@article {gomaa2022crispr,
	title = {CRISPR/Cas9-induced disruption of Bodo saltans paraflagellar rod-2 gene reveals its importance for cell survival},
	journal = {Environmental Microbiology},
	year = {2022},
	publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
	author = {Gomaa, Fatma and Li, Zhu-Hong and Beaudoin, David J and Alzan, Heba and Girguis, Peter R. and Docampo, Roberto and Edgcomb, Virginia P}
}
@article {baker2022evidence,
	title = {Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria},
	journal = {mBio},
	volume = {13},
	year = {2022},
	pages = {e02904{\textendash}21},
	publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
	author = {Baker, Isabel R and Conley, Bridget E and Gralnick, Jeffrey A and Girguis, Peter R.}
}
@article {de2022novel,
	title = {Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome},
	journal = {Molecular biology and evolution},
	volume = {39},
	year = {2022},
	pages = {msab347},
	publisher = {Oxford University Press},
	author = {de Oliveira, Andr{\'e} Luiz and Mitchell, Jessica and Peter Girguis and Bright, Monika}
}
@article {marlow2021carbonate,
	title = {Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	year = {2021},
	publisher = {National Academy of Sciences},
	author = {Marlow, Jeffrey J and Hoer, Daniel and Jungbluth, Sean P and Reynard, Linda M and Gartman, Amy and Chavez, Marko S and El-Naggar, Mohamed Y and Tuross, Noreen and Orphan, Victoria J and Girguis, Peter R.}
}
@article {leonard2021cooccurring,
	title = {Cooccurring Activities of Two Autotrophic Pathways in Symbionts of the Hydrothermal Vent Tubeworm Riftia pachyptila},
	journal = {Applied and Environmental Microbiology},
	volume = {87},
	year = {2021},
	pages = {e00794{\textendash}21},
	publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
	author = {Leonard, Juliana M and Mitchell, Jessica and Beinart, Roxanne A and Delaney, Jennifer A and Sanders, Jon G and Ellis, Greg and Goddard, Ethan A and Girguis, Peter R. and Scott, Kathleen M}
}
@article {smith2021grayness,
	title = {The grayness of the origin of life},
	journal = {Life},
	volume = {11},
	year = {2021},
	pages = {498},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Smith, Hillary H and Hyde, Andrew S and Simkus, Danielle N and Libby, Eric and Maurer, Sarah E and Graham, Heather V and Kempes, Christopher P and Sherwood Lollar, Barbara and Chou, Luoth and Ellington, Andrew D and others}
}
@article {picard2021interactions,
	title = {Interactions Between Iron Sulfide Minerals and Organic Carbon: Implications for Biosignature Preservation and Detection},
	journal = {Astrobiology},
	volume = {21},
	year = {2021},
	pages = {587{\textendash}604},
	publisher = {Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~{\textellipsis}},
	author = {Picard, Aude and Gartman, Amy and Girguis, Peter R.}
}
@article {trembath2021multiple,
	title = {Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids},
	journal = {Science Advances},
	volume = {7},
	year = {2021},
	pages = {eabg0153},
	publisher = {American Association for the Advancement of Science},
	author = {Trembath-Reichert, Elizabeth and Shah Walter, Sunita R and Ortiz, Marc Alec Font{\'a}nez and Carter, Patrick D and Girguis, Peter R. and Huber, Julie A}
}
@article {helm2021protect,
	title = {Protect high seas biodiversity},
	journal = {Science},
	volume = {372},
	year = {2021},
	pages = {1048{\textendash}1049},
	publisher = {American Association for the Advancement of Science},
	author = {Helm, Rebecca R and Clark, Nichola and Harden-Davies, Harriet and Amon, Diva and Peter Girguis and Bordehore, Cesar and Earle, Sylvia and Gibbons, Mark J and Golbuu, Yimnang and Haddock, Steven H. D. and others}
}
@article {marlow2021spatially,
	title = {Spatially resolved correlative microscopy and microbial identification reveal dynamic depth-and mineral-dependent anabolic activity in salt marsh sediment},
	journal = {Environmental microbiology},
	volume = {23},
	year = {2021},
	pages = {4756{\textendash}4777},
	publisher = {John Wiley \& Sons, Inc. Hoboken, USA},
	author = {Marlow, Jeffrey and Spietz, Rachel and Kim, Keun-Young and Ellisman, Mark and Peter Girguis and Hatzenpichler, Roland}
}
@article {leprich2021sulfur,
	title = {Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps},
	journal = {The ISME journal},
	volume = {15},
	year = {2021},
	pages = {2043{\textendash}2056},
	publisher = {Nature Publishing Group},
	author = {Leprich, Dalton J and Flood, Beverly E and Schroedl, Peter R and Ricci, Elizabeth and Marlow, Jeffery J and Girguis, Peter R. and Bailey, Jake V}
}
@article {chou2021towards,
	title = {Towards a more universal life detection strategy},
	journal = {Bulletin of the American Astronomical Society},
	volume = {53},
	year = {2021},
	publisher = {American Astronomical Society},
	author = {Chou, Luoth and Grefenstette, Natalie and Johnson, Sarah S and Graham, Heather and Mahaffy, Paul and Kempes, Christopher and Elsila, Jamie E and Libby, Eric and Ellington, Andrew and Anslyn, Eric and others}
}
@article {girguis2020fundamentals,
	title = {Fundamentals of benthic microbial fuel cells: theory, development and application},
	year = {2020},
	publisher = {Springer Verlag Press},
	author = {Girguis, Peter R. and Nielsen, Mark and Reimers, Clare}
}
@conference {graham2020agnostic,
	title = {Agnostic approaches to extant life detection on Ocean Worlds},
	booktitle = {Ocean Sciences Meeting 2020},
	year = {2020},
	publisher = {AGU},
	organization = {AGU},
	author = {Graham, Heather and Johnson, Sarah and Anslyn, Eric and Conrad, Pamela and Cronin, Leroy and Ellington, Andrew and Cook, Jamie Elsila and Girguis, Peter R. and House, Christopher H and Kempes, Chris and others}
}
@article {meyer2020author,
	title = {Author Correction: A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge},
	journal = {Scientific Reports},
	volume = {10},
	year = {2020},
	pages = {1{\textendash}1},
	publisher = {Nature Publishing Group},
	author = {Meyer, Julie L and Jaekel, Ulrike and Tully, Benjamin J and Glazer, Brian T and Wheat, C Geoffrey and Lin, Huei-Ting and Hsieh, Chih-Chiang and Cowen, James P and Hulme, Samuel M and Girguis, Peter R. and others}
}
@article {meyer2020distinct,
	title = {A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge (vol 6, 22541, 2016)},
	journal = {SCIENTIFIC REPORTS},
	volume = {10},
	year = {2020},
	publisher = {NATURE PUBLISHING GROUP MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
	author = {Meyer, Julie L and Jaekel, Ulrike and Tully, Benjamin J and Glazer, Brian T and Wheat, C Geoffrey and Lin, Huei-Ting and Hsieh, Chih-Chiang and Cowen, James P and Hulme, Samuel M and Girguis, Peter R. and others}
}
@conference {michel2020seafloor,
	title = {From the Seafloor to the Surface: In situ Chemical Analysis of Rising Bubbles along the Cascadia Margin},
	booktitle = {Ocean Sciences Meeting 2020},
	year = {2020},
	publisher = {AGU},
	organization = {AGU},
	author = {Michel, Anna and Johnson, Andrew Stafford and Fauria, Kristen and Preston, Victoria and Nicholson, David P and Hoer, Daniel and Girguis, Peter R. and Wankel, Scott D}
}
@article {girguis2020fundamentals,
	title = {Fundamentals of benthic microbial fuel cells: theory, development and application},
	year = {2020},
	publisher = {Springer Verlag Press},
	author = {Girguis, Peter R. and Nielsen, Mark and Reimers, Clare}
}
@article {faktorova2020genetic,
	title = {Genetic tool development in marine protists: emerging model organisms for experimental cell biology},
	journal = {Nature methods},
	volume = {17},
	year = {2020},
	pages = {481{\textendash}494},
	publisher = {Nature Publishing Group},
	author = {Faktorov{\'a}, Drahom{\'{\i}ra and Nisbet, R Ellen R and Fern{\'a}ndez Robledo, Jos{\'e} A and Casacuberta, Elena and Sudek, Lisa and Allen, Andrew E and Ares, Manuel and Arest{\'e}, Cristina and Balestreri, Cecilia and Barbrook, Adrian C and others}
}
@article {beam2020mud,
	title = {Mud, microbes, and macrofauna: seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat},
	journal = {Frontiers in Marine Science},
	year = {2020},
	pages = {921},
	publisher = {Frontiers},
	author = {Beam, Jacob P and George, Sarabeth and Record, Nicholas R and Countway, Peter D and Johnston, David T and Girguis, Peter R. and David Emerson}
}
@article {breusing2020physiological,
	title = {Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails},
	journal = {The ISME journal},
	volume = {14},
	year = {2020},
	pages = {2568{\textendash}2579},
	publisher = {Nature Publishing Group},
	author = {Breusing, Corinna and Mitchell, Jessica and Delaney, Jennifer and Sylva, Sean P and Seewald, Jeffrey S and Girguis, Peter R. and Beinart, Roxanne A}
}
@article {murray2020roadmap,
	title = {Roadmap for naming uncultivated Archaea and Bacteria},
	journal = {Nature microbiology},
	volume = {5},
	year = {2020},
	pages = {987{\textendash}994},
	publisher = {Nature Publishing Group},
	author = {Murray, Alison E and Freudenstein, John and Gribaldo, Simonetta and Hatzenpichler, Roland and Hugenholtz, Philip and K{\"a}mpfer, Peter and Konstantinidis, Konstantinos T and Lane, Christopher E and Papke, R Thane and Parks, Donovan H and others}
}
@conference {picard2020role,
	title = {Role of Pressure in the Formation of Organo-Mineral Interactions: Implications for Organic Preservation in the Anoxic Subsurface},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2020},
	year = {2020},
	pages = {B098{\textendash}01},
	author = {Picard, Aude and Girguis, Peter R.}
}
@article {waterston2020undersea,
	title = {Undersea Supercharger{\texttrademark} Network?: A Commentary Promoting In-Situ Methane to Fuel Expansion of Seafloor Robotics},
	journal = {Marine Technology Society Journal},
	volume = {54},
	year = {2020},
	pages = {5{\textendash}7},
	publisher = {Marine Technology Society},
	author = {Waterston, John and Florea, Rachel and Peter Girguis}
}
@article {totoiu2020vortex,
	title = {Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens},
	journal = {PloS one},
	volume = {15},
	year = {2020},
	pages = {e0225807},
	publisher = {Public Library of Science San Francisco, CA USA},
	author = {Totoiu, Christian A and Phillips, Jessica M and Reese, Aspen T and Majumdar, Sudipta and Girguis, Peter R. and Raston, Colin L and Gregory A. Weiss}
}
@article {picard2019authigenic,
	title = {Authigenic metastable iron sulfide minerals preserve microbial organic carbon in anoxic environments},
	journal = {Chemical Geology},
	volume = {530},
	year = {2019},
	pages = {119343},
	publisher = {Elsevier},
	author = {Picard, Aude and Gartman, Amy and Cosmidis, Julie and Obst, Martin and Vidoudez, Charles and Clarke, David R and Girguis, Peter R.}
}
@article {beinart2019bacterial,
	title = {The bacterial symbionts of closely related hydrothermal vent snails with distinct geochemical habitats show broad similarity in chemoautotrophic gene content},
	journal = {Frontiers in microbiology},
	year = {2019},
	pages = {1818},
	publisher = {Frontiers},
	author = {Beinart, Roxanne A and Luo, Chengwei and Konstantinidis, Konstantinos T and Stewart, Frank J and Girguis, Peter R.}
}
@conference {german2019exploring,
	title = {Exploring ocean worlds: a systems-level approach for the search for life beyond Earth},
	booktitle = {2019 Astrobiology Science Conference},
	year = {2019},
	publisher = {AGU},
	organization = {AGU},
	author = {German, Christopher R and Blackman, Donna K and Fisher, Andrew T and Girguis, Peter R. and Hand, Kevin P and Hoehler, Tori M and Huber, Julie A and Marshall, John C and Seewald, Jeffrey and Shock, Everett and others}
}
@article {mitchell2019hydrogen,
	title = {Hydrogen does not appear to be a major electron donor for symbiosis with the deep-sea hydrothermal vent tubeworm Riftia pachyptila},
	journal = {Applied and environmental microbiology},
	volume = {86},
	year = {2019},
	pages = {e01522{\textendash}19},
	publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
	author = {Mitchell, Jessica H and Leonard, Juliana M and Delaney, Jennifer and Girguis, Peter R. and Scott, Kathleen M}
}
@article {le2019hydrothermal,
	title = {Hydrothermal energy transfer and organic carbon production at the deep seafloor},
	journal = {Frontiers in Marine Science},
	volume = {5},
	year = {2019},
	pages = {531},
	publisher = {Frontiers},
	author = {Lebris, Nadine and Y{\"u}cel, Mustafa and Das, Anindita and Sievert, Stefan M and LokaBharathi, PonnaPakkam and Girguis, Peter R.}
}
@conference {wankel2019situ,
	title = {In situ Chemical Analysis of Rising Bubbles Along the Cascadia Margin},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2019},
	year = {2019},
	pages = {OS23C{\textendash}1798},
	author = {Wankel, Scott D and Johnson, Andrew S and Hoer, Daniel and Girguis, Peter R. and Michel, AP}
}
@conference {johnson2019laboratory,
	title = {The Laboratory for Agnostic Biosignatures Project},
	booktitle = {2019 Astrobiology Science Conference},
	year = {2019},
	publisher = {AGU},
	organization = {AGU},
	author = {Johnson, Sarah and Graham, Heather and Anslyn, Eric and Conrad, Pamela and Cronin, Leroy and Ellington, Andrew and Elsila, Jamie and Girguis, Peter R. and House, Christopher H and Kempes, Chris and others}
}
@conference {marlow2019methane,
	title = {Methane Hydrates as an Astrobiological Target: Lessons from Seafloor Methane Seeps},
	booktitle = {2019 Astrobiology Science Conference},
	year = {2019},
	publisher = {AGU},
	organization = {AGU},
	author = {Marlow, Jeffrey J and Hoer, Daniel and Reynard, Linda and Girguis, Peter R.}
}
@article {rowe2019methane,
	title = {Methane-linked mechanisms of electron uptake from cathodes by Methanosarcina barkeri},
	journal = {MBio},
	volume = {10},
	year = {2019},
	pages = {e02448{\textendash}18},
	publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
	author = {Rowe, Annette R and Xu, Shuai and Gardel, Emily and Bose, Arpita and Peter Girguis and Amend, Jan P and El-Naggar, Mohamed Y}
}
@conference {girguis2019peak,
	title = {A peak behind the curtain: What Earth{\textquoteright}s thin biosphere reveals about the deep subsurface.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2019},
	year = {2019},
	pages = {B51D{\textendash}08},
	author = {Girguis, Peter R.}
}
@article {bowles2019remarkable,
	title = {Remarkable capacity for anaerobic oxidation of methane at high methane concentration},
	journal = {Geophysical Research Letters},
	volume = {46},
	year = {2019},
	pages = {12192{\textendash}12201},
	author = {Bowles, MW and Samarkin, V. A. and Hunter, K. S. and Finke, N and Teske, AP and Girguis, P. R. and Joye, S. B.}
}
@article {park2019synergistic,
	title = {Synergistic substrate cofeeding stimulates reductive metabolism},
	journal = {Nature Metabolism},
	volume = {1},
	year = {2019},
	pages = {643{\textendash}651},
	publisher = {Nature Publishing Group},
	author = {Park, Junyoung O and Liu, Nian and Holinski, Kara M and Emerson, David F and Qiao, Kangjian and Woolston, Benjamin M and Xu, Jingyang and Lazar, Zbigniew and Islam, M Ahsanul and Vidoudez, Charles and others}
}
@conference {girguis2019water,
	title = {Water, Water Everywhere: Bioelectrochemical Processes at Some of Earth{\textquoteright}s most Extreme Aquatic Environments, and Implications for Astrobiological Research},
	booktitle = {2019 Astrobiology Science Conference},
	year = {2019},
	publisher = {AGU},
	organization = {AGU},
	author = {Girguis, Peter R. and Reimers, Clare E and Gulay, Arda and Baker, Isabel}
}
@conference {girguis2018200,
	title = {200,000 KB Under The Sea: Combining High-speed Underwater Communications and Biogeochemical Sensors/Samplers for Deep-Sea Autonomous Exploration},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2018},
	year = {2018},
	pages = {P42B{\textendash}01},
	author = {Girguis, Peter R. and Hoer, Daniel and Farr, Norman and Wankel, Scott D and Michel, Anna}
}
@article {raineault2018advancing,
	title = {Advancing ocean science and exploration through telepresence},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	volume = {150},
	year = {2018},
	pages = {1{\textendash}3},
	author = {Raineault, Nicole A and Bell, Katherine LC and Peter Girguis}
}
@conference {girguis2018development,
	title = {Development and deployment of the autonomous biogeochemical in-situ sensing system (ABISS)},
	booktitle = {2018 Ocean Sciences Meeting},
	year = {2018},
	publisher = {AGU},
	organization = {AGU},
	author = {Girguis, Peter R. and Michel, Anna and Wankel, Scott D and Farr, Norman and Hoer, Daniel and Pontbriand, Clifford}
}
@article {soule2018exploration,
	title = {Exploration of the northern guaymas basin},
	journal = {Oceanography},
	volume = {31},
	year = {2018},
	pages = {39{\textendash}41},
	publisher = {OCEANOGRAPHY SOC PO BOX 1931, ROCKVILLE, MD USA},
	author = {Soule, S Adam and Seewald, Jeff and Wankel, Scott and Michel, Anna and Beinart, Roxanne and Briones, Elva Escobar and Dominguez, Esmerelda Morales and Peter Girguis and Coleman, Dwight and Raineault, Nicole A and others}
}
@conference {wankel2018first,
	title = {First-time combination of underwater sensors for carbon biogeochemistry in deep-sea environments},
	booktitle = {2018 Ocean Sciences Meeting},
	year = {2018},
	publisher = {AGU},
	organization = {AGU},
	author = {Wankel, Scott D and Michel, Anna and Hoer, Daniel and Girguis, Peter R.}
}
@article {marlow2018harnessing,
	title = {Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas},
	journal = {Biotechnology and bioengineering},
	volume = {115},
	year = {2018},
	pages = {1450{\textendash}1464},
	author = {Marlow, Jeffrey J and Kumar, Amit and Enalls, Brandon C and Reynard, Linda M and Tuross, Noreen and Stephanopoulos, Gregory and Peter Girguis}
}
@article {nadine2018hydrothermal,
	title = {Hydrothermal energy transfer and organic carbon production at the deep seafloor},
	journal = {Front Microbiol},
	volume = {5},
	year = {2018},
	pages = {392{\textendash}531},
	author = {Nadine, LB and Yucel, M. and Das, A and Sievert, S. M. and Girguis, P. R.}
}
@article {michel2018situ,
	title = {In situ carbon isotopic exploration of an active submarine volcano},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	volume = {150},
	year = {2018},
	pages = {57{\textendash}66},
	publisher = {Pergamon},
	author = {Michel, Anna PM and Wankel, Scott D and Kapit, Jason and Sandwith, Zoe and Girguis, Peter R.}
}
@article {marlow2018linking,
	title = {Linking Metabolic Activity, Microbial Identity, and Microscale Spatial Arrangements in Chemosynthetic Seafloor Habitats},
	journal = {Ocean Worlds},
	volume = {2085},
	year = {2018},
	pages = {6005},
	author = {Marlow, J and Hatzenpichler, R and Girguis, P.}
}
@article {shah2018microbial,
	title = {Microbial decomposition of marine dissolved organic matter in cool oceanic crust},
	journal = {Nature Geoscience},
	volume = {11},
	year = {2018},
	pages = {334{\textendash}339},
	publisher = {Nature Publishing Group},
	author = {Shah Walter, Sunita R and Jaekel, Ulrike and Osterholz, Helena and Fisher, Andrew T and Huber, Julie A and Pearson, Ann and Dittmar, Thorsten and Girguis, Peter R.}
}
@conference {shah2018microbial,
	title = {Microbial Preference for Dissolved Organic Matter that is 14 C-enriched, 13 C-enriched and Molecularly Distinct in the North Pond Subsurface},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2018},
	year = {2018},
	pages = {B23F{\textendash}2572},
	author = {Shah Walter, SR and Osterholz, Helena and Dittmar, Thorsten and Girguis, Peter R.}
}
@conference {baillard2018new,
	title = {New Insights into Oceanic Spreading Centers from Seafloor Observatories Posters},
	booktitle = {AGU Fall Meeting 2018},
	year = {2018},
	publisher = {AGU},
	organization = {AGU},
	author = {Baillard, Christian and Barreyre, Thibaut and Matabos, Marjolaine and Butterfield, David A and Reysenbach, Anna-Louise and Girguis, Peter R.}
}
@article {reese2018nitrogen,
	title = {Nitrogen cycling of active bacteria within oligotrophic sediment of the Mid-Atlantic Ridge flank},
	journal = {Geomicrobiology Journal},
	volume = {35},
	year = {2018},
	pages = {468{\textendash}483},
	publisher = {Taylor \& Francis},
	author = {Reese, Brandi Kiel and Zinke, Laura A and Sobol, Morgan S and LaRowe, Doug E and Orcutt, Beth N and Zhang, Xinxu and Jaekel, Ulrike and Wang, Fengping and Dittmar, Thorsten and Defforey, Delphine and others}
}
@article {girguis2018peering,
	title = {Peering into the abyss: studying our own ocean to advance astrobiology},
	journal = {Oceanography},
	volume = {31},
	year = {2018},
	pages = {32{\textendash}33},
	publisher = {OCEANOGRAPHY SOC PO BOX 1931, ROCKVILLE, MD USA},
	author = {Girguis, Peter R. and Fundis, Allison}
}
@conference {marlow2018rock,
	title = {Rock-hosted microbial communities possess substantial methane oxidizing potential at geologically diverse methane seep sites},
	booktitle = {2018 Ocean Sciences Meeting},
	year = {2018},
	publisher = {AGU},
	organization = {AGU},
	author = {Marlow, Jeffrey J and Gartman, Amy and Jungbluth, Sean and Hoer, Daniel and Reynard, Linda and Tuross, Noreen and Orphan, Victoria J and Girguis, Peter R.}
}
@conference {girguis2018seas,
	title = {The seas we{\textquoteright}ve hardly seen: Advancing our understanding of deep sea processes through advanced underwater and shipboard communications},
	booktitle = {2018 Ocean Sciences Meeting},
	year = {2018},
	publisher = {AGU},
	organization = {AGU},
	author = {Girguis, Peter R. and Hoer, Daniel and Beinart, Roxanne and Pontbriand, Clifford and Farr, Norman and Panzarino, Jessica}
}
@article {weitz2018sequencing,
	title = {Sequencing of bacteria or other species},
	year = {2018},
	author = {Weitz, David A and Zhang, Huidan and CUI, Nai Wen and Cai, Yamei and Peter Girguis and Stewart, Frank and Sarode, Neha and Kraft, Beate}
}
@article {girguis2018somewhere,
	title = {Somewhere, Beyond the Sea: Advancing Geochemical Sensor Technologies for Biological and Abiotic Analyses on Ocean Worlds},
	journal = {Ocean Worlds},
	volume = {2085},
	year = {2018},
	pages = {6027},
	author = {Girguis, Peter R. and Hoer, Daniel and Michel, Anna and Wankel, Scott D and Baker, Izzy and Farr, Norm}
}
@article {picard2018sulfate,
	title = {Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {220},
	year = {2018},
	pages = {367{\textendash}384},
	publisher = {Pergamon},
	author = {Picard, Aude and Gartman, Amy and Clarke, David R and Girguis, Peter R.}
}
@article {bourbonnais2017citation,
	title = {Citation: Padilla, CC, Bristow LA, Sarode, N., Garcia-Robledo, E., Benson, CR},
	journal = {UNRECOGNIZED DIVERSITY OF MICROBES LINKING METHANOTROPHY TO NITROGEN LOSS IN MARINE OXYGEN MINIMUM ZONES},
	year = {2017},
	pages = {53},
	publisher = {Georgia Institute of Technology},
	author = {Bourbonnais, A and Altabet, M.A. and Girguis, P. R. and Thamdrup, B and Stewart, F. J.}
}
@article {olins2017co,
	title = {Co-registered geochemistry and metatranscriptomics reveal unexpected distributions of microbial activity within a hydrothermal vent field},
	journal = {Frontiers in microbiology},
	volume = {8},
	year = {2017},
	pages = {1042},
	publisher = {Frontiers},
	author = {Olins, Heather C and Rogers, Daniel R and Preston, Christina and Ussler III, William and Pargett, Douglas and Jensen, Scott and Roman, Brent and Birch, James M and Scholin, Christopher A and Haroon, M Fauzi and others}
}
@article {meier2017environmental,
	title = {Environmental parameters of deep-sea hydrothermal vents from the Manus Basin},
	year = {2017},
	author = {Meier, Dimitri V and Pjevac, Petra and Bach, Wolfgang and Hourdez, St{\'e}phane and Girguis, Peter R. and Vidoudez, Charles and Amann, Rudolf and Meyerdierks, Anke and others}
}
@article {raineault2017exploration,
	title = {Exploration of central california basins, cold seeps, and san juan seamount},
	journal = {Oceanography (Wash. DC)},
	volume = {30},
	year = {2017},
	pages = {36{\textendash}37},
	author = {Raineault, Nicole and Peter Girguis and Auscavitch, Steve and Castillo, Chris and Lubetkin, Megan and Marlow, Jeffrey and Kane, R}
}
@article {tang2017geochemically,
	title = {Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically},
	journal = {Geobiology},
	volume = {15},
	year = {2017},
	pages = {324{\textendash}339},
	author = {Tang, T and Mohr, W and Sattin, SR and Rogers, D. R. and Girguis, P. R. and Pearson, A}
}
@article {guan2017iron,
	title = {Iron sulfide formation on iron substrates by electrochemical reaction in anoxic conditions},
	journal = {Crystal Growth \& Design},
	volume = {17},
	year = {2017},
	pages = {6332{\textendash}6340},
	publisher = {American Chemical Society},
	author = {Guan, Xiaofei and Enalls, Brandon C and Clarke, David R and Peter Girguis}
}
@conference {picard2017iron,
	title = {Iron Sulfide Minerals Record Microbe-Mineral Interactions in Anoxic Environments},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2017},
	year = {2017},
	pages = {P43G{\textendash}04},
	author = {Picard, Aude and Gartman, Amy and Cosmidis, Julie and Clarke, David R and Girguis, Peter R.}
}
@article {gartman2017microbes,
	title = {Microbes facilitate mineral deposition in bioelectrochemical systems},
	journal = {ACS Earth and Space Chemistry},
	volume = {1},
	year = {2017},
	pages = {277{\textendash}287},
	publisher = {American Chemical Society},
	author = {Gartman, A. and Picard, A and Olins, H. C. and Sarode, N and Clarke, DR and Girguis, P. R.}
}
@article {orcutt2017microbial,
	title = {Microbial response to oil enrichment in Gulf of Mexico sediment measured using a novel long-term benthic lander system},
	journal = {Elementa: Science of the Anthropocene},
	volume = {5},
	year = {2017},
	publisher = {University of California Press},
	author = {Orcutt, Beth N and Lapham, Laura L and Delaney, Jennifer and Sarode, Neha and Marshall, Kathleen S and Whaley-Martin, Kelly J and Slater, Greg and Wheat, C Geoff and Girguis, Peter R. and Thomsen, Laurenz}
}
@article {bell2017new,
	title = {New Frontiers in Ocean Exploration The E/V Nautilus, NOAA Ship Okeanos Explorer, and R/V Falkor 2016 Field Season},
	journal = {Oceanography},
	volume = {30},
	year = {2017},
	pages = {1{\textendash}+},
	publisher = {OCEANOGRAPHY SOC PO BOX 1931, ROCKVILLE, MD USA},
	author = {Bell, Katherine LC and Mowitt, William and Zykov, Victor and Delgado, James P and Tartt, Mitchell and Stout, Matthew and Wagner, Katie and Marquis, Sarah and Bell, Katherine LC and Phillips, Brennan and others}
}
@article {meier2017niche,
	title = {Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents},
	journal = {The ISME journal},
	volume = {11},
	year = {2017},
	pages = {1545{\textendash}1558},
	publisher = {Nature Publishing Group},
	author = {Meier, Dimitri V and Pjevac, Petra and Bach, Wolfgang and Hourdez, Stephane and Girguis, Peter R. and Vidoudez, Charles and Amann, Rudolf and Meyerdierks, Anke}
}
@article {marlow2017opinion,
	title = {Opinion: Telepresence is a potentially transformative tool for field science},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {114},
	year = {2017},
	pages = {4841{\textendash}4844},
	publisher = {National Academy of Sciences},
	author = {Marlow, Jeffrey and Borrelli, Chiara and Jungbluth, Sean P and Hoffman, Colleen and Marlow, Jennifer and Girguis, Peter R. and others}
}
@article {fontanillas2017proteome,
	title = {Proteome evolution of deep-sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages},
	journal = {Genome Biology and Evolution},
	volume = {9},
	year = {2017},
	pages = {279{\textendash}296},
	publisher = {Oxford University Press},
	author = {Fontanillas, Eric and Galzitskaya, Oxana V and Lecompte, Odile and Lobanov, Mikhail Y and Tanguy, Arnaud and Mary, Jean and Girguis, Peter R. and Hourdez, St{\'e}phane and Jollivet, Didier}
}
@conference {girguis2017there,
	title = {There and back again: An oceanographer{\textquoteright}s approach to delving into-and returning from-the unknown.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2017},
	year = {2017},
	pages = {P51F{\textendash}02},
	author = {Girguis, Peter R. and Hoer, Daniel and Michel, Anna and Wankel, Scott D and Farr, Norman and Pontbriand, Clifford and Raineault, Nicole}
}
@article {gomaa2017toward,
	title = {Toward establishing model organisms for marine protists: Successful transfection protocols for Parabodo caudatus (Kinetoplastida: Excavata)},
	journal = {Environmental microbiology},
	volume = {19},
	year = {2017},
	pages = {3487{\textendash}3499},
	author = {Gomaa, Fatma and Garcia, Paulo A and Delaney, Jennifer and Girguis, Peter R. and Buie, Cullen R and Edgcomb, Virginia P}
}
@article {padilla2016activity,
	title = {Activity and diversity of aerobic methanotrophs in a coastal marine oxygen minimum zone},
	journal = {American Geophysical Union},
	volume = {2016},
	year = {2016},
	pages = {ME34D{\textendash}0829},
	author = {Padilla,Cory C and Bristow,Laura A and Sarode, Neha D and Garcia-Robledo,Emilio and Girguis, Peter R. and Thamdrup,Bo and Stewart, Frank J}
}
@article {michel2016advancing,
	title = {Advancing an In situ Laser Spectrometer for Carbon Isotope Analyses in the Deep Ocean},
	journal = {American Geophysical Union},
	volume = {2016},
	year = {2016},
	pages = {IS52A{\textendash}03},
	author = {Michel, A and Wankel, S. D. and Kapit, J and Girguis, P. R.}
}
@article {maher2016arsenic,
	title = {Arsenic concentrations and species in three hydrothermal vent worms, Ridgeia piscesae, Paralvinella sulficola and Paralvinella palmiformis},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	volume = {116},
	year = {2016},
	pages = {41{\textendash}48},
	publisher = {Pergamon},
	author = {Maher, WA and Duncan, Elliott and Dilly, Geoffrey and Foster, Simon and Krikowa, Frank and Lombi, E and Scheckel, Kirk and Peter Girguis}
}
@conference {girguis2016closing,
	title = {Closing in on the limits of life through open-access instrumentation.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2016},
	year = {2016},
	pages = {V34A{\textendash}06},
	author = {Girguis, Peter R. and Hoer, Daniel}
}
@article {meyer2016distinct,
	title = {A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge},
	journal = {Scientific reports},
	volume = {6},
	year = {2016},
	pages = {1{\textendash}14},
	publisher = {Nature Publishing Group},
	author = {Meyer, Julie L and Jaekel, Ulrike and Tully, Benjamin J and Glazer, Brian T and Wheat, C Geoffrey and Lin, Huei-Ting and Hsieh, Chih-Chiang and Cowen, James P and Hulme, Samuel M and Girguis, Peter R. and others}
}
@conference {kane2016v,
	title = {E/V Nautilus Mapping and ROV Dives Reveal Hundreds of Vents along the West Coast of the United States},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2016},
	year = {2016},
	pages = {OS41A{\textendash}1943},
	author = {Kane, Renato and Raineault, Nicole and Embley, Robert W and Merle, Susan G and Girguis, Peter R. and Irish, Onni and Lubetkin, Megan and German, Christopher R and Levin, Lisa A and Cormier, Marie-Helene and others}
}
@booklet {levin2016exploration,
	title = {Exploration and discovery of methane seeps and associated communities in the California Borderland},
	howpublished = {Oceanography},
	volume = {29},
	year = {2016},
	pages = {40{\textendash}43},
	publisher = {OCEANOGRAPHY SOC PO BOX 1931, ROCKVILLE, MD USA},
	author = {Levin, Lisa and Girguis, Peter R. and German, Christopher R and Brennan, Michael L and Tuzun, Suna and Wagner, Jamie and Smart, Clara and Kruger, Avery and Inderbitzen, Katherine and Le, Jennifer and others}
}
@article {meier2016heterotrophic,
	title = {Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting},
	journal = {Environmental microbiology},
	volume = {18},
	year = {2016},
	pages = {4348{\textendash}4368},
	author = {Meier, Dimitri V and Bach, Wolfgang and Girguis, Peter R. and Gruber-Vodicka, Harald R and Reeves, Eoghan P and Richter, Michael and Vidoudez, Charles and Amann, Rudolf and Meyerdierks, Anke}
}
@article {schrader2016independent,
	title = {Independent benthic microbial fuel cells powering sensors and acoustic communications with the MARS underwater observatory},
	journal = {Journal of Atmospheric and Oceanic Technology},
	volume = {33},
	year = {2016},
	pages = {607{\textendash}617},
	author = {Schrader, Paul S and Reimers, Clare E and Peter Girguis and Delaney, Jennifer and Cody Doolan and Michael Wolf and Dale Green}
}
@article {tang2016intracellular,
	title = {Intracellular carbon isotope distributions of continuous-culture Allochromatium vinosum grown on acetate vs. CO 2.},
	journal = {American Geophysical Union},
	volume = {2016},
	year = {2016},
	pages = {MM44C{\textendash}0508},
	author = {Tang, T and Mohr, W and Sattin, S and Rogers, D and Girguis, P. R. and Pearson, A}
}
@article {sobol2016investigating,
	title = {Investigating the Differences in the Total and Active Microbial Community of Mid-Atlantic Ridge Sediments},
	journal = {American Geophysical Union},
	volume = {2016},
	year = {2016},
	pages = {MM24B{\textendash}0443},
	author = {Sobol, Morgan S and Zinke, Laura A and Orcutt, Beth and Mills, Heath Jordan and Edwards, Katrina J and Girguis, Peter R. and Reese, BK}
}
@conference {tully2016metagenomic,
	title = {Metagenomic Assessment of a Dynamic Microbial Population from Subseafloor Aquifer Fluids in the Cold, Oxygenated Crust},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2016},
	year = {2016},
	pages = {B13J{\textendash}02},
	author = {Tully, Benjamin J and Heidelberg, John F and Kraft, Beate and Girguis, Peter R. and Huber, Julie A}
}
@article {seston2016metatranscriptional,
	title = {Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes},
	journal = {Frontiers in microbiology},
	volume = {7},
	year = {2016},
	pages = {1074},
	publisher = {Frontiers},
	author = {Seston, Sherry L and Beinart, Roxanne A and Sarode, Neha and Shockey, Abigail C and Ranjan, Piyush and Ganesh, Sangita and Girguis, Peter R. and Stewart, Frank J}
}
@article {girguis2016microbial,
	title = {Microbial ecology: Here, there and everywhere},
	journal = {Nature Microbiology},
	volume = {1},
	year = {2016},
	pages = {1{\textendash}2},
	publisher = {Nature Publishing Group},
	author = {Peter Girguis}
}
@article {ge2016nanoporous,
	title = {Nanoporous microscale microbial incubators},
	journal = {Lab on a Chip},
	volume = {16},
	year = {2016},
	pages = {480{\textendash}488},
	publisher = {Royal Society of Chemistry},
	author = {Ge, Zhifei and Girguis, Peter R. and Buie, Cullen R}
}
@article {padilla2016nc10,
	title = {NC10 bacteria in marine oxygen minimum zones},
	journal = {The ISME journal},
	volume = {10},
	year = {2016},
	pages = {2067{\textendash}2071},
	publisher = {Nature Publishing Group},
	author = {Padilla,Cory C and Bristow,Laura A and Sarode, Neha and Garcia-Robledo,Emilio and G{\'o}mez Ram{\'{\i}rez, Eddy and Benson,Catherine R and Bourbonnais,Annie and Altabet,Mark A and Girguis, Peter R. and Thamdrup,Bo and others}
}
@article {bradley2016patterns,
	title = {Patterns of sulfur isotope fractionation during microbial sulfate reduction},
	journal = {Geobiology},
	volume = {14},
	year = {2016},
	pages = {91{\textendash}101},
	author = {Bradley, A. S. and Leavitt, WD and Schmidt, M. and Knoll, Andrew Herbert and Girguis, Peter R. and Johnston, David T}
}
@article {cordes2016rov,
	title = {ROV Hercules Investigates Brine Lakes on the Bottom of the Ocean},
	journal = {Oceanography},
	volume = {29},
	year = {2016},
	pages = {30{\textendash}31},
	author = {Cordes, E and Michel, A and Petersen, J and Wankel, S and Ansorge, Rebecca and Girguis, P. and Leisch, Nikolaus and Smart, Clara and Roman, Chris and Wetzel, Silke and others}
}
@conference {fisher2016stability,
	title = {Stability of Hydrothermal Vent Communities on the Eastern Lau Spreading Center},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2016},
	year = {2016},
	pages = {OS34A{\textendash}03},
	author = {Fisher, Charles R and Du Preez, Cherisse and Ferrini, Vicki Lynn and Beinart, Roxanne and Seewald, Jeffrey and Hoer, Daniel and Girguis, Peter R.}
}
@article {levin2016tele,
	title = {(Tele) presenting Secrets from the Deep Southern California Margin},
	journal = {American Geophysical Union},
	volume = {2016},
	year = {2016},
	pages = {ED24A{\textendash}1655},
	author = {Levin, Lisa A and Girguis, Peter R. and Brennan, Michael and German, Christopher R and Raineault, Nicole and Le, Jennifer Tran and Grupe, Benjamin and Gallo, Natalya and Inderbitzen, Katherine E and Tuzun, Suna and others}
}
@article {picard2016we,
	title = {What do we really know about the role of microorganisms in iron sulfide mineral formation?},
	journal = {Frontiers in Earth Science},
	volume = {4},
	year = {2016},
	pages = {68},
	publisher = {Frontiers},
	author = {Picard, Aude and Gartman, Amy and Girguis, Peter R.}
}
@article {Maher201641,
	title = {Arsenic concentrations and species in three hydrothermal vent worms, Ridgeia piscesae, Paralvinella sulficola and Paralvinella palmiformis},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	volume = {116},
	year = {2016},
	pages = {41 - 48},
	abstract = {Abstract Hydrothermal vents are surficial expressions of subsurface geological and hydrological processes. Fluids emitting from active vents are chemically distinct from bottom seawater, and are enriched in dissolved metals and metalloids, including arsenic. Vent organisms accumulate arsenic but the arsenic speciation in these non-photosynthetic organisms is largely unknown. Here, arsenic concentrations and chemical species were measured in three deep sea hydrothermal vent worms (Ridgeia piscesae, Paralvinella sulfincola and Paralvinella palmiformis ) from the Juan de Fuca Ridge in the Northwest pacific. R. piscesae has similar arsenic concentrations (3.8{\textendash}35 {\textmu}g g-1) to shallow water polychaetes while P. sulfincola and P. palmiformis have significantly higher arsenic concentrations (420{\textendash}1417 and 125{\textendash}321 {\textmu}g g-1 respectively). R. piscesae contains appreciable quantities of inorganic arsenic (36{\textpm}14\%), monomethyl arsenic (2{\textpm}2\%), dimethyl arsenic (34{\textpm}21\%), an unknown methyl arsenical (7{\textpm}16\%), OSO3-arsenosugar (5{\textpm}9\%), \TETRA\ (4{\textpm}5\%), ThioPO4/ThioDMAE (1{\textpm}2\%) and an unknown thio-arsenical (12{\textpm}14\%). These results suggests that host and symbionts are either involved in the methylation of arsenic, or are bathed in fluids enriched in methylated arsenic as a result of free-living microbial activity. The host carrying out methylation, however, cannot be ruled out. In contrast, 96{\textendash}97\% of the arsenic in P. sulfincola and P. palmiformis is inorganic arsenic, likely the result of arsenic precipitation within and upon the mucus they ingest while feeding. While all worms have oxo- and thio arsenosugars (2{\textendash}30\%), Paralvinella also have small amounts of arsenobetaine (\&lt;0.001{\textendash}0.21\%). The presence of arsenosugars, arsenobetaine and other minor arsenic species in the absence of photosynthesising algae/bacteria indicates that they may be formed by vent animals in the absence of sunlight, but at this time their formation cannot be explained.},
	issn = {0967-0637},
	doi = {http://dx.doi.org/10.1016/j.dsr.2016.07.009},
	url = {http://www.sciencedirect.com/science/article/pii/S0967063716301194},
	author = {W.A. Maher and E. Duncan and G. Dilly and S. Foster and F. Krikowa and E. Lombi and K. Scheckel and Girguis, P.}
}
@article {928296,
	title = {Microbial ecology: Here, there and everywhere},
	journal = {Nature Microbiology},
	volume = {1},
	year = {2016},
	month = {2016/07/26/onlin},
	pages = {16123 - },
	publisher = {Macmillan Publishers Limited},
	url = {http://dx.doi.org/10.1038/nmicrobiol.2016.123},
	author = {Peter Girguis}
}
@article {EMI:EMI13304,
	title = {Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting},
	journal = {Environmental Microbiology},
	year = {2016},
	pages = {n/a{\textendash}n/a},
	abstract = {Deep-sea hydrothermal vents are highly dynamic habitats characterized by steep temperature and chemical gradients. The oxidation of reduced compounds dissolved in the venting fluids fuels primary production providing the basis for extensive life. Until recently studies of microbial vent communities have focused primarily on chemolithoautotrophic organisms. In our study, we targeted the change of microbial community compositions along mixing gradients, focusing on distribution and capabilities of heterotrophic microorganisms. Samples were retrieved from different venting areas within the Menez Gwen hydrothermal field, taken along mixing gradients, including diffuse fluid discharge points, their immediate surroundings and the buoyant parts of hydrothermal plumes. High throughput 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization, and targeted metagenome analysis were combined with geochemical analyses. Close to diffuse venting orifices dominated by chemolithoautotrophic Epsilonproteobacteria, in areas where environmental conditions still supported chemolithoautotrophic processes, we detected microbial communities enriched for versatile heterotrophic Alpha- and Gammaproteobacteria. The potential for alkane degradation could be shown for several genera and yet uncultured clades. We propose that hotspots of chemolithoautotrophic life support a {\textquoteleft}belt{\textquoteright} of heterotrophic bacteria significantly different from the dominating oligotrophic microbiota of the deep sea.},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.13304},
	url = {http://dx.doi.org/10.1111/1462-2920.13304},
	author = {Meier, Dimitri V. and Bach, Wolfgang and Peter R. Girguis and Gruber-Vodicka, Harald R. and Reeves, Eoghan P. and Richter, Michael and Vidoudez, Charles and Amann, Rudolf and Meyerdierks, Anke}
}
@article {doi:10.1175/JTECH-D-15-0102.1,
	title = {Independent Benthic Microbial Fuel Cells Powering Sensors and Acoustic Communications with the MARS Underwater Observatory},
	journal = {Journal of Atmospheric and Oceanic Technology},
	volume = {33},
	year = {2016},
	pages = {607-617},
	abstract = {AbstractMost oceanographic instruments on the seafloor have no connections with the surface and therefore have to run on batteries and store data until recovery. To demonstrate a developing technology, sensors and acoustic modems were powered with energy harvested from the seafloor, and data were relayed acoustically in near{\textendash}real time to the Monterey Accelerated Research System (MARS) observatory in Monterey Bay, California, and to surface research vessels. MARS is a cabled observatory in deep water (~890 m) at the edge of Monterey Canyon. An acoustic modem was attached to the MARS node and configured to send out commands to, and relay data received from, remote modems. Two benthic microbial fuel cells (BMFCs) positioned approximately 0.5 km away from MARS supplied power to the remote modems and sensors. At their peak performance, these BMFCs produced continuous power densities of ~35 mW m-2 (footprint area). The modems utilized in this study contained an integrated power management platform (PMP) designed to manage and store the electrical energy generated by each BMFC and to record BMFC performance parameters and sensor data on an hourly basis. Temperature and either oxygen or conductivity sensors were chosen because of their common use and environmental relevance. Acoustically transmitted data records show that the BMFCs renewed energy stores and that the oceanographic sensors measured dissolved oxygen, temperature, and conductivity reliably throughout the operational life of each BMFC system (~6 months). These systems remained in place for more than 12 months.},
	doi = {10.1175/JTECH-D-15-0102.1},
	url = {http://dx.doi.org/10.1175/JTECH-D-15-0102.1},
	author = {Paul S. Schrader and Clare E. Reimers and Peter Girguis and Delaney, Jennifer and Cody Doolan and Michael Wolf and Dale Green}
}
@article {928281,
	title = {NC10 bacteria in marine oxygen minimum zones},
	journal = {ISME J},
	volume = {10},
	year = {2016},
	note = {Supplementary information available for this article at http://www.nature.com/ismej/journal/v10/n8/suppinfo/ismej2015262s1.html},
	month = {2016/08//print},
	pages = {2067 - 2071},
	publisher = {International Society for Microbial Ecology},
	abstract = {Bacteria of the NC10 phylum link anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. A niche for NC10 in the pelagic ocean has not been confirmed. We show that NC10 bacteria are present and transcriptionally active in oceanic oxygen minimum zones (OMZs) off northern Mexico and Costa Rica. NC10 16S rRNA genes were detected at all sites, peaking in abundance in the anoxic zone with elevated nitrite and methane concentrations. Phylogenetic analysis of particulate methane monooxygenase genes further confirmed the presence of NC10. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes of the putative nitrite-dependent intra-aerobic pathway, with high representation of transcripts containing the unique motif structure of the nitric oxide (NO) reductase of NC10 bacteria, hypothesized to participate in O2-producing NO dismutation. These findings confirm pelagic OMZs as a niche for NC10, suggesting a role for this group in OMZ nitrogen, methane and oxygen cycling.},
	isbn = {1751-7362},
	url = {http://dx.doi.org/10.1038/ismej.2015.262},
	author = {Padilla,Cory C and Bristow,Laura A and Sarode, Neha and Garcia-Robledo,Emilio and Gomez Ramirez,Eddy and Benson,Catherine R and Bourbonnais,Annie and Altabet,Mark A and Girguis, Peter R. and Thamdrup,Bo and Stewart, Frank J}
}
@article {928276,
	title = {Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes},
	journal = {Frontiers in Microbiology},
	volume = {7},
	year = {2016},
	month = {2016/06/27/accep},
	pages = {1074},
	publisher = {Frontiers Media S.A.},
	abstract = {Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO(2) fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O(2) scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.},
	isbn = {1664-302X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4949241/},
	author = {Seston, Sherry L and Beinart, Roxanne A and Sarode, Neha and Shockey, Abigail C and Ranjan, Piyush and Ganesh, Sangita and Girguis, Peter R. and Stewart, Frank J}
}
@article {10.3389/feart.2016.00068,
	title = {What Do We Really Know about the Role of Microorganisms in Iron Sulfide Mineral Formation?},
	journal = {Frontiers in Earth Science},
	volume = {4},
	year = {2016},
	pages = {68},
	abstract = {Iron sulfide mineralization in low-temperature systems is a result of biotic and abiotic processes, though the delineation between these two modes of formation is not always straightforward. Here we review the role of microorganisms in the precipitation of extracellular iron sulfide minerals. We summarize the evidence that links sulfur-metabolizing microorganisms and sulfide minerals in nature and we present a critical overview of laboratory-based studies of the nucleation and growth of iron sulfide minerals in microbial cultures. We discuss whether biologically derived minerals are distinguishable from abiotic minerals, possessing attributes that are uniquely diagnostic of biomineralization. These inquiries have revealed the need for additional thorough, mechanistic and high-resolution studies to understand microbially mediated formation of a variety of sulfide minerals across a range of natural environments.},
	issn = {2296-6463},
	doi = {10.3389/feart.2016.00068},
	url = {http://journal.frontiersin.org/article/10.3389/feart.2016.00068},
	author = {Picard, Aude and Gartman, Amy and Peter R. Girguis}
}
@article {928266,
	title = {A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	month = {2016/02/15/accep},
	pages = {22541},
	publisher = {Nature Publishing Group},
	abstract = {The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 {\textdegree}C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.},
	isbn = {2045-2322},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776111/},
	author = {Meyer, Julie L and Jaekel, Ulrike and Tully, Benjamin J and Glazer, Brian T and Wheat, C Geoffrey and Lin, Huei-Ting and Hsieh, Chih-Chiang and Cowen, James P and Hulme, Samuel M and Girguis, Peter R. and Huber, Julie A}
}
@article {C5LC00978B,
	title = {Nanoporous microscale microbial incubators},
	journal = {Lab Chip},
	volume = {16},
	year = {2016},
	pages = {480-488},
	publisher = {The Royal Society of Chemistry},
	abstract = {Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals abundant microbial diversity that has not been cultured in the laboratory. Many attribute this so-called {\textquoteright}great plate count anomaly{\textquoteright} to traditional microbial cultivation techniques, which largely facilitate the growth of a single species. Yet, it is widely recognized that bacteria in nature exist in complex communities. One technique to increase the pool of cultivated bacterial species is to co-culture multiple species in a simulated natural environment. Here, we present nanoporous microscale microbial incubators (NMMI) that enable high-throughput screening and real-time observation of multi-species co-culture. The key innovation in NMMI is that they facilitate inter-species communication while maintaining physical isolation between species, which is ideal for genomic analysis. Co-culture of a quorum sensing pair demonstrates that the NMMI can be used to culture multiple species in chemical communication while monitoring the growth dynamics of individual species.},
	doi = {10.1039/C5LC00978B},
	url = {http://dx.doi.org/10.1039/C5LC00978B},
	author = {Ge, Zhifei and Peter R. Girguis and Buie, Cullen R.}
}
@article {GBI:GBI12149,
	title = {Patterns of sulfur isotope fractionation during microbial sulfate reduction},
	journal = {Geobiology},
	volume = {14},
	year = {2016},
	pages = {91{\textendash}101},
	abstract = {Studies of microbial sulfate reduction have suggested that the magnitude of sulfur isotope fractionation varies with sulfate concentration. Small apparent sulfur isotope fractionations preserved in Archean rocks have been interpreted as suggesting Archean sulfate concentrations of <200~μm, while larger fractionations thereafter have been interpreted to require higher concentrations. In this work, we demonstrate that fractionation imposed by sulfate reduction can be a function of concentration over a millimolar range, but that nature of this relationship depends on the organism studied. Two sulfate-reducing bacteria grown in continuous culture with sulfate concentrations ranging from 0.1 to 6~mm showed markedly different relationships between sulfate concentration and isotope fractionation. Desulfovibrio vulgaris str. Hildenborough showed a large and relatively constant isotope fractionation (34εSO4-H2S ≅ 25{\textperthousand}), while fractionation by Desulfovibrio alaskensis G20 strongly correlated with sulfate concentration over the same range. Both data sets can be modeled as Michaelis{\textendash}Menten (MM)-type relationships but with very different MM constants, suggesting that the fractionations imposed by these organisms are highly dependent on strain-specific factors. These data reveal complexity in the sulfate concentration{\textendash}fractionation relationship. Fractionation during MSR relates to sulfate concentration but also to strain-specific physiological parameters such as the affinity for sulfate and electron donors. Previous studies have suggested that the sulfate concentration{\textendash}fractionation relationship is best described with a MM fit. We present a simple model in which the MM fit with sulfate concentration and hyperbolic fit with growth rate emerge from simple physiological assumptions. As both environmental and biological factors influence the fractionation recorded in geological samples, understanding their relationship is critical to interpreting the sulfur isotope record. As the uptake machinery for both sulfate and electrons has been subject to selective pressure over Earth history, its evolution may complicate efforts to uniquely reconstruct ambient sulfate concentrations from a single sulfur isotopic composition.},
	issn = {1472-4669},
	doi = {10.1111/gbi.12149},
	url = {http://dx.doi.org/10.1111/gbi.12149},
	author = {Bradley, A. S. and Leavitt, W. D. and Schmidt, M. and Knoll, A. H. and Girguis, P. R. and Johnston, D. T.}
}
@conference {michel2015advancing,
	title = {Advancing a deep sea near-infrared laser spectrometer for dual isotope measurements},
	booktitle = {CLEO: Applications and Technology},
	year = {2015},
	pages = {ATu4J{\textendash}6},
	publisher = {Optical Society of America},
	organization = {Optical Society of America},
	author = {Michel, Anna PM and Wankel, Scott D and Kapit, Jason and Girguis, Peter R. and Manish Gupta}
}
@article {sanders2015baleen,
	title = {Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores},
	journal = {Nature communications},
	volume = {6},
	year = {2015},
	pages = {1{\textendash}8},
	publisher = {Nature Publishing Group},
	author = {Sanders, Jon G and Beichman, Annabel C and Joe Roman and Scott, Jarrod J and David Emerson and McCarthy, James J and Girguis, Peter R.}
}
@article {lu2015biological,
	title = {Biological capacitance studies of anodes in microbial fuel cells using electrochemical impedance spectroscopy},
	journal = {Bioprocess and biosystems engineering},
	volume = {38},
	year = {2015},
	pages = {1325{\textendash}1333},
	publisher = {Springer Berlin Heidelberg},
	author = {Lu, Zhihao and Peter Girguis and Liang, Peng and Shi, Haifeng and Huang, Guangtuan and Cai, Lankun and Zhang, Lehua}
}
@article {orcutt2015carbon,
	title = {Carbon fixation by basalt-hosted microbial communities},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	pages = {904},
	publisher = {Frontiers},
	author = {Orcutt, Beth N and Sylvan, Jason B and Rogers, Daniel and Delaney, Jennifer and Lee, Raymond W and Girguis, Peter R.}
}
@article {girguis2015collaborative,
	title = {Collaborative Research: Ecosystem dynamics of Western Pacific hydrothermal vent communities associated with polymetallic sulfide deposits},
	year = {2015},
	author = {Peter Girguis and others}
}
@article {girguis2015collaborative,
	title = {COLLABORATIVE RESEARCH: The role of iron-oxidizing bacteria in the sedimentary iron cycle: ecological, physiological and biogeochemical implications.},
	year = {2015},
	author = {Peter Girguis and others}
}
@article {sperling2015ecological,
	title = {The ecological physiology of Earth{\textquoteright}s second oxygen revolution},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	volume = {46},
	year = {2015},
	pages = {215{\textendash}235},
	publisher = {Annual Reviews},
	author = {Sperling, Erik A and Knoll, Andrew H and Girguis, Peter R.}
}
@article {jiang2015enhancing,
	title = {Enhancing the response of microbial fuel cell based toxicity sensors to Cu (II) with the applying of flow-through electrodes and controlled anode potentials},
	journal = {Bioresource technology},
	volume = {190},
	year = {2015},
	pages = {367{\textendash}372},
	publisher = {Elsevier},
	author = {Jiang, Yong and Liang, Peng and Zhang, Changyong and Bian, Yanhong and Yang, Xufei and Huang, Xia and Girguis, Peter R.}
}
@article {qiao2015graphite,
	title = {Graphite Anodes Activated by Melamine, Carbamide, ZnCl2 and H3PO4 in Microbial Fuel Cells},
	journal = {Int. J. Electrochem. Sci},
	volume = {10},
	year = {2015},
	pages = {5001{\textendash}5012},
	author = {Qiao, Junjing and Peter Girguis and Li, Dongmei and Ma, Jingxing and Cai, Lankun and Zhang, Lehua}
}
@conference {frank2015key,
	title = {Key Factors Influencing Rates of Heterotrophic Sulfate Reduction in Hydrothermal Massive Sulfide Deposits},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2015},
	year = {2015},
	pages = {B11I{\textendash}0554},
	author = {Frank, Kiana L and Rogers, Karyn L and Rogers, Daniel and Johnston, David T and Girguis, Peter R.}
}
@article {frank2015key,
	title = {Key factors influencing rates of heterotrophic sulfate reduction in active seafloor hydrothermal massive sulfide deposits},
	journal = {Frontiers in microbiology},
	volume = {6},
	year = {2015},
	pages = {1449},
	publisher = {Frontiers},
	author = {Frank, Kiana L and Rogers, Karyn L and Rogers, Daniel R and Johnston, David T and Girguis, Peter R.}
}
@conference {shah2015microbe,
	title = {Microbe-mediated transformations of marine dissolved organic matter during 2,100 years of natural incubation in the cold, oxic crust of the Mid-Atlantic Ridge.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2015},
	year = {2015},
	pages = {OS42A{\textendash}04},
	author = {Shah Walter, SR and Jaekel, Ulrike and Huber, Julie A and Dittmar, Thorsten and Girguis, Peter R.}
}
@article {gittel2015ubiquitous,
	title = {Ubiquitous presence and novel diversity of anaerobic alkane degraders in cold marine sediments},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	pages = {1414},
	publisher = {Frontiers},
	author = {Gittel, Antje and Donhauser, Johanna and R{\o}y, Hans and Girguis, Peter R. and J{\o}rgensen, Bo B and Kjeldsen, Kasper U}
}
@article {beinart2015uptake,
	title = {The uptake and excretion of partially oxidized sulfur expands the repertoire of energy resources metabolized by hydrothermal vent symbioses},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {282},
	year = {2015},
	pages = {20142811},
	publisher = {The Royal Society},
	author = {Beinart, R. A. and Gartman, A. and Sanders, J. G. and Luther, G. W. and Girguis, P. R.}
}
@conference {girguis2015worlds,
	title = {When Worlds Collide: Microbial Ecophysiology at the Aerobic/Anaerobic Interface},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2015},
	year = {2015},
	pages = {OS42A{\textendash}01},
	author = {Girguis, Peter R.}
}
@article {928251,
	title = {Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores},
	journal = {Nature Communications},
	volume = {6},
	year = {2015},
	month = {2015/09/22/onlin},
	pages = {8285 - },
	publisher = {The Author(s)},
	url = {http://dx.doi.org/10.1038/ncomms9285},
	author = {Jon G. Sanders and Annabel C. Beichman and Joe Roman and Jarrod J. Scott and David Emerson and James J. McCarthy and Peter R. Girguis}
}
@article {10.3389/fmicb.2015.01449,
	title = {Key Factors Influencing Rates of Heterotrophic Sulfate Reduction in Active Seafloor Hydrothermal Massive Sulfide Deposits},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	pages = {1449},
	abstract = {Hydrothermal vents are thermally and geochemically dynamic habitats, and the organisms therein are subject to steep gradients in temperature and chemistry. To date, the influence of these environmental dynamics on microbial sulfate reduction has not been well constrained. Here, via multivariate experiments, we evaluate the effects of key environmental variables (temperature, pH, H2S, SO42-, DOC) on sulfate reduction rates and metabolic energy yields in material recovered from a hydrothermal flange from the Grotto edifice in the Main Endeavor Field, Juan de Fuca Ridge. Sulfate reduction was measured in batch reactions across a range of physico-chemical conditions. Temperature and pH were the strongest stimuli, and maximum sulfate reduction rates were observed at 50 {\textdegree}C and pH 6, suggesting that the in situ community of sulfate-reducing organisms in Grotto flanges may be most active in a slightly acidic and moderate thermal/chemical regime. At pH 4, sulfate reduction rates increased with sulfide concentrations most likely due to the mitigation of metal toxicity. While substrate concentrations also influenced sulfate reduction rates, energy-rich conditions muted the effect of metabolic energetics on sulfate reduction rates. We posit that variability in sulfate reduction rates reflect the response of the active microbial consortia to environmental constraints on in situ microbial physiology, toxicity, and the type and extent of energy limitation. These experiments help to constrain models of the spatial contribution of heterotrophic sulfate reduction within the complex gradients inherent to seafloor hydrothermal deposits.},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2015.01449},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2015.01449},
	author = {Frank, Kiana L. and Rogers, Karyn L. and Rogers, Daniel R. and Johnston, David T. and Peter R. Girguis}
}
@article {10.3389/fmicb.2015.01414,
	title = {Ubiquitous Presence and Novel Diversity of Anaerobic Alkane Degraders in Cold Marine Sediments},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	pages = {1414},
	abstract = {Alkanes are major constituents of crude oil and are released to the marine environment by natural seepage and from anthropogenic sources. Due to their chemical inertness, their removal from anoxic marine sediments is primarily controlled by the activity of anaerobic alkane-degrading microorganisms. To conduct a comprehensive cultivation-independent survey of the diversity and distribution of anaerobic alkane degraders, we designed novel PCR primers that cover all known diversity of the 1-methylalkyl succinate synthase gene (masD/assA), which catalyzes the initial activation of alkanes. We studied masD/assA gene diversity in pristine and seepage-impacted Danish coastal sediments, as well as in sediments and alkane-degrading enrichment cultures from the Middle Valley (MV) hydrothermal vent system in the Pacific Northwest. MasD/assA genes were ubiquitously present, and the primers captured the diversity of both known and previously undiscovered masD/assA gene diversity. Seepage sediments were dominated by a single masD/assA gene cluster, which is presumably indicative of a substrate-adapted community, while pristine sediments harbored a diverse range of masD/assA phylotypes including those present in seepage sediments. This rare biosphere of anaerobic alkane degraders will likely increase in abundance in the event of seepage or accidental oil spillage. Nanomolar concentrations of short-chain alkanes (SCA) were detected in pristine and seepage sediments. Interestingly, anaerobic alkane degraders closely related to strain BuS5, the only SCA degrader in pure culture, were found in mesophilic MV enrichments, but not in cold sediments from Danish waters. We propose that the new masD/assA gene lineages in these sediments represent novel phylotypes that are either fueled by naturally occurring low levels of SCA or that metabolize medium- to long-chain alkanes. Our study highlights that masD/assA genes are a relevant diagnostic marker to identify seepage and microseepage, e.g. during prospecting for oil and gas, and may act as an indicator of anthropogenic oil spills in marine sediments.},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2015.01414},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2015.01414},
	author = {Gittel, Antje and Donhauser, Johanna and R{\o}y, Hans and Peter R. Girguis and J{\o}rgensen, Bo B. and Kjeldsen, Kasper U.}
}
@article {928236,
	title = {Carbon fixation by basalt-hosted microbial communities},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	month = {2015/08/19/accep},
	pages = {904},
	publisher = {Frontiers Media S.A.},
	abstract = {Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1{\textendash}10 nmol C g(-1)(rock) d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9){\textendash}10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.},
	isbn = {1664-302X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561358/},
	author = {Orcutt, Beth N and Sylvan, Jason B and Rogers, Daniel R and Delaney, Jennifer and Lee, Raymond W and Girguis, Peter R.}
}
@article {713401,
	title = {Biological capacitance studies of anodes in microbial fuel cells using electrochemical impedance spectroscopy.},
	journal = {Bioprocess and Biosystems Engineering},
	volume = {38},
	year = {2015},
	pages = {1325-1333},
	author = {Lu, Z. and Girguis, P. and Liang, P. and Shi, H. and Huang, G. and Cai, L. and Zhang, L.}
}
@article {713501,
	title = {Enhancing the response of microbial fuel cell based toxicity sensors to Cu (II) with the applying of flow-through electrodes and controlled anode potentials.},
	journal = {Bioresource Technology},
	volume = {190},
	year = {2015},
	pages = {367-372},
	author = {Jiang, Y. and Liang, P. and Zhang, C. and Bian, Y. and Yang, X. and Huang, X. and Girguis, PR.}
}
@article {713511,
	title = {Patterns of microbial sulfur isotope fractionation at low sulfate concentrations.},
	journal = {Geobiology},
	year = {2015},
	author = {Bradley, AS. and Leavitt, WD. and Schmidt, M. and Knoll, AH. and Girguis, PR. and Johnston, DT.}
}
@article {713491,
	title = {The uptake and excretion of partially oxidized sulfur expands the repertoire of energy resources metabolized by hydrothermal vent symbioses.},
	journal = {Proceedings of the Royal Society Biological Sciences},
	volume = {282},
	year = {2015},
	author = {Beinart, RA. and Gartman, A. and Sanders, JG. and Luther, GW. and Girguis, PR.}
}
@conference {desilva2014access,
	title = {Access to the Sea: A Roadmap for Expedition Planning},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {OS41A{\textendash}1187},
	author = {DeSilva, Annette M and Girguis, Peter R.}
}
@conference {orcutt2014carbon,
	title = {Carbon fixation in oceanic crust: Does it happen, and is it important?},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {B23G{\textendash}04},
	author = {Orcutt, Beth and Sylvan, Jason B and Rogers, Daniel and Lee, Ray and Girguis, Peter R. and Carr, Stephanie A and Jungbluth, Sean and Rappe, Michael S}
}
@article {liao2014characterizing,
	title = {Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses R idgeia piscesae},
	journal = {Molecular ecology},
	volume = {23},
	year = {2014},
	pages = {1544{\textendash}1557},
	author = {Liao, Li and Wankel, Scott D and Wu, Min and Cavanaugh, Colleen M and Girguis, Peter R.}
}
@booklet {girguis2014citation,
	title = {Citation for Scientific Excellence: Victoria J. Bertics},
	year = {2014},
	author = {Girguis, Peter R.}
}
@conference {vidoudez2014constraining,
	title = {Constraining geochemistry and biological primary productivity in hydrothermal systems via in situ mass spectrometric geochemical mapping},
	booktitle = {EGU General Assembly Conference Abstracts},
	year = {2014},
	pages = {9955},
	author = {Vidoudez, Charles and Marcon, Yann and Bach, Wolfgang and Lebris, Nadine and Dubilier, Nicole and Peter Girguis}
}
@article {bose2014electron,
	title = {Electron uptake by iron-oxidizing phototrophic bacteria},
	journal = {Nature communications},
	volume = {5},
	year = {2014},
	pages = {1{\textendash}7},
	publisher = {Nature Publishing Group},
	author = {Bose, Arpita and Gardel, Emily Jeanette and Vidoudez, Charles and Parra, E. A. and Girguis, Peter R.}
}
@conference {olins2014finding,
	title = {Finding the best windows: An apparent environmental threshold determines which diffuse flows are dominated by subsurface microbes},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {B21L{\textendash}04},
	author = {Olins, Heather C and Rogers, Daniel and Scholin, Chris A and Preston, Chris J and Vidoudez, Charles and Ussler, William and Pargett, Doug and Jensen, Scott and Roman, Brent and Birch, James M and others}
}
@conference {girguis2014mantle,
	title = {From Mantle to Microbe to Mollusc: How Animal-Microbial Symbioses Influence Carbon and Sulfur Cycling in Hydrothermal Vent Flows.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {OS51E{\textendash}07},
	author = {Girguis, Peter R. and Beinart, Roxanne}
}
@article {beinart2014intracellular,
	title = {Intracellular O ceanospirillales inhabit the gills of the hydrothermal vent snail A lviniconcha with chemosynthetic, $\gamma$-P roteobacterial symbionts},
	journal = {Environmental Microbiology Reports},
	volume = {6},
	year = {2014},
	pages = {656{\textendash}664},
	author = {Beinart, R. A. and Nyholm, S. V. and Dubilier, Nicole and Girguis, Peter R.}
}
@conference {girguis2014islands,
	title = {Islands in the Sea: the Patchy Distribution and Physiological Poise of Vent Microbes and the Implications for Carbon Cycling},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {OS21D{\textendash}04},
	author = {Girguis, Peter R.}
}
@conference {kraft2014microbial,
	title = {Microbial Turnover of Fixed Nitrogen Compounds in Oceanic Crustal Fluids},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {B21H{\textendash}0167},
	author = {Kraft, Beate and Wankel, Scott D and Glazer, Brian T and Huber, Julie A and Girguis, Peter R.}
}
@conference {sperling2014oxygen,
	title = {Oxygen, ecology, and the Cambrian radiation of animals},
	booktitle = {INTEGRATIVE AND COMPARATIVE BIOLOGY},
	volume = {54},
	year = {2014},
	pages = {E198{\textendash}E198},
	publisher = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	organization = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	author = {Sperling, E. A. and Frieder, C. A. and Raman, A and Girguis, P. R. and Levin, L. A. and Knoll, A. H.}
}
@conference {vidoudez2014perspectives,
	title = {Perspectives on Applying Metabolomics to Understand Carbon Cycling and Process Rates in Deep-Sea Microorganisms},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {B13A{\textendash}0166},
	author = {Vidoudez, Charles and Saghatelian, Alan and Girguis, Peter R.}
}
@article {brooks2014project,
	title = {Project Summary: Investigations of Chemosynthetic Communities on the Lower Continental Slope of the Gulf of Mexico},
	year = {2014},
	publisher = {United States. Bureau of Ocean Energy Management.},
	author = {Brooks, JM and Fisher, C and Roberts, H and Bernard, B and McDonald, I and Carney, R and Joye, S and Cordes, E and Wolff, G and Bright, M. and others}
}
@conference {picard2014sulfate,
	title = {Sulfate Reduction and Sulfide Biomineralization by Deep-Sea Hydrothermal Vent Microorganisms},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2014},
	year = {2014},
	pages = {B13A{\textendash}0164},
	author = {Picard, Aude and Gartman, Amy and Clarke, David R and Girguis, Peter R.}
}
@article {510941,
	title = {Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae},
	journal = {Molecular Ecology},
	volume = {23},
	number = {6},
	year = {2014},
	note = {<p>Sp. Iss. SIAc8hiTimes Cited:2Cited References Count:68</p>},
	month = {Mar},
	pages = {1544-1557},
	abstract = {<p>Chemoautotrophic symbionts of deep sea hydrothermal vent tubeworms are known to provide their hosts with all their primary nutrition. While studies have examined how chemoautotrophic symbionts provide the association with nitrogen, fewer have examined if symbiont nitrogen metabolism varies as a function of environmental conditions. Ridgeia piscesae tubeworms flourish at Northeastern Pacific vents, occupy a range of microhabitats, and exhibit a high degree of morphological plasticity [e.g. long-skinny (LS) and short-fat (SF) phenotypes] that may relate to environmental conditions. This plasticity affords an opportunity to examine whether symbiont nitrogen metabolism varies among host phenotypes. LS and SF R.piscesae were recovered from the Axial and Main Endeavour Field hydrothermal vents. Nitrate and ammonium were quantified in Ridgeia blood, and the expression of key nitrogen metabolism genes, as well as stable nitrogen isotope ratios, was quantified in host branchial plume and symbiont-containing tissues. Nitrate and ammonium were abundant in the blood of both phenotypes though environmental ammonium concentrations were, paradoxically, lowest among individuals with the highest blood ammonium. Assimilatory nitrate reductase transcripts were always below detection, though in both LS and SF R.piscesae symbionts, we observed elevated expression of dissimilatory nitrate reductase genes, as well as symbiont and host ammonium assimilation genes. Site-specific differences in expression, along with tissue stable isotope analyses, suggest that LS and SF Ridgeia symbionts are engaged in both dissimilatory nitrate reduction and ammonia assimilation to varying degrees. As such, it appears that environmental conditions -not host phenotype-primarily dictates symbiont nitrogen metabolism.</p>},
	keywords = {bacterial endosymbiont, de-fuca ridge, guaymas basin, hydrothermal vent, inorganic nitrogen, isotope fractionation, marine diatoms, nitrate reductases, nitrogen, physiological proteomics, ridgeia, symbiosis, tubeworm, tubeworm riftia-pachyptila, vestimentiferan tubeworms},
	isbn = {0962-1083},
	author = {Liao, L. and Wankel, S. D. and Wu, M. and Cavanaugh, C. M. and Girguis, P. R.}
}
@article {510946,
	title = {Electron uptake by iron-oxidizing phototrophic bacteria.},
	journal = {Nature Communications},
	volume = {5},
	year = {2014},
	note = {<p>Ac6xzTimes Cited:2Cited References Count:39</p>},
	month = {Feb},
	pages = {1-7},
	abstract = {<p>Oxidation-reduction reactions underlie energy generation in nearly all life forms. Although most organisms use soluble oxidants and reductants, some microbes can access solid-phase materials as electron-acceptors or -donors via extracellular electron transfer. Many studies have focused on the reduction of solid-phase oxidants. Far less is known about electron uptake via microbial extracellular electron transfer, and almost nothing is known about the associated mechanisms. Here we show that the iron-oxidizing photoautotroph Rhodopseudomonas palustris TIE-1 accepts electrons from a poised electrode, with carbon dioxide as the sole carbon source/electron acceptor. Both electron uptake and ruBisCo form I expression are stimulated by light. Electron uptake also occurs in the dark, uncoupled from photosynthesis. Notably, the pioABC operon, which encodes a protein system essential for photoautotrophic growth by ferrous iron oxidation, influences electron uptake. These data reveal a previously unknown metabolic versatility of photoferrotrophs to use extracellular electron transfer for electron uptake.</p>},
	keywords = {atom exchange, co2 fixation, electricity, metabolism, microorganisms, oxidation, reduction, regulatory twist, rhodopseudomonas-palustris cga010, tie-1},
	isbn = {2041-1723},
	author = {Bose, A. and Gardel, E. J. and Vidoudez, C. and Parra, E. A. and Girguis, P. R.}
}
@article {510951,
	title = {Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, gamma-Proteobacterial symbionts},
	journal = {Environmental Microbiology Reports},
	volume = {6},
	number = {6},
	year = {2014},
	note = {<p>Au6guTimes Cited:0Cited References Count:51</p>},
	month = {Dec},
	pages = {656-664},
	abstract = {<p>Associations between bacteria from the -Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic - or epsilon-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for AlviniconchaOceanospirillales phylotype{\textquoteright}) in membrane-bound vacuoles that were separate from the known - or epsilon-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting -Proteobacterial symbionts and 102 hosting epsilon-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53\% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting -Proteobacterial symbionts than in those hosting epsilon-Proteobacterial symbionts (96\% and 5\% of individuals respectively). The high incidence of AOP in -Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.</p>},
	keywords = {Bacteria, coral stylophora-pistillata, diversity, endosymbionts, genus alviniconcha, indian-ocean, provannidae, sea, sp nov., targeted oligonucleotide probes},
	isbn = {1758-2229},
	author = {Beinart, R. A. and Nyholm, S. V. and Dubilier, N. and Girguis, P. R.}
}
@article {510936,
	title = {Oxygen, ecology, and the Cambrian radiation of animals},
	journal = {Integrative and Comparative Biology},
	volume = {54},
	year = {2014},
	note = {<p>Suppl. 1Ad2fpTimes Cited:0Cited References Count:0</p>},
	pages = {E198-E198},
	isbn = {1540-7063},
	author = {Sperling, E. A. and Frieder, C. A. and Raman, A. V. and Girguis, P. R. and Levin, L. A. and Knoll, A. H.}
}
@article {adams2013anaerobic,
	title = {Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity},
	journal = {Frontiers in Microbiology},
	volume = {4},
	year = {2013},
	pages = {110},
	publisher = {Frontiers},
	author = {Adams, Melissa M and Hoarfrost, Adrienne L and Bose, Arpita and Joye, Samantha B and Girguis, Peter R.}
}
@article {olins2013assessing,
	title = {Assessing the influence of physical, geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys},
	journal = {Geobiology},
	volume = {11},
	year = {2013},
	pages = {279{\textendash}293},
	author = {Olins, H. C. and Rogers, D. R. and Frank, K. L. and Vidoudez, C. and Girguis, P. R.}
}
@article {ussler2013autonomous,
	title = {Autonomous application of quantitative PCR in the deep sea: in situ surveys of aerobic methanotrophs using the deep-sea environmental sample processor},
	journal = {Environmental science \& technology},
	volume = {47},
	year = {2013},
	pages = {9339{\textendash}9346},
	publisher = {American Chemical Society},
	author = {Ussler III, William and Preston, Christina and Tavormina, Patricia and Pargett, Doug and Jensen, Scott and Roman, Brent and Marin III, Roman and Shah, Sunita R and Girguis, Peter R. and Birch, James M and others}
}
@booklet {girguis2013biochemical,
	title = {Biochemical systems for sulfur and carbon sequestration},
	year = {2013},
	note = {US Patent App. 13/991,785},
	author = {Peter Girguis and Reimers, Clare E}
}
@conference {adams2013biogeography,
	title = {Biogeography and diversity of methane and sulfur-cycling ecotypes in deep subsurface sediments},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2013},
	year = {2013},
	pages = {B13C{\textendash}0484},
	author = {Adams, M. M. and Biddle, J and Girguis, P. R.}
}
@article {robidart2013characterizing,
	title = {Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers},
	journal = {Environmental science \& technology},
	volume = {47},
	year = {2013},
	pages = {4399{\textendash}4407},
	publisher = {American Chemical Society},
	author = {Robidart, Julie and Callister, Stephen J and Song, Pengfei and Nicora, Carrie D and Wheat, Charles G and Girguis, Peter R.}
}
@article {frank2013characterizing,
	title = {Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents},
	journal = {The ISME journal},
	volume = {7},
	year = {2013},
	pages = {1391{\textendash}1401},
	publisher = {Nature Publishing Group},
	author = {Frank, Kiana L and Rogers, Daniel R and Olins, Heather C and Vidoudez, Charles and Girguis, Peter R.}
}
@article {wankel2013characterizing,
	title = {Characterizing the distribution of methane sources and cycling in the deep sea via in situ stable isotope analysis},
	journal = {Environmental science \& technology},
	volume = {47},
	year = {2013},
	pages = {1478{\textendash}1486},
	publisher = {American Chemical Society},
	author = {Wankel, Scott D and Huang, Yi-wen and Manish Gupta and Provencal, Robert and Leen, J Brian and Fahrland, Andrew and Vidoudez, Charles and Girguis, Peter R.}
}
@conference {pargett2013deep,
	title = {Deep water instrument for microbial identification, quantification, and archiving},
	booktitle = {2013 OCEANS-San Diego},
	year = {2013},
	pages = {1{\textendash}6},
	publisher = {IEEE},
	organization = {IEEE},
	author = {Pargett, Douglas M and Jensen, Scott D and Roman, Brent A and Preston, Christina M and Ussler, William and Girguis, Peter R. and Marin, Roman and Birch, James M and Scholin, Christopher A}
}
@article {bose2013geomicrobiological,
	title = {Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments},
	journal = {Frontiers in microbiology},
	volume = {4},
	year = {2013},
	pages = {386},
	publisher = {Frontiers},
	author = {Bose, Arpita and Rogers, Daniel R and Adams, Melissa M and Joye, Samantha B and Girguis, Peter R.}
}
@article {perner2013situ,
	title = {In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from I rina II in the L ogatchev field},
	journal = {Environmental Microbiology},
	volume = {15},
	year = {2013},
	pages = {1551{\textendash}1560},
	author = {Perner, Mirjam and Gonnella, Giorgio and Hourdez, Stephane and B{\"o}hnke, Stefanie and Kurtz, Stefan and Peter Girguis}
}
@article {sylvan2013low,
	title = {Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin},
	journal = {Frontiers in Microbiology},
	volume = {4},
	year = {2013},
	pages = {61},
	publisher = {Frontiers},
	author = {Sylvan, Jason B and Sia, Tiffany Y and Haddad, Amanda G and Briscoe, Lindsey J and Toner, Brandy M and Girguis, Peter R. and Edwards, Katrina J}
}
@article {sanders2013metatranscriptomics,
	title = {Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts},
	journal = {The ISME journal},
	volume = {7},
	year = {2013},
	pages = {1556{\textendash}1567},
	publisher = {Nature Publishing Group},
	author = {Sanders, J. G. and Beinart, R. A. and Stewart, F. J. and Delong, E. F. and Girguis, P. R.}
}
@conference {girguis2013microbial,
	title = {Microbial transformations of carbon in crustal aquifer fluids at North Pond, Mid-Atlantic Ridge},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2013},
	year = {2013},
	pages = {B23G{\textendash}02},
	author = {Girguis, P. R. and Jaekel, U and Dittmar, T and Meyer, JL and Glazer, BT and Huber, JA}
}
@article {sperling2013oxygen,
	title = {Oxygen, ecology, and the Cambrian radiation of animals},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {110},
	year = {2013},
	pages = {13446{\textendash}13451},
	publisher = {National Academy of Sciences},
	author = {Sperling, Erik A and Frieder, Christina A and Raman, Akkur V and Girguis, Peter R. and Levin, Lisa A and Knoll, Andrew H}
}
@article {reimers2013redox,
	title = {Redox effects on the microbial degradation of refractory organic matter in marine sediments},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {121},
	year = {2013},
	pages = {582{\textendash}598},
	publisher = {Pergamon},
	author = {Reimers, Clare E and Alleau, Yvan and Bauer, James E and Delaney, Jennifer and Girguis, Peter R. and Schrader, Paul S and Stecher III, Hilmar A}
}
@article {kolodkin2013respiration,
	title = {Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase},
	journal = {Genes \& development},
	volume = {27},
	year = {2013},
	pages = {887{\textendash}899},
	publisher = {Cold Spring Harbor Lab},
	author = {Kolodkin-Gal, Ilana and Elsholz, Alexander KW and Muth, Christine and Girguis, Peter R. and Kolter, Roberto and Losick, Richard}
}
@conference {schrader2013sensors,
	title = {Sensors and acoustic modems powered by Benthic Microbial Fuel Cells at the MARS observatory},
	booktitle = {2013 OCEANS-San Diego},
	year = {2013},
	pages = {1{\textendash}6},
	publisher = {IEEE},
	organization = {IEEE},
	author = {Schrader, Paul S and Cody Doolan and Reimers, Clare E and Girguis, Peter R. and Michael Wolf and Dale Green}
}
@article {bell2013workshop,
	title = {Workshop on telepresence-enabled exploration of the Caribbean region},
	journal = {Oceanography},
	volume = {26},
	year = {2013},
	pages = {50{\textendash}+},
	publisher = {OCEANOGRAPHY SOC PO BOX 1931, ROCKVILLE, MD USA},
	author = {Bell, Katherine LC and Brennan, Michael L and Peter Girguis and Austin Jr, James A and Carey, Steven N and Coleman, Dwight F and Mayer, Larry and Ballard, Robert D and Martinez, Catalina and Russell, Craig}
}
@article {714276,
	title = {Capitalizing on Expertise in Marine Education and Outreach to Broaden Impacts.},
	journal = {The Journal of Marine Education},
	volume = {28},
	year = {2013},
	pages = {39-40},
	author = {Girguis, P. R. and DeCharon, A. and Herren, C.M.}
}
@proceedings {714311,
	title = {The Science and Applications of Microbial Genomics},
	year = {2013},
	note = {<p>The</p>},
	publisher = {The National Academies Press},
	address = {Washington, D.C.},
	author = {Girguis, P. R. and Choffnes, E.R. and LeighAnne, O. and Wizemann, T.M.}
}
@article {511026,
	title = {Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity},
	journal = {Frontiers in Microbiology},
	volume = {4},
	year = {2013},
	note = {<p>Aa5buTimes Cited:5Cited References Count:58</p>},
	month = {May 14},
	pages = {1-11},
	abstract = {<p>Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C-2), propane (C-3), and butane (C-4) in anoxic sediments in contrast to methane (C-1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C-1-C-4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C-1-C-4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75 degrees C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C-1-C-4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C-2-C-4 alkanes. Maximum C-1-C-4 alkane oxidation rates occurred at 55 degrees C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C-3 was oxidized at the highest rate over time, then C-4, C-2, and C-1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C-2-C(4)alkanes with AOM for available oxidants and the influence on the fate of C-1 derived from these hydrothermal systems.</p>},
	keywords = {cold seeps, de-fuca ridge, gas hydrate, gulf-of-mexico, hydrothermal vent, intrinsic bioremediation, juan de fuca ridge, marine methane oxidation, metalliferous sediments, middle valley, molecular-weight hydrocarbons, short-chain alkanes, sulfate reduction, vent fluids},
	isbn = {1664-302X},
	author = {Adams, M. M. and Hoarfrost, A. L. and Bose, A. and Joye, S. B. and Girguis, P. R.}
}
@article {511006,
	title = {Assessing the influence of physical, geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys.},
	journal = {Geobiology},
	volume = {11},
	number = {3},
	year = {2013},
	note = {<p>123ZATimes Cited:1Cited References Count:101</p>},
	month = {May},
	pages = {279-293},
	abstract = {<p>Chemosynthetic primary production supports hydrothermal vent ecosystems, but the extent of that productivity and its governing factors have not been well constrained. To better understand anaerobic primary production within massive vent deposits, we conducted a series of incubations at 4, 25, 50 and 90 degrees C using aggregates recovered from hydrothermal vent structures. We documented in situ geochemistry, measured autochthonous organic carbon stable isotope ratios and assessed microbial community composition and functional gene abundances in three hydrothermal vent chimney structures from Middle Valley on the Juan de Fuca Ridge. Carbon fixation rates were greatest at lower temperatures and were comparable among chimneys. Stable isotope ratios of autochthonous organic carbon were consistent with the CalvinBensonBassham cycle being the predominant mode of carbon fixation for all three chimneys. Chimneys exhibited marked differences in vent fluid geochemistry and microbial community composition, with structures being differentially dominated by gamma () or epsilon (epsilon) proteobacteria. Similarly, qPCR analyses of functional genes representing different carbon fixation pathways showed striking differences in gene abundance among chimney structures. Carbon fixation rates showed no obvious correlation with observed in situ vent fluid geochemistry, community composition or functional gene abundance. Together, these data reveal that (i) net anaerobic carbon fixation rates among these chimneys are elevated at lower temperatures, (ii) clear differences in community composition and gene abundance exist among chimney structures, and (iii) tremendous spatial heterogeneity within these environments likely confounds efforts to relate the observed rates to in situ microbial and geochemical factors. We also posit that microbes typically thought to be mesophiles are likely active and growing at cooler temperatures, and that their activity at these temperatures comprises the majority of endolithic anaerobic primary production in hydrothermal vent chimneys.</p>},
	keywords = {autotrophic carbon fixation, chemoautotrophic symbionts, de-fuca ridge, east pacific rise, epsilon-proteobacteria, flank crustal fluids, low-temperature, mid-atlantic ridge, riftia-pachyptila, sulfur-oxidizing chemolithoautotroph},
	isbn = {1472-4677},
	author = {Olins, H. C. and Rogers, D. R. and Frank, K. L. and Vidoudez, C. and Girguis, P. R.}
}
@article {510961,
	title = {Autonomous Application of Quantitative PCR in the Deep Sea: In Situ Surveys of Aerobic Methanotrophs Using the Deep-Sea Environmental Sample Processor},
	journal = {Environmental Science \& Technology},
	volume = {47},
	number = {16},
	year = {2013},
	note = {<p>205VATimes Cited:2Cited References Count:24</p>},
	month = {Aug 20},
	pages = {9339-9346},
	abstract = {<p>Recent advances in ocean observing systems and genomic technologies have led to the development of the deep-sea environmental sample processor (D-ESP). The DESP filters particulates from seawater at depths up to 4000 m and applies a variety of molecular assays to the particulates, including quantitative PCR (qPCR), to identify particular organisms and genes in situ. Preserved samples enable laboratory-based validation of in situ results and expanded studies of genomic diversity and gene expression. Tests of the D-ESP at a methane-rich mound in the Santa Monica Basin centered on detection of 16S rRNA and particulate methane monooxygenase (pmoA) genes for two putative aerobic methanotrophs. Comparison of in situ qPCR results with laboratory-based assays of preserved samples demonstrates the D-ESP generated high-quality qPCR data while operating autonomously on the seafloor. Levels of 16S rRNA and pmoA cDNA detected in preserved samples are consistent with an active community of aerobic methanotrophs near the methane-rich mound. These findings are substantiated at low methane sites off Point Conception and in Monterey Bay where target genes are at or below detection limits. Successful deployment of the D-ESP is a major step toward developing autonomous systems to facilitate a wide range of marine microbiological investigations.</p>},
	keywords = {esp, harmful algae, oxygen minimum zone, remote detection},
	isbn = {0013-936X},
	author = {Ussler, W. and Preston, C. and Tavormina, P. and Pargett, D. and Jensen, S. and Roman, B. and Marin, R. and Shah, S. R. and Girguis, P. R. and Birch, J. M. and Orphan, V. and Scholin, C.}
}
@article {510986,
	title = {Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers},
	journal = {Environmental Science \& Technology},
	volume = {47},
	number = {9},
	year = {2013},
	note = {<p>141WATimes Cited:2Cited References Count:36</p>},
	month = {May 7},
	pages = {4399-4407},
	abstract = {<p>Microbes play a key role in mediating aquatic biogeochemical cycles. However, our understanding of the relationships between microbial phylogenetic/physiological diversity and habitat physicochemical characteristics is restrained by our limited capacity to concurrently collect microbial and geochemical samples at appropriate spatial and temporal scales. Accordingly, we have developed a low-cost, continuous fluid sampling system (the Biological OsmoSampling System, or BOSS) to address this limitation. The BOSS does not use electricity, can be deployed in harsh/remote environments, and collects/preserves samples with daily resolution for \&gt;1 year. Here, we present data on the efficacy of DNA and protein preservation during a 1.5 year laboratory study as well as the results of two field deployments at deep-sea hydrothermal vents, wherein we examined changes in microbial diversity, protein expression, and geochemistry over time. Our data reveal marked changes in microbial composition co-occurring with changes in hydrothermal fluid composition as well as the temporal dynamics of an enigmatic sulfide-oxidizing symbiont in its free-living state. We also present the first data on in situ protein preservation and expression dynamics highlighting the BOSS{\textquoteright}s potential utility in meta-proteomic studies. These data illustrate the value of using BOSS to study relationships among microbial and geochemical phenomena and environmental conditions.</p>},
	keywords = {bacterial, diversity, dominance, field, growth, high-resolution, mid-atlantic ridge, population-dynamics, quantification},
	isbn = {0013-936X},
	author = {Robidart, J. and Callister, S. J. and Song, P. F. and Nicora, C. D. and Wheat, C. G. and Girguis, P. R.}
}
@article {511016,
	title = {Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents.},
	journal = {ISME Journal},
	volume = {7},
	number = {7},
	year = {2013},
	note = {<p>170LMTimes Cited:5Cited References Count:70</p>},
	month = {Jul},
	pages = {1391-1401},
	abstract = {<p>Few studies have directly measured sulfate reduction at hydrothermal vents, and relatively little is known about how environmental or ecological factors influence rates of sulfate reduction in vent environments. A better understanding of microbially mediated sulfate reduction in hydrothermal vent ecosystems may be achieved by integrating ecological and geochemical data with metabolic rate measurements. Here we present rates of microbially mediated sulfate reduction from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. Maximum rates of sulfate reduction occurred at 90 degrees C in all three deposits. Pyrosequencing and functional gene abundance data revealed differences in both biomass and community composition among sites, including differences in the abundance of known sulfate-reducing bacteria. The abundance of sequences for Thermodesulfovibro-like organisms and higher sulfate reduction rates at elevated temperatures suggests that Thermodesulfovibro-like organisms may have a role in sulfate reduction in warmer environments. The rates of sulfate reduction presented here suggest that-within anaerobic niches of hydrothermal deposits-heterotrophic sulfate reduction may be quite common and might contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents.</p>},
	keywords = {anaerobic oxidation, dissolved organic-carbon, epsilon-proteobacteria, estuarine sediments, guaymas basin, hydrothermal vent, microbial ecology, molecular characterization, phylogenetic diversity, primary productivity, reducing bacteria, ribosomal-rna analysis, sp-nov., sulfate reduction},
	isbn = {1751-7362},
	author = {Frank, K. L. and Rogers, D. R. and Olins, H. C. and Vidoudez, C. and Girguis, P. R.}
}
@article {510956,
	title = {Characterizing the Distribution of Methane Sources and Cycling in the Deep Sea via in Situ Stable Isotope Analysis},
	journal = {Environmental Science \& Technology},
	volume = {47},
	number = {3},
	year = {2013},
	note = {<p>086HUTimes Cited:4Cited References Count:54</p>},
	month = {Feb 5},
	pages = {1478-1486},
	abstract = {<p>The capacity to make in situ geo-referenced measurements of methane concentration and stable isotopic composition (delta C-13(CH4)) would greatly improve our understanding of the distribution and type of methane sources in the environment, allow refined determination of the extent to which microbial production and consumption contributes to methane cycling, and enable the testing of hypotheses about the sensitivity of methane cycling to changes in environmental conditions. In particular, characterizing biogeochemical methane cycling dynamics in the deep ocean is hampered by a number of challenges, especially in environments where high methane concentrations preclude intact recovery of undisturbed samples. To that end, we have developed an in situ analyzer capable of delta C-13(CH4) measurements in the deep ocean. Here we present data from laboratory and field studies in which we characterize the instrument{\textquoteright}s analytical capabilities and performance and provide the first in situ stable isotope based characterization of the influence of anaerobic methane oxidation on methane flux from seep sediments. These data illustrate how in situ measurements can permit finer-scale analyses of variations in AOM activity, and facilitate advances in using delta C-13(CH4) and other isotopic systems to interrogate biogeochemical cycles in the deep sea and other remote or challenging environments.</p>},
	keywords = {anaerobic oxidation, carbon-dioxide, cavity-output spectroscopy, dissolved-gases, inlet mass-spectrometry, laser absorption spectrometer, monterey-bay, n2o isotopomers, organic-compounds, quantum-cascade laser},
	isbn = {0013-936X},
	author = {Wankel, S. D. and Huang, Y. W. and Gupta, M. and Provencal, R. and Leen, J. B. and Fahrland, A. and Vidoudez, C. and Girguis, P. R.}
}
@proceedings {511001,
	title = {Deep Water Instrument for Microbial Identification, Quantification, and Archiving},
	year = {2013},
	note = {<p>Ba3erTimes Cited:0Cited References Count:8Oceans-Ieee</p>},
	abstract = {<p>A deep ocean robotic platform capable of in situ microbial identification and quantification at depths to 4000 m has been developed. The platform is a free benthic lander, containing a low pressure microbial instrument and deep ocean sampling systems that can monitor and collect raw seawater from multiple sources, then decompress the raw seawater for processing by the detection instrument. This has enabled the autonomous collection, processing, and archiving of microbes from multiple sites. This allows for direct, time correlated comparison of different microbial populations along with the seawater physical and chemical composition.</p>},
	keywords = {autonomous sampling, deep ocean, ecogenomic sensor, harmful algae, in situ instrumentation, remote detection, sample processor esp},
	isbn = {0197-7385},
	author = {Pargett, D. M. and Jensen, S. D. and Roman, B. A. and Preston, C. M. and Ussler, W. and Girguis, P. R. and Marin, R. and Birch, J. M. and Scholin, C. A.}
}
@article {511021,
	title = {Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments},
	journal = {Frontiers in Microbiology},
	volume = {4},
	year = {2013},
	note = {<p>Ab1kqTimes Cited:4Cited References Count:53</p>},
	month = {Dec 12},
	abstract = {<p>Marine hydrocarbon seeps are ecosystems that are rich in methane, and, in some cases, short-chain (C-2-C-5) and longer alkanes. C-2-C-4 alkanes such as ethane, propane, and butane can be significant components of seeping fluids. Some sulfate-reducing microbes oxidize short-chain alkanes anaerobically, and may play an important role in both the competition for sulfate and the local carbon budget. To better understand the anaerobic oxidation of short-chain n-alkanes coupled with sulfate-reduction, hydrocarbon-rich sediments from the Gulf of Mexico (GoM) were amended with artificial, sulfate-replete seawater and one of four n-alkanes (C-1-C-4) then incubated under strict anaerobic conditions. Measured rates of alkane oxidation and sulfate reduction closely follow stoichiometric predictions that assume the complete oxidation of alkanes to CO2 (though other sinks for alkane carbon likely exist). Changes in the delta C-13 of all the alkanes in the reactors show enrichment over the course of the incubation, with the C-3 and C-4 incubations showing the greatest enrichment (4.4 and 4.5 parts per thousand, respectively). The concurrent depletion in the delta C-13 of dissolved inorganic carbon (DIC) implies a transfer of carbon from the alkane to the DIC pool (-3.5 and -6.7 parts per thousand for C-3 and C-4 incubations, respectively). Microbial community analyses reveal that certain members of the class Deltaproteobacteria are selectively enriched as the incubations degrade C-1-C-4 alkanes. Phylogenetic analyses indicate that distinct phylotypes are enriched in the ethane reactors, while phylotypes in the propane and butane reactors align with previously identified C-3-C-4 alkane-oxidizing sulfate-reducers. These data further constrain the potential influence of alkane oxidation on sulfate reduction rates (SRRs) in cold hydrocarbon-rich sediments, provide insight into their contribution to local carbon cycling, and illustrate the extent to which short-chain alkanes can serve as electron donors and govern microbial community composition and density.</p>},
	keywords = {16s ribosomal-rna, anaerobic oxidation, butane, c-1-c-4 hydrocarbons, cold seeps, ethane, gas hydrate, gulf of mexico, gulf-of-mexico, methane, methane oxidation, microbial diversity, microbial sulfate reduction, phylogenetic analysis, propane, reducing bacteria, short-chain alkanes, spectrophotometric determination},
	isbn = {1664-302X},
	author = {Bose, A. and Rogers, D. R. and Adams, M. M. and Joye, S. B. and Girguis, P. R.}
}
@article {510966,
	title = {Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin},
	journal = {Frontiers in Microbiology},
	volume = {4},
	year = {2013},
	note = {<p>Aa3pxTimes Cited:2Cited References Count:60</p>},
	month = {Mar 27},
	abstract = {<p>The East Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. We studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila, and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. alpha-proteobacteria, epsilon-proteobacteria, and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (\&lt;90\% sequence similarity) to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing alpha-proteobacteria, gamma-proteobacteria, and epsilon-proteobacteria, while the interior of one chimney is dominated by putative sulfur-reducing delta-proteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.</p>},
	keywords = {back-arc basin, bacteroidetes, basalt, community diversity, deep-sea, east pacific rise, epsilon-proteobacteria, geomicrobiology, hydrothermal, hydrothermal plume, inactive sulfides, microbial diversity, oxidizing bacteria, sea-floor basalt, sp-nov.},
	isbn = {1664-302X},
	author = {Sylvan, J. B. and Sia, T. Y. and Haddad, A. G. and Briscoe, L. J. and Toner, B. M. and Girguis, P. R. and Edwards, K. J.}
}
@article {510981,
	title = {Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts},
	journal = {ISME Journal},
	volume = {7},
	number = {8},
	year = {2013},
	note = {<p>187LFTimes Cited:6Cited References Count:67</p>},
	month = {Aug},
	pages = {1556-1567},
	abstract = {<p>Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host-symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts{\textquoteright} metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts{\textquoteright} interaction with regional-scale differences in geochemistry.</p>},
	keywords = {alviniconcha, Bacteria, calyptogena-magnifica, chemoautotrophy, deep-sea vents, escherichia-coli, gene-expression, genome, hydrothermal vents, metatranscriptomics, nitrate respiration, riftia-pachyptila endosymbiont, sulfurimonas-denitrificans, symbiosis, tube worm},
	isbn = {1751-7362},
	author = {Sanders, J. G. and Beinart, R. A. and Stewart, F. J. and Delong, E. F. and Girguis, P. R.}
}
@article {510971,
	title = {Oxygen, ecology, and the Cambrian radiation of animals},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {110},
	number = {33},
	year = {2013},
	note = {<p>200LATimes Cited:13Cited References Count:57</p>},
	month = {Aug 13},
	pages = {13446-13451},
	abstract = {<p>The Proterozoic-Cambrian transition records the appearance of essentially all animal body plans (phyla), yet to date no single hypothesis adequately explains both the timing of the event and the evident increase in diversity and disparity. Ecological triggers focused on escalatory predator-prey "arms races" can explain the evolutionary pattern but not its timing, whereas environmental triggers, particularly ocean/atmosphere oxygenation, do the reverse. Using modern oxygen minimum zones as an analog for Proterozoic oceans, we explore the effect of low oxygen levels on the feeding ecology of polychaetes, the dominant macrofaunal animals in deep-sea sediments. Here we show that low oxygen is clearly linked to low proportions of carnivores in a community and low diversity of carnivorous taxa, whereas higher oxygen levels support more complex food webs. The recognition of a physiological control on carnivory therefore links environmental triggers and ecological drivers, providing an integrated explanation for both the pattern and timing of Cambrian animal radiation.</p>},
	keywords = {bathyal macrofauna, Community structure, continental-margin, diversity, ediacaran, Evolution, hypoxia, life, metazoa, minimum zone, organic-matter, origin},
	isbn = {0027-8424},
	author = {Sperling, E. A. and Frieder, C. A. and Raman, A. V. and Girguis, P. R. and Levin, L. A. and Knoll, A. H.}
}
@article {510991,
	title = {Redox effects on the microbial degradation of refractory organic matter in marine sediments},
	journal = {Geochimica Et Cosmochimica Acta},
	volume = {121},
	year = {2013},
	note = {<p>226ZRTimes Cited:0Cited References Count:91</p>},
	month = {Nov 15},
	pages = {582-598},
	abstract = {<p>Microbially mediated reduction-oxidation (redox) reactions are often invoked as being the mechanisms by which redox state influences the degradation of sedimentary organic matter (OM) in the marine environment. To evaluate the effects of elevated, oscillating and reduced redox potentials on the fate of primarily aged, mineral-adsorbed OM contained in continental shelf sediments, we used microbial fuel cells to control redox state within and around marine sediments, without amending the sediments with reducing or oxidizing substances. We subsequently followed electron fluxes in the redox elevated and redox oscillating treatments, and related sediment chemical, isotopic and bacterial community changes to redox conditions over a 748-day experimental period.The electron fluxes of the elevated and oscillating redox cells were consistent with models of organic carbon (OC) oxidation with time-dependent first-order rate constants declining from 0.023 to 0.005 y(-1), in agreement with rate constants derived from typical OC profiles and down core ages of offshore sediments, or from sulfate reduction rate measurements in similar sediments. Moreover, although cumulative electron fluxes were higher in the continuously elevated redox treatment, incremental rates of electron harvesting in the two treatments converged over the 2 year experiment. These similar rates were reflected in chemical indicators of OM metabolism such as dissolved OC and ammonia, and particulate OC concentrations, which were not significantly different among all treatments and controls over the experimental time-scale. In contrast, products of carbonate and opal dissolution and metal mobilization showed greater enrichments in sediments with elevated and oscillating redox states.Microbial community composition in anode biofilms and surrounding sediments was assessed via high-throughput 16S rRNA gene sequencing, and these analyses revealed that the elevated and oscillatory redox treatments led to the enrichment of Deltaproteobacteria on the sediment-hosted anodes over time. Many Deltaproteobacteria are capable of using electrodes as terminal electron acceptors to completely oxidize organic substrates. Notably, Deltaproteobacteria were not measurably enriched in the sediments adjacent to anodes, suggesting that - in these experiments - electron-shuttling bacterial networks did not radiate out away from the electrodes, affecting millimeters or centimeters of sediment. Rather, microbial phylotypes allied to the Clostridia appeared to dominate in the sediment amongst all treatments, and likely played essential roles in converting complex dissolved and particulate sources of OM to simple fermentation products. Thus, we advance that the rate at which fermentation products are generated and migrate to oxidation fronts is what limits the remineralization of OM in many subsurface sediments removed from molecular oxygen. This is a diagenetic scenario that is consistent with the discharging behavior of redox oscillating sediment MFCs. It is also compatible with hypotheses that molecular O-2 - and not just the resulting elevated redox potential - may be required to effectively catalyze the degradation of refractory OM. Such decomposition reactions have been suggested to depend on substrate interactions with highly reactive oxygen- containing radicals and/or with specialized extracellular enzymes produced by aerobic prokaryotic or eukaryotic cells. (c) 2013 Elsevier Ltd. All rights reserved.</p>},
	keywords = {carbon preservation, communities, continental-margin sediments, energy, extracellular electron-transfer, fuel-cells, hydrogen sulfide, oxygen, sea-floor, shelf sediments},
	isbn = {0016-7037},
	author = {Reimers, C. E. and Alleau, Y. and Bauer, J. E. and Delaney, J. and Girguis, P. R. and Schrader, P. S. and Stecher, H. A.}
}
@article {511011,
	title = {Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase},
	journal = {Genes \& Development},
	volume = {27},
	number = {8},
	year = {2013},
	note = {<p>134NBTimes Cited:11Cited References Count:61</p>},
	month = {Apr 15},
	pages = {887-899},
	abstract = {<p>Bacillus subtilis forms organized multicellular communities known as biofilms wherein the individual cells are held together by a self-produced extracellular matrix. The environmental signals that promote matrix synthesis remain largely unknown. We discovered that one such signal is impaired respiration. Specifically, high oxygen levels suppressed synthesis of the extracellular matrix. In contrast, low oxygen levels, in the absence of an alternative electron acceptor, led to increased matrix production. The response to impaired respiration was blocked in a mutant lacking cytochromes caa(3) and bc and markedly reduced in a mutant lacking kinase KinB. Mass spectrometry of proteins associated with KinB showed that the kinase was in a complex with multiple components of the aerobic respiratory chain. We propose that KinB is activated via a redox switch involving interaction of its second transmembrane segment with one or more cytochromes under conditions of reduced electron transport. In addition, a second kinase (KinA) contributes to the response to impaired respiration. Evidence suggests that KinA is activated by a decrease in the nicotinamide adenine dinucleotide (NAD(+))/NADH ratio via binding of NAD(+) to the kinase in a PAS domain A-dependent manner. Thus, B. subtilis switches from a unicellular to a multicellular state by two pathways that independently respond to conditions of impaired respiration.</p>},
	keywords = {activation, amyloid fibers, Bacillus subtilis, biofilm formation, biofilms, cytochromes, gene-expression, histidine kinase, initiation, master regulator, phosphorelay, Respiration, saccharomyces-cerevisiae, sensor kinase, sporulation},
	isbn = {0890-9369},
	author = {Kolodkin-Gal, I. and Elsholz, A. K. W. and Muth, C. and Girguis, P. R. and Kolter, R. and Losick, R.}
}
@article {510976,
	title = {Sensors and Acoustic Modems Powered by Benthic Microbial Fuel Cells at the MARS Observatory},
	journal = {2013 Oceans - San Diego},
	year = {2013},
	note = {<p>Ba3erTimes Cited:0Cited References Count:14Oceans-Ieee</p>},
	abstract = {<p>The goals of this project were three-fold: 1) to power underwater instruments with energy harvested from deep sea, organic poor sediments using Benthic Microbial Fuel Cells (BMFCs); 2) to relay instrument data acoustically -and in near-real time-through a cabled seafloor observatory or surface vessel, as appropriate; and 3) to characterize the operational performance of these interactive systems during in situ deployments. Two BMFC-underwater sensing/communications packages were demonstrated near the Monterey Accelerated Research System (MARS) observatory in Monterey Bay, California. MARS is a cabled observatory that resides in deep water (similar to 890 m), about 37 km (23 miles) seaward of the Monterey Bay Aquarium Research Institute (MBARI).The BMFCs were constructed using a cylindrical chamber design with a 0.28 m(2) footprint. Each BMFC was used to power an Aanderaa dissolved O-2/temperature or conductivity/temperature sensor, as well as a Teledyne Benthos compact acoustic modem which contained an integrated power management platform (PMP) for the complete system. The packages were deployed from a surface vessel and allowed to descend freely to the seafloor, at locations approximately 0.5 km away from the MARS node, at depths of 863 and 895 m. The PMPs were programmed to record data from both the sensors and the BMFC (whole cell voltage, capacitor voltage, and battery voltage) on an hourly basis, and to monitor overall microbial fuel cell energy production on a daily basis. Post-deployment, BMFC 1 generated a net surplus of energy from days 98 through 166, and remained operational for 210 days. BMFC 2 began generating a surplus of energy on day 54 and remained operational for 158 days. Data recovered from the oceanographic sensors was transmitted acoustically over both the MARS node and to a research vessel, underscoring the utility of this technology.</p>},
	keywords = {benthic microbial fuel cells (bmfcs), deep water deployment, electricity, electrodes, energy, energy production, geobacter-sulfurreducens, microorganisms, monterey accelerated research system (mars) observatory},
	isbn = {0197-7385},
	author = {Schrader, P. S. and Doolan, C. and Reimers, C. E. and Girguis, P. R. and Wolf, M. and Green, D.}
}
@article {wankel2012anaerobic,
	title = {Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and decoupling from sulfate reduction},
	journal = {Environmental microbiology},
	volume = {14},
	year = {2012},
	pages = {2726{\textendash}2740},
	publisher = {Blackwell Publishing Ltd Oxford, UK},
	author = {Wankel, Scott D and Adams, Melissa M and Johnston, David T and Hansel, Colleen M and Joye, Samantha B and Girguis, Peter R.}
}
@conference {german2012being,
	title = {Being There \& Getting Back Again: Half a Century of Deep Ocean Research \& Discovery with the Human Occupied Vehicle" Alvin"},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {OS53E{\textendash}06},
	author = {German, CR and Fornari, DJ and Fryer, P and Girguis, P. R. and Humphris, S. E. and Kelley, DS and Tivey, M and Van Dover, C. L. and Von Damm, K}
}
@conference {adams2012distribution,
	title = {Distribution, activity and function of short-chain alkane degrading phylotypes in hydrothermal vent sediments},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B43G{\textendash}0497},
	author = {Adams, M. M. and Joye, S. B. and Hoarfrost, A and Girguis, P. R.}
}
@article {gardel2012duty,
	title = {Duty cycling influences current generation in multi-anode environmental microbial fuel cells},
	journal = {Environmental science \& technology},
	volume = {46},
	year = {2012},
	pages = {5222{\textendash}5229},
	publisher = {American Chemical Society},
	author = {Gardel, Emily J and Nielsen, Mark E and Grisdela Jr, Phillip T and Girguis, Peter R.}
}
@article {beinart2012evidence,
	title = {Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {109},
	year = {2012},
	pages = {E3241{\textendash}E3250},
	publisher = {National Academy of Sciences},
	author = {Beinart, Roxanne A and Sanders, Jon G and Faure, Baptiste and Sylva, Sean P and Lee, Raymond W and Becker, Erin L and Gartman, Amy and Luther, George W and Seewald, Jeffrey S and Fisher, Charles R and others}
}
@article {dilly2012exploring,
	title = {Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {279},
	year = {2012},
	pages = {3347{\textendash}3356},
	publisher = {The Royal Society},
	author = {Dilly, Geoffrey F and Young, C Robert and Lane, William S and Pangilinan, Jasmyn and Girguis, Peter R.}
}
@conference {dilly2012exploring,
	title = {Exploring the limit of metazoan thermal tolerance via comparative proteomics: Thermally induced expression shifts in hydrothermal vent polychaetes P. sulfincola and P. palmiformis},
	booktitle = {INTEGRATIVE AND COMPARATIVE BIOLOGY},
	volume = {52},
	year = {2012},
	pages = {E47{\textendash}E47},
	publisher = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	organization = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	author = {Dilly, G. F. and Young, C. R. and Lane, W. S. and Pangalinan, J and Girguis, P. R.}
}
@article {nyholm2012expression,
	title = {Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae},
	journal = {PloS one},
	volume = {7},
	year = {2012},
	pages = {e38267},
	publisher = {Public Library of Science},
	author = {Nyholm, Spencer V. and Song, Pengfei and Dang, Jeanne and Bunce, Corey and Girguis, Peter R.}
}
@article {nyholm2012expression,
	title = {Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the},
	year = {2012},
	author = {Nyholm, S. V. and Song, P. and Dang, J and Bunce, C. and Girguis, P. R.}
}
@conference {beinart2012isotopic,
	title = {Isotopic Approaches to Allying Productivity and Sulfur Metabolism in Three Symbiotic Hydrothermal Vent Molluscs},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B43L{\textendash}08},
	author = {Beinart, R. and Gartman, A. and Sanders, J. G. and Luther, G. W. and Girguis, P. R.}
}
@conference {frank2012key,
	title = {Key factors influencing rates of heterotrophic sulfate reduction in hydrothermal massive sulfide deposits},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B43G{\textendash}0498},
	author = {Frank, K. L. and Rogers, D and Girguis, P. R.}
}
@conference {breier2012linking,
	title = {Linking hydrothermal plume geochemistry with deep-sea microbial community structure along the Eastern Lau Spreading Center},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B44B{\textendash}05},
	author = {Breier, JA and Toner, B. M. and Sheik, C and Anantharaman, K and Sylvan, J. B. and Edwards, K. J. and Girguis, P. R. and Wendt, K and Sorensen, J and Madison, A and others}
}
@article {tivey2012links,
	title = {Links from mantle to microbe at the Lau Integrated Study Site: Insights from a back-arc spreading center},
	journal = {Oceanography},
	volume = {25},
	year = {2012},
	pages = {62{\textendash}77},
	publisher = {The Oceanography Society},
	author = {Tivey, Margaret K and Becker, Erin and Beinart, Roxanne and Fisher, Charles R and Girguis, Peter R. and Langmuir, Charles H and Michael, Peter J and Reysenbach, Anna-Louise}
}
@conference {meyer2012microbial,
	title = {Microbial life in cold, hydrologically active oceanic crustal fluids},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B42C{\textendash}05},
	author = {Meyer, JL and Jaekel, U and Girguis, P. R. and Glazer, BT and Huber, JA}
}
@conference {olins2012microbial,
	title = {Microbial Primary Productivity in Hydrothermal Vent Chimneys at Middle Valley, Juan de Fuca Ridge},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B43G{\textendash}0496},
	author = {Olins, H. C. and Rogers, D and Frank, K. L. and Girguis, P. R. and Vidoudez, C.}
}
@article {girguis2012potential,
	title = {On the potential for bioenergy and biofuels from hydrothermal vent microbes},
	journal = {Oceanography},
	volume = {25},
	year = {2012},
	pages = {213{\textendash}217},
	publisher = {Oceanography Society},
	author = {Girguis, Peter R. and Holden, James F}
}
@conference {jaekel2012transformations,
	title = {Transformations of organic matter in the deep biosphere at North Pond},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2012},
	year = {2012},
	pages = {B43G{\textendash}0486},
	author = {Jaekel, U and Dittmar, T and Meyer, JL and Huber, JA and Glazer, BT and Girguis, P. R.}
}
@article {511031,
	title = {Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and decoupling from sulfate reduction},
	journal = {Environmental Microbiology },
	volume = {14},
	number = {10},
	year = {2012},
	note = {<p>Sp. Iss. SI015KYTimes Cited:10Cited References Count:71</p>},
	month = {Oct},
	pages = {2726-2740},
	abstract = {<p>The anaerobic oxidation of methane (AOM) is a globally significant sink that regulates methane flux from sediments into the oceans and atmosphere. Here we examine mesophilic to thermophilic AOM in hydrothermal sediments recovered from the Middle Valley vent field, on the Juan de Fuca Ridge. Using continuous-flow sediment bioreactors and batch incubations, we characterized (i) the degree to which AOM contributes to net dissolved inorganic carbon flux, (ii) AOM and sulfate reduction (SR) rates as a function of temperature and (iii) the distribution and density of known anaerobic methanotrophs (ANMEs). In sediment bioreactors, inorganic carbon stable isotope mass balances results indicated that AOM accounted for between 16\% and 86\% of the inorganic carbon produced, underscoring the role of AOM in governing inorganic carbon flux from these sediments. At 90 degrees C, AOM occurred in the absence of SR, demonstrating a striking decoupling of AOM from SR. An abundance of Fe(III)-bearing minerals resembling mixed valent Fe oxides, such as green rust, suggests the potential for a coupling of AOM to Fe(III) reduction in these metalliferous sediments. While SR bacteria were only observed in cooler temperature sediments, ANMEs allied to ANME-1 ribotypes, including a putative ANME-1c group, were found across all temperature regimes and represented a substantial proportion of the archaeal community. In concert, these results extend and reshape our understanding of the nature of high temperature methane biogeochemistry, providing insight into the physiology and ecology of thermophilic anaerobic methanotrophy and suggesting that AOM may play a central role in regulating biological dissolved inorganic carbon fluxes to the deep ocean from the organic-poor, metalliferous sediments of the global mid-ocean ridge hydrothermal vent system.</p>},
	keywords = {de-fuca ridge, guaymas basin, gulf-of-mexico, in-vitro, marine-sediments, middle valley, molecular-weight hydrocarbons, organic-matter, reducing bacteria, skagerrak denmark},
	isbn = {1462-2912},
	author = {Wankel, S. D. and Adams, M. M. and Johnston, D. T. and Hansel, C. M. and Joye, S. B. and Girguis, P. R.}
}
@article {511056,
	title = {Duty Cycling Influences Current Generation in Multi-Anode Environmental Microbial Fuel Cells.},
	journal = {Environmental Science \& Technology},
	volume = {46},
	number = {9},
	year = {2012},
	note = {<p>933GOTimes Cited:9Cited References Count:66</p>},
	month = {May 1},
	pages = {5222-5229},
	abstract = {<p>Improving microbial fuel cell (MFC) performance continues to be the subject of research, yet the role of operating conditions, specifically duty cycling, on MFC performance has been modestly addressed. We present a series of studies in which we use a 15-anode environmental MFC to explore how duty cycling (variations in the time an anode is connected) influences cumulative charge, current, and microbial composition. The data reveal particular switching intervals that result in the greatest time-normalized current. When disconnection times are sufficiently short, there is a striking decrease in current due to an increase in the overall electrode reaction resistance. This was observed over a number of whole cell potentials. Based on these results, we posit that replenishment of depleted electron donors within the biofilm and surrounding diffusion layer is necessary for maximum charge transfer, and that proton flux may be not limiting in the highly buffered aqueous phases that are common among environmental MFCs. Surprisingly, microbial diversity analyses found no discernible difference in gross community composition among duty cycling treatments, suggesting that duty cycling itself has little or no effect. Such duty cycling experiments are valuable in determining which factors govern performance of bioelectrochemical systems and might also be used to optimize field-deployed systems.</p>},
	keywords = {biofuel cells, communities, elemental sulfur, extracellular electron-transfer, geobacter-sulfurreducens, harvesting electricity, power-generation, sediment, sulfate-reducing bacteria, waste-water treatment},
	isbn = {0013-936X},
	author = {Gardel, E. J. and Nielsen, M. E. and Grisdela, P. T. and Girguis, P. R.}
}
@article {511066,
	title = {Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	number = {47},
	year = {2012},
	note = {<p>049PZTimes Cited:11Cited References Count:88</p>},
	month = {Nov 20},
	pages = {E3241-E3250},
	abstract = {<p>Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus Alviniconcha) in the Lau Basin. We extensively surveyed Alviniconcha holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one epsilon-proteobacteria and two gamma-proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with epsilon-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with gamma-proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.</p>},
	keywords = {chemoautotrophic symbionts, chemoautotrophy, Community structure, east pacific rise, endosymbiosis, epsilon-proteobacteria, host-plant use, lau-spreading-center, mussel bathymodiolus-thermophilus, riftia-pachyptila jones, rose garden vent, symbiosis, tube worm},
	isbn = {0027-8424},
	author = {Beinart, R. A. and Sanders, J. G. and Faure, B. and Sylva, S. P. and Lee, R. W. and Becker, E. L. and Gartman, A. and Luther, G. W. and Seewald, J. S. and Fisher, C. R. and Girguis, P. R.}
}
@article {511061,
	title = {Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes},
	journal = {Proceedings of the Royal Society B-Biological Sciences},
	volume = {279},
	number = {1741},
	year = {2012},
	note = {<p>973DQTimes Cited:8Cited References Count:53</p>},
	month = {Aug 22},
	pages = {3347-3356},
	abstract = {<p>Temperatures around hydrothermal vents are highly variable, ranging from near freezing up to 300 degrees C. Nevertheless, animals thrive around vents, some of which live near the known limits of animal thermotolerance. Paralvinella sulfincola, an extremely thermotolerant vent polychaete, and Paralvinella palmiformis, a cooler-adapted congener, are found along the Juan de Fuca Ridge in the northwestern Pacific. We conducted shipboard high-pressure thermotolerance experiments on both species to characterize the physiological adaptations underlying P. sulfincola{\textquoteright}s pronounced thermotolerance. Quantitative proteomics, expressed sequence tag (EST) libraries and glutathione assays revealed that P. sulfincola (i) exhibited an upregulation in the synthesis and recycling of glutathione with increasing temperature, (ii) downregulated nicotinamide adenine dinucleotide (NADH) and succinate dehydrogenases (key enzymes in oxidative phosphorylation) with increasing temperature, and (iii) maintained elevated levels of heat shock proteins (HSPs) across all treatments. In contrast, P. palmiformis exhibited more typical responses to increasing temperatures (e. g. increasing HSPs at higher temperatures). These data reveal differences in how a mesotolerant and extremely thermotolerant eukaryote respond to thermal stress, and suggest that P. sulfincola{\textquoteright}s capacity to mitigate oxidative stress via increased synthesis of antioxidants and decreased flux through the mitochondrial electron transport chain enable pronounced thermotolerance. Ultimately, oxidative stress may be the key factor in limiting all metazoan thermotolerance.</p>},
	keywords = {Animals, climate-change, fishes, Heat-Shock Proteins, hydrothermal vents, mitochondria, Molecular Chaperones, oxidative stress, oxygen limitation, paralvinella, proteomics, redox, temperature-dependent biogeography, thermotolerance},
	isbn = {0962-8452},
	author = {Dilly, G. F. and Young, C. R. and Lane, W. S. and Pangilinan, J. and Girguis, P. R.}
}
@article {511041,
	title = {Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae},
	journal = {Plos One},
	volume = {7},
	number = {6},
	year = {2012},
	note = {<p>959TUTimes Cited:3Cited References Count:86</p>},
	month = {Jun 11},
	abstract = {<p>The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular "dialogue{\textquoteright}{\textquoteright} between the partners that includes interactions between the host{\textquoteright}s innate immune system and the symbiont.</p>},
	keywords = {bacterial symbiosis, carbonic-anhydrase, chemoautotrophic symbionts, host, localization, metabolite uptake, recognition, sulfide binding, toll-like receptors, worm riftia-pachyptila},
	isbn = {1932-6203},
	author = {Nyholm, S. V. and Song, P. F. and Dang, J. N. and Bunce, C. and Girguis, P. R.}
}
@article {510996,
	title = {In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field},
	journal = {Environmental Microbiology},
	volume = {15},
	number = {5},
	year = {2012},
	note = {<p>Perner, MirjamGonnella, GiorgioHourdez, StephaneBohnke, StefanieKurtz, StefanGirguis, PeterengResearch Support, Non-U.S. Gov{\textquoteright}tEngland2012/11/23 06:00Environ Microbiol. 2013 May;15(5):1551-60. doi: 10.1111/1462-2920.12038. Epub 2012 Nov 22.</p>},
	month = {May},
	pages = {1551-60},
	abstract = {<p>We present data on the co-registered geochemistry (in situ mass spectrometry) and microbiology (pyrosequencing of 16S rRNA genes; V1, V2, V3 regions) in five fluid samples from Irina II in the Logatchev hydrothermal field. Two samples were collected over 24 min from the same spot and further three samples were from spatially distinct locations (20 cm, 3 m and the overlaying plume). Four low-temperature hydrothermal fluids from the Irina II are composed of the same core bacterial community, namely specific Gammaproteobacteria and Epsilonproteobacteria, which, however, differs in the relative abundance. The microbial composition of the fifth sample (plume) is considerably different. Although a significant correlation between sulfide enrichment and proportions of Sulfurovum (Epsilonproteobacteria) was found, no other significant linkages between abiotic factors, i.e. temperature, hydrogen, methane, sulfide and oxygen, and bacterial lineages were evident. Intriguingly, bacterial community compositions of some time series samples from the same spot were significantly more similar to a sample collected 20 cm away than to each other. Although this finding is based on three single samples only, it provides first hints that single hydrothermal fluid samples collected on a small spatial scale may also reflect unrecognized temporal variability. However, further studies are required to support this hypothesis.</p>},
	keywords = {*Biodiversity, Hydrogen-Ion Concentration, Hydrothermal Vents/*chemistry/*microbiology, Magnesium/analysis, Oxygen/analysis, Proteobacteria/genetics/isolation \& purification, RNA, Ribosomal, 16S/genetics, Seawater/*chemistry/*microbiology, Temperature, Time Factors},
	isbn = {1462-2920 (Electronic)1462-2912 (Linking)},
	author = {Perner, M. and Gonnella, G. and Hourdez, S. and Bohnke, S. and Kurtz, S. and Girguis, P.}
}
@article {511036,
	title = {Links from Mantle to Microbe at the Lau Integrated Study Site: Insights from a Back-Arc Spreading Center},
	journal = {Oceanography},
	volume = {25},
	number = {1},
	year = {2012},
	note = {<p>Sp. Iss. SI903DCTimes Cited:8Cited References Count:70</p>},
	month = {Mar},
	pages = {62-77},
	abstract = {<p>The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna.</p>},
	keywords = {basin, crustal structure, de-fuca ridge, east pacific rise, endeavor segment, flow, growth, rose garden vent, sea hydrothermal vents, Speciation},
	isbn = {1042-8275},
	author = {Tivey, M. K. and Becker, E. and Beinart, R. and Fisher, C. R. and Girguis, P. R. and Langmuir, C. H. and Michael, P. J. and Reysenbach, A. L.}
}
@article {511051,
	title = {On the Potential for Bioenergy and Biofuels from Hydrothermal Vent Microbes.},
	journal = {Oceanography},
	volume = {25},
	number = {1},
	year = {2012},
	note = {<p>Sp. Iss. SI903DCTimes Cited:2Cited References Count:17</p>},
	month = {Mar},
	pages = {213-217},
	keywords = {energy, fuel-cells},
	isbn = {1042-8275},
	author = {Girguis, P. R. and Holden, J. F.}
}
@article {gong2011benthic,
	title = {Benthic microbial fuel cell as direct power source for an acoustic modem and seawater oxygen/temperature sensor system},
	journal = {Environmental science \& technology},
	volume = {45},
	year = {2011},
	pages = {5047{\textendash}5053},
	publisher = {American Chemical Society},
	author = {Gong, Yanming and Radachowsky, Sage E and Michael Wolf and Nielsen, Mark E and Girguis, Peter R. and Reimers, Clare E}
}
@conference {nielsen2011characterizing,
	title = {Characterizing Electrosynthetic Microbial Production of Acetate},
	booktitle = {ECS Meeting Abstracts},
	year = {2011},
	pages = {144},
	publisher = {IOP Publishing},
	organization = {IOP Publishing},
	author = {Nielsen, Mark E and Peter Girguis}
}
@article {wankel2011influence,
	title = {Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids},
	journal = {Nature Geoscience},
	volume = {4},
	year = {2011},
	pages = {461{\textendash}468},
	publisher = {Nature Publishing Group},
	author = {Wankel, Scott D and Germanovich, Leonid N and Lilley, Marvin D and Genc, Gence and DiPerna, Christopher J and Bradley, Alexander S and Olson, Eric J and Girguis, Peter R.}
}
@article {robidart2011linking,
	title = {Linking hydrothermal geochemistry to organismal physiology: physiological versatility in Riftia pachyptila from sedimented and basalt-hosted vents},
	journal = {PLoS One},
	volume = {6},
	year = {2011},
	pages = {e21692},
	publisher = {Public Library of Science},
	author = {Robidart, Julie C. and Roque, Annelys and Song, Pengfei and Girguis, Peter R.}
}
@inbook {scott2011measuring,
	title = {Measuring isotope fractionation by autotrophic microorganisms and enzymes},
	booktitle = {Methods in Enzymology},
	volume = {494},
	year = {2011},
	pages = {281{\textendash}299},
	publisher = {Academic Press},
	organization = {Academic Press},
	author = {Scott, Kathleen M and Fox, Gordon and Girguis, Peter R.}
}
@article {rabaey2011metabolic,
	title = {Metabolic and practical considerations on microbial electrosynthesis},
	journal = {Current opinion in biotechnology},
	volume = {22},
	year = {2011},
	pages = {371{\textendash}377},
	publisher = {Elsevier Current Trends},
	author = {Rabaey, Korneel and Peter Girguis and Nielsen, Lars K}
}
@article {childress2011metabolic,
	title = {The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities},
	journal = {Journal of Experimental Biology},
	volume = {214},
	year = {2011},
	pages = {312{\textendash}325},
	publisher = {Company of Biologists},
	author = {Childress, J. J. and Girguis, Peter R.}
}
@booklet {girguis2011methane,
	title = {Methane-powered microbial fuel cells},
	year = {2011},
	note = {US Patent App. 12/994,598},
	author = {Peter Girguis and Reimers, Clare E}
}
@article {luther2011thermodynamics,
	title = {Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment},
	journal = {Frontiers in microbiology},
	volume = {2},
	year = {2011},
	pages = {62},
	publisher = {Frontiers},
	author = {Luther, George W and Findlay, Alyssa J and MacDonald, Daniel J and Owings, Shannon M and Hanson, Thomas E and Beinart, Roxanne A and Girguis, Peter R.}
}
@article {gong2011benthic,
	title = {Benthic microbial fuel cell as direct power source for an acoustic modem and seawater oxygen/temperature sensor system},
	journal = {Environmental science \& technology},
	volume = {45},
	year = {2011},
	pages = {5047{\textendash}5053},
	publisher = {American Chemical Society},
	author = {Gong, Yanming and Radachowsky, Sage E and Michael Wolf and Nielsen, Mark E and Girguis, Peter R. and Reimers, Clare E}
}
@conference {nielsen2011characterizing,
	title = {Characterizing Electrosynthetic Microbial Production of Acetate},
	booktitle = {ECS Meeting Abstracts},
	year = {2011},
	pages = {144},
	publisher = {IOP Publishing},
	organization = {IOP Publishing},
	author = {Nielsen, Mark E and Peter Girguis}
}
@article {petersen2011hydrogen,
	title = {Hydrogen is an energy source for hydrothermal vent symbioses},
	journal = {Nature},
	volume = {476},
	year = {2011},
	pages = {176{\textendash}180},
	publisher = {Nature Publishing Group},
	author = {Petersen, Jillian M and Zielinski, Frank U and Pape, Thomas and Seifert, Richard and Moraru, Cristina and Amann, Rudolf and Hourdez, Stephane and Girguis, Peter R. and Wankel, Scott D and Barbe, Valerie and others}
}
@conference {nielsen2011increased,
	title = {Increased carbon uptake in marine sediment enabled by naturally occurring electrical conductors},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2011},
	year = {2011},
	pages = {B43H{\textendash}08},
	author = {Nielsen, M. E. and Cahoon, DP and Girguis, P. R.}
}
@article {wankel2011influence,
	title = {Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids},
	journal = {Nature Geoscience},
	volume = {4},
	year = {2011},
	pages = {461{\textendash}468},
	publisher = {Nature Publishing Group},
	author = {Wankel, Scott D and Germanovich, Leonid N and Lilley, Marvin D and Genc, Gence and DiPerna, Christopher J and Bradley, Alexander S and Olson, Eric J and Girguis, Peter R.}
}
@conference {wankel2011influence,
	title = {Influence Of Subsurface Biosphere On Geochemical Fluxes From Diffuse Hydrothermal Fluids: Direct Measurement Of Subsurface Hydrogen Oxidation},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2011},
	year = {2011},
	pages = {B22A{\textendash}03},
	author = {Wankel, S. D. and Germanovich, L. N. and Lilley, M. D. and Genc, G. and DiPerna, C. J. and Bradley, A. S. and Olson, E. J. and Girguis, P. R.}
}
@article {robidart2011linking,
	title = {Linking hydrothermal geochemistry to organismal physiology: physiological versatility in Riftia pachyptila from sedimented and basalt-hosted vents},
	journal = {PLoS One},
	volume = {6},
	year = {2011},
	pages = {e21692},
	publisher = {Public Library of Science},
	author = {Robidart, Julie C. and Roque, Annelys and Song, Pengfei and Girguis, Peter R.}
}
@inbook {scott2011measuring,
	title = {Measuring isotope fractionation by autotrophic microorganisms and enzymes},
	booktitle = {Methods in Enzymology},
	volume = {494},
	year = {2011},
	pages = {281{\textendash}299},
	publisher = {Academic Press},
	organization = {Academic Press},
	author = {Scott, Kathleen M and Fox, Gordon and Girguis, Peter R.}
}
@article {rabaey2011metabolic,
	title = {Metabolic and practical considerations on microbial electrosynthesis},
	journal = {Current opinion in biotechnology},
	volume = {22},
	year = {2011},
	pages = {371{\textendash}377},
	publisher = {Elsevier Current Trends},
	author = {Rabaey, Korneel and Peter Girguis and Nielsen, Lars K}
}
@article {childress2011metabolic,
	title = {The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities},
	journal = {Journal of Experimental Biology},
	volume = {214},
	year = {2011},
	pages = {312{\textendash}325},
	publisher = {Company of Biologists},
	author = {Childress, J. J. and Girguis, Peter R.}
}
@booklet {girguis2011methane,
	title = {Methane-powered microbial fuel cells},
	year = {2011},
	note = {US Patent App. 12/994,598},
	author = {Peter Girguis and Reimers, Clare E}
}
@conference {sia2011microbiology,
	title = {Microbiology of Low Temperature Seafloor Deposits Along a Geochemical Gradient in Lau Basin},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2011},
	year = {2011},
	pages = {OS23B{\textendash}03},
	author = {Sia, T. Y. and Haddad, A and Briscoe, L. J. and Girguis, P. R. and Edwards, K. J. and others}
}
@conference {girguis2011nature,
	title = {Nature and extent of electrogenic microbial communities recovered from Juan de Fuca hydrothermal sulfides},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2011},
	year = {2011},
	pages = {V14C{\textendash}02},
	author = {Girguis, P. R. and Nielsen, M. E.}
}
@conference {frank2011physico,
	title = {Physico-chemical gradients within the hydrothermal chimney Roane define sharp boundaries for microbial community ecology},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2011},
	year = {2011},
	pages = {B22A{\textendash}06},
	author = {Frank, K. L. and Kelley, DS and Girguis, P. R.}
}
@article {gartman2011sulfide,
	title = {Sulfide oxidation across diffuse flow zones of hydrothermal vents},
	journal = {Aquatic Geochemistry},
	volume = {17},
	year = {2011},
	pages = {583{\textendash}601},
	publisher = {Springer Netherlands},
	author = {Gartman, Amy and Y{\"u}cel, Mustafa and Madison, Andrew S and Chu, David W and Ma, Shufen and Janzen, Christopher P and Becker, Erin L and Beinart, Roxanne A and Girguis, Peter R. and Luther, George W}
}
@article {luther2011thermodynamics,
	title = {Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment},
	journal = {Frontiers in microbiology},
	volume = {2},
	year = {2011},
	pages = {62},
	publisher = {Frontiers},
	author = {Luther, George W and Findlay, Alyssa J and MacDonald, Daniel J and Owings, Shannon M and Hanson, Thomas E and Beinart, Roxanne A and Girguis, Peter R.}
}
@article {511101,
	title = {Benthic Microbial Fuel Cell as Direct Power Source for an Acoustic Modem and Seawater Oxygen/Temperature Sensor System.},
	journal = {Environmental Science \& Technology},
	volume = {45},
	number = {11},
	year = {2011},
	note = {<p>771ADTimes Cited:18Cited References Count:36</p>},
	month = {Jun 1},
	pages = {5047-5053},
	abstract = {<p>Supported by the natural potential difference between anoxic sediment and oxic seawater, benthic microbial fuel cells (BMFCs) promise to be ideal power sources for certain low-power marine sensors and communication devices. In this study a chambered BMFC with a 0.25 m(2) footprint was used to power an acoustic modem interfaced with an oceanographic sensor that measures dissolved oxygen and temperature. The experiment was conducted in Yaquina Bay, Oregon over 50 days. Several improvements were made in the BMFC design and power management system based on lessons learned from earlier prototypes. The energy was harvested by a dynamic gain charge pump circuit that maintains a desired point on the BMFC{\textquoteright}s power curve and stores the energy in a 200 F supercapacitor. The system also used an ultralow power microcontroller and quartz clock to read the oxygen/temperature sensor hourly, store data with a time stamp, and perform daily polarizations. Data records were transmitted to the surface by the acoustic modem every 1-5 days after receiving an acoustic prompt from a surface hydrophone. After jump-starting energy production with supplemental macroalgae placed in the BMFC{\textquoteright}s anode chamber, the average power density of the BMFC adjusted to 44 mW/m(2) of seafloor area which is better than past demonstrations at this site. The highest power density was 158 mW/m(2), and the useful energy produced and stored was \&gt;= 1.7 times the energy required to operate the system.</p>},
	keywords = {anode, electricity production, energy, generation, in-situ, microorganisms, sea-floor},
	isbn = {0013-936X},
	author = {Gong, Y. M. and Radachowsky, S. E. and Wolf, M. and Nielsen, M. E. and Girguis, P. R. and Reimers, C. E.}
}
@article {511091,
	title = {Hydrogen is an energy source for hydrothermal vent symbioses.},
	journal = {Nature},
	volume = {476},
	number = {7359},
	year = {2011},
	note = {<p>805MUTimes Cited:47Cited References Count:48</p>},
	month = {Aug 11},
	pages = {176-180},
	abstract = {<p>The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.</p>},
	keywords = {Bacteria, dual symbiosis, fluids, h-2, membrane-bound hydrogenase, mid-atlantic ridge, molecular-hydrogen, mussels, riftia-pachyptila jones, tube worm},
	isbn = {0028-0836},
	author = {Petersen, J. M. and Zielinski, F. U. and Pape, T. and Seifert, R. and Moraru, C. and Amann, R. and Hourdez, S. and Girguis, P. R. and Wankel, S. D. and Barbe, V. and Pelletier, E. and Fink, D. and Borowski, C. and Bach, W. and Dubilier, N.}
}
@article {511071,
	title = {Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids},
	journal = {Nature Geoscience},
	volume = {4},
	number = {7},
	year = {2011},
	note = {<p>785PVTimes Cited:28Cited References Count:50</p>},
	month = {Jul},
	pages = {461-468},
	abstract = {<p>Hydrothermal vents along mid-ocean systems host unique, highly productive biological communities, based on microbial chemoautotrophy, that thrive on the sulphur, metals, nitrogen and carbon emitted from the vents into the deep ocean. Geochemical studies of vents have centred on analyses of high-temperature, focused hydrothermal vents, which exhibit very high flow rates and are generally considered too hot for microbial life. Geochemical fluxes and metabolic activity associated with habitable, lower temperature diffuse fluids remain poorly constrained. As a result, little is known about the extent to which microbial communities, particularly in the subsurface, influence geochemical flux from more diffuse flows. Here, we estimate the net flux of methane, carbon dioxide and hydrogen from diffuse and focused hydrothermal vents along the Juan de Fuca ridge, using an in situ mass spectrometer and flowmeter. We show that geochemical flux from diffuse vents can equal or exceed that emanating from hot, focused vents. Notably, hydrogen concentrations in fluids emerging from diffuse vents are 50\% to 80\% lower than predicted. We attribute the loss of hydrogen in diffuse vent fluids to microbial consumption in the subsurface, and suggest that subsurface microbial communities can significantly influence hydrothermal geochemical fluxes to the deep ocean.</p>},
	keywords = {de-fuca-ridge, east pacific rise, heat, isotopic evidence, main endeavor field, mass-spectrometry, riftia-pachyptila, sea-floor, temporal variability, vent fluids},
	isbn = {1752-0894},
	author = {Wankel, S. D. and Germanovich, L. N. and Lilley, M. D. and Genc, G. and DiPerna, C. J. and Bradley, A. S. and Olson, E. J. and Girguis, P. R.}
}
@article {511081,
	title = {Linking Hydrothermal Geochemistry to Organismal Physiology: Physiological Versatility in Riftia pachyptila from Sedimented and Basalt-hosted Vents},
	journal = {Plos One},
	volume = {6},
	number = {7},
	year = {2011},
	note = {<p>pgirguis@oeb.harvard.edu</p>},
	pages = {e21692, 1-12},
	abstract = {<p>Much of what is known regarding Riftia pachyptila physiology is based on the wealth of studies of tubeworms living at diffuse flows along the fast-spreading, basalt-hosted East Pacific Rise (EPR). These studies have collectively suggested that Riftia pachyptila and its chemoautotrophic symbionts are physiologically specialized, highly productive associations relying on hydrogen sulfide and oxygen to generate energy for carbon fixation, and the symbiont{\textquoteright}s nitrate reduction to ammonia for energy and biosynthesis. However, Riftia also flourish in sediment-hosted vents, which are markedly different in geochemistry than basalt-hosted systems. Here we present data from shipboard physiological studies and global quantitative proteomic analyses of Riftia pachyptila trophosome tissue recovered from tubeworms residing in the EPR and the Guaymas basin, a sedimented, hydrothermal vent field. We observed marked differences in symbiont nitrogen metabolism in both the respirometric and proteomic data. The proteomic data further suggest that Riftia associations in Guaymas may utilize different sulfur compounds for energy generation, may have an increased capacity for energy storage, and may play a role in degrading exogenous organic carbon. Together these data reveal that Riftia symbionts are far more physiologically plastic than previously considered, and that -contrary to previous assertions- Riftia do assimilate reduced nitrogen in some habitats. These observations raise new hypotheses regarding adaptations to the geochemical diversity of habitats occupied by Riftia, and the degree to which the environment influences symbiont physiology and evolution.</p>},
	keywords = {Abiotic factors, Annelids, Associations, Evolution, Habitat, Invertebrates, Marine habitat, Marine zones, Pacific Ocean, Whole animal physiology},
	author = {Robidart, Julie C. and Roque, Annelys and Song, Pengfei and Girguis, Peter R.}
}
@article {511076,
	title = {Measuring Isotope Fractionation by Autotrophic Microorganisms and Enzymes},
	journal = {Methods in Enzymology: Methods in Methane Metabolism, Pt A},
	volume = {494},
	year = {2011},
	note = {<p>Bui30Times Cited:1Cited References Count:78Methods in Enzymology</p>},
	pages = {281-299},
	abstract = {<p>Physical, chemical, and biological processes commonly discriminate among stable isotopes. Therefore, the stable isotope compositions of biomass, growth substrates, and products often carry the isotopic fingerprints of the processes that shape them. Therefore, measuring isotope fractionation by enzymes and cultures of autotrophic microorganisms can provide insights at many levels, from metabolism to ecosystem function. Discussed here are considerations relevant to measuring isotope discrimination by enzymes as well at, intact cells, with an emphasis on stable one-carbon isotopes and autotrophic microorganisms.</p>},
	keywords = {atmospheric methane, carbon-dioxide, continuous-flow bioreactor, form ia-rubisco, gas-chromatography, high-precision, inlet mass-spectrometry, ribulose bisphosphate, tricarboxylic-acid cycle, tubeworm riftia-pachyptila},
	isbn = {0076-6879},
	author = {Scott, K. M. and Fox, G. and Girguis, P. R.}
}
@article {511086,
	title = {Metabolic and practical considerations on microbial electrosynthesis},
	journal = {Current Opinion in Biotechnology},
	volume = {22},
	number = {3},
	year = {2011},
	note = {<p>Rabaey, KorneelGirguis, PeterNielsen, Lars KengResearch Support, Non-U.S. Gov{\textquoteright}tResearch Support, U.S. Gov{\textquoteright}t, Non-P.H.S.ReviewEngland2011/03/01 06:00Curr Opin Biotechnol. 2011 Jun;22(3):371-7. doi: 10.1016/j.copbio.2011.01.010. Epub 2011 Feb 23.</p>},
	month = {Jun},
	pages = {371-7},
	abstract = {<p>The production of biofuels and biochemicals is highly electron intensive. To divert fermentative and respiratory pathways to the product of interest, additional electrons (i.e. reducing power) are often needed. Meanwhile, the past decade has seen the breakthrough of sustainable electricity sources such as solar and wind. Microbial electrosynthesis (MES) is at the nexus of both, as it uses electrical energy as source of reducing power for microorganisms. This review addresses the key opportunities and challenges for MES. While exciting as a concept, MES needs to overcome many biological, electrochemical, logistical and economic challenges. Particularly the latter is critical, as on a {\textquoteright}per electron basis{\textquoteright} MES does not yet appear to deliver a substantial benefit relative to existing approaches.</p>},
	keywords = {*Electricity, *Microbiological Phenomena, Biofuels/economics, Biosynthetic Pathways, Carbon/metabolism, Cost-Benefit Analysis, Dexfenfluramine, Electrons, Fermentation, Glucose/metabolism},
	isbn = {1879-0429 (Electronic)0958-1669 (Linking)},
	author = {Rabaey, K. and Girguis, P. and Nielsen, L. K.}
}
@article {511111,
	title = {The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities},
	journal = {Journal of Experimental Biology},
	volume = {214},
	number = {2},
	year = {2011},
	note = {<p>childres@lifesci.ucsb.edu</p>},
	pages = {312-325},
	abstract = {<p>While chemoautotrophic endosymbioses of hydrothermal vents and other reducing environments have been well studied, little attention has been paid to the magnitude of the metabolic demands placed upon the host by symbiont metabolism and the adaptations necessary to meet such demands. Here we make the first attempt at such an evaluation, and show that moderate to high rates of chemoautotrophic or methanotrophic metabolism impose oxygen uptake and proton equivalent elimination demands upon the hosts that are much higher than is typical for the non-symbiotic annelid, bivalve and gastropod lineages to which they are related. The properties of the hosts are described and compared to determine which properties are associated with and predictive of the highest rates. We suggest that the high oxygen demand of these symbionts is perhaps the most limiting flux for the symbioses. Among the consequences of such demands has been the widespread presence of circulating and/or tissue hemoglobins in these symbioses that are necessary to support high metabolic rates in thioautotrophic endosymbioses. We also compare photoautotrophic with chemoautotrophic and methanotrophic endosymbioses to evaluate the differences and similarities in physiologies. These analyses suggest that the high demand for oxygen by chemoautotrophic and methanotrophic symbionts is likely a major factor precluding their endosymbiosis with cnidarians.</p>},
	keywords = {Annelids, Associations, Biochemistry, Evolution, Invertebrates, Molluscs},
	author = {Childress, J. J. and Girguis, P. R.}
}
@article {511106,
	title = {Sulfide Oxidation across Diffuse Flow Zones of Hydrothermal Vents},
	journal = {Aquatic Geochemistry},
	volume = {17},
	number = {4-5},
	year = {2011},
	note = {<p>Sp. Iss. SI814MYTimes Cited:12Cited References Count:57</p>},
	month = {Sep},
	pages = {583-601},
	abstract = {<p>The sulfide (H(2)S/HS(-)) that is emitted from hydrothermal vents begins to oxidize abiotically with oxygen upon contact with ambient bottom water, but the reaction kinetics are slow. Here, using in situ voltammetry, we report detection of the intermediate sulfur oxidation products polysulfides [S(x)(2-)] and thiosulfate [S(2)O(3)(2-)], along with contextual data on sulfide, oxygen, and temperature. At Lau Basin in 2006, thiosulfate was identified in less than one percent of approximately 10,500 scans and no polysulfides were detected. Only five percent of 11,000 voltammetric scans taken at four vent sites at Lau Basin in May 2009 show either thiosulfate or polysulfides. These in situ data indicate that abiotic sulfide oxidation does not readily occur as H(2)S contacts oxic bottom waters. Calculated abiotic potential sulfide oxidation rates are \&lt; 10(-3) mu M/min and are consistent with slow oxidation and the observed lack of sulfur oxidation intermediates. It is known that the thermodynamics for the first electron transfer step for sulfide and oxygen during sulfide oxidation in these systems are unfavorable, and that the kinetics for two electron transfers are not rapid. Here, we suggest that different metal catalyzed and/or biotic reaction pathways can readily produce sulfur oxidation intermediates. Via shipboard high-pressure incubation experiments, we show that snails with chemosynthetic endosymbionts do release polysulfides and may be responsible for our field observations of polysulfides.</p>},
	keywords = {aqueous-solution, diffuse flow, east pacific rise, elemental sulfur, hydrogen-sulfide, hydrothermal vents, in situ chemistry, in-situ, Kinetics, lau basin, lau spreading center, riftia-pachyptila, species distributions, sulfide oxidation, sulfur speciation, voltammetric microelectrode},
	isbn = {1380-6165},
	author = {Gartman, A. and Yucel, M. and Madison, A. S. and Chu, D. W. and Ma, S. F. and Janzen, C. P. and Becker, E. L. and Beinart, R. A. and Girguis, P. R. and Luther, G. W.}
}
@article {511096,
	title = {Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment},
	journal = {Frontiers in Microbiology},
	volume = {2},
	year = {2011},
	note = {<p>V31deTimes Cited:13Cited References Count:51</p>},
	abstract = {<p>The thermodynamics for the first electron transfer step for sulfide and oxygen indicates that the reaction is unfavorable as unstable superoxide and bisulfide radical ions would need to be produced. However, a two-electron transfer is favorable as stable S(0) and peroxide would be formed, but the partially filled orbitals in oxygen that accept electrons prevent rapid kinetics. Abiotic sulfide oxidation kinetics improve when reduced iron and/or manganese are oxidized by oxygen to form oxidized metals which in turn oxidize sulfide. Biological sulfur oxidation relies on enzymes that have evolved to overcome these kinetic constraints to affect rapid sulfide oxidation. Here we review the available thermodynamic and kinetic data for H2S and HS center dot as well as O-2, reactive oxygen species, nitrate, nitrite, and NOx species. We also present new kinetic data for abiotic sulfide oxidation with oxygen in trace metal clean solutions that constrain abiotic rates of sulfide oxidation in metal free solution and agree with the kinetic and thermodynamic calculations. Moreover, we present experimental data that give insight on rates of chemolithotrophic and photolithotrophic sulfide oxidation in the environment. We demonstrate that both anaerobic photolithotrophic and aerobic chemolithotrophic sulfide oxidation rates are three or more orders of magnitude higher than abiotic rates suggesting that in most environments biotic sulfide oxidation rates will far exceed abiotic rates due to the thermodynamic and kinetic constraints discussed in the first section of the paper. Such data reshape our thinking about the biotic and abiotic contributions to sulfide oxidation in the environment.</p>},
	keywords = {abiotic, biotic, chemolithotrophy, chlorobaculum tepidum, oxidation, photolithotrophy, sulfide},
	isbn = {1664-302X},
	author = {Luther, G. W. and Findlay, A. J. and MacDonald, D. J. and Owings, S. M. and Hanson, T. E. and Beinart, R. A. and Girguis, P. R.}
}
@conference {blumenfeld2010abundance,
	title = {Abundance and Distribution of Diagnostic Carbon Fixation Genes in a Deep-Sea Hydrothermal Gradient Ecosystem},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B21B{\textendash}0318},
	author = {Blumenfeld, HN and Kelley, DS and Girguis, P. R. and Schrenk, MO}
}
@conference {ussler2010autonomous,
	title = {Autonomous in-situ qPCR in the Deep Sea},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {P13B{\textendash}1386},
	author = {Ussler, W. and Tavormina, P. and Preston, C. and Shah, S and Girguis, P. R. and Birch, J. M. and Orphan, V. and Scholin, C.}
}
@conference {guzman2010benthic,
	title = {Benthic microbial fuel cells: Long-term power sources for wireless marine sensor networks},
	booktitle = {Sensors, and command, control, communications, and intelligence (C3I) technologies for homeland security and homeland defense IX},
	volume = {7666},
	year = {2010},
	pages = {76662M},
	publisher = {International Society for Optics and Photonics},
	organization = {International Society for Optics and Photonics},
	author = {Guzman, Juan J and Cooke, Keegan G and Gay, Marcus O and Radachowsky, Sage E and Girguis, Peter R. and Chiu, Michael A}
}
@conference {girguis2010capitalizing,
	title = {Capitalizing on Education and Outreach (E/O) Expertise to Broaden Impacts},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {ED34A{\textendash}07},
	author = {Girguis, P. R. and Herren, C and DeCharon, A.}
}
@conference {girguis2010correlating,
	title = {Correlating Community Dynamics and Microbial protein expression With Changes In Hydrothermal Chemistry At The Juan UUUFuca Ridge using Biological Osmotic Sampling Systems(BOSS)},
	booktitle = {Proceedings from the 2010 AGU Ocean Sciences Meeting},
	year = {2010},
	publisher = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	organization = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	author = {Girguis, P. R. and Robidart, J. and Wheat, C. G.}
}
@conference {nielsen2010evidence,
	title = {Evidence for Hydrothermal Vents as" Biogeobatteries"},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {NS33A{\textendash}02},
	author = {Nielsen, M. E. and Girguis, P. R.}
}
@conference {girguis2010geological,
	title = {Geological and geochemical controls on the distribution of Alviniconcha vent snail symbioses: Have we finally linked mantle to microbe?},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {OS13G{\textendash}08},
	author = {Girguis, P. R. and Beinart, R. and Sanders, J. and Seewald, J}
}
@article {girguis2010harnessing,
	title = {Harnessing energy from marine productivity using bioelectrochemical systems},
	journal = {Current Opinion in Biotechnology},
	volume = {21},
	year = {2010},
	pages = {252{\textendash}258},
	publisher = {Elsevier Current Trends},
	author = {Girguis, Peter R. and Nielsen, Mark E and Figueroa, Israel}
}
@conference {wankel2010situ,
	title = {In Situ Stable Isotopic Detection of Anaerobic Oxidation of Methane in Monterey Bay Cold Seeps Via Off-Axis Integrated Cavity Output Spectroscopy},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B23A{\textendash}0385},
	author = {Wankel, S. D. and Gupta, M. and Leen, J and Provencal, RA and Parsotam, V and Girguis, P. R.}
}
@conference {johnston2010recalibrating,
	title = {Recalibrating the concentration of Precambrian seawater sulfate},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B51G{\textendash}0422},
	author = {Johnston, D. T. and Bradley, A. S. and Hoarfrost, A and Girguis, P. R.}
}
@conference {blumenfeld2010abundance,
	title = {Abundance and Distribution of Diagnostic Carbon Fixation Genes in a Deep-Sea Hydrothermal Gradient Ecosystem},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B21B{\textendash}0318},
	author = {Blumenfeld, HN and Kelley, DS and Girguis, P. R. and Schrenk, MO}
}
@conference {nielsen2010hydrothermal,
	title = {Are hydrothermal vents natural microbial fuel cells?},
	booktitle = {GEOCHIMICA ET COSMOCHIMICA ACTA},
	volume = {74},
	year = {2010},
	pages = {A759{\textendash}A759},
	publisher = {PERGAMON-ELSEVIER SCIENCE LTD THE BOULEVARD, LANGFORD LANE, KIDLINGTON~{\textellipsis}},
	organization = {PERGAMON-ELSEVIER SCIENCE LTD THE BOULEVARD, LANGFORD LANE, KIDLINGTON~{\textellipsis}},
	author = {Nielsen, Mark E and Girguis, Peter R.}
}
@conference {ussler2010autonomous,
	title = {Autonomous in-situ qPCR in the Deep Sea},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {P13B{\textendash}1386},
	author = {Ussler, W. and Tavormina, P. and Preston, C. and Shah, S and Girguis, P. R. and Birch, J. M. and Orphan, V. and Scholin, C.}
}
@conference {guzman2010benthic,
	title = {Benthic microbial fuel cells: Long-term power sources for wireless marine sensor networks},
	booktitle = {Sensors, and command, control, communications, and intelligence (C3I) technologies for homeland security and homeland defense IX},
	volume = {7666},
	year = {2010},
	pages = {76662M},
	publisher = {International Society for Optics and Photonics},
	organization = {International Society for Optics and Photonics},
	author = {Guzman, Juan J and Cooke, Keegan G and Gay, Marcus O and Radachowsky, Sage E and Girguis, Peter R. and Chiu, Michael A}
}
@conference {girguis2010capitalizing,
	title = {Capitalizing on Education and Outreach (E/O) Expertise to Broaden Impacts},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {ED34A{\textendash}07},
	author = {Girguis, P. R. and Herren, C and DeCharon, A.}
}
@conference {girguis2010correlating,
	title = {Correlating Community Dynamics and Microbial protein expression With Changes In Hydrothermal Chemistry At The Juan UUUFuca Ridge using Biological Osmotic Sampling Systems(BOSS)},
	booktitle = {Proceedings from the 2010 AGU Ocean Sciences Meeting},
	year = {2010},
	publisher = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	organization = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	author = {Girguis, P. R. and Robidart, J. and Wheat, C. G.}
}
@conference {nielsen2010evidence,
	title = {Evidence for Hydrothermal Vents as" Biogeobatteries"},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {NS33A{\textendash}02},
	author = {Nielsen, M. E. and Girguis, P. R.}
}
@conference {girguis2010evidence,
	title = {Evidence for seismicity influencing deep sea primary productivity: A year-long study of microbial processes at the Juan de Fuca ridge using biological osmotic samplers},
	booktitle = {GEOCHIMICA ET COSMOCHIMICA ACTA},
	volume = {74},
	year = {2010},
	pages = {A335{\textendash}A335},
	publisher = {PERGAMON-ELSEVIER SCIENCE LTD THE BOULEVARD, LANGFORD LANE, KIDLINGTON~{\textellipsis}},
	organization = {PERGAMON-ELSEVIER SCIENCE LTD THE BOULEVARD, LANGFORD LANE, KIDLINGTON~{\textellipsis}},
	author = {Peter Girguis and Robidart, Julie and Wheat, Geoffrey and Frank, Kiana}
}
@conference {girguis2010geological,
	title = {Geological and geochemical controls on the distribution of Alviniconcha vent snail symbioses: Have we finally linked mantle to microbe?},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {OS13G{\textendash}08},
	author = {Girguis, P. R. and Beinart, R. and Sanders, J. and Seewald, J}
}
@article {girguis2010harnessing,
	title = {Harnessing energy from marine productivity using bioelectrochemical systems},
	journal = {Current Opinion in Biotechnology},
	volume = {21},
	year = {2010},
	pages = {252{\textendash}258},
	publisher = {Elsevier Current Trends},
	author = {Girguis, Peter R. and Nielsen, Mark E and Figueroa, Israel}
}
@conference {wankel2010situ,
	title = {In Situ Stable Isotopic Detection of Anaerobic Oxidation of Methane in Monterey Bay Cold Seeps Via Off-Axis Integrated Cavity Output Spectroscopy},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B23A{\textendash}0385},
	author = {Wankel, S. D. and Gupta, M. and Leen, J and Provencal, RA and Parsotam, V and Girguis, P. R.}
}
@booklet {girguis2010linking,
	title = {Linking mantle to microbe: a community-wide effort to ally hydrothermal vent microbial identity and ecology to geochemical cycles via metagenomics},
	year = {2010},
	publisher = {DOE Joint Genome Institute},
	author = {Peter Girguis}
}
@booklet {girguis2010methods,
	title = {Methods and apparatus for stimulating and managing power from microbial fuel cells},
	year = {2010},
	note = {US Patent App. 12/311,165},
	author = {Girguis, Peter Riad and Kauffman, Peter Carr}
}
@article {wankel2010new,
	title = {New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	volume = {57},
	year = {2010},
	pages = {2022{\textendash}2029},
	publisher = {Pergamon},
	author = {Wankel, Scott D and Joye, Samantha B and Samarkin, Vladimir A and Shah, Sunita R and Friederich, Gernot and Melas-Kyriazi, John and Girguis, Peter R.}
}
@conference {johnston2010recalibrating,
	title = {Recalibrating the concentration of Precambrian seawater sulfate},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2010},
	year = {2010},
	pages = {B51G{\textendash}0422},
	author = {Johnston, D. T. and Bradley, A. S. and Hoarfrost, A and Girguis, P. R.}
}
@conference {birch2010searching,
	title = {Searching for microbes in deep-sea seep and hydrothermal vents using the Environmental Sample Processor},
	booktitle = {Astrobiology Science Conference},
	volume = {201},
	year = {2010},
	author = {Birch, J and Preston, C. and Pargett, D. and Jensen, S. and Roman, B. and Everloce, C and Marin III, R and Orphan, V. and Girguis, P. and Scholin, C.}
}
@conference {edwards2010subsurface,
	title = {Subsurface microbial observatories to investigate the deep ocean crust biosphere- development, testing, and future},
	booktitle = {Proceedings from the 2010 AGU Ocean Sciences Meeting},
	year = {2010},
	publisher = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	organization = {American Geophysical Union, 2000 Florida Ave., N. W. Washington DC 20009 USA,},
	author = {Edwards, Katrina J and Bach, W. and Cowen, JP and Fisher, A and Girguis, P. R. and Glazer, BT and Huber, JA and Nealson, KH and Orcutt, B and Pettigrew, T and others}
}
@proceedings {511121,
	title = {Are hydrothermal vents natural microbial fuel cells?},
	volume = {74},
	number = {12},
	year = {2010},
	note = {<p>Suppl. 1676TLTimes Cited:0Cited References Count:0</p>},
	month = {Jun},
	pages = {A759-A759},
	isbn = {0016-7037},
	author = {Nielsen, M. E. and Girguis, P. R.}
}
@article {511126,
	title = {Benthic Microbial Fuel Cells: Long-Term Power Sources for Wireless Marine Sensor Networks},
	journal = {Sensors, and Command, Control, Communications, and Intelligence (C3i) Technologies for Homeland Security and Homeland Defense Ix},
	volume = {7666},
	year = {2010},
	note = {<p>Bss37Times Cited:2Cited References Count:13Proceedings of SPIE-The International Society for Optical Engineering</p>},
	abstract = {<p>Wireless marine sensor networks support an assortment of services in industries ranging from national security and defense to communications and environmental stewardship. Expansion of marine sensor networks has been inhibited by the limited availability and high cost of long-term power sources. Benthic Microbial Fuel Cells (BMFCs) are a novel form of energy harvesting for marine environments. Through research conducted in-lab and by academic collaborators, Trophos Energy has developed a series of novel BMFC architectures to improve power generation capability and overall system robustness. When integrated with Trophos{\textquoteright} power management electronics, BMFCs offer a robust, long-term power solution for a variety of remote marine applications. The discussions provided in this paper outline the architectural evolution of BMFC technology to date, recent experimental results that will govern future BMFC designs, and the present and future applicability of BMFC systems as power sources for wireless marine sensor networks.</p>},
	keywords = {benthic microbial fuel cell, energy, environmental fuel cell, marine power, marine sensor network, remote power source, remote sensor network},
	isbn = {0277-786X},
	author = {Guzman, J. J. and Cooke, K. G. and Gay, M. O. and Radachowsky, S. E. and Girguis, P. R. and Chiu, M. A.}
}
@inbook {511131,
	title = {Fundamentals of Benthic Microbial Fuel Cells: Theory, Development, and Applications},
	booktitle = {Bioelectrochemical systems},
	year = {2010},
	publisher = {Springer Verlag Press},
	organization = {Springer Verlag Press},
	edition = {First edition},
	author = {Girguis, P. R. and Nielsen, M. E. and Reimers, C. E.}
}
@article {511136,
	title = {Harnessing energy from marine productivity using bioelectrochemical systems.},
	journal = {Current Opinion in Biotechnology},
	volume = {21},
	number = {3},
	year = {2010},
	note = {<p>613CKTimes Cited:9Cited References Count:81</p>},
	month = {Jun},
	pages = {252-258},
	abstract = {<p>Over the past decade, studies have shown that devices called microbial fuel cells (MFCs) can harness electricity from microbially mediated degradation of organic carbon, in both lab cultures and natural environments. Other studies have shown that MFCs can harness power from coastal and deep ocean sediments, as well as from plankton, without any fuel supplementation or microbial inoculation. The fuel for these systems is organic matter resulting from oceanic primary productivity. Models suggest that MFCs may operate for decades on endogenous organic carbon. In light of their capacity to generate power in natural milieus by tapping into biogeochemical cycles, MFCs may one day provide an efficient means of generating power (or high value biofuels) directly from marine productivity.</p>},
	keywords = {cathode materials, electron-transfer, escherichia-coli, generating electricity, iron, microbial fuel-cell, organic-matter, power, reduction, waste-water},
	isbn = {0958-1669},
	author = {Girguis, P. R. and Nielsen, M. E. and Figueroa, I.}
}
@article {511116,
	title = {New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry},
	journal = {Deep-Sea Research Part II -Topical Studies in Oceanography},
	volume = {57},
	number = {21-23},
	year = {2010},
	note = {<p>694TZTimes Cited:21Cited References Count:52</p>},
	month = {Nov},
	pages = {2022-2029},
	abstract = {<p>Deep-sea biogeochemical cycles are, in general, poorly understood owing to the difficulties of making measurements in situ, recovering samples with minimal perturbation, and, in many cases, coping with high spatial and temporal heterogeneity. In particular, biogeochemical fluxes of volatiles such as methane remain largely unconstrained because of the difficulties with accurate quantification in situ and the patchiness of point sources such as seeps and brine pools. To better constrain biogeochemical fluxes and cycling, we have developed a deep-sea in situ mass spectrometer (ISMS) to enable high-resolution quantification of volatiles in situ. Here we report direct measurements of methane concentrations made in a Gulf of Mexico brine pool located at a depth of over 2300 m. Concentrations of up to 33 mM methane were observed within the brine pool, whereas concentrations in the water directly above were three orders of magnitude lower. These direct measurements enabled us to make the first accurate estimates of the diffusive flux from a brine pool, calculated to be 1.1 +/- 0.2 mol m(-2) yr(-1). Integrated rate measurements of aerobic methane oxidation in the water column overlying the brine pool were similar to 320 mu mol m(-2) yr(-1), accounting at most for just 0.03\% of the diffusive methane flux from the brine pool. Calculated rates of anaerobic methane oxidation were 600-1200 mu M yr(-1), one to two orders of magnitude higher than previously published values of AOM in anoxic fluids. These findings suggest that brine pools are enormous point sources of methane in the deep sea, and may, in aggregate, have a pronounced impact on the global marine methane cycle. (C) 2010 Elsevier Ltd. All rights reserved.</p>},
	keywords = {biogeochemistry, brine pool, cold seeps, dissolved-gases, gas hydrate, gulf of mexico, mass spectrometer, methane flux, methane oxidation, riftia-pachyptila, saanich inlet, sea-floor brines, sediments, slope, sulfate reduction},
	isbn = {0967-0645},
	author = {Wankel, S. D. and Joye, S. B. and Samarkin, V. A. and Shah, S. R. and Friederich, G. and Melas-Kyriazi, J. and Girguis, P. R.}
}
@article {girguis2009coupling,
	title = {Coupling metabolite flux to proteomics: Insights into the molecular mechanisms underlying primary productivity by tubeworm symbionts},
	journal = {Geochimica et Cosmochimica Acta Supplement},
	volume = {73},
	year = {2009},
	pages = {A439},
	author = {Girguis, Peter Riad and Robidart, Julie and Nyholm, Spencer}
}
@article {bradley2009methane,
	title = {Methane cycling at Lost City: A biological view of geochemistry},
	journal = {Geochimica et Cosmochimica Acta Supplement},
	volume = {73},
	year = {2009},
	pages = {A154},
	author = {Bradley, Alexander S and Song, Pengfei and Summons, Roger E and Girguis, Peter R.}
}
@article {seibel2009variation,
	title = {Variation in evolved {\textquotedblleft}limits to life{\textquotedblright} preclude universal tolerance indices: a critique of the {\textquotedblleft}Respiration Index{\textquotedblright}},
	journal = {Science},
	year = {2009},
	author = {Seibel, Brad A and Girguis, Peter R. and Childress, James J.}
}
@conference {sylvan2009bacterial,
	title = {Bacterial community composition in hydrothermal plume environments is heterogeneous and distinct},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2009},
	year = {2009},
	pages = {V51D{\textendash}1739},
	author = {Sylvan, J. B. and Toner, B. M. and Girguis, P. R. and Edwards, K. J.}
}
@article {girguis2009coupling,
	title = {Coupling metabolite flux to proteomics: Insights into the molecular mechanisms underlying primary productivity by tubeworm symbionts},
	journal = {Geochimica et Cosmochimica Acta Supplement},
	volume = {73},
	year = {2009},
	pages = {A439},
	author = {Girguis, Peter Riad and Robidart, Julie and Nyholm, Spencer}
}
@conference {dilly2009exploring,
	title = {Exploring the Boundaries of Metazoan Thermotolerance at Hydrothermal Vents: Respiration and Protein Expression of Paralvinellid Worms},
	booktitle = {INTEGRATIVE AND COMPARATIVE BIOLOGY},
	volume = {49},
	year = {2009},
	pages = {E222{\textendash}E222},
	publisher = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	organization = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	author = {Dilly, G. F. and Girguis, P. R.}
}
@conference {girguis2009metabolite,
	title = {From metabolite flux to gene expression and proteomics: insights into the molecular mechanisms underlying primary productivity in hydrothermal vent tubeworms},
	booktitle = {INTEGRATIVE AND COMPARATIVE BIOLOGY},
	volume = {49},
	year = {2009},
	pages = {E63{\textendash}E63},
	publisher = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	organization = {OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
	author = {Girguis, P. R. and Nyholm, S. and Robidart, J. A. and Girguis}
}
@article {nielsen2009influence,
	title = {Influence of substrate on electron transfer mechanisms in chambered benthic microbial fuel cells},
	journal = {Environmental science \& technology},
	volume = {43},
	year = {2009},
	pages = {8671{\textendash}8677},
	publisher = {American Chemical Society},
	author = {Nielsen, Mark E and Wu, Di M and Girguis, Peter R. and Reimers, Clare E}
}
@article {bradley2009methane,
	title = {Methane cycling at Lost City: A biological view of geochemistry},
	journal = {Geochimica et Cosmochimica Acta Supplement},
	volume = {73},
	year = {2009},
	pages = {A154},
	author = {Bradley, Alexander S and Song, Pengfei and Summons, Roger E and Girguis, Peter R.}
}
@booklet {girguis2009peering,
	title = {Peering Into the Private Lives of Microbes: From Microbial Activity to Geochemical Cycles},
	year = {2009},
	publisher = {Organismic \& Evolutionary Biology, Harvard University},
	author = {Peter Girguis}
}
@article {white2009quantitative,
	title = {Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells},
	journal = {The ISME journal},
	volume = {3},
	year = {2009},
	pages = {635{\textendash}646},
	publisher = {Nature Publishing Group},
	author = {White, Helen K and Reimers, Clare E and Cordes, Erik E and Dilly, Geoffrey F and Girguis, Peter R.}
}
@article {wankel2009real,
	title = {Real-time in situ volatile characterization and methane carbon stable isotopic composition in the deep sea},
	journal = {Geochimica et Cosmochimica Acta Supplement},
	volume = {73},
	year = {2009},
	pages = {A1418},
	author = {Wankel, Scott D and Lilley, Marvin D and Olson, Eric and Girguis, Peter R.}
}
@article {yancey2009thiotaurine,
	title = {Thiotaurine and hypotaurine contents in hydrothermal-vent polychaetes without thiotrophic endosymbionts: correlation With sulfide exposure},
	journal = {Journal of Experimental Zoology Part A: Ecological Genetics and Physiology},
	volume = {311},
	year = {2009},
	pages = {439{\textendash}447},
	publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
	author = {Yancey, Paul H and Ishikawa, Joanne and Meyer, Brigitte and Girguis, Peter R. and Lee, Raymond W}
}
@article {seibel2009variation,
	title = {Variation in evolved {\textquotedblleft}limits to life{\textquotedblright} preclude universal tolerance indices: a critique of the {\textquotedblleft}Respiration Index{\textquotedblright}},
	journal = {Science},
	year = {2009},
	author = {Seibel, Brad A and Girguis, Peter R. and Childress, James J.}
}
@proceedings {511166,
	title = {Coupling metabolite flux to proteomics: Insights into the molecular mechanisms underlying primary productivity by tubeworm symbionts},
	volume = {73},
	number = {13},
	year = {2009},
	note = {<p>460YSTimes Cited:0Cited References Count:0</p>},
	month = {Jun},
	pages = {A439-A439},
	isbn = {0016-7037},
	author = {Girguis, P. R. and Robidart, J. and Nyholm, S.}
}
@proceedings {511176,
	title = {Exploring the Boundaries of Metazoan Thermotolerance at Hydrothermal Vents: Respiration and Protein Expression of Paralvinellid Worms},
	volume = {49},
	year = {2009},
	note = {<p>481KLTimes Cited:0Cited References Count:0</p>},
	month = {Feb},
	pages = {E222-E222},
	isbn = {1540-7063},
	author = {Dilly, G. F. and Girguis, P. R.}
}
@article {511171,
	title = {From metabolite flux to gene expression and proteomics: insights into the molecular mechanisms underlying primary productivity in hydrothermal vent tubeworms},
	journal = {Integrative and Comparative Biology},
	volume = {49},
	year = {2009},
	note = {<p>481KLTimes Cited:0Cited References Count:0</p>},
	month = {Feb},
	pages = {E63-E63},
	isbn = {1540-7063},
	author = {Girguis, P. R. and Nyholm, S. V. and Robidart, J. A. and Girguis}
}
@article {511161,
	title = {Influence of Substrate on Electron Transfer Mechanisms in Chambered Benthic Microbial Fuel Cells.},
	journal = {Environmental Science \& Technology},
	volume = {43},
	number = {22},
	year = {2009},
	note = {<p>516ZVTimes Cited:22Cited References Count:45</p>},
	month = {Nov 15},
	pages = {8671-8677},
	abstract = {<p>This research investigated whether the addition of an exogenous electron donor would affect power production in laboratory-scale benthic microbial fuel cells (BMFC) by differentially influencing microbially mediated electron transfer processes. Six BMFCs were operated for over one year in a temperature-controlled laboratory. Three BMFCs relied on endogenous electron donors, and three were supplemented with lactate. The supplemented BMFCs generated more cumulative charge, but did not generate higher average current between periods of lactate enrichment Coulombic efficiencies during the lactate treatments ranged from 25 to 65\% suggesting that lactate utilization was variably coupled to power production. Cumulative electron flux resulting from lactate additions and chemical changes within the anode chamber, as well as a difference in the anode-hosted microbial communities indicated that lactate supplementation promoted sulfate reduction. After the addition of molybdate to suppress sulfate reduction and sulfur disproportionation, all BMFCs continued to produce current but no longer responded to lactate additions. Chemical data support a two-step cycle in which endogenous organic carbon and/or supplemented lactate fuel sulfate reduction resulting in sulfide and simple organic molecules (such as acetate) that can act as the electron donors for the BMFC.</p>},
	keywords = {biofilm, communities, energy-metabolism, harvesting electricity, hydrogen-sulfide, marine-sediments, oxidation, reduction, sea-floor, sulfate-reducing bacteria},
	isbn = {0013-936X},
	author = {Nielsen, M. E. and Wu, D. M. and Girguis, P. R. and Reimers, C. E.}
}
@proceedings {511181,
	title = {Methane cycling at Lost City: A biological view of geochemistry},
	volume = {73},
	number = {13},
	year = {2009},
	note = {<p>460YSTimes Cited:0Cited References Count:4</p>},
	month = {Jun},
	pages = {A154-A154},
	keywords = {hydrothermal field},
	isbn = {0016-7037},
	author = {Bradley, A. S. and Song, P. and Summons, R. E. and Girguis, P. R.}
}
@article {511146,
	title = {Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells.},
	journal = {Isme Journal},
	volume = {3},
	number = {6},
	year = {2009},
	note = {<p>452HITimes Cited:25Cited References Count:31</p>},
	month = {Jun},
	pages = {635-646},
	abstract = {<p>This study examines changes in diversity and abundance of bacteria recovered from the anodes of microbial fuel cells (MFCs) in relation to anode potential, power production and geochemistry. MFCs were batch-fed with plankton, and two systems were maintained at different potentials whereas one was at open circuit for 56.8 days. Bacterial phylogenetic diversity during peak power was assessed from 16S rDNA clone libraries. Throughout the experiment, microbial community structure was examined using terminal restriction fragment length polymorphism. Changes in cell density of key phylotypes, including representatives of delta-, epsilon-, gamma-proteobacteria and Flavobacterium-Cytophaga-Bacteroides, were enumerated by quantitative PCR. Marked differences in phylogenetic diversity were observed during peak power versus the final time point, and changes in microbial community structure were strongly correlated to dissolved organic carbon and ammonium concentrations within the anode chambers. Community structure was notably different between the MFCs at different anode potentials during the onset of peak power. At the final time point, however, the anode-hosted communities in all MFCs were similar. These data demonstrate that differences in growth, succession and population dynamics of key phylotypes were due to anode potential, which may relate to their ability to exploit the anode as an electron acceptor. The geochemical milieu, however, governs overall community diversity and structure. These differences reflect the physiological capacity of specific phylotypes to catabolize plankton-derived organic matter and exploit the anode of an MFC for their metabolism directly or indirectly through syntrophy. The ISME Journal (2009) 3, 635-646; doi: 10.1038/ismej.2009.12; published online 26 February 2009</p>},
	keywords = {bacterial communities, cell, diversity, Ecology, electricity, electron-transfer, energy, fuel, generation, plankton, power, real-time pcr, reduction, sediments},
	isbn = {1751-7362},
	author = {White, H. K. and Reimers, C. E. and Cordes, E. E. and Dilly, G. F. and Girguis, P. R.}
}
@proceedings {511151,
	title = {Real-time in situ volatile characterization and methane carbon stable isotopic composition in the deep sea},
	volume = {73},
	number = {13},
	year = {2009},
	note = {<p>460YSTimes Cited:0Cited References Count:0</p>},
	month = {Jun},
	pages = {A1418-A1418},
	isbn = {0016-7037},
	author = {Wankel, S. D. and Lilley, M. D. and Olson, E. and Girguis, P. R.}
}
@article {511141,
	title = {Thiotaurine and Hypotaurine Contents in Hydrothermal-Vent Polychaetes Without Thiotrophic Endosymbionts: Correlation With Sulfide Exposure.},
	journal = {Journal of Experimental Zoology Part a-Ecological Genetics and Physiology},
	volume = {311A},
	number = {6},
	year = {2009},
	note = {<p>473VXTimes Cited:4Cited References Count:46</p>},
	month = {Jul 1},
	pages = {439-447},
	abstract = {<p>Invertebrates at hydrothermal vents and cold seeps must cope with toxic H(2)S. One proposed protection mechanism involves taurine derivatives: At vents and seeps, many animals have high levels of hypotaurine and thiotaurine (a product of hypotaurine and HS), originally found in animals with thiotrophic endosymbionts. To further test the role of these compounds, we analyzed them in vent polychaetes without endosymbionts: Paralvinella sulfincola, P. palmiformis and P. pandorae (paralvinellids) and Nicomache venticola (maldanid). P. sulfincola were collected from a high temperature (42-68 degrees C) and a warm site (21-35 degrees C). P. plamiformis and pandorae were from cool sites (12-18 degrees C) and N. venticola were from a cold site (4 degrees C). H(2)S concentrations in vent effluent largely correlate with temperature. Some specimens were frozen; other ones were kept alive in laboratory chambers, with and without sulfide. Tissues were analyzed for taurine derivatives and other solutes that serve as organic osmolytes. The major osmolyte of all species was glycine. Thiotaurine contents were significantly different among all species, in the order P. sulfincola hot \&gt; P. sulfincola warm \&gt; P. pandorae \&gt; P. palmiformis \&gt; N. venticola. P. sulfincola also had high levels of sarcosine; others species had none. Sarcosine and hypotaurine contents of P. sulfincola{\textquoteright}s branchiae were higher, while glycine contents were lower, than in main body. In P. palmiformis kept in pressure chambers with sulfide, thiotaurine contents were higher and hypotaurine lower than in those. kept without sulfide. These results support the hypothesis that conversion of hypotaurine to thiotaurine detoxifies sulfide in vent animals without endosymbionts. J. Exp. Zool. 311A:439-447, 2009, (C) 2009 Wiley-Liss, Inc.</p>},
	keywords = {amino-acids, cold seeps, de-fuca ridge, hydrostatic-pressure, northeast pacific, organic osmolytes, riftia-pachyptila, sea animals, symbiotic bacteria, tolerance},
	isbn = {1932-5223},
	author = {Yancey, P. H. and Ishikawa, J. and Meyer, B. and Girguis, P. R. and Lee, R. W.}
}
@booklet {511156,
	title = {Variation in evolved limits to life preclude universal tolerance indices: a critque of the Respiration Index},
	howpublished = {Science e-Letters},
	year = {2009},
	author = {Seibel, B. A. and Girguis, P. R. and Childress, J. J.}
}
@article {dilly2008hydrothermal,
	title = {Hydrothermal vents and eukaryotic thermotolerance: Profiling heat shock proteins expression in Paralvinella sulfincola},
	journal = {Comparative Biochemistry and Physiology, Part A},
	volume = {1},
	year = {2008},
	pages = {S39},
	author = {Dilly, G and Girguis, P.}
}
@conference {wolfe2008iron,
	title = {Iron, Sulfur, Arsenic and Water: Geochemical Implications of Facultative Anoxygenic Photosynthesis in Cyanobacteria and the Slow Rise of Oxygen},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2008},
	year = {2008},
	pages = {B21B{\textendash}0344},
	author = {Wolfe-Simon, F and Johnston, D. T. and Girguis, P. R. and Pearson, A and Knoll, A. H.}
}
@conference {girguis2008boss,
	title = {The BOSS: a novel approach to coupling temporal changes in geochemistry and microbiology in the deep subsurface biosphere.},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2008},
	year = {2008},
	pages = {B51F{\textendash}03},
	author = {Girguis, P. R. and Robidart, J. and Wheat, G}
}
@article {newton2008comparative,
	title = {Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts},
	journal = {BMC genomics},
	volume = {9},
	year = {2008},
	pages = {1{\textendash}12},
	publisher = {BioMed Central},
	author = {Newton, Irene LG and Girguis, Peter R. and Cavanaugh, Colleen M}
}
@article {nyholm2008coupling,
	title = {Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae},
	journal = {The Biological Bulletin},
	volume = {214},
	year = {2008},
	pages = {255{\textendash}265},
	publisher = {Marine Biological Laboratory},
	author = {Nyholm, Spencer V. and Robidart, Julie and Girguis, Peter R.}
}
@conference {schulte2008earth,
	title = {Earth{\textquoteright}s Deep Biosphere and Life in the Solar System},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2008},
	year = {2008},
	pages = {B52B{\textendash}08},
	author = {Schulte, M and Orcutt, B and Girguis, P.}
}
@article {dilly2008hydrothermal,
	title = {Hydrothermal vents and eukaryotic thermotolerance: Profiling heat shock proteins expression in Paralvinella sulfincola},
	journal = {Comparative Biochemistry and Physiology, Part A},
	volume = {1},
	year = {2008},
	pages = {S39},
	author = {Dilly, G and Girguis, P.}
}
@conference {wolfe2008iron,
	title = {Iron, Sulfur, Arsenic and Water: Geochemical Implications of Facultative Anoxygenic Photosynthesis in Cyanobacteria and the Slow Rise of Oxygen},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2008},
	year = {2008},
	pages = {B21B{\textendash}0344},
	author = {Wolfe-Simon, F and Johnston, D. T. and Girguis, P. R. and Pearson, A and Knoll, A. H.}
}
@conference {girguis2008power,
	title = {Power Production by Sediment-Hosted Microbial Fuel Cells: The Influence of Substrate Availability and Microbial Ecology},
	booktitle = {2008 Joint Meeting of The Geological Society of America, Soil Science Society of America, American Society of Agronomy, Crop Science Society of America, Gulf Coast Association of Geological Societies with the Gulf Coast Section of SEPM},
	year = {2008},
	author = {Girguis, Peter R.}
}
@article {nielsen2008sustainable,
	title = {Sustainable energy from deep ocean cold seeps},
	journal = {Energy \& Environmental Science},
	volume = {1},
	year = {2008},
	pages = {584{\textendash}593},
	publisher = {Royal Society of Chemistry},
	author = {Nielsen, Mark E and Reimers, Clare E and White, Helen K and Sharma, Sonam and Girguis, Peter R.}
}
@article {511196,
	title = {Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts},
	journal = {Bmc Genomics},
	volume = {9},
	year = {2008},
	note = {<p>417VSTimes Cited:13Cited References Count:62</p>},
	month = {Dec 4},
	abstract = {<p>Background: The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible.Results: To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents.Conclusion: The results of this comparative genomics analysis emphasize the importance of the symbionts{\textquoteright} chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.</p>},
	keywords = {blochmannia, buchnera-aphidicola, calyptogena-magnifica, deep-sea clam, endosymbiotic bacteria, Evolution, hydrothermal vent, nitrate reductase, sequence, transmission},
	isbn = {1471-2164},
	author = {Newton, I. L. G. and Girguis, P. R. and Cavanaugh, C. M.}
}
@article {511186,
	title = {Coupling metabolite flux to transcriptomics: Insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae},
	journal = {Biological Bulletin},
	volume = {214},
	number = {3},
	year = {2008},
	note = {<p>319TOTimes Cited:13Cited References Count:73</p>},
	month = {Jun},
	pages = {255-265},
	abstract = {<p>Deep-sea hydrothermal vents host highly productive ecosystems. Many of these communities are dominated by vestimentiferan tubeworms that house endosymbiotic chemoautotrophic bacteria that provide the hosts with their primary nutritional needs. Rates of carbon fixation by these symbioses are also among the highest recorded. Despite the breadth of physiological and biochemical research on these associations, the underlying molecular mechanisms that regulate host and symbiont metabolite flux and carbon fixation are largely unknown. Here we present metabolite flux and transcriptomics data from shipboard high-pressure respirometry experiments in which we maintained Ridgeia piscesae tubeworms at conditions comparable to those in situ. Host trophosome was used for cDNA library construction and sequencing. Of the 19,132 clones sequenced, 10,684 represented unique expressed sequence tags (ESTs). The highest proportions of genes are involved with translation, ribosomal structure and biogenesis, cellular processing, and signal transduction. There was moderate representation of genes involved in metabolite exchange and acid-base regulation. These data represent the first concomitant surveys of metabolite flux rates and gene expression for a chemoautotrophic symbiosis during net autotrophy, and they suggest that-in the case of Riageia piscesae-host-symbiont interactions such as cell cycle regulation may play a significant role in maintaining physiological poise during high productivity.</p>},
	keywords = {alvinella-pompejana, carbonic-anhydrase, chemoautotrophic symbionts, community, deep-sea vents, east pacific rise, fuca ridge, methanococcus-jannaschii, sulfide binding, worm riftia-pachyptila},
	isbn = {0006-3185},
	author = {Nyholm, S. V. and Robidart, J. and Girguis, P. R.}
}
@article {511191,
	title = {Sustainable energy from deep ocean cold seeps},
	journal = {Energy \& Environmental Science},
	volume = {1},
	number = {5},
	year = {2008},
	note = {<p>414TOTimes Cited:26Cited References Count:46</p>},
	pages = {584-593},
	abstract = {<p>Two designs of benthic microbial fuel cell (BMFC) were deployed at cold seeps in Monterey Canyon, CA, unattended for between 68 and 162 days. One design had a cylindrical solid graphite anode buried vertically in sediment, and the other had a carbon fiber brush anode semi-enclosed in a chamber above the sediment-water interface. Each chamber included two check valves to allow fluid flow from the sediment into the chamber. On average, power outputs were 0.2 mW (32 mW m(-2) normalized to cross sectional area) from the solid anode BMFC and from 11 to 56 mW (27-140 mW m(-2)) during three deployments of the chambered design. The range in power produced with the chambered BMFC was due to different valve styles, which appear to have permitted different rates of chemical seepage from the sediments into the anode chamber. Valves with the lowest breaking pressure led to the highest power production and presumably the highest inputs of electron donors. The increase in power coincided with a significant change in the microbial community associated with the anode from being dominated by epsilonproteobacteria to a more diverse community with representatives from deltaproteobacteria, epsilonproteobacteria, firmicutes, and flavobacterium/cytophaga/bacterioides (FCB). The highest levels of power delivered by the chambered BMFC would meet the energy requirements of many oceanographic sensors marketed today. In addition, these BMFCs did not exhibit signs of electrochemical passivation or progressive substrate depletion as is often observed with buried anodes.</p>},
	keywords = {california, communities, electron-transfer, geobacter-sulfurreducens, harvesting electricity, microbial fuel-cells, monterey bay, power, sea-floor, sediment-water interface},
	isbn = {1754-5692},
	author = {Nielsen, M. E. and Reimers, C. E. and White, H. K. and Sharma, S. and Girguis, P. R.}
}
@conference {kelley2007towards,
	title = {Towards Determining the Upper Temperature Limit to Life},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2007},
	year = {2007},
	pages = {V23D{\textendash}02},
	author = {Kelley, DS and Girguis, P. R. and Wheat, G and Cordes, E and Schrenk, MO and Lin, M and Baross, JA and Delaney, JR}
}
@conference {girguis2007tracing,
	title = {Tracing The Fate Of Methane-Derived Carbon: Insights Into The Ecological Physiology Of Anaerobic Methanotrophy Via Quantitative Molecular and Geochemical Approaches},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2007},
	year = {2007},
	pages = {B51D{\textendash}07},
	author = {Girguis, P. R. and Nyholm, S. V. and Delong, E. F.}
}
@article {white2007examining,
	title = {Examining the efficiency and biochemistry of plankton-fed microbial fuel cells},
	year = {2007},
	author = {White, Helen K and Reimers, Clare E and Stecher III, HA and Girguis, P. R.}
}
@conference {reimers2007examining,
	title = {Examining the efficiency and biogeochemistry of plankton-fed microbial fuel cells},
	booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
	volume = {234},
	year = {2007},
	publisher = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	author = {Reimers, Clare E and Stecher III, Hilmar A and White, Helen K and Peter Girguis}
}
@conference {reimers2007ocean,
	title = {Ocean Microbial Fuel Cell: Power Source and Research Tool for Studying Marine Biogeochemistry},
	booktitle = {AGU Spring Meeting Abstracts},
	volume = {2007},
	year = {2007},
	pages = {NS44A{\textendash}01},
	author = {Reimers, C. E. and Girguis, P. and Westall, J. C. and Nielsen, M. E.}
}
@article {fisher2007proteomic,
	title = {A proteomic snapshot of life at a vent},
	journal = {science},
	volume = {315},
	year = {2007},
	pages = {198{\textendash}199},
	publisher = {American Association for the Advancement of Science},
	author = {Fisher, Charles R and Peter Girguis}
}
@article {reimers2007substrate,
	title = {Substrate degradation kinetics, microbial diversity, and current efficiency of microbial fuel cells supplied with marine plankton},
	journal = {Applied and Environmental Microbiology},
	volume = {73},
	year = {2007},
	pages = {7029{\textendash}7040},
	publisher = {American Society for Microbiology},
	author = {Reimers, Clare E and Stecher III, Hilmar A and Westall, John C and Alleau, Yvan and Howell, Kate A and Soule, Leslie and White, Helen K and Girguis, Peter R.}
}
@conference {kelley2007towards,
	title = {Towards Determining the Upper Temperature Limit to Life},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2007},
	year = {2007},
	pages = {V23D{\textendash}02},
	author = {Kelley, DS and Girguis, P. R. and Wheat, G and Cordes, E and Schrenk, MO and Lin, M and Baross, JA and Delaney, JR}
}
@conference {girguis2007tracing,
	title = {Tracing The Fate Of Methane-Derived Carbon: Insights Into The Ecological Physiology Of Anaerobic Methanotrophy Via Quantitative Molecular and Geochemical Approaches},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2007},
	year = {2007},
	pages = {B51D{\textendash}07},
	author = {Girguis, P. R. and Nyholm, S. V. and Delong, E. F.}
}
@article {511206,
	title = {Microbiology. A proteomic snapshot of life at a vent},
	journal = {Science},
	volume = {315},
	number = {5809},
	year = {2007},
	note = {<p>Fisher, Charles RGirguis, PeterengCommentNew York, N.Y.2007/01/16 09:00Science. 2007 Jan 12;315(5809):198-9.</p>},
	month = {Jan 12},
	pages = {198-9},
	keywords = {*Ecosystem, *Proteomics, *Symbiosis, Animals, Bacterial Proteins/analysis/*metabolism, Carbon Isotopes/analysis, Carbon/metabolism, Chemoautotrophic Growth, Citric Acid Cycle, Gammaproteobacteria/*metabolism, Metabolic Networks and Pathways, Oxidation-Reduction, Pacific Ocean, Polychaeta/*microbiology/*physiology, Proteome, Reproduction, Sulfides/metabolism, Temperature},
	isbn = {1095-9203 (Electronic)0036-8075 (Linking)},
	author = {Fisher, C. R. and Girguis, P.}
}
@article {511201,
	title = {Substrate degradation kinetics, microbial diversity, and current efficiency of microbial fuel cells supplied with marine plankton.},
	journal = {Applied and Environmental Microbiology},
	volume = {73},
	number = {21},
	year = {2007},
	note = {<p>228AZTimes Cited:34Cited References Count:52</p>},
	month = {Nov},
	pages = {7029-7040},
	abstract = {<p>The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture of freshly captured phytoplankton and zooplankton (0.21 to 1 mm) added at an initial batch concentration of 27.5 mmol liter(-1) particulate organic carbon (OC). After 56.7 days, between 19.6 and 22.2\% of the initial OC remained, sulfate reduction coupled to OC oxidation accounted for the majority of the OC that was degraded, and current efficiencies (of the active MFCs) were between 11.3 and 15.5\%. In the open-circuit control cell, anaerobic plankton decomposition (as quantified by the decrease in total OQ could be modeled by three terms: two first-order reaction rate expressions (0.79 day(-1) and 0.037 day(-1), at 15 degrees C) and one constant, no-reaction term (representing 10.6\% of the initial 0Q. However, in each active MFC, decomposition rates increased during the third week, lagging just behind periods of peak electricity generation. We interpret these decomposition rate changes to have been due primarily to the metabolic activity of sulfur-reducing microorganisms at the anode, a finding consistent with the electrochemical oxidization of sulfide to elemental sulfur and the elimination of inhibitory effects of dissolved sulfide. Representative phylotypes, found to be associated with anodes, were allied with Delta-, Epsilon-, and Gamma-proteobacteria as well as the Flavobacterium-Cytophaga-Bacteroides and Fusobacteria. Based upon these results, we posit that higher current efficiencies can be achieved by optimizing plankton-fed MFCs for direct electron transfer from organic matter to electrodes, including microbial precolonization of high-surface-area electrodes and pulsed flowthrough additions of biomass.</p>},
	keywords = {communities, electricity-generation, energy, hydrogen-sulfide, methane production, organic-matter, phytoplankton, sea-floor, sediments, sulfate reduction},
	isbn = {0099-2240},
	author = {Reimers, C. E. and Stecher, H. A. and Westall, J. C. and Alleau, Y. and Howell, K. A. and Soule, L. and White, H. K. and Girguis, P. R.}
}
@article {girguis2006metabolite,
	title = {Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature},
	journal = {Journal of experimental biology},
	volume = {209},
	year = {2006},
	pages = {3516{\textendash}3528},
	publisher = {Company of Biologists},
	author = {Girguis, Peter R. and Childress, James J.}
}
@article {reimers2006microbial,
	title = {Microbial fuel cell energy from an ocean cold seep},
	journal = {Geobiology},
	volume = {4},
	year = {2006},
	pages = {123{\textendash}136},
	publisher = {Blackwell Publishing Ltd Oxford, UK},
	author = {Reimers, C. E. and Girguis, P. and Stecher, H. A. and Tender, L. M. and Ryckelynck, N. and Whaling, P.}
}
@conference {mcbride2006power,
	title = {Power storage and conversion from an ocean microbial energy source},
	booktitle = {OCEANS 2006},
	year = {2006},
	pages = {1{\textendash}5},
	publisher = {IEEE},
	organization = {IEEE},
	author = {McBride, LR and Girguis, P. and Reimers, C. E.}
}
@article {girguis2006thermal,
	title = {Thermal preference and tolerance of alvinellids},
	journal = {Science},
	volume = {312},
	year = {2006},
	pages = {231{\textendash}231},
	publisher = {American Association for the Advancement of Science},
	author = {Girguis, Peter R. and Lee, Raymond W}
}
@article {717076,
	title = {Power Storage and Conversion from an Ocean Microbial Energy Source.},
	journal = {Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers},
	year = {2006},
	author = {McBride, L. R. and Girguis, P. R. and Reimers, C. E.}
}
@article {511221,
	title = {Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature},
	journal = {Journal of Experimental Biology},
	volume = {209},
	number = {18},
	year = {2006},
	note = {<p>079CXTimes Cited:27Cited References Count:47</p>},
	month = {Sep 15},
	pages = {3516-3528},
	abstract = {<p>The hydrothermal vent tubeworm Riftia pachyptila is a dominant member of many hydrothermal vent communities along the East Pacific rise and is one of the fastest growing metazoans known. Riftia flourish in diffuse hydrothermal fluid flows, an environment with high spatial and temporal heterogeneity in physical and chemical conditions. To date, physiological and biochemical studies of Riftia have focused on Riftia{\textquoteright}s adaptations to its chemoautotrophic bacterial symbionts. However the relation between in situ physico-chemical heterogeneity and Riftia host and symbiont metabolism, in particular symbiont chemoautotrophic function, remain poorly understood. Accordingly, we conducted experiments using shipboard high-pressure respirometers to ascertain the effect of varying substrate concentrations and temperature on Riftia metabolite uptake and symbiont carbon fixation. Our results show that substrate concentrations can strongly govern Riftia oxygen and sulfide uptake rates, as well as net carbon uptake (which is a proxy for chemoautotrophic primary production). However, after sufficient exposure to sulfide and oxygen, Riftia were capable of sustaining symbiont autotrophic function for several hours in seawater devoid of sulfide or oxygen, enabling the association to support symbiont metabolism through brief periods of substrate deficiency. Overall, temperature had the largest influence on Riftia metabolite uptake and symbiont autotrophic metabolism. In sum, while Riftia requires sufficient availability of substrates to support symbiont chemoautotrophic function, it is extremely well poised to buffer the temporal and spatial heterogeneity in environmental substrate concentrations, alleviating the influence of environmental heterogeneity on symbiont chemoautotrophic function.</p>},
	keywords = {autotrophic carbon fixation, bacterial symbiont, chemoautotrophy, habitats, hydrothermal vent, inorganic carbon, jones, metabolism, oxidation, riftia, rose garden, stoichiometry, sulfide-binding, symbiosis, vestimentifera, worm},
	isbn = {0022-0949},
	author = {Girguis, P. R. and Childress, J. J.}
}
@article {511211,
	title = {Microbial fuel cell energy from an ocean cold seep},
	journal = {Geobiology},
	volume = {4},
	year = {2006},
	pages = {123-136},
	author = {Reimers, C. E. and Girguis, P. R. and Stecher, H. A. and Tender, L. M. and Ryckelynck, N. and Whaling, P.}
}
@article {511216,
	title = {Thermal preference and tolerance of alvinellids},
	journal = {Science},
	volume = {312},
	number = {5771},
	year = {2006},
	note = {<p>032HKTimes Cited:36Cited References Count:10</p>},
	month = {Apr 14},
	pages = {231},
	keywords = {pompeii worms, Temperature},
	isbn = {0036-8075},
	author = {Girguis, P. R. and Lee, R. W.}
}
@article {reimers2005using,
	title = {Using electrochemical methods to study redox processes and harvest energy from marine sediments},
	journal = {Geochim Cosmochim Acta},
	volume = {69},
	year = {2005},
	pages = {A575{\textendash}A575},
	author = {Reimers, C and Girguis, P. and Westall, J and Newman, D and Stecher, H and Howell, K and Alleau, Y.}
}
@conference {reimers2005electrochemical,
	title = {Electrochemical power generation and microbial communities at seafloor seeps},
	booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
	volume = {230},
	year = {2005},
	pages = {U1749{\textendash}U1749},
	publisher = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	organization = {AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	author = {Reimers, C. E. and Hilmar, AS and Girguis, P. and Tender, L. M.}
}
@article {girguis2005growth,
	title = {Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor},
	journal = {Applied and environmental microbiology},
	volume = {71},
	year = {2005},
	pages = {3725{\textendash}3733},
	publisher = {American Society for Microbiology},
	author = {Girguis, Peter R. and Cozen, Aaron E and DeLong, Edward F}
}
@article {reimers2005using,
	title = {Using electrochemical methods to study redox processes and harvest energy from marine sediments},
	journal = {Geochim Cosmochim Acta},
	volume = {69},
	year = {2005},
	pages = {A575{\textendash}A575},
	author = {Reimers, C and Girguis, P. and Westall, J and Newman, D and Stecher, H and Howell, K and Alleau, Y.}
}
@article {511231,
	title = {Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor},
	journal = {Applied and Environmental Microbiology},
	volume = {71},
	number = {7},
	year = {2005},
	note = {<p>944RETimes Cited:78Cited References Count:41</p>},
	month = {Jul},
	pages = {3725-3733},
	abstract = {<p>The consumption of methane in anoxic marine sediments is a biogeochemical phenomenon mediated by two archaeal groups (ANME-1 and ANME-2) that exist syntrophically with sulfate-reducing bacteria. These anaerobic methanotrophs have yet to be recovered in pure culture, and key aspects of their ecology and physiology remain poorly understood. To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-How bioreactor during two experiments at different advective porewater flow rates. We examined the growth kinetics of anaerobic methanotrophs and Desulfosarcina-like sulfate-reducing bacteria using quantitative PCR as a proxy for cell counts, and measured methane oxidation rates using membrane-inlet mass spectrometry. Our data show that the specific growth rates of ANME-1 and ANME-2 archaea differed in response to porewater How rates. ANME-2 methanotrophs had the highest rates in lower-flow regimes (mu(ANME-2) 0.167 center dot week(-1)), whereas ANME-1 methanotrophs had the highest rates in higher-flow regimes (mu(ANME-1) = 0.218 center dot week(-1)). In both incubations, Desulfosarcina-like sulfate-reducing bacterial growth rates were approximately 0.3 center dot week(-1), and their growth dynamics suggested that sulfate-reducing bacterial growth might be facilitated by, but not dependent upon, an established anaerobic methanotrophic population. ANME-1 growth rates corroborate field observations that ANME-1 archaea flourish in higher-flow regimes. Our growth and methane oxidation rates jointly demonstrate that anaerobic methanotrophs are capable of attaining substantial growth over a range of environmental conditions used in these experiments, including relatively low methane partial pressures.</p>},
	keywords = {anoxic marine-sediments, carbon isotopic evidence, communities, consortium, consumption, Ecology, identification, oxidation rates, reduction, sea-floor},
	isbn = {0099-2240},
	author = {Girguis, P. R. and Cozen, A. E. and Delong, E. F.}
}
@inbook {childress2004edge,
	title = {On the edge of a deep biosphere: Real animals in extreme environments},
	booktitle = {The Subseafloor Biosphere at Mid-Ocean Ridges, 2004},
	year = {2004},
	pages = {41{\textendash}49},
	publisher = {Blackwell Publishing Ltd},
	organization = {Blackwell Publishing Ltd},
	author = {Childress, James J. and Fisher, Charles F and Felbeck, Horst and Peter Girguis}
}
@conference {kelley2004towards,
	title = {Towards Determining the Upper Temperature Limits to Life on Earth: An In-situ Sulfide-Microbial Incubator},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2004},
	year = {2004},
	pages = {OS42A{\textendash}05},
	author = {Kelley, D and Baross, J and Delaney, J. and Girguis, P. and Schrenk, M}
}
@inbook {childress2004edge,
	title = {On the edge of a deep biosphere: Real animals in extreme environments},
	booktitle = {The Subseafloor Biosphere at Mid-Ocean Ridges, 2004},
	year = {2004},
	pages = {41{\textendash}49},
	publisher = {Blackwell Publishing Ltd},
	organization = {Blackwell Publishing Ltd},
	author = {Childress, James J. and Fisher, Charles F and Felbeck, Horst and Peter Girguis}
}
@conference {kelley2004towards,
	title = {Towards Determining the Upper Temperature Limits to Life on Earth: An In-situ Sulfide-Microbial Incubator},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2004},
	year = {2004},
	pages = {OS42A{\textendash}05},
	author = {Kelley, D and Baross, J and Delaney, J. and Girguis, P. and Schrenk, M}
}
@article {girguis2003growth,
	title = {Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	year = {2003},
	pages = {5472{\textendash}5482},
	publisher = {American Society for Microbiology},
	author = {Girguis, Peter R. and Orphan, Victoria J and Hallam, Steven J and DeLong, Edward F}
}
@article {hallam2003identification,
	title = {Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea},
	journal = {Applied and environmental microbiology},
	volume = {69},
	year = {2003},
	pages = {5483{\textendash}5491},
	publisher = {American Society for Microbiology},
	author = {Hallam, Steven J and Girguis, Peter R. and Preston, Christina M and Richardson, Paul M and DeLong, Edward F}
}
@article {511241,
	title = {Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	number = {9},
	year = {2003},
	note = {<p>723MWTimes Cited:74Cited References Count:39</p>},
	month = {Sep},
	pages = {5472-5482},
	abstract = {<p>Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that simulates the majority of in situ conditions and supports the metabolism and growth of anaerobic methanotrophic archaea. We incubated sediments collected from within and outside a methane cold seep in Monterey Canyon, Calif., for 24 weeks on the AMIS system. Anaerobic methane oxidation was measured in all sediments after incubation on AMIS, and quantitative molecular techniques verified the increases in methane-oxidizing archaeal populations in both seep and nonseep sediments. Our results demonstrate that the AMIS system stimulated the maintenance and growth of anaerobic methanotrophic archaea, and possibly their syntrophic, sulfate-reducing partners. Our data demonstrate the utility of combining physiological and molecular techniques to quantify the growth and metabolic activity of anaerobic microbial consortia. Further experiments with the AMIS system should provide a better understanding of the biological mechanisms of methane oxidation in anoxic marine environments. The AMIS may also enable the enrichment, purification, and isolation of methanotrophic archaea as pure cultures or defined syntrophic consortia.</p>},
	keywords = {anoxic marine-sediments, cells, cold seeps, consortium, consumption, diversity, identification, monterey bay, sulfate reduction, water chemistry},
	isbn = {0099-2240},
	author = {Girguis, P. R. and Orphan, V. J. and Hallam, S. J. and Delong, E. F.}
}
@article {511236,
	title = {Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	number = {9},
	year = {2003},
	note = {<p>723MWTimes Cited:166Cited References Count:36</p>},
	month = {Sep},
	pages = {5483-5491},
	abstract = {<p>Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 and ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about anaerobic methane oxidation at the molecular level, the evolutionary relationship between methane-oxidizing archaea (MOA) and methanogenic archaea raises the possibility that MOA have co-opted key elements of the methanogenic pathway, reversing many of its steps to oxidize methane anaerobically. In order to explore this hypothesis, the existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in ANME-1 and ANME-2 archaea isolated from various marine environments. Clone libraries targeting a conserved region of the alpha subunit of MCR (mcrA) were generated and compared from environmental samples, laboratory-incubated microcosms, and fosmid libraries. Four out of five novel mcrA types identified from these sources were associated with ANME-1 or ANME-2 group members. Assignment of mcrA types to specific phylogenetic groups was based on environmental clone recoveries, selective enrichment of specific MOA and mcrA types in a microcosm, phylogenetic congruence between mcrA and small-subunit rRNA tree topologies, and genomic context derived from fosmid sequences. Analysis of the ANME-1 and ANME-2 mcrA sequences suggested the potential for catalytic activity based on conservation of active-site amino acids. These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea.</p>},
	keywords = {anoxic marine-sediments, Bacteria, Biochemistry, consumption, environments, methanogenesis, oxidation, pcr amplification, phylogenetic analysis, ribosomal-rna},
	isbn = {0099-2240},
	author = {Hallam, S. J. and Girguis, P. R. and Preston, C. M. and Richardson, P. M. and Delong, E. F.}
}
@conference {girguis2002anaerobic,
	title = {Anaerobic enrichment of methane-oxidizing archaeal/bacterial consortia in deep-sea marine sediments},
	booktitle = {General Meeting of the American Society for Microbiology},
	volume = {102},
	year = {2002},
	pages = {327},
	author = {Girguis, P. R. and Delong, E. F.}
}
@conference {sessions2002connecting,
	title = {Connecting genomics and biogeochemistry via the carbon-isotopic composition of ribosomal RNA},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2002},
	year = {2002},
	pages = {B51B{\textendash}0721},
	author = {Sessions, AL and Pearson, A and Hayes, J. M. and Delong, E. F. and Girguis, P.}
}
@conference {girguis2002anaerobic,
	title = {Anaerobic enrichment of methane-oxidizing archaeal/bacterial consortia in deep-sea marine sediments},
	booktitle = {General Meeting of the American Society for Microbiology},
	volume = {102},
	year = {2002},
	pages = {327},
	author = {Girguis, P. R. and Delong, E. F.}
}
@conference {sessions2002connecting,
	title = {Connecting genomics and biogeochemistry via the carbon-isotopic composition of ribosomal RNA},
	booktitle = {AGU Fall Meeting Abstracts},
	volume = {2002},
	year = {2002},
	pages = {B51B{\textendash}0721},
	author = {Sessions, AL and Pearson, A and Hayes, J. M. and Delong, E. F. and Girguis, P.}
}
@article {girguis2002effects,
	title = {Effects of metabolite uptake on proton-equivalent elimination by two species of deep-sea vestimentiferan tubeworm, Riftia pachyptila and Lamellibrachia cf luymesi: proton elimination is a necessary adaptation to sulfide-oxidizing chemoautotrophic symbiont},
	journal = {Journal of experimental biology},
	volume = {205},
	year = {2002},
	pages = {3055{\textendash}3066},
	publisher = {Company of Biologists},
	author = {Girguis, P. R. and Childress, J. J. and Freytag, J. K. and Klose, K. and Stuber, R.}
}
@article {511246,
	title = {Effects of metabolite uptake on proton-equivalent elimination by two species of deep-sea vestimentiferan tubeworm, Riftia pachyptila and Lamellibrachia cf luymesi: proton elimination is a necessary adaptation to sulfide-oxidizing chemoautotrophic symbiont},
	journal = {Journal of Experimental Biology},
	volume = {205},
	number = {19},
	year = {2002},
	note = {<p>604ZZTimes Cited:28Cited References Count:38</p>},
	month = {Oct},
	pages = {3055-3066},
	abstract = {<p>Intracellular symbiosis requires that the host satisfy the symbiont{\textquoteright}s metabolic requirements, including the elimination of waste products. The hydrothermal vent tubeworm Riftia pachyptila and the hydrocarbon seep worm Lamellibrachia cf luymesi are symbiotic with chemolithoautotrophic bacteria that produce sulfate and protons as end-products. In this report, we examine the relationship between symbiont metabolism and host proton equivalent elimination in R. pachyptila and L cf luymesi, and the effects of sulfide exposure on proton-equivalent elimination by Urechis caupo, an echiuran worm that lacks intracellular symbionts (for brevity, we will hereafter refer to proton-equivalent elimination as {\textquoteright}proton elimination{\textquoteright}). Proton elimination by R. pachyptila and L. cf luymesi constitutes the worms{\textquoteright} largest mass-specific metabolite flux, and R. pachyptila proton elimination is, to our knowledge, the most rapid reported for any metazoan. Proton elimination rates by R. pachyptila and L. cf luymesi correlated primarily with the rate of sulfide oxidation. Prolonged exposure to low environmental oxygen concentrations completely inhibited the majority of proton elimination by R. pachyptila, demonstrating that proton elimination does not result primarily from anaerobic metabolism. Large and rapid increases in environmental inorganic carbon concentrations led to short-lived proton elimination by R. pachyptila, as a result of the equilibration between internal and external inorganic carbon pools. U. caupo consistently exhibited proton elimination rates 5-20 times lower than those, of L cf luymesi and R. pachyptila upon exposure to sulfide. Treatment with specific ATPase inhibitors completely inhibited a fraction of proton elimination and sulfide and inorganic carbon uptake by R. pachyptila, suggesting that proton elimination occurs in large part via K+/H+-ATPases and Na+/H+-ATPases. In the light of these results, we suggest that protons are the primary waste product of the symbioses of R. pachyptila and L cf luymesi, and that proton elimination is driven by symbiont metabolism, and may be the largest energetic cost incurred by the worms.</p>},
	keywords = {acquisition, bacterial symbiont, Biochemistry, carbon-dioxide, chemoautotrophy, hydrothermal vent, hydrothermal vent tubeworm, ion-transport, jones, lamellibrachia cf luymesi, metabolite uptake, oxidation, physiology, proton-equivalent, riftia pachyptila, sensitivity, sulfide, symbiosis, tubeworm, urechis caupo, vestimentiferan, worm},
	isbn = {0022-0949},
	author = {Girguis, P. R. and Childress, J. J. and Freytag, J. K. and Klose, K. and Stuber, R.}
}
@article {freytag2001paradox,
	title = {A paradox resolved: sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {98},
	year = {2001},
	pages = {13408{\textendash}13413},
	publisher = {National Academy of Sciences},
	author = {Freytag, John K and Girguis, Peter R. and Bergquist, Derk C and Andras, Jason P and Childress, James J. and Fisher, Charles R}
}
@article {511251,
	title = {A paradox resolved: Sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {98},
	number = {23},
	year = {2001},
	note = {<p>490WMTimes Cited:82Cited References Count:37</p>},
	month = {Nov 6},
	pages = {13408-13413},
	abstract = {<p>Vestimentiferan tubeworms, symbiotic with sulfur-oxidizing chemoautotrophic bacteria, dominate many cold-seep sites in the Gulf of Mexico. The most abundant vestimentiferan species at these sites, Lamellibrachia cf. luymesi, grows quite slowly to lengths exceeding 2 meters and lives in excess of 170-250 years. L. cf. luymesi can grow a posterior extension of its tube and tissue, termed a "root," down into sulfidic sediments below its point of original attachment. This extension can be longer than the anterior portion of the animal. Here we show, using methods optimized for detection of hydrogen sulfide down to 0.1 muM in seawater, that hydrogen sulfide was never detected around the plumes of large cold-seep vestimentiferans and rarely detectable only around the bases of mature aggregations. Respiration experiments, which exposed the root portions of L. cf. luymesi to sulfide concentrations between 51-561 muM, demonstrate that L. cf. luymesi use their roots as a respiratory surface to acquire sulfide at an average rate of 4.1 mu mol.g(-1).h(-1). Net dissolved inorganic carbon uptake across the plume of the tubeworms was shown to occur in response to exposure of the posterior (root) portion of the worms to sulfide, demonstrating that sulfide acquisition by roots of the seep vestimentiferan L. cf. luymesi can be sufficient to fuel net autotrophic total dissolved inorganic carbon uptake.</p>},
	keywords = {biology, calyptogena-magnifica, communities, gulf, hydrothermal vent, mexico, organisms, symbioses, transport, worm riftia-pachyptila},
	isbn = {0027-8424},
	author = {Freytag, J. K. and Girguis, P. R. and Bergquist, D. C. and Andras, J. P. and Childress, J. J. and Fisher, C. R.}
}
@mastersthesis {girguis2000metabolite,
	title = {Metabolite flux of the tubeworm Riftia pachyptila: Stoichiometric balance of the chemoautotrophic symbiosis and the potential rates of primary production},
	year = {2000},
	school = {University of California, Santa Barbara},
	type = {phd},
	author = {Girguis, Peter Riad}
}
@article {girguis2000fate,
	title = {Fate of nitrate acquired by the tubeworm Riftia pachyptila},
	journal = {Applied and environmental microbiology},
	volume = {66},
	year = {2000},
	pages = {2783{\textendash}2790},
	publisher = {American Society for Microbiology},
	author = {Girguis, Peter R. and Lee, Raymond W and Desaulniers, Nicole and Childress, James J. and Pospesel, Mark and Felbeck, Horst and Zal, Franck}
}
@mastersthesis {girguis2000metabolite,
	title = {Metabolite flux of the tubeworm Riftia pachyptila: Stoichiometric balance of the chemoautotrophic symbiosis and the potential rates of primary production},
	year = {2000},
	school = {University of California, Santa Barbara},
	type = {phd},
	author = {Girguis, Peter Riad}
}
@article {freytag2000paradox,
	title = {A paradox resolved: sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy},
	journal = {Comparative Biochemistry and Physiology{\textendash}Part B: Biochemistry and Molecular Biology},
	year = {2000},
	pages = {S37},
	author = {Freytag, John K and Girguis, Peter R. and Bergquist, Derk C and Andras, Jason P and Childress, James J. and Fisher, Charles R}
}
@article {511256,
	title = {Fate of nitrate acquired by the tubeworm Riftia pachyptila.},
	journal = {Applied and Environmental Microbiology},
	volume = {66},
	number = {7},
	year = {2000},
	note = {<p>332DETimes Cited:38Cited References Count:36</p>},
	month = {Jul},
	pages = {2783-2790},
	abstract = {<p>The hydrothermal vent tubeworm Riftia pachyptila lacks a mouth and gut and lives in association with intracellular, sulfide-oxidizing chemoautotrophic bacteria. Growth of this tubeworm requires an exogenous source of nitrogen for biosynthesis, and, as determined in previous studies, environmental ammonia and free amino acids appear to be unlikely sources of nitrogen. Nitrate, however, is present in situ (K, Johnson, J. Childress, R. Hessler, C. Sakamoto-Arnold, and C. Beehler, Deep-Sea Res. 35:1723-1744, 1988), is taken up by the host, and can be chemically reduced by the symbionts (U. Hentschel and H. Felbeck, Nature 366:338-340, 1993), Here we report that at an in situ concentration of 40 mu M, nitrate is acquired by R, pachyptila at a rate of 3.54 mu mol g(-1) h(-1), while elimination of nitrite and elimination of ammonia occur at much lower rates (0.017 and 0.21 mu mol g(-1) h(-1), respectively), We also observed reduction of nitrite (and accordingly nitrate) to ammonia in the trophosome tissue. When R. pachyptila tubeworms are exposed to constant in situ conditions for 60 h, there is a difference between the amount of nitrogen acquired via nitrate uptake and the amount of nitrogen lost via nitrite and ammonia elimination, which indicates that there is a nitrogen "sink" Our results demonstrate that storage of nitrate does not account for the observed stoichiometric differences in the amounts of nitrogen, Nitrate uptake was not correlated with sulfide or inorganic carbon flux, suggesting that nitrate is probably not an important oxidant in metabolism of the symbionts, Accordingly, we describe a nitrogen flux model for this association, in which the product of symbiont nitrate reduction, ammonia, is the primary source of nitrogen for the host and the symbionts and fulfills the association{\textquoteright}s nitrogen needs via incorporation of ammonia into amino acids.</p>},
	keywords = {assimilation, blood, chemoautotrophic symbionts, hydrothermal vent animals, inorganic nitrogen, Respiration, rose garden, sulfide, uric-acid, worm},
	isbn = {0099-2240},
	author = {Girguis, P. R. and Lee, R. W. and Desaulniers, N. and Childress, J. J. and Pospesel, M. and Felbeck, H. and Zal, F.}
}
@article {goffredi1999physiological,
	title = {Physiological functioning of carbonic anhydrase in the hydrothermal vent tubeworm Riftia pachyptila},
	journal = {The Biological Bulletin},
	volume = {196},
	year = {1999},
	pages = {257{\textendash}264},
	publisher = {MBL},
	author = {Goffredi, Shana K and Girguis, Peter R. and Childress, James J. and Desaulniers, Nicole T}
}
@article {511261,
	title = {Physiological functioning of carbonic anhydrase in the hydrothermal vent tubeworm Riftia pachyptila},
	journal = {Biological Bulletin},
	volume = {196},
	number = {3},
	year = {1999},
	note = {<p>210KRTimes Cited:20Cited References Count:32</p>},
	month = {Jun},
	pages = {257-264},
	abstract = {<p>On the basis of our experiments, it is clear that carbonic anhydrase (CA) plays an important role in the CO2-concentrating mechanisms in Riftia pachyptila. Plume tissue from freshly collected animals had the highest CA activity, 253.7 +/- 36.0 mu mol CO2 min(-1) g(-1) wet wt, and trophosome activity averaged 109.4 +/- 17.9 mu mol CO2 min(-1) g(-1) wet wt. Exposure of living worms to ethoxyzolamide, a carbonic anhydrase inhibitor, resulted in a 99\% decrease in CA activity (from 103.9 +/- 38.6 to 0.7 +/- 0.2 mu mol CO2 min(-1) g(-1) wet wt in the plume tissue and 57.6 +/- 17.9 to 0.03 +/- 0,11 mu mol CO2 min(-1) g(-1) wet wt in the trophosome) and essentially a complete cessation of Sigma CO2, uptake. High concentrations of CA appear to facilitate the equilibration between inorganic carbon (Ci) in the external and internal environments, greatly enhancing the diffusion of CO2 into the animal. In summary, R. pachyptila demonstrates very effective acquisition of inorganic carbon from the environment, thereby providing the symbionts with large amounts of CO2. This effective acquisition is made possible by three factors: extremely effective pH regulation, a large external pool of CO2, and, described in this paper, high levels of carbonic anhydrase.</p>},
	keywords = {blood, co2 excretion, facilitation, gill, inorganic carbon, jones, symbiont, transport, worm},
	isbn = {0006-3185},
	author = {Goffredi, S. K. and Girguis, P. R. and Childress, J. J. and Desaulniers, N. T.}
}
@article {girguis1998h+,
	title = {H+ equivalent elimination by the tubeworm Riftia pachyptila},
	journal = {Cah. Biol. Mar},
	volume = {39},
	year = {1998},
	pages = {295},
	author = {Girguis, Peter R. and Childress, James J.}
}
@article {girguis1998h+,
	title = {H+ equivalent elimination by the tubeworm Riftia pachyptila},
	journal = {Cah. Biol. Mar},
	volume = {39},
	year = {1998},
	pages = {295},
	author = {Girguis, Peter R. and Childress, James J.}
}
@article {511266,
	title = {H+ equivalent elimination by the tube-worm Riftia pachyptila.},
	journal = {Cahiers de Biologie Marine},
	volume = {39},
	number = {3-4},
	year = {1998},
	pages = {295-296},
	keywords = {Annelids, Biochemistry, Invertebrates, Marine zones, Pacific Ocean},
	author = {Girguis, P. R. and Childress, J. J.}
}
