The SAR92 clade: An abundant coastal clade of culturable marine bacteria possessing proteorhodopsin

Applied and Environmental Microbiology

Volumn 73, Issue 7, 2007, Pages 2290-2296

  Stingl, Ulrich ^b   Desiderio, Russell A ^a   Cho, Jang Cheon ^b   Vergin, Kevin L ^a   Giovannoni, Stephen J ^a  

^a Inha University   (South Korea)

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BATCH CULTURE; ENERGY PRODUCTION; PROTEORHODOPSIN (PR); PROTON PUMPS;

CHROMOPHORES; COASTAL ZONES; GENE ENCODING; MARINE BIOLOGY; PROTEINS; RNA; SURFACE WATERS;

BACTERIA;

CARBON; PROTEORHODOPSIN; RETINAL; RHODOPSIN; UNCLASSIFIED DRUG;

ASSAY; BACTERIOPLANKTON; BACTERIUM; CARBON; CLADISTICS; COASTAL ZONE; GENE; GENETIC ANALYSIS; GENOME; HYBRIDIZATION; PHYLOGENETICS; PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; CELL LINE; CHROMATOPHORE; CLADISTICS; CULTURE MEDIUM; FLUORESCENCE IN SITU HYBRIDIZATION; GAMMAPROTEOBACTERIA; GENE SEQUENCE; GENETIC TRANSCRIPTION; MARINE BACTERIUM; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; POLYMERASE CHAIN REACTION; SEASHORE; SEQUENCE ANALYSIS; SYNTHESIS; UNINDEXED SEQUENCE;

GAMMAPROTEOBACTERIA; GENOME, BACTERIAL; LIGHT; PHYLOGENY; POLYMERASE CHAIN REACTION; RETINALDEHYDE; RHODOPSIN; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY;

NORTH AMERICA; OREGON; UNITED STATES;

BACTERIA (MICROORGANISMS); CANDIDATUS PELAGIBACTER UBIQUE;

EID: 34247488726     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02559-06     Document Type: Article

References (30)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
4. Arrigo, K. R. 2005. Marine microorganisms and global nutrient cycles. Nature 437:349-355.
5. Beja, O., L. Aravind, E. V. Koonin, M. T. Suzuki, A. Hadd, L. P. Nguyen, S. B. Jovanovich, C. M. Gates, R. A. Feldman, J. L. Spudich, E. N. Spudich, and E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-1906.
6. Beja, O., E. N. Spudich, J. L. Spudich, M. Leclerc, and E. F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411:786-789.
7. Cho, J.-C., and S. J. Giovannoni. 2004. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl. Environ. Microbiol. 70:432-440.
8. Connon, S. A., and S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:3878-3885.
9. de la Torre, J. R., L. M. Christianson, O. Beja, M. T. Suzuki, B. M. Karl, J. Heidelberg, and E. F. DeLong. 2003. Proteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc. Natl. Acad. Sci. USA 100:12830-12835.
10. Frigaard, N. U., A. Martinez, T. J. Mincer, and E. F. DeLong. 2006. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439:847-850.
11. Giovannoni, S. J., L. Bibbs, J. C. Cho, M. D. Stapels, R. Desiderio, K. L. Vergin, M. S. Rappe, S. Laney, L. J. Wilhelm, H. J. Tripp, E. J. Mathur, and D. F. Barofsky. 2005. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438:82-85.
12. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 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. 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. Lane, D. J., A. P. Harrison, Jr., D. Stahl, B. Pace, S. J. Giovannoni, G. J. Olsen, and N. R. Pace. 1992. Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J. Bacteriol. 174:269-278.
16. Loy, A., M. Horn, and M. Wagner. 2003. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31:514-516.
17. Morris, R. M., M. S. Rappe, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson, and S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.
18. Morris, R. M., M. S. Rappé, E. Urbach, S. A. Connon, and S. J. Giovannoni. 2004. Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl. Environ. Microbiol. 70:2836-2842.
19. Oesterhelt, D., and W. Stoeckenius. 1971. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat. New Biol. 233:149-152.
20. Peck, R. F., E. A. Johnson, and M. P. Krebs. 2002. Identification of a lycopene β-cyclase required for bacteriorhodopsin biogenesis in the archaeon Halobacterium salinarum. J. Bacteriol. 184:2889-2897.
21. Pernthaler, J., F. O. Glockner, W. Schonhuber, and R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30:207-226.
22. Rappe, M. S., S. A. Connon, K. L. Vergin, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633.
23. Rappe, M. S., and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369-394.
24. Relief, J. D. 2000. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132:243-258.
25. Sabehi, G., O. Beja, M. T. Suzuki, C. M. Preston, and E. F. DeLong. 2004. Different SAR86 subgroups harbour divergent proteorhodopsins. Environ. Microbiol. 6:903-910.
26. Sabehi, G., A. Loy, K. H. Jung, R. Partha, J. L. Spudich, T. Isaacson, J. Hirschberg, M. Wagner, and O. Beja. 2005. New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol. 3:e273.
27. Sabehi, G., R. Massana, J. P. Bielawski, M. Rosenberg, E. F. Delong, and O. Beja. 2003. Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ. Microbiol. 5:842-849.
28. Schwalbach, M. S., M. Brown, and J. A. Fuhrman. 2005. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39:235-245.
29. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
30. Wright, T. D., K. L. Vergin, P. W. Boyd, and S. J. Giovannoni. 1997. A novel 8-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. Environ. Microbiol. 63:1441-1448.