Using the SeqCode to validate the names of reclassified lineages of rhizobia and agrobacteria

Abstract

Genome-based taxonomy offers a powerful means to resolve long-standing ambiguities in the classifications of agrobacteria and rhizobia, two bacterial groups with major ecological and agricultural significance. We applied a robust phylogenomic framework to genomes of the families Bartonellaceae and Rhizobiaceae to comprehensively reassess evolutionary relationships. Species trees were constructed using nucleotide sequences of 92 conserved genes and amino acid sequences of 120 ubiquitous proteins, clarifying relationships that were previously obscured by marker-limited historical classifications. These analyses demonstrated several instances of taxonomic inconsistencies across genera, most notably within Mesorhizobium, which forms a paraphyletic assemblage spanning multiple divergent lineages. These findings were further reinforced by the genome-wide similarity metric, average amino acid identity (AAI), which supported reclassifications at both genus and species levels, reflecting natural discontinuities between lineages. We propose the reclassification of eight species and five new genera and the validation of their names primarily under the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). As genome-based resources expand, and with the availability of new nomenclatural frameworks such as the SeqCode, genome-informed taxonomy offers a powerful approach to delineate taxa into biologically meaningful groups that can be formally recognised. The revised taxonomy presented here brings greater coherence to the systematics of agrobacteria and rhizobia and provides a framework for future evolutionary investigations into these agriculturally and ecologically significant bacterial groups. • Genome-based analyses confirm persistent paraphyly within the families Bartonellaceae and Rhizobiaceae. • Several lineages remain effectively, but not validly published under the ICNP. • The SeqCode was used to formally validate genome-based taxonomic reassessments. • The names of five genera and eight species are validated using the SeqCode.