Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS)

The marine Roseobacter clade bacteria comprise up to 20% of the microbial community in coastal surface seawater. Marine Roseobacter clade bacteria are known to catalyse some important biogeochemical transformations in marine carbon and sulfur cycles. Using a comparative genomic approach, this study revealed that many marine Roseobacter clade bacteria have the genetic potential to utilize methylated amines (MAs) as alternative nitrogen sources. These MAs represent a significant pool of dissolved organic carbon and nitrogen in the marine environment. The marine Roseobacter clade bacterial genomes also encode full sets of genes providing them with the potential to generate energy from complete oxidation of the methyl groups of MAs. Representative species of the marine Roseobacter clade were tested and their abilities to use MAs are directly linked to the presence in their genomes of genes encoding key enzymes involved in MA metabolism, including trimethylamine monooxygenase (tmm) and gamma-glutamylmethylamide synthetase (gmaS). These two genes were chosen as functional markers for detecting MA-utilizing marine Roseobacter clade bacteria in the environment. PCR primers targeting these two genes were designed and used successfully to retrieve corresponding gene sequences from MA-utilizing isolates of the marine Roseobacter clade, as well as directly from DNA extracted from surface seawater obtained from Station L4 off the coast of Plymouth, UK. Taken together, the results suggest that MAs may serve as important nitrogen and possibly energy sources for marine Roseobacter clade bacteria, which helps to explain their global success in the marine environment.