Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment.
Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment.
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DOI：
10.1038/s41396-018-0269-8
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发表时间：
2019-03
期刊：
影响因子：
--
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
Jameson E;Stephenson J;Jones H;Millard A;Kaster AK;Purdy KJ;Airs R;Murrell JC;Chen Y
沿海盐沼沉积物是天然甲烷排放的重要来源，其中大部分来自季胺和甲基胺，例如胆碱和三甲胺。在本研究中，我们将 DNA 稳定同位素探测与 16S rRNA 基因和富含 13C2 胆碱的宏基因组的高通量测序相结合，然后进行宏基因组数据组装，以确定负责胆碱产甲烷作用的关键微生物。与 13C2-胆碱一起孵育的微观世界导致三甲胺的形成和随后的甲烷产生，这表明胆碱依赖性产甲烷是一个以三甲胺为关键中间体的两步过程。扩增子测序分析确定 Pelobacter 属的 Deltaproteobacteria 是主要的胆碱利用者。甲烷球菌属的产甲烷古菌在胆碱修饰的微观世界中富集，表明它们在三甲胺形成甲烷中的作用。宏基因组 DNA 的分类导致分类为 Pelobacter 和 Methanococcoides 的分类的识别。对这些箱的分析表明，Pelobacter 具有利用胆碱-三甲胺裂解酶途径将胆碱降解为三甲胺的遗传潜力，而甲烷球菌能够利用含有吡咯赖氨酸的三甲胺甲基转移酶途径产生甲烷。总之，我们的数据提供了关于沿海沉积物中胆碱利用生物多样性的新见解，并支持细菌和古细菌之间的互养关系，作为该环境中胆碱产甲烷的主要途径。
Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.
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DOI：
10.1038/ismej.2015.37
发表时间：
2015-11
期刊：
The ISME journal
影响因子：
--
作者：
Eyice Ö;Namura M;Chen Y;Mead A;Samavedam S;Schäfer H
通讯作者：
Schäfer H
影响因子：
5.2
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影响因子：
2.7
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影响因子：
4.8
作者：
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Tars, Kaspars
DOI：
10.1099/ijs.0.058289-0
发表时间：
2014-06-01
影响因子：
2.8
作者：
L'Haridon, Stephane;Chalopin, Morgane;Toffin, Laurent
通讯作者：
Toffin, Laurent