Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Surveying, Culturing, and Sequencing Root Microbiomes Associated with Switchgrass, a Native North American Biofuel Feedstock


Joseph Edwards1,2* (, Adam Healey3, Usha Saran1, Jane Grimwood3, Jeremy Schmutz3, Thomas Juenger1


1Integrative Biology Department, University of Texas–Austin; 2Plant Pathology and Microbiology, Texas A&M University–College Station; 3HudsonAlpha Institute for Biotechnology


Root-associated bacteria play a central role in plant health, affecting ecosystem processes and impacting agricultural sustainability. The group aims to better understand the interactions between root-associated bacterial communities (i.e., microbiota) and switchgrass, a biofuel feedstock C4 grass native to North America. Researchers have surveyed root microbiota from a population of re-sequenced, natural switchgrass accessions growing across its native range (Edwards et al 2023). The team found that root microbiomes of switchgrass are dependent upon the field site the plants are growing in. Within field sites, researchers found that the abundance for many different microbes depend on the genetic background of the host plant. Genome-wide association studies (GWAS) identified several host genetic loci of interest which may impact microbiome assembly.

The above study helped researchers understand how host plants modulate their bacterial communities, yet researchers still know little about the bacterial strains that colonize switchgrass, their genomic information, or the interactions they have with the plants and with other members of the microbial community. In this study, the team used a high-throughput bacterial isolation approach to culture members of the switchgrass microbiome across genotypes. Researchers are using a full-genome sequencing approach to identify the bacterial isolates in the collection, so far sequencing over 3,500 genomes. In this poster, researchers present the phylogenetic diversity of the culture collection and how it relates to the field surveying efforts, the catalogue and diversity of the biosynthetic gene clusters of the culture collection, and an example of how synthetic communities can be formed and inoculated on plants to evaluate assembly patterns. Researchers envision these bacterial isolates with their corresponding genomes to be an important resource for the switchgrass microbiome community.


Edwards, J., et al. 2023. “Genetic Determinants of Switchgrass Root-Associated Microbiota in Field Sites Spanning Its Natural Range,” Current Biology 33(10), 1926–38. DOI:10.1016/j.cub.2023.03.078.