Habitat, plant height, and soil nutrients are important determinants of the Hypericum perforatum microbiome

Abstract Aims Saint John’s wort, Hypericum perforatum, is a medicinally and ecologically important perennial plant species that has a broad global distribution. Despite the species’ importance, little is known about the factors that structure its microbial communities and the identity of microbes that enhance plant growth and fitness. Here we aim to describe the microbial communities associated with Hypericum perforatum and elucidate factors that structure these communities.Methods We collected H. perforatum root samples in three adjacent habitat types: wet and dry alvars (two types of limestone barren) and fallow agricultural fields (i.e. old-fields), in Jefferson County, New York. We used high-throughput amplicon sequencing of the SSU-rRNA gene (16S, bacteria) and the internal transcribed spacer region 1 (ITS1, fungi) to characterize the root microbiome of H. perforatum. At each root sampling location, we quantified aspects of the plant phenotype and soil characteristics to evaluate habitat variables that correlate with root microbial communities.Results Alvars had ~ 13% higher bacterial richness compared to old-fields. In contrast, old-fields had 28% higher fungal richness than dry alvars, but similar fungal richness to wet alvars. Habitat and plant height were important predictors of microbial community composition. We identified two bacterial taxa positively associated with plant height, both belonging to the bacterial phylum Actinobacteria.Conclusions This work contributes to our understanding of the environmental determinants of microbial community composition. Additionally, we were able to identify bacterial taxa that are correlated with plant health and should be investigated further as indicators of soil health or plant-growth promoting rhizobacteria.