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决定微生物的行为，包括土壤微生物是否抑制植物病害、促进作物生长或依靠特定的土壤养分生长。 然而，人们对介导这些行为的具体化学信号知之甚少，限制了实际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这个项目的目标是开发和测试一套 100 个新颖的微生物记录器，它们可以感知特定信号并报告微生物中 100 个特定基因中的每一个是否做出反应。 该项目将提供一种有价值的方法来识别土壤微生物中的特定化学信号，从而优化有益功能或抑制有害功能。 该研究将揭示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组如何支持健康的作物和生态系统，并为利用微生物组发挥有益功能提供新颖、实用的方法。 这里创建的工具还将指导改进对农业和自然栖息地土壤微生物组的生态和功能潜力的理解。 美国和英国科学家之间的交流对于研究工作的成功至关重要，可以加强两国科学家的能力和产出。 该研究将为信号在调节土壤微生物生态和抑制植物病害中的作用提供基本见解。这项工作为精准农业的功能性土壤微生物组工程奠定了基础。 具体目标是： 1) 开发和测试基因记录器 (GR) 菌株，以“监听和报告”土壤中调节链霉菌属初级和次级代谢途径的信号。从抑制疾病的土壤中分离出来； 2) 建模并测试依赖初级和次级代谢诱导的物种间相互作用如何影响多物种群落； 3) 发现潜在信号对链霉菌代谢的影响，并利用信号来优化土壤中微生物的功能能力。 方法： 1) 将创建 GR，以使用丝氨酸整合酶介导的重组来检测土壤微生物中感兴趣的基因/途径的激活。 GR 将使用下一代测序技术进行量化，并且能够在单个高通量实验中同时记录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与功能联系起来。 现有的代谢建模平台将进行扩展，以纳入新的功能，以了解信号如何影响单个细菌的生理学并改变新兴的生态系统动态。 3）潜在信号将在体外筛选对链霉菌抗生素抑制和营养利用表型的直接影响，提供信号发现平台并与表型数据直接比较。 该项目是通过“土壤信号（SitS）机会”获得的，这是一项合作招标，涉及美国国家科学基金会（NSF）、美国农业部国家食品和药物管理局的 ENG/CBET 和 BIO/IOS 部门。农业 (USDA NIFA) 和以下英国研究与创新 (UKRI) 研究委员会：1) 自然环境研究委员会 (NERC)，2) 生物技术和生物科学研究委员会 (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 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。