Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

Nature

Volumn 424, Issue 6952, 2003, Pages 1042-1047

  Rocap, Gabrielle ^a   Larimer, Frank W ^b,c   Lamerdin, Jane ^c   Malfatti, Stephanie ^c   Chain, Patrick ^c,d   Ahlgren, Nathan A ^a   Arellano, Andrae ^c   Coleman, Maureen ^e   Hauser, Loren ^b,c   Hess, Wolfgang R ^g,j   Johnson, Zackary I ^e   Land, Miriam ^b,c   Lindell, Debbie ^e   Post, Anton F ^h   Regala, Warren ^c   Shah, Manesh ^b,c   Shaw, Stephanie L ^f,k   Steglich, Claudia ^g   Sullivan, Matthew B ^f   Ting, Claire S ^f   Tolonen, Andrew ^f   Webb, Eric A ⁱ   Zinser, Erik R ^e   Chisholm, Sallie W ^e,f   more..

^a UNIVERSITY OF WASHINGTON   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^e Massachusetts Institute of Technology Cambridge   (United States)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^g HUMBOLDT UNIVERSITY   (Germany)

^h The Interuniversity Institute for Marine Science Eilat   (Israel)

ⁱ WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^j Ocean Genome Legacy   (United States)

^k UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

GENES; OXYGEN; PHOTOSYNTHESIS;

GENOME DIVERGENCE;

ECOSYSTEMS;

CHLOROPHYLL; GENOMIC DNA; RIBOSOME DNA;

CYANOBACTERIUM; GENOME; MARINE ENVIRONMENT; NICHE PARTITIONING; PHYTOPLANKTON;

ARTICLE; BACTERIAL GENOME; BACTERIOPLANKTON; CYANOBACTERIUM; EVOLUTION; GENE TRANSFER; GENETIC VARIABILITY; GENOME; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEANIC REGIONS; PHOTOSYNTHESIS; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCHLOROCOCCUS; STRAIN DIFFERENCE;

ADAPTATION, PHYSIOLOGICAL; CYANOBACTERIA; ENVIRONMENT; EVOLUTION; GENES, BACTERIAL; GENOME, BACTERIAL; LIGHT; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROCHLOROCOCCUS; PROKARYOTA;

EID: 0042878464     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01947     Document Type: Article

References (30)

1. Chisholm, S. W. et al. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334, 340-343 (1988).
2. Campbell, L., Liu, H., Nolla, H. & Vaulot, D. Annual variability of phytoplankton and bacteria in the subtropical North Pacific Ocean at Station ALOHA during the 1991-1994 ENSO event. Deep Sea Res. I 44, 167-192 (1997).
3. DuRand, M. D., Olson, R. J. & Chisholm, S. W. Phytoplankton population dynamics at the Bermuda Atlantic Time-series Station in the Sargasso Sea. Deep Sea Res. II 48, 1983-2003 (2001).
4. Rocap, G., Distel, D. L., Waterbury, J. B. & Chisholm, S. W. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S rDNA internal transcribed spacer (ITS) sequences. Appl. Environ. Microbiol. 68, 1180-1191 (2002).
5. Moore, L. R. & Chisholm, S. W. Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates. Limnol. Oceanogr. 44, 628-638 (1999).
6. Moore, L. R., Rocap, G. & Chisholm, S. W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393, 464-467 (1998).
7. Moore, L. R., Goericke, R. E. & Chisholm, S. W. Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties. Mar. Ecol. Prog. Ser. 116, 259-275 (1995).
8. Mann, E. L., Ahlgren, N., Moffett, J. W. & Chisholm, S. W. Copper toxicity and cyanobacteria ecology in the Sargasso Sea. Limnol. Oceanogr. 47, 976-988 (2002).
9. Moore, L. R., Post, A. F., Rocap, G. & Chisholm, S. W. Utilization of different nitrogen sources by the marine cyanobacteria, Prochlorococcus and Synechococcus. Limnol. Oceanogr. 47, 989-996 (2002).
10. Sullivan, M. B., Waterbury, J. B. & Chisholm, S. W. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424, 1047-1051 (2003).
11. Hagström, Å. et al. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl. Environ. Microbiol. 68, 3628-3633 (2002).
12. West, N. J. et al. Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology 147, 1731-1744 (2001).
13. Palenik, B. et al. The genome of a motile marine Synechococcus. Nature 424, 1037-1042 (2003).
14. La Roche, J. et al. Independent evolution of the prochlorophyte and green plant chlorophyll a/b light harvesting proteins. Proc. Natl Acad. Sci. USA 93, 15244-15248 (1996).
15. Hess, W. et al. The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics. Photosynth. Res. 70, 53-71 (2001).
16. Stickforth, P., Steiger, S., Hess, W. R. & Sandmann, G. A novel type of lycopene ε-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch. Microbiol. 179, 407-415 (2003).
17. Frankenberg, N., Mukougawa, K., Kohchi, T. & Lagarias, J. C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13, 965-978 (2001).
18. Ting, C., Rocap, G., King, J. & Chisholm, S. W. Phycobiliprotein genes of the marine prokaryote Prochlorococcus: Evidence for rapid evolution of genetic heterogeneity. Microbiology 147, 3171-3182 (2001).
19. Golden, S. S., Brusslan, J. & Haselkorn, R. Expression of a family of psbA genes encoding a photosystem II polypeptide in the cyanobacterium Anacystis nidulans R2. EMBO J. 5, 2789-2798 (1986).
20. Shen, J. R., Qian, M., Inoue, Y. L. & Burnap, R. L. Functional characterization of Synechocystis sp. PCC 6803 ΔpsbU and ΔpsbV mutants reveals important roles of cytochrome c-550 in cyanobacterial oxygen evolution. Biochemistry 37, 1551-1558 (1998).
21. Garczarek, L., van der Staay, G. W. M., Hess, W. R., Le Gall, F. & Partensky, F. Expression and phylogeny of the multiple antenna genes of the low-light-adapted strain Prochlorococcus marinus SS120 (Oxyphotobacteria). Plant Mol. Biol. 46, 683-693 (2001).
22. Nakamura, Y. et al. Complete genome structure of the thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1. DNA Res. 9, 123-130 (2002).
23. Ishiura, M. et al. Expression of a gene cluster kaiABC as a circadian feedback process in cyanobateria. Science 281, 1519-1523 (1998).
24. Vaulot, D., Marie, D., Olson, R. J. & Chisholm, S. W. Growth of Prochlorococcus, a photosynthetic prokaryote, in the Equatorial Pacific Ocean. Science 268, 1480-1482 (1995).
25. Michaels, M. L. & Miller, J. H. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-Hydroxyguanine (7,8-Dihydro-8-Oxoguanine). J. Bacteriol. 174, 6321-6325 (1992).
26. Lindell, D. & Post, A. F. Ultraphytoplankton succession is triggered by deep winter mixing in the Gulf of Aqaba (Eilat). Red Sea. Limnol. Oceanogr. 40, 1130-1141 (1995).
27. Karl, D. M., Bidigare, R. R. & Letelier, R. M. Long-term changes in plankton community structure and productivity in the North Pacific Subtropical Gyre: The domain shift hypothesis. Deep Sea Res. II 48, 1449-1470 (2001).
28. Scanlan, D. J., Mann, N. H. & Carr, N. G. The response of the picoplanktonic marine cyanobacterium Synechococcus species WH7803 to phosphate starvation involves a protein homologous to the periplasmic phosphate binding protein of Echerichia coli. Mol. Microbiol. 10, 181-191 (1993).
29. Johnson, Z. et al. Energetics and growth kinetics of a deep Prochlorococcus spp. population in the Arabian Sea. Deep Sea Res. II 46, 1719-1743 (1999).
30. Dufresne, A. et al. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120. a near minimal oxyphototrophic genome. Proc. Natl Acad. Sci. USA (in the press).