PEER-REVIEWED PUBLICATIONS

 

Amend Lab Post-doc (@), Graduate Student (#), Undergraduate Student ($)

 

2021

  • LaRowe, DE, Carlson, HK$, Amend, JP, The energetic potential for undiscovered manganese metabolisms in nature. Frontiers in Microbiology (in revision).

  • Lu, G-S#, LaRowe, DE, Amend, JP, Bioenergetic potentials in terrestrial, shallow-sea and deep-sea hydrothermal systems. Chemical Geology (in review).

  • Osburn, MR, Casar, CP, Kruger, B, Momper, L, Flynn, T, Amend, JP, Contrasting variable and stable subsurface microbial populations: an ecological time series from the Deep Mine Microbial Observatory, South Dakota, USA. Environmental Microbiology (in revision).

  • Perez-Rodriguez, IM, Choi, JK, Abuyen, K$, Tyler, M$, Ronkowski, C$, Romero, E$, Trujillo, A$, Tremblay, J$, Savalia, P, 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 (in press).

  • 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.

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

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)

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)

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)