Research Assistant Lawrence Berkeley National Lab, California
Body of Abstract: Beneficial plant-microbe interactions in the rhizosphere, or root microbiome, improve a plant’s nutrient cycling and stress tolerance capabilities. Rhizosphere engineering thus represents a potential avenue to improve crop performance. This can be especially relevant when developing bioenergy crops, which are often planted in marginal or degraded land not fit for growing food crops. While previous investigations of plant-microbe interactions have focused on the role of endophytic bacteria or plant exudates, less is known about the role of root cell walls in mediating a commensal microbial community. Cell wall engineering is a large focus of bioenergy crop research. Approaches include reducing the amount of a secondary cell wall component, lignin, which improves the conversion of the cell wall sugars into fuel. However, little is known about the impact of these modifications on the root microbiome. In this study, we used a lignin biosynthetic mutant of the model grass Brachypodium distachyon to study the effects of the cell wall on rhizosphere assembly in bioenergy crops. We first inoculated wildtype and lignin mutant roots with a 17-member bacterial synthetic community. We then developed a single inoculation platform using fabricated ecosystems (EcoFABs) and semi-automated epifluorescence microscopy to generate nondestructive and quantitative spatiotemporal data on root colonization. This system enables higher-throughput study of the interactions between commensal bacteria and bioenergy crops, and has potential for clarifying the effect of the cell wall on assembly of the root microbiome.