Quantitative analysis of bacterial DMSP-degrading gene diversity, abundance, and expression in marine surface water environments
Varaljay, Vanessa Ann
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Dimethylsulfoniopropionate (DMSP) is an algal-derived sulfur compound degraded by marine bacterioplankton in surface waters via two competing mechanisms: (1) DMSP cleavage that produces the climatically-relevant sulfur gas dimethylsulfide (DMS); and (2) DMSP demethylation that produces less-volatile intermediates used for amino acid synthesis or energy. Given the implications for climate, the discovery of the genes mediating the first steps in each pathway, dddP (DMSP cleavage) and dmdA (DMSP demethylation), provided the basis to quantify the diversity, abundance, and expression of this genetic capability in the environment. Using an in silico pipeline based on marine metagenomic data, 10 primer sets for environmental clades of dmdA were iteratively optimized to target sequences in a southeastern U.S. coastal ocean. Using pyrosequencing, >700 total sequence clusters (~90% sequence similarity) were retrieved and thousands of sequences per primer exhibited specificity to the correct group, signifying the importance of environmental sequence data in primer design. The vetted primer sets were used in quantitative PCR in the North Pacific Ocean over 10 months in the upper and lower euphotic zones. DMSP-degrading genes were more abundant at the surface (maximum of ~16% (dmdA) and ~2% (dddP) of cells harboring a gene), consistent with higher DMSP concentrations, temperature, and solar radiation. The dmdA pool was dominated by genes from the SAR11 clade with lesser but consistent contributions of roseobacters and Gammaproteobacteria. In Monterey Bay, an autonomous sampling instrument captured near-daily abundance and expression of DMSP-degrading genes from two taxa, roseobacters (dmdA and dddP) and SAR11 (dmdA) during highly variable DMSP concentrations due to sequential phytoplankton blooms. SAR11 genes were more abundant than Roseobacter genes, but expression levels per gene were lower, particularly in particle-associated vs. free-living fractions. Expression ratios for all genes were best correlated with particulate DMSP relative to the total phytoplankton pool, a proxy for high-DMSP-producing phytoplankton. Overall, PCR analysis with environmentally-relevant primer sets indicated DMSP-degrading genes are abundant in marine surface waters. Taxon-specific spatial and temporal trends in gene diversity, abundance, and expression in association with DMSP, phytoplankton, and other environmental variables were observed, providing new insights into the bacteria that cycle sulfur in the surface ocean.