The transparent soil microcosm: a window into the spatial distribution and dynamics of carbon utilization and microbial interspecies interactions

Soil is a rich ecosystem of bacteria, fungi, and plants interacting within a complex and highly variable physical environment. The microbial interactions and metabolic activities of these soil inhabitants have profound effects on ecosystem-level processes such as global carbon and nutrient cycling. A deeper understanding of how organisms physically and chemically interact with one another and soil nutrients has been hindered by the opacity of soil, which prevents the direct visualization of these interactions. To overcome this challenge and improve our understanding of interkingdom soil communities, we propose to develop an innovative imaging platform that will enable the real-time, non-destructive visualization of microbial activities in a model soil system. We will create microcosms composed of transparent soil-like particles, plant roots, and microbial communities that can be perturbed using microfluidics, and monitored using confocal fluorescence microscopy, Raman microspectroscopy, and isotopic carbon tracing. We will address key questions about community assembly and carbon cycling (e.g. how do microbes physically and chemically interact with one another? how are plant-microbe communities established? how does carbon flow between the members of soil ecosystems? how do microbes degrade complex carbon substrates?). Our approach will provide a unique imaging tool that bridges the gap between traditional laboratory and field experiments and will allow us to generate and test hypotheses to improve agricultural productivity and facilitate ecosystem management.