Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (=DSM 106348T=CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments.
Highlights
Bacteria of the family Rhizobiaceae (Alphaproteobacteria) are usually soil-borne and found in association with plant roots, where they mostly rely on a saprophytic lifestyle degrading soil organic compounds and plant exudates, including aromatic compounds [6,7,50]
From the SML571 tree, we identified the well-supported clade grouping 41 genomes including all representative of Neorhizobium spp. and Pseudorhizobium spp. and our new isolates
Khangiran2 has a average identity (AAI) similarity score of 97.1% with R. halotolerans AB21T (96.5% with R. flavum YW14T), values that are similar to the within-species scores we report above
Summary
Bacteria of the family Rhizobiaceae (Alphaproteobacteria) are usually soil-borne and found in association with plant roots, where they mostly rely on a saprophytic lifestyle degrading soil organic compounds and plant exudates, including aromatic compounds [6,7,50]. This particular versatility in using various organic compounds likely stems from the presence of some of the largest known sets of carbohydrate transporter genes in Rhizobiaceae genomes [38,74].
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