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Volumn 5, Issue JULY, 2014, Pages

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

Author keywords

Co occurrence; Community assembly; MGRAST; Microbial communities; Network theory

Indexed keywords

RNA 16S;

EID: 84905396568     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00358     Document Type: Article
Times cited : (285)

References (58)
  • 1
    • 0002154022 scopus 로고    scopus 로고
    • A new method for non-parametric multivariate analysis of variance
    • doi: 10.1111/j.1442-9993.2001.01070.pp.x
    • Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Aust. Ecol. 26, 32-46. doi: 10.1111/j.1442-9993.2001.01070.pp.x
    • (2001) Aust. Ecol. , vol.26 , pp. 32-46
    • Anderson, M.J.1
  • 2
    • 84891355477 scopus 로고    scopus 로고
    • PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing?
    • doi: 10.1890/12-2010.1
    • Anderson, M. J., and Walsh, D. C. I. (2013). PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol. Monogr. 83, 557-574. doi: 10.1890/12-2010.1
    • (2013) Ecol. Monogr. , vol.83 , pp. 557-574
    • Anderson, M.J.1    Walsh, D.C.I.2
  • 3
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • doi: 10.1186/1471-2105-4-2
    • Bader, G. D., and Hogue, C. W. V. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 1-27. doi: 10.1186/1471-2105-4-2
    • (2003) BMC Bioinformatics , vol.4 , pp. 1-27
    • Bader, G.D.1    Hogue, C.W.V.2
  • 4
    • 84855949949 scopus 로고    scopus 로고
    • Using network analysis to explore co-occurrence patterns in soil microbial communities
    • doi: 10.1038/ismej.2011.119
    • Barberán, A., Bates, S. T., Casamayor, E. O., and Fierer, N. (2012). Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6, 343-351. doi: 10.1038/ismej.2011.119
    • (2012) ISME J. , vol.6 , pp. 343-351
    • Barberán, A.1    Bates, S.T.2    Casamayor, E.O.3    Fierer, N.4
  • 5
    • 84897149362 scopus 로고    scopus 로고
    • lme4: Linear Mixed-effects Models Using Eigen and S4.
    • R package version 1.0-6.
    • Bates, D., Maechler, M., Bolker, B., and Walker, S. (2014). lme4: Linear Mixed-effects Models Using Eigen and S4. R package version 1.0-6. Available online at: http://CRAN.R-project.org/package=lme4
    • (2014)
    • Bates, D.1    Maechler, M.2    Bolker, B.3    Walker, S.4
  • 6
    • 78049465387 scopus 로고    scopus 로고
    • Node centrality indices in food webs: rank orders versus distributions
    • doi: 10.1016/j.ecocom.2009.11.006
    • Bauer, B., Jordán, F., and Podani, J. (2010). Node centrality indices in food webs: rank orders versus distributions. Ecol. Complex 7, 471-477. doi: 10.1016/j.ecocom.2009.11.006
    • (2010) Ecol. Complex , vol.7 , pp. 471-477
    • Bauer, B.1    Jordán, F.2    Podani, J.3
  • 7
    • 84890261691 scopus 로고    scopus 로고
    • Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments.
    • doi: 10.3389/fmicb.2013.00342
    • Bowen, J. L., Byrnes, J. E. K., Weisman, D., and Colaneri, C. (2013). Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments. Front. Microbiol. 4:342. doi: 10.3389/fmicb.2013.00342
    • (2013) Front. Microbiol. , vol.4 , pp. 342
    • Bowen, J.L.1    Byrnes, J.E.K.2    Weisman, D.3    Colaneri, C.4
  • 9
  • 10
    • 77954238817 scopus 로고    scopus 로고
    • A global network of coexisting microbes from environmental and whole-genome sequence data
    • doi: 10.1101/gr.104521.109
    • Chaffron, S., Rehrauer, H., Pernthaler, J., and Von Mering, C. (2010). A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947-959. doi: 10.1101/gr.104521.109
    • (2010) Genome Res. , vol.20 , pp. 947-959
    • Chaffron, S.1    Rehrauer, H.2    Pernthaler, J.3    Von Mering, C.4
  • 11
    • 84888200521 scopus 로고    scopus 로고
    • Temporal variability and coherence of euphotic zone bacterial communities over a decade in the southern california bight
    • doi: 10.1038/ismej.2013.122
    • Chow, C. E. T., Sachdeva, R., Cram, J. A., Steele, J. A., Needham, D. M., Patel, A., et al. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the southern california bight. ISME J. 7, 2259-2273. doi: 10.1038/ismej.2013.122
    • (2013) ISME J. , vol.7 , pp. 2259-2273
    • Chow, C.E.T.1    Sachdeva, R.2    Cram, J.A.3    Steele, J.A.4    Needham, D.M.5    Patel, A.6
  • 12
    • 84888782821 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing.
    • Core Team, R. (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna. Available online at: http://www.r-project.org/
    • (2013) R Foundation for Statistical Computing. Vienna
    • Core Team, R.1
  • 13
    • 72949091232 scopus 로고    scopus 로고
    • Bacterial community variation in human body habitats across space and time
    • doi: 10.1126/science.1177486
    • Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., and Knight, R. (2009). Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697. doi: 10.1126/science.1177486
    • (2009) Science , vol.326 , pp. 1694-1697
    • Costello, E.K.1    Lauber, C.L.2    Hamady, M.3    Fierer, N.4    Gordon, J.I.5    Knight, R.6
  • 14
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research.
    • Csardi, G., and Nepusz, T. (2006). The igraph software package for complex network research. Int. J. Complex Syst. 1695.
    • (2006) Int. J. Complex Syst. 1695
    • Csardi, G.1    Nepusz, T.2
  • 16
    • 82855163972 scopus 로고    scopus 로고
    • Correlation network analysis applied to complex biofilm communities.
    • doi: 10.1371/journal.pone.0028438
    • Duran-Pinedo, A. E., Paster, B., Teles, R., and Frias-Lopez, J. (2011). Correlation network analysis applied to complex biofilm communities. PLoS ONE 6:e28438. doi: 10.1371/journal.pone.0028438
    • (2011) PLoS ONE , vol.6
    • Duran-Pinedo, A.E.1    Paster, B.2    Teles, R.3    Frias-Lopez, J.4
  • 17
    • 84855951093 scopus 로고    scopus 로고
    • Coherent dynamics and association networks among lake bacterioplankton taxa
    • doi: 10.1038/ismej.2011.113
    • Eiler, A., Heinrich, F., and Bertilsson, S. (2012). Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J. 6, 330-342. doi: 10.1038/ismej.2011.113
    • (2012) ISME J. , vol.6 , pp. 330-342
    • Eiler, A.1    Heinrich, F.2    Bertilsson, S.3
  • 18
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: from networks to models
    • doi: 10.1038/nrmicro2832
    • Faust, K., and Raes, J. (2012). Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538-550. doi: 10.1038/nrmicro2832
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 19
    • 77954241658 scopus 로고    scopus 로고
    • The large-scale organization of the bacterial network of ecological co-occurrence interactions
    • doi: 10.1093/nar/gkq118
    • Freilich, S., Kreimer, A., Meilijson, I., Gophna, U., Sharan, R., and Ruppin, E. (2010). The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res. 38, 3857-3868. doi: 10.1093/nar/gkq118
    • (2010) Nucleic Acids Res. , vol.38 , pp. 3857-3868
    • Freilich, S.1    Kreimer, A.2    Meilijson, I.3    Gophna, U.4    Sharan, R.5    Ruppin, E.6
  • 20
    • 84865733148 scopus 로고    scopus 로고
    • Inferring correlation networks from genomic survey data
    • doi: 10.1371/journal.pcbi.1002687
    • Friedman, J., and Alm, E. J. (2012). Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8:e1002687. doi: 10.1371/journal.pcbi.1002687
    • (2012) PLoS Comput. Biol. , vol.8
    • Friedman, J.1    Alm, E.J.2
  • 21
    • 66149150877 scopus 로고    scopus 로고
    • Microbial community structure and its functional implications
    • doi: 10.1038/nature08058
    • Fuhrman, J. A. (2009). Microbial community structure and its functional implications. Nature 459, 193-199. doi: 10.1038/nature08058
    • (2009) Nature , vol.459 , pp. 193-199
    • Fuhrman, J.A.1
  • 22
    • 54549105879 scopus 로고    scopus 로고
    • Community structure of marine bacterioplankton: patterns, networks, and relationships to function
    • doi: 10.3354/ame01222
    • Fuhrman, J. A., and Steele, J. A. (2008). Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat. Microb. Ecol. 53, 69-81. doi: 10.3354/ame01222
    • (2008) Aquat. Microb. Ecol. , vol.53 , pp. 69-81
    • Fuhrman, J.A.1    Steele, J.A.2
  • 23
    • 84855958621 scopus 로고    scopus 로고
    • Defining seasonal marine microbial community dynamics
    • doi: 10.1038/ismej.2011.107
    • Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbrück, L., Reeder, J., Temperton, B., et al. (2012). Defining seasonal marine microbial community dynamics. ISME J. 6, 298-308. doi: 10.1038/ismej.2011.107
    • (2012) ISME J. , vol.6 , pp. 298-308
    • Gilbert, J.A.1    Steele, J.A.2    Caporaso, J.G.3    Steinbrück, L.4    Reeder, J.5    Temperton, B.6
  • 24
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • doi: 10.1073/pnas.122653799
    • Girvan, M., and Newman, M. E. J. (2002). Community structure in social and biological networks. Proc. Natl. Acad. Sci. U.S.A. 99, 7821-7826. doi: 10.1073/pnas.122653799
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 7821-7826
    • Girvan, M.1    Newman, M.E.J.2
  • 25
    • 80053569422 scopus 로고    scopus 로고
    • Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance.
    • doi: 10.3389/fmicb.2011.00094
    • Goldfarb, K. C., Karaoz, U., Hanson, C. A., Santee, C. A., Bradford, M. A., Treseder, K. K., et al. (2011). Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front. Microbiol. 2:94. doi: 10.3389/fmicb.2011.00094
    • (2011) Front. Microbiol. , vol.2 , pp. 94
    • Goldfarb, K.C.1    Karaoz, U.2    Hanson, C.A.3    Santee, C.A.4    Bradford, M.A.5    Treseder, K.K.6
  • 26
    • 84872550978 scopus 로고    scopus 로고
    • Rethinking community assembly through the lens of coexistence theory
    • doi: 10.1146/annurev-ecolsys-110411-160411
    • HilleRisLambers, J., Adler, P. B., Harpole, W. S., Levine, J. M., and Mayfield, M. M. (2012). Rethinking community assembly through the lens of coexistence theory. Annu. Rev. Ecol. Evol. Syst. 43, 227-248. doi: 10.1146/annurev-ecolsys-110411-160411
    • (2012) Annu. Rev. Ecol. Evol. Syst. , vol.43 , pp. 227-248
    • HilleRisLambers, J.1    Adler, P.B.2    Harpole, W.S.3    Levine, J.M.4    Mayfield, M.M.5
  • 27
    • 34547626761 scopus 로고    scopus 로고
    • A comparison of taxon co-occurrence patterns for macro-and microorganisms
    • doi: 10.1890/06-0286
    • Horner-Devine, M. C., Silver, J. M., Leibold, M. A., Bohannan, B. J. M., Colwell, R. K., Fuhrman, J. A., et al. (2007). A comparison of taxon co-occurrence patterns for macro-and microorganisms. Ecology 88, 1345-1353. doi: 10.1890/06-0286
    • (2007) Ecology , vol.88 , pp. 1345-1353
    • Horner-Devine, M.C.1    Silver, J.M.2    Leibold, M.A.3    Bohannan, B.J.M.4    Colwell, R.K.5    Fuhrman, J.A.6
  • 28
    • 84875829000 scopus 로고    scopus 로고
    • Co-occurrence patterns of plants and soil bacteria in the high-alpine subnival zone track environmental harshness.
    • doi: 10.3389/fmicb.2012.00347
    • King, A. J., Farrer, E. C., Suding, K. N., and Schmidt, S. K. (2012). Co-occurrence patterns of plants and soil bacteria in the high-alpine subnival zone track environmental harshness. Front. Microbiol. 3:347. doi: 10.3389/fmicb.2012.00347
    • (2012) Front. Microbiol. , vol.3 , pp. 347
    • King, A.J.1    Farrer, E.C.2    Suding, K.N.3    Schmidt, S.K.4
  • 29
    • 84873684861 scopus 로고    scopus 로고
    • Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.
    • doi: 10.1371/journal.pone.0047879
    • Kittelmann, S., Seedorf, H., Walters, W. A., Clemente, J. C., Knight, R., Gordon, J. I., et al. (2013). Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS ONE 8:e47879. doi: 10.1371/journal.pone.0047879
    • (2013) PLoS ONE , vol.8
    • Kittelmann, S.1    Seedorf, H.2    Walters, W.A.3    Clemente, J.C.4    Knight, R.5    Gordon, J.I.6
  • 30
    • 84864582440 scopus 로고    scopus 로고
    • Lineage-dependent ecological coherence in bacteria
    • doi: 10.1111/j.1574-6941.2012.01387.x
    • Koeppel, A. F., and Wu, M. (2012). Lineage-dependent ecological coherence in bacteria. FEMS Microbiol. Ecol. 81, 574-582. doi: 10.1111/j.1574-6941.2012.01387.x
    • (2012) FEMS Microbiol. Ecol. , vol.81 , pp. 574-582
    • Koeppel, A.F.1    Wu, M.2
  • 31
    • 79959619241 scopus 로고    scopus 로고
    • Species sorting and neutral processes are both important during the initial assembly of bacterial communities
    • doi: 10.1038/ismej.2010.207
    • Langenheder, S., and Székely, A. J. (2011). Species sorting and neutral processes are both important during the initial assembly of bacterial communities. ISME J. 5, 1086-1094. doi: 10.1038/ismej.2010.207
    • (2011) ISME J. , vol.5 , pp. 1086-1094
    • Langenheder, S.1    Székely, A.J.2
  • 32
    • 84861990785 scopus 로고    scopus 로고
    • Predicting bacterial community assemblages using an artificial neural network approach
    • doi: 10.1038/nmeth.1975
    • Larsen, P. E., Field, D., and Gilbert, J. A. (2012). Predicting bacterial community assemblages using an artificial neural network approach. Nat. Methods 9, 621-625. doi: 10.1038/nmeth.1975
    • (2012) Nat. Methods , vol.9 , pp. 621-625
    • Larsen, P.E.1    Field, D.2    Gilbert, J.A.3
  • 33
    • 49249124904 scopus 로고    scopus 로고
    • The influence of soil properties on the structure of bacterial and fungal communities across land-use types
    • doi: 10.1016/j.soilbio.2008.05.021
    • Lauber, C. L., Strickland, M. S., Bradford, M. A., and Fierer, N. (2008). The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40, 2407-2415. doi: 10.1016/j.soilbio.2008.05.021
    • (2008) Soil Biol. Biochem. , vol.40 , pp. 2407-2415
    • Lauber, C.L.1    Strickland, M.S.2    Bradford, M.A.3    Fierer, N.4
  • 34
    • 33746021304 scopus 로고    scopus 로고
    • Coexistence of the niche and neutral perspectives in community ecology
    • doi: 10.1890/0012-9658(2006)87[1399:COTNAN]2.0.CO;2
    • Leibold, M. A., and McPeek, M. A. (2006). Coexistence of the niche and neutral perspectives in community ecology. Ecology 87, 1399-1410. doi: 10.1890/0012-9658(2006)87[1399:COTNAN]2.0.CO;2
    • (2006) Ecology , vol.87 , pp. 1399-1410
    • Leibold, M.A.1    McPeek, M.A.2
  • 35
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
    • doi: 10.1186/1471-2105-9-386
    • Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., et al. (2008). The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi: 10.1186/1471-2105-9-386
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5    Kubal, M.6
  • 36
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • doi: 10.1103/PhysRevE.69.026113
    • Newman, M. E. J., and Girvan, M. (2004). Finding and evaluating community structure in networks. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 69:026113. doi: 10.1103/PhysRevE.69.026113
    • (2004) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. , vol.69 , pp. 026113
    • Newman, M.E.J.1    Girvan, M.2
  • 37
    • 77957270949 scopus 로고    scopus 로고
    • Combined niche and neutral effects in a microbial wastewater treatment community
    • doi: 10.1073/pnas.1000604107
    • Ofiteru, I. D., Lunn, M., Curtis, T. P., Wells, G. F., Criddle, C. S., Francis, C. A., et al. (2010). Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl. Acad. Sci. U.S.A. 107, 15345-15350. doi: 10.1073/pnas.1000604107
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 15345-15350
    • Ofiteru, I.D.1    Lunn, M.2    Curtis, T.P.3    Wells, G.F.4    Criddle, C.S.5    Francis, C.A.6
  • 40
    • 79960987794 scopus 로고    scopus 로고
    • Using false discovery rates for multiple comparisons in ecology and evolution
    • doi: 10.1111/j.2041-210X.2010.00061.x
    • Pike, N. (2011). Using false discovery rates for multiple comparisons in ecology and evolution. Method Ecol. Evol. 2, 278-282. doi: 10.1111/j.2041-210X.2010.00061.x
    • (2011) Method Ecol. Evol. , vol.2 , pp. 278-282
    • Pike, N.1
  • 41
    • 20144380698 scopus 로고    scopus 로고
    • Network thinking in ecology and evolution
    • doi: 10.106/j.tree.2005.04.004
    • Proulx, S., Promislow, D., and Phillips, P. (2005). Network thinking in ecology and evolution. Trends Ecol. Evol. 20, 345-353. doi: 10.106/j.tree.2005.04.004
    • (2005) Trends Ecol. Evol. , vol.20 , pp. 345-353
    • Proulx, S.1    Promislow, D.2    Phillips, P.3
  • 42
    • 49649089054 scopus 로고    scopus 로고
    • Molecular eco-systems biology: towards an understanding of community function
    • doi: 10.1038/nrmicro1935
    • Raes, J., and Bork, P. (2008). Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 6, 693-699. doi: 10.1038/nrmicro1935
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 693-699
    • Raes, J.1    Bork, P.2
  • 43
    • 83755163018 scopus 로고    scopus 로고
    • Detecting novel associations in large data sets
    • doi: 10.1126/science.1205438
    • Reshef, D. N., Reshef, Y. A., Finucane, H. K., Grossman, S. R., McVean, G., Turnbaugh, P. J., et al. (2011). Detecting novel associations in large data sets. Science 334, 1518-1524. doi: 10.1126/science.1205438
    • (2011) Science , vol.334 , pp. 1518-1524
    • Reshef, D.N.1    Reshef, Y.A.2    Finucane, H.K.3    Grossman, S.R.4    McVean, G.5    Turnbaugh, P.J.6
  • 44
    • 75149120711 scopus 로고    scopus 로고
    • NeMo: network module identification in Cytoscape
    • doi: 10.1186/1471-2105-11-S1-S61
    • Rivera, C. G., Vakil, R., and Bader, J. S. (2010). NeMo: network module identification in Cytoscape. BMC Bioinformatics 11:S61. doi: 10.1186/1471-2105-11-S1-S61
    • (2010) BMC Bioinformatics , vol.11
    • Rivera, C.G.1    Vakil, R.2    Bader, J.S.3
  • 45
    • 84864440400 scopus 로고    scopus 로고
    • Metagenomic microbial community profiling using unique clade-specific marker genes
    • doi: 10.1038/nmeth.2066
    • Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., and Huttenhower, C. (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811-814. doi: 10.1038/nmeth.2066
    • (2012) Nat. Methods , vol.9 , pp. 811-814
    • Segata, N.1    Waldron, L.2    Ballarini, A.3    Narasimhan, V.4    Jousson, O.5    Huttenhower, C.6
  • 46
    • 84880917983 scopus 로고    scopus 로고
    • A meta-analysis of changes in bacterial and archaeal communities with time
    • doi: 10.1038/ismej.2013.54
    • Shade, A., Caporaso, J. G., Handelsman, J., Knight, R., and Fierer, N. (2013a). A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 7, 1493-1506. doi: 10.1038/ismej.2013.54
    • (2013) ISME J. , vol.7 , pp. 1493-1506
    • Shade, A.1    Caporaso, J.G.2    Handelsman, J.3    Knight, R.4    Fierer, N.5
  • 47
    • 84886895932 scopus 로고    scopus 로고
    • Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil
    • doi: 10.1128/AEM.02017-13
    • Shade, A., Klimowicz, A. K., Spear, R. N., Linske, M., Donato, J. J., Hogan, C. S., et al. (2013b). Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil. Appl. Environ. Microbiol. 79, 6617-6625. doi: 10.1128/AEM.02017-13
    • (2013) Appl. Environ. Microbiol. , vol.79 , pp. 6617-6625
    • Shade, A.1    Klimowicz, A.K.2    Spear, R.N.3    Linske, M.4    Donato, J.J.5    Hogan, C.S.6
  • 48
    • 84864241592 scopus 로고    scopus 로고
    • Distinct soil bacterial communities revealed under a diversely managed agroecosystem
    • doi: 10.1371/journal.pone.0040338
    • Shange, R. S., Ankumah, R. O., Ibekwe, A. M., Zabawa, R., and Dowd, S. E. (2012). Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS ONE 7:e40338. doi: 10.1371/journal.pone.0040338
    • (2012) PLoS ONE , vol.7
    • Shange, R.S.1    Ankumah, R.O.2    Ibekwe, A.M.3    Zabawa, R.4    Dowd, S.E.5
  • 49
    • 80052061077 scopus 로고    scopus 로고
    • Marine bacterial, archaeal and protistan association networks reveal ecological linkages
    • doi: 10.1038/ismej.2011.24
    • Steele, J. A., Countway, P. D., Xia, L., Vigil, P. D., Beman, J. M., Kim, D. Y., et al. (2011). Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. 5, 1414-1425. doi: 10.1038/ismej.2011.24
    • (2011) ISME J. , vol.5 , pp. 1414-1425
    • Steele, J.A.1    Countway, P.D.2    Xia, L.3    Vigil, P.D.4    Beman, J.M.5    Kim, D.Y.6
  • 50
    • 84865345637 scopus 로고    scopus 로고
    • Stochastic and deterministic assembly processes in subsurface microbial communities
    • doi: 10.1038/ismej.2012.22
    • Stegen, J. C., Lin, X., Konopka, A. E., and Fredrickson, J. K. (2012). Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 6, 1653-1664. doi: 10.1038/ismej.2012.22
    • (2012) ISME J. , vol.6 , pp. 1653-1664
    • Stegen, J.C.1    Lin, X.2    Konopka, A.E.3    Fredrickson, J.K.4
  • 51
    • 0025622072 scopus 로고
    • The checkerboard score and species distributions
    • doi: 10.1007/BF00317345
    • Stone, L., and Roberts, A. (1990). The checkerboard score and species distributions. Oecologia 85, 74-79. doi: 10.1007/BF00317345
    • (1990) Oecologia , vol.85 , pp. 74-79
    • Stone, L.1    Roberts, A.2
  • 52
    • 45449097447 scopus 로고    scopus 로고
    • fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
    • doi: 10.1093/bioinformatics/btn209
    • Strimmer, K. (2008). fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24, 1461-1462. doi: 10.1093/bioinformatics/btn209
    • (2008) Bioinformatics , vol.24 , pp. 1461-1462
    • Strimmer, K.1
  • 53
    • 84883558425 scopus 로고    scopus 로고
    • Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients
    • doi: 10.1111/1462-2920.12133
    • Sun, M. Y., Dafforn, K. A., Johnston, E. L., and Brown, M. V. (2013). Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients. Environ. Microbiol. 15, 2517-2531. doi: 10.1111/1462-2920.12133
    • (2013) Environ. Microbiol. , vol.15 , pp. 2517-2531
    • Sun, M.Y.1    Dafforn, K.A.2    Johnston, E.L.3    Brown, M.V.4
  • 55
    • 80051856839 scopus 로고    scopus 로고
    • The human gut microbiome: ecology and recent evolutionary changes
    • doi: 10.1146/annurev-micro-090110-102830
    • Walter, J., and Ley, R. (2011). The human gut microbiome: ecology and recent evolutionary changes. Annu. Rev. Microbiol. 65, 411-429. doi: 10.1146/annurev-micro-090110-102830
    • (2011) Annu. Rev. Microbiol. , vol.65 , pp. 411-429
    • Walter, J.1    Ley, R.2
  • 56
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • doi: 10.1038/30918
    • Watts, D. J., and Strogatz, S. H. (1998). Collective dynamics of 'small-world' networks. Nature 393, 440-442. doi: 10.1038/30918
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 57
    • 84884242904 scopus 로고    scopus 로고
    • Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments.
    • doi: 10.3389/fmicb.2013.00104
    • Zhalnina, K., de Quadros, P. D., Gano, K. A., Davis-Richardson, A., Fagen, J. R., Brown, C. T., et al. (2013). Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front. Microbiol. 4:104. doi: 10.3389/fmicb.2013.00104
    • (2013) Front. Microbiol. , vol.4 , pp. 104
    • Zhalnina, K.1    de Quadros, P.D.2    Gano, K.A.3    Davis-Richardson, A.4    Fagen, J.R.5    Brown, C.T.6
  • 58
    • 84878318466 scopus 로고    scopus 로고
    • Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes
    • doi: 10.1038/ismej.2012.176
    • Zimmerman, A. E., Martiny, A. C., and Allison, S. D. (2013). Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J. 7, 1187-1199. doi: 10.1038/ismej.2012.176
    • (2013) ISME J. , vol.7 , pp. 1187-1199
    • Zimmerman, A.E.1    Martiny, A.C.2    Allison, S.D.3


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