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Our laboratory seeks to understand the role of environmental engineering by microbial populations in microbial community assembly and microbial evolution.

Microbes secrete many different kinds of molecules to their environment, from metabolic byproducts to extracellular enzymes. These molecules collectively modify the extracellular environment, and mediate either direct or indirect ecological interactions. Our lab is interested in how these excreted molecules structure microbial communities and determine the evolutionary trajectories of the species in these communities. Our current work includes:

1) Ecosystem engineering in evolution: Eco-evolutionary feedbacks in microbial populations. We are trying to understand how microbes adapt to their own metabolic secretions, using a combination of theory (consumer-resource models), computation (dynamic FBA) and evolution experiments with model organisms such as E. coli (Bajic et al 2018).

2) Effect of ecosystem engineering in microbial community assembly. Metabolic secretions produce new niches that can be occupied by other species, potentially leading to facilitation. By cultivating large environmental microbial communities ex vivo in synthetic media, we are investigating: (a) How environmental engineering by metabolic secretions affects microbial community assembly (Goldford et al 2018); (b) how environmental engineering affects the outcome of microbial invasions (Lu et al 2018); and (c) how environmental engineering leads to emergent properties of microbial ecosystems (Sanchez-Gorostiaga et al 2018).

3) Systems Biology of public goods production in microbial populations. In addition to metabolic byproducts, microbes also secrete costly exoenzymes that also are critical in environmental engineering. These lead to public goods interactions, and we are trying to understand: (a) How their expression is regulated and what consequences this has for community assembly (Rauch et al 2017); (b) how enzymes secreted by different species interact with each other outside the cell (in preparation: stay tuned!); and (c) how variability in single-cell behavior affects microbial evolution.


More about our publications