Updated taxonomy of the family Rhizobiaceae with proposals for 10 novel genera and 35 novel combinations

Abstract

The family Rhizobiaceae of the class Alphaproteobacteria is highly diverse and currently consists of at least 276 validly published or proposed species across 38 genera. Despite several recent studies proposing revisions to the family Rhizobiaceae, anomalies and inconsistencies in the taxonomy of this family remain. Here, we revisit the taxonomy of the family Rhizobiaceae with a focus on the genus Rhizobium. First, we generated whole genome sequences for 12 Rhizobium type strains that previously lacked publicly available genome sequences. We then applied an established phylogenomic framework to reappraise the taxonomic classification of 242 Rhizobiaceae type strains. Our data suggest that Rhizobium aegyptiacum is a later heterotypic synonym of Rhizobium aethiopicum, and they contradict a recent suggestion that Rhizobium azibense and Rhizobium gallicum are synonymous. In addition, we propose the formation of ten new genera (Allohoeflea gen. nov., Arminia gen. nov., Fluviimicrobium gen. nov., Gillisella gen. nov., Limnomicrobium gen. nov., Martinezia gen. nov., Neohoeflea gen. nov., Parahoeflea gen. nov., Velazquezia gen. nov., and Yannia gen. nov.) and 35 novel combinations to fix paraphyletic genera or account for monophyletic type strains that are clearly distinguishable based on core-proteome average amino acid identity (cpAAI) comparisons. Lastly, our data suggest that the type strain of Rhizobium arsenicireducens may have been lost, and that either a neotype should be designated or the taxonomic status of this species should be revised.