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Open Access item Genome characteristics of a generalist marine bacterial lineage
|Authors:||Newton, R. J.|
Griffin, L. E.
Bowles, K. M.
Givens, C. E.
Howard, E. C.
Oakley, C. A.
Reisch, C. R.
Rinta-Kanto, J. M.
Westrich, J. R.
Moran, M. A.
|Keywords:||Phylogeny, Roseobacter, Genome, Marine|
|Publisher:||Nature Publishing Group|
|Citation:||ISME Journal 4 : 784-798 (2010)|
|Abstract:||Members of the marine Roseobacter lineage have been characterized as ecological generalists,
suggesting that there will be challenges in assigning well-delineated ecological roles and
biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter
isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/
pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy
and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply
branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat
surprisingly, phylogenetic tree topology was not the best model for organizing genome
characteristics or distribution patterns of individual genes/pathways, although it provided some
predictive power. The lifestyle framework, established by grouping isolates according to evidence
for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this
lineage. The environment framework had a weak predictive power for the overall genome content of
each strain, but explained the distribution of several individual genes/pathways, including those
related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled
sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale
geographical signal in some Roseobacter genes. The primary findings emerging from this
comparative genome analysis are that members of the lineage cannot be easily collapsed into
just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates);
the strongest framework for predicting genome content is trophic strategy, but no single framework
gives robust predictions; and previously unknown homologs to genes for H2 oxidation,
proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO2 fixation by Form
IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms
for energy and carbon acquisition in this remarkably versatile bacterial lineage.|
|Description:||15 páginas, 6 figuras, 1 tabla.|
|Publisher version (URL):||http://dx.doi.org/10.1038/ismej.2009.150|
|E-ISSNmetadata.dc.identifier.doi = DOI:||1751-7370|
|Appears in Collections:||(CEAB) Artículos|
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