This paper will discuss the findings from the studies carried out as part of the soil biodiversity programme (SBP) in examining the diversity and functions of soil microbes. We will discuss the results obtained describing the taxonomic diversity of organisms found at the site and the consequences of experimental perturbations on microbial community structure. Much of the work carried out utilised molecular methods to describe or ‘fingerprint’ the microbial communities without the biases associated with traditional culture-based assays. One of the fundamental aims of the SBP was to link the activity and diversity of microbes with functional roles in the cycling of plant derived carbon through the soil food web. For this purpose novel isotope tracer approaches were applied, whereby stable isotope (13C) labelled CO2 was fed to plants and the root-released labelled carbon was traced into soil microbial biomarkers. We will review the data obtained and show how agricultural practices or trophic manipulations impact upon soil biodiversity and community functioning, and discuss the potential merit of these approaches in increasing our understanding of soil ecosystems.