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Title: Development and Integration of Genome-Enabled Techniques to Track and Predict the Cycling of Carbon in Model Microbial Communities

The primary objective of this project was to establish widely applicable, high-throughput “omics” methods for tracking carbon flow in microbial communities at a strain-resolved molecular level. We developed and applied these methods to study a well-established microbial community model system with a long history of “omics” innovation: chemoautotrophic biofilms grown in an acid mine drainage (AMD) environment. The methods are now being transitioned (in a new project) to study soil. Using metagenomics, stable-isotope proteomics, stable-isotope metabolomics, transcriptomics, and microscopy, we tracked carbon flow during initial biofilm growth involving CO 2 fixation, through the maturing biofilm community consisting of multiple trophic levels, and during an anaerobic degradative phase after biofilms sink. This work included explicit consideration of the often overlooked roles of archaea and microbial eukaryotes (fungi) in carbon turnover. We also analyzed where the eosystem begins to fail in response to thermal perturbation, and how perturbation propagates through a carbon cycle. We investigated the form of strain variation in microbial communities, the importance of strain variants, and the rate and form of strain evolution. Overall, the project generated an array of new, integrated ‘omics’ approaches and provided unprecedented insight into the functioning of a natural ecosystem. This project supported graduatemore » training for five Ph.D. students and three post doctoral fellows and contributed directly to at least 26 publications (two in Science).« less
  1. Univ. of California, Berkeley, CA (United States)
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Technical Report
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Univ. of California, Berkeley, CA (United States)
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United States