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

二甲基硫化物（DMS）是一种大气微量气体，有助于气候调节。这种气体的氧化产物通过将热辐射反向散射到太空中而起到气候冷却剂的作用。它们还会影响云的凝结，改变云的反射特性，从而减少到达地球表面的光量，从而产生冷却效果。大气DMS的主要来源是海洋环境，它是由各种微观藻类和海藻的细胞成分形成的。然而，大多数可用于海洋到空气转移的DMS会被海水中的细菌迅速降解，因此不会从海洋中排放出来。申请人之前的工作表明，与甲基噬菌相关的细菌与海洋中DMS降解的环境相关，并且具有未表征的DMS降解途径。因此，噬甲基细菌（可能还有海水中的其他类似细菌）的DMS降解活动正在影响全球气候，因为它们阻止了更多的DMS从海洋排放到大气中。为了更好地了解这些细菌的生理机能，需要对甲基噬菌中DMS降解的关键酶和基因进行更详细的表征。这将通过甲基噬菌分离物的基因组测序（目前正在进行中，数据将于2007年获得）和基因组序列分析来实现。基因组序列将允许比已经实现的更详细地鉴定由该细菌在DMS上生长期间诱导的特定酶。酶将被纯化以表征其活性，编码这些酶的基因将被敲除，它们的调控将被研究。这些互补的策略将导致对这种模式生物中DMS降解的详细了解。随后，将研究编码特定dms降解酶的基因在环境样品中的分布。微生物学家面临的一个普遍问题是环境中存在的大多数细菌无法培养。因此，微生物学家使用分子生物学技术来规避这些问题，并允许在不需要培养的情况下识别环境样本中的生物体。当海水中的DMS降解细菌在DMS上生长时，它们会将DMS中的碳吸收到它们的生物量中。这将通过在海水样品中加入同位素重的DMS来开发，这将使吸收DMS的细菌的DNA比那些不吸收重DMS的细菌的DNA重。随后，吸收DMS的细菌的“重”DNA可以从其他细菌的DNA（不吸收DMS）中物理分离出来。然后将应用许多分子生物学方法来描述利用重DNA吸收DMS的细菌的物种组成。这也将包括对他们的基因组DNA进行测序。通过应用一种新的显微镜技术，可以检测吸收重同位素的细胞，还将对吸收dms的细菌数量进行直接量化。综上所述，对模式生物及其降解DMS的酶和基因的分析将有助于了解DMS在环境相关海洋生物中的降解机制。将这些见解与环境中的生物进行比较，将大大增强我们对海洋细菌如何影响海洋排放的DMS量的理解，这对全球气候的调节很重要。

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.