Exploration of the genomic diversity of Rhizobium isolates that are the closest known relatives to arsenite-oxidizing Rhizobium strain NT-26.

Bacteria from the Rhizobiaceae family are often carrying large plasmids, called megaplasmids or even chromids when they carry essential genes, which confer them a variety of phenotypes, including highly specialized ones such as nodule symbiosis, plant pathogenicity and metabolism of heavy-metals. The distribution of these plasmids correlates to some extent with their host bacterium phylogeny, even though transfers between closely related species are frequent. This suggest long-term co-evolutionary dynamics between the chromosomal and megaplasmid compartments of the rhizobial genomes, potentially leading to strong epistatic interactions. This is even more likely considering the large gene cargo of these plasmids (usually hundreds of genes), which expression is tightly regulated and co-ordinated with that of the core-genome in relation to the host bacterium environmental perception. In that sense, megaplasmids come as large packages of adaptive 'apps' that are relatively specific of a genomic 'operating sytem' (Young 2016, PMID: 27680981). However it is not clear wether these confer a specialized adaptation to a well-define ecological niche, or rather provide the bacterial host with a sets of functions that would prove adaptive in the many different environments it is likely to encounter.The arsenite-oxidizing strain Rhizobium sp. NT-26 (Santini et al. 2000, PMID: 10618208) is an example of high ecological specialization, from the usual soil-dwelling, plant root commensal rhizobia towards heavy-metal resistance and arsenic and sulfur chemolithotrophism, which is in part geared by the presence of a megaplasmid (Andres et al. 2013, PMID: 23589360). Here we sequence the genomes of Rhizobium isolates that are the closely related to Rhizobium sp. NT-26, to reconstruct its evolutionary pathway to niche specialization, and to explore the diversity of genomic assemblages of chromosomal and megaplasmid genotypes.