Genetic variation in plants can influence associated soil microbial communities, especially in species-depauperate ecosystems like coastal marshes where intraspecific variation can exert greater influence than differences among species. Yet the functional bridges linking plant genotype with microbial community structure are not well understood. Here we examined whether genotypic differences and associated heritable traits in a foundational coastal marsh plant affect colonization of root endophytic microbes under environmental stress. In a common-garden greenhouse experiment, we assessed endosphere microbial communities that colonized roots of 11 genotypes of the sedge Schoenoplectusamericanus following salinity stress. We drew comparisons between endosphere bacteria and fungi to determine whether plant genotype exerts similar influences that manifest as parallel patterns of diversity and community structure. We further determined whether genotypic differences in plants elicit differences in rhizosphere soil microbial communities.
Results/Conclusions We found evidence that variation in endosphere and rhizosphere microbial communities reflect genotypic and phenotypic trait variation in S. americanus, but that the differences were context-dependent. For example, the diversity of root fungal endosphere communities exhibited differences across S. americanus genotypes regardless of salinity stress whereas the diversity of root endosphere bacterial communities did not differ across plant genotypes. Correlation analyses between microbial communities and plants traits similarly revealed different associations with fungi and bacteria as well as rhizosphere and endosphere communities. Endosphere fungal diversity were negatively correlated with plants traits such as belowground biomass and stem height, in contrast, endosphere bacterial diversity was positively correlated with all plant traits. Our results highlight the potential relevance of plant intraspecific variation in plant–microbe–soil feedbacks in shaping naturally depauperate ecosystems like salt marshes.