Host species and environmental variation can influence rhizobial community composition

Abstract

Summary Nitrogen‐fixing rhizobial mutualists display high levels of genetic and phenotypic diversity at multiple spatial scales. Identifying the ecological and environmental drivers of variation in the genetic composition and function of rhizobial communities is critical to understanding rhizobial impacts on community and ecosystem productivity. In this study, we examined how environmental factors and host species jointly affect rhizobial phenotypic diversity and community structure. Individual host plants of two native Australian legumes, Acacia salicina and A. stenophylla, were inoculated with a community of six rhizobial strains (belonging to three genera) previously characterized for symbiotic effectiveness. The plants were grown in a fully factorial experiment under high and low phosphorus and water, and high or no nitrogen. Half the plants were harvested after 19 weeks and the other half after 30 weeks. The relative abundance of the six rhizobial strains was characterized using amplicon sequencing of the rhizobial 16S rRNA gene from DNA extracted from the root nodules of plants after each harvest. Variation in the relative abundance of the six rhizobial strains was best explained by host species, although interactions between environment and host species also emerged as significant predictors of variation in rhizobial community composition. We detected strong host‐specific interactions for two strains, while two other strains were clearly generalists, being relatively abundant in both host species. For both host species, the two generalist strains were as abundant as the best specialist strain within the rhizobial community. Synthesis. Our study show host species identity as the key determinant of rhizobial community structure within the root nodules of Acacia plants. Strains that were efficient at promoting the growth of their host plant had high relative abundance in experimental communities. Furthermore, interaction among host species, rhizobial host‐range, and environmental variation determine the structure of rhizobial communities, although not in clearly predictable ways. Such interactions contributed to the maintenance (albeit at relatively low frequencies) of ineffective strains in nodule communities. These interacting effects could help to explain why rhizobial communities are functionally diverse, such that specialists, generalists and seemingly ineffective rhizobia, can be simultaneously maintained in rhizosphere communities.