UC San Diego

Microbial communities play a key role in the natural environment. However, the study of these communities if often limited by the inability to cultivate individual community members. Although culture-independent meta-level analyses are useful for establishing the basic structure of the community, they often mask the role individual species fulfill within the community, stymieing our ability to understand and thus manipulate the community phenotype. Within this dissertation, microbial communities involved in global carbon cycling are studied from a species-centric perspective. First, the ferric uptake regulator (Fur) is studied in Fe(III)-reducing Geobacter sulfurreducens, a common member of subsurface soil environments. Chromatin immunopreciptation was utilized to establish the genome-wide binding profile of Fur. This dataset coupled with gene expression datasets derived from a variety of iron conditions was used to elucidate the iron stimulon and Fur regulon of G.sulfurreducens. Additional physiological and transcriptional analyses of G. sulfurreducens grown with various Fe(II) concentrations revealed the depth of Fur's involvement in energy metabolism. Next, single cell de novo sequencing and metatranscriptomics was used to reveal the intricate metabolic interactions of a 15-year-old alkane-degrading methanogenic consortium. The methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus far unknown biochemical process. The genome sequence of a dominant bacterial member belonging to the family of Syntrophace was sequenced and served as the basis for metabolic reconstruction. Metatranscriptomic data highlighted metabolically active genes of this bacterium. Subsequent genome analysis assisted in the identification of critical genes and pathways involved in anaerobic alkane metabolism. When perturbed by butyric or caprylic acid, the species composition of the alkane- degrading community shifts to accommodate the change. Although some species persist and remain active despite the shift, major ecological succession by these dormant microbes leads to a new, stable community optimized to digest the newly added substrate. The final chapter of this thesis describes the study of these poorly characterized genera from the species perspective using metagenomic binning, metatranscriptomics, and metabolic modeling. Subsequent community analysis revealed that energetic requirements, amino acid auxotrophies, and strategic antimicrobial usage all contribute to the robustness of the community. Collectively, these results suggest that the multidimensional interactions utilized by natural communities bolster their stability during environmental perturbation and promote the maintenance of high species richness