10.5: References
- Page ID
- 131905
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Achtnich, C., Bak, F., Conrad, R., 1995. Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers, and methanogens in anoxic paddy soil. Biol. Fert. Soils 19, 65–72. https://doi.org/10.1007/bf00336349
Averill, C., Bhatnagar, J.M., Dietze, M.C., Pearse, W.D., Kivlin, S.N., 2019. Global imprint of mycorrhizal fungi on whole-plant nutrient economics. Proc. Natl. Acad. Sci. U.S.A. 116, 23163–23168. https://doi.org/10.1073/pnas.1906655116
Bethke, C.M., Ding, D., Jin, Q., Sanford, R.A., 2008. Origin of microbiological zoning in groundwater flows. Geology 36, 739–742.
Bethke, C.M., Sanford, R.A., Kirk, M.F., Jin, Q., Flynn, T.M., 2011. The thermodynamic ladder in geomicrobiology. Am. J. Sci. 311, 183–210. https://doi.org/10.2475/03.2011.01 \
Chapin, F.S., 1980. The Mineral Nutrition of Wild Plants. Annu. Rev. Ecol. Syst. 11, 233–260. https://doi.org/10.1146/annurev.es.11.110180.001313
Chen, H., Williams, H.N., 2012. Sharing of Prey: Coinfection of a Bacterium by a Virus and a Prokaryotic Predator. mBio 3. https://doi.org/10.1128/mBio.00051-12
Danczak, R.E., Daly, R.A., Borton, M.A., Stegen, J.C., Roux, S., Wrighton, K.C., Wilkins, M.J., 2020. Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems. mSystems 5, e00098-20. https://doi.org/10.1128/mSystems.00098-20
Fernandez, L., Rodriguez, A., Garcia, P., 2018. Phage or foe: an insight into the impact of viral predation on microbial communities. ISME Journal 12, 1171–1179. https://doi.org/10.1038/s41396-018-0049-5
Flynn, T.M., Sanford, R.A., Ryu, H., Bethke, C.M., Levine, A.D., Ashbolt, N.J., Santo Domingo, J.W., 2013. Functional microbial diversity explains groundwater chemistry in a pristine aquifer. BMC Microbiol. 13. https://doi.org/10.1186/1471-2180-13-146
Fredrickson, A.G., Stephanopoulos, G., 1981. Microbial competition. Science 213, 972–979. https://doi.org/10.1126/science.7268409
García, F.C., Clegg, T., O’Neill, D.B., Warfield, R., Pawar, S., Yvon-Durocher, G., 2023. The temperature dependence of microbial community respiration is amplified by changes in species interactions. Nature Microbiology 8, 272–283. https://doi.org/10.1038/s41564-022-01283-w
Garcia, S.L., Buck, M., McMahon, K.D., Grossart, H.-P., Eiler, A., Warnecke, F., 2015. Auxotrophy and intrapopulation complementary in the "interactome’ of a cultivated freshwater model community. Molecular Ecology 24, 4449–4459. https://doi.org/10.1111/mec.13319
González-Cabaleiro, R., Ofiţeru, I.D., Lema, J.M., Rodríguez, J., 2015. Microbial catabolic activities are naturally selected by metabolic energy harvest rate. The ISME Journal 9, 2630–2641. https://doi.org/10.1038/ismej.2015.69
Herndon, E.M., Yang, Z.M., Bargar, J., Janot, N., Regier, T., Graham, D., Wullschleger, S., Gu, B.H., Liang, L.Y., 2015. Geochemical drivers of organic matter decomposition in arctic tundra soils. Biogeochemistry 126, 397–414. https://doi.org/10.1007/s10533-015-0165-5
Hibbing, M.E., Fuqua, C., Parsek, M.R., Peterson, S.B., 2010. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25. https://doi.org/10.1038/nrmicro2259
Jakobsen, R., Postma, D., 1999. Redox zoning, rates of sulfate reduction and interactions with Fereduction and methanogenesis in a shallow sandy aquifer, Romo, Denmark. Geochim. Cosmochim. Acta 63, 137–151.
Johnson, N.C., Graham, J.-H., Smith, F.A., 1997. Functioning of mycorrhizal associations along the mutualism–parasitism continuum*. New Phytologist 135, 575–585. https://doi.org/10.1046/j.1469-8137.1997.00729.x
Kehe, J., Ortiz, A., Kulesa, A., Gore, J., Blainey, P.C., Friedman, J., 2021. Positive interactions are common among culturable bacteria. Science Advances 7, eabi7159. https://doi.org/10.1126/sciadv.abi7159
Kirk, M.F., Santillan, E.F.U., Sanford, R.A., Altman, S.J., 2013. CO2-induced shift in microbial activity affects carbon trapping and water quality in anoxic bioreactors. Geochim. Cosmochim. Acta 122, 198–208. https://doi.org/10.1016/j.gca.2013.08.018
Konopka, A., 2009. What is microbial community ecology? ISME Journal 3, 1223–1230. https://doi.org/10.1038/ismej.2009.88
Kuenen, J.G., 2020. Anammox and beyond. Environmental Microbiology 22, 525–536. https://doi.org/10.1111/1462-2920.14904
Küsel, K., Blöthe, M., Schulz, D., Reiche, M., Drake, H.L., 2008. Microbial reduction of iron and porewater biogeochemistry in acidic peatlands. Biogeosciences 5, 1537–1549.
Lovley, D.R., Goodwin, S., 1988. Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochim. Cosmochim. Acta 52, 2993–3003.
Marquart, K.A., Haller, B.R., Paper, J.M., Flynn, T.M., Boyanov, M.I., Shodunke, G., Gura, C., Jin, Q., Kirk, M.F., 2019. Influence of pH on the balance between methanogenesis and iron reduction. Geobiology 17, 185–198. https://doi.org/10.1111/gbi.12320
Marzocchi, U., Trojan, D., Larsen, S., Louise Meyer, R., Peter Revsbech, N., Schramm, A., Peter Nielsen, L., Risgaard-Petersen, N., 2014. Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment. The ISME Journal 8, 1682–1690. https://doi.org/10.1038/ismej.2014.19
Metje, M., Frenzel, P., 2007. Methanogenesis and methanogenic pathways in a peat from subarctic permafrost. Environ. Microbiol. 9, 954–964. https://doi.org/10.1111/j.1462-2920.2006.01217.x
Moënne-Loccoz, Y., Mavingui, P., Combes, C., Normand, P., Steinberg, C., 2014. Microorganisms and Biotic Interactions. Environmental Microbiology: Fundamentals and Applications, 395–444. https://doi.org/10.1007/978-94-017-9118-2_11
Morris, B.E.L., Henneberger, R., Huber, H., Moissl-Eichinger, C., 2013. Microbial syntrophy: interaction for the common good. FEMS Microbiology Reviews 37, 384–406. https://doi.org/10.1111/1574-6976.12019
Nair, R.R., Vasse, M., Wielgoss, S., Sun, L., Yu, Y.-T.N., Velicer, G.J., 2019. Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences. Nature Communications 10. https://doi.org/10.1038/s41467-019-12140-6
Nielsen, L.P., Risgaard-Petersen, N., Fossing, H., Christensen, P.B., Sayama, M., 2010. Electric currents couple spatially separated biogeochemical processes in marine sediment. Nature 463, 1071– 1074. https://doi.org/10.1038/nature08790
Orphan, V., 2009. Methods for unveiling cryptic microbial partnerships in nature. Current Opinion in Microbiology 12.
Orsi, W.D., 2018. Ecology and evolution of seafloor and subseafloor microbial communities. Nature Reviews Microbiology 16, 671–683. https://doi.org/10.1038/s41579-018-0046-8
Paper, J.M., Flynn, T.M., Boyanov, M.I., Kemner, K.M., Haller, B.R., Crank, K., Lower, A., Jin, Q., Kirk, M.F., 2021. Influences of pH and substrate supply on the ratio of iron to sulfate reduction. Geobiology 19. https://doi.org/10.1111/gbi.12444
Paul, S., Küsel, K., Alewell, C., 2006. Reduction processes in forest wetlands: Tracking down heterogeneity of source/sink functions with a combination of methods. Soil Biol. Biochem. 38, 1028–1039. https://doi.org/10.1016/j.soilbio.2005.09.001
Pfeffer, C., Larsen, S., Song, J., Dong, M., Besenbacher, F., Meyer, R.L., Kjeldsen, K.U., Schreiber, L., Gorby, Y.A., El-Naggar, M.Y., Leung, K.M., Schramm, A., Risgaard-Petersen, N., Nielsen, L.P., 2012. Filamentous bacteria transport electrons over centimetre distances. Nature 491, 218–221. https://doi.org/10.1038/nature11586
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
Smercina, D.N., Evans, S.E., Friesen, M.L., Tiemann, L.K., 2019. To Fix or Not To Fix: Controls on FreeLiving Nitrogen Fixation in the Rhizosphere. Applied and Environmental Microbiology 85, e02546-18. https://doi.org/10.1128/AEM.02546-18
Van Der Heijden, M.G.A., Bardgett, R.D., Van Straalen, N.M., 2008. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters 11, 296–310. https://doi.org/10.1111/j.1461-0248.2007.01139.x
Velicer, G.J., Mendes-Soares, H., 2009. Bacterial predators. Current Biology 19, R55–R56. https://doi.org/10.1016/j.cub.2008.10.043
Yan, J., Haaijer, S.C.M., Op den Camp, H.J.M., van Niftrik, L., Stahl, D.A., Könneke, M., Rush, D., Sinninghe Damsté, J.S., Hu, Y.Y., Jetten, M.S.M., 2012. Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system. Environmental Microbiology 14, 3146–3158. https://doi.org/10.1111/j.1462-2920.2012.02894.x