OCE-PRF Biological methane sinks in the deep ocean: Linking genomic diversity and ecophysiology in syntrophic methane-oxidizing consortia

该奖项的全部或部分资金来自《2021年美国救援计划法案》(公法117-2)。微生物是每个生物地球化学周期背后的主力，它们控制着不同营养物质和其他化合物的可获得性。深海的甲烷渗漏就是这样一个系统，甲烷和其他气体从海洋沉积物中渗出，它们占全球甲烷预算的很大一部分。在这些渗漏处，不同的微生物群落茁壮成长，并能代谢从海底释放的甲烷。然而，人们对控制这些微生物分布的特定力量和过程以及它们执行重要新陈代谢的能力知之甚少。本项目研究甲烷降解系统中微生物多样性与环境之间的联系，重点是厌氧甲烷营养古菌(ANME)和硫酸盐还原细菌(SRB)的组合。这些结果将澄清微生物群落组成的基本决定因素，并提高对海洋甲烷动力学的理解。拟议的工作将以几种方式吸引更广泛的公众。来自STEM背景不足的本科生将通过加州理工大学的WAVE项目在暑期研究项目中得到指导。研究人员还将通过加州理工学院CTL；O办公室和环境微生物相互作用中心(CEMI)与当地的小学、高中和本科服务项目合作，鼓励学生参与与拟议工作相关的研究机会。通过ANSEP计划和孤儿实验室之间的现有合作，研究人员将参与ANSEP中学海洋科学职业探索计划。该项目旨在确定1)ANME/SRB伙伴的基因组多样性是如何在从单个联合体到环境梯度的范围内构建的，以及2)决定每个伙伴的生态结果的基因和生态因素。含有ANME/SRB联合体的样品以前是从甲烷渗漏沉积物中获得的，具有一系列生物地球化学参数。将对单个联合体进行分类和测序，以产生高质量的超基因组组装基因组(MAG)进行比较分析，以揭示单个联合体的菌株水平组成，以及不同沉积物样本中每个菌株在不同甲烷渗漏中的比例。MAGS的功能图谱将使比较基因组学方法能够识别最有可能对每个种群在各种环境中的成功至关重要的基因。预测将通过一系列实验室实验得到实验验证，包括纳米级二次离子质谱仪(NanoSIMS)、生物正交非典型氨基酸标记(BONCAT)和荧光原位杂交(FISH)。这里确定的基因和相关的生态生理学将使我们更好地理解在渗漏和盆地尺度上控制甲烷的因素，以及更广泛地说，微生物如何适应异质环境的普遍原则。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).Microbes are the workhorses behind every biogeochemical cycle, where they control the availability of different nutrients and other compounds. Methane seeps in the deep sea are one such system, where methane and other gases seep out from marine sediments, and they account for a significant fraction of the global methane budget. At these seeps, diverse microbial communities thrive and can metabolize the methane released from the seafloor. However, little is known about the specific forces and processes controlling the distribution of these microbes and their ability to perform their important metabolisms. This project investigates the links between microbial diversity and the environment in a methane-degrading system, focusing on consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). The results will clarify the fundamental determinants of microbial community composition and improve understanding of marine methane dynamics. The proposed work will engage the broader public in several ways. Undergraduate students from backgrounds underrepresented in STEM will be mentored over a summer research project through the Caltech WAVE program. The researcher will also partner with local elementary, high school, and undergraduate-serving programs through the Caltech CTL&O office and the Center for Environmental Microbial Interactions (CEMI) to encourage student participation in research opportunities related to the proposed work. Through existing collaborations between the ANSEP program and the Orphan lab, the researcher will participate in the ANSEP middle school Career Exploration in Marine Science program. This project aims to identify 1) how the genomic diversity of ANME/SRB partners is structured across scales ranging from individual consortia to environmental gradients and 2) the genes and ecological factors determining ecological outcomes for each partner. Samples containing ANME/SRB consortia have been previously obtained from methane seep sediments with a range of biogeochemical parameters. Individual consortia will be sorted and sequenced to produce high-quality metagenome-assembled genomes (MAGs) for comparative analysis to reveal the strain-level composition of individual consortia and the proportion of each strain across different sediment samples to different methane seeps. Functional profiling of MAGs will then allow comparative genomic approaches to identify the genes most likely to be critical to each population’s success in each environment. Predictions will be experimentally tested by a range of laboratory experiments including nanoscale secondary ion mass spectroscopy (NanoSIMS), bioorthogonal non-canonical amino acid tagging (BONCAT), and fluorescence in situ hybridization (FISH). The genes and associated ecophysiology identified here will result in greater understanding of the factors controlling methane at seep- and basin-scales, and more broadly, the generalizable principles of how microbes adapt to heterogeneous environments.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.