Refining the taxonomy of the orderHyphomicrobiales(Rhizobiales) based on whole genome comparisons of over 130 genus type strains

Abstract

ABSTRACTThe alphaproteobacterial orderHyphomicrobialesconsists of 38 families comprising 155 validly published genera as of June 2023. The orderHyphomicrobialeswas first described in 1957 and underwent important revisions in 2020. However, several inconsistencies in the taxonomy of this order remain, and there is a need for a consistent framework for defining families within the order. We propose a common genome-based framework for defining families within the orderHyphomicrobiales, suggesting that families represent monophyletic groups in core-genome phylogenies that share pairwise average amino acid identity values above ∼75% when calculated from a core set of 59 proteins. Applying this framework, we propose the formation of four new families and to reassign the generaSalaquimonas,Rhodoblastus, andRhodoligotrophosintoSalaquimonadaceaefam. nov.,Rhodoblastaceaefam. nov., andRhodoligotrophaceaefam. nov., respectively, and the generaAlbibacter,Chenggangzhangella,Hansschlegelia, andMethylopilaintoMethylopilaceaefam. nov.. We further propose to unify the familiesBartonellaceae,Brucellaceae,Phyllobacteriaceae, andNotoacmeibacteraceaeasBartonellaceae; the familiesSegnochrobactraceaeandPseudoxanthobacteraceaeasSegnochrobactraceae; the familiesLichenihabitantaceaeandLichenibacteriaceaeasLichenihabitantaceae; and the familiesBreoghaniaceaeandStappiaceaeasStappiaceae. Lastly, we propose to reassign several genera to existing families. Specifically, we propose to reassign the genusPseudohoefleato the familyRhizobiaceae; the generaOricola,Roseitalea, andOceaniradiusto the familyAhrensiaceae; the genusLimoniibacterto the emended familyBartonellaceae; the genusFaunimonasto the familyAfifellaceae; and the genusPseudochelatococcusto the familyChelatococcaceae. Our data also support the recent proposal to reassign the genusProsthecomicrobiumto the familyKaistiaceae.