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

• Published in: The ISME Journal Vol. 11; no. 6; pp. 1483 - 1499
• Main Authors: Simon, Meinhard, Scheuner, Carmen, Meier-Kolthoff, Jan P, Brinkhoff, Thorsten, Wagner-Döbler, Irene, Ulbrich, Marcus, Klenk, Hans-Peter, Schomburg, Dietmar, Petersen, Jörn, Göker, Markus
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.06.2017; Oxford University Press; Nature Publishing Group
• Subjects: 45/23; 631/158/855; 631/181/757; Acclimatization - genetics; Acetic acid; Adaptation; Aquatic habitats; Bacteria; Base Sequence; Biogeochemical cycles; Biological evolution; Biomedical and Life Sciences; DNA, Bacterial - genetics; Ecological adaptation; Ecology; Ecosystem; Enzymes; Eukaryotes; Evolution, Molecular; Evolutionary Biology; Fucoidan; Gene sequencing; Genes; Genomes; Habitats; Indoleacetic acid; Life Sciences; Metabolic pathways; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Molecular Sequence Data; Oligotrophy; Original; original-article; Phylogeny; Plant hormones; Players; Rhodobacteraceae - genetics; Sodium chloride; Solutes
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2016.198

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.