In the Schomer lab, we are motivated to understand the microbial ecology and bacterial physiology behind the formation and maintenance of soil microbiomes. We use molecular and genetic techniques to understand how bacteria integrate complex environmental and host signals into behavioral and metabolic responses. Motile, soil-dwelling bacteria exploit chemotaxis (chemical-driven migration up or down gradients) to move to suitable environments, such as the rhizosphere (root surface). Our work deciphers the mechanisms that allow bacteria to perceive complex signals to locate and colonize preferred niches like the rhizosphere or host plants.

Decoding complex chemotaxis

Linking chemoreceptors to attractants. ​Environmental microorganisms have complex chemotactic systems. Metabolically versatile bacteria have dozens of structurally diverse chemoreceptors that detect unique or overlapping environmental chemical signals. ​

We leverage high-throughput chemical genomics approaches to identify chemoreceptor ligands from targeted soil microorganisms (e.g., root-associated pathogens, bacterial strains with unique biodegradative capabilities, etc.). We are interested not only in what signals drive bacterial behavioral responses, but also how this behavior influence microbial physiology, soil ecology, and bacteria-plant host interactions. 

Host Specificity. We use plant-pathogenic Ralstonia as a model to understand the role of chemosensing and motility in host range and host discovery. During its life cycle Ralstonia must travel from the soil into a plant host. Ralstonia uses chemotaxis to detect gradients of host root exudates to locate hosts. Individual Ralstonia strains have broad host ranges and as a species complex can infect hundreds of different botanical families. We are interested in identifying the adaptations that result in dissimilar host ranges across the phylogenetically diverse clades of Ralstonia. To understand the plant-Ralstonia chemical language, we use a variety of comparative genomics, functional genomics, and metabolomics approaches.
 
Microbial Ecology. Metabolic versatility is a common survival tactic that is often associated with motility and chemotactic phenotypes. We are interested in how soil communities react to disturbances and chemical fluctuations. Using high-throughput chemical genomics, we mine and characterize agricultural and contaminated soils bacterial to understand how microbial chemosensing contributes to bioremediation, soil sustainability and community formation & maintenance.