We explore the potential for applying broad ecological theories to interactions between soil animals and micro-organisms to generate a predictive framework within which more hypothesis led research can be undertaken. The paper stems from discussions during a workshop at the XIVth International Symposium on Soil Zoology. The possible linkage between biodiversity and ecosystem functions forms a good example of how soil zoology research can be productively stimulated by addressing a broader ecological concept but also how the concept can be tested below ground at fundamentally different scales to those commonly used above ground. Other areas of theory rapidly developing above ground, which are yet to be fully tested below ground, include: spatial variability in food webs; indirect interactions mediated through changes in plant secondary chemistry; signalling, including tritrophic interactions; optimal foraging theory, including depletion theory when patches differ in quality as well as quantity; adaptive plasticity in life history traits in relation to temporal variability in resources; trade-offs and facultative non-symbiotic and symbiotic mutualism. We identify modelling of effects of climate change on the soil compartment of the global carbon cycle as an area in which understanding of soil fauna-microbe interaction may outstrip current ecological theory and as a major challenge facing soil biologists in the future. © 2006.