SITS-NSF-UKRI: Reverse engineering the soil microbiome: detecting, modeling, and optimizing signal impacts on microbiome metabolic functions

SITS-NSF-UKRI：土壤微生物组逆向工程：检测、建模和优化信号对微生物组代谢功能的影响

• 批准号: 1935458
• 负责人: Linda Kinkel
• 金额: $ 79.93万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-15 至 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1935458&HistoricalAwards=false
• 关键词: SITS; NSF; UKRI; Reverse; engineering

Chemical signaling among microorganisms in the soil determines microbial behavior, including whether or not soil microbes suppress plant diseases, enhance crop growth, or grow on particular soil nutrients. However, little is known about the specific chemical signals that mediate these behaviors, limiting the potential for practical management to optimize microbial activities to support healthy crops and ecosystems. The objectives of this project at the University of Minnesota and the University of Manchester in the UK are to develop and test a set of 100 novel, microbial recorders that can sense specific signals and report on whether each of 100 particular genes in the microbe responds. This project will provide a valuable means of identifying specific chemical signals among soil microbes that can optimize beneficial functions or suppress detrimental functions. The research will shed light on the complex chemical and metabolic interactions that determine how well soil microbiomes can support healthy crops and ecosystems, and provide insight into novel, practical ways to harness microbiomes for beneficial functions. Tools created here will also guide improvements in understanding the ecology and functional potential of soil microbiomes in agricultural and natural habitats. Exchanges between U.S. and U.K. scientists will be integral to the success of the research effort, strengthening the capacities and output of scientists in both countries. The research will provide fundamental insights into the roles of signals in mediating the ecology of soil microbes and suppression of plant diseases. This work establishes a foundation for engineering functional soil microbiomes for precision agriculture. Specific objectives are to: 1) Develop and test genetic recorder (GR) strains to "listen and report" on signals in the soil that regulate primary and secondary metabolic pathways in Streptomyces spp. isolated from disease suppressive soils; 2) Model and test how species-species interactions that rely on primary and secondary metabolic induction impact multi-species communities; and 3) Discover effects of potential signals on Streptomyces metabolism and harness signals to optimize microbial functional capacities in soil. Methods: 1) GRs will be created to detect the activation of genes/pathways of interest in soil microbes using serine integrase-mediated recombination. The GRs will be quantified using Next-Generation Sequencing technology, and will be able to simultaneously record the activation of hundreds of metabolic activities in a single high-throughput experiment. 2) Genome-scale metabolic models, transcriptomics, and metabolomics will be used to connect signals to functions. Existing metabolic modeling platforms will be extended to incorporate novel functionality to understand how signals influence the physiology of individual bacteria and alter emergent ecosystem dynamics. 3) Potential signals will be screened for their direct effects on Streptomyces antibiotic inhibitory and nutrient use phenotypes in vitro, providing both a signal discovery platform and a direct comparison with phenotypic data. This project was awarded through the "Signals in the Soil (SitS) opportunity, a collaborative solicitation that involves the ENG/CBET and BIO/IOS divisions of the National Science Foundation (NSF), the United States Department of Agriculture National Institute of Food and Agriculture (USDA NIFA) and the following United Kingdom Research and Innovation (UKRI) research councils: 1) The Natural Environment Research Council (NERC), 2) the Biotechnology and Biological Sciences Research Council (BBSRC), 3) the Engineering and Physical Sciences Research Council (EPSRC), and the Science and Technology Facilities Council (STFC).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.

土壤中微生物之间的化学信号传导决定了微生物行为，包括土壤微生物是否抑制植物疾病，增强作物生长或在特定土壤养分上生长。 但是，对于介导这些行为的特定化学信号知之甚少，限制了实践管理优化微生物活动以支持健康作物和生态系统的潜力。明尼苏达大学和英国曼彻斯特大学的该项目的目标是开发和测试一组100种小说，微生物录音机，它们可以感知特定的信号并报告微生物中100个特定基因中的每个基因中的每个基因。 该项目将提供一种有价值的方法，以识别土壤微生物之间的特定化学信号，以优化有益功能或抑制有害功能。 这项研究将阐明复杂的化学和代谢相互作用，这些相互作用决定了土壤微生物可以如何支持健康的农作物和生态系统，并洞悉利用微生物的新型，实用的方法来实现有益的功能。 这里创建的工具还将指导改善农业和自然栖息地中土壤微生物组的生态和功能潜力。 美国和英国科学家之间的交流将是研究工作成功的组成部分，增强了两国科学家的能力和产出。 这项研究将提供有关信号在介导土壤微生物生态和抑制植物疾病中的作用的基本见解。这项工作为精确农业的工程功能土壤微生物组奠定了基础。 特定目标是：1）开发和测试遗传记录仪（GR）菌株，以“倾听和报告”土壤中调节链霉菌属链霉菌原代和次级代谢途径的信号。从抑制性土壤中分离出来； 2）模型并测试依赖原代和次级代谢诱导影响多种物种群落的物种种类相互作用如何； 3）发现潜在信号对链霉菌代谢和线束信号的影响，以优化土壤中的微生物功能能力。 方法：1）将创建GRS，以检测使用丝氨酸积分酶介导的重组的土壤微生物中感兴趣的基因/途径的激活。 GRS将使用下一代测序技术进行量化，并能够同时记录单个高通量实验中数百种代谢活动的激活。 2）基因组规模的代谢模型，转录组学和代谢组学将用于将信号连接到功能。 现有的代谢建模平台将扩展以结合新功能，以了解信号如何影响单个细菌的生理和改变新兴生态系统动力学。 3）潜在信号将在体外筛选其对链霉菌抗生素抑制和营养用途表型的直接影响，从而提供信号发现平台以及与表型数据的直接比较。 该项目是通过“土壤中的信号（SITS）机会授予的，这是一个合作的招标，涉及美国国家科学基金会（NSF）的Eng/CBET和CBET和BIO/IOS部门，美国农业国家科学系食品和农业研究所（USDA NIFA）以及随后的英国研究和企业研究所（UKRIE委员会）（UKRI INFERT）：1）生物技术与生物学科学研究委员会（BBSRC），3）工程与物理科学研究委员会（EPSRC）和科学技术设施委员会（STFC）。该奖项反映了NSF的法定任务，并被认为是通过基金会的智力功能和广泛影响的评估来评估Criteria，并被认为是值得通过评估的支持。