Host genetics play a significant role in the composition of switchgrass root microbiomes

Featured article | 27-Jun-2023

The study points to traits and genes in the control of the root microbiome of switchgrass, a biofuel feedstock and native North American prairie grass.

DOE/US Department of Energy


Plants provide a home for a wide variety of microbes, especially in their roots. In turn, these communities can provide important benefits for the host. This study investigated how host plant genetics determine the composition of bacterial communities associated with plant roots. The study identified a core of bacterial strains that colonize switchgrass roots. Many of these bacteria differ in abundance between plant genotypes. The study then mapped the genes in the host genome that appear to influence the abundance of these microbes. This mapping revealed that genes involved in host immunity, plant development and hormone signaling play a role in how plants acquire their microbiome.

The impact

Plants rely on their microbiomes to perform vital functions. Researchers try to breed plant varieties to increase beneficial associations with bacteria. However, scientists have limited knowledge of the extent to which host genetics influence the composition of the microbiome. This study found that the genotype of a switchgrass host plant affects much of the plant’s microbiome. The study also identified switchgrass genes that appear to influence the abundance of these microbes. These findings may help design or breed plant varieties that form stronger beneficial associations with their microbiomes.


Plant-associated microbiota can contribute significantly to plant growth and yield. How host genetic variation affects root-microbiome assembly is an open question. In this study, the researchers used a common garden approach with field sites in Texas, Missouri, and Michigan to uncover the composition of the switchgrass root microbiome, characterize the effect of environment versus host genetics on the composition of the root microbiome and identifying the putative loci in the host genome implied the differential composition of the microbiome. The team included scientists from the University of Texas at Austin, the HudsonAlpha Institute for Biotechnology, the Joint Genome Institute of Lawrence Berkeley National Laboratory, the University of Missouri and Michigan State University.

Through sequencing efforts at the Joint Genome Institute, researchers have found that the microbiota composition of switchgrass roots is largely site dependent. However, there is a conserved array of core bacteria found in great abundance on roots at all sites. Most of these foundational microbes differ in abundance between host genotypes in an environment-dependent manner. Finally, the researchers used a genome-wide association study (GWAS) framework to identify loci in the host genome associated with the differing abundance of these microbes. Variation in genes implicated in plant immunity, development and signaling has been associated with differences in microbiome composition. These results provide a deeper understanding of the mechanisms plants use to modify their microbiota and offer an avenue for breeding host plants to adapt their microbiome.


This research was supported by the Department of Energy’s Office of Science; Office of Biological and Environmental Research; the National Science Foundation’s long-term ecological research program; and the Department of Agriculture National Institute of Food and Agriculture.

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