Bacterial assembly in the switchgrass rhizosphere is shaped by phylogeny, host genotype, and growing site.

Since microbial traits are conserved at different taxonomic levels, plant hosts may influence microbiome composition differently at different levels to broadly promote or resist microbiota with traits that impact host fitness. We tested this hypothesis by assessing signals of host genetic influence on bacterial composition in the switchgrass rhizosphere using 128 genotypes in dissimilar growing sites. We employed three common gardens, combined with host genetic mapping, 16S rRNA gene sequence analysis, hierarchical modeling, tests of phylogenetic conservation of host influence, and genome-wide association analyses to determine the contributions of host genetics in shaping rhizosphere bacterial composition at different taxonomic levels. Modeling bacterial assembly showed that growing site was a strong factor shaping bacterial composition in the rhizosphere, though host genetic influence played a significant role. The heritability of bacterial abundance was strongest at the genus level. Phylogenetic signal for heritability was detected within the bacterial phylogeny but conserved clades differed between common gardens. We identified shared host genetic variants associated with bacterial abundance and host traits related to plant metabolism. Our results suggest further investigation is required regarding the genotype-by-environment-by-microbiome relationship to elucidate the factors shaping rhizosphere microbiome composition and the agroecological dynamics shaping plant phenotype. ### Competing Interest Statement The authors have declared no competing interest.