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Volumn 15, Issue 10, 2013, Pages 2642-2657

A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales

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GENETIC MARKER;

EID: 84885185599     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12156     Document Type: Short Survey
Times cited : (19)

References (93)
  • 1
    • 70149113478 scopus 로고    scopus 로고
    • A new phylogenetic diversity measure generalizing the shannon index and its application to phyllostomid bats
    • Allen, B., Kon, M., and Bar-Yam, Y. (2009) A new phylogenetic diversity measure generalizing the shannon index and its application to phyllostomid bats. Am Nat 174: 236-243.
    • (2009) Am Nat , vol.174 , pp. 236-243
    • Allen, B.1    Kon, M.2    Bar-Yam, Y.3
  • 2
    • 42349093774 scopus 로고    scopus 로고
    • Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
    • Amann, R., and Fuchs, B.M. (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6: 339-348.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 339-348
    • Amann, R.1    Fuchs, B.M.2
  • 3
    • 78650061319 scopus 로고    scopus 로고
    • Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist
    • Anderson, M.J., Crist, T.O., Chase, J.M., Vellend, M., Inouye, B.D., Freestone, A.L., etal. (2011) Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecol Lett 14: 19-28.
    • (2011) Ecol Lett , vol.14 , pp. 19-28
    • Anderson, M.J.1    Crist, T.O.2    Chase, J.M.3    Vellend, M.4    Inouye, B.D.5    Freestone, A.L.6
  • 4
    • 34247520067 scopus 로고    scopus 로고
    • Functional diversity of crustacean zooplankton communities: towards a trait-based classification
    • Barnett, A.J., Finlay, K., and Beisner, B.E. (2007) Functional diversity of crustacean zooplankton communities: towards a trait-based classification. Freshwater Biol 52: 796-813.
    • (2007) Freshwater Biol , vol.52 , pp. 796-813
    • Barnett, A.J.1    Finlay, K.2    Beisner, B.E.3
  • 5
    • 24144447031 scopus 로고    scopus 로고
    • The contribution of species richness and composition to bacterial services
    • Bell, T., Newman, J.A., Silverman, B.W., Turner, S.L., and Lilley, A.K. (2005) The contribution of species richness and composition to bacterial services. Nature 436: 1157-1160.
    • (2005) Nature , vol.436 , pp. 1157-1160
    • Bell, T.1    Newman, J.A.2    Silverman, B.W.3    Turner, S.L.4    Lilley, A.K.5
  • 6
    • 77956309161 scopus 로고    scopus 로고
    • The partitioning of diversity: showing Theseus a way out of the labyrinth
    • de Bello, F., Lavergne, S., Meynard, C.N., Lepš, J., and Thuiller, W. (2010) The partitioning of diversity: showing Theseus a way out of the labyrinth. J Veg Sci 21: 992-1000.
    • (2010) J Veg Sci , vol.21 , pp. 992-1000
    • de Bello, F.1    Lavergne, S.2    Meynard, C.N.3    Lepš, J.4    Thuiller, W.5
  • 7
    • 34247477605 scopus 로고    scopus 로고
    • Measuring species richness based on microbial community fingerprints: the emperor has no clothes
    • Bent, S.J., Pierson, J.D., and Forney, L.J. (2007) Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol 73: 2399-2401.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 2399-2401
    • Bent, S.J.1    Pierson, J.D.2    Forney, L.J.3
  • 8
    • 77957236681 scopus 로고    scopus 로고
    • Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales
    • Bissett, A., Richardson, A.E., Baker, G., Wakelin, S., and Thrall, P.H. (2011) Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Mol Ecol 19: 4315-4327.
    • (2011) Mol Ecol , vol.19 , pp. 4315-4327
    • Bissett, A.1    Richardson, A.E.2    Baker, G.3    Wakelin, S.4    Thrall, P.H.5
  • 9
    • 84866035770 scopus 로고    scopus 로고
    • Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets
    • Bonilla-Rosso, G., Eguiarte, L.E., Romero, D., Travisano, M., and Souza, V. (2012) Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets. FEMS Microbiol Ecol 82: 37-49.
    • (2012) FEMS Microbiol Ecol , vol.82 , pp. 37-49
    • Bonilla-Rosso, G.1    Eguiarte, L.E.2    Romero, D.3    Travisano, M.4    Souza, V.5
  • 10
    • 50049085522 scopus 로고    scopus 로고
    • Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity
    • Bryant, J.A., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., and Green, J.L. (2008) Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci USA 105: 11505-11511.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 11505-11511
    • Bryant, J.A.1    Lamanna, C.2    Morlon, H.3    Kerkhoff, A.J.4    Enquist, B.J.5    Green, J.L.6
  • 11
    • 84867808440 scopus 로고    scopus 로고
    • Application of metatranscriptomics to soil environments
    • Carvalhais, L.C., Dennis, P.G., Tyson, G.W., and Schenk, P.M. (2012) Application of metatranscriptomics to soil environments. J Microbiol 91: 246-251.
    • (2012) J Microbiol , vol.91 , pp. 246-251
    • Carvalhais, L.C.1    Dennis, P.G.2    Tyson, G.W.3    Schenk, P.M.4
  • 12
    • 84874758926 scopus 로고    scopus 로고
    • Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny
    • Chang, Q., Luan, Y., and Sun, F. (2011) Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics 12: 118.
    • (2011) BMC Bioinformatics , vol.12 , pp. 118
    • Chang, Q.1    Luan, Y.2    Sun, F.3
  • 13
    • 66249131497 scopus 로고    scopus 로고
    • Global sequencing: a review of current molecular data and new methods available to assess microbial diversity
    • Christen, R. (2008) Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ 23: 253-268.
    • (2008) Microbes Environ , vol.23 , pp. 253-268
    • Christen, R.1
  • 14
    • 84891283567 scopus 로고    scopus 로고
    • Physiological structure and single-cell activity in marine bacterioplankton
    • Kirchman, D.L. (ed.). New York, USA: John Wiley & Sons
    • Del Giorgio, P.A., and Gasol, J.M. (2008) Physiological structure and single-cell activity in marine bacterioplankton. In Microbial Ecology of the Oceans. Kirchman, D.L. (ed.). New York, USA: John Wiley & Sons, pp. 243-298.
    • (2008) Microbial Ecology of the Oceans , pp. 243-298
    • Del Giorgio, P.A.1    Gasol, J.M.2
  • 15
    • 17144420448 scopus 로고    scopus 로고
    • Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray
    • DeSantis, T.Z., Brodie, E.L., Moberg, J.P., Zubieta, I.X., Piceno, Y.M., and Andersen, G.L. (2005) Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett 245: 271-278.
    • (2005) FEMS Microbiol Lett , vol.245 , pp. 271-278
    • DeSantis, T.Z.1    Brodie, E.L.2    Moberg, J.P.3    Zubieta, I.X.4    Piceno, Y.M.5    Andersen, G.L.6
  • 16
    • 77954788862 scopus 로고    scopus 로고
    • Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world
    • Devictor, V., Mouillot, D., Meynard, C., Jiguet, F., Thuiller, W., and Mouquet, N. (2010) Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecol Lett 13: 1030-1040.
    • (2010) Ecol Lett , vol.13 , pp. 1030-1040
    • Devictor, V.1    Mouillot, D.2    Meynard, C.3    Jiguet, F.4    Thuiller, W.5    Mouquet, N.6
  • 18
    • 79952751932 scopus 로고    scopus 로고
    • The generation and maintenance of diversity in microbial communities
    • Fierer, N., and Lennon, J.T. (2011) The generation and maintenance of diversity in microbial communities. Am J Bot 98: 439-448.
    • (2011) Am J Bot , vol.98 , pp. 439-448
    • Fierer, N.1    Lennon, J.T.2
  • 19
  • 20
    • 66149150877 scopus 로고    scopus 로고
    • Microbial community structure and its functional implications
    • Fuhrman, J.A. (2009) Microbial community structure and its functional implications. Nature 459: 193-199.
    • (2009) Nature , vol.459 , pp. 193-199
    • Fuhrman, J.A.1
  • 21
    • 42149121333 scopus 로고    scopus 로고
    • Phylogenetic and genomic analysis
    • Hurst, C.J., Crawford, R.L., Garland, J.L., Lipson, D.A., Mills, A.L., and Stetzenbach, L.D. (eds). Washington, DC, USA: ASM Press
    • Gevers, D., and Coenye, T. (2007) Phylogenetic and genomic analysis. In Manual of Environmental Microbiology. Hurst, C.J., Crawford, R.L., Garland, J.L., Lipson, D.A., Mills, A.L., and Stetzenbach, L.D. (eds). Washington, DC, USA: ASM Press, pp. 157-168.
    • (2007) Manual of Environmental Microbiology , pp. 157-168
    • Gevers, D.1    Coenye, T.2
  • 22
    • 0141676315 scopus 로고    scopus 로고
    • Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil
    • Gremion, F., Chatzinotas, A., and Harms, H. (2003) Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ Microbiol 5: 896-907.
    • (2003) Environ Microbiol , vol.5 , pp. 896-907
    • Gremion, F.1    Chatzinotas, A.2    Harms, H.3
  • 24
    • 84862324907 scopus 로고    scopus 로고
    • High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
    • Handley, K.M., Wrighton, K.C., Piceno, Y.M., Andersen, G.L., DeSantis, T.Z., Williams, K.H., etal. (2012) High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiol Ecol 81: 188-204.
    • (2012) FEMS Microbiol Ecol , vol.81 , pp. 188-204
    • Handley, K.M.1    Wrighton, K.C.2    Piceno, Y.M.3    Andersen, G.L.4    DeSantis, T.Z.5    Williams, K.H.6
  • 25
    • 58649116646 scopus 로고    scopus 로고
    • Development and application of functional gene arrays for microbial community analysis
    • He, Z.L., Van Nostrand, J.D., Wu, L.Y., and Zhou, J.Z. (2008) Development and application of functional gene arrays for microbial community analysis. T Nonferr Metal Soc 18: 1319-1327.
    • (2008) T Nonferr Metal Soc , vol.18 , pp. 1319-1327
    • He, Z.L.1    Van Nostrand, J.D.2    Wu, L.Y.3    Zhou, J.Z.4
  • 26
    • 77950595690 scopus 로고    scopus 로고
    • Culture-independent molecular techniques for soil microbial ecology
    • Hirsch, P.R., Mauchline, T.H., and Clark, I.M. (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42: 878-887.
    • (2010) Soil Biol Biochem , vol.42 , pp. 878-887
    • Hirsch, P.R.1    Mauchline, T.H.2    Clark, I.M.3
  • 27
    • 84872896954 scopus 로고    scopus 로고
    • Visualization and statistical comparisons of microbial communities using R packages on phylochip data
    • Holmes, S., Alekseyenko, A., Timme, A., Nelson, T., Pasricha, P.J., and Spormann, A. (2010) Visualization and statistical comparisons of microbial communities using R packages on phylochip data. Pac Symp Biocomput: 142-153.
    • (2010) Pac Symp Biocomput , pp. 142-153
    • Holmes, S.1    Alekseyenko, A.2    Timme, A.3    Nelson, T.4    Pasricha, P.J.5    Spormann, A.6
  • 28
    • 57149093416 scopus 로고    scopus 로고
    • Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing
    • Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A., and Sogin, M.L. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
    • (2008) PLoS Genet , vol.4
    • Huse, S.M.1    Dethlefsen, L.2    Huber, J.A.3    Welch, D.M.4    Relman, D.A.5    Sogin, M.L.6
  • 29
    • 84873558890 scopus 로고    scopus 로고
    • Spatial and temporal scales of aquatic bacterial beta diversity
    • Jones, S.E., Cadkin, T.A., Newton, R.J., and McMahon, K.D. (2012) Spatial and temporal scales of aquatic bacterial beta diversity. Front Microbiol 3: 318.
    • (2012) Front Microbiol , vol.3 , pp. 318
    • Jones, S.E.1    Cadkin, T.A.2    Newton, R.J.3    McMahon, K.D.4
  • 30
    • 38449096471 scopus 로고    scopus 로고
    • Partitioning diversity into independent alpha and beta components
    • Jost, L. (2007) Partitioning diversity into independent alpha and beta components. Ecology 88: 2427-2439.
    • (2007) Ecology , vol.88 , pp. 2427-2439
    • Jost, L.1
  • 31
    • 77954580286 scopus 로고    scopus 로고
    • Independence of alpha and beta diversities
    • Jost, L. (2010) Independence of alpha and beta diversities. Ecology 91: 1969-1974.
    • (2010) Ecology , vol.91 , pp. 1969-1974
    • Jost, L.1
  • 32
    • 58549098885 scopus 로고    scopus 로고
    • Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity
    • Jurasinski, G., Retzer, V., and Beierkuhnlein, C. (2009) Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity. Oecologia 159: 15-26.
    • (2009) Oecologia , vol.159 , pp. 15-26
    • Jurasinski, G.1    Retzer, V.2    Beierkuhnlein, C.3
  • 34
    • 68849099915 scopus 로고    scopus 로고
    • Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests
    • Kembel, S.W. (2009) Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol Lett 12: 949-960.
    • (2009) Ecol Lett , vol.12 , pp. 949-960
    • Kembel, S.W.1
  • 37
    • 0038054120 scopus 로고    scopus 로고
    • Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences
    • Kisand, V., and Wikner, J. (2003) Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences. J Microbiol Methods 54: 183-191.
    • (2003) J Microbiol Methods , vol.54 , pp. 183-191
    • Kisand, V.1    Wikner, J.2
  • 38
    • 0038670419 scopus 로고    scopus 로고
    • Measuring beta diversity for presence-absence data
    • Koleff, P., Gaston, K.J., and Lennon, J.J. (2003) Measuring beta diversity for presence-absence data. J Anim Ecol 72: 367-382.
    • (2003) J Anim Ecol , vol.72 , pp. 367-382
    • Koleff, P.1    Gaston, K.J.2    Lennon, J.J.3
  • 39
    • 77950121887 scopus 로고    scopus 로고
    • A morphological classification capturing functional variation in phytoplankton
    • Kruk, C., Huszar, V.L.M., Peeters, E.T.H.M., Bonilla, S., Costa, L., etal. (2010) A morphological classification capturing functional variation in phytoplankton. Freshwater Biol 55: 614-627.
    • (2010) Freshwater Biol , vol.55 , pp. 614-627
    • Kruk, C.1    Huszar, V.L.M.2    Peeters, E.T.H.M.3    Bonilla, S.4    Costa, L.5
  • 41
    • 0030303753 scopus 로고    scopus 로고
    • Statistics and partitioning of species diversity, and similarity among multiple communities
    • Lande, R. (1996) Statistics and partitioning of species diversity, and similarity among multiple communities. Oikos 76: 5-13.
    • (1996) Oikos , vol.76 , pp. 5-13
    • Lande, R.1
  • 42
    • 77956993764 scopus 로고    scopus 로고
    • Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores
    • Liggenstoffer, A.S., Youssef, N.H., Couger, M.B., and Elshahed, M.S. (2010) Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 4: 1225-1235.
    • (2010) ISME J , vol.4 , pp. 1225-1235
    • Liggenstoffer, A.S.1    Youssef, N.H.2    Couger, M.B.3    Elshahed, M.S.4
  • 43
    • 80051471111 scopus 로고    scopus 로고
    • Empirical approaches to metacommunities: a review and comparison with theory
    • Logue, J.B., Mouquet, N., Peter, H., Hillebrand, H., and Working, M. (2011) Empirical approaches to metacommunities: a review and comparison with theory. Trends Ecol Evol 26: 482-491.
    • (2011) Trends Ecol Evol , vol.26 , pp. 482-491
    • Logue, J.B.1    Mouquet, N.2    Peter, H.3    Hillebrand, H.4    Working, M.5
  • 44
    • 33644838781 scopus 로고    scopus 로고
    • Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
    • Loisel, P., Harmand, J., Zemb, O., Latrille, E., Lobry, C., Delgenes, J.P., and Godon, J.J. (2006) Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8: 720-731.
    • (2006) Environ Microbiol , vol.8 , pp. 720-731
    • Loisel, P.1    Harmand, J.2    Zemb, O.3    Latrille, E.4    Lobry, C.5    Delgenes, J.P.6    Godon, J.J.7
  • 45
    • 34547433545 scopus 로고    scopus 로고
    • Global patterns in bacterial diversity
    • Lozupone, C.A., and Knight, R. (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104: 11436-11440.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 11436-11440
    • Lozupone, C.A.1    Knight, R.2
  • 46
    • 44849128805 scopus 로고    scopus 로고
    • Species divergence and the measurement of microbial diversity
    • Lozupone, C.A., and Knight, R. (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 32: 557-578.
    • (2008) FEMS Microbiol Rev , vol.32 , pp. 557-578
    • Lozupone, C.A.1    Knight, R.2
  • 47
    • 33947269742 scopus 로고    scopus 로고
    • Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
    • Lozupone, C.A., Hamady, M., Kelley, S.T., and Knight, R. (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 1576-1585
    • Lozupone, C.A.1    Hamady, M.2    Kelley, S.T.3    Knight, R.4
  • 48
    • 0036324293 scopus 로고    scopus 로고
    • Phylogenetic approaches for describing and comparing the diversity of microbial communities
    • Martin, A.P. (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-3682.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 3673-3682
    • Martin, A.P.1
  • 49
    • 84858079785 scopus 로고    scopus 로고
    • Functional diversity across space and time: trends in wader communities on British estuaries
    • Mendez, V., Gill, J.A., Burton, N.H.K., Austin, G.E., Petchey, O.L., and Davies, R.G. (2012) Functional diversity across space and time: trends in wader communities on British estuaries. Divers Distrib 18: 356-365.
    • (2012) Divers Distrib , vol.18 , pp. 356-365
    • Mendez, V.1    Gill, J.A.2    Burton, N.H.K.3    Austin, G.E.4    Petchey, O.L.5    Davies, R.G.6
  • 50
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker, M.L. (2010) Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 51
    • 78751664289 scopus 로고    scopus 로고
    • Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules
    • Mouchet, M.A., Villéger, S., Mason, N.W.H., and Mouillot, D. (2010) Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules. Funct Ecol 24: 867-876.
    • (2010) Funct Ecol , vol.24 , pp. 867-876
    • Mouchet, M.A.1    Villéger, S.2    Mason, N.W.H.3    Mouillot, D.4
  • 52
    • 78751664289 scopus 로고    scopus 로고
    • Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules
    • Mouchet, M.A., Bouvier, C., Bouvier, T., Troussellier, M., Escalas, A., and Mouillot, D. (2012) Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules. Funct Ecol 24: 867-876.
    • (2012) Funct Ecol , vol.24 , pp. 867-876
    • Mouchet, M.A.1    Bouvier, C.2    Bouvier, T.3    Troussellier, M.4    Escalas, A.5    Mouillot, D.6
  • 54
    • 34547579868 scopus 로고    scopus 로고
    • Genotypic microbial community profiling: a critical technical review
    • Nocker, A., Burr, M., and Camper, A.K. (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54: 276-289.
    • (2007) Microb Ecol , vol.54 , pp. 276-289
    • Nocker, A.1    Burr, M.2    Camper, A.K.3
  • 55
    • 0028782146 scopus 로고
    • Theoretical and practical aspects of the quantification of biodiversity among microorganisms
    • Odonnell, A.G., Goodfellow, M., and Hawksworth, D.L. (1994) Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Philos Trans R Soc Lond B Biol Sci 345: 65-73.
    • (1994) Philos Trans R Soc Lond B Biol Sci , vol.345 , pp. 65-73
    • Odonnell, A.G.1    Goodfellow, M.2    Hawksworth, D.L.3
  • 56
    • 18844397307 scopus 로고    scopus 로고
    • Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable?
    • Pavoine, S.A., Ollier, S., and Pontier, D. (2005) Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable? Theor Popul Biol 67: 231-239.
    • (2005) Theor Popul Biol , vol.67 , pp. 231-239
    • Pavoine, S.A.1    Ollier, S.2    Pontier, D.3
  • 59
    • 79951811101 scopus 로고    scopus 로고
    • Inter-laboratory evaluation of the ISO standard 11063 'Soil quality - method to directly extract DNA from soil samples'
    • Petric, I., Philippot, L., Abbate, C., Bispo, A., Chesnot, T., Hallin, S., etal. (2011) Inter-laboratory evaluation of the ISO standard 11063 'Soil quality - method to directly extract DNA from soil samples'. J Microbiol Methods 84: 454-460.
    • (2011) J Microbiol Methods , vol.84 , pp. 454-460
    • Petric, I.1    Philippot, L.2    Abbate, C.3    Bispo, A.4    Chesnot, T.5    Hallin, S.6
  • 61
    • 84864421488 scopus 로고    scopus 로고
    • Environment drives high phylogenetic turnover among oceanic bacterial communities
    • Pommier, T., Douzery, E.J.P., and Mouillot, D. (2012) Environment drives high phylogenetic turnover among oceanic bacterial communities. Biol Lett 8: 562-566.
    • (2012) Biol Lett , vol.8 , pp. 562-566
    • Pommier, T.1    Douzery, E.J.P.2    Mouillot, D.3
  • 62
    • 84870006986 scopus 로고    scopus 로고
    • Functional assignment of metagenomic data: challenges and applications
    • Prakash, T., and Taylor, T.D. (2012) Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 13: 711-727.
    • (2012) Brief Bioinform , vol.13 , pp. 711-727
    • Prakash, T.1    Taylor, T.D.2
  • 63
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team. Vienna, Austria: Foundation for Statistical Computing [WWW document]. URL
    • R Development Core Team (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: Foundation for Statistical Computing [WWW document]. URL http://www.r-project.org/.
    • (2011) R: A Language and Environment for Statistical Computing
  • 64
    • 0003143622 scopus 로고
    • Diversity and dissimilarity coefficients: a unified approach
    • Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theor Popul Biol 21: 24-43.
    • (1982) Theor Popul Biol , vol.21 , pp. 24-43
    • Rao, C.R.1
  • 65
    • 0242523909 scopus 로고    scopus 로고
    • The uncultured microbial majority
    • Rappe, M.S., and Giovannoni, S.J. (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 369-394
    • Rappe, M.S.1    Giovannoni, S.J.2
  • 66
    • 70449528633 scopus 로고    scopus 로고
    • Diversity partitioning of Rao's quadratic entropy
    • Ricotta, C., and Szeidl, L. (2009) Diversity partitioning of Rao's quadratic entropy. Theor Popul Biol 76: 299-302.
    • (2009) Theor Popul Biol , vol.76 , pp. 299-302
    • Ricotta, C.1    Szeidl, L.2
  • 67
    • 77953121795 scopus 로고    scopus 로고
    • Comparing microarrays and next-generation sequencing technologies for microbial ecology research
    • Roh, S.W., Abell, G.C.J., Kim, K.H., Nam, Y.D., and Bae, J.W. (2010) Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol 28: 291-299.
    • (2010) Trends Biotechnol , vol.28 , pp. 291-299
    • Roh, S.W.1    Abell, G.C.J.2    Kim, K.H.3    Nam, Y.D.4    Bae, J.W.5
  • 68
    • 72949116825 scopus 로고    scopus 로고
    • Community niche predicts the functioning of denitrifying bacterial assemblages
    • Salles, J.F., Poly, F., Schmid, B., and Le Roux, X. (2009) Community niche predicts the functioning of denitrifying bacterial assemblages. Ecology 90: 3324-3332.
    • (2009) Ecology , vol.90 , pp. 3324-3332
    • Salles, J.F.1    Poly, F.2    Schmid, B.3    Le Roux, X.4
  • 69
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 71
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J., and Ji, H. (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 73
    • 0001974895 scopus 로고    scopus 로고
    • Molecular approaches for the measurement of density, diversity, and phylogeny
    • Garland, J.L. (ed.). Washington, DC, USA: ASM Press
    • Stahl, D.A. (2007) Molecular approaches for the measurement of density, diversity, and phylogeny. In Manual of Environmental Microbiology. Garland, J.L. (ed.). Washington, DC, USA: ASM Press, pp. 139-156.
    • (2007) Manual of Environmental Microbiology , pp. 139-156
    • Stahl, D.A.1
  • 74
    • 84865345637 scopus 로고    scopus 로고
    • Stochastic and deterministic assembly processes in subsurface microbial communities
    • 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.
    • (2012) ISME J , vol.6 , pp. 1653-1664
    • Stegen, J.C.1    Lin, X.2    Konopka, A.E.3    Fredrickson, J.K.4
  • 75
    • 84856373733 scopus 로고    scopus 로고
    • Culture-independent methods for studying environmental microorganisms: methods, application, and perspective
    • Su, C., Lei, L., Duan, Y., Zhang, K.Q., and Yang, J. (2012) Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 93: 993-1003.
    • (2012) Appl Microbiol Biotechnol , vol.93 , pp. 993-1003
    • Su, C.1    Lei, L.2    Duan, Y.3    Zhang, K.Q.4    Yang, J.5
  • 76
    • 84855295480 scopus 로고    scopus 로고
    • Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities
    • Suenaga, H. (2012) Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ Microbiol 14: 13-22.
    • (2012) Environ Microbiol , vol.14 , pp. 13-22
    • Suenaga, H.1
  • 77
    • 34548349181 scopus 로고    scopus 로고
    • Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities
    • Szabo, K.E., Itor, P.O.B., Bertilsson, S., Tranvik, L., and Eiler, A. (2007) Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities. Aquat Microb Ecol 47: 1-10.
    • (2007) Aquat Microb Ecol , vol.47 , pp. 1-10
    • Szabo, K.E.1    Itor, P.O.B.2    Bertilsson, S.3    Tranvik, L.4    Eiler, A.5
  • 78
    • 77953953850 scopus 로고    scopus 로고
    • A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity
    • Tuomisto, H.A. (2010a) A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography 33: 2-22.
    • (2010) Ecography , vol.33 , pp. 2-22
    • Tuomisto, H.A.1
  • 79
    • 77953923721 scopus 로고    scopus 로고
    • A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena
    • Tuomisto, H.A. (2010b) A diversity of beta diversities: straightening up a concept gone awry. Part 2. Quantifying beta diversity and related phenomena. Ecography 33: 23-45.
    • (2010) Ecography , vol.33 , pp. 23-45
    • Tuomisto, H.A.1
  • 80
    • 0034753958 scopus 로고    scopus 로고
    • Do commonly used indices of β-diversity measure species turnover?
    • Vellend, M. (2001) Do commonly used indices of β-diversity measure species turnover? J Veg Sci 12: 545-552.
    • (2001) J Veg Sci , vol.12 , pp. 545-552
    • Vellend, M.1
  • 82
    • 84863615315 scopus 로고    scopus 로고
    • Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities
    • Villéger, S., Ramos Miranda, J., Flores Hernandez, D., and Mouillot, D. (2012) Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities. PLoS ONE 7: e40679.
    • (2012) PLoS ONE , vol.7
    • Villéger, S.1    Ramos Miranda, J.2    Flores Hernandez, D.3    Mouillot, D.4
  • 83
    • 33847291893 scopus 로고    scopus 로고
    • Quantitative phylogenetic assessment of microbial communities in diverse environments
    • Von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., etal. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-1130.
    • (2007) Science , vol.315 , pp. 1126-1130
    • Von Mering, C.1    Hugenholtz, P.2    Raes, J.3    Tringe, S.G.4    Doerks, T.5    Jensen, L.J.6
  • 84
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
    • Von Wintzingerode, F., Göbel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
    • (1997) FEMS Microbiol Rev , vol.21 , pp. 213-229
    • Von Wintzingerode, F.1    Göbel, U.B.2    Stackebrandt, E.3
  • 85
    • 84857067661 scopus 로고    scopus 로고
    • A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity
    • Vos, M., Quince, C., Pijl, A.S., de Hollander, M., and Kowalchuk, G.A. (2012) A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS ONE 7: e30600.
    • (2012) PLoS ONE , vol.7
    • Vos, M.1    Quince, C.2    Pijl, A.S.3    de Hollander, M.4    Kowalchuk, G.A.5
  • 86
    • 0025366456 scopus 로고
    • 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community
    • Ward, D.M., Weller, R., and Bateson, M.M. (1990) 16S ribosomal-RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 63-65.
    • (1990) Nature , vol.345 , pp. 63-65
    • Ward, D.M.1    Weller, R.2    Bateson, M.M.3
  • 87
    • 0001226978 scopus 로고
    • Vegetation of the Siskiyou Mountains, Oregon and California
    • Whittaker, R.H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecol Monogr 30: 279-338.
    • (1960) Ecol Monogr , vol.30 , pp. 279-338
    • Whittaker, R.H.1
  • 88
    • 0000594195 scopus 로고
    • Evolution and measurement of species diversity
    • Whittaker, R.H. (1972) Evolution and measurement of species diversity. Taxon 21: 213-251.
    • (1972) Taxon , vol.21 , pp. 213-251
    • Whittaker, R.H.1
  • 89
    • 78149458009 scopus 로고    scopus 로고
    • Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L
    • Xiong, J., Wu, L., Tu, S., Van Nostrand, J.D., He, Z., Zhou, J., and Wang, G. (2010) Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L. Appl Environ Microbiol 76: 7277-7284.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 7277-7284
    • Xiong, J.1    Wu, L.2    Tu, S.3    Van Nostrand, J.D.4    He, Z.5    Zhou, J.6    Wang, G.7
  • 90
    • 84860113191 scopus 로고    scopus 로고
    • Methanogen diversity and community composition in peatlands of the central to northern Appalachian Mountain region, North America
    • Yavitt, J.B., Yashiro, E., Cadillo-Quiroz, H., and Zinder, S.H. (2012) Methanogen diversity and community composition in peatlands of the central to northern Appalachian Mountain region, North America. Biogeochemistry 109: 117-131.
    • (2012) Biogeochemistry , vol.109 , pp. 117-131
    • Yavitt, J.B.1    Yashiro, E.2    Cadillo-Quiroz, H.3    Zinder, S.H.4
  • 91
    • 0037772204 scopus 로고    scopus 로고
    • Microarrays for bacterial detection and microbial community analysis
    • Zhou, J. (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 288-294
    • Zhou, J.1
  • 92
    • 84862820580 scopus 로고    scopus 로고
    • Non-linear response of microbial activity across a gradient of nitrogen addition to a soil from the Gurbantunggut Desert, northwestern China
    • Zhou, X., Zhang, Y., and Downing, A. (2012) Non-linear response of microbial activity across a gradient of nitrogen addition to a soil from the Gurbantunggut Desert, northwestern China. Soil Biol Biochem 47: 67-77.
    • (2012) Soil Biol Biochem , vol.47 , pp. 67-77
    • Zhou, X.1    Zhang, Y.2    Downing, A.3
  • 93
    • 84859605159 scopus 로고    scopus 로고
    • Two decades of describing the unseen majority of aquatic microbial diversity
    • Zinger, L., Gobet, A., and Pommier, T. (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol 21: 1878-1896.
    • (2012) Mol Ecol , vol.21 , pp. 1878-1896
    • Zinger, L.1    Gobet, A.2    Pommier, T.3


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