Decoding the mechanisms of disease-suppressive soil microbial communities

Abstract

As the global population is expected to reach 9.4 billion by 2050, food demand is expected to requirea doubling of food production. One of the main obstacles in achieving this goal is the prevalence of diseases caused by plant pests and pathogens, which are responsible for approximately 30% of pre-harvest crop loss. This study seeks to learn the design rules for engineering disease-suppressive soils (DSS), soils in which plants thrive despite the presence of pathogens. Microbial communities and their interactions contribute to the establishment, pathogen-suppressive properties, and maintenance of DSS. This work focuses on members of the bacterial genus Streptomyces. Streptomyces is well-known as a source of numerous antibiotics, and has previously been implicated in DSS. We examine the genomes of three distinct Streptomyces isolates from unique soil environments, including DSS. The isolates were selected for their exquisite inhibitory effects, and ability to interact with a wide range of Streptomyces species. Interestingly, comparative genomic analysis does not reflect their phenotypic distinctiveness, suggesting that their unique characteristics may arise from specific gene expression responses to environmental stimuli, including other microbial taxa. We explore how gene expression changes in Streptomyces communities of varying complexities. We measure genome-wide transcriptional changes, with a focus on biosynthetic gene clusters, the source of small molecules like antibiotics. A key finding is the potential role of iron in influencing microbial community interactions, shedding new light on the complex dynamics within DSS. This work includes a study focused on simulation modeling techniques to optimize gene expression within engineered multi-gene systems. This approach, while initially inspired by small molecule titer improvement, could be extended to the design of microbial consortia for environmental and agricultural applications. The dissertation concludes by integrating these findings within the context of soil microbial ecology and the potential for engineering microbial consortia. Finally, we propose promising threads to follow as future research directions.