A comprehensive genome-centred taxonomy for agrobacteria and rhizobia in the Bartonellaceae and Rhizobiaceae families

Abstract

To clarify the taxonomy of agrobacteria and rhizobia – assemblages of bacteria critical for sustainable agriculture and biotechnology – we applied a phylogenomic approach to reassess their current classifications. By phylogenetically analysing two marker gene sets based on both nucleotide (UBCG) and amino acid levels (bac120) of the type strains within the families Bartonellaceae and Rhizobiaceae, we found that both marker sets led to congruent phylogenies that consistently recovered the same lineages. These generic boundaries of the proposed lineages were strongly supported by average amino acid identities of ≥76%. Our results corroborate with previously proposed genus-level thresholds and provided a robust foundation for taxonomic revision. Several taxonomic changes are proposed to minimize the disruption to current classifications while also reflecting the evolutionary histories of these organisms. These include the emendation of ‘Paramesorhizobium’ to better reflect its distinction from Ochrobactrum and Phyllobacterium. Two Rhizobium species were also reassigned to the novel genera Fluviirhizobium gen. nov. and Phytoamicus gen. nov., reflecting the deep phylogenetic divergence and distinct ecological origins. Other taxonomic refinements include new combinations for species previously assigned to Rhizobium and Mesorhizobium, now shown to belong to Paenirhizobium and Terribium. We further clarified the classifications of Allorhizobium, Neorhizobium and Mesorhizobium sensu GTDB that were based on relative evolutionary divergence and were likely too broad. This demonstrates the need for an integrative genome-based approach to classify organisms that do not solely rely on numerical thresholds to produce biologically meaningful groups that enhance taxonomic stability.