UC Santa Barbara

Macroalgae are important primary producers in the ocean and form expansive underwater forests to support diverse organisms in the ecosystem. They also contribute to a large amount of carbon export below the euphotic zone and carbon sequestration in the deep ocean in the form of detritus. As a result, there is an increasing number of studies suggesting long-term storage of carbon in macroalgae as a carbon dioxide removal strategy to mitigate climate change. However, in contrast to the growing attention of macroalgae as one of the blue carbon ecosystems, the fate of macroalgal-derived carbon after entering the deep ocean remains largely unexplored. Polysaccharides are a major component of both living and detrital macroalgae, and the degradation of these complex polymers is an important process for the turnover of carbon in the ocean. Macroalgal polysaccharides have diverse structures varying significantly in their monomeric saccharides, glycosidic linkages, branching sites, and modifications by chemical groups like sulfate. Therefore, the degradation of macroalgal polysaccharides requires an extensive number of enzymes produced by microorganisms specialized in this process. Carbohydrate-active enzymes (CAZymes) and sulfatases are the key enzymes typically organized in polysaccharide utilization loci (PULs) that mediate a cascade of pathways to degrade polymers to oligosaccharides and eventually to monosaccharides. However, we still have knowledge gaps in the details of the degradation processes and the various enzymes involved. In this dissertation, approaches like cultivation, genomic, and transcriptomic sequencing were applied to study the microbial degradation of macroalgal polysaccharides from cultures grown in the laboratory to marine sediments collected in the deep Santa Barbara Basin. A novel anaerobic bacterial strain NLcol2 was isolated from microbial mats in sediments offshore Santa Barbara, California, USA, and the name Pontiella agarivorans sp. nov. was proposed. It is the fifth cultivated representative in the phylum Kiritimatiellota with the ability to degrade macroalgal polysaccharides including agar and iota-carrageenan and is the first strain reported to be capable of nitrogen fixation. More than 10% of its genome also encodes CAZymes, sulfatases and nitrogenases that facilitate these metabolisms. To further study the enzymes and pathways involved in macroalgae degradation, a transcriptomic study was performed on strain NLcol2 growing with macroalgal polymers of agar and dried seaweeds compared with the monosaccharide D-galactose as control condition. During the growth of strain NLcol2 on polymers, 55% of the genome was expressed differentially, among which many CAZymes and sulfatases involved in the degradation pathways were significantly up-regulated. 12 putative PULs were identified and a selfish mechanism for agar degradation was proposed. The highly expressed genes involved in flagella formation and capsule polysaccharide synthesis with growth on seaweeds could promote motility and biofilm formation for better access and attachment to seaweed particles. To explore the ecological role of P. agarivorans and its relatives in the natural marine environment and to investigate the microbial communities enriched in kelp detritus on the seafloor, marine sediments with and without kelp detritus were sampled in the deep Santa Barbara Basin. The 16S rRNA gene survey showed an enrichment of phyla (Bacteroidota, Spirochaetota, Desulfobacterota, Campylobacterota, Verrucomicrobiota etc.) in kelp-laden sediments with cultivated relatives specializing in polysaccharide degradation, dissimilatory sulfate reduction and nitrogen fixation. Close relatives of P. agarivorans are widely distributed across the basin in low abundance in general but exhibited a high relative abundance in carbon-rich sediments with kelp detritus and at shallower depths. These microbial communities together contribute to the coupled biogeochemical cycling of carbon, sulfur, and nitrogen in the Santa Barbara Basin sediments in low oxygen conditions.