We propose that a holistic view be taken to the study and implementation of ecological research into soils, soil organisms and plant growth. This builds upon the spatial and temporal aspects of soil physical and biological characteristics at the micro- and macroaggregate scales. This has major implications for the interactions of the soil biota and also for the possibilities of soil organic matter (SOM) dynamics, including gradual accumulation of SOM across decades and centuries. One of the key integrating factors in the role of soil biota in plant nutrition is the centrality of detrital and soil food webs in fostering nutrient cycling and ecosystem stability. We conclude with a five-dimension approach to studying key factors in soil biological interactions that affect plant nutrition and also long-term carbon balance in natural and agricultural ecosystems.