Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques

Environmental Microbiology

Volumn 16, Issue 9, 2014, Pages 2672-2681

  Gobet, Angélique ^a,b,d   Boetius, Antje ^a,c   Ramette, Alban ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b JACOBS UNIVERSITY BREMEN   (Germany)

^c ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^d STATION BIOLOGIQUE DE ROSCOFF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

BACTERIAL DNA; SEA WATER;

BACTERIUM; BACTERIUM IDENTIFICATION; BIODIVERSITY; CLASSIFICATION; COMPARATIVE STUDY; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; PROCEDURES; SEDIMENT;

BACTERIA; BACTERIAL TYPING TECHNIQUES; BIODIVERSITY; DNA FINGERPRINTING; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84904746353     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12308     Document Type: Article

References (43)

1. Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., and Polz, M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
2. Avaniss-Aghajani, E., Jones, K., Chapman, D., and Brunk, C. (1994) A molecular technique for identification of bacteria using small-subunit ribosomal-RNA sequences. Biotechniques 17: 144-149.
3. Bent, S.J., and Forney, L.J. (2008) The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J 2: 689-695.
4. Bienhold, C., Boetius, A., and Ramette, A. (2012) The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISME J 6: 724-732.
5. Böer, S.I., Hedtkamp, S.I.C., van Beusekom, J.E.E., Fuhrman, J.A., Boetius, A., and Ramette, A. (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3: 780-791.
6. Bray, J.R., and Curtis, J.T. (1957) An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr 27: 326-349.
7. Brown, M.V., Schwalbach, M.S., Hewson, I., and Fuhrman, J.A. (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7: 1466-1479.
8. Cardinale, M., Brusetti, L., Quatrini, P., Borin, S., Puglia, A.M., Rizzi, A., etal. (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70: 6147-6156.
9. Clarke, K.R. (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18: 117-143.
10. Crosby, L.D., and Criddle, C.S. (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-794.
11. Curtis, T.P., and Sloan, W.T. (2005) Exploring microbial diversity - a vast below. Science 309: 1331-1333.
12. Degnan, P.H., and Ochman, H. (2012) Illumina-based analysis of microbial community diversity. ISME J 6: 183-194.
13. Fisher, M.M., and Triplett, E.W. (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65: 4630-4636.
14. Gilbert, J.A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., etal. (2009) The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol 11: 3132-3139.
15. Gobet, A., Quince, C., and Ramette, A. (2010) Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Res 38: e155.
16. Gobet, A., Böer, S.I., Huse, S.M., van Beusekom, J.E.E., Quince, C., Sogin, M.L., etal. (2012) Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6: 542-553.
17. Gower, J.C. (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325-338.
18. Gürtler, V., and Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142: 3-16.
19. Huber, J.A., Morrison, H.G., Huse, S.M., Neal, P.R., Sogin, M.L., Welch, D.B.M., and Mark Welch, D.B. (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 11: 1292-1302.
20. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L., and Mark Welch, D. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
21. Koopman, M.M., Fuselier, D.M., Hird, S., and Carstens, B.C. (2010) The carnivorous pale pitcher plant harbors diverse, distinct, and time-dependent bacterial communities. Appl Environ Microbiol 76: 1851-1860.
22. Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
23. Legendre, L., and Legendre, P. (1998) Numerical Ecology Edition, 2nd English (ed). Amsterdam, The Netherlands: Elsevier Science BV.
24. Legendre, P., and Gallagher, E.D. (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.
25. Legendre, P., Borcard, D., and Peres-Neto, P.R. (2005) Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecol Monogr 75: 435-450.
26. Musat, N., Werner, U., Knittel, K., Kolb, S., Dodenhof, T., van Beusekom, J.E.E., etal. (2006) Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Romo Basin, Wadden Sea. Syst Appl Microbiol 29: 333-348.
27. Oksanen, J., Guillaume Blanchet, F., Kindt, R., Legendre, P., O'Hara, R.B., Simpson, G.L., etal. (2013) VEGAN: Community Ecology Package. R package version 2.0-7.
28. Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.R., and Stahl, D.A. (1986) Microbial ecology and evolution - a ribosomal-rna approach. Annu Rev Microbiol 40: 337-365.
29. Pearson, K. (1901) Mathematical contributions to the theory of evolution - VII on the correlation of characters of not quantitatively measurable. Philos Trans R Soc Lond A 195: 1-47.
30. Quince, C., Curtis, T.P., and Sloan, W.T. (2008) The rational exploration of microbial diversity. ISME J 2: 997-1006.
31. Quince, C., Lanzén, A., Curtis, T.P., Davenport, R.J., Hall, N., Head, I.M., etal. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
32. Quinlan, A.R., Stewart, D.A., Stromberg, M.P., Marth, G.T., Strömberg, M.P., and Marth, T. (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 5: 179-181.
33. R Development Core Team. (2013) R: a Language and Environment for Statistical Computing.
34. Ramette, A. (2009) Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. Appl Environ Microbiol 75: 2495-2505.
35. Ramette, A., and Tiedje, J.M. (2007) Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci USA 104: 2761-2766.
36. Roesch, L.F.W., Lorca, G.L., Casella, G., Giongo, A., Naranjo, A., Pionzio, A.M., etal. (2009) Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J 3: 536-548.
37. Shepard, R.N. (1966) Metric structures in ordinal data. J Math Psychol 3: 287-315.
38. Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., etal. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere. Proc Natl Acad Sci USA 103: 12115-12120.
39. Stackebrandt, E., and Goebel, B.M. (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846-849.
40. Urakawa, H., Kita-Tsukamoto, K., and Ohwada, K. (1999) Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145: 3305-3315.
41. Yannarell, A.C., and Triplett, E.W. (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71: 227-239.
42. Zinger, L., Amaral-Zettler, L.A., Fuhrman, J.A., Horner-Devine, M.C., Huse, S.M., Welch, D.B.M., etal. (2011) Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6: e24570.
43. Zinger, L., Gobet, A., and Pommier, T. (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol 21: 1878-1896.