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Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels. [ABSTRACT FROM AUTHOR]

Abstract Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources). HGT-based genetic conversions therefore causes homogenization, while genetic introductions drive divergence of populations upon fixation of genetic variants. The impact of HGT in different prokaryotic species may vary substantially and can range from very low levels to rampant HGT, producing chimeric groups of isolates. Combined with other evolutionary processes, these varying levels of HGT causes diversity space to be occupied by unique groups that are mostly incomparable in terms of genetic similarity, genomic cohesion and evolutionary age. As a result, the conventional, cut-off based metrics for species delineation are not adequate. Rather, a pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokaryotic species. Following this approach, all prokaryotic species may be regarded as unique and each of their own kind (sui generis). Taxonomic decisions thus require evolutionary information that integrates vertical inheritances with all possible sources of genetic heterogeneity to ultimately produce robust and biologically meaningful classifications. [ABSTRACT FROM AUTHOR]