Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: Development and application to a time series

Environmental Microbiology

Volumn 7, Issue 9, 2005, Pages 1466-1479

  Brown, Mark V ^a   Schwalbach, Michael S ^a   Hewson, Ian ^a   Fuhrman, Jed A ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOSOMAL SPACER DNA; RNA 16S; SEA WATER;

ARTICLE; AUTOMATION; CLASSIFICATION; DNA SEQUENCE; GENE LIBRARY; GENETICS; MICROBIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; PHYLOGENY; PROTEOBACTERIA; SEASON; UNITED STATES;

AUTOMATION; CALIFORNIA; CLONING, MOLECULAR; DNA, RIBOSOMAL SPACER; GENE LIBRARY; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEOBACTERIA; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; SEQUENCE ANALYSIS, DNA;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); CYANOBACTERIA; CYANOBACTERIUM (GENUS); GAMMAPROTEOBACTERIA; PROCHLOROCOCCUS;

EID: 23944517269     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00835.x     Document Type: Article

References (39)

1. Amann, R.I., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143-169.
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: 144-146.
3. Beja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
4. Beja, O., Suzuki, M.T., Heidelberg, J.F., Nelson, W.C., Preston, C.M., and Hamada, T. (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.
5. Binder, B.J., Chisholm, S.W., Olson, R.J., Frankel, S.L., and Worden, A.Z. (1996) Dynamics of picophytoplankton, ultraphytoplankton and bacteria in the central equatorial Pacific. Deep-Sea Res II 43: 907-931.
6. Campbell, L., Nolla, H.A., and Vaulot, D. (1994) The importance of Prochlorococcus to community structure in the central North Pacific-Ocean. Limnol Oceanogr 39: 954-961.
7. Dufresne, A., Salanoubat, M., Partensky, F., Artiguenave, F., Axmann, I.M., Barbe, V., et al. (2003) Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Nat Acad Sci USA 100: 10020-10025.
8. 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.
9. Fuhrman, J.A., Comeau, D.E., Hagstrom, A., and Chan, A.M. (1988) Extraction of DNA suitable for molecular biological studies from natural planktonic microorganisms. Appl Environ Microbiol 54: 1426-1429.
10. Fuhrman, J.A., McCallum, K., and Davis, A.A. (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol 59: 1294-1302.
11. Garcia-Martinez, J., and Rodriguez-Valera, F. (2000) Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol Ecol 9: 935-948.
12. Giovanonni, S., and Rappe, M. (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In Molecular Ecology of the Oceans. Kirchman, D.L. (ed.), New York, USA: John Wiley and Sons, pp. 47-84.
13. Gonzalez, J.M., Simo, R., Massana, R., Covert, J.S., Casamayor, E.O., Pedros-Alio, C., and Moran, M.A. (2000) Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66: 4237-4246.
14. Grant, A., and Olgivie, L.A. (2004) Name that Microbe: rapid identification of taxa responsible for individual fragments in fingerprints of microbial community structure. Mol Ecol Notes 4: 133-136.
15. Hayward, T.L., and Venrick, E.L. (1998) Near-surface pattern in the California Current: coupling between physical and biological structure. Deep-Sea Res II 45: 1617-1638.
16. Hewson, I., and Fuhrman, J.A. (2004) Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70: 3425-3433.
17. Hewson, I., Vargo, G.A., and Fuhrman, J.A. (2003) Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment and nutrient enrichment. Microb Ecol 46: 322-336.
18. Hugenholtz, P. (2002) Exploring prokaryotic diversity in the genomic era. Genom Biol 3: Reviews 0003.1-0003.8.
19. Jaspers, E., and Overmann, K. (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbial 70: 4831-4839.
20. Kent, A.D., and Triplett, E.W. (2002) Microbial communities and their interactions in soil and rhizoshphere ecosystmes. Annu Rev Microbiol 56: 211-236.
21. Klappenbach, J.A., Dunbar, J.M., and Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
22. Kolber, Z.S., Van Dover, C.L., Niederman, R.A., and Falkowski, P.G. (2000) Bacterial photosynthesis in surface waters of the open ocean. Nature 407: 177-179.
23. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Technology in Bacterial Sysematics. Stackebrandt, E., and Goodfellow, M. (eds). New York, USA: John Wiley and Sons, pp. 115-175.
24. Moran, M.A., Buchan, A., Gonzalez, J.M., Heidelberg, J.F., Whitman, W.B., Kiene, R.P., et al. (2004) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910-913.
25. Muyzer, G.E., DeWaal, C., and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
26. Palenik, B., Brahamsha, B., Larimer, F.W., Land, M., Hauser, L., Chain, P., et al. (2003) The genome of a motile marine Synechococcus. Nature 424: 1037-1042.
27. Partensky, F., Hess, W.R., and Vaulot, D. (1999) Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Molec Biol Rev 63: 106-124.
28. Ranjard, L., Brothier, A., and Nazaret, S. (2000) Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. Appl Environ Microbiol 66: 5334-5339.
29. Rocap, G., Distel, D.L., Waterbury, J.B., and Chisholm, S.W. (2002) Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbiol 68: 1180-1191.
30. Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
31. Schloter, M., Lebuhn, M., Heulin, T., and Hartmann, A. (2000) Ecology and evolution of bacterial microdiversity. FEMS Microbiol Rev 24: 647-660.
32. Schwalbach, M.S., Hewson, I., and Fuhrman, J.A. (2004) Viral effects on bacterial community composition in marine planktonic microcosms. Aquat Microb Ecol 34: 117-127.
33. Staley, J.T., and Konopka, A. (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39: 321-346.
34. Suzuki, T.M., Beja, O., Taylor, L.T., and DeLong, E.F. (2001) Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3: 323-331.
35. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
36. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
37. Vila, M., Simo, R., Kiene, R.P., Pinhassi, J., Gonzalez, J.M., Moran, M.A., and Pedros-Alio, C. (2004) Use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incroporation by marine bacterioplankton taxa. Appl Environ Mirocbiol 70: 4648-4657.
38. 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.
39. Zubkov, M.V., Fuchs, B.M., Tarran, G.A., Burkhill, P.H., and Amann, R. (2003) High rate of uptake of organic nitrogen by Prochlorococcus cyanobacteria as key to their dominance in oligotrophic oceanic waters. Appl Environ Microbiol 69: 1299-1304.