title: Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.
abstract: Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-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 difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
authors.forename: Meinhard
authors.initials: M
authors.lastname: Simon
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Carmen
authors.initials: C
authors.lastname: Scheuner
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Brinkhoff
authors.affiliation: Helmholtz Centre for Infection Research, Research Group Microbial Communication, Braunschweig, Germany.
authors.forename: Irene
authors.initials: I
authors.lastname: Wagner-Döbler
authors.affiliation: Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Ulbrich
authors.affiliation: School of Biology, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Hans-Peter
authors.identifier: 0000-0001-6758-8150
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Institute of Biochemical Engineering, Technical University Braunschweig, Braunschweig, Germany.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Petersen
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D017753:Ecosystem; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D041902:Rhodobacteraceae / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial