Genomic and Physiological Characterization of Lignin-Derived Aromatic Catabolism Pathways in Roseobacters

Lignin provides vascular plants with structural rigidity and is the most abundant aromatic polymer on Earth. Lignin is rich in phenolic structures and its structural complexity contributes to its biological recalcitrance, yet it is susceptible to degradation via microbial enzymes. Biogeochemically relevant marine bacteria in the Roseobacter clade are capable of transforming lignin and mineralizing lignin-derived aromatic monomers. Roseobacters are prevalent in temperate and polar oceans, marine sediments, sea ice, and hydrothermal vents, and representatives are readily cultivated in the lab. Roseobacter abundances are frequently highest in coastal oceans, including the salt marshes of the Southeastern United States, where the dissolved organic carbon pool is enriched in aromatic moeities. This dissertation provides new insight into the aromatic compound catabolism potential by members of the Roseobacter lineage through both genomic analyses of publicly available genome sequences and genetic and physiological characterization of the Roseobacter strain Sagitulla stellata. Approximately 85% of the 311 Roseobacter genomes analyzed in this study have genes that encode for enzymes for at least one ring-cleaving pathway. These findings highlight the prevalence of this trait amongst lineage members, but also revealed little correlation between phylogeny, based on 89 conserved protein sequences, and genomic potential. Laboratory-based studies focused on the ligninolytic Roseobacter, S. stellata, with an emphasis on pathways mediating the degradation of the hydroxycinnamates (HCAs) ferulate and p-coumarate, which are important for cross-linking in lignin. Two genes annotated as feruloyl-CoA-synthases, enzymes that catalyze the first step of HCA degradation, were found to have overlapping specificities for the two HCAs in S. stellata, highlighting a functional redundancy not yet reported for other aromatic compound degrading bacteria. Additional studies were performed to examine the physiological response of S. stellata to mixtures of aromatic monomers. A series of studies performed with binary mixtures of aromatic compounds revealed a strong substrate preference for HCAs and their catabolic intermediates relative to benzoate. Collectively, these data indicate S. stellata is adapted to growing on a mixture of lignin-derived aromatics, which would be advantageous in the aromatic compound-rich salt marshes in which it and its relatives are found.