overlying horizons and methane-rich sediment beneath the transition zone. Comparison of the Santa Barbara Basin SMTZ microbial assemblage to microbial assemblages of methane seeps and other organic matter-rich sedimentary environments suggests that bacterial groups not typically associated with AOM, such as Planctomycetes and candidate division JS1, are additionally enriched within the SMTZ and may represent a common bacterial signature of many SMTZ environments worldwide.", "doi": "10.1128/AEM.01812-08", "pmcid": "PMC2655439", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2009-03", "series_number": "6", "volume": "75", "issue": "6", "pages": "1487-1499" }, { "id": "authors:24twa-xdb92", "collection": "authors", "collection_id": "24twa-xdb92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090427-131232717", "type": "article", "title": "Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Jahnke", "given_name": "L. L.", "clpid": "Jahnke-L-L" }, { "family_name": "Embaye", "given_name": "T.", "clpid": "Embaye-T" }, { "family_name": "Turk", "given_name": "K. A.", "clpid": "Turk-K-A" }, { "family_name": "Pernthaler", "given_name": "A.", "clpid": "Pernthaler-A" }, { "family_name": "Summons", "given_name": "R. E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Des Marais", "given_name": "D. J.", "clpid": "Des-Marais-D-J" } ], "abstract": "Well-developed hypersaline cyanobacterial mats from Guerrero Negro, Baja California Sur, sustain active methanogenesis in the presence of high rates of sulfate reduction. Very little is known about the diversity and distribution of the microorganisms responsible for methane production in these unique ecosystems. Applying a combination of 16S rRNA and metabolic gene surveys, fluorescence in situ hybridization, and lipid biomarker analysis, we characterized the diversity and spatial relationships of methanogens and other archaea in the mat incubation experiments stimulated with methanogenic substrates. The phylogenetic and chemotaxonomic diversity established within mat microcosms was compared with the archaeal diversity and lipid biomarker profiles associated with different depth horizons in the in situ mat. Both archaeal 16S rRNA and methyl coenzyme M reductase gene (mcrA) analysis revealed an enrichment of diverse methanogens belonging to the Methanosarcinales in response to trimethylamine addition. Corresponding with DNA-based detection methods, an increase in lipid biomarkers commonly synthesized by methanogenic archaea was observed, including archaeol and sn-2-hydroxyarchaeol polar lipids, and the free, irregular acyclic isoprenoids, 2,6,10,15,19-pentamethylicosene (PMI) and 2,6,11,15-tetramethylhexadecane (crocetane). Hydrogen enrichment of a novel putative archaeal polar C_(30) isoprenoid, a dehydrosqualane, was also documented. Both DNA and lipid biomarker evidence indicate a shift in the dominant methanogenic genera corresponding with depth in the mat. Specifically, incubations of surface layers near the photic zone predominantly supported Methanolobus spp. and PMI, while Methanococcoides and hydroxyarchaeol were preferentially recovered from microcosms of unconsolidated sediments underlying the mat. Together, this work supports the existence of small but robust methylotrophic methanogen assemblages that are vertically stratified within the benthic hypersaline mat and can be distinguished by both their DNA signatures and unique isoprenoid biomarkers.", "doi": "10.1111/j.1472-4669.2008.00166.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2008-09", "series_number": "4", "volume": "6", "issue": "4", "pages": "376-393" }, { "id": "authors:fhgcy-h6c51", "collection": "authors", "collection_id": "fhgcy-h6c51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:JAHgbi08", "type": "article", "title": "Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment", "author": [ { "family_name": "Jahnke", "given_name": "L. L.", "clpid": "Jahnke-L-L" }, { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Embaye", "given_name": "T.", "clpid": "Embaye-T" }, { "family_name": "Kubo", "given_name": "M. D.", "clpid": "Kubo-M-D" }, { "family_name": "Summons", "given_name": "R. E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Des Marais", "given_name": "D. J.", "clpid": "Des-Marais-D-J" } ], "abstract": "This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (~10 : 1) in the 4\u201317 mm and 100\u2013130 mm horizons, and highest (132 : 1) in the surface 0\u20132 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C30 isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2\u201310 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0\u20132 mm and 35\u201365 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35\u201365 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis.", "doi": "10.1111/j.1472-4669.2008.00165.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2008-09", "series_number": "4", "volume": "6", "issue": "4", "pages": "394-410" }, { "id": "authors:tn3q6-cts13", "collection": "authors", "collection_id": "tn3q6-cts13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130510-110748396", "type": "article", "title": "Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach", "author": [ { "family_name": "Fike", "given_name": "David Andrew", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Gammon", "given_name": "Crystal Lynn", "clpid": "Gammon-C-L" }, { "family_name": "Ziebis", "given_name": "Wiebke", "clpid": "Ziebis-W" }, { "family_name": "Orphan", "given_name": "Victoria Jeanne", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "The metabolic activities of microbial mats have likely regulated biogeochemical cycling over most of Earth's history. However, the relationship between metabolic activity and the establishment of isotopic geochemical gradients in these mats remains poorly constrained. Here we present a parallel microgeochemical and microbiological study of micron-scale sulfur cycling within hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. Dissolved sulfide within the mats was captured on silver discs and analyzed for its abundance and \u03b4^(34)S isotopic composition using high-resolution secondary ion mass spectrometry (nanoSIMS). These results were compared to sulfide and oxygen microelectrode profiles. Two-dimensional microgeochemical mapping revealed well-defined laminations in sulfide concentration (on scales from 1 to 200\u2009\u03bcm), trending toward increased sulfide concentrations at depth. Sulfide \u03b4^(34)S decreased from ~+10\u2030 to \u221220\u2030 in the uppermost 3\u2009mm and oscillated repeatedly between \u221210\u2030 and \u221230\u2030 down to a depth of 8\u2009mm. These variations are attributed to spatially variable bacterial sulfate reduction within the mat. A parallel examination of the spatial distribution of known sulfate-reducing bacteria within the family Desulfobacteraceae was conducted using catalyzed reporter deposition fluorescence in situ hybridization. Significant concentrations of Desulfobacteraceae were observed in both oxic and anoxic zones of the mat and occurred in several distinct layers, in large aggregates and heterogeneously dispersed as single cells throughout. The spatial distribution of these microorganisms is consistent with the variation in sulfide concentration and isotopic composition we observed. The parallel application of the methodologies developed here can shed light on micron-scale sulfur cycling within microbially dominated sedimentary environments.", "doi": "10.1038/ismej.2008.39", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2008-07", "series_number": "7", "volume": "2", "issue": "7", "pages": "749-759" }, { "id": "authors:ykwyb-rzz38", "collection": "authors", "collection_id": "ykwyb-rzz38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TAVaem08", "type": "article", "title": "Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L." }, { "family_name": "Ussler", "given_name": "William, III" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Methane vents are of significant geochemical and ecological importance. Notable progress has been made towards understanding anaerobic methane oxidation in marine sediments, however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. Both environments play an essential role in regulating methane release from the oceans to the atmosphere. In this study, the diversity of particulate methane monooxygenase (pmoA) and 16S rRNA genes from two methane vent environments along the California continental margin was characterized. The pmoA phylotypes recovered from methane-rich sediments and the overlying water column differed. Sediments harbored the greatest number of unique pmoA phylotypes broadly affiliated with the Methylococcaceae family, whereas planktonic pmoA phylotypes formed three clades that were distinct from the sediment-hosted methanotrophs, and distantly related to established methanotrophic clades. Water-column associated phylotypes were highly similar between field sites, suggesting that planktonic methanotroph diversity is controlled primarily by environmental factors rather than geographical proximity. Analysis of 16S rRNA genes from methane-rich waters did not readily recover known methanotrophic lineages, with only a few phylotypes demonstrating distant relatedness to Methylococcus. The development of new pmo primers increased the recovery of monooxygenase genes from the water column and led to the discovery of a highly diverged monooxygenase sequence which is phylogenetically intermediate to Amo and pMMO. This sequence potentiates insight into the amo/pmo superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment.", "doi": "10.1128/AEM.00069-08", "pmcid": "PMC2446507", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2008-07", "series_number": "13", "volume": "74", "issue": "13", "pages": "3985-3995" }, { "id": "authors:fgewr-m1z45", "collection": "authors", "collection_id": "fgewr-m1z45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130402-154755386", "type": "article", "title": "Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat", "author": [ { "family_name": "Fike", "given_name": "David A.", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Gammon", "given_name": "Crystal L.", "clpid": "Gammon-C-L" }, { "family_name": "Finke", "given_name": "Niko", "clpid": "Finke-N" }, { "family_name": "Hoehler", "given_name": "Tori", "clpid": "Hoehler-T-M" }, { "family_name": "Turk", "given_name": "Kendra", "clpid": "Turk-K-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "We present a parallel microgeochemical and\nmicrobiological study of \u03bcm-scale sulfur cycling within\nhypersaline microbial mats from Guerrero Negro, Baja\nCalifornia Sur, Mexico. Diel variations (day/night) in sulfur cycling were investigated in field incubations as well as in mats grown under controlled conditions in the laboratory at NASA Ames Research Center. Sulfur cycling in the laboratory mats was examined under a variety of different sulfate concentrations to evaluate the role this had on sulfide concentration and isotopic composition. Sulfate levels in the overlying water column were: 80 mM SO_4 (natural level at\nGuerrero Negro); 1 mM SO_4; and 200 uM SO_4. Dissolved\nsulfide within the mat was captured on silver discs and\nanalyzed for its abundance and \u03b4^(34)S isotopic composition\nusing high resolution secondary ion mass spectrometry\n(SIMS) on a Cameca 7F Geo.", "doi": "10.1016/j.gca.2008.05.009", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2008-07", "series_number": "12", "volume": "72", "issue": "12", "pages": "A268" }, { "id": "authors:07y94-pd065", "collection": "authors", "collection_id": "07y94-pd065", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PERpnas08", "type": "article", "title": "Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics", "author": [ { "family_name": "Pernthaler", "given_name": "Annelie", "clpid": "Pernthaler-A" }, { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Brown", "given_name": "C. Titus", "orcid": "0000-0001-6001-2677", "clpid": "Brown-C-T" }, { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Embaye", "given_name": "Tsegereda", "clpid": "Embaye-T" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of 15N2 incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.", "doi": "10.1073/pnas.0711303105", "pmcid": "PMC2383945", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2008-05-13", "series_number": "19", "volume": "105", "issue": "19", "pages": "7052-7057" }, { "id": "authors:pgda9-nmw38", "collection": "authors", "collection_id": "pgda9-nmw38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-080517687", "type": "article", "title": "Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California", "author": [ { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Wilpiszeski", "given_name": "Regina", "clpid": "Wilpiszeski-R" }, { "family_name": "Lee", "given_name": "Ray", "clpid": "Lee-Ray" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic; however, we demonstrate that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon was enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding sea floor to at least 10\u2009m, forming a 'bulls eye' of elevated carbon. The diversity of sedimentary archaea associated with the 2893\u2009m whale-fall in Monterey Canyon (California) varied both spatially and temporally. 16S rRNA diversity, determined by both sequencing and terminal restriction fragment length polymorphism analysis, as well as quantitative PCR of the methyl-coenzyme M reductase gene, revealed that methanogens, including members of the Methanomicrobiales and Methanosarcinales, were the dominant archaea (up to 98%) in sediments immediately beneath the whale-fall. Temporal changes in this archaeal community included the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10\u2009m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group I and marine benthic group B. Overall, these results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages, resulting in an active near-seafloor methane cycle in the deep sea.", "doi": "10.1038/ismej.2007.103", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2008-02", "series_number": "2", "volume": "2", "issue": "2", "pages": "204-220" }, { "id": "authors:gb0f3-42r69", "collection": "authors", "collection_id": "gb0f3-42r69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-081544064", "type": "article", "title": "Methyl sulfides as intermediates in the anaerobic oxidation of methane", "author": [ { "family_name": "Moran", "given_name": "James J.", "clpid": "Moran-J-J" }, { "family_name": "Beal", "given_name": "Emily J.", "clpid": "Beal-E-J" }, { "family_name": "Vrentas", "given_name": "Jennifer M.", "clpid": "Vrentas-J-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Freeman", "given_name": "Katherine H.", "orcid": "0000-0002-3350-7671", "clpid": "Freeman-K-H" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" } ], "abstract": "While it is clear that microbial consortia containing Archaea and sulfate-reducing bacteria (SRB) can mediate the anaerobic oxidation of methane (AOM), the interplay between these microorganisms remains unknown. The leading explanation of the AOM metabolism is 'reverse methanogenesis' by which a methanogenesis substrate is produced and transferred between species. Conceptually, the reversal of methanogenesis requires low H_2 concentrations for energetic favourability. We used ^(13)C-labelled CH_4 as a tracer to test the effects of elevated H_2 pressures on incubations of active AOM sediments from both the Eel River basin and Hydrate Ridge. In the presence of H_2, we observed a minimal reduction in the rate of CH_4 oxidation, and conclude H_2 does not play an interspecies role in AOM. Based on these results, as well as previous work, we propose a new model for substrate transfer in AOM. In this model, methyl sulfides produced by the Archaea from both CH_4 oxidation and CO_2 reduction are transferred to the SRB. Metabolically, CH_4 oxidation provides electrons for the energy-yielding reduction of CO_2 to a methyl group ('methylogenesis'). Methylogenesis is a dominantly reductive pathway utilizing most methanogenesis enzymes in their forward direction. Incubations of seep sediments demonstrate, as would be expected from this model, that methanethiol inhibits AOM and that CO can be substituted for CH_4 as the electron donor for methylogenesis.", "doi": "10.1111/j.1462-2920.2007.01441.x", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2008-01", "series_number": "1", "volume": "10", "issue": "1", "pages": "162-173" }, { "id": "authors:pg442-v0j13", "collection": "authors", "collection_id": "pg442-v0j13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130403-085441691", "type": "article", "title": "Archaea, Methane, and Oases of the Deep", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" } ], "abstract": "The deep sea, fed by a slow trickling input of photosynthetically derived carbon, has historically been considered\na low energy, oligotrophic environment. In localized areas, however, oases of elevated microbial biomass and activity\nwithin the deep sea do exist. Perhaps the most famous are hydrothermal vents, emerging along spreading\ncenters and subduction zones, fueled by hot reduced fluids re-circulated within the Earth's crust. Equally rich,\nalthough less well known, areas of stimulated biomass production and activity also occur in the psychrophilic\ndepths of the seafloor, fueled by large organic accumulations (i.e. food falls) and subsurface reservoirs of methane.\nThe microbial ecology within these locally active deep-sea habitats is unique, supporting novel microbial\nassociations and diverse pathways for carbon remineralization.", "issn": "0369-5034", "publisher": "Deutsche Akademie der Naturforscher Leopoldina", "publication": "Nova Acta Leopoldina", "publication_date": "2008", "series_number": "356", "volume": "96", "issue": "356", "pages": "19-23" }, { "id": "authors:xwn8f-abh34", "collection": "authors", "collection_id": "xwn8f-abh34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130211-144010988", "type": "article", "title": "Micron-scale resolution of sulfur cycling in a microbial mat", "author": [ { "family_name": "Fike", "given_name": "David", "orcid": "0000-0003-2848-0328", "clpid": "Fike-D-A" }, { "family_name": "Ussler", "given_name": "William", "clpid": "Ussler-W-III" }, { "family_name": "Eiler", "given_name": "John", "clpid": "Eiler-J-M" }, { "family_name": "Guan", "given_name": "Yunbin", "orcid": "0000-0002-7636-3735", "clpid": "Guan-Yunbin" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Microbial mats consist of finely laminated layers of\ndiverse microbial communities. Mat organization is thought\nto result from strong spatial gradients in light intensity and\nredox in the uppermost few millimeters Optical examination\nreveals microbial laminations on scales between 5mm and\n5um throughout the thickness of the microbial mat. However,\nsuch fine laminations at depth have usually been regarded as a\n'relict architecture' inherited from an older mat surface. To\nfurther our understanding of microbial processes within this\nlaminated architecture, we have investigated sulfur cycling (as\nrecorded by sulfide production) within a benthic microbial\nmat.", "doi": "10.1016/j.gca.2007.06.015", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2007-08", "series_number": "15", "volume": "71", "issue": "15", "pages": "A278" }, { "id": "authors:phwbh-vah76", "collection": "authors", "collection_id": "phwbh-vah76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327312", "type": "article", "title": "The ties that bind: Dynamics of syntrophic associations in marine methane seeps", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Pernthaler", "given_name": "Annelie", "clpid": "Pernthaler-A" }, { "family_name": "Dekas", "given_name": "Anne E.", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-A-E" }, { "family_name": "Gammon", "given_name": "Crystal", "clpid": "Gammon-C-L" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" } ], "abstract": "The deep-sea methane seep environment supports active\nand diverse microbial assemblages supported by the anaerobic\noxidation of methane (AOM). Unknown to science less than a\ndecade ago, the microorganisms and the molecular\nmechanisms underlying this enigmatic and globally important\nbiogeochemical process have been the subject of intensive\nstudy worldwide. The identification, activity, distribution, and\npartial metabolic pathway reconstruction of methanotrophic\narchaea and co-associated sulfate reducing bacteria has been\ncharacterized. However fundamental questions still remain\nregarding the necessity of a physically coupled syntrophic\nassociation between sulfate reducing bacteria and methane\noxidizing archaea, the underlying biochemistry enabling\nsulfate-coupled methane oxidation, and the extent of the\ndiversity of microbial assemblages involved in AOM. Using\nmicroanalytical stable isotope analyses of whole cells in\ntandem with genomics enabled molecular methods, we\nexamined the variation in metabolic activity between\nindividual aggregations of microorganisms recovered from\nmethane seep sediments. Significant differences in activity\nwere observed between archaeal-bacterial associations and\nmono-specific aggregations of putative methanotrophic\narchaea and sulfate-reducing populations, supporting\nenhanced metabolism in multi-species aggregates.\nApplication of a new SSU rRNA targeted method for\ncapturing and concentrating specific uncultured microbial\npopulations from methane seep sediments has uncovered\nnovel partnerships and additional insights into the metabolic\npotential of the methanotrophic archaea and co-associated\nbacteria.", "doi": "10.1016/j.gca.2007.06.023", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2007-08", "series_number": "15, S", "volume": "71", "issue": "15, S", "pages": "A743" }, { "id": "authors:503ht-1et86", "collection": "authors", "collection_id": "503ht-1et86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130429-140926092", "type": "article", "title": "Authigenic carbonate formation at hydrocarbon seeps in continental margin sediments: A comparative study", "author": [ { "family_name": "Naehr", "given_name": "Thomas H.", "clpid": "Naehr-T-H" }, { "family_name": "Eichhubl", "given_name": "Peter", "clpid": "Eichhubl-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Hovland", "given_name": "Martin", "clpid": "Hovland-M" }, { "family_name": "Paull", "given_name": "Charles K.", "clpid": "Paull-C-K" }, { "family_name": "Ussler", "given_name": "William, III", "clpid": "Ussler-W-III" }, { "family_name": "Lorenson", "given_name": "Thomas D.", "clpid": "Lorensen-T-D" }, { "family_name": "Greene", "given_name": "H. Gary", "clpid": "Greene-H-G" } ], "abstract": "Authigenic carbonates from five continental margin locations, the Eel River Basin, Monterey Bay, Santa Barbara Basin, the Sea of Okhotsk, and the North Sea, exhibit a wide range of mineralogical and stable isotopic compositions. These precipitates include aragonite, low- and high-Mg calcite, and dolomite. The carbon isotopic composition of carbonates varies widely, ranging from \u221260\u2030 to +26\u2030, indicating complex carbon sources that include ^(13)C-depleted microbial and thermogenic methane and residual, 13C-enriched, bicarbonate. A similarly large variability of \u03b4^(18)O values (\u22125.5\u2030 to +8.9\u2030) demonstrates the geochemical complexity of these sites, with some samples pointing toward an ^(18)O-enriched oxygen source possibly related to advection of ^(18)O-enriched formation water or to the decomposition of gas hydrate. Samples depleted in ^(18)O are consistent with formation deeper in the sediment or mixing of pore fluids with meteoric water during carbonate precipitation.\n\nA wide range of isotopic and mineralogical variation in authigenic carbonate composition within individual study areas but common trends across multiple geographic areas suggest that these parameters alone are not indicative for certain tectonic or geochemical settings. Rather, the observed variations probably reflect local controls on the flux of carbon and other reduced ions, such as faults, fluid conduits, the presence or absence of gas hydrate in the sediment, and the temporal evolution of the local carbon reservoir.\n\nAreas with seafloor carbonates that indicate formation at greater depth below the sediment\u2013water interface must have undergone uplift and erosion in the past or are still being uplifted. Consequently, the occurrence of carbonate slabs on the seafloor in areas of active hydrocarbon seepage is commonly an indicator of exhumation following carbonate precipitation in the shallow subsurface. Therefore, careful petrographic and geochemical analyses are critical components necessary for the correct interpretation of processes related to hydrocarbon seepage in continental margin environments and elsewhere.", "doi": "10.1016/j.dsr2.2007.04.010", "issn": "0967-0645", "publisher": "Elsevier", "publication": "Deep-Sea Research. Part II, Topical Studies in Oceanography", "publication_date": "2007-06", "series_number": "11-13", "volume": "54", "issue": "11-13", "pages": "1268-1291" }, { "id": "authors:ecfff-zf524", "collection": "authors", "collection_id": "ecfff-zf524", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TREaem07", "type": "article", "title": "Consumption of Methane and CO_2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea", "author": [ { "family_name": "Treude", "given_name": "Tina", "clpid": "Treude-T" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Knittel", "given_name": "Katrin", "clpid": "Knittel-K" }, { "family_name": "Gieseke", "given_name": "Armin", "clpid": "Gieseke-A" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Boetius", "given_name": "Antje", "clpid": "Boetius-A" } ], "abstract": "The deep anoxic shelf of the northwestern Black Sea has numerous gas seeps, which are populated by methanotrophic microbial mats in and above the seafloor. Above the seafloor, the mats can form tall reef-like structures composed of porous carbonate and microbial biomass. Here, we investigated the spatial patterns of CH_4 and CO_2 assimilation in relation to the distribution of ANME groups and their associated bacteria in mat samples obtained from the surface of a large reef structure. A combination of different methods, including radiotracer incubation, beta microimaging, secondary ion mass spectrometry, and catalyzed reporter deposition fluorescence in situ hybridization, was applied to sections of mat obtained from the large reef structure to locate hot spots of methanotrophy and to identify the responsible microbial consortia. In addition, CO_2 reduction to methane was investigated in the presence or absence of methane, sulfate, and hydrogen. The mat had an average \u03b4^(13)C carbon isotopic signature of \u221267.1\u2030, indicating that methane was the main carbon source. Regions dominated by ANME-1 had isotope signatures that were significantly heavier (\u221266.4\u2030 \u00b1 3.9 \u2030 [mean \u00b1 standard deviation; n = 7]) than those of the more central regions dominated by ANME-2 (\u221272.9\u2030 \u00b1 2.2 \u2030; n = 7). Incorporation of ^(14)C from radiolabeled CH_4 or CO_2 revealed one hot spot for methanotrophy and CO2 fixation close to the surface of the mat and a low assimilation efficiency (1 to 2% of methane oxidized). Replicate incubations of the mat with ^(14)CH_4 or ^(14)CO_2 revealed that there was interconversion of CH_4 and CO_2. The level of CO_2 reduction was about 10% of the level of anaerobic oxidation of methane. However, since considerable methane formation was observed only in the presence of methane and sulfate, the process appeared to be a rereaction of anaerobic oxidation of methane rather than net methanogenesis.", "doi": "10.1128/AEM.02685-06", "pmcid": "PMC1855681", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2007-04", "series_number": "7", "volume": "73", "issue": "7", "pages": "2271-2283" }, { "id": "authors:8ay3m-a1608", "collection": "authors", "collection_id": "8ay3m-a1608", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140723-162327093", "type": "article", "title": "Linking molecular taxonomy with environmental geochemsitry in environments relevant to astrobiology: The anaerobic oxidation of methane in cold seeps & deeply buried marine sediments", "author": [ { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Biddle", "given_name": "Jennifer F.", "clpid": "Biddle-J-F" }, { "family_name": "Lipp", "given_name": "Julius S.", "clpid": "Lipp-J-S" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "McKeegan", "given_name": "Kevin D.", "clpid": "McKeegan-K-D" }, { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" } ], "abstract": "The linking of molecular taxonomy (including 16s rRNA) to environmental geochemistry\nis a powerful way to work out the interactions, metabolic activities, and food webs of microorganisms in their natural setting, whether it is sediment, soil,\nor a water column. To this end, we developed a method for coupling an extant microorganism's\ngenetic information with geochemical data derived from the direct\nanalysis of its cell. FISH\u2013SIMS combines fluorescent in-situ hybridization (FISH)\nwith secondary ion mass spectrometry (SIMS). FISH is a culture-independent technique\nused to visually identify naturally occurring microorganisms by staining their\nribosomal RNA. Secondary ion mass spectrometry (SIMS) is a method by which\ngeochemical information can be obtained from microsamples. Using FISH-SIMS, a\nresearcher can measure a target cell's isotopic or elemental composition in a mixed\nenvironment.\nThe identification and study of methane-consuming microorganisms is an important\nstep toward understanding the methane cycle and microbial response to\nmethane release. The recent identification of two distinct Archaea capable of anaerobic\nmethane oxidationwas in part accomplished using FISH-SIMS. Because natural\nmethane is highly depleted in 13C, FISH-SIMS is particularly powerful at determining\nif a particular cell, collected from the environment, and consumed methane\nas a substrate for its cell carbon. This research demonstrated that both the ANME-1\nand ANME\u20132 Archaea from the Eel River Methane Seep are highly depleted in\n13C due to growth on methane.\nThe deep marine biosphere is thought to contain abundant microbial inhabitants,\nestimated to be a tenth of the Earth's total biomass. Sediments from this\nenvironment were recovered during Ocean Drilling Program (ODP) Leg 201, and\nwere analyzed by both molecular biological and organic geochemical techniques.\nOf particular interest in these sediments were four sulfate/methane transition zones\nseen at ODP Sites 1227, 1229 and 1230, two of which coincided with strongly elevated\ncell counts. Archaeal cells in these zones were analyzed for abundance and\nd13C composition by whole cell analysis (FISH-SIMS) and intact membrane lipids\n(HPLC-ESI-MSn). Cell counts showed greater archaeal abundance than bacterial,\nwhich was reflected by intact membrane lipid abundance. Isotopic compositions\nby both techniques (often around \u221220\u2030) suggest that methane is not an important\ncarbon source for these cells. Autotrophic carbon fixation appears to be an unlikely\nmetabolism given the relationship between the isotopic composition of DIC and\narchaeal biomass. The isotopic evidence suggests that the bulk archaeal community\nis heterotrophic, possibly mediating the oxidation of methane without consuming\nit as a carbon source.\nThe importance of these techniques is that the cells targeted for study can be\nenvironmental species that cannot currently be grown in the laboratory. These\ntechniques promises to become critical for working out the interactions, metabolic\nactivities, and food webs of microorganisms in their natural setting, whether it is\nsediment, soil, or a water column.", "issn": "0169-6149", "publisher": "Springer", "publication": "Origins of life and evolution of the biosphere", "publication_date": "2006-06", "series_number": "3", "volume": "36", "issue": "3", "pages": "314-315" }, { "id": "authors:jvp7z-j6572", "collection": "authors", "collection_id": "jvp7z-j6572", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130402-081618805", "type": "article", "title": "Evolutionary innovation: a bone-eating marine symbiosis", "author": [ { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Rouse", "given_name": "Greg W.", "clpid": "Rouse-G-W" }, { "family_name": "Jahnke", "given_name": "Linda", "clpid": "Jahnke-L" }, { "family_name": "Embaye", "given_name": "Tsegeria", "clpid": "Embaye-T" }, { "family_name": "Turk", "given_name": "Kendra", "clpid": "Turk-K-A" }, { "family_name": "Lee", "given_name": "Ray", "clpid": "Lee-Ray" }, { "family_name": "Vrijenhoek", "given_name": "Robert C.", "clpid": "Vrijenhoek-R-C" } ], "abstract": "Symbiotic associations between microbes and invertebrates have resulted in some of the most unusual physiological and morphological adaptations that have evolved in the animal world. We document a new symbiosis between marine polychaetes of the genus Osedax and members of the bacterial group Oceanospirillales, known for heterotrophic degradation of complex organic compounds. These organisms were discovered living on the carcass of a grey whale at 2891 m depth in Monterey Canyon, off the coast of California. The mouthless and gutless worms are unique in their morphological specializations used to obtain nutrition from decomposing mammalian bones. Adult worms possess elaborate posterior root-like extensions that invade whale bone and contain bacteriocytes that house intracellular symbionts. Stable isotopes and fatty acid analyses suggest that these unusual endosymbionts are likely responsible for the nutrition of this locally abundant and reproductively prolific deep-sea worm.", "doi": "10.1111/j.1462-2920.2005.00824.x", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2005-09", "series_number": "9", "volume": "7", "issue": "9", "pages": "1369-1378" }, { "id": "authors:xjv3s-9v076", "collection": "authors", "collection_id": "xjv3s-9v076", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-085250919", "type": "article", "title": "Geological, geochemical, and microbiological heterogeneity of the seafloor around methane vents in the Eel River Basin, offshore California", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Ussler", "given_name": "W., III", "clpid": "Ussler-W-III" }, { "family_name": "Naehr", "given_name": "T. H.", "clpid": "Naehr-T-H" }, { "family_name": "House", "given_name": "C. H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Hinrichs", "given_name": "K.-U.", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "Paull", "given_name": "C. K.", "clpid": "Paull-C-K" } ], "abstract": "Marine methane vents and cold seeps are common features along continental margins worldwide, serving as localized sites for methane release and colonization by microbial and chemosynthetic megafaunal communities. The Eel River Basin (ERB), located on the continental slope off Northern California, contains active methane vents and seep-associated chemosynthetic biological communities (CBC) on the crests of anticlines in \u223c520-m water depth. Seep-related features on the seafloor have a patchy distribution and include active bubbling vents, chemosynthetic clam beds, and sulfide-oxidizing bacterial mats. Methane sources supplying local seeps are heterogeneous on all spatial scales and support a large and diverse microbial assemblage involved in the anaerobic oxidation of methane (AOM).\n\nTo develop a comprehensive understanding of the complex biological, geochemical and physical processes associated with, and influencing seafloor methane seepage, a multidisciplinary approach is required. Here we present an integrative, multidisciplinary study that illustrates the diverse processes associated with seafloor methane seepage within the Eel River Basin and the complex interactions defining the geochemistry, mineralogy and microbiology within this environment.", "doi": "10.1016/j.chemgeo.2003.12.035", "issn": "0009-2541", "publisher": "Elsevier", "publication": "Chemical Geology", "publication_date": "2004-05-14", "series_number": "3-4", "volume": "205", "issue": "3-4", "pages": "265-289" }, { "id": "authors:vkava-9nk56", "collection": "authors", "collection_id": "vkava-9nk56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GOFaem04", "type": "article", "title": "Novel Forms of Structural Integration between Microbes and a Hydrothermal Vent Gastropod from the Indian Ocean", "author": [ { "family_name": "Goffredi", "given_name": "Shana K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "War\u00e9n", "given_name": "Anders", "clpid": "War\u00e9n-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Van Dover", "given_name": "Cindy L.", "clpid": "Van-Dover-C-L" }, { "family_name": "Vrijenhoek", "given_name": "Robert C.", "clpid": "Vrijenhoek-R-C" } ], "abstract": "Here we describe novel forms of structural integration between endo- and episymbiotic microbes and an unusual new species of snail from hydrothermal vents in the Indian Ocean. The snail houses a dense population of {gamma}-proteobacteria within the cells of its greatly enlarged esophageal gland. This tissue setting differs from that of all other vent mollusks, which harbor sulfur-oxidizing endosymbionts in their gills. The significantly reduced digestive tract, the isotopic signatures of the snail tissues, and the presence of internal bacteria suggest a dependence on chemoautotrophy for nutrition. Most notably, this snail is unique in having a dense coat of mineralized scales covering the sides of its foot, a feature seen in no other living metazoan. The scales are coated with iron sulfides (pyrite and greigite) and heavily colonized by {epsilon}- and {delta}-proteobacteria, likely participating in mineralization of the sclerites. This novel metazoan-microbial collaboration illustrates the great potential of organismal adaptation in chemically and physically challenging deep-sea environments.", "doi": "10.1128/AEM.70.5.3082-3090.2004", "pmcid": "PMC404406", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2004-05", "series_number": "5", "volume": "70", "issue": "5", "pages": "3082-3090" }, { "id": "authors:8g9h2-z6y27", "collection": "authors", "collection_id": "8g9h2-z6y27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GIRaem03", "type": "article", "title": "Growth and Methane Oxidation Rates of Anaerobic Methanotrophic Archaea in a Continuous-Flow Bioreactor", "author": [ { "family_name": "Girguis", "given_name": "Peter R.", "clpid": "Girguis-P-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Hallam", "given_name": "Steven J.", "clpid": "Hallam-S-J" }, { "family_name": "DeLong", "given_name": "Edward F.", "clpid": "DeLong-E-F" } ], "abstract": "Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that simulates the majority of in situ conditions and supports the metabolism and growth of anaerobic methanotrophic archaea. We incubated sediments collected from within and outside a methane cold seep in Monterey Canyon, Calif., for 24 weeks on the AMIS system. Anaerobic methane oxidation was measured in all sediments after incubation on AMIS, and quantitative molecular techniques verified the increases in methane-oxidizing archaeal populations in both seep and nonseep sediments. Our results demonstrate that the AMIS system stimulated the maintenance and growth of anaerobic methanotrophic archaea, and possibly their syntrophic, sulfate-reducing partners. Our data demonstrate the utility of combining physiological and molecular techniques to quantify the growth and metabolic activity of anaerobic microbial consortia. Further experiments with the AMIS system should provide a better understanding of the biological mechanisms of methane oxidation in anoxic marine environments. The AMIS may also enable the enrichment, purification, and isolation of methanotrophic archaea as pure cultures or defined syntrophic consortia.", "doi": "10.1128/AEM.69.9.5472-5482.2003", "pmcid": "PMC194967", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2003-09", "series_number": "9", "volume": "69", "issue": "9", "pages": "5472-5482" }, { "id": "authors:dxjxy-8zt41", "collection": "authors", "collection_id": "dxjxy-8zt41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130419-103230121", "type": "article", "title": "Geochemical Influence on Diversity and Microbial Processes in High Temperature Oil Reservoirs", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Goffredi", "given_name": "S. K.", "orcid": "0000-0002-9110-9591", "clpid": "Goffredi-S-K" }, { "family_name": "DeLong", "given_name": "E. F.", "clpid": "DeLong-E-F" }, { "family_name": "Boles", "given_name": "J. R.", "clpid": "Boles-J-R" } ], "abstract": "The diversity of thermophilic microbial assemblages detected within two neighboring high temperature petroleum formations was shown to closely parallel the different geochemical regimes existing in each. A high percentage of archaeal 16S rRNA gene sequences, related to thermophilic aceticlastic and hydrogenotrophic methanogens, were detected in the natural gas producing Rincon Formation. In contrast, rRNA gene libraries from the highly sulfidogenic Monterey Formation contained primarily sulfur-utilizing and fermentative archaea and bacteria. In addition to the variations in microbial community structure, microbial activities measured in microcosm experiments using high temperature production fluids from oil-bearing formations also demonstrated fundamental differences in the terminal respiratory and redox processes. Provided with the same suite of basic energy substrates, production fluids from the South Elwood Rincon Formation actively generated methane, while thermophilic microflora within the Monterey production fluids were dominated by hydrogen sulfide producing microorganisms. In both cases, molecular hydrogen appeared to play a central role in the stimulation of carbon and sulfur cycling in these systems. In methanogenic production fluids, the addition of sulfur compounds induced a rapid shift in the terminal electron accepting process, stimulating hydrogen sulfide formation and illustrating the metabolic versatility of the subsurface thermophilic assemblage. The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurface physicochemical conditions and may actively influence the geochemical environment in situ.", "doi": "10.1080/01490450303898", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "2003-07", "series_number": "4", "volume": "20", "issue": "4", "pages": "295-311" }, { "id": "authors:nrark-rt445", "collection": "authors", "collection_id": "nrark-rt445", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140715-170201332", "type": "article", "title": "Direct phylogenetic and isotopic evidence for multiple groups of archaea involved in the anaerobic oxidation of methane", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "House", "given_name": "C. H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Hinrichs", "given_name": "K.-U.", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "McKeegan", "given_name": "K. D.", "clpid": "McKeegan-K-D" }, { "family_name": "DeLong", "given_name": "E. F.", "clpid": "DeLong-E-F" } ], "abstract": "The biological oxidation of methane by anaerobic\nmicroorganisms is a significant sink for methane in the marine\nenvironment. Although there is convincing biogeochemical\nevidence for anaerobic oxidation of methane (AOM) by\nmethanotrophic archaea and sulfate-reducing bacteria, the\nidentity of these uncultured microorganisms is only now being\ndescribed. In this study, we examined the diversity archaeal\nand bacterial assemblages involved in AOM using directly\ncoupled isotopic and phylogenetic analyses at the level of\nsingle cells. The combined application of fluorescent in situ\nhybridization and secondary ion mass spectrometry (FISHSIMS)\nidentified two phylogenetically distinct groups of\narchaea (ANME-1 and ANME-2) from marine methane seeps\nthat were extremely depleted in carbon-13 (-83\u2030) and appear\nto be capable of directly oxidizing methane. These archaeal\ngroups were observed to exist as monospecies aggregates or\nsingle cells as well as in physical association with bacteria\nincluding, but not limited to, members of the sulfate-reducing\nDesulfosarcina. The results from this work illustrate the\ncomplexity of the microbial communities and possible\nmechanisms involved in AOM. FISH-SIMS is an effective\napproach for understanding the dynamic microbial interactions\nwithin diverse methane-associated communities and may\nprovide a useful culture-independent tool for deciphering the\nmetabolic function of other environmentally significant\nmicroorganisms in situ.", "doi": "10.1016/S0016-7037(02)01016-5", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2002-08-15", "series_number": "S1", "volume": "66", "issue": "S1", "pages": "A571" }, { "id": "authors:9ynm5-3d092", "collection": "authors", "collection_id": "9ynm5-3d092", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ORPpnas02", "type": "article", "title": "Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "McKeegan", "given_name": "Kevin D.", "clpid": "McKeegan-K-D" }, { "family_name": "DeLong", "given_name": "Edward F.", "clpid": "DeLong-E-F" } ], "abstract": "No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated. Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples. Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM). Here we use combined fluorescent in situ hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments. The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps. Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells. The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner. Bacteria associated with both archaeal groups included, but were not limited to, close relatives of Desulfosarcina species. Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia. In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex. The data also clearly show that highly structured ANME-2/Desulfosarcina consortia are not the sole entities responsible for AOM at marine methane seeps. Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia.", "doi": "10.1073/pnas.072210299", "pmcid": "PMC124316", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2002-05-28", "series_number": "11", "volume": "99", "issue": "11", "pages": "7663-7668" }, { "id": "authors:830e2-vsw47", "collection": "authors", "collection_id": "830e2-vsw47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130410-080805831", "type": "article", "title": "Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis", "author": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "House", "given_name": "Christopher H.", "orcid": "0000-0002-4926-4985", "clpid": "House-C-H" }, { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "McKeegan", "given_name": "Kevin D.", "clpid": "McKeegan-K-D" }, { "family_name": "DeLong", "given_name": "Edward F.", "clpid": "DeLong-E-F" } ], "abstract": "Microorganisms living in anoxic marine sediments consume more than 80% of the methane produced in the world's oceans. In addition to single-species aggregates, consortia of metabolically interdependent bacteria and archaea are found in methane-rich sediments. A combination of fluorescence in situ hybridization and secondary ion mass spectrometry shows that cells belonging to one specific archaeal group associated with the Methanosarcinales were all highly depleted in ^(13)C (to values of \u201396\u2030). This depletion indicates assimilation of isotopically light methane into specific archaeal cells. Additional microbial species apparently use other carbon sources, as indicated by significantly higher ^(13)C/^(12)C ratios in their cell carbon. Our results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms.", "doi": "10.1126/science.1061338", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2001-07-20", "series_number": "5529", "volume": "293", "issue": "5529", "pages": "484-487" }, { "id": "authors:v7tq9-q2b65", "collection": "authors", "collection_id": "v7tq9-q2b65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ORPaem01", "type": "article", "title": "Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Hinrichs", "given_name": "K.-U.", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "Ussler", "given_name": "W., III", "clpid": "Ussler-W-III" }, { "family_name": "Paull", "given_name": "C. K.", "clpid": "Paull-C-K" }, { "family_name": "Taylor", "given_name": "L. T.", "clpid": "Taylor-L-T" }, { "family_name": "Sylva", "given_name": "S. P.", "clpid": "Sylva-S-P" }, { "family_name": "Hayes", "given_name": "J. M.", "clpid": "Hayes-J-M" }, { "family_name": "DeLong", "given_name": "E. F.", "clpid": "DeLong-E-F" } ], "abstract": "The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant 13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. 13C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta -proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant 13C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.", "doi": "10.1128/AEM.67.4.1922-1934.2001", "pmcid": "PMC92814", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2001-04", "series_number": "4", "volume": "67", "issue": "4", "pages": "1922-1934" }, { "id": "authors:exe0n-r3842", "collection": "authors", "collection_id": "exe0n-r3842", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130429-141001775", "type": "article", "title": "Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments", "author": [ { "family_name": "Hinrichs", "given_name": "Kai-Uwe", "orcid": "0000-0002-0739-9291", "clpid": "Hinrichs-K-U" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Orphan", "given_name": "Victoria", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Sylva", "given_name": "Sean P.", "clpid": "Sylva-S-P" }, { "family_name": "Hayes", "given_name": "John M.", "clpid": "Hayes-J-M" } ], "abstract": "Convergent lines of molecular, carbon-isotopic, and phylogenetic evidence have previously indicated (Hinrichs, K.-U., Hayes, J.M., Sylva, S.P., Brewer, P.G., DeLong, E. F., 1999. Methane-consuming archaebacteria in marine sediments. Nature 398, 802\u2013805.) that archaea are involved in the anaerobic oxidation of methane in sediments from the Eel River Basin, offshore northern California. Now, further studies of those same sediments and of sediments from a methane seep in the Santa Barbara Basin have confirmed and extended those results. Mass spectrometric and chromatographic analyses of an authentic standard of sn-2-hydroxyarchaeol (hydroxylated at C-3 in the sn-2 phytanyl moiety) have confirmed our previous, tentative identification of this compound but shown that the previously examined product was the mono-TMS, rather than di-TMS, derivative. Further analyses of ^(13)C-depleted lipids, appreciably more abundant in samples from the Santa Barbara Basin, have shown that the archaeal lipids are accompanied by two sets of products that are only slightly less depleted in ^(13)C. These are additional glycerol ethers and fatty acids. The alkyl substituents in the ethers (mostly monoethers, with some diethers) are non-isoprenoidal. The carbon-number distributions and isotopic compositions of the alkyl substituents and of the fatty acids are similar, suggesting strongly that they are produced by the same organisms. Their structures, n-alkyl and methyl-branched n-alkyl, require a bacterial rather than archaeal source. The non-isoprenoidal glycerol ethers are novel constituents in marine sediments but have been previously reported in thermophilic, sulfate- and nitrate-reducing organisms which lie near the base of the rRNA-based phylogenetic tree. Based on previous observations that the anaerobic oxidation of methane involves a net transfer of electrons from methane to sulfate, it appears likely that the non-archaeal, ^(13)C-depleted lipids are products of one or more previously unknown sulfate-reducing bacteria which grow syntrophically with the methane-utilizing archaea. Their products account for 50% of the fatty acids in the sample from the Santa Barbara Basin. At all methane-seep sites examined, the preservation of aquatic products is apparently enhanced because the methane-oxidizing consortium utilizes much of the sulfate that would otherwise be available for remineralization of materials from the water column.", "doi": "10.1016/S0146-6380(00)00106-6", "issn": "0146-6380", "publisher": "Elsevier", "publication": "Organic Geochemistry", "publication_date": "2000-12", "series_number": "12", "volume": "31", "issue": "12", "pages": "1685-1701" }, { "id": "authors:yqm05-4cn54", "collection": "authors", "collection_id": "yqm05-4cn54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-083124041", "type": "article", "title": "Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs", "author": [ { "family_name": "Orphan", "given_name": "V. J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Taylor", "given_name": "L. T.", "clpid": "Taylor-L-T" }, { "family_name": "Hafenbradl", "given_name": "D.", "clpid": "Hafenbradl-D" }, { "family_name": "DeLong", "given_name": "E. F.", "clpid": "DeLong-E-F" } ], "abstract": "Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90\u00b0C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resembling Thermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H_2, acetate, and CO_2 as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium, Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter, Thermococcus, Desulfothiovibrio, Aminobacterium, Acidaminococcus, Pseudomonas, Halomonas, Acinetobacter, Sphingomonas, Methylobacterium, and Desulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.", "doi": "10.1128/AEM.66.2.700-711.2000", "pmcid": "PMC91884", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2000-02", "series_number": "2", "volume": "66", "issue": "2", "pages": "700-711" } ]