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

Overview: Our project 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. Our team consists of experts in soil ecology, genetic engineering, metabolomics, and community modeling from the UK and USA.

Objectives: 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) We will create GRs to detect the activation of genes/pathways of interest in soil microbes using serine integrase-mediated recombination. The GRs will be triggered by yet unknown chemical, physical, and biological signals to produce a state change that can be easily quantified using Next-Generation Sequencing technology. Using these GRs, we will be able to simultaneously record the activation of hundreds of metabolic activities, across diverse microbial species, in a single high-throughput experiment. 2) We will utilize genome-scale metabolic models,
transcriptomics, and metabolomics to connect signals to functions. We will extend existing metabolic modeling platforms to incorporate novel functionality to understand how signals will influence the physiology of individual bacteria and alter emergent ecosystem dynamics. Transcriptomic and metabolomic data will be used to validate and extend current knowledge of exo-metabolite roles in system behavior and advance systems-level understanding of soil microbiomes. 3) We will screen potential signals for their direct effects on Streptomyces antibiotic inhibitory and nutrient use phenotypes in vitro. We will use the GRs to screen presumptive signals for their role in mediating Streptomyces primary and secondary metabolic activities, providing both a signal discovery platform and a direct comparison with phenotypic data. We will create signal-optimized isolate combinations or isolate/signal combinations and test their capacities to reduce plant diseases on wheat and radish seedlings in soil. Finally, we will test the effectiveness of the GRs in detecting signals in complex soil communities.

Intellectual Merit: The proposed research will advance fundamental understanding of the roles of signals in mediating the assembly, dynamics, and functional behaviors of complex soil microbiomes; provide novel tools for studying signaling dynamics in vivo, with potential to serve as sensors of microbial activities in soil; enhance systems-level understanding and modeling of primary and secondary metabolic activities within microbiomes; and test the capacity of signal-optimized inoculants to enhance plant health and productivity in soil systems.
sustainable cropping systems worldwide.

Education, training, and participation of underrepresented groups: We will recruit and train five post- doctoral research associates (PDRA), while actively recruiting additional graduate students and undergraduate researchers to our project. At both institutions, the PDRA and graduate students will work within highly-collaborative interdisciplinary teams, and gain experiences in biotechnology, agriculture, and synthetic biology. We have budgeted funds to support each PDRA for a cross-institution short-term research exchange to enhance scientific training. To encourage participation of nderrepresented groups, the UMN team will work with the McNair Scholars Program, which provides fellowships for undergraduates from underrepresented groups. The U-M team will participate in the Life Sciences Teachers Summer School to engage local school teachers with the research undertaken on this project, and will be involved in the U-M Work Experience program which mentors 14-15 year-old students in the opportunity for hands-on research. The U-M team will participate in outreach events such as `Discover Day' (targeting students planning to go to University) and `Science Star Days' (to inspire younger children to pursue science). Finally, all PIs will incorporate our research findings into undergraduate courses and offer opportunities for undergraduate research experiences throughout the term of the project.

Outreach and stakeholder interactions: Relevant findings from this project will be shared in twice-annual meetings with Minnesota crop producers. PI Kinkel is the co-founder of a small business (Jord Bioscience) that could potentially license IP generated within this proposal to commercialize and facilitate its adaptation in precision agriculture domestically and internationally.

Dissemination of research to enhance understanding: The PIs will disseminate results to the scientific community through diverse, high-impact scientific journals. PIs, postdocs, and graduate students will present research findings at major national and international conferences. We will communicate our work to the general public via UMN and U-M press offices to highlight project findings. We will propose a UMN Bell Museum of Natural History Café Scientifique (CS) session, which provides a unique happy hour program at for adults to learn about cutting-edge research. Finally, the project partners are committed to the use of social media, including Twitter, to disseminate project findings.

Sponsored Research Symposia and events: In conjunction with the visit of the U-M team to the UMN, we will sponsor a full-day research symposium for students, staff, PDRA, and faculty, focusing on "Convergent Research to Advance Understanding and Applications in Microbiome Science". In addition, all PDRA will present departmental or program seminars on their cross-institutional visit, and seminars will be required to be in an academic discipline outside of the student's home institution. This will challenge students to take a truly interdisciplinary approach to the presentation of their research project. Finally, post-doctoral scientists at UMN will jointly develop and teach a one-semester Special Topics course on the soil microbiome, with an emphasis on the biotic signals of plant/microbial origin.