PAPM EAGER: Microfluidic Root Exudate Sampler with High Spatio-Temporal Sampling Resolution


Roots interact with and respond to the biotic and abiotic environment in which they live (the rhizosphere) by qualitatively and quantitatively modulating material exuded by roots. These exudates use the language of chemistry to communicate between and among the biotic and abiotic components. Powerful DNA sequencing platforms and analytical tools for identifying chemical components are now available for profiling these interactions among the rhizosphere and the root components. The integrated application of these analytical strategies is limited by the ability to access and isolate exudates from roots and the rhizosphere. Existing exudate sampling tools are bulky, require large amounts of soil, and significantly alter the soil structure. This difficulty of sampling exudates has slowed the process of linking plant genetic determinants to rhizosphere microbiome genomic and metabolic features. This project addresses key design, fabrication, integration, and operation problems faced in developing next-generation root exudate sampling tools. The research will develop greatly-needed tools for probing the chemical exchange between plants and the micro- and macro-organisms in the rhizosphere. The root exudates are critical drivers of microbiome assembly and plant-pest/pathogen outcomes. The dynamic and environmentally responsive nature of root exudates illustrates the importance of developing sampling tools that are functional in a real-world situation, rather than the current tools that are limited to use in primarily artificial hydroponic and polymer-embedded systems. The samplers that will be developed will significantly impact the pace of research on rhizosphere microbiome by enabling continuous, spatially-resolved sampling of the microbes and exudates on roots grown in real-world conditions. This enhanced capability will meet societal needs to increase agricultural productivity for an increasing global population in the face of the uncertainties associated with climate-change, and thus develop new strategies to impact gains in agricultural productivity. This research will enhance interdisciplinary STEM workforce development by hosting at least two under-represented students in an undergraduate Howard Hughes Medical Institute summer internship program, providing research opportunities to four undergraduate senior students, and providing hands-on workshops to a high school Science Bound program to engage students in tech-transfer endeavors, while highlighting plant-microbe contributions to agriculture and global food security.

This project will elaborate advanced technology for gathering high spatiotemporal resolution data of metabolites and microbes in the rhizosphere. This objective will be met by developing a modular toolkit for the localized sampling of rhizosphere exudates from roots grown in soil matrices. This toolkit will consist of (i) a single site exudate sampler, which will serve as a building block of more complex modular sampling systems; (ii) distributed exudate samplers able to extract exudates from key locations with high spatial resolution; (iii) spine-like flexible exudate samplers, providing conformational fitting at the root-soil interface, which will maximize sampling at this crucial interface; and (iv) parallel gradient samplers positioned radially outward from a root, providing access to radial gradients of exudates. These samplers will be uniquely coupled with microfluidic sorters to enable automated separation and isolation of microbes from the collected exudates for simultaneous analysis of both the microbes and the soluble exudates. Furthermore, these samplers will integrate miniature tensiometers, which will allow monitoring of local soil potential condition at the sampling sites, and trigger the automatic start of sampling. Rendering such a "smart" device will improve temporal resolution of sampling. Validating the utility of these integrated devices will involve installing them, collecting and sorting samples, and analyzing the interactions between the rhizosphere and genetically specified maize roots, grown under gnotobiotic conditions with and without microbes. The multidisciplinary research has drawn expertise ranging from microsystems design and construction, microbiome and metabolomics, to address the proposed goal and deliver on the specific aims.