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Volumn 73, Issue 16, 2007, Pages 5276-5283

Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: Insights from Simulated Microbial Communities

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CORRELATION METHODS; MICROBIOLOGY; MOLECULAR STRUCTURE; POLYMORPHISM;

EID: 34548235824     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00514-07     Document Type: Article
Times cited : (175)

References (40)
  • 1
    • 33751434274 scopus 로고    scopus 로고
    • Evaluating the physical capture method of terminal restriction fragment length polymorphism for comparison of soil microbial communities
    • Blackwood, C. B., and J. S. Buyer. 2007. Evaluating the physical capture method of terminal restriction fragment length polymorphism for comparison of soil microbial communities. Soil Biol. Biochem. 39:590-599.
    • (2007) Soil Biol. Biochem , vol.39 , pp. 590-599
    • Blackwood, C.B.1    Buyer, J.S.2
  • 2
    • 0037313539 scopus 로고    scopus 로고
    • Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities
    • Blackwood, C. B., T. Marsh, S.-H. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69:926-932.
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 926-932
    • Blackwood, C.B.1    Marsh, T.2    Kim, S.-H.3    Paul, E.A.4
  • 4
    • 0033941482 scopus 로고    scopus 로고
    • Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis
    • Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2000. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66:2943-2950.
    • (2000) Appl. Environ. Microbiol , vol.66 , pp. 2943-2950
    • Dunbar, J.1    Ticknor, L.O.2    Kuske, C.R.3
  • 5
    • 0035163587 scopus 로고    scopus 로고
    • Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities
    • Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2001. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67:190-197.
    • (2001) Appl. Environ. Microbiol , vol.67 , pp. 190-197
    • Dunbar, J.1    Ticknor, L.O.2    Kuske, C.R.3
  • 6
    • 0036269049 scopus 로고    scopus 로고
    • Empirical and theoretical bacterial diversity in four Arizona soils
    • Dunbar, J., S. M. Barns, L. O. Ticknor, and C. R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68:3035-3045.
    • (2002) Appl. Environ. Microbiol , vol.68 , pp. 3035-3045
    • Dunbar, J.1    Barns, S.M.2    Ticknor, L.O.3    Kuske, C.R.4
  • 7
    • 0031981808 scopus 로고    scopus 로고
    • Santa Rosalia revisited: Why are there so many species of bacteria?
    • Dykhuizen, D. E. 1998. Santa Rosalia revisited: why are there so many species of bacteria? Antonie Leeuwenhoek 73:25-33.
    • (1998) Antonie Leeuwenhoek , vol.73 , pp. 25-33
    • Dykhuizen, D.E.1
  • 8
    • 0043031094 scopus 로고    scopus 로고
    • Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism
    • Engebretson, J. J., and C. L. Moyer. 2003. Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Appl. Environ. Microbiol. 69:4823-4829.
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 4823-4829
    • Engebretson, J.J.1    Moyer, C.L.2
  • 9
    • 31444447130 scopus 로고    scopus 로고
    • The diversity and biogeography of soil bacterial communities
    • Fierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103:626-631.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 626-631
    • Fierer, N.1    Jackson, R.B.2
  • 10
    • 0037270927 scopus 로고    scopus 로고
    • Influence of drying-rewetting frequency on soil bacterial community structure
    • Fierer, N., J. P. Schimel, and P. A. Holden. 2003. Influence of drying-rewetting frequency on soil bacterial community structure. Microb. Ecol. 45:63-71.
    • (2003) Microb. Ecol , vol.45 , pp. 63-71
    • Fierer, N.1    Schimel, J.P.2    Holden, P.A.3
  • 11
    • 33747802455 scopus 로고    scopus 로고
    • Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses
    • Frey, J. C, E. R. Angert, and A. N. Pell. 2006. Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses. J. Microbiol. Methods 67: 9-19.
    • (2006) J. Microbiol. Methods , vol.67 , pp. 9-19
    • Frey, J.C.1    Angert, E.R.2    Pell, A.N.3
  • 13
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans, J., M. Wolinsky, and J. Dunbar. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
    • (2005) Science , vol.309 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 14
    • 0034870192 scopus 로고    scopus 로고
    • Quantifying biodiversity: Procedures and pitfalls in the measurement and comparison of species richness
    • Gotelli, N. J., and R. K. Colwell. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4:379-391.
    • (2001) Ecol. Lett , vol.4 , pp. 379-391
    • Gotelli, N.J.1    Colwell, R.K.2
  • 15
    • 22044440860 scopus 로고    scopus 로고
    • Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees
    • Graff, A., and R. Conrad. 2005. Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees. FEMS Microbiol. Ecol. 53:401-415.
    • (2005) FEMS Microbiol. Ecol , vol.53 , pp. 401-415
    • Graff, A.1    Conrad, R.2
  • 16
    • 33747843979 scopus 로고    scopus 로고
    • Influence of plant diversity and elevated carbon dioxide levels on belowground bacterial diversity
    • Grüter, D., B. Schmid, and H. Brandl. 2006. Influence of plant diversity and elevated carbon dioxide levels on belowground bacterial diversity. BMC Microbiol. 6:68.
    • (2006) BMC Microbiol , vol.6 , pp. 68
    • Grüter, D.1    Schmid, B.2    Brandl, H.3
  • 17
    • 4644363590 scopus 로고    scopus 로고
    • Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils
    • Hackl, E., S. Zechmeister-Boltenstern, L. Bodrossy, and A. Sessitsch. 2004. Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl. Environ. Microbiol. 70:5057-5065.
    • (2004) Appl. Environ. Microbiol , vol.70 , pp. 5057-5065
    • Hackl, E.1    Zechmeister-Boltenstern, S.2    Bodrossy, L.3    Sessitsch, A.4
  • 18
    • 33845521652 scopus 로고    scopus 로고
    • Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices
    • Hartmann, M., and F. Widmer. 2006. Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl. Environ. Microbiol. 72:7804-7812.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 7804-7812
    • Hartmann, M.1    Widmer, F.2
  • 21
    • 33646876613 scopus 로고    scopus 로고
    • Entropy and diversity
    • Jost, L. 2006. Entropy and diversity. Oikos 113:363-375.
    • (2006) Oikos , vol.113 , pp. 363-375
    • Jost, L.1
  • 22
    • 0037728487 scopus 로고    scopus 로고
    • Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content
    • Kaplan, C. W., and C. L. Kitts. 2003. Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J. Microbiol. Methods 54:121-125.
    • (2003) J. Microbiol. Methods , vol.54 , pp. 121-125
    • Kaplan, C.W.1    Kitts, C.L.2
  • 23
    • 0036405388 scopus 로고    scopus 로고
    • Microbial communities and their interactions in soil and rhizosphere ecosystems
    • Kent, A. G., and E. W. Triplett. 2002. Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu. Rev. Microbiol. 56: 211-236.
    • (2002) Annu. Rev. Microbiol , vol.56 , pp. 211-236
    • Kent, A.G.1    Triplett, E.W.2
  • 24
    • 26844546416 scopus 로고    scopus 로고
    • The analysis of microbial communities with terminal restriction fragment length polymorphism (T-RFLP)
    • G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. Akkermans, and J. D. van Elsas ed, 2nd ed. Springer, New York, NY
    • Kim, S. H., and T. L. Marsh. 2004. The analysis of microbial communities with terminal restriction fragment length polymorphism (T-RFLP), p. 789-808. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. Akkermans, and J. D. van Elsas (ed.), Molecular microbial ecology manual, 2nd ed. Springer, New York, NY.
    • (2004) Molecular microbial ecology manual , pp. 789-808
    • Kim, S.H.1    Marsh, T.L.2
  • 25
    • 0141438984 scopus 로고    scopus 로고
    • Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes
    • LaMontagne, M. G., J. P. Schimel, and P. A. Holden. 2003. Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microb. Ecol. 46:216-227.
    • (2003) Microb. Ecol , vol.46 , pp. 216-227
    • LaMontagne, M.G.1    Schimel, J.P.2    Holden, P.A.3
  • 26
    • 33644838781 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
    • Loisel, P., J. Harmand, O. Zemb, E. Latrille, C. Lobry, J. Delgenès, and J. Godon. 2006. Denaturing gradient gel 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    Delgenès, J.6    Godon, J.7
  • 28
    • 2542523843 scopus 로고    scopus 로고
    • Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
    • Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
  • 30
    • 0032812081 scopus 로고    scopus 로고
    • Optimization of terminal restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis
    • Moeseneder, M. M., J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl. 1999. Optimization of terminal restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525.
    • (1999) Appl. Environ. Microbiol , vol.65 , pp. 3518-3525
    • Moeseneder, M.M.1    Arrieta, J.M.2    Muyzer, G.3    Winter, C.4    Herndl, G.J.5
  • 31
    • 26844488070 scopus 로고    scopus 로고
    • Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags
    • Neufeld, J. D., and W. W. Mohn. 2005. Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl. Environ. Microbiol. 71:5710-5718.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 5710-5718
    • Neufeld, J.D.1    Mohn, W.W.2
  • 32
    • 33144466522 scopus 로고    scopus 로고
    • New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities
    • Osborne, C. A., G. N. Rees, Y. Bernstein, and P. H. Janssen. 2006. New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl. Environ. Microbiol. 72:1270-1278.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 1270-1278
    • Osborne, C.A.1    Rees, G.N.2    Bernstein, Y.3    Janssen, P.H.4
  • 33
    • 33744745905 scopus 로고    scopus 로고
    • Marine microbial diversity: Can it be determined?
    • Pedrós-Alió, C. 2006. Marine microbial diversity: can it be determined? Trends Microbiol. 14:257-263.
    • (2006) Trends Microbiol , vol.14 , pp. 257-263
    • Pedrós-Alió, C.1
  • 34
    • 0001572401 scopus 로고
    • The commonness, and rarity, of species
    • Preston, F. W. 1948. The commonness, and rarity, of species. Ecology 29: 254-283.
    • (1948) Ecology , vol.29 , pp. 254-283
    • Preston, F.W.1
  • 35
    • 0242676205 scopus 로고    scopus 로고
    • Sampling strategy in molecular microbial ecology: Influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities
    • Ranjard, L., D. P. H. Lejon, C. Mougel, L. Schehrer, D. Merdinoglu, and R. Chaussod. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ. Microbiol. 5:1111-1120.
    • (2003) Environ. Microbiol , vol.5 , pp. 1111-1120
    • Ranjard, L.1    Lejon, D.P.H.2    Mougel, C.3    Schehrer, L.4    Merdinoglu, D.5    Chaussod, R.6
  • 36
    • 15444366206 scopus 로고    scopus 로고
    • Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil
    • Ricke, P., S. Kolb, and G. Braker. 2005. Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil. Appl. Environ. Microbiol. 71:1671-1673.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 1671-1673
    • Ricke, P.1    Kolb, S.2    Braker, G.3
  • 37
    • 0030303752 scopus 로고    scopus 로고
    • A consumer's guide to evenness indices
    • Smith, B., and J. B. Wilson. 1996. A consumer's guide to evenness indices. Oikos 76:70-82.
    • (1996) Oikos , vol.76 , pp. 70-82
    • Smith, B.1    Wilson, J.B.2
  • 38
    • 34548277392 scopus 로고    scopus 로고
    • Reference deleted
    • Reference deleted.
  • 40
    • 27444435260 scopus 로고    scopus 로고
    • Physiological and molecular characterisation of microbial communities associated with different water-stable aggregate size classes
    • Väisänen, R. K., M. S. Roberts, J. L. Garland, S. D. Frey, and L. A. Dawson. 2005. Physiological and molecular characterisation of microbial communities associated with different water-stable aggregate size classes. Soil Biol. Biochem. 37:2007-2016.
    • (2005) Soil Biol. Biochem , vol.37 , pp. 2007-2016
    • Väisänen, R.K.1    Roberts, M.S.2    Garland, J.L.3    Frey, S.D.4    Dawson, L.A.5


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