Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the “Roseobacter Clade” Into a Novel Family, Roseobacteraceae fam. nov.

Abstract

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

“…The most common order is that of the Rhizobiales, which are widespread in earth environments and have been studied predominantly because of their economic (agricultural) and medical impact [6,7]. The second most common order is that of Rhodobacterales, including purple photosynthetic bacteria that have traditionally dominated the biochemical and genetic studies on Alphaproteobacteria [1,4], plus an ever-increasing number of marine non-photosynthetic bacteria [8,9].…”

The Influence of Genes on the “Killer Plasmid” of Dinoroseobacter shibae on Its Symbiosis With the Dinoflagellate Prorocentrum minimum

“…Because vitamin concentrations in the ocean water are low, algae are therefore dependent on symbiosis with bacteria (Croft et al, 2006;Smith et al, 2007). One bacterial group frequently associated with algae are the Roseobacters, which have recently been renamed Roseobacteraceae, and represent the marine family of the Rhodobacterales, consisting of more than 300 species (Pujalte et al, 2014;Simon et al, 2017;Hördt et al, 2020;Liang et al, 2021).…”

Mesobacterium pallidum gen. nov., sp. nov., Heliomarina baculiformis gen. nov., sp. nov. and Oricola indica sp. nov., three novel Alphaproteobacteria members isolated from deep-sea water in the southwest Indian ridge

“…The DNA G+C contents of strains T40-1 T and T40-3 T were 66.5 and 60.1 mol%, respectively, which were in the range of 51.7–72.1 mol% for the family Roseobacteraceae [3]. The ANI and in silico DDH values between strains T40-1 T , T40-3 T and closely related type strains of the family Roseobacteraceae were 70.0–73.9 % and 18.7–22.6 % (Table S2), respectively.…”

“…The members of this group also possess a great deal of physiological diversity, which is capable of metabolizing a large number of carbon sources, synthesizing B vitamins to facilitate eukaryotic interactions, assimilatory and dissimilatory nitrate reduction, and phototrophic growth [14]. The G+C content is 51.7–72.1 mol % [3].…”