<p>This thesis details a study of saprophytic competence in the Gram-negative bacterium Sinorhizobium meliloti, and comprises three main areas of research. The B-ketoadipate pathway is required for the catabolism of a wide range of aromatic compounds that are released into soil through the degradation of lignin. We demonstrate that S. meliloti encodes enzymes associated with the protocatechuate branch of the B-ketoadipate pathway within two operons (pcaDCHGB and pcaIJF) whose expression is regulated by the LysR-protein PcaQ and the IclR-type regulator PcaR, respectively. We show that purified PcaQ recognizes a motif with partial dyad symmetry (5' ATAACCN4-GGTTAA 3') positioned upstream of the pcaD promoter, and that this site is required for the regulated expression of pcaD in vivo. We report that PcaQ also regulates the expression of a protocatechuate-inducible ABC-type transport system that we infer is involved in the uptake of this aromatic acid, and we extend this analysis to identify PcaQbinding motifs in the genomes of a-,B-, and y-proteobacteria. </p> <p>In addition to protocatechuate, S. meliloti may utilize hydroxyproline as an energy source, as this amino acid is released into soil during the natural decay of plant tissue. We demonstrate that S. meliloti encodes a hydroxyproline-inducible ABC-type transport system that mediates the uptake of trans-4-hydrox-L-proline, as determined via growth and transport assays. </p> <p>As a more comprehensive method of examining saprophytic competence, we assayed the growth of S. meliloti upon inoculation into sterile bulk soil. We screened 40 S. meliloti strains carrying deletions within the pSymA or pSymB megaplasmids for growth in soil, and report that the majority of strains establish a stable population (greater than or equal to 10^8 cells g^(-1) soil) that persists for several weeks. In contrast, two S. meliloti strains exhibited a decreased ability to colonize soil, indicating that loci within the deleted regions play a role in saprophytic competence. </p> / Thesis / Doctor of Philosophy (PhD)