CAREER:Fractured Shales as Portals into Cryptic Carbon and Nitrogen Cycling in the Deep Biosphere

陆地环境中的微生物群落催化着无数具有全球意义的生物地球化学循环。然而，在许多生态系统中，生物和化学复杂性的结合可能会妨碍对微生物如何相互作用、受病毒影响和交换代谢物的真正机制性理解。这些见解对于我们操纵微生物组以获得有益结果的能力至关重要，并更好地预测生物地球化学循环在不同环境条件下可能如何变化。深断裂页岩宿主更受约束的微生物财团，更容易审问，并提供了新的科学见解和开发工具，可应用于日益复杂的系统的机会。事实上，研究人员先前已经揭示，甲胺-简单的碳和氮化合物-的循环是一种保守的代谢策略，在阿巴拉契亚盆地的深层页岩地层中为甲基营养型甲烷生成提供燃料。本提案中概述的工作将确定地理上不同页岩的功能保护程度，并使用广泛的深生物圈微生物分离物库来研究微生物代谢的相互依赖性，使生命能够在这些极端环境中持续存在。还将研究病毒在驱动微生物群落动态和代谢物循环中的作用。最后，在页岩生态系统中开发的新工具和见解将应用于更复杂的湿地系统，以进一步阐明陆地环境中甲胺代谢的程度。该项目将培养一名研究生，并为本科研究人员提供机会。工业合作伙伴的参与将使研究生能够实习，并有助于课程材料，旨在告知学生在地下科学的各种职业机会。考虑到公众对水力压裂和深层生物圈问题的兴趣，还计划在当地组织开展一系列外联活动。基因组解析宏基因组和代谢组分析，加上实验室实验，揭示了深层陆地页岩中的甲胺循环是整个阿巴拉契亚盆地的一个保守的功能过程，使微生物群落能够持续数百天。使用多组学方法，这项工作将扩大对美国西部页岩区的调查，并确定在不同的盐度和温度条件下功能性状是如何改变的。对这些系统中代谢物交换和甲烷同位素分馏的基因组见解将在实验室中使用环境分离物和高压孵育装置进行测试，该装置能够实现原位条件（例如，压力、温度、盐度）来重建。新的分析工具，包括高压实时核磁共振将被用来跟踪高时间分辨率的基板的循环。还将使用生物信息学工具和实验室实验相结合的方法，研究新的和丰富的病毒种群在深层生物圈中介导碳和氮循环的能力。从这些研究中获得的数据将为微生物和病毒种群的功能提供独特的见解，以及微生物代谢对地球深层次表面下难以解决的碳和氮循环的影响。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Microbial communities in terrestrial environments catalyze myriad biogeochemical cycles with global implications. However, in many ecosystems the combination of biological and chemical complexity can preclude a true mechanistic understanding of how microorganisms interact, are affected by viruses, and exchange metabolites. These kinds of insights are critical for our ability to manipulate microbiomes for beneficial outcomes, and better predict how biogeochemical cycles might change under varying environmental conditions. Deep fractured shales host more constrained microbial consortia that are more amenable to interrogation, and offer opportunities for new scientific insights and development of tools that can be applied to increasingly complex systems. Indeed, the investigator has previously revealed that the cycling of methylamines--simple carbon and nitrogen compounds--is a conserved metabolic strategy that fuels methylotrophic methanogenesis in deep shale formations across the Appalachian Basin. Work outlined in this proposal will determine the extent of functional conservation across geographically distinct shales, and use an extensive library of deep biosphere microbial isolates to investigate microbial metabolic interdependencies that enable persistence of life in these extreme environments. The role of viruses in driving microbial community dynamics and metabolite cycling will also be investigated. Finally, novel tools and insights developed in the shale ecosystem will be applied to a more complex wetland system to further illuminate the extent of methylamine metabolism in terrestrial environments. This project will train a graduate student and offer opportunities to undergraduate researchers. The involvement of industrial partners will enable internship placements for graduate students, and contribute to curriculum materials aimed at informing students of diverse career opportunities in subsurface science. Given the level of public interest in hydraulic fracturing and deep biosphere topics, a series of outreach events at local organizations are also planned.Genome-resolved metagenomic and metabolomic analyses, coupled with laboratory experimentation, has revealed that methylamine cycling in deep terrestrial shales is a conserved functional process across the Appalachian Basin that enables microbial communities to persist for many hundreds of days. Using multiomic approaches, this work will expand investigations into western US shale plays, and determine how functional traits are altered under varying salinity and temperature conditions. Genomic insights into metabolite exchange and methane isotope fractionation in these systems will be tested in the laboratory using environmental isolates and high-pressure incubation apparatus that enables in situ conditions (e.g., pressure, temperature, salinity) to be recreated. Novel analytical tools including high-pressure real-time NMR will be used to track the cycling of substrates at high temporal resolution. The ability of novel and abundant viral populations to mediate carbon and nitrogen cycling in the deep biosphere will also be investigated using a combination of bioinformatic tools and laboratory experimentation. Data resulting from these studies will offer unique insights into the functioning of microbial and viral populations, and the impact of microbial metabolism on poorly-resolved carbon and nitrogen cycles in the deep terrestrial subsurface.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.