Metagenome data from DNA stable isotope probing of Stiffkey saltmarsh sediment microcosms to investigate methanogenesis from choline

Coastal saltmarsh sediments represent an important source of natural methane emissions, much of the methanogenesis originates from quaternary and methylated amines, such as choline and trimethylamine. However, the key microbes involved in choline-dependent methanogenesis remain poorly characterized and the metabolic pathways by which the saltmarsh microbes degrade choline and form methane are yet to be determined. In this study, we combined DNA stable isotope probing microcosms with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by binning of the microbial population genomes to identify the microbes responsible for methanogenesis. 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 identified Deltaproteobacteria, of the genera Pelobacter and Desulfuromonas were the major choline-utilizers. The methanogenic Archaea, of the genera Methanococcoides became enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of the microbial population genomes from metagenomic DNA resulted in the identification of bins that are classified as Pelobacter, Desulfuromonas, Methanococcoides and their associated viruses. Analyses of these bins revealed that Pelobacter and Desulfuromonas 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.

海岸盐沼沉积物是天然甲烷排放的重要来源，其中大部分甲烷生成起源于四元和甲基化胺类，例如胆碱和三甲胺。然而，参与胆碱依赖性甲烷生成的关键微生物尚缺乏详细表征，而盐沼微生物降解胆碱形成甲烷的代谢途径尚未明确。在本研究中，我们结合了DNA稳定同位素探针微生态系统与16S rRNA基因的高通量测序以及13C2-胆碱富集的宏基因组的高通量测序，随后对微生物种群基因组进行分箱，以识别负责甲烷生成的微生物。13C2-胆碱的微生态系统培养导致三甲胺的形成以及随后的甲烷产生，表明胆碱依赖性甲烷生成是一个涉及三甲胺作为关键中间体的两步过程。扩增子测序分析鉴定出德尔塔变形菌门，属于Pelobacter和Desulfuromonas属的细菌是主要的胆碱利用者。甲烷生成古菌，属于Methanococcoides属，在胆碱添加的微生态系统中富集，表明其在从三甲胺形成甲烷中的作用。从宏基因组DNA中微生物种群基因组的分箱导致了被分类为Pelobacter、Desulfuromonas、Methanococcoides及其相关病毒的箱子的识别。对这些箱子的分析揭示了Pelobacter和Desulfuromonas具有使用胆碱-三甲胺裂解酶途径降解胆碱为三甲胺的遗传潜力，而Methanococcoides则能够通过含有吡咯赖氨酸的三甲胺甲基转移酶途径进行甲烷生成。