Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean

Applied and Environmental Microbiology

Volumn 65, Issue 7, 1999, Pages 3192-3204

  Crump, Byron C ^a   Armbrust, E Virginia ^a   Baross, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIVER WATER; RNA 16S;

BACTERIUM; MICROBIAL COMMUNITY; PHYLOGENETICS;

ARTICLE; BACTERIUM; BIODIVERSITY; CHLOROPLAST; CYANOBACTERIUM; ESTUARY; FLEXIBACTERACEAE; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RIVER; SEA;

COLUMBIA RIVER; UNITED STATES;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CYTOPHAGA; FLEXIBACTERACEAE; POSIBACTERIA; PROTEOBACTERIA; RHODOBACTER; VERRUCOMICROBIUM;

EID: 0032976388     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.7.3192-3204.1999     Document Type: Article

References (50)

1. Abee, T., R. Palmen, K. J. Hellingwerf, and W. N. Konings. 1990. Osmoregulation in Rhodobacter sphaeroides. J. Bacteriol. 172:149-154.
2. Bahr, M., J. E. Hobbie, and M. L. Sogin. 1996. Bacterial diversity in an arctic lake: a freshwater SAR11 cluster. Aquat. Microb. Ecol. 11:271-277.
3. Baross, J. A., B. Crump, and C. A. Simenstad. 1994. Elevated 'microbial loop' activities in the Columbia River estuarine turbidity maximum, p. 495-464. In K. R. Dyer and B. J. Orth (ed.), Changes in fluxes in estuaries: implications from science to management (ECSA22/ERF symposium, Plymouth, September 1992). Olsen & Olsen, Fredensborg, Denmark.
4. Berner, E. K., and R. A. Berner. 1996. Marginal marine environments: estuaries, p. 284-311. In Global environment: water, air, and geochemical cycles. Prentice Hall, Englewood Cliffs, N.J.
5. Crump, B. C., and J. A. Baross. 1996. Particle-attached bacteria and heterotrophic plankton in the Columbia River estuary. Mar. Ecol. Prog. Ser. 138: 265-273.
6. Crump, B. C., C. A. Simenstad, and J. A. Baross. 1998. Particle-attached bacteria dominate the Columbia River estuary. Aquat. Microb. Ecol. 14:7-18.
7. 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.
8. Felske, A., A. Wolterink, R. Van Lis, and A. D. L. Akkermans. 1998. Phytogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl. Environ. Microbiol. 64:871-879.
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. Gauthier, M. J., B. Lafay, R. Christen, L. Fernandez, M. Acquaviva, P. Bonin, and J.-C. Bertrand. 1992. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new extremely halotolerent, hydrocarbon-degrading marine bacterium. Int. J. Syst. Bacteriol. 42:568-576.
12. Gilbert, D. G. 11 July 1994, posting date. [Online.] SeqApp program, version 1.9a169. http://ftp.bio.indiana.edu/IUBio-software+Data/molbio/seqapp [27 May 1999, last day accessed.]
13. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
14. González, J. M., F. Mayer, M. A. Moran, R. E. Hodson, and W. B. Whitman. 1997. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int. J. Syst. Bacteriol. 47:369-376.
15. González, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
16. Hansen, M. C., T. Tolker-Nielsen, M. Givskov, and S. Molin. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26:141-149.
17. Hansen, T. A., and J. F. Imhoff. 1985. Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int. J. Syst. Bacteriol. 35:115-116.
18. Hiorns, W. D., B. A. Methé, S. A. Nierzwicki-Bauer, and J. P. Zehr. 1997. Bacterial diversity in Adirondack Mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63:2957-2960.
19. Hiraishi, A., and Y. Ueda. 1994. Intrageneric structure of the genus Rhodobacter: transfer of Rhodobacter sulfidophilus and related marine species to the genus Rhodovulum gen. nov. Int. J. Syst. Bacteriol. 44:15-23.
20. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.
21. Igeño, M. I., C. González del Moral, F. Castillo, and F. J. Caballero. 1995. Halotolerence of the phototrophic bacterium Rhodobacter capsulatus E1F1 is dependent on the nitrogen source. Appl. Environ. Microbiol. 61:2970-2975.
22. Imhoff, J. F. 1988. Halophilic phototrophic bacteria, p. 85-108. In F. Rodriguez-Valera (ed.), Halophilic bacteria, vol. 1. CRC Press, Boca Raton, Fla.
23. Kopczynski, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
24. Krieg, N. R. 1984. Genus Oceanospirillum Hylemon, Wells, Krieg and Jannasch 1973, 361 (AL), p. 104-110. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. Williams & Wilkins, Baltimore, Md.
25. Liesack, W., and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:5072-5078.
26. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
27. Methé, B. A., W. D. Hiorns, and J. P. Zehr. 1998. Contrasts between marine and freshwater bacterial community composition: analyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43:386-374.
28. Moore, L. R., G. Rocap, and S. W. Chisholm. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393:464-467.
29. 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.
30. Munson, M. A., D. B. Nedwell, and T. M. Embley. 1997. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63:4729-4733.
31. National Center for Biotechnology Information. 13 April 1997, revision date. [Online.] Programs. National Center for Biotechnology Information, Bethesda, Md. http://www.ncbi.nlm.nih.gov. [27 May 1999, last date accessed.]
32. Neal, V. T. 1972. Physical aspects of the Columbia River and its estuary. In A. T. Pruter and D. L. Alverson (ed.), The Columbia River estuary and adjacent ocean waters. University of Washington Press, Seattle.
33. Nold, S. C., and G. Zwart. 1998. Patterns and governing forces in aquatic microbial communities. Aquat. Ecol. 32:17-35.
34. Pedersen, K., J. Arlinger, L. Hallbeck, and C. Pettersson. 1996. Diversity and distribution of subterranean bacteria in groundwater at Oklo in Gabon, as determined by 16S rRNA gene sequencing. Mol. Ecol. 5:427-436.
35. Prahl, F. G., L. F. Small, and B. Eversrmeyer. 1997. Biogeochemical characterization of suspended particulate mater in the Columbia River estuary. Mar. Ecol. Prog. Ser. 160:173-184.
36. Rappé, M. S., P. F. Kemp, and S. J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 165 rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42:811-826.
37. Reed, D. J. Personal communication.
38. Reichenbach, H. 1989. Genus 1. Cytophaga Winogradsky 1929, 577, (AL) emend, p. 2015-2050. In J. T. Staley, M. P. Bryant, N. Pfenning, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams & Wilkins, Baltimore, Md.
39. Simenstad, C. A., L. F. Small, C. D. McIntire, D. A. Jay, and C. Sherwood. 1990. Columbia River estuary studies: an introduction to the estuary, a brief history, and prior studies. Prog. Oceanog. 25:1-13.
40. Simenstad, C. A., C. A. Morgan, J. R. Cordell, and J. A. Baross. 1994. Flux, passive retention, and active residence of zooplankton in Columbia River estuarine turbidity maxima, p. 473-484. In K. R. Dyer and B. J. Orth (ed.), Changes in fluxes in estuaries: implications from science to management (ECSA22/ERF symposium, Plymouth, September 1992). Olsen & Olsen, Fredensborg, Denmark.
41. Small, L. F., C. D. McIntire, K. B. MacDonald, J. R. Lara-Lara, B. R. Frey, M. C. Amspoker, and T. Wenfield. 1990. Primary production, plant and detrital biomass, and particle transport in the Columbia River estuary. Prog. Oceanogr. 25:175-210.
42. Stackebrandt, E., W. Liesack, and B. M. Goebel. 1993. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:232-236.
43. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
44. Suzuki, M. T., M. S. Rappé, Z. W. Haimberger, H. Winfield, N. Adair, J. Ströbel, and S. J. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63:983-989.
45. Tanner, M. A., B. M. Goebel, M. A. Dojka, and N. R. Pace. 1998. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64:3110-3113.
46. von Wintzingerode, F., U. B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
47. Wilson, K. H., and R. B. Blitchington. 1996. Human colonie biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:2273-2278.
48. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.
49. Zwart, G., W. D. Hiorns, B. A. Methe, M. P. van Agterveld, R. Huismans, S. C. Nold, J. P. Zehr, and H. J. Laanbroek. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst. Appl. Microbiol. 21:546-556.
50. Zwart, G., R. Huismans, M. P. van Agterveld, Y. Van de Peer, P. De Rijk, H. Eenhoorn, G. Muyzer, E. J. van Hannen, H. J. Gons, and H. J. Laanbroek. 1998. Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol. Ecol. 25:159-169.