By some accounts exploring the origins of soil microbial diversity represents a scientific frontier similar to that of space exploration in its scope, described by Curtis and Sloan (2004) as ”an immense and unexplored frontier in science of astronomical dimensions and of astonishing complexity”. The complexity is attributed to soil ecological heterogeneity reflecting interplay of spatio-temporal, physical, and nutritional variables delineating spheres of influence that define microbial habitats and function. Key to microbial life in soil is a flickering aqueous network that defines nutrient diffusional pathways and shapes microbial dispersion and interactions. We propose to develop an individual-based and spatially resolved modeling platform that explicitly considers soil pore structure and aqueous phase configuration and associated biophysical processes forming a virtual soil microcosm. The assembly of these complex ingredients into a computational platform will enable systematic hypotheses testing concerning central questions in microbial ecology that are neither addressed by present ecological theories nor emerge from standard continuum models. Specifically, the project will provide quantitative insights into effects of hydration extremes on survival strategies, the roles of space and diffusional heterogeneity, aspects of dispersion and trophic interactions, self-organization of consortia, and emergence of temporal niches in soil. The research will transform quantitative understanding of soil biophysical processes, a gap that presently limits coherent interpretation of the rapidly growing molecular-based estimates of soil biodiversity, and is essential for guiding future data collection. The research lies at the interface between environmental microbiology and soil physics cutting across disciplinary boundaries and addressing broad issues impacting soil and water quality, the functioning of global bio-geochemical cycles, and the fate of anthropogenic pollutants.