Background It is well established that the functioning of terrestrial ecosystems depends on biophysical and biogeochemical feedbacks occurring at the soil-plant-atmosphere (SPA) interface. However, dynamic biophysical and biogeochemical processes that operate at local scales are seldom studied in conjunction with structural ecosystem properties that arise from broad environmental constraints. As a result, the effect of SPA interactions on how ecosystems respond to, and exert influence on, the global environment remains difficult to predict. Scope We review recent findings that link structural and functional SPA interactions and evaluate their potential for predicting ecosystem responses to chronic environmental pressures. Specifically, we propose a quantitative framework for the integrated analysis of three major plant functional groups (evergreen conifers, broadleaf deciduous, and understory shrubs) and their distinct mycorrhizal symbionts under rising levels of carbon dioxide, changing climate, and disturbance regime. First, we explain how symbiotic and competitive strategies involving plants and soil microorganisms influence scale-free patterns of carbon, nutrient, and water use from individual organisms to landscapes. We then focus on the relationship between those patterns and structural traits such as specific leaf area, leaf area index, and soil physical and chemical properties that constrain root connectivity and canopy gas exchange. Finally, we use those relationships to predict how changes in ecosystem structure may affect processes that are important for climate stability. Conclusions On the basis of emerging ecological theory and empirical biophysical and biogeochemical knowledge, we propose ten interpretive hypotheses that serve as a primary set of hierarchical relationships (or scaling rules), by which local SPA interactions can be spatially and temporally aggregated to inform broad climate change mitigation efforts. To this end, we provide a series of numerical formulations that simplify the net outcome of complex SPA interactions as a first step towards anticipating shifts in terrestrial carbon, water, and nutrient cycles.