Studying and Engineering the Rhizosphere

The soil is a vast and complex ecosystem that plays a major role in global biogeochemical processes and is the literal foundation of our own human society. Within this environment, microbial metabolism is the major bridge that links the biotic and abiotic aspects of the soil ecosystem together— whether one wants to understand how global nutrient cycling processes affect greenhouse gas production, wants to remediate environments contaminated by toxins, or wants to increase the resilience and yield of crop plants to better feed our growing population, microbes will be a key player in the solutions to any of these challenges.

Visualizing microbial gene expression in the rhizosphere

One of the central challenges associated with studying the rhizosphere is that the opacity of soil prevents the use of conventional readout modalities for measuring the dynamics of gene expression over time. I am currently leading a collaborative project across the Hay, Pierce, Meyerowitz, and Demirer groups at Caltech to develop a general platform that enables the minimally-invasive montoring of the expression dynamics of target genes from the rhizosphere microbial community, by combining broad host range biosensors with microbe-plant communication systems to infer the activity of underground microbes from the aboveground response of engineered reporter plants.

Nematodes as delivery vectors for microbes into the soil

Applications in agriculture and bioremediation often involve the introduction of nonnative microbes into a soil ecosystem, but ensuring that these microbes can conduct their intended function before being outcompeted is a major challenge. Together with Mengyi Cao’s group at the Carnegie Institute for Science, I am exploring the potential for using nematodes as a delivery vector that can protect internalized microbes from competition while still enabling them to influence the soil ecosystem.