Linking sequence to function in microbial genomics

Abstract

Microbial genomes show high plasticity due to horizontal transfer, large community sizes, and rapid growth paired with adaptive mutations. Despite this mutability of gene content, most studies of microbial communities still rely on bulk, single-gene amplicon sequencing. In this thesis, I present methods that interrogate the gene content of single cells derived from complex natural communities. In the first project, I present a novel molecular biology method to link a bacterial functional gene to its host species with single-cell resolution. This high-throughput protocol is applied to assess the distribution of anaerobic respiration genes in a lake ecosystem. In the second project, I demonstrate extensions of this methodology to link genes between spatially proximal microbial cells, and apply this approach to probe the spatial organization of human dental plaque using DNA sequencing. In the final project, I completed whole-genome sequencing of environmental isolates derived from single, cultivable cells and employ mutational and horizontal transfer analysis to demonstrate adaptation to harsh environmental conditions in contaminated groundwater. These projects demonstrate the rich information stored within each microbial genome and the impact of spatial distribution in the environment. Each effort also contributes or highlights new molecular biology techniques to generate genomic data from individual microbial cells.