Diversity patterns of R hizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes

Summary Current knowledge about rhizobial diversity patterns in non‐nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation‐dependent and independent approaches to analyse alpha and beta diversity patterns of R hizobiaceae communities from a conserved seasonally dry tropical forest site in central M exico and two nearby agricultural fields. Lineage‐specific rec A amplicon libraries were generated from soil DNA and their sequences compared with those from root surface and nodule isolates recovered in trapping experiments from two native A cacia species and two P haseolus vulgaris cultivars. Rarefaction analyses revealed that R hizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A ‘rare biosphere'‐like distribution of species was found in the three habitats. Multivariate statistical analyses demonstrated that the plant genus exerted a stronger influence than the land‐usage regime on the diversity of rhizobia associated with hosts. R hizobium etli was the dominant R hizobiaceae found in the soil libraries. It dominated nodulation of A cacia spp. and predominately harboured symbiovar mimosae‐like nod C genes. A novel R hizobium lineage ( R sp1) dominated bean nodulation. Specialist and generalist genotypes for host nodulation were detected in both species.