Surveying plant microbiomes
Plants represent a rich environment for soil microbes. Some microbes trade services to the plant in exchange for energy and nutrients while other microbes take advantage of energy resource and harm the plant. How the host plant balances and controls the assembly of different microorganisms on its roots is an important question with implications for sustainable agriculture and ecosystem processes. We are particularly interested to identify genetic pathways in crop and bioenergy grasses impacting microbiome acquisition using GWAS and QTL mapping.
Prospecting root-associated bacteria
Surveying microbiomes through sequencing allows us to characterize which microbes have strong associations with the plants. We utilize automated, high-throughput culturing of bacteria to retrieve these bacteria from root and soil samples. The bacterial isolates undergo full-genome sequencing which allows us to identify the organisms, characterize genetic variation within and between bacterial species, and to build synthetic communities to test parameters of microbiome assembly across plants and environments.
Visualizing microbial colonization
Where do different strains of microbes establish on plant roots? Are there structures which attract some bacteria but not others? We are developing strains and tools to visualize microbial colonization in native grasses.
Natural variation of plant immunity
Plants posses an immune system which protects against pathogen and pest damage. We are characterizing pattern triggered immunity in native C4 grasses, exploring genotypic responses to elicitors and bacterial strains.