Transitions: Modeling microbial community metabolic interactions under extreme conditions

Duke University, Durham NC

Investigators

Abstract

This goal of this research is to determine how microbes living in extreme conditions communicate metabolically. Microbial extremophiles are remarkable examples of life’s resilience, thriving in hot springs at boiling temperatures, in brine lakes saturated with salt, and in deserts once thought to be sterile. This project uses extremophiles that live in high salt as a test system to map and model how nutrients flow through microbial communities, enabling resilience during times of food scarcity. The metabolism of salt-adapted microbes is poorly understood but produces chemicals and enzymes of interest to biotechnology. The proposed research is therefore expected to reveal general principles of biological resilience and present novel approaches for future industrial applications of extremophile metabolic products. These activities will enable a transition in the PI's research direction from molecular experiments in pure laboratory cultures to field ecology and metabolic modeling. The goal of the education plan is to foster inclusive learning experiences that span disciplinary lines. Together with students and postdocs from her group, the PI will form “co-learning teams" in which the team leader learns, alongside students in the field, how to sample and collect data. In these vertically integrated teams, the perspective that everyone is learning together is expected to lessen power dynamics and promote a positive research culture where all team members feel welcome and valued. The proposed research tests the hypothesis that hypersaline microbial communities interact to maintain stability despite changes in salinity and nutrient availability. Hypersaline-adapted archaea, or halophiles, provide a unique model for investigating the metabolic interactions in microbial communities. Member species share a common hypersaline habitat but exhibit extensive diversity in how they generate energy. Nutrients are intermittently available in hypersaline lakes during seasonal variation, resulting in severe energy stress. In response, halophiles have evolved a wide array of possible metabolic solutions to survive on the same pool of scarce resources. Hypersaline microbial communities have great potential to reveal general principles of community resilience to environmental perturbation. However, knowledge regarding the mechanisms of community interactions remain largely uncharacterized. In the proposed work, the PI and collaborators address these questions by pursuing the following objectives: (a) constructing constraint-based models for hypersaline communities to explain and predict metabolic interactions; (b) sampling the Great Salt Lake microbial communities over temporal and spatial gradients to test model predictions; (c) testing model predictions in synthetic communities grown in the lab under ecologically relevant conditions. To accomplish these aims, a comprehensive Professional Development Plan is proposed, including intensive study in metabolic modeling and training in field ecology during trips to the Great Salt Lake. The proposed models are expected to enable highly accurate predictions of flux distributions in microbial communities. This research enables the PI to launch a new and exciting research direction, building on prior work that discovered mechanisms of transcriptional regulation of metabolic networks in archaeal extremophiles. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.