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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). We are developing computational tools to simulate evolution in complex communities in silico, and to address questions such as (a) how horizontal gene transfer affects the stability and dynamics of microbial communities, (b) how metabolic networks evolve, or (c) how the complexity of a microbial community affects the strength and directionality of eco-evolutionary feedbacks.

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 numbers of environmental microbial communities in synthetic laboratory environments, 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. Ecological and evolutionary effects of cellular decision-making in microbial populations. By altering their shared environments through their metabolic activity, microbes can influence the phenotypes expressed by other cells in their proximity, e.g. which metabolites they choose to utilize or which enzymes to express. Evolutionary changes in the genetic and biochemical circuits that control microbial behavior may thus affect ecological interactions between species, and are an essential component of microbial communities. Our lab is interested understanding the relationship between the evolution of microbial behavior and microbial ecology. For instance, we ask questions such as: How conserved are metabolic decisions across the bacterial tree of life? How does the behavior of individuals from one species affect the behavior of other species in the community?  (Rauch et al 2017);


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