7.8: References

Aciego, S.M., Riebe, C.S., Hart, S.C., Blakowski, M.A., Carey, C.J., Aarons, S.M., Dove, N.C., Botthoff, J.K., Sims, K.W.W., Aronson, E.L., 2017. Dust outpaces bedrock in nutrient supply to montane forest ecosystems. Nat. Commun. 8, 14800. https://doi.org/10.1038/ncomms14800

Aeppli, M., Babey, T., Engel, M., Lacroix, E.M., Tolar, B.B., Fendorf, S., Bargar, J.R., Boye, K., 2022. Export of Organic Carbon from Reduced Fine-Grained Zones Governs Biogeochemical Reactivity in a Simulated Aquifer. Environ. Sci. Technol. 56, 2738–2746. https://doi.org/10.1021/acs.est.1c04664

Akob, D.M., Kuesel, K., 2011. Where microorganisms meet rocks in the Earth’s Critical Zone. Biogeosciences 8, 3531–3543. https://doi.org/10.5194/bg-8-3531-2011

Andersen, I.M., Williamson, T.J., González, M.J., Vanni, M.J., 2020. Nitrate, ammonium, and phosphorus drive seasonal nutrient limitation of chlorophytes, cyanobacteria, and diatoms in a hypereutrophic reservoir. Limnol. Oceanogr. 65, 962–978. https://doi.org/10.1002/lno.11363

Arndt, S., Jørgensen, B., LaRowe, D.E., Middelburg, J., Pancost, R.D., Regnier, P., 2013. Quantifying the degradation of organic matter in marine sediments: A review and synthesis. Earth-Sci. Rev. 123, 53–86. https://doi.org/10.1016/j.earscirev.2013.02.008

Baker, B.J., Banfield, J.F., 2003. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44, 139–152. https://doi.org/10.1016/s0168-6496(03)00028-x

Bay, S.K., Waite, D.W., Dong, X., Gillor, O., Chown, S.L., Hugenholtz, P., Greening, C., 2021. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. ISME J. 15, 3339–3356. https://doi.org/10.1038/s41396-021-01001-0

Beatty, J., Overmann, J., Lince, M., Manske, A., Lang, A., Blankenship, R., Dover, C., Martinson, T., Plumley, F., 2005. An Obligately Photosynthetic Bacterial Anaerobe from a Deep-Sea Hydrothermal Vent. Proc. Natl. Acad. Sci. U.S.A. 102, 9306–10. https://doi.org/10.1073/pnas.0503674102

Bekker, A., Holland, H.D., 2012. Oxygen overshoot and recovery during the early Paleoproterozoic. Earth Planet. Sci. Lett. 317–318, 295–304. https://doi.org/10.1016/j.epsl.2011.12.012

Beulig, F., Schubert, F., Adhikari, R.R., Glombitza, C., Heuer, V.B., Hinrichs, K.-U., Homola, K.L., Inagaki, F., Jørgensen, B.B., Kallmeyer, J., Krause, S.J.E., Morono, Y., Sauvage, J., Spivack, A.J., Treude, T., 2022. Rapid metabolism fosters microbial survival in the deep, hot subseafloor biosphere. Nat. Commun. 13, 312. https://doi.org/10.1038/s41467-021-27802-7

Bose, A., Gardel, E.J., Vidoudez, C., Parra, E.A., Girguis, P.R., 2014. Electron uptake by iron-oxidizing phototrophic bacteria. Nat. Commun. 5, 3391. https://doi.org/10.1038/ncomms4391

Brazelton, W.J., Morrill, P.L., Szponar, N., Schrenk, M.O., 2013. Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs. Appl. Environ. Microbiol. 79, 3906. https://doi.org/10.1128/AEM.00330-13

Burns, R.G., DeForest, J.L., Marxsen, J., Sinsabaugh, R.L., Stromberger, M.E., Wallenstein, M.D., Weintraub, M.N., Zoppini, A., 2013. Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biol. Biochem. 58, 216–234. https://doi.org/10.1016/j.soilbio.2012.11.009

Canarini, A., Kaiser, C., Merchant, A., Richter, A., Wanek, W., 2019. Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli. Front. Plant Sci. 10.

Ciani, A., Goss, K.-U., Schwarzenbach, R., 2005. Light penetration in soil and particulate minerals. Eur. J. Soil Sci. 56, 561–574. https://doi.org/10.1111/j.1365-2389.2005.00688.x

Cleveland, C.C., Liptzin, D., 2007. C:N:P stoichiometry in soil: is there a “Redfield ratio” for the microbial biomass? Biogeochemistry 85, 235–252. https://doi.org/10.1007/s10533-007-9132-0

Colman, D.R., Lindsay, M.R., Amenabar, M.J., Boyd, E.S., 2019. The intersection of geology, geochemistry, and microbiology in continental hydrothermal systems. Astrobiology. https://doi.org/10.1089/ast.2018.2016

Colman, D.R., Poudel, S., Stamps, B.W., Boyd, E.S., Spear, J.R., 2017. The deep, hot biosphere: Twenty-five years of retrospection. Proc. Natl. Acad. Sci. 201701266. https://doi.org/10.1073/pnas.1701266114

Conrad, R., 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1, 285–292. https://doi.org/10.1111/j.1758-2229.2009.00038.x

Conrad, R., 1996. Soil microorganisms as controllers of atmospheric trace gases (H₂, CO, CH₄, OCS, N₂O, and NO). Microbiol. Rev. 60, 609–640.

Crossey, L.J., Karlstrom, K.E., Schmandt, B., Crow, R.R., Colman, D.R., Cron, B., Takacs-Vesbach, C.D., Dahm, C.N., Northup, D.E., Hilton, D.R., Ricketts, J.W., Lowry, A.R., 2016. Continental smokers couple mantle degassing and distinctive microbiology within continents. Earth Planet. Sci. Lett. 435, 22–30. https://doi.org/10.1016/j.epsl.2015.11.039

Dick, H.J.B., Lin, J., Schouten, H., 2003. An ultraslow-spreading class of ocean ridge. Nature 426, 405–412. https://doi.org/10.1038/nature02128

Dunham, E.C., Dore, J.E., Skidmore, M.L., Roden, E.E., Boyd, E.S., 2020. Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments. Proc. Natl. Acad. Sci. 202007051. https://doi.org/10.1073/pnas.2007051117

Dzaugis, M.E., Spivack, A.J., Dunlea, A.G., Murray, R.W., D’Hondt, S., 2016. Radiolytic Hydrogen Production in the Subseafloor Basaltic Aquifer. Front. Microbiol. 7.

Edwards, K.J., Bach, W., McCollom, T.M., Rogers, D.R., 2004. Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats, Diversity, and Roles in Mineral Deposition, Rock Alteration, and Biomass Production in the Deep-Sea. Geomicrobiol. J. 21, 393–404. https://doi.org/10.1080/01490450490485863

Edwards, K.J., Rogers, D.R., Wirsen, D.O., McCollom, T.M., 2003. Isolation and Characterization of Novel Psychrophilic, Neutrophilic, Fe-Oxidizing, Chemolithoautotrophic α- and γ-Proteobacteria from the Deep Sea. Appl. Environ. Microbiol. 69, 2906–2913. https://doi.org/10.1128/AEM.69.5.2906-2913.2003

Falkowski, P., 2012. Ocean Science: The power of plankton. Nature 483, S17–S20. https://doi.org/10.1038/483S17a

Freeman, C., Ostle, N., Kang, H., 2001. An enzymic “latch” on a global carbon store. Nature 409, 149. https://doi.org/10.1038/35051650

Gold, T., 1992. The deep, hot biosphere. Proc. Natl. Acad. Sci. 89, 6045–6049.

Gruber, N., Galloway, J.N., 2008. An Earth-system perspective of the global nitrogen cycle. Nature 451, 293–296. https://doi.org/10.1038/nature06592

Haichar, F. el Z., Marol, C., Berge, O., Rangel-Castro, J.I., Prosser, J.I., Balesdent, J., Heulin, T., Achouak, W., 2008. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2, 1221–1230. https://doi.org/10.1038/ismej.2008.80

Horsfield, B., Schenk, H.J., Zink, K., Ondrak, R., Dieckmann, V., Kallmeyer, J., Mangelsdorf, K., di Primlo, R., Wilkes, H., Parkes, R.J., Fry, J., Cragg, B., 2006. Living microbial ecosystems within the active zone of catagenesis: Implications for feeding the deep biosphere. Earth Planet. Sci. Lett. 246, 55–69. https://doi.org/10.1016/j.epsl.2006.03.040

Jannasch, H.W., Mottl, M.J., 1985. Geomicrobiology of deep-sea hydrothermal vents. Science 229, 717– 725.

Keiluweit, M., Wanzek, T., Kleber, M., Nico, P., Fendorf, S., 2017. Anaerobic microsites have an unaccounted role in soil carbon stabilization. Nat. Commun. Lond. 8, 1–10. http://dx.doi.org.er.lib.k-state.edu/10.1038/s41467-017-01406-6

Kita, I., Matsuo, S., Wakita, H., 1982. H₂ generation by reaction between H₂O and crushed rock: An experimental study on H₂ degassing from the active fault zone. J. Geophys. Res. Solid Earth 87, 10789–10795. https://doi.org/10.1029/JB087iB13p10789

Krumholz, L.R., McKinley, J.P., Ulrich, F.A., Suflita, J.M., 1997. Confined subsurface microbial communities in Cretaceous rock. Nature 386, 64–66. https://doi.org/10.1038/386064a0

Lappan, R., Shelley, G., Islam, Z.F., Leung, P.M., Lockwood, S., Nauer, P.A., Jirapanjawat, T., Ni, G., Chen, Y.-J., Kessler, A.J., Williams, T.J., Cavicchioli, R., Baltar, F., Cook, P.L.M., Morales, S.E., Greening, C., 2023. Molecular hydrogen in seawater supports growth of diverse marine bacteria. Nat. Microbiol 8, 581–595. https://doi.org/10.1038/s41564-023-01322-0

Lee, C.-T.A., Jiang, H., Ronay, E., Minisini, D., Stiles, J., Neal, M., 2018. Volcanic ash as a driver of enhanced organic carbon burial in the Cretaceous. Sci. Rep. 8, 4197. https://doi.org/10.1038/s41598-018-22576-3

Lin Li-Hung, Wang Pei-Ling, Rumble Douglas, Lippmann-Pipke Johanna, Boice Erik, Pratt Lisa M., Lollar Barbara Sherwood, Brodie Eoin L., Hazen Terry C., Andersen Gary L., DeSantis Todd Z., Moser Duane P., Kershaw Dave, Onstott T. C., 2006. Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome. Science 314, 479–482. https://doi.org/10.1126/science.1127376

Lovley, D.R., 2017. Happy together: microbial communities that hook up to swap electrons. ISME J. 11, 327–336. https://doi.org/10.1038/ismej.2016.136

Lovley, D.R., Holmes, D.E., 2021. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat. Rev. Microbiol. 20, 5–19. https://doi.org/10.1038/s41579-021-00597-6

Madigan, M.T., Martinko, J.M., Parker, J., 2003. Brock Biology of Microorganisms, 10th ed. Pearson Education, Inc., Upper Saddle River.

Martinović, T., Mašínová, T., López-Mondéjar, R., Jansa, J., Štursová, M., Starke, R., Baldrian, P., 2022. Microbial utilization of simple and complex carbon compounds in a temperate forest soil. Soil Biol. Biochem. 173, 108786. https://doi.org/10.1016/j.soilbio.2022.108786

McCollom, T., Seewald, J., 2013. Serpentinites, Hydrogen, and Life. Elements 9, 129–134. https://doi.org/10.2113/gselements.9.2.129

McCollom, T.M., Bach, W., 2009. Thermodynamic constraints on hydrogen generation during serpentinization of ultramafic rocks. Geochim. Cosmochim. Acta 73, 856–875. https://doi.org/10.1016/j.gca.2008.10.032

McMahon, P.B., Chapelle, F.H., 1991. Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry. Nature 349, 233–235.

Napieralski, S.A., Buss, H.L., Brantley, S.L., Lee, S., Xu, H., Roden, E.E., 2019. Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock. Proc. Natl. Acad. Sci. 116, 26394. https://doi.org/10.1073/pnas.1909970117

Naughton, H., Keiluweit, M., Tfaily, M., Dynes, J., Regier, T., Fendorf, S., 2021. Development of energetic and enzymatic limitations on microbial carbon cycling in soils. Biogeochemistry 153, 191–213. https://doi.org/10.1007/s10533-021-00781-z

Newell, D., Crossey, L., Karlstrom, K., Fischer, T., Hilton, D., 2005. Continental-scale links between the mantle and groundwater systems of the western United States: Evidence from travertine springs and regional He isotope data. GSA Today 15, 4–10.

Ortiz, M., Leung, P.M., Shelley, G., Jirapanjawat, T., Nauer, P.A., Van Goethem, M.W., Bay, S.K., Islam, Z.F., Jordaan, K., Vikram, S., Chown, S.L., Hogg, I.D., Makhalanyane, T.P., Grinter, R., Cowan, D.A., Greening, C., 2021. Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc. Natl. Acad. Sci. 118, e2025322118. https://doi.org/10.1073/pnas.2025322118

Parkes, R.J., Wellsbury, P., Mather, I.D., Cobb, S.J., Cragg, B.A., Hornibrook, E.R.C., Horsfield, B., 2007. Temperature activation of organic matter and minerals during burial has the potential to sustain the deep biosphere over geological timescales. Org. Geochem. 38, 845–852. https://doi.org/10.1016/j.orggeochem.2006.12.011

Percak-Dennett, E., He, S., Converse, B., Konishi, H., Xu, H., Corcoran, A., Noguera, D., Chan, C., Bhattacharyya, A., Borch, T., Boyd, E., Roden, E.E., 2017. Microbial acceleration of aerobic pyrite oxidation at circumneutral pH. Geobiology 15, 690–703. https://doi.org/10.1111/gbi.12241

Pett-Ridge, J.C., 2009. Contributions of dust to phosphorus cycling in tropical forests of the Luquillo Mountains, Puerto Rico. Biogeochemistry 94, 63–80. https://doi.org/10.1007/s10533-009-9308-x

Popa, R., Smith, A., Popa, R., Boone, J., Fisk, M., 2012. Olivine-Respiring Bacteria Isolated from the Rock-Ice Interface in a Lava-Tube Cave, a Mars Analog Environment. Astrobiology 12, 9–18. https://doi.org/10.1089/ast.2011.0639

Proskurowski, G., Lilley, M.D., Seewald, J.S., Früh-Green, G.L., Olson, E.J., Lupton, J.E., Sylva, S.P., Kelley, D.S., 2008. Abiogenic Hydrocarbon Production at Lost City Hydrothermal Field. Science 319, 604–607. https://doi.org/10.1126/science.1151194

Rotaru, A.E., Shrestha, P.M., Liu, F., Markovaite, B., Chen, S., Nevin, K.P., Lovley, D.R., 2014a. Direct Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri. Appl. Environ. Microbiol. 80, 4599–4605. https://doi.org/10.1128/aem.00895-14

Rotaru, A.E., Shrestha, P.M., Liu, F.H., Shrestha, M., Shrestha, D., Embree, M., Zengler, K., Wardman, C., Nevin, K.P., Lovley, D.R., 2014b. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energy Environ. Sci. 7, 408–415. https://doi.org/10.1039/c3ee42189a

Rotaru, A.-E., Yee, M.O., Musat, F., 2021. Microbes trading electricity in consortia of environmental and biotechnological significance. Curr. Opin. Biotechnol. 67, 119–129. https://doi.org/10.1016/j.copbio.2021.01.014

Santelli, C.M., Orcutt, B.N., Banning, E., Bach, W., Moyer, C.L., Sogin, M.L., Staudigel, H., Edwards, K.J., 2008. Abundance and diversity of microbial life in ocean crust. Nature 453, 653–656. https://doi.org/10.1038/nature06899

Sauvage, J.F., Flinders, A., Spivack, A.J., Pockalny, R., Dunlea, A.G., Anderson, C.H., Smith, D.C., Murray, R.W., D’Hondt, S., 2021. The contribution of water radiolysis to marine sedimentary life. Nat. Commun. 12, 1297. https://doi.org/10.1038/s41467-021-21218-z

Scheller, S., Yu, H., Chadwick, G.L., McGlynn, S.E., Orphan, V.J., 2016. Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction. Science 351, 703–707. https://doi.org/10.1126/science.aad7154

Schlesinger, W.H., Bernhardt, E.S., 2013. Biogeochemistry: An analysis of global change, 3rd ed. Elsevier, New York.

Schmidt, M.W.I., Torn, M.S., Abiven, S., Dittmar, T., Guggenberger, G., Janssens, I.A., Kleber, M., KogelKnabner, I., Lehmann, J., Manning, D.A.C., Nannipieri, P., Rasse, D.P., Weiner, S., Trumbore, S.E., 2011. Persistence of soil organic matter as an ecosystem property. Nature 478, 49–56. https://doi.org/10.1038/nature10386

Seewald, J.S., Zolotov, M.Yu., McCollom, T., 2006. Experimental investigation of single carbon compounds under hydrothermal conditions. Geochim. Cosmochim. Acta 70, 446–460. https://doi.org/10.1016/j.gca.2005.09.002

Shelobolina, Xu, H., Konishi, H., Kukkadapu, R., Wu, T., Blöthe, M., Roden, E., 2012. Microbial Lithotrophic Oxidation of Structural Fe(II) in Biotite. Appl. Environ. Microbiol. 78, 5746–5752. https://doi.org/10.1128/AEM.01034-12

Shen, L., Zhao, Q.C., Wu, X.E., Li, X.Z., Li, Q.B., Wang, Y.P., 2016. Interspecies electron transfer in syntrophic methanogenic consortia: From cultures to bioreactors. Renew. Sustain. Energy Rev. 54, 1358–1367. https://doi.org/10.1016/j.rser.2015.10.102

Shock, E., Holland, M., Meyer-Dombard, D., Amend, J., Osburn, G.R., Fischer, T., 2010. Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA. Geochim. Cosmochim. Acta 74, 4005–4043. https://doi.org/10.1016/j.gca.2009.08.036

Sinsabaugh, R.L., Hill, B.H., Follstad Shah, J.J., 2009. Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature 462, 795–798. https://doi.org/10.1038/nature08632

Sleep, N.H., Meibom, A., Fridriksson, Th., Coleman, R.G., Bird, D.K., 2004. H₂-rich fluids from serpentinization: Geochemical and biotic implications. Proc. Natl. Acad. Sci. U.S.A. 101, 12818. https://doi.org/10.1073/pnas.0405289101

Timmers, P.H.A., Suarez-Zuluaga, D.A., van Rossem, M., Diender, M., Stams, A.J.M., Plugge, C.M., 2016. Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source. Isme J. 10, 1400–1412. https://doi.org/10.1038/ismej.2015.213

Turner, B.L., 2008. Resource partitioning for soil phosphorus: a hypothesis. J. Ecol. 96, 698–702. https://doi.org/10.1111/j.1365-2745.2008.01384.x

Tveit, A.T., Hestnes, A.G., Robinson, S.L., Schintlmeister, A., Dedysh, S.N., Jehmlich, N., von Bergen, M., Herbold, C., Wagner, M., Richter, A., Svenning, M.M., 2019. Widespread soil bacterium that oxidizes atmospheric methane. Proc. Natl. Acad. Sci. U.S.A. 116, 8515. https://doi.org/10.1073/pnas.1817812116

Welch, S.A., Taunton, A.E., Banfield, J.F., 2002. Effect of Microorganisms and Microbial Metabolites on Apatite Dissolution. Geomicrobiol. J. 19, 343–367. https://doi.org/10.1080/01490450290098414

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