Soil biota, including roots, control the complex set of soil nitrogen transformations that regulate the production, flow, and loss of nitrate (NO3-) in ecosystems. This research addresses the spatial arrangement of belowground organisms and soil resources, and its implications for soil N cycling. One aspect is the functioning of arbuscular mycorrhizal fungi (AMF) for plant nutrition, soil ecology and nutrient cycling, using a previously well characterized mycorrhizal defective tomato mutant and its mycorrhizal wildtype progenitor. These were grown on a long term organic fresh market tomato farm (Yolo County, CA), with different levels of nutrient addition in root in-growth cores of field soil. While biomass of the two genotypes was very similar, AMF increased plant N, P and Zn, and decreased Mg and Mn concentrations. Effects on the wider soil community including nematodes, fungi and microbial biomass C were less pronounced. Detailed molecular analysis of ammonia oxidizing bacteria was also carried out at the community (DGGE) and population (quantitative real-time PCR) levels; this approach revealed no significant mycorrhizal effects. A second field experiment was conducted in which the short term fates of NO3- in soils were quantified. Using 15N-NO3- we found that rapid interception of NO3- by roots, irrespective of mycorrhizal colonization, lead to decreased N2O emissions from soils, especially close to plants, relative to root-free soils. Finally, the contribution of roots and mycorrhizae to soil respiration, over a 64 day time course, were quantified using a glasshouse-based continuous CO2 monitoring system. While roots contributed significantly to soil respiration, relative to plant free controls, mycorrhizal colonization of roots had little effect on soil respiration, although AMF did enhance plant nutrient uptake. Results from each of these studies are discussed in the context of organic and conventional production systems, with respect to the spatio-temporal arrangement of soil biota and nutrients.