Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

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  2. Professor Hans-Peter Klenk
Author(s)Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M
Publication type Article
JournalThe ISME Journal
Year2017
Volume11
Issue
Pages1483–1499
ISSN (print)1751-7362
ISSN (electronic)1751-7370
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Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling,comprise up to 30% of bacterial communities in pelagic environments and are often mutualists ofeukaryotes. As ‘Roseobacter clade’, these ‘roseobacters’ are assumed to be monophyletic, but nonmarineRhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, weanalysed 106 genome sequences, particularly emphasizing gene sampling and its effect onphylogenetic stability, and investigated relationships between marine versus non-marine habitat,evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence forthe monophyly of roseobacters, indicate several shifts between marine and non-marine habitats thatoccurred independently and were accompanied by characteristic changes in genomic content oforthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinitytransporters to cope with much lower sulphate concentrations and lost genes related to the reducedsodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceaegained genes required for fucoidan desulphonation and synthesis of the plant hormone indole3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition,even though typical for the family, nor the degree of oligotrophy shows a systematic differencebetween marine and non-marine Rhodobacteraceae. We suggest the operational term ‘Roseobactergroup’ for the marine Rhodobacteraceae strains.
PublisherNature Publishing Group
URLhttps://doi.org/10.1038/ismej.2016.198
DOI10.1038/ismej.2016.198
PubMed id28106881
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