CBIOMES Project: Constraint-based Modeling of Marine Microbial Community Metabolism and Physiology
Marine microbial communities mediate the transformations of Earth’s major bioelements through an intricate web of inorganic and organic ‘conduits,’ connecting microbes to microbes, and connecting microbes to global biogeochemical cycles. Within the SC-CBIOMES project, my objective is to identify and quantify the fluxes through each conduit within and between the numerically dominant microbial taxa of the oligotrophic ocean gyres: Prochlorococcus, Synechococcus, Crocosphaera, SAR11 and Roseobacter. Genome-scale metabolic networks, detailed and stoichiometrically balanced networks of the many biochemical transformations within a cell, will be reconstructed from the ‘pangenomes’ of each taxonomic group. From each pangenome, hundreds of randomized in silico strains and sequenced strains will be reconstructed in an effort to capture the phylogenetic, physiological and metabolic microdiversity within each group. By leveraging laboratory and field data, including environmental ‘omics datasets, realistic simulations will be designed to predict the winners and losers within the broad environmental niche spaces they occupy. Using a convex optimization approach (dynamic flux balance analysis and its family of variants) to predict fluxes and growth rates within and between each network, the costs and benefits associated with metabolic interactions of in silico representatives of microbial consortia will be quantified. Ultimately, reduced-complexity metabolic models will be designed to complement ecosystem-scale modeling approaches developed within the SC-CBIOMES project.
John R. Casey is a postdoctoral fellow in the Department of Earth, Atmospheric and Planetary Sciences at the Massachusetts Institute of Technology. He received his B.S. at the College of Charleston in 2007 and received his Ph.D. from the University of Hawai’i in 2017.
Casey’s research focuses on microbial oceanography, especially in the fundamental principles guiding the organization and function of microbial metabolisms and their influence on marine ecosystems and biogeochemical cycles. Combining observations, experimental approaches and emerging computational methods, Casey has made contributions to the understanding of long-term microbial community dynamics, of patterns underlying heterotrophic growth and respiration of dissolved organic matter, and the metabolism of Prochlorococcus, a globally important cyanobacterium. Casey is developing and applying optimization tools to integrate environmental, physiological and multi-‘omics measurements from cultivated and natural microbial communities into a network-based computational framework. By expanding network coverage of the metabolic functional diversity, and by exploring the thermodynamic objectives of microbial growth, he is working to develop quantitative systems-level predictions of phenotypes, activities and interactions within marine microbial communities.