The microbial ecology of soil still presents a challenge to microbiologists attempting to establish the ways in which bacteria and fungi actively metabolise substrates, link into food webs and recycle plant and animal remains and provide essential nutrients for plants. Extraction and in situ analysis of rRNA has enabled identification of active taxa, and detection of mRNA has provided an insight into the expression of key functional genes in soil. Recent advances in genomic analysis and stable isotope probing are the first steps in resolving the linkage between structure and function in microbial communities.