The structure-function problem in microbial communities

The very persistence of ecosystems requires nutrient cycling. On a global scale microbial communities are the evolved metabolic engines that drive these cycles. The flow of nutrients around these cycles are defined by and defines microbial community structure and metabolic function. As such, a primary concern of microbial ecology is understanding the eco-evolutionary process by which functional microbial communities arise. How does the metabolic function of a microbial community emerge from the genes, species, and interactions present? How are communities organized by and for nutrient fluxes? We address these questions experimentally and theoretically in two model systems. In our first study, we ask: can we predict the flow of metabolites through a community from the genes each community member possesses? We take a bottom-up approach using denitrification as a model process whereby bacterial communities reduce oxidized nitrogen compounds through a cascade of four reactions. Using natural isolates, sequencing and metabolite measurements we develop a statistical approach to quantitatively map community level denitrification rates to genomic composition. In our second study, we ask: how do communities self-organize to sustain nutrient cycles? To address this question we take a top-down approach using closed microbial communities - hermetically sealed microbial biospheres which persist indefinitely when supplied with only light - as model systems. Closed ecosystem persistence relies on the sustained cycling of carbon driven by photosynthesis. Closed ecosystems provide tractable, model systems for understanding how emergent nutrient cycles arise from metabolic interactions in communities. We present a new, high-precision, measurement of carbon cycling in closed ecosystems. Using this approach, we show that complex microbial consortia can self-organize to persistently cycle carbon. Sequencing and metabolic measurements show that self-organized closed ecosystems that cycle carbon are taxonomically diverse but all harbor a shared set of conserved metabolic capabilities. In essence, the composition of the community is flexible, but the metabolic capabilities are conserved.

If you would like to participate, please contact Britta Baron for Zoom link and password (baron@evolbio.mpg.de).