The implications of micro-habitat architecture for soil microbial community structure and function

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Soil health refers to the capacity of soil to sustain life. It is a topic of great scientific and societal importance. Healthy soils have hordes of tiny, beneficial microorganisms that access and recycle the building blocks of life, including nutrients and carbon, and make them available to the next generation of plants. Beneficial soil microorganisms form intricate relationships with plants, supporting crop growth and productivity. Although they comprise some of the most biologically diverse communities on Earth, many details regarding the ways which microorganisms help maintain soil health and promote plant growth remain mysterious. For example, how do microbial communities cope with variations in the water and chemical content of soil, which can change drastically over small distances? This research project will use state-of-the-art methods and recently developed x-ray technology to examine soil micro-scale properties including the number and size of soil pores, pH, and nutrient and carbon quality and availability. These measurements will be coupled with high through-put genome sequencing to examine the impact of these properties on microbial diversity and soil health. This project will serve national interests through advancing fundamental knowledge about the roles that microorganisms play to support soil health, food security and agriculture. The project will also advance the field of soil ecosystem science, and will support education and workforce training through authentic laboratory research opportunities for undergraduates.The relationship between spatial heterogeneity of soil micro-habitats and microbial diversity will be investigated by dissecting precise physical and chemical micro-environmental variables and the structure and function of their associated microorganisms. The research will determine associations between microorganisms (bacteria and archaea) and micro-environmental variables as a function of soil associations with plants (specifically the microscale distribution of plant-derived carbon in rhizosphere versus bulk soils); and identify the micro-environmental characteristics responsible for suitability of distinct micro-habitats to certain microbial groups. This research offers a fundamentally new approach of combining synchrotron-based X-ray computed micro-tomography information with microbial metagenomics to achieve an improved understanding of the role that physical micro-environmental conditions play in determining compositional and functional diversity of soil microbial communities. This study will pioneer quantitative, combined analysis of key elements important for microbial functioning, including the architecture and characteristics of soil pores, their relationship to micro-biogeographic patterns in microbial structure, and spatial micro-biogeographic patterns that emerge given associations with plant roots. One unique feature of the project is that observed spatial patterns of micro-habitats will be studied with specific reference to local characteristics of soil pores ("geo-referencing"), which are the avenues enabling air, water, and nutrient fluxes and soil microbial migration. Broader impacts will include potential benefits to agriculture, forestry and food security, as well as multidisciplinary undergraduate research training via internships.