The epidemicity of facultative microsymbionts in faba bean rhizosphere soils

•No significant biogeography of bacteria was found in rhizosphere soils of faba bean.•A strong biogeography of nodD genotypes exists in rhizosphere soils and nodules.•The biogeography of nodD is incoherent with that of Rhizobium species in nodules.•Hosts shed hierarchical selections on nodD genotypes and Rhizobium species.

The epidemicity of bacteria facultatively associated with eukaryotes, involves not only housekeeping genes but also genes linked with the pathogenesis and symbiosis. Here, by characterizing both housekeeping (rpoB and 16S rRNA gene) and nodulation (nodD) genes, we explore processes shaping epidemic patterns of facultative microsymbionts from rhizosphere soils of faba bean in three ecoregions. Although total bacterial communities in rhizosphere were not significantly differentiated across ecoregions, rpoB amplicon sequencing uncovered that Rhizobium laguerreae and Rhizobium anhuiense were predominant in different samples with contrasting pH or salt content. However, R. anhuiense can outcompete R. laguerreae in certain sterilized soils where R. laguerreae originally dominated, and viceversa. Contrasting bacterial taxa associated with either R. laguerreae or R. anhuiense in soils. The biogeographical pattern of nodD was more clear than that of rhizobial species in both rhizosphere soils and nodules. Competitive nodulation experiments demonstrated a hierarchical selection on nodD genotypes and their genomic backgrounds by faba bean cultivars. Taken together, abiotic and biotic factors in soils and the selection by legume hosts are either indirectly or directly involved in shaping rhizobial species-level taxonomic biogeography, which however cannot be used to infer spatial patterns of nodulation gene.