Publications
Scientific publications provide an in-depth look into the details of our research. We strive to ensure that all our publications are open-access.
A list of our publications with their respective DOIs can be found below.
For our latest publications please visit Google Scholar.
Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts
Mitchell, J.H., Freedman, A.H., Delaney, J.A., and Girguis, P.R., 2024. Nature Microbiology, 9(6), pp.1526-1539. doi:10.1038/s41564-024-01704-y
Sulfur cycling likely obscures dynamic biologically‐driven iron redox cycling in contemporary methane seep environments
Baker, I.R. and Girguis, P.R. 2024. Environmental Microbiology Reports, 16(3), p.e13263. doi:10.1111/1758-2229.13263
Genomic language model predicts protein co-regulation and function
Hwang, Y., Cornman, A.L., Kellogg, E.H., Ovchinnikov, S., and Girguis, P.R. 2024. Nature Communications, 15(1), p.2880. doi:10.1038/s41467-024-46947-9
Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation
Baker, I.R., Matzen, S.L., Schuler, C.J., Toner, B.M., and Girguis, P.R. 2023. PNAS nexus, 2(12), pgad421. doi:10.1093/pnasnexus/pgad421
Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment
Frates, E.S., Spietz, R.L., Silverstein, M.R., Girguis, P., Hatzenpichler, R., and Marlow, J.J. 2023. Frontiers in Microbiology, 14. doi:10.3389/fmicb.2023.1235906
A molluscan class struggle: exploring the surprisingly uneven distribution of chemosymbiosis among two major mollusk groups
Hughes, I.V. and Girguis, P.R. 2023. Frontiers in Marine Science, 10, 1167803. doi:10.3389/fmars.2023.1167803
The metabolic rate of the biosphere and its components
Hoehler, T.M., Mankel, D.J., Girguis, P.R., McCollom, T.M., Kiang, N.Y., and Jørgensen, B.B. 2023. Proceedings of the National Academy of Sciences, 120(25), e2303764120. doi:10.1073/pnas.2303764120
Proterozoic acquisition of archaeal genes for extracellular electron transfer: A metabolic adaptation of aerobic ammonia-oxidizing bacteria to oxygen limitation
Gulay, A., Fournier, G., Smets, B.F., and Girguis, P.R. 2023. Molecular Biology and Evolution, 40(8), msad161. doi:10.1093/molbev/msad161
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats
Hwang, Y., Roux, S., Coclet, C., Krause, S.J., and Girguis, P.R. 2023. Nature Microbiology, 1-12. doi:10.1038/s41564-023-01347-5
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis
Osvatic, J.T., Yuen, B., Kunert, M., Wilkins, L., Hausmann, B., Girguis, P.R., Lundin, K., Taylor, J., Jospin, G., and Petersen, J.M. 2023. The ISME Journal. doi:10.1038/s41396-022-01355-z
Probing the Santa Barbara Basin benthos Hydrocarbon seeps
Bernhard, J.M., Edgcomb, V.P., Powers, C.C., Travis, B., Lott, S., Yousavich, D., Haiat, K., Raineault, N., and Girguis, P.R. 2022. Oceanography, (35)1, 26-27.
Ocean system science to inform the exploration of ocean worlds
German, C.R., Blackman, D.K., Fisher, A.T., Girguis, P.R., Hand, K.P., Hoehler, T.M., Huber, J.A., Marshall, J.C., Pietro, K.R., Seewald, J.S., and Shock, E.L. 2022. Oceanography, 35(1), 16-22. doi:10.5670/oceanog.2021.411
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Shaffer, J.P., Nothias, L-F., Thompson, L.R., Sanders, J.G., et al. and the Earth Microbiome Project 500 (EMP500) Consortium. 2022. Nature Microbiology, 7, 2128–2150. doi:10.1038/s41564-022-01266-x
Discovering hydrothermalism from Afar: In Situ methane instrumentation and change-point detection for decision-making
Preston, Victoria, Flaspohler, G., Kapit, J., Pardis, W.,Youngs, S., Martocello III, D.E., Roy, N., Girguis, P.R., Wankel, S.D., and Michel, A.P.M. 2022. Frontiers in Earth Science, 1965. doi:10.3389/feart.2022.984355
Using deep-sea images to examine ecosystem services associated with methane seeps
Le, J.T., Girguis, P.R., and Levin, L.A. 2022. Marine Environmental Research, 105740. doi:10.1016/j.marenvres.2022.105740
Impacts of bioturbation on iron biogeochemistry and microbial communities in coastal sediment mesocosms under varying degrees of hypoxia
Beam, J.P., Michaud, A.B., Johnston, D.T., Girguis, P.R., and Emerson, D. 2022. Estuarine, Coastal and Shelf Science, 108032. doi:10.1016/j.ecss.2022.108032
Low-cost, deep-sea imaging and analysis tools for deep-sea exploration: A collaborative design study
Bell, K.L.C., Chow, J.S., Hope, A., Quinzin, M.C., Cantner, K.A., Amon, D.J., Cramp J.E., Rotjan R.D., Kamalu L., de Vos, A., Talma S., Buglass S., Wade V., Filander Z., Noyes K., Lynch M., Knight A., Lourenço N., Girguis P.R., de Sousa J.B., Blake C., Kennedy B.R.C., Noyes T.J., and McClain C.R. 2022. Frontier in Marine Science. doi:10.3389/fmars.2022.873700
Concentrations, d13C and D14C data for DOC and DIC in fluids collected from North Pond Cork Observatories U1382A and U1383C and from bottom seawater in 2012, 2014 and 2017
Girguis, P.R., and Shah Walter, S.R. 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-08-10. doi:10.26008/1912/bco-dmo.876729.1. (NOTE: This is a publicly available dataset)
Differentiated evolutionary strategies of genetic diversification in atlantic and pacific thaumarchaeal populations
Hwang, Y. and Girguis, P.R. 2022. Msystems, e01477-21. doi:10.1128/msystems.01477-21
Evidence for horizontal and vertical transmission of Mtr-mediated extracellular electron transfer among the Bacteria
Baker, I.R., Conley, B.E., Gralnick, J.A., and Girguis, P.R. 2022. Mbio, 13(1), e02904-21. doi:10.1128/mbio.02904-21
Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genomede
de Oliveira, A.L., Mitchell, J., Girguis, P.R., and Bright, M. 2022. Molecular Biology and Evolution, 39(1), msab347. doi:10.1093/molbev/msab347
CRISPR/Cas9‐induced disruption of Bodo saltansparaflagellar rod‐2 gene reveals its importance for cell survival
Gomaa, F., Li, Z.H., Beaudoin, D.J., Alzan, H., Girguis, P.R., Docampo, R., and Edgcomb, V.P., 2022. Environmental Microbiology. doi:10.1111/1462-2920.15918
Spatially resolved correlative microscopy and microbial identification reveal dynamic depth‐and mineral‐dependent anabolic activity in salt marsh sediment
Marlow, J., Spietz, R., Kim, K.Y., Ellisman, M., Girguis, P.R., and Hatzenpichler, R. 2021. Environmental Microbiology, 23(8), 4756-4777. doi:10.1111/1462-2920.15667
The grayness of the origin of life
Smith, H.H., Hyde, A.S., Simkus, D.N. Libby, E., Maurer, S.E., Graham, H.V., Kempes, C.P., Lollar, B.S. Chou, L., Ellington, A.D., Fricke, G.M., Girguis, P.R., Grefenstette, N.M., Pozarycki, C.I., House, C.H., and Johnson, S.S. 2021. Life, 11(6), 498. doi:10.3390/life11060498
Co-occurring activities of two autotrophic pathways in symbionts of the hydrothermal vent tubeworm Riftia pachyptila
Leonard, J.M., Mitchell, J., Beinart, R.A., Delaney, J.A., Sanders, J.G., Ellis, G., Goddard, E.A., Girguis, P.R., and Scott, K.M. 2021. Applied and Env. Microbiology, 87(17), e00794-21. doi:10.1128/AEM.00794-21
Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites
Marlow, J.J., Hoer, D., Jungbluth, S.P., Reynard, L.M., Gartman, A., Chavez, M.S., El-Naggar, M.Y., Tuross, N., Orphan, V.J. and Girguis, P.R. 2021. Proceedings of the National Academy of Sciences, 118(25). doi:10.1073/pnas.2006857118
Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps
Leprich, D.J., Flood, B.E., Schroedl, P.R., Ricci, E., Marlow, J.J., Girguis, P.R., and Bailey, J.V. 2021. The ISME Journal. doi:10.1038/s41396-021-00903-3
Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids
Trembath-Reichert E., Shah-Walter S.R., Ortiz M.A.F., Carter P.D., Girguis P.R., and Huber J.A. 2021. Science Advances, Apr;7(18). doi:10.1126/sciadv.abg0153
Interactions between iron sulfide minerals and organic carbon: Implications for biosignature preservation and detection
Picard, A., Gartman, A., and Girguis, P.R. 2021. Astrobiology. doi:10.1089/ast.2020.2276
Mud, microbes, and macrofauna: seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat
Beam, J.P., George, S., Record, N.R., Countway, P.D., Johnston,D.T., Girguis, P.R., and Emerson D. 2020. Frontiers in Marine Science. doi:10.3389/fmars.2020.562617
A genomic catalog of Earth’s microbiomes
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu1, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J.P., Edirisinghe, J.N., Henry, C.S., Jungbluth, S.P., Chivian, D., Dehal, P., Wood-Charlson, E.M., Arkin, A.P., Tringe, S., Visel, A., and the IMG/M Data Consortium. Nature Biotechnology, 1-11. doi:10.1038/s41587-020-0718-6
Undersea Supercharger™ network?: A commentary promoting in-situ methane to fuel expansion of seafloor robotics
Waterston, J., Florea, R., and Girguis, P.R. 2020. Marine Technology Society Journal, 54.5, 5-7. doi:10.4031/MTSJ.54.5.1
Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails
Breusing, C., Mitchell, J., Delaney, J., Sylva, S., Seewald, J., Girguis, P.R., and Beinart, R. 2020. The ISME Journal. doi:10.1038/s41396-020-0707-2
Roadmap for naming uncultivated Archaea and Bacteria
Murray, A.E., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K.T., Lane, C.E., Papke, R.T., Parks, D.H., Rossello-Mora, R., et al. 2020. Nature Microbiology, 1-7. doi:10.1038/s41564-020-0733-x
Genetic tool development in marine protists: Emerging model organisms for experimental cell biology
Faktorová, D., Nisbet, R.E.R., Robledo, J.A.F., Casacuberta, E., Sudek, L., Allen, A.E., Ares, M., Aresté, C., Balestreri, C., Barbrook, A.C. Beardslee, P., et al. 2020. Nature Methods, 17(5), 481-494. doi:10.1038/s41592-020-0796-x
Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens
Totoiu, C.A., Phillips, J.M., Reese, A.T., Majumdar, S., Girguis, P.R., Raston, C.L., and Weiss, G.A. 2020. PloS ONE, 15(1), e0225807. doi:10.1371/journal.pone.0225807
Authigenic metastable iron sulfide minerals preserve microbial organic carbon in anoxic environments
Picard, A., Gartman, A., Cosmidis, J., Obst, M., Vidoudez, C., Clarke, D.R., and Girguis, P.R. 2019. Chemical Geology, 530, 119343. doi:10.1016/j.chemgeo.2019.119343
Hydrogen does not appear to be a major electron donor for symbiosis with the deep-sea hydrothermal vent tubeworm Riftia pachyptila
Mitchell, J.H., Leonard, J.M., Delaney, J., Girguis, P.R.*, and Scott, K.M.* 2020. Applied and Environmental Microbiology, 86(1). doi:10.1128/AEM.01522-19
Synergistic substrate cofeeding stimulates reductive metabolism
Park, J.O., Liu, N., Holinski, K.M., Emerson, D.F., Qiao, K., Woolston, B.M., Xu, J., Lazar, Z., Islam, M.A., Vidoudez, C., and Girguis, P.R. 2019. Nature Metabolism, 1(6), 643-651. doi:10.1038/s42255-019-0077-0
The bacterial symbionts of closely related hydrothermal vent snails with distinct geochemical habitats show broad similarity in chemoautotrophic gene content
Beinart, R.A., Luo, C., Konstantinidis, K., Stewart, F., and Girguis, P.R. 2019. Frontiers in Microbiology, 10, 1818. doi:10.3389/fmicb.2019.01818
Methane-linked mechanisms of electron uptake from cathodes by Methanosarcina barkeri
Rowe, A.R., Xu, S., Gardel, E., Bose, A., Girguis, P.R., Amend, J.P., and El-Naggar, M.Y. 2019. mBio, 10(2), e02448-18. doi:10.1128/mBio.02448-18
Remarkable capacity for anaerobic oxidation of methane at high methane concentration
Bowles, M.W., Samarkin, V.A., Hunter, K.S., Finke, N., Teske, A.P., Girguis, P.R., and Joye, S.B. 2019. Geophysical Research Letters, 46(21), 12192-12201. doi:10.1029/2019GL084375
Hydrothermal energy transfer and organic carbon production at the deep seafloor
LeBris, N., Yucel, M., Das, A., Sievert, S.M., and Girguis, P.R. 2019. Frontiers in Marine Science, 5, 531. doi:10.3389/fmars.2018.00531
Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite
Picard, A., Gartman, A., Clarke, D.R., and Girguis, P.R. 2018. Geochimica et Cosmochimica Acta, 220, 367-384. doi:10.1016/j.gca.2017.10.006
Microbial decomposition of marine dissolved organic matter in cool oceanic crust
Shah Walter, S.R., Jaekel, U., Osterholz, H., Fisher, A.T., Huber, J.A., Pearson, A., Dittmar, T., and Girguis, P.R. 2018. Nature Geoscience. doi:10.1038/s41561-018-0109-5
Nitrogen cycling of active bacteria within oligotrophic sediment of the mid-Atlantic Ridge flank
Reese, B.K., Zinke, L.A., Sobol, M.S., LaRowe, D.E., Orcutt, B.N., Zhang, X., Jaekel, U., Wang, F., Dittmar, T., Defforey, D., Tully, B., Paytan, A., Sylvan, J.B., Amend, J.P., Edwards, K.J., and Girguis, P.R. 2018. Geomicrobiology Journal. doi:10.1080/01490451.2017.1392649
Harnessing a methane‐fueled, sediment‐free mixed microbial community for utilization of distributed sources of natural gas
Marlow, J.J., Kumar, A., Enalls, B., Reynard, L.M., Tuross, N., Stephanopoulos, G., and Girguis, P.R. 2017. Biotechnology and Bioengineering, 1-15. doi:10.1002/bit.26576
* Top downloaded paper
Iron sulfide formation on iron substrates by electrochemical reaction in anoxic conditions
Guan, X., Enalls, B.C., Clarke, D.R., and Girguis, P.R. 2017. Crystal Growth & Design, 17(12), 6332-6340. doi:10.1021/acs.cgd.7b01013
Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite
Picard, A., Gartman, A., Clarke, D.R., and Girguis, P.R. 2017. Geochimica et Cosmochimica Acta. doi:10.1016/j.gca.2017.10.006
In situ carbon isotopic exploration of an active submarine volcano
Michel, A.P.M., Wankel, S.D., Kapit, J., Sandwith, Z., and Girguis, P.R. 2017. Deep Sea Research Part II: Topical Studies in Oceanography. doi:10.1016/j.dsr2.2017.10.004
Microbes facilitate mineral deposition in bioelectrochemical systems
Gartman, A., Picard, A., Olins, H.C., Sarode, N., Clarke, D.R., and Girguis, P.R. 2017. ACS Earth and Space Chemistry. doi:10.1021/acsearthspacechem.7b00042
Telepresence is a potentially transformative tool for field science
Marlow, J., Borrelli, C., Jungbluth, S.P., Hoffman, C., Marlow, J., Girguis, P.R., Dekas, A., Skarke, A., Blackman, D., Fornari, D., and Soule, A. 2017. Proceedings of the National Academy of Sciences, 114(19), 4841-4844. doi:10.1073/pnas.1703514114
Toward establishing model organisms for marine protists: successful transfection protocols for Parabodo caudatus (Kinetoplastida: Excavata)
Gomaa, F., Garcia, P.A., Delaney, J., Girguis, P.R., Buie, C.R., and Edgcomb, V.P. 2017. Environmental Microbiology. doi:10.1111/1462-2920.13830
Co-registered geochemistry and metatranscriptomics reveal unexpected distributions of microbial activity within a hydrothermal vent field
Olins, H.C., Rogers, D.R., Preston, C., Ussler III, W., Pargett, D., Jensen, S., Roman, B., Birch, J.M., Scholin, C.A., Haroon, M.F., and Girguis, P.R. 2017. Frontiers in Microbiology, 8, 1042. doi:10.3389/fmicb.2017.01042
Microbial response to oil enrichment in Gulf of Mexico sediment measured using a novel long-term benthic lander system
Orcutt, B.N., Lapham, L.L., Delaney, J., Sarode, N., Marshall, K.S., Whaley-Martin, K.J., Slater, G., Wheat, C.G., and Girguis, P.R. 2017. Elementa Science of the Anthropocene, 5. doi:10.1525/elementa.129
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents
Meier, D.V., Pjevac, P., Bach, W., Hourdez, S., Girguis, P.R., Vidoudez, C., Amann, R., and Meyerdierks, A. 2017. The ISME Journal. doi:10.1038/ismej.2017.37
Geochemically distinct carbon isotope distributions in Allochromatium vinosumDSM 180T grown photoautotrophically and photoheterotrophically
Tang, T., Mohr, W., Sattin, S.R., Rogers, D.R., Girguis, P.R., and Pearson, A. 2017. Geobiology, 15(2), 324-339. doi:10.1111/gbi.12221
Proteome evolution of deep-sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages
Fontanillas, E. Galzitskaya, O.V., Lecompte, O., Lobanov, M.Y., Tanguy, A., Mary, J., Girguis, P.R., Hourdez, S., and Jollivet, D. 2017. Genome Biology and Evolution. doi:10.1093/gbe/evw298
Microbial ecology: Here, there and everywhere
Girguis, P.R. 2016. Nature Microbiology, 1, 16123. doi:10.1038/nmicrobiol.2016.123
What do we really know about the role of microorganisms in iron sulfide mineral formation?
Picard, A., Gartman, A., and Girguis, P.R. 2016. Frontiers in Earth Science, 4, 68. doi:10.3389/feart.2016.00068
Patterns of sulfur isotope fractionation during microbial sulfate reduction
Bradley, A.S., Leavitt, W.D., Schmidt, M., Knoll, A.H., Girguis, P.R., and Johnston, D.T. 2016. Geobiology, 14(1), 91-101. doi:10.1111/gbi.12149
Arsenic concentrations and species in three hydrothermal vent worms, Ridgeia piscesae, Paralvinella sulfincola and Paralvinella palmiformis
Maher, W.A., Duncan, E., Dilly, G., Foster, S., Krikowa, F., Lombi, E., Scheckel, K., and Girguis, P.R. 2016. Deep Sea Research Part I: Oceanographic Research Papers, 116, 41-48. doi:10.1016/j.dsr.2016.07.009
NC10 bacteria in marine oxygen minimum zones
Padilla, C.C., Bristow, L.A., Sarode, N., Garcia-Robledo, E., Ramírez, E.G., Benson, C.R., Bourbonnais, A., Altabet, M.A., Girguis, P.R., Thamdrup, B., and Stewart, F.J. 2016. The ISME Journal. doi:10.1038/ismej.2015.262
Independent benthic microbial fuel cells powering sensors and acoustic communications with the MARS underwater observatory
Schrader, P.S., Reimers, C.E., Girguis, P.R., Delaney, J., Doolan, C., Wolf, M., and Green, D. 2016. Journal of Atmospheric and Oceanic Technology, 33(3), 607-617. doi:10.1175/JTECH-D-15-0102.1
Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes
Seston, S.L., Beinart, R.A., Sarode, N., Shockey, A.C., Ranjan, P., Ganesh, S., Girguis, P.R., and Stewart, F.J. 2016. Frontiers in Microbiology, 7. doi:10.3389/fmicb.2016.01074
Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting
Meier, D.V., Bach, W., Girguis, P.R., Gruber‐Vodicka, H.R., Reeves, E.P., Richter, M., Vidoudez, C., Amann, R., and Meyerdierks, A. 2016. Environmental Microbiology. doi:10.1111/1462-2920.13304
Nanoporous microscale microbial incubators
Ge, Zhifei, Girguis, P.R., and Buie, C.R. 2016. Lab on a Chip. doi:10.1039/C5LC00978B
A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge
Meyer, J.L., Jaekel, U., Tully, B.J., Glazer, B.T., Wheat, C.G., Lin, H.T., Hsieh, C.C., Cowen, J.P., Hulme, S.M., Girguis, P.R., and Huber, J.A., 2016. Scientific Reports, 6. doi:10.1038/s41598-020-63127-z
Exploration and discovery of methane seeps and associated communities in the California Borderland
Levin, L., Girguis, P.R., German, C.R., Brennan, M.L., Tuzun, S., Wagner, J., Smart, C., Kruger, A., Inderbitzen, K., Le, J., and Martinez, M. 2016. Oceanography, 29(1), 40-43.
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores
Sanders, J.G., Beichman, A.C., Roman, J., Scott, J.J., Emerson, D., McCarthy, J.J., and Girguis, P.R. 2015. Nature Communications, 6. doi:10.1038/ncomms9285
Ubiquitous presence and novel diversity of anaerobic alkane degraders in cold marine sediments
Gittel, A., Donhauser, J., Røy, H., Girguis, P.R., Jørgensen, B.B., and Kjeldsen, K.U., 2015. Frontiers in Microbiology, 6, 1414. doi:10.3389/fmicb.2015.01414
Key factors influencing rates of heterotrophic sulfate reduction in active seafloor hydrothermal massive sulfide deposits
Frank, K.L., Rogers, K.L., Rogers, D.R., Johnston, D.T., and Girguis, P.R. 2015. Frontiers in Microbiology, 6. doi:10.3389/fmicb.2015.01449
The ecological physiology of Earth’s second oxygen revolution
Sperling, E.A., Knoll, A.H., and Girguis, P.R. 2015. Annual Review of Ecology, Evolution, and Systematics, 46(1). doi:10.1146/annurev-ecolsys-110512-135808
Carbon fixation by basalt-hosted microbial communities
Orcutt, B.N., Sylvan, J.B., Rogers, D.R., Delaney, J., Lee, R.W., and Girguis, P.R. 2015. Frontiers in Microbiology, 6. doi:10.3389/fmicb.2015.00904
The uptake and excretion of partially oxidized sulfur expands the repertoire of energy resources metabolized by hydrothermal vent symbioses
Beinart, R.A., Gartman, A., Sanders, J.G., Luther, G.W., and Girguis, P.R. 2015. Proceedings of the Royal Society of London B: Biological Sciences, 282(1806), 20142811. doi:10.1098/rspb.2014.2811
Patterns of sulfur isotope fractionation during Microbial Sulfate Reduction
Bradley, A.S., Leavitt, W.D., Schmidt, M., Knoll, A.H., Girguis, P.R., and Johnston, D.T. 2015. Geobiology. doi:10.1111/gbi.12149
Enhancing the response of microbial fuel cell based toxicity sensors to Cu (II) with the applying of flow-through electrodes and controlled anode potentials
Jiang, Y., Liang, P., Zhang, C., Bian, Y., Yang, X., Huang, X., and Girguis, P.R. 2015. Bioresource Technology, 190, 367-372. doi:10.1016/j.biortech.2015.04.127
Biological capacitance studies of anodes in microbial fuel cells using electrochemical impedance spectroscopy
Lu, Z., Girguis, P.R., Liang, P., Shi, H., Huang, G., Cai, L., and Zhang, L. 2015. Bioprocess and Biosystems Engineering, 1-9. doi:10.1007/s00449-015-1373-z
Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ‐Proteobacterial symbionts
Beinart, R.A., Nyholm, S.V., Dubilier, N., and Girguis, P.R. 2014. Environmental Microbiology Reports, 6(6), 656-664. doi:10.1111/1758-2229.12183
Electron uptake by Rhodopseudomonas palustris TIE-1
Bose, A., Vidoudez, C., Parra, E.A., Gardel, E.J., and Girguis. P.R. 2014. Nature Communications. doi:10.1038/ncomms4391
Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae
Liao, L., Wankel, S.D., Wu, M., Cavanaugh, C.M., and Girguis, P.R. 2014. Molecular Ecology, 23(6), 1544-1557. doi:10.1111/mec.12460
Deep water instrument for microbial identification, quantification, and archiving
Pargett, D.M., Jensen, S.D., Roman, B.A., Preston, C.M., Ussler, W., Girguis, P.R., Marin, R., Birch, J.M., and Scholin, C.A., 2013, September. In 2013 OCEANS-San Diego, 1-6. IEEE.
Microbial anaerobic degradation of short chain alkanes in marine hydrocarbon cold seeps
Bose, A., Rogers, D.R., Adams, M.M., Joye, S.B., and Girguis, P.R. 2013. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00386
Capitalizing on expertise in marine education and outreach to broaden impacts
Girguis, P.R., deCharon, A., and Herren, C.M. 2013. Current: The Journal of Marine Education, 28(3), 39-40.
Redox effects on the microbial degradation of refractory organic matter in marine sediments
Reimers, C.E., Alleau, Y., Bauer, J., Delaney, J., Schrader, P., Stecher, H.A., and Girguis, P.R. 2013. Geochimica et Cosmochimica Acta, 121(15), 582-598. doi:10.1016/j.gca.2013.08.004
Sensors and acoustic modems powered by Benthic Microbial Fuel Cells at the MARS observatory
Schrader, P.S., Doolan, C., Reimers, C.E., Girguis, P.R., Wolf, M., and Green, D., 2013, September. In 2013 OCEANS-San Diego, 1-6. IEEE.
Oxygen, ecology, and the Cambrian radiation of animals
Sperling, E.A., Frieder, C.A., Raman, A.V., Girguis, P.R., Levin, L.A., and Knoll, A.H. 2013. Proceedings of the National Academy of Sciences 10(33), 13446-13451. doi:10.1073/pnas.1312778110
Autonomous in situ quantitative PCR in the deep sea: Molecular surveys of aerobic methanotroph genes and gene expression using the deep-sea environmental processor
Ussler III, W., Tavormina, P., Preston, C., Marin III, R., Pargett, D., Jensen, S., Roman, B., Shah, S., Girguis, P.R., Birch, J.M., Orphan, and V., Scholin, C. 2013. Environmental Science and Technology. doi:10.1021/es4023199
Anaerobic oxidation of short-chain alkanes in hydrothermal sediment: potential influences on sulfur cycling and microbial diversity
Adams, M., Hoarfrost, A.L., Bose, A., Joye, S.B., and Girguis, P.R. 2013. Frontiers of Microbiology. doi:10.3389/fmicb.2013.00110
Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase
Kolodkin-Gal, I., Alex Elsholz, A., Muth, C., Girguis, P.R., Kolter, R., and Losick, R. 2013. Genes and Development. doi:10.1101/gad.215244.113
Characterizing the distribution and rates of heterotrophic sulfate reduction at Middle Valley hydrothermal vents
Frank, K., Rogers, D.R., Olins, H.C., Vidoudez, C. P-M., and Girguis, P.R. 2013. The ISME Journal. doi:10.1038/ismej.2013.17
Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts
Sanders, J.G., Beinart, R.A., Stewart, F.J., Delong, E.F., and Girguis, P.R. 2013. The ISME Journal. doi:10.1038/ismej.2013.45
Investigating microbial community and geochemical dynamics at hydrothermal vents using osmotically-driven continuous fluid samplers
Robidart, J.R., Song, P., Callister, S.J., Wheat, C.G., and Girguis, P.R. 2013. Environmental Science and Technology. doi:10.1021/es3037302
The science and applications of microbial genomics
Girguis, P.R., Choffnes, Eileen R., Leigh Anne Olsen, and Theresa M. Wizemann, et. al. Washington, D.C: The National Academies Press, 2013.
Characterizing the distribution of methane sources and cycling in the deep sea via in situ stable isotope analysis
Wankel, S.D., Huang, Y., Gupta, M., Leen, J.B., Provencal, B., Vidoudez, C., and Girguis, P.R. 2013. Environmental Science and Technology. doi:10.1021/es303661w
Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin
Sylvan, J.B., Sia, T.Y., Haddad, A.G., Briscoe, L.J., Toner, B.M., Girguis, P.R., and Edwards, K.J. 2013. Frontiers of Microbiology, 236. doi:10.3389/fmicb.2013.00061
Assessing the influence of physical, geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys
Olins, H.C., Rogers, D.R., Frank, K., Vidoudez, C. P-M., and Girguis, P.R. 2013. Geobiology. doi:10.1111/gbi.12034
In situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field
Perner, M., Gonnella, G., Hourdez, S., Bohnke, S., Kurtz, S., and Girguis, P.R. 2013. Environmental Microbiology. doi:10.1111/1462-2920.12038
Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses
Beinart, R.A., Sanders, J.G., Faure, B., Sylva, S., Lee, R.W., Becker, E.L., Gartman, A., Luther III, G.W., Seewald, J.S., Fisher, C.R., and Girguis, P.R. 2012. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1202690109
Links from mantle to microbe at the Lau Integrated Study Site: Insights from a back-arc spreading center
Tivey, M.K., Becker, E., Beinart, R., Fisher, C.R., Girguis, P.R., Langmuir, C.H., Michael, P.J., and Reysenbach, A.-L. 2012. Oceanography, 25(1), 62–77. doi:10.5670/oceanog.2012.04
Anaerobic methane oxidation in metalliferous hydrothermal sediment: influences on carbon flux and decoupling from sulfate reduction
Wankel, S.D., Adams, M.A., Johnston, D., Joye, S.B., and Girguis P.R. 2012. Environmental Microbiology. doi:10.1111/j.1462-2920.2012.02825.x
Duty cycling influences current generation in multi-anode environmental microbial fuel cells
Gardel, E.J., Nielsen, M.E., Griselda, P.T., and Girguis, P.R. 2012. Environmental Science and Technology, 46(9), 5222–5229. doi:10.1021/es204622m
On the potential for bioenergy and biofuels from hydrothermal vent microbes
Girguis, P.R. and Holden, J. 2012. Oceanography, 25(1), 213-217. doi:10.5670/oceanog.2012.20
Hydrogen is an energy source for vent symbioses
Petersen J.M., Zielinski, F.U., Pape, T., Seifert, R., Moraru, C., Amann, R., Hourdez, S., Girguis, P.R., Barbe,V., Pelletier, E., Fink, D., Borowski, C., Bach, W., and Dubilier, N. 2011. Nature, 474, 176-180, 11 August 2011. doi:10.1038/nature10325
Exploring the thermal limits of metazoan life: thermally induced changes in global protein expression of hydrothermal vent polychaetes
Dilly, G.F., Young, C.F., Lane, W.S., Pangilinan, J., Lee, R.W., and Girguis, P.R. 2012. Proceedings of the Royal Society of London Series B, 279, 3347-3356. doi:10.1098/rspb.2012.0098
Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids
Wankel, S.D., Germanovich, L.N., Lilley, M.D., Genc, G., DiPerna, C.J., Bradley, A.S., Olson, E.J., and Girguis, P.R. 2011. Nature Geosciences, 4, 461-468. doi:10.1038/Ngeo1183
Linking hydrothermal geochemistry to organismal physiology: physiological versatility in Riftia pachyptilafrom sedimented and basalt-hosted vents
Robidart, J.C., Roque, A., Song, P., and Girguis, P.R. 2011. PLoS ONE, 6(7), e21692. doi:10.1371/journal.pone.0021692
Sulfide oxidation across diffuse flow zones of hydrothermal vents
Gartman, A., Yucel, M., Madison, A.S., Chu, D.W., Ma, S., Janzen, C.P., Becker, E.L., Beinart, R.A., Girguis, P.R., and Luther III. G.W. 2011. Aquatic Geochemistry, 17(4), 583-601. doi:10.1007/s10498-011-9136-1
Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment
Findlay, A.J., Luther III, G.W., MacDonald, D.J., Owings, S.M., Hanson, T.E., Beinart, R.A., and Girguis, P.R. 2011. Frontiers in Microbiology, 2(62), 1-9. doi:10.3389/fmicb.2011.00062
Benthic microbial fuel cell as direct power source for an acoustic modem and seawater oxygen/temperature sensor system
Gong, Y., Radachowsky, S.E., Wolf, M., Nielsen, M.E., Girguis, P.R., and Reimers, C.E. 2011. Environmental Science and Technology, 45(11), 5047–5053. doi:10.1021/es104383q
The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities
Childress, J.J. and Girguis, P.R. 2011. Journal of Experimental Biology, 214, 312-325. doi:10.1242/jeb.049023
Metabolic and practical considerations on microbial electrosynthesis
Rabaey, K., Girguis, P.R., and Nielsen, L.K. 2011. Current Opinion in Biotechnology, 22, 1-7. doi:10.1016/j.copbio.2011.01.010
Measuring isotope fractionation by autotrophic microorganisms and enzymes
Scott, K.M., Fox, G., and Girguis, P.R. 2010. Methods in Enzymology, 494, 281-299. (Edited by Amy Rosenzweig and Stephen Ragsdale). doi:10.1016/B978-0-12-385112-3.00014-7
New constraints on methane fluxes and rates of anaerobic methane oxidation in a Gulf of Mexico brine pool via in situ mass spectrometry
Wankel, S.D., Joye, S.B., Samarkin, V.A., Shah, S.A., Friederich, G., Melas-Kyriazi, J., and Girguis, P.R. 2010. Deep Sea Research II, 57(21-23), 2022-2029. doi:10.1016/j.dsr2.2010.05.009
Harnessing energy from marine productivity using bioelectrochemical systems
Girguis, P.R., Nielsen, M.E., and Figueroa, I. 2010. Current Opinion in Biotechnology, 21(3), 252-258. doi:10.1016/j.copbio.2010.03.015
Fundamentals of sediment-hosted microbial fuel cells
Girguis, P.R., Nielsen, M.E., and Reimers, C.E. 2010. In Bioelectrochemical Systems, First Edition (Ed. K. Raebey). Springer Verlag Press, 327-346.
Benthic microbial fuel cells: long-term power sources for wireless marine sensor networks
Guzman, J.J., Cooke, K.G., Gay, M.O., Radachowsky, S.E., Girguis, P.R., and Chiu, M.A. 2010. SPIE Defense, Security, and Sensing, 76662. doi:10.1117/12.854896
Influence of substrate on electron transfer mechanisms in chambered benthic microbial fuel cells
Nielsen, M.E., Wu, D.M., Girguis, P.R., and Reimers, C.E. 2009. Environmental Science and Technology, 43(22), 8671–8677. doi:10.1021/es9013773
Thiotaurine and hypotaurine contents in hydrothermal-vent polychaetes without thiotrophic endosymbionts: correlation with sulfide exposure
Yancey, P.H., Ishikawa, J., Meyer, B., Girguis, P.R., and Lee, R. 2009. Journal of Experimental Zoology, 311A(6), 439-447. doi:10.1002/jez.541
Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells: examining the relationship between power production, geochemistry and microbial ecology
White, H.K., Reimers, C.E., Cordes, E.E., Dilly, G.F., and Girguis, P.R. 2009. The ISME Journal, 3, 635-646. doi:10.1038/ismej.2009.12
Variation in evolved limits to life preclude universal tolerance indices
Seibel, B.A., Girguis, P.R., and Childress, J.J. 2009. Science.
Sustainable energy from deep ocean cold seeps
Nielsen, M.E., Reimers, C.E., White, H.K., Sharma, S., and Girguis, P.R. 2008. Energy and Environmental Science, 1(5): 584-593. doi:10.1039/B811899J
Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae
Nyholm, S.V., Robidart, J., and Girguis, P.R. 2008. Biological Bulletin, 214(3), 255–265. doi:10.2307/25470667
Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts
Newton, I.L.G., Girguis, P.R., and Cavanaugh, C.M. 2008. BMC Genomics, 9, 585. doi:10.1186/1471-2164-9-585
Substrate degradation kinetics, microbial diversity and the current efficiency of microbial fuel cells supplied with marine plankton
Reimers, C.E., Stecher III, H.A., Westall, J.C., Alleau, Y., Howell, K.A., Soule, L., White, H.K., and Girguis, P.R. 2007. Applied and Environmental Microbiology, 73(21), 7029-7040. doi:10.1128/AEM.01209-07
A proteomic snapshot of life at a vent
Fisher, C.R. and Girguis, P.R. 2007. Science, 315(5809), 198-199 (Perspectives). doi:10.1126/science.1137739
Power storage and conversion from an ocean microbial energy source
McBride, L.R.*, Girguis, P.R.*, and Reimers, C.E. 2006. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers, 1-5. doi:10.1109/OCEANS.2006.306847 (* = authors contributed equally)
Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature
Girguis, P.R. and Childress, J.J. 2006. Journal of Experimental Biology, 209(18), 3516-28. doi:10.1242/jeb.02404
Microbial fuel cell energy from an ocean cold seep
Reimers, C.E., Girguis, P.R., Stecher III, H.A., Tender, L.M., Ryckelynck, N., and Whaling, P. 2006. Geobiology, 4, 123-136. doi:10.1111/j.1472-4669.2006.00071.x
Thermal tolerance and preference of alvinellids
Girguis, P.R. and Lee, R.W. 2006. Science, 312(5771), 231. doi:10.1126/science.1125286
Growth rates of methane-oxidizing archaeal-bacterial consortia in deep-sea marine sediments: insights into the physiology of microbially-mediated anaerobic methane oxidation
Girguis, P.R., Cozen, A., and DeLong, E.E. 2005. Applied and Environmental Microbiology, 71, 3725-3733. doi:10.1128/AEM.71.7.3725-3733.2005
On the edge of a deep biosphere: true animals in extreme environments
Childress J.J., Fisher C.R., and Girguis, P.R. 2003. In The Subseafloor Biosphere at Mid-Ocean Ridges (eds. W.D. Wilcock, D.S. Kelley, J.A. Baross, E. DeLong, and C. Cary), American Geophysical Union Monographs, 144, 41-49. doi:10.1029/144GM04
Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor
Girguis, P.R., Orphan, V.J., Hallam, S.J., and DeLong, E.F. 2003. Applied and Environmental Microbiology, 69(9), 5472-5482. doi:10.1128/AEM.69.9.5472-5482.2003
Identification of methyl coenzyme M reductase A (mcrA) genes in methane oxidizing archaea
Hallam, S.J., Girguis, P.R., Preston, C.M., Richardson, P.M., and DeLong. E.F. 2003. Applied and Environmental Microbiology, 69(9), 5483-5491. doi:10.1128/AEM.69.9.5483-5491.2003
Effects of metabolite uptake on proton-equivalent elimination by two species of deep-sea vestimentiferan tubeworm, Riftia pachyptila and Lamellibrachia cf luymesi
Girguis, P.R., Childress, J.J., Freytag, J.A., Klose, K.A., and Stuber, R. 2002. Journal of Experimental Biology, 205, 3055-3066. doi:10.1242/jeb.205.19.3055
A paradox resolved: sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy
Freytag, J.K., Girguis, P.R., Bergquist, D.C., Andras, J.P., Childress, J.J., and Fisher, C.R. 2001. Proceedings of the National Academies of Sciences, 98(23), 13408–13413. doi:10.1073/pnas.231589498
Fate of nitrate acquired by the tubeworm Riftia pachyptila
Girguis, P.R., Lee, R.W., Desaulniers, N., Childress, J.J., Pospesel, M., Felbeck, H., and Zal, F. 2000. Applied and Environmental Microbiology, 66(7), 2783-27909. doi:10.1128/AEM.66.7.2783-2790.2000
Physiological functioning of carbonic anhydrase in the hydrothermal vent tubeworm Riftia pachyptila
Goffredi, S.K., Girguis, P.R., Childress. J.J., and Desaulniers, N.T. 1999. Biological Bulletin, 196(3), 257-264. doi:10.2307/1542950
H+ equivalent elimination by the tubeworm Riftia pachyptila
Girguis, P.R. and Childress, J.J. 1998. Cahiers de Marine Biologie, 39, 285-296.