The soil environment is arguably the most complex biological community because of the extremely high diversity at small scales and a chemical environment of complex and changing gradients housed in a heterogenous physical environment. Some basic important facts regarding the complexity of soil communities are presented. For a better understanding of the soil community and its activity, the role of soil matrix in structuring microbial communities, geographical characteristics of heterotrophic communities, and the application of DNA microarray technology to environmental microbiology are discussed. The highlights of soil organic matter research within the soil science community and the inter-disciplinary nature of soil science per se, is briefly reviewed and the main conclusions are outlined.