Submitted by Mary K. FIRESTONE on
Most microorganisms live in biofilms composed primarily of extracellular polysaccharides. Polysaccharide biosynthesis is an important part of microbial physiology as well as a substantial fraction of carbon flux in many ecosystems. In soil in particular, microbial polysaccharides constitute upwards of half of soil organic carbon and polysaccharide production mediates agronomic and ecologically relevant soil properties, including water retention and nutrient availability. The research work described below is part of a larger project to predict polysaccharide classes produced by soil microbes from environmental-DNA derived genomes, and to quantify population-specific polysaccharide production under a range of experimental conditions.
Project Description:
The project will begin by surveying the diversity of extracellular polysaccharide biosynthetic gene clusters in soil microbial genomes. This will require curating a set of reference genomes of common soil microbial organisms from cultured and uncultured taxa. We will identify polysaccharide biosynthesis gene clusters using existing pipelines and analyze what features of biosynthetic gene clusters suggest the structures of their products, based on relationships to operons of known polysaccharides and latent features of machine learning models of polysaccharide gene cluster structure and diversity. Student will be working with Alex Greenlon a post doctoral scholar in the Firestone and Banfield labs.
The proposed SPUR project will be entirely computational. The student researcher will be primarily responsible for assembling and curating a reference set of soil microbial genomes from microbial cultures as well as metagenomic databases, as well as for documenting polysaccharide biosynthetic gene cluster annotations for structurally-characterized extracellular polysaccharides. There will also be opportunities to participate in writing code to execute annotations of polysaccharide synthesis and analyze gene-content composition of polysaccharide biosynthesis clusters related to know diversity.
Potential student researchers should have familiarity with molecular biology and an interest or background in soil science and microbial ecology. Prior experience with programming languages including at least one of python, r, unix shells or willingness to learn.