The small genome of an abundant coastal ocean methylotroph.

@article{Giovannoni2008TheSG,
  title={The small genome of an abundant coastal ocean methylotroph.},
  author={Stephen J. Giovannoni and Darin H. Hayakawa and H. James Tripp and Ulrich Stingl and Scott A. Givan and Jang-Cheon Cho and Hyun-Myung Oh and Joshua B. Kitner and Kevin L. Vergin and Michael S. Rapp{\'e}},
  journal={Environmental microbiology},
  year={2008},
  volume={10 7},
  pages={
          1771-82
        }
}
OM43 is a clade of uncultured beta-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was… Expand
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References

SHOWING 1-10 OF 58 REFERENCES
Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis
TLDR
The genome analysis of C. litoralis strain KT71 identifies the gammaproteobacterial marine AAnPs, postulated based on BAC sequences, as members of the NOR5/OM60 clade. Expand
The SAR92 Clade: an Abundant Coastal Clade of Culturable Marine Bacteria Possessing Proteorhodopsin
TLDR
Genome sequencing and analysis of HTCC2207 showed that the PR gene is present as a lone transcriptional unit directly followed by an operon containing genes that are presumably involved in the synthesis of retinal, the chromophore of PR. Expand
Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707
TLDR
Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. Expand
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
TLDR
The genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade, is described, indicating that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds to supplement heterotrophy. Expand
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
TLDR
The isolation of representatives of the SAR11 clade is reported, which indicates that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study. Expand
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
TLDR
Evidence is gained for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential, in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. Expand
SAR11 clade dominates ocean surface bacterioplankton communities
TLDR
Quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters support the conclusion that this microbial group is among the most successful organisms on Earth. Expand
Methylotrophy in Methylobacterium extorquens AM1 from a Genomic Point of View
TLDR
In the 20 years following the publication of Biochemistry of Methylotrophs, a few additional methylotrophy biochemical pathways have been discovered, such as the pathway for C1 transfer linked to methanopterin and methanofuran, which solved the long-standing mystery of formaldehyde oxidation in many methylotrophic organisms. Expand
The first methane-oxidizing bacterium from the upper mixing layer of the deep ocean:Methylomonas pelagica sp. nov.
Methane enrichment of twenty-three 100-ml portions of seawater from three stations in the Sargasso Sea yielded the same obligate type I methanotroph. It is pigmented white, requires NaCl, grows wellExpand
Genome Streamlining in a Cosmopolitan Oceanic Bacterium
TLDR
P. ubique, the first cultured member of the SAR11 clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. Expand
...
1
2
3
4
5
...