Towards an understanding of methylotrophic methane production in anoxic coastal sediments

甲烷是一种强大的温室气体，对全球变暖有重大贡献。海岸沉积物是一种动态的生态系统，具有大量的甲烷生产。然而，我们对这些生态系统中产生甲烷的微生物的多样性知之甚少。这阻碍了我们理解在不断变化的环境条件下沿海沉积物中甲烷的产生是如何调节的，也阻碍了我们开发模型来准确预测气候变化下未来全球甲烷的收支。沿海沉积物中甲烷产生的主要途径是甲基化化合物的微生物降解，主要是甲醇、三甲胺（TMA）和二甲硫醚（DMS）。这些化合物在环境中非常丰富，因此导致大量甲烷的产生。我们最近发现，这些化合物在河口和盐沼沉积物中的甲烷生产的贡献可能被低估，几种不同的微生物在这些沉积物中将TMA和DMS转化为甲烷。然而，我们不知道哪些微生物积极地将这些丰富的甲基化化合物转化为甲烷。这限制了对这一过程的代谢途径以及这些途径如何受环境条件（例如温度和盐度）调节的进一步研究。在本项目中，我们的目标是揭示缺氧海岸沉积物中降解甲醇，TMA和DMS为甲烷的活性微生物的身份。这不仅将为全球甲烷生产开辟新的研究途径，而且还将允许开发模型来预测缺氧沿海沉积物中未来的甲烷生产。我们非常适合这项研究，因为：-我们表明甲醇，TMA和DMS在一系列缺氧沉积物中降解为甲烷。- 我们研究了缺氧沉积物中甲烷产生的关键基因，使我们能够确定潜在的微生物多样性。我们开发并广泛使用了先进的微生物学工具，如稳定同位素探针，以满足本研究的需要。定量分析缺氧海岸沉积物中甲醇、TMA、DMS和甲烷的浓度：我们将定量分析河口、海岸湿地和盐沼沉积物中甲醇、TMA、DMS和甲烷浓度的深度分布。这将显示每种化合物在取样点的重要性。这将使我们能够设计稳定同位素探测（SIP）实验（目标2）。确定在缺氧的沿海沉积物中积极降解甲醇，TMA和DMS为甲烷的产甲烷菌：我们将使用我们开发的SIP测序方法来阐明降解甲醇，TMA和DMS为甲烷的活性微生物的身份。我们将用13 C-甲醇、13 C-TMA和13 C-DMS对样品进行修饰，并跟踪13 C掺入降解这些化合物的微生物的遗传物质（DNA）中。对13 C标记的DNA进行测序，我们将获得有关这些微生物身份的前所未有的细节。确定缺氧沉积物中活性甲基营养型产甲烷菌的全球分布模式：使用生物信息学工具，我们将在公开的序列数据集中搜索我们在目标2中确定的活性产甲烷菌的遗传标记。这将包括来自海洋和沿海生态系统的几个先进的序列数据集。研究结果将揭示全球缺氧沉积物中降解甲醇、TMA和DMS的优势产甲烷菌的全球分布，并将回答关于沿海沉积物中普遍存在的化合物降解为甲烷的活性微生物的身份及其全球分布模式的关键问题。这项研究计划的结果将为未来的研究铺平道路，这些研究将重点关注这些关键微生物物种的代谢以及它们如何应对不断变化的环境条件。这将有助于开发模型，更好地预测未来气候变化中的甲烷产量。

Methane is a powerful greenhouse gas which significantly contributes to global warming. Coastal sediments are dynamic ecosystems with substantial methane production. Yet, we know very little about the diversity of microbes producing methane in these ecosystems. This prohibits our understanding of how methane production in coastal sediments is regulated under changing environmental conditions and the development of models for accurate prediction of the future global methane budget under climate change. The major route to methane production in coastal sediments is the microbial degradation of methylated compounds, mainly methanol, trimethylamine (TMA) and dimethylsulfide (DMS). These compounds are highly abundant in the environment therefore lead to the production of substantial amount of methane. We recently found that the contribution of these compounds to the methane production in estuarine and saltmarsh sediments is likely underestimated and several different microbes convert TMA and DMS to methane in these sediments. Yet, we do not know which microbes actively convert these abundant methylated compounds to methane. This limits further research on the metabolic pathways of this process and how these pathways are regulated by environmental conditions (e.g. temperature and salinity). In this project, we aim to reveal the identity of the active microbes degrading methanol, TMA and DMS to methane in anoxic coastal sediments. This will not only open up new research avenues on global methane production but will also allow to develop models to predict future methane production in anoxic coastal sediments.We are well suited for this study, because:-we showed methanol, TMA and DMS are degraded to methane in a range of anoxic sediments. -we studied the key gene in methane production in anoxic sediments, allowing us to pinpoint the underlying microbial diversity.-we developed and used extensively the advanced microbiology tools such as stable isotope probing required for this study.Our objectives:1. Quantify the concentrations of methanol, TMA, DMS and methane in anoxic coastal sediments: We will quantify the depth distribution of methanol, TMA, DMS and methane concentrations in estuarine, coastal wetland and saltmarsh sediments. This will show the significance of each compound at sampling sites. This will enable us to design the stable isotope probing (SIP) experiments (Objective 2).2. Identify the methanogens that actively degrade methanol, TMA and DMS to methane in anoxic coastal sediments: We will use the SIP-sequencing approach that we developed to elucidate the identity of active microbes that degrade methanol, TMA and DMS to methane. We will amend the samples with 13C-methanol, 13C-TMA and 13C-DMS, and follow the incorporation of 13C into the genetic material (DNA) of microbes degrading these compounds. Sequencing the 13C-labelled DNA, we will obtain unprecedented detail about these microbes' identity.3. Determine the global distribution patterns of active methylotrophic methanogens in anoxic sediments: Using bioinformatics tools, we will search the publicly available sequence datasets for genetic markers from the active methanogens that we identify in Objective 2. This will include several advanced sequence datasets from marine and coastal ecosystems. Results will reveal the global distribution of dominant methanogens that degrade methanol, TMA and DMS in anoxic sediments across the world.This project will answer critical questions as to the identity of the active microorganisms degrading ubiquitous compounds to methane in coastal sediments as well as their global distribution patterns. The outcome of this research programme will pave the way for future research that would focus on the metabolism of these key microbial species and how they response to changing environmental conditions. This will allow developing models for better prediction of future methane production in a changing climate.