[ { "id": "thesis:17294", "collection": "thesis", "collection_id": "17294", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292025-055458332", "primary_object_url": { "basename": "silverman_shaelyn_2025_thesis.pdf", "content": "final", "filesize": 35182409, "license": "other", "mime_type": "application/pdf", "url": "/17294/3/silverman_shaelyn_2025_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "From Pure Cultures to Particles: Tracing Microbial Metabolism Through Amino Acid \u00b2H/\u00b9H Ratios", "author": [ { "family_name": "Silverman", "given_name": "Shaelyn Nicole", "orcid": "0000-0001-9201-6904", "clpid": "Silverman-Shaelyn-Nicole" } ], "thesis_advisor": [ { "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" } ], "thesis_committee": [ { "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" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Microbial metabolisms exert profound impact on our planet\u2019s atmosphere and surface geochemistry. Most available tools to study microbial metabolism in the environment provide only snapshots of activity at the time of sampling. However, holistic understanding of microbial function requires the ability to quantitatively reconstruct their activities prior to sampling, for which tools are currently limited. The overarching research presented in this thesis addresses this challenge through development of a new isotopic tool, amino acid hydrogen isotope (\u03b42HAA) analysis, into a useful tracer of microbial metabolism in the environment. We begin by solving a major analytical challenge: correcting for contributions of exchangeable amine-bound hydrogen in derivatized amino acids, which unlocks the ability to accurately measure \u03b42HAA values in organisms via gas chromatography-pyrolysis-isotope ratio mass spectrometry. We demonstrate in aerobic heterotrophic bacteria and phytoplankton that \u03b42HAA values are controlled by metabolism (specifically, carbon flow in cells), and we apply this isotopic tool to natural samples of marine particulate organic matter (POM), demonstrating substantial potential turnover of photoautotrophic proteins into heterotrophic proteins (up to 57 \u00b1 18%) in POM with depth at different ocean sites. We further explore the microscale dynamics of marine bacteria on diatom aggregates to contextualize our understanding of controls on marine POM degradation. In particular, we find that both intra- and interspecies interactions profoundly shape microbial colonization dynamics, which in turn likely affect bulk particle degradation rates. Together, this body of work demonstrates the profound utility of \u03b42HAA analysis as a tracer of microbial metabolism\u2014a timely development given the need to trace and quantify the metabolic responses of microbial communities to ongoing environmental perturbations.", "doi": "10.7907/5v12-1149", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17375", "collection": "thesis", "collection_id": "17375", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022025-214449948", "type": "thesis", "title": "Exploring Versatility of Energy Metabolism and Dynamics of Anabolism and Growth in Anaerobic Methanotrophic Consortia", "author": [ { "family_name": "Guo", "given_name": "Yongzhao", "orcid": "0009-0005-3983-8382", "clpid": "Guo-Yongzhao" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Two main questions are asked in this thesis, how environmental microorganisms respond and persist in an energy-limiting condition, and how we can investigate and disentangle the dynamics of these microbes\u2019 activity and growth at a high spatiotemporal resolution. To the end, this thesis focuses on a symbiosis of methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB), who mediate the anaerobic oxidation of methane (AOM), an important process in the global methane cycle. For the former question, Chapter 2 first found that carbon monoxide (CO) was able to serve as an alternative electron donor for ANME-SRB, and notably CO can even reverse the direction of AOM in ANME archaea to produce methane by the reduction of CO\u2082. Chapter 3 then explored and verified from the other side the potential role of pyrite (nano)particles in supporting AOM via a predicted reaction at the pyrite-water interface to generate sulfate and iron oxides as electron sinks. For the latter question, Chapter 4 took advantage of stable isotopic probing combined with the high sensitivity and spatial resolution of nanometer-scale secondary ion mass spectrometry (nanoSIMS) approach, and proposed a pipeline of multi-isotope imaging to record and in situ read out the single cell activity in the past. Chapter 5 as an in progress work attempts to disentangle the native division process in the yet uncultured ANME archaea by means of serial block face electron microscopy (SBEM) and deep learning imaging analysis. Taken together, this work provides more evidence of the versatile energy metabolism for ANME-SRB symbiosis and at the same time offers solutions to capturing the dynamics of activity and growth in natural microorganisms for the field of environmental microbiology.", "doi": "10.7907/fz82-xt77", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17045", "collection": "thesis", "collection_id": "17045", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03052025-175659528", "primary_object_url": { "basename": "ParraSergio_PhdThesis_Final.pdf", "content": "final", "filesize": 9240598, "license": "other", "mime_type": "application/pdf", "url": "/17045/1/ParraSergio_PhdThesis_Final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Location, Location, Location: Insights from Spatially-Resolved Observations of Marine Seep Carbonate Ecosystems and Carbonaceous Chondrite Surfaces", "author": [ { "family_name": "Parra", "given_name": "Sergio Alexander", "orcid": "0000-0002-2637-7960", "clpid": "Parra-Sergio-Alexander" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Ehlmann", "given_name": "Bethany L.", "orcid": "0000-0002-2745-3240", "clpid": "Ehlmann-B-L" } ], "thesis_committee": [ { "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" }, { "family_name": "Ehlmann", "given_name": "Bethany L.", "orcid": "0000-0002-2745-3240", "clpid": "Ehlmann-B-L" }, { "family_name": "Meile", "given_name": "Christof", "orcid": "0000-0002-0825-4596", "clpid": "Meile-C" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Spatially heterogeneous, multi-component systems are prevalent topics of study in geobiology and planetary science. However, previous studies of these systems often represent limited measurements that abstract or separate the sample from its localized context, thereby obscuring or precluding insights into the drivers ultimately shaping these systems. This challenge motivates the work presented in this thesis, where we provide an extensive and spatially-resolved examination of two complex, heterogeneous systems in geobiology and planetary science: marine seep carbonates and carbonaceous chondrite surfaces, respectively. In marine seep systems worldwide, seep carbonates are a mineral byproduct of a microbial metabolism (the anaerobic oxidation of methane, or AOM) and can continue hosting metabolically active microbial communities, including methane-oxidizing microbes. However, much of our understanding of these endolithic microbial communities stems from bulk, centimeter-scale evaluations of microbial identity and/or metabolic activity across a limited number of samples. As such, the range of structural and environmental conditions that ultimately shape the degree and extent of microbial activity in seep carbonates, including AOM, remains relatively under-constrained. To address this gap, Chapters 1-3 investigate carbonate-hosted microbial communities at a methane seep site in Santa Monica. In Chapter 1, we explore carbonate \u2018nodules\u2019 from methane seep sediments at and below the sulfate-methane transition zone (SMTZ), analyzing their mineral composition, internal structures, and hosted microbial communities compared to their host sediment communities and porewater chemistry. We also discuss key implications of the connectivity of seep sediments to nodules over geologic timescales and the preservation of microbial \u2018thumbprints\u2019. Chapter 2 describes rare tripartite associations between two groups of anaerobic methanotrophic archaea (ANME-1 and ANME-2) and a bacterial partner within seep carbonate crusts and other substrates at the seafloor, with implications towards understudied diversity in the syntrophic interactions governing AOM beyond seep carbonates. Chapter 3 examines the impact of seep carbonate internal structure on endolithic communities from various carbonate crusts, revealing similarities and differences between surface and interior communities that may reflect the importance of pore networks in maintaining favorable local environments. In Chapter 4, we pivot to an extensive analysis of spectra from carbonaceous chondrite surfaces. Carbonaceous chondrites (CCs) are a group of meteorites that represent the oldest materials in the solar system, whose mineralogy preserves a record of early alteration processes thought to be shared with certain asteroids. However, most studies connecting specific CCs to specific asteroids have relied on spectroscopic measurements of bulk powder CCs, which are spatially unresolved and destroy textures, thereby hindering tying shared spectral features to particular phases, petrologic contexts, and alteration histories. As such, Chapter 4 presents an analysis of CCs measured using microimaging hyperspectral visible-and-shortwave-infrared (VSWIR) spectroscopy, where we capture chondrite surfaces features at high spatial resolution. We also compare CC spectral features with asteroids using the Expanded Bus-DeMeo taxonomy, which provides a systematic framework to examine and identify shared drivers of spectral diversity within this spectral range, including Fe-bearing minerals from both original and terrestrial alteration processes. Together, these studies emphasize the importance of spatially-resolved sampling across disciplines, specifically in geobiology and planetary science, thereby capturing and highlighting the heterogenous nature of key systems in these fields and bettering our understanding of the factors shaping them.", "doi": "10.7907/c0w0-ns76", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17274", "collection": "thesis", "collection_id": "17274", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272025-172840679", "primary_object_url": { "basename": "Narayanan_AK_Thesis.pdf", "content": "final", "filesize": 22695777, "license": "other", "mime_type": "application/pdf", "url": "/17274/3/Narayanan_AK_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Diversity, Activity, and Adaptations of Phage Communities in Anoxic Hydrocarbon-Rich Marine Sediments", "author": [ { "family_name": "Narayanan", "given_name": "Aditi Kalpagam", "orcid": "0000-0003-0627-1859", "clpid": "Narayanan-Aditi-Kalpagam" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Parker", "given_name": "Joseph", "orcid": "0000-0001-9598-2454", "clpid": "Parker-J" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The viruses of the global ocean, especially those infecting prokaryotic taxa, are known to play an important role in maintaining the genetic and taxonomic diversity of their host communities and in the cycling of atmospheric carbon and key nutrients like nitrogen and iron. However, the vast majority of these conclusions are drawn from the surface ocean and upper water column, while the sediments, which constitute one of the largest biomes on earth, are understudied in comparison. Of special interest are areas on the ocean floor where methane and other hydrocarbons are produced and released by geological activity and oxidized by a consortium of archaea and bacteria. Using direct genomic sequencing of the viruses from a variety of simplified sediment-free enrichments of hydrocarbon oxidizers, I compare viral communities sampled from different locations and incubated under a range of temperatures to understand the role these parameters might play in shaping distribution and community structure. I then present the most comprehensive picture thus far of viral diversity and distribution from a methane cold seep and discuss whether the viral assemblages are influenced by the steep geochemical gradients that characterize seep sediments. From these datasets, I propose that viral communities in methane-oxidizing sediments are tailored specifically to the physical constraints of the sediment matrix rather than to the dominant members of the cellular community or to other physicochemical parameters such as temperature, sampling location, or depth below the seafloor. I then outline the development of two methods, stable-isotope probing coupled to nanoSIMS and biorthogonal non-canonical amino acid tagging, to work in heterogenous sediment virus samples rather than the liquid pure cultures on which they had previously relied. Implementation of these methods, which allow us to temporally constrain viral production and virus-influenced nutrient flow, resulted in the hypothesis that viral production likely responds to shifts in the major metabolic processes within an ecosystem and may influence cellular community composition.", "doi": "10.7907/v5x8-7447", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16357", "collection": "thesis", "collection_id": "16357", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04172024-164449548", "primary_object_url": { "basename": "Lim_thesis_2024.pdf", "content": "final", "filesize": 10822139, "license": "other", "mime_type": "application/pdf", "url": "/16357/5/Lim_thesis_2024.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "The Impact of Energy Availability and Substrate Complexity on Anaerobic Microbial Communities in Marine Sediment", "author": [ { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "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" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This thesis probes the interplay of organic matter complexity (Chapters 1 and 2) and local redox gradients (Chapter 3) with the community structure and function of the anaerobic marine sediment microbiome. Deep marine sediments, despite being generally organic-poor, harbor a vast diversity of microorganisms that are critical to the global nutrient cycle. Transient nutrient inputs such as whale falls result in hotspots of microbial community activity in an environment that normally processes heavily degraded organic material from the upper ocean. These organic loading events result in transitions down redox gradients and dynamic shifts in the local energy availability of the microbial communities. Through in situ seafloor and laboratory microcosm experiments, we provide insights into the impact of energy availability and carbon complexity on maintaining hierarchical and complex community interactions, community activity, and systematic and functional diversity.", "doi": "10.7907/67j6-4885", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:13962", "collection": "thesis", "collection_id": "13962", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09232020-172452048", "type": "thesis", "title": "Spatial and Temporal Dynamics of Microorganisms Living Along Steep Energy Gradients and Implications for Ecology and Geologic Preservation in the Deep Biosphere", "author": [ { "family_name": "Mullin", "given_name": "Sean William Alexander", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-William-Alexander" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

The deep biosphere represents a massive repository of life with unknown effects on global biogeochemical cycles. Even the fundamental life strategies of the endemic microorganisms that inhabit this biome remain enigmatic; some studies have indicated that subsurface organisms subsist in energetic regimes below the theoretical lower limit for life. A boom-bust life cycle, mediated by tectonic disturbances and subsurface fractures, may help explain these phenomena. This work addresses and expands on this question, first by exploring the response of continental deep biosphere microorganisms to an in situ organic matter amendment, then by analyzing the microbial community dynamics of the sediments and carbonate along a naturally-occurring energy gradient at a methane seep. Our experiments in the continental deep biosphere confirmed that mineralogical heterogeneity can drive differential colonization of the native microorganisms, implying that selection and adaptation to in situ conditions occurs, differentiating individual microbial niches. We also observed the formation of secondary framboidal iron sulfide minerals, a well-known phenomenon in marine sediments but not extensively observed in the deep subsurface, that were correlated to the presence of abundant sulfur-metabolizing microorganisms. Chapters 2 and 3 are instead focused on the microbial ecology of a methane seep on the Pacific margin of Costa Rica. Cold methane seeps themselves represent sharp boundaries between the generally low-energy background seafloor and abundant chemical energy in the form of methane. Chapter 2 describes that the microorganisms living at these seeps occupy a significantly narrower spatial scale than the endemic megafauna. In addition, by correlating community dissimilarity and geographic distance, the functional center of the seep was identified, allowing for insight into the ecological differentiation between clades of anaerobic methanotrophic archaea (ANME). Chapter 3 examines in greater detail the endolithic microbial community, principally composed of ANME-1. By conducting transplantation experiments of carbonates on the seafloor, we tested the response of the in situ endolithic communities and found that carbonates moved distinctly outside the active zone changed less than communities moved to regions of less activity.

", "doi": "10.7907/f3k8-ck13", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13842", "collection": "thesis", "collection_id": "13842", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07182020-211405749", "primary_object_url": { "basename": "Chadwick_Thesis_v3.pdf", "content": "final", "filesize": 58503253, "license": "other", "mime_type": "application/pdf", "url": "/13842/37/Chadwick_Thesis_v3.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "How to Beat Diffusion: Explorations of Energetics and Spatial Relationships in Microbial Ecosystems", "author": [ { "family_name": "Chadwick", "given_name": "Grayson Lee", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-Lee" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

This thesis investigates four microbial systems, with a particular focus for how spatial considerations shape the behavior and evolution of microorganisms. After a general introduction in Chapter 1, Chapter 2 presents the results of experiments demonstrating how cellular activity varies through space within an anode-reducing biofilm. Chapter 3 presents a comprehensive comparative genomic analysis of all known marine anaerobic methanotrophic archaea, supporting the notion that these organisms share many energetic similarities with the anode reducing organisms in Chapter 2. These are interpreted as specific adaptations to life in highly structured microbial communities. Chapter 4 describes the enrichment and characterization of a new member of the purple sulfur bacteria, and the adaptations that may improve substrate acquisition beyond the normal limitations of diffusion. Chapter 5 describes the convergent evolution of novel Complex I gene clusters that have incorporated new proton pumping subunits, and the modifications made to the protein structure to facilitate the incorporation of these new subunits into the quaternary structure of the complex.

", "doi": "10.7907/svrp-rb07", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13854", "collection": "thesis", "collection_id": "13854", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08122020-110818529", "primary_object_url": { "basename": "Metcalfe_PhD.pdf", "content": "final", "filesize": 248598908, "license": "other", "mime_type": "application/pdf", "url": "/13854/37/Metcalfe_PhD.pdf", "version": "v17.0.0" }, "type": "thesis", "title": "Symbiotic Diversity and Mineral-Associated Microbial Ecology in Marine Microbiomes", "author": [ { "family_name": "Metcalfe", "given_name": "Kyle Shuhert", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-Shuhert" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This thesis investigates ecological interactions in the seafloor between microbial taxa (Chapters 1 and 2) and between these microorganisms and their mineral hosts (Chapters 2 through 4). In seafloor sediments, electron acceptors are often limited, forcing microorganisms inhabiting these sediments to acquire symbiotic partners and/or perform extracellular electron transfer to insoluble electron acceptors. Seafloor methane seeps present an endmember case wherein extremely reducing fluids charged with methane advect through sediment. In these benthic ecosystems, anaerobic methanotrophic archaea (ANME) form symbiotic partnerships with sulfate-reducing bacteria (SRB), but it remained unclear if certain ANME exhibit a preference for certain SRB partners. In Chapter 1, I present results documenting such a pattern of partnership specificity in ANME-SRB consortia. In Chapter 2, I further examine these patterns in rare ANME taxa through development and application of a density-separation protocol refined from published work. This protocol exploits the co-association of microbial taxa on mineral surfaces to aid in the detection of novel symbioses, and further is useful to detect microbial interactions with certain minerals. In Chapter 3, I focus on the interaction between ANME-SRB consortia and authigenic silicates that have been observed on consortium exteriors, finding evidence to support that the precipitation of these silicates is actively mediated by ANME-SRB. In Chapter 4, I perform geochemical modeling benchmarked by synchrotron X-ray analysis to examine the imprint of extracellular electron transport by metal-reducing microorganisms on Precambrian manganese-rich sedimentary rocks.", "doi": "10.7907/ve4r-k526", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:10212", "collection": "thesis", "collection_id": "10212", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262017-143517395", "type": "thesis", "title": "Insights into Pathways of Nitrous Oxide Generation from Novel Isotopologue Measurements", "author": [ { "family_name": "Magyar", "given_name": "Paul Macdonald", "orcid": "0000-0003-0234-247X", "clpid": "Magyar-Paul-Macdonald" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "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" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

The accumulation of nitrous oxide (N2O) in the atmosphere is a significant manifestation of human perturbations of the nitrogen cycle. This thesis reports the development and first applications of a novel isotopic technique for characterizing nitrous oxide sources. Chapter 1 describes the development of methods to use the newly available technology of high- resolution dual-inlet multi-collector mass spectrometry to measure six isotopic parameters in nitrous oxide. It reports the standardization and initial biological application of these methods. Chapter 2 presents a model for the generation of isotope effects in an important N2O generating enzyme, the bacterial nitric oxide reductase; this model and published isotopic constraints are used to provide insights into the mechanism of that enzyme. Chapter 3 describes the six-dimensional isotopic characterization of nitrous oxide from bacterial denitrifiers, while Chapter 4 describes nitrous oxide generated by ammonia oxidizing bacteria.

", "doi": "10.7907/Z93776RJ", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10319", "collection": "thesis", "collection_id": "10319", "cite_using_url": "https://resolver.caltech.edu/CaltechThesis:06082017-134458390", "primary_object_url": { "basename": "Thesis_Hang_Yu.pdf", "content": "final", "filesize": 16027895, "license": "other", "mime_type": "application/pdf", "url": "/10319/18/Thesis_Hang_Yu.pdf", "version": "v11.0.0" }, "type": "thesis", "title": "Understanding the Symbiosis in Anaerobic Oxidation of Methane Through Metabolic, Biosynthetic and Transcriptomic Activities", "author": [ { "family_name": "Yu", "given_name": "Hang Hank", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang-Hank" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "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": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

Microorganisms provide essential ecological services to our planet. Their combined activities control and shape our environment as we know today. In the deep sea, a microbial mediated process known as anaerobic oxidation of methane (AOM) consumes large amounts of methane, a potent greenhouse gas and a valuable energy resource. How this symbiosis works is poorly understood.

\r\n\r\n

In this thesis, I tested current hypotheses on the symbiotic mechanisms in AOM microbial consortia, consisting of a partnership between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Sediments collected from methane seeps offshore Oregon and California and dominated by AOM consortia were used in these investigations. A range of compounds were amended to sediment microcosms, and their effects on the metabolic activities of ANME or SRB were monitored by tracking the rates of methane oxidation or sulfate reduction on timescales varying from hours to months. A lack of stimulation or inhibition on the AOM consortia, combined with long-term community profiles, suggest that diffusible compounds are unlikely to be involved in the symbiosis in AOM. I further examine ANME genomes, focusing the role of sulfur in methane seep ecosystems. Phylogenetic analyses revealed multiple poorly characterized genes in the sulfur pathway, and comparisons with methanogenic archaea related to ANME provided a better understanding of their roles in the cell. Transcriptional responses combined with protein modeling were used to predict the potential substrate of a sulfite reductase related enzyme. These predictions were validated using genetics, and together point to an assimilatory rather than dissimilatory sulfur pathway in methane-utilizing archaea in general. Then, the AOM symbiosis was decoupled for the first time using soluble electron acceptors. ANME remained metabolically and biosynthetically active without their SRB partner, suggesting that the electrons are transferred directly in this partnership. This observation was investigated to a greater depth with transcriptomics. Membrane proteins and multiheme cytochromes critical in extracellular electron transfer in ANME and SRB were expressed. These results together illuminate the path electrons may take to exit or enter the AOM consortia. Overall, multiple activity analyses used here piece together a clearer view on how the symbiosis in AOM works, with potential applications in future energy generation from methane.

\r\n", "doi": "10.7907/Z9XD0ZQQ", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9768", "collection": "thesis", "collection_id": "9768", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-132232540", "primary_object_url": { "basename": "ETR_Thesis_Final.pdf", "content": "final", "filesize": 120182434, "license": "other", "mime_type": "application/pdf", "url": "/9768/43/ETR_Thesis_Final.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Molecular and Geochemical Insights into Microbial Life Centimeters to Kilometers Below the Seafloor", "author": [ { "family_name": "Trembath-Reichert", "given_name": "Elizabeth", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

At the broadest scale, this thesis is an investigation of how life modulates the movement of essential elements (carbon, sulfur, nitrogen, and silicon) on modern and geologic timescales. Chapters 1 and 2 explore carbon and sulfur cycling microbial communities found centimeters below the seafloor in hydrocarbon-rich methane seep ecosystems. At the Hydrate Ridge methane seep, we investigated how microbial partnerships direct the flow of methane and sulfide in these benthic oases by using identity-based physical separation methods developed in our lab (Magneto-FISH) in conjunction with community profiling and metagenomic sequencing. This method explores the middle ground between single cell and bulk sediment analysis by separating target microbes and their physically associated community for downstream sequencing applications. Magneto-FISH captures were done at a range of microbial taxonomic group specificities and sequenced with both clone library and next-gen iTag 16S rRNA gene methods. Chapter 1 provides a demonstration of how FISH probe taxonomic specificity correlates to resultant Archaeal taxonomic diversity in Magneto-FISHed seep sediments, with specific attention to preparation of Archaea-enriched samples for downstream metagenomic sequencing. In Chapter 2, a Bacteria-focused parallel environmental isolation and sequencing effort was subjected to co-occurrence analyses which suggested there may be far more microbial associations in methane seep systems than are currently appreciated, including partnerships that do not involve the canonical anaerobic methane oxidizing archaea and sulfate reducing bacteria. With samples from IODP Expedition 337 Shimokita coalbed biosphere, Chapter 3 provides evidence for an active microbial assemblage kilometers below the sea floor in the deepest samples ever collected by marine scientific ocean drilling. Using in situ temperature Stable Isotope Probing (SIP) incubations and NanoSIMS, we investigated whole community activity (with the passive tracer D2O) and substrate specific activity with C1-carbon compounds methylamine and methanol. We found deuterium-based turnover times to be faster (years) than previous deep biosphere estimates (hundreds to thousands of years), but methylotrophy rates to be slower than previous carbon metabolic rates.

", "doi": "10.7907/Z96Q1V6Q", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9064", "collection": "thesis", "collection_id": "9064", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07212015-103405937", "type": "thesis", "title": "Physical, Metabolic, and Energetic Investigations of Methane-Metabolizing Microbial Communities", "author": [ { "family_name": "Marlow", "given_name": "Jeffrey James", "clpid": "Marlow-Jeffrey-James" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Hoehler", "given_name": "Tori M.", "clpid": "Hoehler-T-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Understanding the roles of microorganisms in environmental settings by linking phylogenetic identity to metabolic function is a key challenge in delineating their broad-scale impact and functional diversity throughout the biosphere. This work addresses and extends such questions in the context of marine methane seeps, which represent globally relevant conduits for an important greenhouse gas. Through the application and development of a range of culture-independent tools, novel habitats for methanotrophic microbial communities were identified, established settings were characterized in new ways, and potential past conditions amenable to methane-based metabolism were proposed. Biomass abundance and metabolic activity measures \u2013 both catabolic and anabolic \u2013 demonstrated that authigenic carbonates associated with seep environments retain methanotrophic activity, not only within high-flow seep settings but also in adjacent locations exhibiting no visual evidence of chemosynthetic communities. Across this newly extended habitat, microbial diversity surveys revealed archaeal assemblages that were shaped primarily by seepage activity level and bacterial assemblages influenced more substantially by physical substrate type. In order to reliably measure methane consumption rates in these and other methanotrophic settings, a novel method was developed that traces deuterium atoms from the methane substrate into aqueous medium and uses empirically established scaling factors linked to radiotracer rate techniques to arrive at absolute methane consumption values. Stable isotope probing metaproteomic investigations exposed an array of functional diversity both within and beyond methane oxidation- and sulfate reduction-linked metabolisms, identifying components of each proposed enzyme in both pathways. A core set of commonly occurring unannotated protein products was identified as promising targets for future biochemical investigation. Physicochemical and energetic principles governing anaerobic methane oxidation were incorporated into a reaction transport model that was applied to putative settings on ancient Mars. Many conditions enabled exergonic model reactions, marking the metabolism and its attendant biomarkers as potentially promising targets for future astrobiological investigations. This set of inter-related investigations targeting methane metabolism extends the known and potential habitat of methanotrophic microbial communities and provides a more detailed understanding of their activity and functional diversity.", "doi": "10.7907/Z9W66HPS", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9776", "collection": "thesis", "collection_id": "9776", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-170051580", "primary_object_url": { "basename": "Case_David_2016_Thesis_Full_Revised.pdf", "content": "final", "filesize": 23212031, "license": "other", "mime_type": "application/pdf", "url": "/9776/54/Case_David_2016_Thesis_Full_Revised.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Carbonate-Associated Microbial Ecology at Methane Seeps: Assemblage Composition, Response to Changing Environmental Conditions, and Implications for Biomarker Longevity", "author": [ { "family_name": "Case", "given_name": "David Hamilton", "orcid": "0000-0002-1023-0040", "clpid": "Case-David-Hamilton" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Levin", "given_name": "Lisa A.", "clpid": "Levin-L-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

Methane seeps are globally distributed geologic features in which reduced fluid from below the seafloor is advected upward and meets the oxidized bottom waters of Earth\u2019s oceans. This redox gradient fuels chemosynthetic communities anchored by the microbially-mediated anaerobic oxidation of methane (AOM). Both today and in Earth\u2019s past, methane seeps have supported diverse biological communities extending from microorgansisms to macrofauna and adding to the diversity of life on Earth. Simultaneously, the carbon cycling associated with methane seeps may have played a significant role in modulating ancient Earth\u2019s climate, particularly by acting as a control on methane emissions.

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The AOM metabolism generates alkalinity and dissolved inorganic carbon (DIC) and at a 2:1 ratio, promoting the abiogenic, or authigenic, precipitation of carbonate minerals. Over time, these precipitates can grow into pavements covering hundreds of square meters on the seafloor and dominating the volumetric habitat space available in seep ecosystems. Importantly, carbonates are incorporated into the geologic record and therefore preserve an inorganic (i.e., d13C) and organic (i.e., lipid biomarker) history of methane seepage. However, the extent to which preserved biomarkers represent a snapshot of microorganisms present at the time of primary precipitation, a time-integrated history of microbial assemblages across the life cycle of a methane seep, or a view of the final microorganisms inhabiting a carbonate prior to incorporation in the sedimentary record is unresolved.

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This thesis addresses the ecology of carbonate-associated seep microorganisms. Chapters One and Two contextualize the extant microbial diversity on seep carbonates versus within seep sediments, as determined through 16S rRNA gene biomarkers. Small, protolithic carbonate \u201cnodules\u201d recovered from within seep sediments are observed to be capable of capturing surrounding sediment-hosted microbial diversity, but in some cases also diverge from sediments. Meanwhile, lithified carbonate blocks recovered from the seafloor host microbial assemblages demonstrably distinct from seep sediments (and seep nodules). Microbial 16S rRNA gene diversity within carbonate samples is well-differentiated by the extent of contemporary seepage. In situ seafloor transplantation experiments further demonstrated the microbial assemblages associated with seep carbonates to be sensitive to seep quiescence and activation on short (13-month) timescales. This was particularly true for organisms whose 16S rRNA genes imply physiologies dependent on methane or sulfur oxidation. With an improved understanding of the modern ecology of carbonate-associated microorganisms, Chapter Three applies intact polar lipid (IPL) and core lipid analyses to begin describing whether, and to what extent, geologically relevant biomarkers mimic short-term dynamics observed in 16S rRNA gene profiles versus archive a record of historic microbial diversity. Biomarker longevity is determined to increase from 16S rRNA genes to IPLs to core lipids, with IPLs preserving microbial diversity history on timescales more similar to 16S rRNA genes than core lipids. Ultimately, individual IPL biomarkers are identified which may be robust proxies for determining whether the biomarker profile recorded in a seep carbonate represents vestiges of active seepage processes, or the profile of a microbial community persisting after seep quiescence.

", "doi": "10.7907/Z9TD9V84", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:7755", "collection": "thesis", "collection_id": "7755", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282013-062935856", "primary_object_url": { "basename": "SaxenaAbigail2013_thesis.pdf", "content": "final", "filesize": 13911949, "license": "other", "mime_type": "application/pdf", "url": "/7755/31/SaxenaAbigail2013_thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Sulfur-Cycling in Methane-Rich Ecosystems: Uncovering Microbial Processes and Novel Niches", "author": [ { "family_name": "Saxena", "given_name": "Abigail Green", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-Abigail-Green" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Jensen", "given_name": "Grant J.", "clpid": "Jensen-G-J" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "clpid": "Mazmanian-S-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "clpid": "Rothenberg-E-V" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "

Microbial sulfur cycling communities were investigated in two methane-rich ecosystems, terrestrial mud volcanoes (TMVs) and marine methane seeps, in order to investigate niches and processes that would likely be central to the functioning of these crucial ecosystems. Terrestrial mud volcanoes 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 4 TMVs in Azerbaijan, supporting the presence of active sulfur-oxidizing and sulfate-reducing guilds in all 4 TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. We also found evidence for the anaerobic oxidation of methane coupled to sulfate reduction, a process which we explored further in the more tractable marine methane seeps. 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. Using a combination of molecular, geochemical and fluorescence in situ hybridization coupled to nano-scale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations, we show that the unexplained diversity in SRB associated with ANME cells can be at least partially explained by preferential nitrate utilization by one particular partner, the seepDBB. This discovery reveals that nitrate is likely an important factor in community structuring and diversity in marine methane seep ecosystems. The thesis concludes with a study of the dynamics between ANME and their associated SRB partners. We inhibited sulfate reduction and followed the metabolic processes of the community as well as the effect of ANME/SRB aggregate composition and growth on a cellular level by tracking 15N substrate incorporation into biomass using FISH-NanoSIMS. We revealed that while sulfate-reducing bacteria gradually disappeared over time in incubations with an SRB inhibitor, the ANME archaea persisted in the form of ANME-only aggregates, which are capable of little to no growth when sulfate reduction is inhibited. These data suggest ANME are not able to synthesize new proteins when sulfate reduction is inhibited.

", "doi": "10.7907/Z9125QKD", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7347", "collection": "thesis", "collection_id": "7347", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12192012-141624638", "primary_object_url": { "basename": "Dekas_Anne_2013_thesis.pdf", "content": "final", "filesize": 52021793, "license": "other", "mime_type": "application/pdf", "url": "/7347/1/Dekas_Anne_2013_thesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Diazotrophy in the Deep: An Analysis of the Distribution, Magnitude, Geochemical Controls, and Biological Mediators of Deep-Sea Benthic Nitrogen Fixation", "author": [ { "family_name": "Dekas", "given_name": "Anne Elizabeth", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-Anne-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Kirschvink", "given_name": "Joseph L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "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": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Howard", "given_name": "James B.", "clpid": "Howard-J-B" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

Biological nitrogen fixation (the conversion of N2 to NH3) is a critical process in the oceans, counteracting the production of N2 gas by dissimilatory bacterial metabolisms and providing a source of bioavailable nitrogen to many nitrogen-limited ecosystems. One currently poorly studied and potentially underappreciated habitat for diazotrophic organisms is the sediments of the deep-sea. Although nitrogen fixation was once thought to be negligible in non-photosynthetically driven benthic ecosystems, the present study demonstrates the occurrence and expression of a diversity of nifH genes (those necessary for nitrogen fixation), as well as a widespread ability to fix nitrogen at high rates in these locations. The following research explores the distribution, magnitude, geochemical controls, and biological mediators of nitrogen fixation at several deep-sea sediment habitats, including active methane seeps (Mound 12, Costa Rica; Eel River Basin, CA, USA; Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA), whale-fall sites (Monterey Canyon, CA), and background deep-sea sediment (off-site Mound 12 Costa Rica, off-site Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA). The first of the five chapters describes the FISH-NanoSIMS method, which we optimized for the analysis of closely associated microbial symbionts in marine sediments. The second describes an investigation of methane seep sediment from the Eel River Basin, where we recovered nifH sequences from extracted DNA, and used FISH-NanoSIMS to identify methanotrophic archaea (ANME-2) as diazotrophs, when associated with functional sulfate-reducing bacterial symbionts. The third and fourth chapters focus on the distribution and diversity of active diazotrophs (respectively) in methane seep sediment from Mound 12, Costa Rica, using a combination of 15N-labeling experiments, FISH-NanoSIMS, and RNA and DNA analysis. The fifth chapter expands the scope of the investigation by targeting diverse samples from methane seep, whale-fall, and background sediment collected along the Eastern Pacific Margin, and comparing the rates of nitrogen fixation observed to geochemical measurements collected in parallel. Together, these analyses represent the most extensive investigation of deep-sea nitrogen fixation to date, and work towards understanding the contribution of benthic nitrogen fixation to global marine nitrogen cycling.

", "doi": "10.7907/H9F5-T161", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:6448", "collection": "thesis", "collection_id": "6448", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-085126961", "primary_object_url": { "basename": "BKH_Thesis_110527.pdf", "content": "final", "filesize": 3601319, "license": "other", "mime_type": "application/pdf", "url": "/6448/1/BKH_Thesis_110527.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Microbial Colonization of Minerals in Marine Sediments \u2013 Method Development and Ecological Significance", "author": [ { "family_name": "Harrison", "given_name": "Benjamin Kimball", "clpid": "Harrison-Benjamin-Kimball" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Edwards", "given_name": "Katrina J.", "clpid": "Edwards-K-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "

Interactions between microorganisms and minerals significantly impact microbial diversity and geochemical cycles in diverse settings. However, methodological difficulty has inhibited past study of microbe\u2013mineral interactions in fine-grained subsurface environments. Conventional sampling poorly resolves microbial diversity at the fine scale necessary to perceive overall community differences between mineral substrates that are thoroughly mixed. In particular, the importance of microbial attachment to minerals in unconsolidated marine sediments remains poorly constrained despite extensive geobiological research in these settings. This study presents an approach for characterizing microbial colonization patterns using mineral separation techniques. Differences in density and magnetic susceptibility are used to enrich target minerals from bulk environmental samples, selecting for those minerals which may have importance as substrates for metabolic activity.

\r\n \r\n

The application of this methodology to methane seep sediments of the Eel River Basin (ERB) on the California margin demonstrates that variations in microbial diversity between minerals are comparable to community differences across broad spatial scales and a range of porewater geochemistry. ERB colonization patterns determined by separation are shown to be reproducible and reflect in situ differences in the microbial community. Affinity of putative sulfide-oxidizing bacteria (primarily identified as Gammaproteobacteria) for mineral partitions enriched in authigenic sulfides suggests microbial attachment may reflect a metabolic role in sulfur cycling under reducing conditions. Mineral attachment is also shown to select between key archaeal phylotypes involved in the anaerobic oxidation of methane (AOM), providing insight into physiological differences between these uncultured groups. Preliminary results demonstrate that mineral attachment may be a significant factor in the microbial diversity of the marine subsurface, and that such community differences will be ecologically relevant.

\r\n", "doi": "10.7907/3891-QQ56", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6527", "collection": "thesis", "collection_id": "6527", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06232011-131748079", "primary_object_url": { "basename": "HKLiuSeniorThesis.pdf", "content": "updated", "filesize": 216140, "license": "other", "mime_type": "application/pdf", "url": "/6527/1/HKLiuSeniorThesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Abundance and Behavior of Viruses in Ancient Seawater and Modern Iron-rich Environments", "author": [ { "family_name": "Liu", "given_name": "Hanna Ken-Yuin", "clpid": "Liu-Hanna-Ken-Yuin" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" } ], "thesis_committee": [ { "family_name": "None", "given_name": "None" } ], "local_group": [ { "literal": "Senior Undergraduate Thesis Prize" }, { "literal": "div_gps" } ], "abstract": "The proclivity of silica for ferric hydroxide sorption sites allows for an Archean iron cycle involving iron-silica co-precipitation and deposition of banded iron formations (BIF). Considering the tendency of viruses to also sorb iron, here we investigate the possibility that viruses were involved in the iron cycle and potentially deposited in BIFs. A known concentration of Syn33a cyanophages was introduced into each media and the viral particles remaining in solution after a short centrifugation were enumerated using epifluorescence microscopy. The number of particles sequestered on the siliceous ferric oxide precipitate was estimated by difference. Similar to previous experiments, we observed a strong affinity of viral particles for iron oxides in the absence of silica. However, we also observe competitive inhibition of viral adsorption by silica, though only when silica is raised to concentrations of 670 \u03bcM. Ultimately, our data reveal that interactions between iron, silica, and viruses would have affected virus dynamics and corresponding biogeochemistry in the Archean ocean. Similar dynamics are predicted to occur in iron-rich environments today.", "doi": "10.7907/VTTR-HS63", "publication_date": "2011", "thesis_type": "senior_major", "thesis_year": "2011" } ]