Delineation of Paraburkholderia tuberum and description of Paraburkholderia lebeckiae sp. nov. isolated from the root nodules of South African Lebeckia ambigua.

Paraburkholderia tuberum is a diverse beta-rhizobial species (i.e. rhizobia bacteria belonging to the class Betaproteobacteria) indigenous to South Africa that associates mostly with indigenous papilionoid legume species. The taxonomic boundary of this species was reviewed in 2022, which indicated that it includes a number of diverse strains. In fact, some of these P. tuberum strains appear to have sufficient genetic heterogeneity to belong to separate species. The absence of publicly available whole-genome sequences for the majority of P. tuberum strains during the last review of their taxonomy limited the accuracy of their species delineation. In this study, we revise the species delineation of P. tuberum using a comprehensive genome-based approach. With whole-genome sequences of 28 P. tuberum strains now available, we performed genealogical concordance analysis based on 92 conserved gene regions and conducted analysis of average nucleotide identity, digital DNA-DNA hybridization and pangenome coding content. Overall, our analyses grouped the 28 P. tuberum strains into two separate species clusters, which showed sufficient divergence to allow recognition as separate species. The one cluster represents P. tuberum sensu stricto, while the second cluster was described as a novel species. For this novel species, we propose the name Paraburkholderia lebeckiae sp. nov., with the type strain WSM4175T (=CMW-IA:007206T; DSM 120862T; LMG 34098T). Our results confirm that whole-genome-based information is crucial in determining accurate species boundaries, and its use should be supported and promoted.