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 analyze
alpha and beta diversity patterns of Rhizobiaceae communities from a conserved
seasonally-dry tropical forest site in central Mexico and two nearby agricultural
fields. Lineage-specific recA 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 Acacia species and two
Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae
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. Rhizobium etli was the dominant Rhizobiaceae found in the
soil libraries. It dominated nodulation of Acacia spp. and predominately harbored
symbiovar mimosae-like nodC genes. A novel Rhizobium lineage (Rsp1) dominated
bean nodulation. Specialist and generalist genotypes for host nodulation were
detected in both species.