Orphan, Victoria

Combined from CaltechAUTHORS

• Mueller, Elliott P. and Panehal, Juliann, el al. (2024) Isotopic evidence of acetate turnover in Precambrian continental fracture fluids; Nature Communications; Vol. 15; No. 1; 9130; 10.1038/s41467-024-53438-4
• Hoehler, Tori M. and Amend, Jan P., el al. (2024) Editorial: Studies on life at the energetic edge – from laboratory experiments to field-based investigations, volume II; Frontiers in Microbiology; Vol. 14; 10.3389/fmicb.2023.1351761
• Osorio-Rodriguez, Daniela and Metcalfe, Kyle S., el al. (2023) Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation; Proceedings of the National Academy of Sciences; Vol. 120; No. 51; e2302156120; PMCID PMC10743459; 10.1073/pnas.2302156120
• Candry, Pieter and Chadwick, Grayson L., el al. (2023) Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities; ISME Journal; Vol. 17; No. 11; 2014-2022; PMCID PMC10579388; 10.1038/s41396-023-01508-8
• Murali, Ranjani and Yu, Hang, el al. (2023) Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea; PLOS Biology; Vol. 21; No. 9; e3002292; PMCID PMC10553843; 10.1371/journal.pbio.3002292
• Mangenot, Xavier and Xie, Hao, el al. (2023) ²H-²H clumping in molecular hydrogen method and preliminary results; Chemical Geology; Vol. 621; Art. No. 121278; 10.1016/j.chemgeo.2022.121278
• Laso-Pérez, Rafael and Wu, Fabai, el al. (2023) Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome; Nature Microbiology; Vol. 8; No. 2; 231-245; PMCID PMC9894754; 10.1038/s41564-022-01297-4
• Utter, D. R. and Orphan, V. J. (2023) Gifts hidden in shadowy genome islands; Cell; Vol. 186; No. 1; 5-7; 10.1016/j.cell.2022.12.001
• Murali, Ranjani and Yu, Hang, el al. (2022) Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea; 10.1101/2022.11.23.517749
• McGlynn, Shawn Erin and Perkins, Guy, el al. (2022) A Cristae-Like Microcompartment in Desulfobacterota; mBio; Vol. 13; No. 6; Art. No. 01613-22; PMCID PMC9764997; 10.1128/mbio.01613-22
• Wegener, Gunter and Laso-Pérez, Rafael, el al. (2022) Anaerobic Degradation of Alkanes by Marine Archaea; Annual Review of Microbiology; Vol. 76; No. 1; 553-577; 10.1146/annurev-micro-111021-045911
• Aronson, Heidi S. and Monteverde, Danielle R., el al. (2022) Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA; Geobiology; Vol. 20; No. 5; 707-725; 10.1111/gbi.12512
• Schwartzman, Julia A. and Ebrahimi, Ali, el al. (2022) Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles; Current Biology; Vol. 32; No. 14; 3059-3069.e7; PMCID PMC9496226; 10.1016/j.cub.2022.06.011
• Laso-Pérez, Rafael and Wu, Fabai, el al. (2022) Evolutionary Diversification of Methanotrophic Ca. Methanophagales (ANME-1) and Their Expansive Virome; 10.1101/2022.07.04.498658
• Speth, Daan R. and Yu, Feiqiao B., el al. (2022) Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily; ISME Journal; Vol. 16; 1750-1764; 10.1038/s41396-022-01222-x
• Heryakusuma, Christian and Susanti, Dwi, el al. (2022) A Reduced F₄₂₀-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon; Journal of Bacteriology; Vol. 204; No. 7; Art. No. e00078-22; PMCID PMC9295563; 10.1128/jb.00078-22
• Yu, Hang and Speth, Daan R., el al. (2022) Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep; Applied and Environmental Microbiology; Vol. 88; No. 11; Art. No. e0210921; PMCID PMC9195934; 10.1128/aem.02109-21
• Case, Nicola T. and Song, Min, el al. (2022) Exploring Space via Astromycology: A Report on the CIFAR Programs Earth 4D and Fungal Kingdom Inaugural Joint Meeting; Astrobiology; Vol. 22; No. 6; 637-640; PMCID PMC9233531; 10.1089/ast.2021.0186
• Lingappa, Usha F. and Stein, Nathaniel T., el al. (2022) Early impacts of climate change on a coastal marine microbial mat ecosystem; Science Advances; Vol. 8; No. 21; Art. No. eabm7826; PMCID PMC9140962; 10.1126/sciadv.abm7826
• Himmler, Tobias and Crémière, Antoine, el al. (2022) Putative fossils of chemotrophic microbes preserved in seep carbonates from Vestnesa Ridge, off northwest Svalbard, Norway; Geology; Vol. 50; No. 2; 169-173; 10.1130/g49620.1
• Wu, Fabai and Speth, Daan R., el al. (2022) Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes; Nature Microbiology; Vol. 7; No. 2; 200-212; 10.1038/s41564-021-01039-y
• Chadwick, Grayson L. and Skennerton, Connor T., el al. (2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea; PLoS Biology; Vol. 20; No. 1; Art. No. e3001508; PMCID PMC9012536; 10.1371/journal.pbio.3001508
• Yu, Hang and Skennerton, Connor T., el al. (2022) Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea; ISME Journal; Vol. 16; No. 1; 168-177; 10.1038/s41396-021-01047-0
• Lloyd, M. K. and Trembath-Reichert, E., el al. (2021) Methoxyl stable isotopic constraints on the origins and limits of coal-bed methane; Science; Vol. 374; No. 6569; 894-897; 10.1126/science.abg0241
• Osorio‐Rodriguez, Daniela and Razo-Mejia, Manuel, el al. (2021) Sulfur isotope fractionations constrain the biological cycling of dimethylsulfoniopropionate in the upper ocean; Limnology and Oceanography; Vol. 66; No. 10; 3607-3618; 10.1002/lno.11901
• Speth, Daan R. and Yu, Feiqiao B., el al. (2021) Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily; 10.1101/2021.08.02.454472
• Jiménez Otero, Fernanda and Chadwick, Grayson L., el al. (2021) Evidence of a Streamlined Extracellular Electron Transfer Pathway from Biofilm Structure, Metabolic Stratification, and Long-Range Electron Transfer Parameters; Applied and Environmental Microbiology; Vol. 87; No. 17; Art. No. AEM.00706-21; PMCID PMC8357294; 10.1128/aem.00706-21
• Phillips, Alexandra A. and Speth, Daan R., el al. (2021) Microbial succession and dynamics in meromictic Mono Lake, California; Geobiology; Vol. 19; No. 4; 376-393; 10.1111/gbi.12437
• Marlow, Jeffrey J. and Hoer, Daniel, el al. (2021) Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites; Proceedings of the National Academy of Sciences; Vol. 118; No. 25; Art. No. e2006857118; PMCID PMC8237665; 10.1073/pnas.2006857118
• He, Xiaojia and Chadwick, Grayson L., el al. (2021) Controls on Interspecies Electron Transport and Size Limitation of Anaerobically Methane-Oxidizing Microbial Consortia; mBio; Vol. 12; No. 3; Art. No. e03620-20; 10.1128/mBio.03620-20
• He, Xiaojia and Chadwick, Grayson, el al. (2021) Spatially Resolved Electron Transport through Anode‐Respiring Geobacter sulfurreducens Biofilms: Controls and Constraints; ChemElectroChem; Vol. 8; No. 10; 1747-1758; 10.1002/celc.202100111
• Ashford, Oliver S. and Guan, Shuzhe, el al. (2021) A chemosynthetic ecotone—"chemotone"—in the sediments surrounding deep-sea methane seeps; Limnology and Oceanography; Vol. 66; No. 5; 1687-1702; 10.1002/lno.11713
• Metcalfe, Kyle S. and Murali, Ranjani, el al. (2021) Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy; ISME Journal; Vol. 15; No. 2; 377-396; PMCID PMC8027057; 10.1038/s41396-020-00757-1
• Sim, Min Sub and Skennerton, Connor T., el al. (2021) Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus; PLoS ONE; Vol. 16; No. 1; Art. No. e0245069; 10.1371/journal.pone.0245069
• Mullin, Sean W. and Wanger, Greg, el al. (2020) Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer; Frontiers in Microbiology; Vol. 11; Art. No. 536535; PMCID PMC7711152; 10.3389/fmicb.2020.536535
• Fincker, Maeva and Huber, Julie A., el al. (2020) Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions; Environmental Microbiology; Vol. 22; No. 8; 3188-3204; 10.1111/1462-2920.15061
• Houghton, J. L. and Jones, C., el al. (2020) Resolving micron-scale heterogeneity in porewater δ³⁴S_(H₂S) by combining films for in-situ sulfide capture and secondary ion mass spectrometry; Marine Chemistry; Vol. 223; Art. No. 103810; 10.1016/j.marchem.2020.103810
• Leu, Andy O. and McIlroy, Simon J., el al. (2020) Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae; mBio; Vol. 11; No. 3; Art. No. e01325-20; PMCID PMC7327174; 10.1128/mBio.01325-20
• Goffredi, Shana K. and Tilic, Ekin, el al. (2020) Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage; Science Advances; Vol. 6; No. 14; Art. No. eaay8562; 10.1126/sciadv.aay8562
• Leu, Andy O. and Cai, Chen, el al. (2020) Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae; ISME Journal; Vol. 14; No. 4; 1030-1041; PMCID PMC7082337; 10.1038/s41396-020-0590-x
• Bird, Laurence R. and Dawson, Katherine S., el al. (2019) Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane‐oxidizing archaea; Geobiology; Vol. 17; No. 6; 611-627; 10.1111/gbi.12354
• Bublitz, DeAnna C. and Chadwick, Grayson L., el al. (2019) Peptidoglycan Production by an Insect-Bacterial Mosaic; Cell; Vol. 179; No. 3; 703-712; PMCID PMC6838666; 10.1016/j.cell.2019.08.054
• Chadwick, Grayson L. and Jiménez-Otero, Fernanda, el al. (2019) NanoSIMS imaging reveals metabolic stratification within current-producing biofilms; Proceedings of the National Academy of Sciences of the United States of America; Vol. 116; No. 41; 20716-20724; PMCID PMC6789570; 10.1073/pnas.1912498116
• Speth, Daan R. and Orphan, Victoria J. (2019) ASM-Clust: classifying functionally diverse protein families using alignment score matrices; 10.1101/792739
• Cavicchioli, Ricardo and Orphan, Victoria J. (2019) Scientists' warning to humanity: microorganisms and climate change; Nature Reviews Microbiology; Vol. 17; No. 9; 569-586; PMCID PMC7136171; 10.1038/s41579-019-0222-5
• Arrojo e Drigo, Rafael and Lev-Ram, Varda, el al. (2019) Age Mosaicism across Multiple Scales in Adult Tissues; Cell Metabolism; Vol. 30; No. 2; 343-351; 10.1016/j.cmet.2019.05.010
• Sapers, Haley M. and Razzell Hollis, Joseph, el al. (2019) The Cell and the Sum of Its Parts: Patterns of Complexity in Biosignatures as Revealed by Deep UV Raman Spectroscopy; Frontiers in Microbiology; Vol. 10; Art. No. 679; PMCID PMC6527968; 10.3389/fmicb.2019.00679
• Boyd, Joel A. and Jungbluth, Sean P., el al. (2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi; ISME Journal; Vol. 13; No. 5; 1269-1279; PMCID PMC6474303; 10.1038/s41396-018-0343-2
• Amend, Jan and Feyhl-Buska, Jayme, el al. (2019) Calorimetric determination of microbial activity in low-energy environments
• Murali, Ranjani and Hemp, James, el al. (2019) FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks; 10.1101/592808
• Sim, Min Sub and Sessions, Alex L., el al. (2019) Precise determination of equilibrium sulfur isotope effects during volatilization and deprotonation of dissolved H_2S; Geochimica et Cosmochimica Acta; Vol. 248; 242-251; 10.1016/j.gca.2019.01.016
• He, Xiaojia and Chadwick, Grayson, el al. (2019) Microbial interactions in the anaerobic oxidation of methane: Model simulations constrained by process rates and activity patterns; Environmental Microbiology; Vol. 21; No. 2; 631-647; 10.1111/1462-2920.14507
• Stamenković, V. and Fischer, W. W., el al. (2019) The next frontier for planetary and human exploration; Nature Astronomy; Vol. 3; No. 2; 116-120; 10.1038/s41550-018-0676-9
• Sim, Min Sub and Ogata, Hideaki, el al. (2019) Role of APS reductase in biogeochemical sulfur isotope fractionation; Nature Communications; Vol. 10; Art. No. 44; PMCID PMC6327049; 10.1038/s41467-018-07878-4
• Yu, Hang and Susanti, Dwi, el al. (2018) Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea; Frontiers in Microbiology; Vol. 9; Art. No. 2917; PMCID PMC6286981; 10.3389/fmicb.2018.02917
• Dekas, Anne E. and Fike, David A., el al. (2018) Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading; Environmental Microbiology; Vol. 20; No. 12; 4281-4296; 10.1111/1462-2920.14342
• Chadwick, Grayson L. and Hemp, James, el al. (2018) Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications; ISME Journal; Vol. 12; No. 11; 2668-2680; PMCID PMC6194058; 10.1038/s41396-018-0210-1
• Yung, Yuk L. and Chen, Pin, el al. (2018) Methane on Mars and Habitability: Challenges and Responses; Astrobiology; Vol. 18; No. 10; 1221-1242; PMCID PMC6205098; 10.1089/ast.2018.1917
• Michel, Alice J. and Ward, Lewis M., el al. (2018) The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch; Microbiome; Vol. 6; Art. No. 167; PMCID PMC6146768; 10.1186/s40168-018-0555-8
• Speth, Daan R. and Orphan, Victoria J. (2018) 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; PeerJ; Vol. 2018; No. 6; Art. No. e5614; PMCID PMC6147122; 10.7717/peerj.5614
• Ijiri, Akira and Case, David H., el al. (2018) Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex; Science Advances; Vol. 4; No. 6; Art. No. eaao4631; PMCID PMC6007163; 10.1126/sciadv.aao4631
• McGlynn, Shawn E. and Chadwick, Grayson L., el al. (2018) Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy; Applied and Environmental Microbiology; Vol. 84; No. 11; Art. No. e00399-18; PMCID PMC5960974; 10.1128/AEM.00399-18
• Zhu, Ying and Zhao, Rui, el al. (2018) Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples; International Journal of Mass Spectrometry; Vol. 427; 4-10; PMCID PMC5863755; 10.1016/j.ijms.2017.08.016
• Pasulka, Alexis L. and Thamatrakoln, Kimberlee, el al. (2018) Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods; Environmental Microbiology; Vol. 20; No. 2; 671-692; 10.1111/1462-2920.13996
• Yung, Yuk L. and Chen, Pin, el al. (2018) Methane on Mars and Habitability: Challenges and Responses; 10.7907/Z990220K
• Fike, D. A. and Houghton, J. L., el al. (2017) Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis; Marine Chemistry; Vol. 197; 26-37; 10.1016/j.marchem.2017.10.004
• Case, David H. and Ijiri, Akira, el al. (2017) Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment; Frontiers in Microbiology; Vol. 8; Art. No. 2569; PMCID PMC5742206; 10.3389/fmicb.2017.02569
• Trembath-Reichert, Elizabeth and Morono, Yuki, el al. (2017) Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds; Proceedings of the National Academy of Sciences of the United States of America; Vol. 114; No. 44; E9206-E9215; PMCID PMC5676895; 10.1073/pnas.1707525114
• Terrado, Ramon and Pasulka, Alexis L., el al. (2017) Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis; ISME Journal; Vol. 11; No. 9; 2022-2034; PMCID PMC5563956; 10.1038/ismej.2017.68
• Skennerton, Connor T. and Chourey, Karuna, el al. (2017) Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea; mBio; Vol. 8; No. 4; Art. No. e00530-17; PMCID PMC5539420; 10.1128/mBio.00530-17
• Marlow, Jeffrey J. and Steele, Joshua A., el al. (2017) Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates; mSphere; Vol. 2; No. 4; Art. No. e00309; PMCID PMC5566838; 10.1128/mSphereDirect.00309-17
• Sim, Min Sub and Paris, Guillaume, el al. (2017) Quantification and isotopic analysis of intracellular sulfur metabolites in the dissimilatory sulfate reduction pathway; Geochimica et Cosmochimica Acta; Vol. 206; 57-72; 10.1016/j.gca.2017.02.024
• Glass, Jennifer B. and Chen, Si, el al. (2017) Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging; Geomicrobiology Journal; Vol. 35; No. 1; 81-89; 10.1080/01490451.2017.1321068
• Smith, Derek A. and Sessions, Alex L., el al. (2017) Rapid Quantification and Isotopic Analysis of Dissolved Sulfur Species; Rapid Communications in Mass Spectrometry; Vol. 31; No. 9; 791-803; 10.1002/rcm.7846
• Tavormina, Patricia L. and Kellermann, Matthias Y., el al. (2017) Starvation and recovery in the deep-sea methanotroph Methyloprofundus sedimenti; Molecular Microbiology; Vol. 103; No. 2; 242-252; 10.1111/mmi.13553
• Skennerton, Connor T. and Haroon, Mohamed F., el al. (2016) Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps; ISME Journal; Vol. 10; No. 11; 2679-2692; PMCID PMC5113845; 10.1038/ismej.2016.55
• Magyar, Paul M. and Orphan, Victoria J., el al. (2016) Measurement of rare isotopologues of nitrous oxide by high-resolution multi-collector mass spectrometry; Rapid Communications in Mass Spectrometry; Vol. 30; No. 17; 1923-1940; 10.1002/rcm.7671
• Pasulka, Alexis L. and Levin, Lisa A., el al. (2016) Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem; Environmental Microbiology; Vol. 18; No. 9; 3022-3043; 10.1111/1462-2920.13185
• Miranda, Priscilla J. and McLain, Nathan K., el al. (2016) Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA; Frontiers in Microbiology; Vol. 7; Art. No. 1163; PMCID PMC4961709; 10.3389/fmicb.2016.01163
• Hatzenpichler, Roland and Connon, Stephanie A., el al. (2016) Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia; Proceedings of the National Academy of Sciences of the United States of America; Vol. 113; No. 28; E4069-E4078; PMCID PMC4948357; 10.1073/pnas.1603757113
• Fradet, Danielle T. and Tavormina, Patricia L., el al. (2016) Members of the methanotrophic genus Methylomarinum inhabit inland mud pots; PeerJ; Vol. 4; Art. No. e2116; PMCID PMC4950536; 10.7717/peerj.2116
• Dawson, Katherine S. and Scheller, Silvan, el al. (2016) Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment; Frontiers in Microbiology; Vol. 7; Art. No. 774; PMCID PMC4881376; 10.3389/fmicb.2016.00774
• Marlow, Jeffrey J. and Skennerton, Connor T., el al. (2016) Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities; Frontiers in Microbiology; Vol. 7; Art. No. 563; PMCID PMC4850331; 10.3389/fmicb.2016.00563
• Trembath-Reichert, Elizabeth and Case, David H., el al. (2016) Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments; PeerJ; Vol. 4; Art. No. e1913; PMCID PMC4841229; 10.7717/peerj.1913
• Dekas, Anne E. and Connon, Stephanie A., el al. (2016) Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses; ISME Journal; Vol. 10; No. 3; 678-692; PMCID PMC4817681; 10.1038/ismej.2015.145
• Scheller, Silvan and Yu, Hang, el al. (2016) Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction; Science; Vol. 351; No. 6274; 703-707; 10.1126/science.aad7154
• Kopf, Sebastian H. and Sessions, Alex L., el al. (2016) Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum; Proceedings of the National Academy of Sciences of the United States of America; Vol. 113; No. 2; E110-E116; PMCID PMC4720290; 10.1073/pnas.1512057112
• Skennerton, Connor T. and Ward, Lewis M., el al. (2015) Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation; Frontiers in Microbiology; Vol. 6; Art. No. 1425; PMCID PMC4688376; 10.3389/fmicb.2015.01425
• Case, David H. and Pasulka, Alexis L., el al. (2015) Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages; mBio; Vol. 6; No. 6; Art. No. e01348-15; PMCID PMC4701829; 10.1128/mBio.01348-15
• Alivisatos, A. P. and Blaser, M. J., el al. (2015) A unified initiative to harness Earth's microbiomes; Science; Vol. 350; No. 6260; 507-508; 10.1126/science.aac8480
• Evans, Paul N. and Parks, Donovan H., el al. (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics; Science; Vol. 350; No. 6259; 434-438; 10.1126/science.aac7745
• McGlynn, Shawn E. and Chadwick, Grayson L., el al. (2015) Single cell activity reveals direct electron transfer in methanotrophic consortia; Nature; Vol. 526; No. 7574; 531-535; 10.1038/nature15512
• Mason, Olivia U. and Case, David H., el al. (2015) Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA; Microbial Ecology; Vol. 70; No. 3; 766-784; 10.1007/s00248-015-0615-6
• Bryson, Samuel Joseph and Thurber, Andrew R., el al. (2015) A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments; Environmental Microbiology; Vol. 17; No. 10; 3708-3721; 10.1111/1462-2920.12758
• Dawson, K. S. and Osburn, M. R., el al. (2015) Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps; Geobiology; Vol. 13; No. 5; 462-477; 10.1111/gbi.12140
• Kopf, Sebastian H. and McGlynn, Shawn E., el al. (2015) Heavy water and ¹⁵N labeling with NanoSIMS analysis reveals growth-rate dependent metabolic heterogeneity in chemostats; Environmental Microbiology; Vol. 17; No. 7; 2542-2556; PMCID PMC4587896; 10.1111/1462-2920.12752
• Marlow, J. and Peckmann, J., el al. (2015) Autoendoliths: a distinct type of rock-hosted microbial life; Geobiology; Vol. 13; No. 4; 303-307; 10.1111/gbi.12131
• Hatzenpichler, Roland and Orphan, Victoria J. (2015) Detection of Protein-Synthesizing Microorganisms in the Environment via Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT); ISBN 978-3-662-49129-4; Hydrocarbon and Lipid Microbiology Protocols: Single-Cell and Single-Molecule Methods; 145-157; 10.1007/8623_2015_61
• Tavormina, Patricia L. and Hatzenpichler, Roland, el al. (2015) Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs; International Journal of Systematic and Evolutionary Microbiology; Vol. 65; No. 1; 251-259; 10.1099/ijs.0.062927-0
• Houghton, J. and Fike, D., el al. (2014) Spatial variability in photosynthetic and heterotrophic activity drives localized δ^(13)C_(org) fluctuations and carbonate precipitation in hypersaline microbial mats; Geobiology; Vol. 12; No. 6; 557-574; 10.1111/gbi.12113
• Wilbanks, Elizabeth G. and Jaekel, Ulrike, el al. (2014) Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh; Environmental Microbiology; Vol. 16; No. 11; 3398-3415; PMCID PMC4262008; 10.1111/1462-2920.12388
• Sivan, Orit and Antler, Gilad, el al. (2014) Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps; Proceedings of the National Academy of Sciences of the United States of America; Vol. 111; No. 40; E4139-E4147; PMCID PMC4209987; 10.1073/pnas.1412269111
• Dekas, Anne E. and Chadwick, Grayson L., el al. (2014) Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea; Environmental Microbiology; Vol. 16; No. 10; 3012-3029; 10.1111/1462-2920.12247
• Marlow, Jeffrey J. and Steele, Joshua A., el al. (2014) Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea; Nature Communications; Vol. 5; No. 10; Art. No. 6094; 10.1038/ncomms6094
• Hatzenpichler, Roland and Scheller, Silvan, el al. (2014) In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry; Environmental Microbiology; Vol. 16; No. 8; 2568-2590; PMCID PMC4122687; 10.1111/1462-2920.12436
• Crespo-Medina, M. and Meile, C. D., el al. (2014) The rise and fall of methanotrophy following a deepwater oil-well blowout; Nature Geoscience; Vol. 7; No. 6; 423-427; 10.1038/ngeo2156
• Glass, Jennifer B. and Yu, Hang, el al. (2014) Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments; Environmental Microbiology; Vol. 16; No. 6; 1592-1633; 10.1111/1462-2920.12314
• Marlow, Jeffrey J. and LaRowe, Douglas E., el al. (2014) The Potential for Biologically Catalyzed Anaerobic Methane Oxidation on Ancient Mars; Astrobiology; Vol. 14; No. 4; 292-307; 10.1089/ast.2013.1078
• Sapir, Amir and Dillman, Adler R., el al. (2014) Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea; Frontiers in Microbiology; Vol. 5; Art. No. 43; PMCID PMC3918590; 10.3389/fmicb.2014.00043
• Green-Saxena, A. and Dekas, A. E., el al. (2014) Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane; ISME Journal; Vol. 8; No. 1; 150-163; PMCID PMC3869021; 10.1038/ismej.2013.147
• Tocheva, Elitza I. and Dekas, Anne E., el al. (2013) Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum; Journal of Bacteriology; Vol. 195; No. 17; 3940-3946; PMCID PMC3754598; 10.1128/JB.00712-13
• Bailey, J. V. and Corsetti, F. A., el al. (2013) Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis; Geobiology; Vol. 11; No. 5; 397-405; 10.1111/gbi.12046
• Ussler, William, III and Preston, Christina, el al. (2013) Autonomous Application of Quantitative PCR in the Deep Sea: In Situ Surveys of Aerobic Methanotrophs Using the Deep-Sea Environmental Sample Processor; Environmental Science and Technology; Vol. 47; No. 16; 9339-9346; 10.1021/es4023199
• Tavormina, Patricia L. and Ussler, William, III, el al. (2013) Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone; Environmental Microbiology Reports; Vol. 5; No. 3; 414-423; 10.1111/1758-2229.12025
• Yang, Song and Matsen, Janet B., el al. (2013) Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study; Frontiers in Microbiology; Vol. 4; Art. No. 70; PMCID PMC3615224; 10.3389/fmicb.2013.00070
• Druschel, Greg K. and Kafantaris, Fotios, el al. (2013) High resolution profiling of sulfur and oxygen speciation in microbial mats: Implications for coupling of hydrogen peroxide with sulfur species
• McGlynn, Shawn E. and Boyd, Eric S., el al. (2013) Classifying the metal dependence of uncharacterized nitrogenases; Frontiers in Microbiology; Vol. 3; Art. No. 419; PMCID PMC3578447; 10.3389/fmicb.2012.00419
• Trembath-Reichert, Elizabeth and Green-Saxena, Abigail, el al. (2013) Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH; ISBN 9780124078635; Microbial Metagenomics, Metatranscriptomics, and Metaproteomics; 21-44; 10.1016/B978-0-12-407863-5.00002-2
• Green-Saxena, A. and Feyzullayev, A., el al. (2012) Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan; Environmental Microbiology; Vol. 14; No. 12; 3271-3286; 10.1111/1462-2920.12015
• Magyar, Paul and Kopf, Sebastian, el al. (2012) Measurement of nitrous oxide isotopologues and isotopomers by the MAT 253 Ultra; Mineralogical Magazine; Vol. 76; No. 6; 2054-2054
• Polz, Martin and Orphan, Victoria, el al. (2012) Environmental Microbiology: evolution of your premier journal; Environmental Microbiology; Vol. 14; No. 10; 2617-2619; 10.1111/j.1462-2920.2012.02869.x
• Thurber, Andrew R. and Levin, Lisa A., el al. (2012) Archaea in metazoan diets: implications for food webs and biogeochemical cycling; ISME Journal; Vol. 6; No. 8; 1602-1612; PMCID PMC3400411; 10.1038/ismej.2012.16
• Levin, Lisa A. and Orphan, Victoria J., el al. (2012) A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems; Proceedings of the Royal Society of London. Series B, Biological Sciences; Vol. 279; No. 1738; 2580-2588; PMCID PMC3350710; 10.1098/rspb.2012.0205
• Harrison, Benjamin K. and Orphan, Victoria J. (2012) Method for Assessing Mineral Composition-Dependent Patterns in Microbial Diversity Using Magnetic and Density Separation; Geomicrobiology Journal; Vol. 29; No. 5; 435-449; 10.1080/01490451.2011.581327
• Glass, Jennifer B. and Orphan, Victoria J. (2012) Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide; Frontiers in Microbiology; Vol. 3; Art. No. 61; PMCID PMC3282944; 10.3389/fmicb.2012.00061
• Newman, Dianne K. and Orphan, Victoria J., el al. (2012) Molecular biology's contributions to geobiology; ISBN 9781118280812; Fundamentals of Geobiology; 228-249
• Bailey, Jake V. and Salman, Verena, el al. (2011) Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria; ISME Journal; Vol. 5; No. 12; 1926-1935; PMCID PMC3223306; 10.1038/ismej.2011.66
• House, Christopher H. and Beal, Emily J., el al. (2011) The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy; Life; Vol. 1; No. 1; 19-33; PMCID PMC4187123; 10.3390/life1010019
• Orphan, Victoria J. and Hoehler, Tori M. (2011) Microbiology: Hydrogen for dinner; Nature; Vol. 476; No. 7359; 154-155; 10.1038/476154a
• Shapiro, Orr H. and Hatzenpichler, Roland, el al. (2011) Multicellular photo-magnetotactic bacteria; Environmental Microbiology Reports; Vol. 3; No. 2; 233-238; 10.1111/j.1758-2229.2010.00215.x
• Orphan, Victoria (2011) Fish-Sims: Characterizing the Metabolic Potential and Interspecies Interactions between Uncultured Environmental Microorganisms; Biophysical Journal; Vol. 100; No. 3, S1; 37a; 10.1016/j.bpj.2010.12.406
• Tavormina, Patricia L. and Orphan, Victoria J., el al. (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs; Environmental Microbiology Reports; Vol. 3; No. 1; 91-100; 10.1111/j.1758-2229.2010.00192.x
• Orphan, Victoria J. (2011) Getting cozy: hidden microbial interactions in nature; Environmental Microbiology Reports; Vol. 3; No. 1; 16-18; 10.1111/j.1758-2229.2010.00236.x
• Dekas, Anne E. and Orphan, Victoria J. (2011) Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS); ISBN 9780123812940; Research on Nitrification and Related Processes; 281-305; 10.1016/B978-0-12-381294-0.00012-2
• Tavormina, Patricia L. and Ussler, William, III, el al. (2010) Distributions of putative aerobic methanotrophs in diverse pelagic marine environments; ISME Journal; Vol. 4; No. 5; 700-710; 10.1038/ismej.2009.155
• Goffredi, Shana K. and Orphan, Victoria J. (2010) Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea; Environmental Microbiology; Vol. 12; No. 2; 344-363; 10.1111/j.1462-2920.2009.02072.x
• Bailey, Jake V. and Raub, Timothy D., el al. (2010) Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia; Palaeogeography, Palaeoclimatology, Palaeoecology; Vol. 285; No. 1-2; 131-142; 10.1016/j.palaeo.2009.11.002
• Bailey, Jake V. and Orphan, Victoria J., el al. (2009) Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record; Astrobiology; Vol. 9; No. 9; 843-859; 10.1089/ast.2008.0314
• Dekas, Anne E. and Poretsky, Rachel S., el al. (2009) Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia; Science; Vol. 326; No. 5951; 422-426; 10.1126/science.1178223
• Fike, David A. and Finke, Niko, el al. (2009) The effect of sulfate concentration on (sub)millimeter-scale sulfide δ^(34)S in hypersaline cyanobacterial mats over the diurnal cycle; Geochimica et Cosmochimica Acta; Vol. 73; No. 20; 6187-6204; 10.1016/j.gca.2009.07.006
• House, Christopher H. and Orphan, Victoria J., el al. (2009) Extensive carbon isotopic heterogeneity among methane seep microbiota; Environmental Microbiology; Vol. 11; No. 9; 2207-2215; 10.1111/j.1462-2920.2009.01934.x
• Beal, Emily J. and House, Christopher H., el al. (2009) Manganese- and iron-dependent marine methane oxidation; Science; Vol. 325; No. 5937; 184-187; 10.1126/science.1169984
• Orphan, Victoria J. and Turk, Kendra A., el al. (2009) Patterns of ^(15)N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS; Environmental Microbiology; Vol. 11; No. 7; 1777-1791; 10.1111/j.1462-2920.2009.01903.x
• Orphan, V. J. and House, C. H. (2009) Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes; Geobiology; Vol. 7; No. 3; 360-372; 10.1111/j.1472-4669.2009.00201.x
• Fike, David A. and Orphan, Victoria J. (2009) High resolution SIMS-based sulfide δ^(34)S: A new tool for characterizing microbial activity in a variety of depositional environments; Geochimica et Cosmochimica Acta; Vol. 73; No. 13, S; A375; 10.1016/j.gca.2009.05.005
• Orphan, Victoria J. (2009) Methods for unveiling cryptic microbial partnerships in nature; Current Opinion in Microbiology; Vol. 12; No. 3; 231-237; 10.1016/j.mib.2009.04.003
• Harrison, Benjamin K. and Zhang, Husen, el al. (2009) Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California); Applied and Environmental Microbiology; Vol. 75; No. 6; 1487-1499; PMCID PMC2655439; 10.1128/AEM.01812-08
• Orphan, V. J. and Jahnke, L. L., el al. (2008) Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California; Geobiology; Vol. 6; No. 4; 376-393; 10.1111/j.1472-4669.2008.00166.x
• Jahnke, L. L. and Orphan, V. J., el al. (2008) Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment; Geobiology; Vol. 6; No. 4; 394-410; 10.1111/j.1472-4669.2008.00165.x
• Fike, David Andrew and Gammon, Crystal Lynn, el al. (2008) Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach; ISME Journal; Vol. 2; No. 7; 749-759; 10.1038/ismej.2008.39
• Fike, David A. and Gammon, Crystal L., el al. (2008) Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat; Geochimica et Cosmochimica Acta; Vol. 72; No. 12; A268; 10.1016/j.gca.2008.05.009
• Tavormina, Patricia L. and Ussler, William, III, el al. (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin; Applied and Environmental Microbiology; Vol. 74; No. 13; 3985-3995; PMCID PMC2446507; 10.1128/AEM.00069-08
• Pernthaler, Annelie and Dekas, Anne E., el al. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 19; 7052-7057; PMCID PMC2383945; 10.1073/pnas.0711303105
• Goffredi, Shana K. and Wilpiszeski, Regina, el al. (2008) Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California; ISME Journal; Vol. 2; No. 2; 204-220; 10.1038/ismej.2007.103
• Moran, James J. and Beal, Emily J., el al. (2008) Methyl sulfides as intermediates in the anaerobic oxidation of methane; Environmental Microbiology; Vol. 10; No. 1; 162-173; 10.1111/j.1462-2920.2007.01441.x
• Orphan, Victoria J. and House, Christopher H., el al. (2008) Archaea, Methane, and Oases of the Deep; Nova Acta Leopoldina; Vol. 96; No. 356; 19-23
• Fike, David and Ussler, William, el al. (2007) Micron-scale resolution of sulfur cycling in a microbial mat; Geochimica et Cosmochimica Acta; Vol. 71; No. 15; A278; 10.1016/j.gca.2007.06.015
• Orphan, Victoria J. and Pernthaler, Annelie, el al. (2007) The ties that bind: Dynamics of syntrophic associations in marine methane seeps; Geochimica et Cosmochimica Acta; Vol. 71; No. 15, S; A743; 10.1016/j.gca.2007.06.023
• Naehr, Thomas H. and Eichhubl, Peter, el al. (2007) Authigenic carbonate formation at hydrocarbon seeps in continental margin sediments: A comparative study; Deep-Sea Research. Part II, Topical Studies in Oceanography; Vol. 54; No. 11-13; 1268-1291; 10.1016/j.dsr2.2007.04.010
• Treude, Tina and Orphan, Victoria J., el al. (2007) Consumption of Methane and CO_2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea; Applied and Environmental Microbiology; Vol. 73; No. 7; 2271-2283; PMCID PMC1855681; 10.1128/AEM.02685-06
• House, Christopher H. and Biddle, Jennifer F., el al. (2006) Linking molecular taxonomy with environmental geochemsitry in environments relevant to astrobiology: The anaerobic oxidation of methane in cold seeps & deeply buried marine sediments; Origins of life and evolution of the biosphere; Vol. 36; No. 3; 314-315
• Goffredi, Shana K. and Orphan, Victoria J., el al. (2005) Evolutionary innovation: a bone-eating marine symbiosis; Environmental Microbiology; Vol. 7; No. 9; 1369-1378; 10.1111/j.1462-2920.2005.00824.x
• Orphan, V. J. and Ussler, W., III, el al. (2004) Geological, geochemical, and microbiological heterogeneity of the seafloor around methane vents in the Eel River Basin, offshore California; Chemical Geology; Vol. 205; No. 3-4; 265-289; 10.1016/j.chemgeo.2003.12.035
• Goffredi, Shana K. and Warén, Anders, el al. (2004) Novel Forms of Structural Integration between Microbes and a Hydrothermal Vent Gastropod from the Indian Ocean; Applied and Environmental Microbiology; Vol. 70; No. 5; 3082-3090; PMCID PMC404406; 10.1128/AEM.70.5.3082-3090.2004
• Girguis, Peter R. and Orphan, Victoria J., el al. (2003) Growth and Methane Oxidation Rates of Anaerobic Methanotrophic Archaea in a Continuous-Flow Bioreactor; Applied and Environmental Microbiology; Vol. 69; No. 9; 5472-5482; PMCID PMC194967; 10.1128/AEM.69.9.5472-5482.2003
• Orphan, V. J. and Goffredi, S. K., el al. (2003) Geochemical Influence on Diversity and Microbial Processes in High Temperature Oil Reservoirs; Geomicrobiology Journal; Vol. 20; No. 4; 295-311; 10.1080/01490450303898
• Orphan, V. J. and House, C. H., el al. (2002) Direct phylogenetic and isotopic evidence for multiple groups of archaea involved in the anaerobic oxidation of methane; Geochimica et Cosmochimica Acta; Vol. 66; No. S1; A571; 10.1016/S0016-7037(02)01016-5
• Orphan, Victoria J. and House, Christopher H., el al. (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. 11; 7663-7668; PMCID PMC124316; 10.1073/pnas.072210299
• Orphan, Victoria J. and House, Christopher H., el al. (2001) Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis; Science; Vol. 293; No. 5529; 484-487; 10.1126/science.1061338
• Orphan, V. J. and Hinrichs, K.-U., el al. (2001) Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments; Applied and Environmental Microbiology; Vol. 67; No. 4; 1922-1934; PMCID PMC92814; 10.1128/AEM.67.4.1922-1934.2001
• Hinrichs, Kai-Uwe and Summons, Roger E., el al. (2000) Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments; Organic Geochemistry; Vol. 31; No. 12; 1685-1701; 10.1016/S0146-6380(00)00106-6
• Orphan, V. J. and Taylor, L. T., el al. (2000) Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs; Applied and Environmental Microbiology; Vol. 66; No. 2; 700-711; PMCID PMC91884; 10.1128/AEM.66.2.700-711.2000