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

二甲基硫醚的海洋微生物降解：通过对模型生物应用后基因组方法来理解过程

基本信息

批准号：
NE/E013333/1
负责人：
Hendrik Schaefer
金额：
$ 62.01万
依托单位：
University of Warwick
依托单位国家：
英国
项目类别：
Fellowship
财政年份：
2007
资助国家：
英国
起止时间：
2007 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=NE%2FE013333%2F1
关键词：
Marine microbial degradation dimethylsulfide Process

项目摘要

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.

二甲基硫（DMS）是一种有助于气候调节的大气痕量气体。这种气体的氧化产物通过将热辐射反向散射到太空中来充当气候冷却剂。它们还影响云的凝结，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。大气中二甲硫醚的主要来源是海洋环境，它是由各种微型藻类和海藻的细胞成分形成的。然而，大多数可通过海洋向空气转移的二甲硫醚会被海水中的细菌迅速降解，因此不会从海洋中排放。申请人先前的工作已经表明，与嗜甲基菌相关的细菌与海洋中的DMS降解具有环境相关性，并且具有未表征的DMS降解途径。因此，甲基噬菌体（可能还有海水中的其他类似细菌）的二甲基硫降解活动正在影响全球气候，因为它们阻止了更多的二甲基硫从海洋排放到大气中。为了更好地了解这些细菌的生理学，需要更详细地描述对Methylophaga中DMS降解至关重要的酶和基因。这将通过对一个嗜甲基菌属分离株进行基因组测序（目前正在进行中，数据将于2007年提供）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在DMS上生长期间由该细菌诱导的特定酶。酶将被纯化以检测它们的活性，编码这些酶的基因将被敲除，它们的调节将被研究。这些补充战略将导致详细了解二甲硫醚降解这一模式生物。随后，将在环境样品中研究编码特定DMS降解酶的基因的分布。微生物学家面临的一个共同问题是，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解决这些问题，并允许在不需要培养的情况下识别环境样品中的生物体。当海水中的二甲硫醚降解细菌在二甲硫醚上生长时，它们将二甲硫醚中的碳纳入其生物量。通过在海水样本中掺入同位素重的二甲基硫醚，这将使吸收二甲基硫醚的细菌的DNA比不吸收重二甲基硫醚的细菌的DNA重。随后，DMS同化细菌的“重”DNA可以与其他细菌（不同化DMS的细菌）的DNA物理分离。然后将应用一些分子生物学方法来鉴定使用重DNA同化DMS的细菌的物种组成。这也将包括其基因组DNA的测序。还将通过应用一种新的显微镜技术直接定量DMS同化细菌的数量，该技术可以检测同化重同位素的细胞。总之，对模式生物及其二甲硫醚降解酶和基因的分析将有助于了解二甲硫醚在与环境相关的海洋生物中的降解机制。将这些见解与环境中的有机体进行比较，将大大增进我们对海洋细菌如何影响海洋排放的二甲基硫醚数量的理解，而二甲基硫醚对于调节全球气候至关重要。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment.

与温带沿海环境中浮游植物大量繁殖相关的活性海洋甲基营养菌的底物特异性分支。

DOI：
10.1128/aem.01266-08
发表时间：
2008
期刊：
Applied and environmental microbiology
影响因子：
4.4
作者：
Neufeld JD
通讯作者：
Neufeld JD

Draft genome sequence of the chemolithoheterotrophic, halophilic methylotroph Methylophaga thiooxydans DMS010.

化学异养型、嗜盐甲基营养型甲基噬菌体 DMS010 的基因组序列草图。

DOI：
10.1128/jb.00388-11
发表时间：
2011
期刊：
Journal of bacteriology
影响因子：
3.2
作者：
Boden R
通讯作者：
Boden R

Microorganisms associated with Sporobolus anglicus, an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide.

DOI：
10.3389/fmicb.2022.950460
发表时间：
2022
期刊：
Frontiers in microbiology
影响因子：
5.2
作者：
通讯作者：

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment.

DOI：
10.1038/ismej.2015.37
发表时间：
2015-11
期刊：
The ISME journal
影响因子：
0
作者：
Eyice Ö;Namura M;Chen Y;Mead A;Samavedam S;Schäfer H
通讯作者：
Schäfer H

Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere.

DOI：
10.1038/ismej.2017.148
发表时间：
2018-01
期刊：
The ISME journal
影响因子：
0
作者：
Eyice Ö;Myronova N;Pol A;Carrión O;Todd JD;Smith TJ;Gurman SJ;Cuthbertson A;Mazard S;Mennink-Kersten MA;Bugg TD;Andersson KK;Johnston AW;Op den Camp HJ;Schäfer H
通讯作者：
Schäfer H