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Soil microbial communities are shaped by plant‐driven changes in resource availability during secondary succession
dc.contributor.authorCline, Lauren C.en_US
dc.contributor.authorZak, Donald R.en_US
dc.date.accessioned2016-02-01T18:48:06Z
dc.date.available2017-01-03T16:21:16Zen
dc.date.issued2015-12en_US
dc.identifier.citationCline, Lauren C.; Zak, Donald R. (2015). "Soil microbial communities are shaped by plant‐driven changes in resource availability during secondary succession." Ecology 96(12): 3374-3385.en_US
dc.identifier.issn0012-9658en_US
dc.identifier.issn1939-9170en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/116975
dc.publisherEcological Society of Americaen_US
dc.publisherWiley Periodicals, Inc.en_US
dc.subject.othersecondary successionen_US
dc.subject.othermetagenomicsen_US
dc.subject.otherCedar Creek Reserve, Minnesota, USAen_US
dc.subject.othersoilen_US
dc.subject.othermicrobial community assemblyen_US
dc.subject.otherold fielden_US
dc.titleSoil microbial communities are shaped by plant‐driven changes in resource availability during secondary successionen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelEcology and Evolutionary Biologyen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.contributor.affiliationumSchool of Natural Resources & Environment, University of Michigan, 440 Church Street, Ann Arbor, Michigan 48109 USAen_US
dc.contributor.affiliationumDepartment of Ecology & Evolution, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109 USAen_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/116975/1/ecy201596123374.pdf
dc.identifier.doi10.1890/15-0184.1en_US
dc.identifier.sourceEcologyen_US
dc.identifier.citedreferenceRousk, J., E. Bååth, P. C. Brookes, C. L. Lauber, C. Lozupone, J. G. Caporaso, R. Knight, and N. Fierer. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME Journal 4: 1340 – 1351.en_US
dc.identifier.citedreferencePorter, T. M., J. E. Skillman, and J. M. Moncalvo. 2008. Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Molecular Ecology 17: 3037 – 3050.en_US
dc.identifier.citedreferencePrice, M. N., P. S. Dehal, and A. P. Arkin. 2010. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.en_US
dc.identifier.citedreferenceQuested, H., O. Eriksson, C. Fortunel, and E. Garnier. 2007. Plant traits relate to whole-community litter quality and decomposition following land use change. Functional Ecology 21: 1016 – 1026.en_US
dc.identifier.citedreferenceR Development Core Team. 2013. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.r-project.orgen_US
dc.identifier.citedreferenceSaiya-Cork, K., R. Sinsabaugh, and D. Zak. 2002. The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biology and Biochemistry 34: 1309 – 1315.en_US
dc.identifier.citedreferenceSchloss, P. D., D. Gevers, and S. L. Westcott. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310.en_US
dc.identifier.citedreferenceTalbot, J. M., et al. 2014. Endemism and functional convergence across the North American soil mycobiome. Proceedings of the National Academy of Sciences USA 111: 6341 – 6346.en_US
dc.identifier.citedreferenceTalbot, J. M., D. J. Yelle, J. Nowick, and K. K. Treseder. 2011. Litter decay rates are determined by lignin chemistry. Biogeochemistry 108: 279 – 295.en_US
dc.identifier.citedreferenceTatusova, T., S. Ciufo, B. Fedorov, K. O'Neill, and I. Tolstoy. 2014. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Research 42: D553 – D559.en_US
dc.identifier.citedreferenceTilman, D. 1980. Resources: a graphical-mechanistic approach to competition and predation. American Naturalist 116: 362 – 393.en_US
dc.identifier.citedreferenceTilman, D. 1988. Plant strategies and the dynamics and structure of plant communities. Princeton University Press, Princeton, New Jersey, USA.en_US
dc.identifier.citedreferenceTravers, K. J., C. S. Chin, D. R. Rank, J. S. Eid, and S. W. Turner. 2010. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Research 38: 1 – 8.en_US
dc.identifier.citedreferenceTscherko, D., U. Hammesfahr, M. C. Marx, and E. Kandeler. 2004. Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence. Soil Biology and Biochemistry 36: 1685 – 1698.en_US
dc.identifier.citedreferenceTwieg, B. D., D. M. Durall, and S. W. Simard. 2007. Ectomycorrhizal fungal succession in mixed temperate forests. New Phytologist 176: 437 – 447.en_US
dc.identifier.citedreferencevan der Wal, A., T. D. Geydan, T. W. Kuyper, and W. de Boer. 2013. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiology Reviews 37: 477 – 494.en_US
dc.identifier.citedreferenceVan Soest, P. J., J. B. Robertson, and B. A. Lewis. 1991. Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition. Journal of Dairy Science 74: 3583 – 3597.en_US
dc.identifier.citedreferenceVoříšková, J., and P. Baldrian. 2013. Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME Journal 7: 477 – 486.en_US
dc.identifier.citedreferenceWaldrop, M. P., D. R. Zak, C. B. Blackwood, C. D. Curtis, and D. Tilman. 2006. Resource availability controls fungal diversity across a plant diversity gradient. Ecology Letters 9: 1127 – 1135.en_US
dc.identifier.citedreferenceWang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73: 5261 – 5267.en_US
dc.identifier.citedreferenceZak, D. R., D. F. Grigal, S. Gleeson, and D. Tilman. 1990. Carbon and nitrogen cycling during old-field succession: constraints on plant and microbial biomass. Biogeochemistry 11: 111 – 129.en_US
dc.identifier.citedreferenceZak, D. R., W. E. Holmes, D. C. White, A. D. Peacock, and D. Tilman. 2003. Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology 84: 2042 – 2050.en_US
dc.identifier.citedreferenceZumsteg, A., J. Luster, H. Göransson, R. H. Smittenberg, I. Brunner, S. M. Bernasconi, J. Zeyer, and B. Frey. 2012. Bacterial, archaeal and fungal succession in the forefield of a receding glacier. Microbial Ecology 63: 552 – 564.en_US
dc.identifier.citedreferenceAltschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403 – 410.en_US
dc.identifier.citedreferenceAmend, A. S., K. A. Seifert, R. Samson, and T. D. Bruns. 2010. Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proceedings of the National Academy of Sciences USA 107: 13748 – 13753.en_US
dc.identifier.citedreferenceBajerski, F., and D. Wagner. 2013. Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica. FEMS Microbiology Ecology 85: 128 – 142.en_US
dc.identifier.citedreferenceBaldrian, P. 2006. Fungal laccases—occurrence and properties. FEMS Microbiology Reviews 30: 215 – 242.en_US
dc.identifier.citedreferenceBardgett, R. D., W. D. Bowman, R. Kaufmann, and S. K. Schmidt. 2005. A temporal approach to linking aboveground and belowground ecology. Trends in Ecology & Evolution 20: 634 – 641.en_US
dc.identifier.citedreferenceBissett, A., A. E. Richardson, G. Baker, S. Wakelin, and P. H. Thrall. 2010. Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Molecular Ecology 19: 4315 – 4327.en_US
dc.identifier.citedreferenceBoddy, L. 2000. Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiology Ecology 31: 185 – 194.en_US
dc.identifier.citedreferenceBurke, C., P. Steinberg, D. Rusch, S. Kjelleberg, and T. Thomas. 2011. Bacterial community assembly based on functional genes rather than species. Proceedings of the National Academy of Sciences USA 108: 14288 – 14293.en_US
dc.identifier.citedreferenceBurns, R. G., J. L. DeForest, J. Marxsen, R. L. Sinsabaugh, M. E. Stromberger, M. D. Wallenstein, M. N. Weintraub, and A. Zoppini. 2013. Soil enzymes in a changing environment: current knowledge and future directions. Soil Biology and Biochemistry 58: 216 – 234.en_US
dc.identifier.citedreferenceChao, A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265 – 270.en_US
dc.identifier.citedreferenceConnell, J. H., and R. O. Slatyer. 1977. Mechanisms of succession in natural communities and their role in community stability and organization. American Naturalist 111: 1119 – 1144.en_US
dc.identifier.citedreferenceCutler, N. A., D. L. Chaput, and C. J. van der Gast. 2014. Long-term changes in soil microbial communities during primary succession. Soil Biology and Biochemistry 69: 359 – 370.en_US
dc.identifier.citedreferenceEdwards, I. P., and D. R. Zak. 2010. Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape. Molecular Ecology 19: 1469 – 1482.en_US
dc.identifier.citedreferenceFawal, N., Q. Li, B. Savelli, M. Brette, G. Passaia, M. Fabre, C. Mathé, and C. Dunand. 2013. PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. Nucleic Acids Research 41: D441 – D444.en_US
dc.identifier.citedreferenceFierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences USA 103: 626 – 631.en_US
dc.identifier.citedreferenceFierer, N., C. L. Lauber, K. S. Ramirez, J. Zaneveld, M. A. Bradford, and R. Knight. 2012. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME Journal 6: 1007 – 1017.en_US
dc.identifier.citedreferenceFish, J. A., B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2013. FunGene: the functional gene pipeline and repository. Frontiers in Microbiology 4: 291.en_US
dc.identifier.citedreferenceGoering, H. K., and P. J. Van Soest. 1970. Forage fiber analysis. Agricultural Research Service Handbook number 379. U.S. Department of Agriculture, Washington, D.C., USA.en_US
dc.identifier.citedreferenceGood, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40: 237 – 264.en_US
dc.identifier.citedreferenceGrigal, D. F., L. M. Chamberlain, H. R. Finney, D. V. Wroblewski, and E. R. Fross. 1974. Soils of the Cedar Creek Natural History Area. Miscellaneous Report 123. University of Minnesota Agricultural Experiment Station, St. Paul, Minnesota, USA.en_US
dc.identifier.citedreferenceGrime, J. P. 1979. Plant strategies, vegetation processes, and ecosystem properties. John Wiley & Sons, New York, New York, USA.en_US
dc.identifier.citedreferenceHopple, J. S., and R. Vilgalys. 1994. Phylogenetic relationships among Coprinoid taxa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia 86: 96 – 107.en_US
dc.identifier.citedreferenceHudson, H. J. 1968. The ecology of fungi on plant remains above the soil. New Phytologist 67: 837 – 874.en_US
dc.identifier.citedreferenceJangid, K., W. B. Whitman, L. M. Condron, B. L. Turner, and M. A. Williams. 2013. Soil bacterial community succession during long-term ecosystem development. Molecular Ecology 22: 3415 – 3424.en_US
dc.identifier.citedreferenceJumpponen, A. 2003. Soil fungal community assembly in a primary successional glacier forefront ecosystem as inferred from rDNA sequence analyses. New Phytologist 158: 569 – 578.en_US
dc.identifier.citedreferenceKnops, J. M. H., and D. Tilman. 2000. Dynamics of soil nitrogen and carbon accumulation for 61 years after agricultural abandonment. Ecology 81: 88 – 98.en_US
dc.identifier.citedreferenceKowalchuk, G. A., D. S. Buma, W. de Boer, P. G. L. Klinkhamer, and J. A. van Veen. 2002. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie van Leeuwenhoek 81: 509 – 520.en_US
dc.identifier.citedreferenceKranabetter, J. M., J. Friesen, S. Gamiet, and P. Kroeger. 2005. Ectomycorrhizal mushroom distribution by stand age in western hemlock–lodgepole pine forests of northwestern British Columbia. Canadian Journal of Forest Research 35: 1527 – 1539.en_US
dc.identifier.citedreferenceKuramae, E., H. Gamper, J. van Veen, and G. Kowalchuk. 2011. Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiology Ecology 77: 285 – 294.en_US
dc.identifier.citedreferenceLane, D. J. 1991. 16S/23S rRNA sequencing. Pages 115 – 175 in E. Stackebrandt and M. Goodfellow, editors. Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, New York, USA.en_US
dc.identifier.citedreferenceLauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75: 5111 – 5120.en_US
dc.identifier.citedreferenceLegendre, P., and M. J. Anderson. 2006. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecological Monographs 69: 1 – 24.en_US
dc.identifier.citedreferenceLombard, V., H. Golaconda Ramulu, E. Drula, P. M. Coutinho, and B. Henrissat. 2013. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Research 42: D490 – D495.en_US
dc.identifier.citedreferenceLozupone, C., M. Hamady, and R. Knight. 2006. UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.en_US
dc.identifier.citedreferenceMartiny, A. C., K. Treseder, and G. Pusch. 2012. Phylogenetic conservatism of functional traits in microorganisms. ISME Journal 7: 830 – 838.en_US
dc.identifier.citedreferenceMcGuire, K. L., E. Bent, J. Borneman, A. Majumder, S. D. Allison, and K. K. Treseder. 2010. Functional diversity in resource use by fungi. Ecology 91: 2324 – 2332.en_US
dc.identifier.citedreferenceMeier, C. L., and W. D. Bowman. 2008. Links between plant litter chemistry, species diversity, and below-ground ecosystem function. Proceedings of the National Academy of Sciences USA 105: 19780 – 19785.en_US
dc.identifier.citedreferenceMeyer, F., et al. 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.en_US
dc.identifier.citedreferenceMitchell, R. J., A. J. Hester, C. D. Campbell, S. J. Chapman, C. M. Cameron, R. L. Hewison, and J. M. Potts. 2010. Is vegetation composition or soil chemistry the best predictor of the soil microbial community? Plant and Soil 333: 417 – 430.en_US
dc.identifier.citedreferenceNemergut, D. R., S. P. Anderson, C. C. Cleveland, A. P. Martin, A. E. Miller, A. Seimon, and S. K. Schmidt. 2007. Microbial community succession in an unvegetated, recently deglaciated soil. Microbial Ecology 53: 110 – 122.en_US
dc.identifier.citedreferenceOksanen, J., F. G. Blanchet, R. Kindt, P. Legendre, R. B. O'Hara, G. L. Simpson, P. Solymos, M. H. H. Stevens, and H. Wagner. 2013. vegan: community ecology package version 2 2.0-7. https://cran.r-project.org/web/packages/vegan/index.htmlen_US
dc.identifier.citedreferenceOsono, T. 2007. Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecological Research 22: 955 – 974.en_US
dc.identifier.citedreferencePaul, E. A., and F. E. Clark. 1996. Soil microbiology and biochemistry. Second edition. Academic Press, New York, New York, USA.en_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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