Towards Modeling of Methane Recycling Lake Washington Microbial Community

The ability to understand and manipulate biological communities is increasingly becoming important as these communities have the capability to address global problems in regards to energy, food, and disease. However, there is still a necessity to adopt a systems-level approach in this regard. The long-term goal of this project is to first better understand the functionality of a microbial community and then design a synthetic community through constructing a multi-faceted approach similar to the ‘biobricks’ method of standardizing biological parts. This approach will characterize the functionality of a microbial strain, its interaction with other members in the community, and ultimately, a specific goal such as over producing a desired product can be achieved by adding, removing, or changing the population of specific strains. The community that this project is interested in is Lake Washington (a fresh lake) community characterized by methane cycling. This community is of interest due to its ability to use sedimentary methane as an energy and carbon source. To achieve this goal, genome-scale metabolic models (GSM) need be reconstructed to understand the role of individual strains in the community and also characterize the interactions between individual strains. Thus far, the draft model for methane-oxidizer Methylobacter Tundripaladum (mbT702), has been reconstructed which has 702 genes, 1298 metabolites, 1167 reactions. Then, flux balance analysis (FBA) and flux variability analysis (FVA) are utilized to identify gaps, errors, and inconsistencies within the draft model as well as optimizing the biomass for the model. These will then be manually fixed through the utilization of literature and gap filling techniques. In addition, a model of another major-player in the Lake Washington community, Methylomonas, will be reconstructed. Our next goal is to use the reconstructed models to construct and analyze a two-member microbial community.