Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere

AimMost culture-independent studies of bacterial biogeography have been at genus or higher taxonomic levels, although many important processes mediated by bacteria are at the strain or species level, such as the competitive nodulation of rhizobia on legumes. Here, at the intra-species level, we characterized the structural variation in rhizobial populations in soybean rhizosphere under field conditions across 32 sampling sites in three eco-regions. LocationNorth-east (Heilongjiang), north (Hebei-Shandong) and south (Jiangxi) China. MethodsThe intra-species diversity of rhizobia in soybean rhizospheres was investigated by rpoB pyrosequencing. Soybean nodule isolates were characterized using repetitive extragenic palindromic PCR, restriction fragment length polymorphism of 16S-23S intergenic sequences and rpoB PCR sequencing. Patterns and processes of biogeography of identified rhizobia were studied. ResultsSignificant biogeographical patterns of rhizosphere rhizobia at the species level were found, and the abundant species in the rhizosphere were generally the dominant microsymbionts in soybean nodules. The distribution of rhizobial species in the rhizosphere across eco-regions correlated with combined effects of spatial, vegetative, edaphic and climatic variables. Gene flow and genetic differentiation analyses revealed that there was no dispersal limitation among geographical populations of the same rhizobial species, and drift or subsequent diversification might be involved in shaping the biogeographical pattern in addition to environmental factors. Main conclusionsThese results constitute the first report of the existence of rhizobial biogeography in legume rhizospheres at the species level, contrasting with most studies, which focused on nodule isolates. The method developed in this study could be used to uncover, at high resolution, the diversity of local rhizobial populations in soils. This information is crucial for choosing suitable strains or species as inoculants for a specific legume host under local field conditions. Moreover, a similar strategy could be used to study other bacteria with important ecological functions.