Publications

2022

2021

• Lu, G.-S., LaRowe, D.E. and Amend, J.P. (2021) Bioenergetic potentials in terrestrial, shallow-sea and deep-sea hydrothermal systems, Chemical Geology 583:120449. https://doi.org/10.1016/j.chemgeo.2021.120449
• Savoie, E.R., Lanclos, V.C., Henson, M.W., Cheng, C., Getz, E., Barnes, S.J., LaRowe, D.E., Rappe, M.S. and Thrash, J.C. (2021) Ecophysiology of the cosmopolitan OM252 bacterioplankton (Gammaproteobacteria), mSystems 6e00276-21. https://doi.org/10.1128/msystems.00276-21
• LaRowe, D.E., Carlson, H.K. and Amend, J.P. (2021) The energetic potential for undiscovered manganese metabolisms in nature. Frontiers in Microbiology 12:636145. https://doi.org/10.3389/fmicb.2021.636145
• Bay, S.K., Dong, X., Bradley, J.A., Leung, P.M., Jirapanjawat, T., Arndt, S.K., Cook, P.L.M., LaRowe, D.E., Nauer, P.A., Chiri, E., Greening, C.  (2021) Trace gas oxidizers are widespread and active members of soil microbial communities, Nature Microbiology, 6: 246-256. https://doi.org/10.1038/s41564-020-00811-w
• Garber AI, Cohen AB, Nealson KH, Ramírez GA, Barco RA, Enzingmüller-Bleyl TC, Gehringer MM, Merino N. (2021) Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats. Front Microbiol. 12:667944. doi: 10.3389/fmicb.2021.667944.
• Meehan CJ, Barco RA, Loh YE, Cogneau S, Rigouts L. (2021) Reconstituting the genus Mycobacterium. Int J Syst Evol Microbiol. 71(9):004922. doi: 10.1099/ijsem.0.004922.

• Perez-Rodriguez, IM, Choi, JK, Abuyen, K, Tyler, M, Ronkowski, C, Romero, E$, Trujillo, A, Tremblay, J, Viney, I, Savalia, P, Amend, JP (2021), Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter. International Journal of Systematic and Evolutionary Microbiology, doi.org/10.1099/ijsem.0.004739.

• Amend, JP, Meyer-Dombard, DR (2021), The shallow-sea hydrothermal system at Vulcano Island (Italy): the ‘type locality’ for several transformative discoveries in geobiology. Italian Journal of Geosciences, doi.org/10.3301/IJG.2020.17.

2020

• Rowe, AR@, Abuyen, K, Lam, BR, Kruger, B, Casar, CP, Osburn, MR, El-Naggar, MY, Amend, JP (2020), Electrochemical evidence for in situ microbial activity at the Deep Mine Microbial Observatory (DeMMO), South Dakota, USA. Geobiology, doi.org/10.1111/gbi.12420.
• Gaidos, E, Johannesson, T, Einarsson, B, Thorsteinsson, Þ, Amend, JP, Skidmore, M (2020), Après nous, le dèluge: a human-triggered jökulhlaup from a subglacial lake. Geophysical Research Letters, doi.org/10.1029/2020GL089876.
• LaRowe, DE, Arndt, S, Bradley, JA, Burwicz, E, Dale, AW, Amend, JP (2020), Organic carbon and microbial activity in marine sediments on a global scale throughout the Quaternary. Geochimica et Cosmochimica Acta, 286, 227-247, doi: org/10.1016/j.gca.2020.07.017.
• Mullin, SW, Wanger, G, Kruger, BR, Sackett, JD, Hamilton-Brehm, SD, Bhartia, R, Amend, JP, Moser, DP, Orphan, VJ (2020), Patterns of in situ mineral colonization by microorganisms in a ~60ºC deep continental subsurface aquifer.  Frontiers in Microbiology, doi: 10.3389/fmicb.2020.536535.
• Bradley, JA, Arndt, S, Amend, JP, Burwicz, E, Dale, AW, Egger, M, LaRowe, DE (2020), Widespread energy limitation to life in global subseafloor sediments. Science Advances, doi: 10.1126/sciadv.aba0697.
• Momper, LM, Semler, A$, Lu, G-S#, Miyazaki, M, Imachi, H, Amend, JP, (2020),  Rectinema subterraneum sp. nov., a chemotrophic spirochaete isolated from the deep terrestrial subsurface. International Journal of Systematic and Environmental Microbiology, doi:10.1099/ijsem.0.004339.
• Lu, G-S#, LaRowe, DE, Gilhooly III, WP, Druschel, GK, Fike, DA, Amend, JP (2020), Bioenergetic characterization of a shallow-sea hydrothermal vent system: Milos Island, Greece. PLOS ONE, doi.org/10.1371/journal/pone.0234175.
• Amend, JP, Aronson, HS, Macalady, J, LaRowe, DE (2020), Another chemolithotrophic metabolism missing in nature: sulfur comproportionation. Environmental Microbiology, 22, 1971-1976, doi: 10.1111/1462-2920.14982.
• Barco, RA@, Garrity, GM, Scott, JJ, Amend, JP, Nealson, KH, Emerson, D (2020), A genus definition for Bacteria and Archaea based on a standard genome relatedness index. mBio, doi: 10.1128/mBio.02475-19.
• LaRowe, DE, Amend, JP (2020), Energy limits for life in the subsurface. In: Whole Earth Carbon: Past to Present (B Orcutt, I Daniel, J Dasgupta eds.). Cambridge University Press, 586-619.
• Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol. 5(8):987-994. doi: 10.1038/s41564-020-0733-x.
• Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D. (2020) A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index. mBio. 2020 Jan 14;11(1):e02475-19. doi: 10.1128/mBio.02475-19.
• Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. (2020) FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol. 11:37. doi: 10.3389/fmicb.2020.00037.

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2019

• Jangir, Y, Karbelkar, AA, Beedle, NM, Zinke, LA, Wanger, G, Anderson, CM, Reese, BK, Amend, JP, El-Naggar, MY (2019), In situ electrochemical studies of the terrestrial deep subsurface biosphere at the Sanford Underground Research Facility, South Dakota, USA.  Frontiers in Energy Research, doi: 10.3389/fenrg.2019.00121.

• Lopez, A, Barco, RA, Tully, B, Albino, D, Beraki, S, Broomell, S, Canela, R, Dingmon, T, Estrada, S, Fernandez, M, Nealson, KH, Emerson, D, Amend, JP (2019), Genome sequence of Mariprofundus sp. strain EBB-1: a novel marine autotroph isolated from an iron-sulfur mineral. Microbiology Resource Announcements, doi: 10.1128/MRA.00995-19.

• Robador, A@, Amend, JP, Finkel, SE (2019), Nanocalorimetry reveals growth dynamics of Escherichia coli cells undergoing adaptive evolution during long-term stationary phase. Applied and Environmental Microbiology, doi: 10.1128/AEM.00968-19.

• Amend, JP, LaRowe, DE (2019), Mini-Review: demystifying microbial reaction energetics. Environmental Microbiology, 21, 3539-3547.

• Osburn, MR, Kruger, B, Masterson, A, Casar, C, Amend, JP, Establishment of the Deep Mine Microbial Observatory (DeMMO), South Dakota, USA, a geochemically stable portal into the deep subsurfaced. Frontiers in Earth Science (in review).

• Jangir, Y, Karbelkar, AA, Beedle, NM, Zinke, LA, Wanger, G, Anderson, CM, Reese, BK, Amend, JP, El-Naggar, MY, In situ electrochemical studies of the terrestrial deep subsurface biosphere at the Sanford Underground Research Facility, South Dakota, USA.  Applied and Environmental Microbiology (in revision).

• LaRowe, DE, Arndt, S, Bradley, J, Burwicz, E, Dale, AW, Amend, JP, Organic carbon and microbial activity in marine sediments on a global scale throughout the Quaternary. Geochimica et Cosmochimica Acta (in review).

• Kotopoulou, E, Godelitsas, A, Göttlicher, J, Steininger, R, Price, RE, Fike, DA, Amend, JP, Gilhooly III, WP, Druschel, GK, Paraskevi, N, Gamaletsos, P, Lozios, S, Geochemistry and nano-mineralogy of shallow-sea hydrothermal precipitates off Milos Island (Greece). Chemical Geology (in review).

• Robador, A, Amend, JP, Finkel, SE, Nanocalorimetry reveals growth dynamics of Escherichia coli cells undergoing adaptive evolution during long-term stationary phase. Applied and Environmental Microbiology (in revision).

• LaRowe, DE, Amend, JP, Energey limits for life in the subsurface. In: Whole Earth Carbon: Past to Present (B Orcutt, ed.). Cambridge University Press (in press).

• Sapers, HM, Razzell Hollis, JJ, Bhartia, R, Beegle, LW, Orphan, VJ, Amend, JP (2019), The cell and the sum of its parts: patterns of complexity in biosignatures as revealed by deep UV Raman spectroscopy. Frontiers in Microbiology, doi: 10.3389/fmicb.2019.00679.

• LaRowe, DE, Amend, JP (2019), The energetics of fermentation in natural settings. Geomicrobiology Journal, doi: 10.1080/01490451.2019.1573278.

• Rowe, AR, Xu, S, Gardel, E, Bose, A, Girguis, P, Amend, JP, El-Naggar, M (2019), Methane-linked mechanisms of electron uptake from cathodes by Methanosarcina barkeri. mBio, 10:e02448-18. doi:https://doi.org/10.1101/415653

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2018

• Zinke, LA, Glombitza, C, Bird, JT, Røy, H, Jørgensen, BB, Lloyd, KG, Amend, JP, Reese, BK (2018), Microbial organic matter degradation potential in Baltic Sea sediments influenced by depositional conditions and in situ geochemistry. Applied and Environmental Microbiology, doi: 10.1128/AEM.02164-18.

• Houghton, JL, Gilhooly III, WP, Kafantaris, FCA, Druschel, GK, Lu, G-S, Amend, JP, Godelitsas, A, Fike, DA (2018), Spatially and temporally variable sulfur cycling in shallow-sea hydrothermal vents, Milos, Greece. Marine Chemistry, doi: 10.1016/j.marchem.2018.11.002.

• Bradley, JA, Amend, JP, LaRowe, DE (2018), Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time. Geobiology, doi: 10.1111/gbi.12313.

• Momper L., Aronson, H.S.#, Amend, JP (2018) Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes. Frontiers in Microbiology. (LINK)

• Reese, B, Zinke, LA#, Sobol, M, LaRowe, DE, Orcutt, BN, Zhang, X, Jaekel, U, Wang, F, Dittmar, T, Defforey, D, Tully, B, Paytan, A, Sylvan, JB, Amend, JP, Edwards, KJ, Girguis, P (2018) Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank. Geomicrobiology Journal. (LINK)

• Zinke, LA#, Reese, B, McManus, J, Wheat, CG, Orcutt, BN, Amend, JP (2018) Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration. Frontiers in Microbiology. (LINK)

• Smith, H, Abuyen, K$, Tremblay, J, Savalia, P, Pérez-Rodríguez, I, Emerson, D, Tully, B, Amend, JP (2018) Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lō‘ihi Seamount, Hawai’i. American Society for Microbiology. (LINK)

• Bradley, J@, Amend, JP, LaRowe, DE (2018) Bioenergetic Controls on Microbial Ecophysiology in Marine Sediments. Frontiers in Microbiology. (LINK)

• Bradley, J@, Amend, JP, LaRowe, DE (2018) Necromass as a Limited Source of Energy for Microorganisms in Marine Sediments. Journal of Geophysical Research – Biogeosciences. (LINK)

• Neely, C, Khalil, CB, Cervantes, A, Diaz, R, Escobar, A, Ho, K, Hoefler, S, Smith, HH, Abuyen, K$, Savalia, P, Nealson, KH, Emerson, D, Tully, B, Barco, RA@, Amend, JP (2018) Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer. American Society for Microbiology. (LINK)

• Robador, A, LaRowe, DE, Finkel, SE, Amend, JP, Nealson, KH (2018) Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions. Frontiers in Microbiology. (LINK)

• Barco, RA@, Garrity, GM, Scott, JJ, Amend, JP, Nealson, KH, Emerson, D (2018) A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation. BioRXIV. (LINK)

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2017

• Price, RE, Boyd, ES, Hoehler, TM, Wehrmann, LM, Bogason, E, Valtysson, HT, Örlygsson, J, Gautason, B, Amend, JP, Ridge-flank basalt alteration can produce alkaline, H2- and CH4-enriched hydrothermal vent fluids with steep Na+ gradients.Geology (in revision).

• Fike, DA, Houghton, JL, Moore, SE, Gilhooly, WP III, Dawson, KS, Druschel, GK,Amend, JP, Orphan, VJ, Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis.Marine Chemistry (in review).

• Zinke, LA, Mullis, MM, Bird, JT, Marshall, IPG, Joergensen, BB, Lloyd, KG, Amend, JP, Reese, BK, Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment. Environmental Microbiology Reports, (LINK)

• Lu, G-S, Price, RE, Houghton, JL,Gilhooly III, WP, Druschel, GK, Fike, DA, Amend, JP, Linking shallow-sea hydrothermal processes and microbial ecology at Milos Island, Greece. Journal of Environmental Chemistry (in revision).

• LaRowe, DE, Koch, BP, Robador, A, Witt, M, Ksionzek, K, Amend, JP, Identification of organic compounds in ocean basement fluids. Organic Geochemistry (in press).

• Momper, LM, Jungbluth, SP, Lee, MD, Amend, JP(2017) Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. International Society for Microbial Ecology Journal, (LINK)

• Tully, B, Savalia, P, Abuyen, K, Baughan, C, Romero, E, Ronkowski, C, Torres, B, Tremblay, J, Trujillo, A, Tyler, M, Perez-Rodriguez, I, Amend, JP (2017), Genome sequence of Geothermobacter sp. strain EPR-M, a deep-sea hydrothermal vent iron reducer. Genome Announcements, 5, e00424-17. (LINK)

• Momper, LM#, Kiel Reese, B, Zinke, LA#, Wanger, GP, Osburn, MR, Moser, D,Amend, JP (2017), Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface. Environmental Microbiology Reports, (LINK)

• Kiel Reese, B, Sobol, MS, Zinke, LA#, LaRowe, DE, Zhang, XX, Jaekel, U, Wang, F, Orcutt, BN, Dittmar, T, Mills, HJ, Amend, JP, Edwards, KJ, Girguis, P (2017), Structure and function of total and active bacteria within oligotrophic Mid-Atlantic Ridge flank sediment. Geomicrobiology Journal (in press).

• Rowe, A@, Yoshimura, M, LaRowe, DE, Bird, L, Amend, JP, Nealson, K, Okamoto, A (2017), In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environmental Microbiology.  (LINK)

• LaRowe, DE, Burwicz, E, Arndt, S, Dale, AW, Amend, JP (2017), The deep biosphere and the global distribution of temperature in marine sediments. Geology, 45, 275-278.

• Kempes, CP@, van Bodegom, P, Wolpert, D, Libby, E, Amend, JP, Hoehler, T (2017), Drivers of bacterial maintenance and minimum energy requirements. Frontiers in Microbiology, 8:31. (LINK)

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2016

• Amend, JP and LaRowe, DE (2016), Ocean sediments—an enormous but underappreciated microbial habitat. Microbe, 11, 427-432. (LINK)

• Jangir, Y, French, S, Momper, LM#, Moser, DP, Amend, JP, El-Naggar, MY (2016), Isolation and characterization of electrochemically active subsurface Delftia and Azonexus. Frontiers in Microbiology, 7:756.  (LINK)

• Kiel Reese, B, Sobol, MS, Zinke, LA, LaRowe, DE, Zhang, XX, Jaekel, U, Wang, F, Orcutt, BN, Dittmar, T, Mills, HJ, Amend, JP, Edwards, KJ, Girguis, P (2016), Structure and function of total and active bacteria within oligotrophic Mid-Atlantic Ridge flank sediment. Frontiers in Microbiology (in revision).

• Robador, A, LaRowe, DE, Jungbluth, SP, Lin, H-T, Rappé, MS, Nealson, KH, Amend, JP (2016), Nanocalorimetric characterization of microbial activity in deep subsurface oceanic crustal fluids. Frontiers in Microbiology (LINK)

• McKay, L, Klokman, VW, Mendlovitz, HP, LaRowe, DE, Hoer, DR, Albert, D, Amend, JP, Teske, A, (2016), Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California. Environmental Microbiology (LINK)

• Kempes, CP@, Wang, L, Amend, JP, Doyle, J, Hoehler T (2016), Evolutionary transitions and shifts in physiological tradeoffs. International Society for Microbial Ecology Journal (LINK)

• LaRowe, DE and Amend, JP(2016), The energetics of anabolism in natural settings.  International Society for Microbial Ecology Journal (LINK)

• Godelitsas, A, Price, RE, Pichler, T, Amend, JP, Gamaletsos, P, Göttlicher, J, Amorphous As-sulfide precipitates from the shallow-water hydrothermal vents off Milos Island (Greece).  Marine Chemistry (LINK)

2015

• Godelitsas, A, Price, RE, Pichler, T, Amend, JP, Gamaletsos, P, Göttlicher, J, Amorphous As-sulfide precipitates from the shallow-water hydrothermal vents off Milos Island (Greece).  Marine Chemistry (LINK).

• LaRowe, DE and Amend, JP (2015), Power limits of microbial life. Frontiers in Microbiology. (LINK).

• Lin, H-T, Amend, JP, LaRowe, DE, Bingham, J-P, Cowen, JP, Dissolved amino acids in oceanic basaltic basement fluids, Geochimica et Cosmochimica Acta, 164, 175-190. (LINK)

• Price, RE@, LaRowe, DE, Italiano, F, Savov, I, Pichler, T, Amend, JP, Subsurface hydrothermal processes and the bioenergetics of chemolithoautotrophy at the shallow-sea vents off Panarea Island (Italy). Chemical Geology, 407-408, 21-45. (LINK)

• Sylvan, JB, Hoffman, CL, Momper, LM#, Toner, BM, Amend, JP, Edwards, KJ, Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halotolerant bacterium isolated from deep subseafloor basaltic crust. International Journal of Systematic and Environmental Microbiology, 65, 1992-1998. (LINK)

• LaRowe, DE and Amend, JP (2015), Catabolic rates, population sizes and doubling/replacement times of microorganisms in the deep subsurface. American Journal of Science, 315, 167-203. (LINK)

• Marlow, J and Amend, JP, (2015) The energy of life, The Scientist, 2, 40-47. (LINK)

• Robador, A@, Jungbluth, SP, LaRowe, DE, Bowers, RM, Rappé, MS, Amend, JP, Cowen, JP (2015) Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust, Frontiers in Microbiology.  (LINK)

• Rusch, A, Islam, S, Savalia, P, Amend, JP (2015), Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system. International Journal of Systematic and Environmental Microbiology, 65, 189-194. (LINK)

• • Amend, JP, Rogers, KL#, Shock, EL, Inguaggiato, S, and Gurrieri, S (2003), Energetics of chemolithoautotrophy in the hydrothermal system of Vulcano Island, southern Italy.  Geobiology, 1, 37-58.  (LINK)

  • Amend, JP, Meyer-Dombard, DR#, Sheth, SN$, Zolotova, N, and Amend, AC (2003), Palaeococcus helgesonii sp. nov., a facultatively anaerobic, hyperthermophilic archaeon from a geothermal well on Vulcano Island, Italy.  Archives of Microbiology, 179, 394-401. (LINK)

  • Tor, JM, Amend, JP, Lovley, DR (2003), Metabolism of organic compounds in anaerobic, hydrothermal sulfate-reducing sediments.  Environmental Microbiology, 5, 583-591. (LINK)

  • Amend, JP (2003), Life through time ­- Geomicrobiology. Geotimes, July, 32-33. (LINK)