RII Track-2 FEC: Single Cell Genome-to-Phenome: Integrating Genome and Phenome Analyses of Individual Microbial Cells in Complex Microbiomes

地球上大多数生物多样性存在于微小的单细胞微生物中，它们负责生物圈中大部分碳、氮和其他元素的循环。然而，使用传统的微生物学工具，只有不到1%的微生物被成功地分离出来，用于实验室培养的详细研究。尽管更新的元经济学？研究工具通过分析整个微生物群落的分子组成来规避实验室培养的需要，这些工具通常混合了来自高度多样化生物体的信息，使得很难将特定微生物的功能（“表型组”）与其DNA密码（“基因组”）直接联系起来。该项目将通过直接将单个微生物细胞的功能和基因组特性联系起来的新方法组合来解决这一技术弱点。这种新方法结合了项目团队？微生物利用与特定生物活动（如呼吸、生长和营养吸收）成比例的特定化合物，对单个细胞的DNA进行排序的能力。研究人员将在从缅因湾到海洋地壳和大陆深层地下等环境中验证这种新方法。该项目将利用缅因州毕格罗实验室单细胞基因组学中心的基因组研究设施、新罕布什尔大学荧光有机探针合成方面的专业知识、内华达州沙漠研究所的大陆地球微生物基础设施，以及缅因州和新罕布什尔正在进行的海洋学研究项目。该项目将有助于为所有三个司法管辖区的国家研究和开发界发展新的分析能力，创造新的就业机会和培训熟练劳动力。该奖项将用于一个多司法管辖区的项目，该项目将利用现有的试点结果，在生物组织的最基本层面（单细胞）实现微生物基因组到表型方法的突破。总体目标是将细胞特异性基因组数据与表达功能联系起来，这样环境过程的速率就可以与特定的微生物谱系相结合。研究小组将：a)开发一种新的、集成的工作流程，用于单个细胞的基因组-表型分析，利用荧光化合物来测量表型；B)在全球重要环境的研究中验证和利用此工作流程；C)通过出版物和核心设施服务与研究界分享新颖的研究工具；d)改善EPSCoR合作辖区的可持续研究基础设施；e)创建一个多方面的劳动力发展计划，以确保这些新研究方法的专业知识。项目将通过利用团队的三个案例研究来建立和验证这个工作流。我们的专业知识和进入不同微生物群复杂环境的途径：沿海海洋、深海、海洋和陆地地下。为了进一步扩大该项目的社会影响和技术潜力，一项额外的试点研究将侧重于表征负责降解环境污染物（聚丙烯酰胺/丙烯酰胺）的单个微生物。最重要的影响将是一种新工具的发展：一种将表型信息与单个微生物细胞联系起来的管道。这将在研究界和工业应用中具有广泛的适用性，并解决了了解环境中微生物关键功能的社会需求。这个项目会利用毕格罗实验室吗？在单细胞基因组学和流式细胞术方面，新罕布什尔？在聚合物的海洋生物地球化学和标记有机分子的合成方面的专业知识，以及沙漠研究所？s （DRI）在研究深层地下环境方面的专业知识和基础设施。新教员将接受指导，其中包括一名将在毕格罗聘请的新高级教员，以及一名目前在新罕布什尔大学的新教员。该奖项反映了美国国家科学基金会的法定使命，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。

Non-technical descriptionThe majority of biological diversity on Earth is found in microscopic, single-celled microbes, which are responsible for most of the cycling of carbon, nitrogen and other elements in the biosphere. However, less than 1% of microbes have been successfully isolated for detailed study in laboratory cultures, using traditional microbiology tools. Although newer ?meta-omics? research tools circumvent the need for laboratory cultivation by analyzing the molecular composition of entire microbial communities, these tools often blend information from highly diverse organisms, making it difficult to directly link the function of specific microbes (the ?phenome?) to their DNA code (the ?genome?). This project will tackle this technological weakness through a new combination of approaches that directly links functional and genomic properties of individual microbial cells. This new approach combines the project team?s ability to sequence the DNA of individual cells with the utilization of specific compounds that microbes incorporate in their cells in proportion to specific biological activities, such as respiration, growth, and uptake of nutrients. The researchers will validate this new approach in environments ranging from the Gulf of Maine to ocean crust and deep continental subsurface. This project will leverage genome research facilities at the Bigelow Laboratory Single Cell Genomics Center in Maine, expertise in the synthesis of fluorescent organic probes at the University of New Hampshire, continental geomicrobiology infrastructure at the Desert Research Institute in Nevada, and ongoing oceanographic research programs in Maine and New Hampshire. The project will contribute to the development of novel analytical capabilities for the national Research and Development (R&D) community, creation of new jobs, and training of skilled workforce in all three jurisdictions.Technical Description This award is for a multi-jurisdictional project that will capitalize on existing pilot results to achieve a breakthrough in microbial genome-to-phenome methodology at the most fundamental level of biological organization: the single cell. The overarching objective is to tie cell-specific genome data to expressed functions such that rates of environmental processes can be coupled to specific microbial lineages. The research team will: a) develop a new, integrated workflow for genome-to-phenome analyses of individual cells that takes advantage of fluorescent compounds to measure phenotypes; b) validate and utilize this workflow in studies of globally significant environments; c) share novel research tools with the research community through publications and core facility services; d) improve sustainable research infrastructure at collaborating EPSCoR jurisdictions; and e) create a multifaceted workforce development program to ensure expertise in these new research approaches. The project will establish and verify this workflow through three case studies that leverage the team?s expertise and access to environments of differing microbiome complexity: the coastal ocean, the deep dark ocean, and the marine and terrestrial subsurface. To further expand the societal impact and technological potential of the project, an added pilot study will focus on characterization of individual microbes responsible for degradation of an environmental contaminant (polyacrylamide/acrylamide). The overarching broader impact will be the development of a new tool: a pipeline for linking phenotype information to single microbial cells. This will have broad applicability across research communities and industrial applications and address a societal need to understand the critical function of microbes in the environment. The project will leverage the Bigelow Laboratory?s capabilities in single cell genomics and flow cytometry, New Hampshire?s expertise in the marine biogeochemistry of polymers and the synthesis of labeled organic molecules, and the Desert Research Institute?s (DRI) expertise and infrastructure in studying deep subsurface environments. New faculty members will be mentored, including a new senior staff member to be hired at Bigelow, and a new faculty member currently at the University of New Hampshire.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.