Atmospheric CO2 concentrations can influence ecosystem carbon storage through net primary production (NPP), soil carbon storage, or both. In assessing the potential for carbon storage in terrestrial ecosystems under elevated CO2, both NPP and processing of soil organic matter (SOM), as well as the multiple links between them, must be examined. Within this context, both the quantity and quality of carbon flux from roots to soil are important, since roots produce specialized compounds that enhance nutrient acquisition (affecting NPP), and since the flux of organic compounds from roots to soil fuels soil microbial activity (affecting processing of SOM). From the perspective of root physiology, a technique is described which uses genetically engineered bacteria to detect the distribution and amount of flux of particular compounds from single roots to non-sterile soils. Other experiments from several labs are noted which explore effects of elevated CO2 on root acid phosphatase, phosphomonoesterase, and citrate production, all associated with phosphorus nutrition. From a soil perspective, effects of elevated CO2 on the processing of SOM developed under a C4 grassland but planted with C3 California grassland species were examined under low (unamended) and high (amended with 20 g m-2 NPK) nutrients; measurements of soil atmosphere delta-13C combined with soil respiration rates show that during vegetative growth in February, elevated CO2 decreased respiration of carbon from C4 SOM in high nutrient soils but not in unamended soils. This emphasis on the impacts of carbon loss from roots on both NPP and SOM processing will be essential to understanding terrestrial ecosystem carbon storage under changing atmospheric CO2 concentrations.