Different ecological processes drive the assembly of dominant and rare root-associated bacteria in a promiscuous legume

Understanding how plant-associated microbial communities assemble and the roles they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, assemblages are mostly determined by filtering by the host as well as abiotic soil conditions. However, for legumes adapted to highly variable environments and nutrient-poor soils, filtering out rhizobial partners may not be an effective strategy to ensure symbiotic benefits. As a consequence, this can lead to net increases in rhizobial diversity driven by stochastic (neutral) assembly processes. Here, we addressed whether symbiotic promiscuity of rooibos (Aspalathus linearis Burm. Dahlgren), reflects increases in rhizobial diversity that are independent of the environmental conditions, following a neutral assembly. We performed a common garden experiment to assess whether root system size and location- and habitat-specific rhizobial propagule pools of rooibos affected rhizobial community diversity and composition. We found a dominance of drift in driving taxonomic turnover in the root nodule communities, but operating at different scales in the dominant Mesorhizobium symbionts and the rest of bacterial taxa. Specifically, drift triggered differentiation between the core rhizobial symbionts of rooibos due to dispersal limitation on a regional scale, whereas it dominated the assembly of non-dominant rhizobial taxa at the root level. This suggests the existence of a significant neutral component in rhizobial community assembly when selectivity by the host plant is low. We conclude that in this promiscuous legume neutral processes govern bacterial community root nodule community assembly, but that these operate at different scales in dominant and rare rhizobial symbionts of the plant.