Increasing agricultural yields to sustainably feed and fuel Earth’s growing population represents a major societal challenge. Plants evolved in the context of complex soil microbial communities, so it is not surprising that microbes confer diverse benefits to plants, including growth promotion, drought tolerance, nutrient acquisition, and pathogen exclusion. In turn, plants release a large fraction of photosynthates (up to 40%) through their roots to support beneficial (“rhizosphere”) microbes. Beneficial microbes are now routinely used in agriculture (predicted to be a $10B market by 2025), thereby providing a natural alternative to fertilizers and pesticides.
Unfortunately, there are enormous gaps in our understanding of plant-microbe interactions that limit our ability to predictably harness beneficial microbial communities. For instance, most of our understanding of microbial gene functions has been obtained from a very small number of organisms that have been studied in isolation. This approach currently excludes most microbial diversity (it is estimated that <1% of microbes have been isolated) and doesn’t provide insights into the functions of genes and metabolites that mediate microbial interactions. Hence, we lack the most basic understanding of how plants attract and maintain beneficial microbiomes and the functions and interactions of the microbes associated with plants.
To address these scientific gaps, the m-CAFEs project is pioneering new technologies and performing laboratory experiments that will provide foundational insights into the activities and interactions of plant-microbial communities. We are developing single-plant-scale, fabricated ecosystems (EcoFABs, www.eco-fab.org) that enable precise and reproducible control and characterization of plant-microbial interactions at a molecular level. Beginning with tractable organisms, we will systematically evaluate the genetic basis for microbial traits that underlie the formation of microbial interaction networks in the rhizosphere. Importantly, to interrogate the function of soil microbiomes, we will develop methods to subtract organisms and alter specific functional capacities from complex networks within controlled laboratory EcoFAB environments.
This combination of approaches allows the precise control of physical, chemical and (micro)biological components of soil ecosystems to facilitate rigorous hypothesis testing of gene, organism, and community function. These systems will be an important resource for the larger scientific community by enabling researchers to reproduce and build on each other’s work, as we have recently shown in a four-lab intra-comparison experiment.
Taking advantage of the contained and controlled laboratory EcoFAB environments, the m-CAFEs team is developing new technologies enabling direct in situ genetic perturbations, such as CRISPR-Cas tools, to dissect the functional basis for soil microbiome interaction networks and move from identifying correlation to demonstrating causation. These technology developments will enable us to remove or inhibit specific microbes and add or remove genes to test predicted interactions and functions within the EcoFABs, thus transforming our understanding of microbial community interactions.
Given the vast array of potential microbes, genes, and metabolites for investigation within the EcoFABs, we will use network and genome-scale modeling to simulate effects and to prioritize targets for testing in both defined and more complex soil communities. A particular strength of the defined rhizosphere communities is the ability to perform leave-one-out experiments and use mutants constructed with classical approaches to determine causal mechanisms of interactions and test the performance of developing in situ methods. We use our EcoFABs for this research because they are designed specifically for sterilization and are compatible with conventional biohazard management approaches. In addition, we are leveraging the expertise of our team, scientific community, and advisory committee to direct our responsible research in developing and applying these in situ methods within our controlled and contained laboratory EcoFAB environments.