The rhizosphere is a complex system in which many diverse and heterogeneous small-scale components (e.g, plant roots, fluids, microbes, and mineral surfaces) interact with one another, often in nonlinear ways, giving rise to emergent system behaviors. Ecosystem-scale perturbations, such as nitrogen limitation or drought, drive changes in micro-environments through a cascade of complex interacting processes, leading to a bidirectional feedback across scales between microbial and plant habitats at the microscale and ecosystem function at the macroscale. We are developing a conceptual and numerical framework for multiscale simulation of organic carbon transport, transformation, and disposition in the soil-microbe-plant continuum. The conceptual model comprises a set of directed graphs, with nodes representing system processes and states and edges representing process-state relationships. The graphs are coded in the graphviz syntax enabling dynamic web visualization. Graph nodes are hyperlinked to metadata pages summarizing current understanding of each process or state and its representation in current numerical codes. This conceptual model is available via a git repository and can guide identification of opportunities for coupling (data exchange) between codes operating at different length scales. The numerical implementation of the conceptual model is based on execution of integrated data processing and multiscale modeling scientific workflows. The numerical framework is enabled by a recent development in information technology known as orchestration, a class of solutions to problems of deployment and execution of cloud-oriented software. Orchestration technology is well-suited to automating complex scientific workflows, both in model-coupling efforts and experimental analysis pipelines. Here it is used to flexibly define workflow steps based on precedent events (such as arrival of a new model output in the data repository). It is being applied to integrate several community software packages spanning scales from molecules to ecosystems, linked to experimental data from the Environmental Molecular Sciences Laboratory (a national scientific user facility), to address critical scientific questions related to soil nutrient cycling.