Abstract
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
Highlights
The genus Burkholderia was originally introduced to accommodate an assemblage of seven Pseudomonas species (Yabuuchi et al, 1992), two of which were later transferred to Ralstonia (Gillis et al, 1995; Yabuuchi et al, 1995)
With their review of the group, Estrada-de los Santos et al (2016) recognized two monophyletic groups [Groups A and B; A consists of Caballeronia and Paraburkholderia as circumscribed by Gyaneshwar et al (2011) and Sawana et al (2014), respectively, while Group B includes most of the notable human, animal and plant pathogens, as well as the so-called “B. cepacia complex”]
We aimed to resolve the relationships within Burkholderia sensu lato, those pertaining to Paraburkholderia and Caballeronia, by making use of whole genome sequence data
Summary
The genus Burkholderia was originally introduced to accommodate an assemblage of seven Pseudomonas species (Yabuuchi et al, 1992), two of which were later transferred to Ralstonia (Gillis et al, 1995; Yabuuchi et al, 1995). The number of Burkholderia species has grown substantially, to about 108 in 2015 (Estrada-de los Santos et al, 2016), spanning a range of Generic Boundaries in Burkholderia Sensu Lato human, animal and plant pathogens, as well as numerous strains with significant biotechnological potential (Depoorter et al, 2016; Estrada-de los Santos et al, 2016) The latter includes the so-called plant beneficial and environmental (PBE) species (Suárez-Moreno et al, 2012), many of which are plant-associated (e.g., those with plant growth promoting activities, the symbiotic diazotrophs and free-living species with diazotrophic, bioremedial and antibiotic activities) (Depoorter et al, 2016; Estrada-de los Santos et al, 2016). To complicate the issue, this new genus was named “Caballeronia” its proposed usage is not synonymous with the one previously proposed by Gyaneshwar et al (2011) for accommodating all the PBE isolates
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