Distinct biogeographic patterns of rhizobia and non-rhizobial endophytes associated with soybean nodules across China

Both rhizobia and non-rhizobial endophytes (NRE) are inhabitants of legume nodules. The biogeography of rhizobia has been well investigated, but little is known about the spatial distribution and community assemblage of NRE. By using high-throughput sequencing, we compared biogeographic patterns of rhizobial and non-rhizobial subcommunities and investigated their bacterial co-occurrence patterns in nodules collected from 50 soybean fields across China. Dispersal probability was lower in NRE than in rhizobia, as revealed by a significant distance-decay relationship found in NRE, but not in rhizobia, in addition to a significant occupancy–abundance relationship in the entire community. Rhizobial and NRE subcommunities were significantly influenced by different environmental and spatial variables. Moreover, the rhizobial subcommunities were grouped into Ensifer- and Bradyrhizobium-dominated clusters that were significantly related to soil pH. The non-rhizobial subcommunities were grouped into Proteobacteria- and Firmicutes-dominated clusters that were more influenced by climatic than by edaphic factors. These results demonstrated that rhizobial and non-rhizobial subcommunities are characterized by distinct biogeographic patterns. Network analysis showed rhizobia and NRE as separately grouped and uncorrelated with each other, suggesting they did not share niche space in soybean nodules. In sum, these results broaden our knowledge of how bacteria are distributed and assemble as a community in root nodules. [Display omitted] •Proteobacteria and Firmicutes dominated non-rhizobial subcommunity.•Rhizobia and non-rhizobial endophytes displayed distinct biogeographic patterns.•Non-rhizobial endophytes had a lower dispersal probability than rhizobia.•Rhizobia and non-rhizobial endophytes grouped separately in association network.