UC Berkeley

Microbes exist in complex, multispecies communities where they participate in nutritional interactions that shape microbial community structure, function and stability. Nutritional interactions can range from competition for shared nutrients, to mutualisms, where nutrients are reciprocally exchanged in ways that benefit both partners. Not all microbes are able to produce all of their required nutrients, and as a result, rely on receiving nutrients from neighboring microbes. I am interested in understanding mechanisms of nutrient release and its implications in supporting microbial communities.

In Chapter 1, I provide background on how microbes interact in communities, and discuss examples of different types of microbial interactions. I then review how microbes impact their surroundings by releasing by-products and metabolites into their environment, that can then be used by other microbes as nutrients. Next, I explore cooperative and mutualistic behaviors, and theories for how we think cooperative interactions evolve overtime, before discussing auxotrophy, and how this trait may have evolved via adaptive evolution. I end Chapter 1 by discussing cell death, different forms of cell lysis, including bacteriophage-mediated lysis, and review what is known about how these processes are related to nutrient release and nutrient cycling in microbial communities.

In Chapter 2, I discuss two theories for how I think metabolites can be released into the environment to facilitate interdependent metabolite sharing. Microbial communities are composed of complex networks of metabolically interdependent organisms. But it is unclear how these nutritional networks evolve. In particular, the incentive for releasing metabolites, such as amino acids, vitamins and nucleobases is not obvious. I discuss that nutrient release could be a by-product of processes, like cell lysis and regulated metabolite efflux, that could facilitate the emergence of interdependent metabolite sharing.

I experimentally test these predictions in Chapter 3 by hypothesizing that bacteriophage-mediated lysis is a dominant mechanism of nutrient release that can support amino acid auxotrophs. I use bacterial growth assays to investigate how well supernatants, mechanical cell lysates, and phage-generated lysates are able to support a set of amino acid auxotrophs. I found that supernatants and mechanical lysates minimally support auxotrophs, and phage lysates release a significant amount of bioavailable nutrients, suggesting that in nature, phage are likely to play a large role in providing auxotrophs with their required nutrient.

Chapter 4 explores secretion as a mechanism of nutrient provisioning. More specifically, I test how nutrient overproduction can occur as result of auxotrophic mutations, and the implications of this nutrient overproduction on co-culture growth. To test this I developed an obligate mutualistic synthetic co-culture using two engineered E. coli that reciprocally exchange vitamin B12 and methionine. I show that co-culture growth is limited by methionine secretion, and reveal how specific auxotrophic mutations are able to increase flux through the methionine biosynthesis pathway to improve co-culture growth.

In addition to exploring mechanisms of nutrient provisioning, I also conducted a sociological project about doctoral students in the biological sciences. In Chapter 5, I investigate key elements of socialization that doctoral students in the biological sciences experience as they navigate their graduate programs. From interviews with over 30 doctoral students, I highlight how informal interactions affect students access to scientific help and expertise.