CAREER: Defining colonization mechanisms and functions of Streptomyces strains in root microbiomes

Michigan State University, East Lansing MI

Investigators

Abstract

The human population is projected to reach 9 billion people by the year 2050. To accommodate this increase in population, global food production will need to increase by 70-100%. Chemical fertilizers, such as phosphate rock, are commonly used to improve crop yields. However, many of these fertilizers are non-renewable resources that will continue to decrease in supply as the demand continually increases. Alternatives to chemical fertilizers are, therefore, necessary to continue improving crop yields into the future. This need, combined with increased public awareness of host-associated microbial communities (microbiomes) and the benefits they provide to their hosts, has turned the attention of the agricultural biotechnology industry towards harnessing plant microbiomes by developing probiotics that increase plant growth and productivity. Before these plant probiotics can have widespread success as an alternative way to improve crop yields, it must be understood how microorganisms inhabit plant tissue consistently and robustly despite encountering various hurdles to colonization. In addition to plant-produced chemicals that can limit microorganism growth, other microorganisms competing for similar niche space can affect each other's growth directly via products such as antibiotics. This research will explore the mechanisms used by microorganisms to protect themselves against these harmful chemical attacks. Planned educational activities will provide education, resources, and training to local and regional communities, targeting underrepresented groups. Together, the intertwined research and educational plans will provide a new perspective to improve and complement product development by agricultural biotechnology companies to expand their potential success to enhance plant productivity. Plants evolved in a microbial world, and, as with many other multicellular organisms, specific subsets of microorganisms assemble into stable host-associated microbiomes. Recent massive parallel sequencing studies using the universal 16S ribosomal RNA gene defined microbiomes for a wide variety of plant species. Results demonstrated clear overlap in internal root (endosphere) microbiome composition, even between the evolutionarily divergent monocots and dicots and across diverse soil reservoir microbial communities. These commonalities suggest that selective pressures, likely imposed by both the plant immune system and competing microbes, exist and limit successful colonization of the endosphere. This work will explore specific interactions between collections of Streptomyces isolates, non-Streptomyces isolates, and genetic mutants of Arabidopsis thaliana as a tractable model system. Streptomyces were chosen based on their ability to: colonize roots from a variety of plants, influence the viability of other soil microbes through production of secondary metabolites, and be controlled the plant immune system. This research will test the hypothesis that Streptomyces species act as keystone members of the endosphere through investigation of how chemicals produced by host plants and/or microbes shape root microbiome membership. The knowledge gained from these studies could facilitate consistent and robust plant colonization by beneficial microbes, even in the face of direct microbial competition and host defenses. Understanding these mechanisms will be critical as we move from basic lab experiments into development of plant biological products to increase crop yields, and thereby, global food security, as the human population continues to rise. 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.