Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga , with ≥96.1 % sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6^T and WSM3557^T was Microvirga flocculans TFB^T, with 97.6–98.0 % similarity, while WSM3693^T was most closely related to Microvirga aerilata 5420S-16^T, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) and cellular fatty acid profiles confirmed the placement of Lut6^T, WSM3557^T and WSM3693^T within the genus Microvirga . DNA–DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6^T, WSM3557^T and WSM3693^T from each other and from other Microvirga species with validly published names. The nodA sequence of Lut6^T was placed in a clade that contained strains of Rhizobium , Mesorhizobium and Sinorhizobium , while the 100 % identical nodA sequences of WSM3557^T and WSM3693^T clustered with Bradyrhizobium , Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that the sequences of Lut6^T, WSM3557^T and WSM3693^T were most closely related to that of Rhizobium etli CFN42^T nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini sp. nov. (type strain Lut6^T = LMG 26460^T = HAMBI 3236^T), Microvirga lotononidis sp. nov. (type strain WSM3557^T = LMG 26455^T = HAMBI 3237^T) and Microvirga zambiensis sp. nov. (type strain WSM3693^T = LMG 26454^T = HAMBI 3238^T).

Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume–rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.

Gram-negative, rod-shaped bacteria were isolated from root nodules of Lupinus polyphyllus, Lathyrus latifolius and Robinia pseudoacacia. Based on the 16S rRNA gene phylogeny, they were closely related to Bosea species (100–97 % similarity), belonging to the class Alphaproteobacteria , family Bradyrhizobiaceae . The closest relatives of LMG 26383^T, LMG 26379^T and LMG 26381^T were respectively the type strains of Bosea thiooxidans (99.6 %), B. eneae (98.3 %) and B. minatitlanensis (99.0 %). Chemotaxonomic data, including major fatty acid profiles, supported the assignment of our strains to the genus Bosea . Analysis of the concatenated sequences of five housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) and the results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from each other and from the five Bosea species with validly published names. No nodA or nodC genes could be amplified, while nifH PCR gave non-specific products. On the basis of genotypic and phenotypic data, three novel species, Bosea lupini sp. nov. (type strain LMG 26383^T = CCUG 61248^T = R-45681^T), Bosea lathyri sp. nov. (type strain LMG 26379^T = CCUG 61247^T = R-46060^T) and Bosea robiniae sp. nov. (type strain LMG 26381^T = CCUG 61249^T = R-46070^T), are proposed.