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

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，人们对调节这些行为的特定化学信号知之甚少，限制了实际管理的潜力，以优化微生物活动以支持健康的作物和生态系统。英国明尼苏达大学和曼彻斯特大学的这个项目的目标是开发和测试一套100种新型的微生物记录器，这些记录器可以感知特定的信号，并报告微生物中的100个特定基因是否都有反应。该项目将提供一种有价值的手段，在土壤微生物中识别特定的化学信号，这些信号可以优化有益功能或抑制有害功能。这项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群支持健康作物和生态系统的程度，并为利用微生物群发挥有益功能的新的、实用的方法提供了洞察。这里创建的工具还将指导改进对农业和自然生境中土壤微生物群的生态和功能潜力的理解。美国和英国科学家之间的交流将是研究工作成功不可或缺的一部分，加强两国科学家的能力和产出。这项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的见解。这项工作为精准农业工程功能土壤微生物群的研究奠定了基础。具体目标是：1)开发和测试遗传记录器(GR)菌株，以“倾听和报告”土壤中调节链霉菌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)模拟和测试依赖初级和次级代谢诱导的物种-物种相互作用如何影响多物种群落；以及3)发现潜在信号对链霉菌新陈代谢的影响，并利用信号来优化土壤中的微生物功能。方法：1)通过丝氨酸整合酶介导的重组，建立GRs来检测土壤微生物中感兴趣的基因/通路的激活。GRs将使用下一代测序技术进行量化，并将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)将使用基因组规模的代谢模型、转录组学和代谢组学将信号与功能联系起来。现有的代谢建模平台将扩展到纳入新的功能，以了解信号如何影响单个细菌的生理并改变新兴的生态系统动态。3)在体外筛选潜在信号对链霉菌的抗生素抑制和营养利用表型的直接影响，提供一个信号发现平台和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”获得的，这是一项合作征集活动，涉及国家科学基金会(NSF)的ENG/CBET和BIO/IOS部门、美国农业部国家粮食和农业研究所(USDA NIFA)以及英国研究与创新(UKRI)研究理事会：1)自然环境研究理事会(NERC)，2)生物技术和生物科学研究理事会(BBSRC)，3)工程和物理科学研究理事会(EPSRC)，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。

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.