Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample

Applied and Environmental Microbiology

Volumn 63, Issue 3, 1997, Pages 983-989

  Suzuki, Marcelino T ^a   Rappé, Michael S ^a   Haimberger, Zara W ^a   Winfied, Harry ^a   Adair, Nanci ^a   Ströbel, Jürgen ^a   Giovannoni, Stephen J ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA; SEA WATER;

ARTICLE; BACTERIUM CULTURE; BACTERIUM ISOLATION; BIODIVERSITY; CELL ISOLATION; DNA LIBRARY; DNA SEQUENCE; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; PSEUDOMONAS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; WATER SAMPLING;

BACTERIA (MICROORGANISMS); PROTEOBACTERIA; PSEUDOMONAS;

EID: 0031035973     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.3.983-989.1997     Document Type: Article

References (34)

1. Ausubel, F. A., R. Brent, R. E. Kingston, D. D. Moore, J. A. Smith, J. G. Seidman, and K. Struhl (ed.). 1988. Current protocols in molecular biology. John Wilev and Sons, Media, Pa.
2. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microhiol. 57:1707-1713.
3. Button, D. K., F. Schut, P. Quang, R. Martin, and B. R. Robertson. 1993. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl. Environ. Microbiol. 59:881-891.
4. Cohan, F. M. 1996. The role of genetic exchange in bacterial evolution. ASM News 62:631-636.
5. DeLong, E. F., D. G. Franks, and A. L. Alldredge. 1993. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol. Oceanogr. 38:924-934.
6. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
7. Felsenstein, J. 1989. PHYLIP - phytogeny inference package (v3.5) Cladistics 5:164-166.
8. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47:49-55.
9. Field, K. G., D. Gordon, T. Wright, M. Rappé, E. Urbach, K. Vergin, and S. J. Giovannoni. 1997. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. Environ. Microbiol. 63:63-70.
10. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1294-1302.
11. Giovannoni, S. J. 1991. The polymerase chain reaction, p. 177-201. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, N.Y.
12. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345: 60-63.
13. Giovannoni, S. J., E. F. DeLong, T. M. Schmidt, and N. R. Pace. 1990. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl. Environ. Microbiol. 56:2572-2575.
14. Giovannoni, S. J., T. D. Mullins, and K. G. Field. 1995. Microbial diversity in oceanic systems: rRNA approaches to the study of unculturable microbes, p. 217-248. In I. Joint (ed.), Molecular ecology of aquatic microbes. Springer, Berlin, Germany.
15. Giovannoni, S. J., M. S. Rappé. D. Gordon, E. Urbach, M. Suzuki, and K. G. Field. 1996. Ribosomal RNA and the evolution of bacterial diversity, p. 63-85. In D. M. Roberts, P. Sharp, G. Alderson, and M. Collins (ed), Evolution of microbial life. Cambridge University Press, Cambridge, United Kingdom.
16. Bobbie, J. E., R. J. Daley, and S. Jasper. 1977. Use of Nucleopore filters for counting bacteria by fluorescence microscopy. Appl. Environ. Microhiol. 33:1225-1228.
17. Ishida, Y., M. Eguchi, and H. Kadota. 1986. Existence of obligately oligotrophic bacteria as a dominant population in the South China Sea and the West Pacific Ocean. Mar. Ecol. Prog. Sci. 30:197-203.
18. Johnson, P. W., and J. M. Sieburth, 1979. Chrooccoid cyanobacteria in the sea: a ubiquitous and diverse phototrophic hiomass. Limnol. Oceanogr. 24:928-935.
19. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
20. Kogure, K., U. Simidu, and N. Taga. 1979. A tentative direct microscopic method for counting living marine bacteria. Can. J. Microbiol. 25:415-420
21. Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K Fogel, J. Blandy, and C. R. Woese. 1994. The Rihosomal Database Project. Nucleic Acids Res. 22:3485-3487.
22. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr 40:148-158
23. Olson, R. J., S. W. Chisholm, E. R. Zettler, M. A. Altabet, and J. A. Dusenberry. 1990. Spatial and temporal distributions of prochlorophyte picoplankton in the North Atlantic Ocean. Deep-Sea Res. 37:1033-1051.
24. Qian, L., and M. Wilkinson. 1991. DNA fragment purification: removal of agarose 10 minutes after electrophoresis. BioTechniques 10:736, 738.
25. Rappé, M. S., P. F. Kemp, and S. J. Giovannoni. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras. North Carolina. Limnol. Oceanogr., in press.
26. Reasoner, D. J., and E. E. Geldreicht. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Micro-biol. 49:1-7.
27. Rehnstam, A. S., S. Backman, D. Smith, F. Azam, and A. Hagstrom. 1993. Blooms of sequence-specific culturable bacteria in the sea. FEMS Microbiol Ecol. 102:161-166.
28. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method tor reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
29. Schmidt, T. E., E. F. DeLong, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene clonings and sequencing. J. Bacteriol. 173:4371-4378.
30. Schut F., E. J. de Vries, J. C. Gottschal, B. R. Robertson, W. Harder, R. A. Prins, and D. K. Button. 1993. Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates unde'r laboratory conditions. Appl. Environ. Microbiol. 59:2150-2161.
31. Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321-346.
32. Stein, J. L., T. L. Marsh, K. Y. Wu, H. Shizuya, and E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591-599.
33. Turley, C. M. 1993. Direct estimates of bacterial numbers in seawater samples without incurring cell loss during cell storage, p. 143-147. In P. F. Kemp. B. F. Sherr, E. B. Sherr, and J. J. Cole (ed.), Handbook of methods in aquatic microbial ecology. Plenum, Boca Raton, Fla.
34. Waterbury, J. B., S. VV. Watson, R. R. L. Guillard, and L. E. Brand. 1979. Widespread occurrence of a unicellular, marine, planktonic. cyanobacterium, Nature, (London) 277:293-294.