Investigating biogeographic patterns of Rhizobium leguminosarum symbiovar viciae within the tribe Fabeae

Abstract

Nodulation is the symbiotic association of plants and diazotrophic bacteria that results in the formation of specialized organs (nodules) and allows fixation of atmospheric nitrogen. Rhizobial nodulation is widespread in Fabaceae with both promiscuous or exclusive hosts and/or rhizobia existing. An ideal group to explore these patterns is tribe Fabeae. Fabeae includes four genera: Ervilia Link, Ervum L., Vicia L., and Lathyrus L., and around 380 species distributed almost globally. They largely nodulate with Rhizobium leguminosarum symbiovar viciae. With the aim of evaluating the biogeographic patterns of rhizobia that colonize Fabeae species using a broader sampling, the genome of 68 strains of R. leguminosarum symbiovar viciae was sequenced. The nodules were collected from Lathyrus and Vicia hosts growing in Argentina, Canada, Chile, Greece (Crete), Japan, Spain, United Kingdom and United States and cultured to single strains. The DNA was extracted and then sent to MicrobesNG for library preparation and sequencing. Reads were trimmed and draft genomes were assembled. From the contigs, three sets of genes were extracted: (1) 120 non-mobile core genes from the chromosome (2) the 16S rRNA sequence, and (3) the nodulation genes nodA, nodC and nodD. The 16S was highly conserved across the accessions and was not informative to distinguish strains or geographical patterns. However, the set of 120 core genes gave a much more resolved picture allowing genospecies identification and revealing geographical patterns. The preliminary results using the core genes indicate a trend for geographical grouping over large areas. Our analysis consistently retrieved a Japanese clade and a South American clade with the remainder (over 50 accessions) belonging to a very widespread group from Europe and North America. Host plants were generally promiscuous and there was no apparent correlation with the evolutionary phylogeny of the hosts and their choice of rhizobial partners.