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.

二甲基硫化物（DMS）是一种有助于气候调节的大气痕量气体。该气体的氧化产物通过将热辐射降低到太空中作为气候冷却剂。它们还会影响云的冷凝并改变云的反射特性，从而减少了到达地球表面的光量，具有冷却效果。大气DM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。但是，大多数可用于海对空的DMS很快被海水中的细菌降解，因此不会从海洋中排放出来。申请人的先前工作表明，与甲基化的细菌在海洋中与DMS降解有关，并且具有DMS降解的未表征。因此，甲基果蝇细菌（以及海水中其他类似细菌）的DMS降解活性会影响全球气候，因为它们阻止了从海洋中发出的其他DMS。为了更好地了解这些细菌的生理学，需要更详细地表征甲基磷中DMS降解的酶和基因。这将通过基因组测序的甲基磷酸分离物测序（目前正在进行的，数据将在2007年提供）以及对基因组序列的分析。基因组序列将允许比已经实现的鉴定在DMS上生长过程中该细菌诱导的特定酶的鉴定。酶将被纯化以表征其活性，并将编码这些酶的基因被淘汰，并研究其调节。这些补充策略将导致对该模型生物体中DMS降解的详细理解。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常见问题是，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其中一些问题，并允许在不需要培养它们的情况下鉴定环境样品中的生物体。当DMS降解在DMS上的DMS降解细菌时，它们将DMS中的碳掺入其生物量中。这将通过尖峰的海水样品具有同位素重的DMS，这将使DMS相比细菌的DNA比没有吸收重型DM的细菌重。随后，DMS象征性细菌的“重” DNA可以从其他细菌的DNA物理分离（没有吸收DMS）。然后，将应用许多分子生物学方法来表征使用重DNA吸收DMS的细菌的物种组成。这还将包括对其基因组DNA的测序。直接量化DMS类似细菌的数量也将通过应用新的显微镜技术来检测吸收沉重同位素的细胞。总而言之，模型生物的分析及其DMS降解的酶和基因将导致对环境相关的海洋生物中DMS降解的机理的理解。这些见解与环境中生物体的比较将大大增强我们对海洋细菌如何对海洋发出的DMS产生影响的理解，这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）

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

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

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：

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

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