6.8: References
- Page ID
- 131849
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Allison, S.D., Martiny, J.B.H., 2008. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. USA 105, 11512. https://doi.org/10.1073/pnas.0801925105
Baker-Austin, C., Dopson, M., 2007. Life in acid: pH homeostasis in acidophiles. Trends in Microbiology 15, 165–171. https://doi.org/10.1016/j.tim.2007.02.005
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. Nature Communications 13, 312. https://doi.org/10.1038/s41467-021-27802-7
Burrows, R.M., van de Kamp, J., Bodrossy, L., Venarsky, M., Coates-Marnane, J., Rees, G., Jumppanen, P., Kennard, M.J., 2021. Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps. FEMS Microbiology Ecology. https://doi.org/10.1093/femsec/fiab130
Dini-Andreote, F., Stegen, J.C., van Elsas, J.D., Salles, J.F., 2015. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc. Natl. Acad. Sci. USA 112, E1326. https://doi.org/10.1073/pnas.1414261112
Fierer, N., Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. Proc. Nat. Acad. Sci. USA 103, 626–631. https://doi.org/10.1073/pnas.0507535103
Fridovich, I., 1999. Fundamental Aspects of Reactive Oxygen Species, or What’s the Matter with Oxygen? Annals of the New York Academy of Sciences 893, 13–18. https://doi.org/10.1111/j.1749-6632.1999.tb07814.x
Hanson, C.A., Fuhrman, J.A., Horner-Devine, M.C., Martiny, J.B.H., 2012. Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews Microbiology 10, 497–506. https://doi.org/10.1038/nrmicro2795
Horikoshi, K., 1999. Alkaliphiles: Some Applications of Their Products for Biotechnology. Microbiology and Molecular Biology Reviews 63, 735–750.
Jin, Q., Kirk, M.F., 2018a. pH as a primary control in environmental microbiology: 1. Thermodynamic perspective. Front. Env. Sci. 6, 1–15. https://doi.org/10.3389/fenvs.2018.00021
Jin, Q., Kirk, M.F., 2018b. pH as a primary control in environmental microbiology: 2. Kinetic perspective. Front. Env. Sci. 6, 1–16. https://doi.org/10.3389/fenvs.2018.00101
Kappler, A., Bryce, C., 2017. Cryptic biogeochemical cycles: unravelling hidden redox reactions. Environmental Microbiology 19, 842–846. https://doi.org/10.1111/1462-2920.13687
Kashefi, K., Lovley, D.R., 2003. Extending the Upper Temperature Limit for Life. Science 301, 934–934. https://doi.org/10.1126/science.1086823
Keiluweit, M., Gee, K., Denney, A., Fendorf, S., 2018. Anoxic microsites in upland soils dominantly controlled by clay content. Soil Biology & Biochemistry 118, 42–50. https://doi.org/10.1016/j.soilbio.2017.12.002
Konhauser, K., 2007. Introduction to Geomicrobiology. Blackwell Publishing, Malden, MA.
Konopka, A., 2009. What is microbial community ecology? ISME Journal 3, 1223–1230. https://doi.org/10.1038/ismej.2009.88
Linn, D.M., Doran, J.W., 1984. Effect of Water-Filled Pore Space on Carbon Dioxide and Nitrous Oxide Production in Tilled and Nontilled Soils. Soil Science Society of America Journal 48, 1267–1272. https://doi.org/10.2136/sssaj1984.03615995004800060013x
Lowe, S.E., Jain, M.K., Zeikus, J.G., 1993. Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates. Microbiol Rev 57, 451–509. https://doi.org/10.1128/mr.57.2.451-509.1993
Madigan, M.T., Martinko, J.M., Parker, J., 2003. Brock Biology of Microorganisms, 10th ed. Pearson Education, Inc., Upper Saddle River.
Min, K., Lehmeier, C.A., Ballantyne, F., Tatarko, A., Billings, S.A., 2014. Differential effects of pH on temperature sensitivity of organic carbon and nitrogen decay. Soil Biology and Biochemistry 76, 193–200. https://doi.org/10.1016/j.soilbio.2014.05.021
Ning, D., Deng, Y., Tiedje, J.M., Zhou, J., 2019. A general framework for quantitatively assessing ecological stochasticity. Proc. Natl. Acad. Sci. USA 116, 16892–16898. https://doi.org/10.1073/pnas.1904623116
Oren, A., 1999. Bioenergetic aspects of halophilism. Microbiol. Molec. Biol. Rev. 63, 334-+.
Picard, A., Daniel, I., 2013. Pressure as an environmental parameter for microbial life – A review. Biophysical Chemistry 183. https://doi.org/10.1016/j.bpc.2013.06.019
Pikuta, E.V., Hoover, R.B., Tang, J., 2007. Microbial extremophiles at the limits of life. Crit. Rev. Microbiol. 33, 183–209. https://doi.org/10.1080/10408410701451948
Power, J.F., Carere, C.R., Lee, C.K., Wakerley, G.L.J., Evans, D.W., Button, M., White, D., Climo, M.D., Hinze, A.M., Morgan, X.C., McDonald, I.R., Cary, S.C., Stott, M.B., 2018. Microbial biogeography of 925 geothermal springs in New Zealand. Nature Communications 9, 2876. https://doi.org/10.1038/s41467-018-05020-y
Rivkina, E.M., Friedmann, E.I., McKay, C.P., Gilichinsky, D.A., 2000. Metabolic Activity of Permafrost Bacteria below the Freezing Point. Applied and Environmental Microbiology 66, 3230–3233. https://doi.org/10.1128/AEM.66.8.3230-3233.2000
Roadcap, G.S., Sanford, R.A., Jin, Q., Pardinas, J.R., Bethke, C.M., 2006. Extremely alkaline (pH > 12) ground water hosts diverse microbial community. Ground Water 44, 511–517. https://doi.org/10.1111/j.1745-6584.2006.00199.x
Roden, E.E., Urrutia, M.M., 1999. Ferrous iron removal promotes microbial reduction of crystalline iron(III) oxides. Environ. Sci. Technol. 33, 1847–1853.
Rosso, L., Lobry, J.R., Bajard, S., Flandrois, J.P., 1995. Convenient model to describe the combined effects of temperature and pH on microbial growth. Appl. Environ. Microbiol. 61, 610–616.
Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N., 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME Journal 4, 1340–1351. https://doi.org/10.1038/ismej.2010.58
Schleper, C., Piihler, G., Kuhlmorgen, B., Zillig, W., 1995. Life at extremely low pH. Nature 375, 741–742. https://doi.org/10.1038/375741b0
Shade, A., Peter, H., Allison, S.D., Baho, D.L., Berga, M., Buergmann, H., Huber, D.H., Langenheder, S., Lennon, J.T., Martiny, J.B.H., Matulich, K.L., Schmidt, T.M., Handelsman, J., 2012. Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology 3. https://doi.org/10.3389/fmicb.2012.00417
Skopp, J., Jawson, M.D., Doran, J.W., 1990. Steady-State Aerobic Microbial Activity as a Function of Soil Water Content. Soil Science Society of America Journal 54, 1619–1625. https://doi.org/10.2136/sssaj1990.03615995005400060018x
Souza, L.F.T., Billings, S.A., 2022. Temperature and pH mediate stoichiometric constraints of organically derived soil nutrients. Global Change Biology 28, 1630–1642. https://doi.org/10.1111/gcb.15985
Takacs-Vesbach, C., Mitchell, K., Jackson-Weaver, O., Reysenbach, A.-L., 2008. Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles. Environmental Microbiology 10, 1681–1689. https://doi.org/10.1111/j.1462-2920.2008.01584.x
Takai, K., Nakamura, K., Toki, T., Tsunogai, U., Miyazaki, M., Miyazaki, J., Hirayama, H., Nakagawa, S., Nunoura, T., Horikoshi, K., 2008. Cell proliferation at 122°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proc. Natl. Acad. Sci. USA 105, 10949. https://doi.org/10.1073/pnas.0712334105
Takami, H., Inoue, A., Fuji, F., Horikoshi, K., 1997. Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiology Letters 152, 279–285. https://doi.org/10.1111/j.1574-6968.1997.tb10440.x
Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill, R.J., Tripathi, A., Gibbons, S.M., Ackermann, G., Navas-Molina, J.A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J.T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M.F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N.A., Lefler, J., Brislawn, C.J., Humphrey, G., Owens, S.M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.A., Clauset, A., Stevens, R.L., Shade, A., Pollard, K.S., Goodwin, K.D., Jansson, J.K., Gilbert, J.A., Knight, R., Rivera, J.L.A., Al-Moosawi, L., Alverdy, J., Amato, K.R., Andras, J., Angenent, L.T., Antonopoulos, D.A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J.K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J.F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D.M., Braun, J., Brazelton, W., Brearley, F.Q., Campbell, A.H., Caporaso, J.G., Cardona, C., Carroll, J., Cary, S.C., Casper, B.B., Charles, T.C., Chu, H., Claar, D.C., Clark, R.G., Clayton, J.B., Clemente, J.C., Cochran, A., Coleman, M.L., Collins, G., Colwell, R.R., Contreras, M., Crary, B.B., Creer, S., Cristol, D.A., Crump, B.C., Cui, D., Daly, S.E., Davalos, L., Dawson, R.D., Defazio, J., Delsuc, F., Dionisi, H.M., Dominguez-Bello, M.G., Dowell, R., Dubinsky, E.A., Dunn, P.O., Ercolini, D., Espinoza, R.E., Ezenwa, V., Fenner, N., Findlay, H.S., Fleming, I.D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E.S., Galindo, G., Garcia, L., Garcia-Amado, M.A., Garshelis, D., Gasser, R.B., Gerdts, G., Gibson, M.K., Gifford, I., Gill, R.T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H.-P., Guyton, K., Haig, S.-J., Hale, V., Hall, R.S., Hallam, S.J., Handley, K.M., Hasan, N.A., Haydon, S.R., Hickman, J.E., Hidalgo, G., Hofmockel, K.S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J.D., Jastrow, J.D., Jex, A.R., Johnson, L.S., Johnston, E.R., Joseph, S., Jurburg, S.D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C.T.E., Kennedy, S.J., Kerkhof, L.J., King, G.M., Kling, G.W., Koehler, A.V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E.M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I.I., Liancourt, P., Liang, W., Linz, A.M., Lipson, D.A., Liu, Y., Lladser, M.E., Lozada, M., Spirito, C.M., MacCormack, W.P., MacRaeCrerar, A., Magris, M., Martín-Platero, A.M., Martín-Vivaldi, M., Martínez, L.M., Martínez-Bueno, M., Marzinelli, E.M., Mason, O.U., Mayer, G.D., McDevitt-Irwin, J.M., McDonald, J.E., McGuire, K.L., McMahon, K.D., McMinds, R., Medina, M., Mendelson, J.R., Metcalf, J.L., Meyer, F., Michelangeli, F., Miller, K., Mills, D.A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R.M., Munroe, P., Myrold, D., Neufeld, J.D., Ni, Y., Nicol, G.W., Nielsen, S., Nissimov, J.I., Niu, K., Nolan, M.J., Noyce, K., O’Brien, S.L., Okamoto, N., Orlando, L., Castellano, Y.O., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J.M., Petraitis, P., Pfister, C., PilonSmits, E., Piombino, P., Pointing, S.B., Pollock, F.J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A.P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K.J., Rodriguezl, S.M., Rohwer, F., Roundstone, W., Safran, R.J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M.D., Scott, N.M., Seger, R.L., Seguin-Orlando, A., Seldin, L., Seyler, L.M., Shakhsheer, B., Sheets, G.M., Shen, C., Shi, Y., Shin, H., Shogan, B.D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D.P., Soler, J.J., Sperling, M., Steinberg, P.D., Stephens, B., Stevens, M.A., Taghavi, S., Tai, V., Tait, K., Tan, C.L., Tas¸, N., Taylor, D.L., Thomas, T., Timling, I., Turner, B.L., Urich, T., Ursell, L.K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Thurber, R.V., Vitaglione, P., Walker, D.A., Walters, W.A., Wang, S., Wang, T., Weaver, T., Webster, N.S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J.J., West, K., Whitehead, A., Whitehead, S.R., Whittingham, L.A., Willerslev, E., Williams, A.E., Wood, S.A., Woodhams, D.C., Yang, Y., The Earth Microbiome Project Consortium, 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463. https://doi.org/10.1038/nature24621
Tiedje, J.M., Sexstone, A.J., Parkin, T.B., Revsbech, N.P., 1984. Anaerobic processes in soil. Plant and Soil 76, 197–212. https://doi.org/10.1007/BF02205580
Triska, F.J., Duff, J.H., Avanzino, R.J., 1993. The role of water exchange between a stream channel and its hyporheic zone in nitrogen cycling at the terrestrial-aquatic interface. Hydrobiologia 251, 167–184. https://doi.org/10.1007/BF00007177
Valett, H.M., Morrice, J.A., Dahm, C.N., Campana, M.E., 1996. Parent lithology, surface–groundwater exchange, and nitrate retention in headwater streams. Limnology and Oceanography 41, 333–345. https://doi.org/10.4319/lo.1996.41.2.0333
Verseux, C., 2020. Bacterial Growth at Low Pressure: A Short Review. Frontiers in Astronomy and Space Sciences 7.
Yayanos, A.A., Dietz, A.S., VAN Boxtel, R., 1979. Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 205, 808–810. https://doi.org/10.1126/science.205.4408.808
Zarnetske, J.P., Haggerty, R., Wondzell, S.M., Baker, M.A., 2011. Dynamics of nitrate production and removal as a function of residence time in the hyporheic zone. Journal of Geophysical Research: Biogeosciences 116. https://doi.org/10.1029/2010JG001356
Zarnetske, J.P., Haggerty, R., Wondzell, S.M., Bokil, V.A., González-Pinzón, R., 2012. Coupled transport and reaction kinetics control the nitrate source-sink function of hyporheic zones. Water Resources Research 48. https://doi.org/10.1029/2012WR011894
Zhang, Horne, R.N., Hawkins, A.J., Primo, J.C., Gorbatenko, Dekas, A.E., 2022. Geological activity shapes the microbiome in deep-subsurface aquifers by advection. Proc. Natl. Acad. Sci. 119, e2113985119. https://doi.org/10.1073/pnas.2113985119
Zobell, C.E., Johnson, F.H., 1949. The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J Bacteriol 57, 179–189. https://doi.org/10.1128/jb.57.2.179-189.1949