Marine microbial degradation of dimethylsulfide: Process understanding through application of postgenomic approaches to a model organism

Dimethylsulfide (DMS) is an atmospheric trace gas that contributes to climate regulation. Oxidation products of this gas act as climate cooling agents by backscattering heat radiation into space. They also effect cloud condensation and alter the reflective properties of clouds which reduces the amount of light that reaches the Earth's surface which has a cooling effect. The main source of atmospheric DMS is the marine environment where it is formed from cellular constituents of a variety of microscopic algae and seaweeds. However, most of the DMS that is available for sea-to-air transfer is quickly degraded by bacteria in seawater and therefore is not emitted from the oceans. Previous work by the applicant has shown that bacteria related to Methylophaga are environmentally relevant for DMS degradation in the ocean and have an uncharacterised pathway of DMS degradation. The DMS-degrading activities of Methylophaga bacteria (and possibly other similar bacteria in seawater) are therefore influencing global climate, since they prevent additional DMS being emitted from the oceans into the atmosphere. In order to better understand the physiology of these bacteria, the enzymes and genes that are key to DMS degradation in Methylophaga need to be characterised in more detail. This will be achieved by genome sequencing of a Methylophaga isolate (currently in progress, data will be available in 2007) and analysis of the genome sequence. The genome sequence will allow in more detail than has already been achieved the identification of specific enzymes that are induced by this bacterium during growth on DMS. Enzymes will be purified to characterise their activity and the genes encoding these enzymes will be knocked out and their regulation will be investigated. These complementing strategies will lead to a detailed understanding of DMS degradation in this model organism. Subsequently, the distribution of the genes encoding specific DMS-degrading enzymes will be studied in environmental samples. A common problem faced by microbiologist is that the majority of bacteria present in the environment cannot be cultured. Therefore, microbiologists use molecular biological techniques that circumvent some of these problems and that allow identification of organisms in environmental samples without the need to culture them. When DMS-degrading bacteria in seawater grow on DMS, they incorporate carbon from DMS into their biomass. This will be exloited by spiking seawater samples with an isotopically heavy version of DMS, which will render the DNA of DMS-assimilating bacteria heavier than that of those that did not assimilate heavy DMS. Subsequently the 'heavy' DNA of DMS-assimilating bacteria can be physically separated from the DNA of other bacteria (that did not assimilate DMS). A number of molecular biological methods will then be applied to characterise the species composition of bacteria that assimilated DMS using the heavy DNA. This will also include sequencing of their genomic DNA. A direct quantification of the number of DMS-assimilating bacteria will also be carried out by applying a new microscopy technique that can detect cells that assimilated heavy isotopes. In summary, the analyses of the model organism, and its enzymes and genes of DMS degradation will lead to understanding of the mechanism of DMS degradation in an environmentally relevant marine organism. The comparison of these insights to organisms in the environment will greatly enhance our understanding of how marine bacteria have an effect on the amount of DMS that is emitted from the oceans which is important for the regulation of global climate.