The rapidly expanding field of metagenomics has revolutionized the ability to analyzemicrobial communities by providing access to ‘true’ microbial diversity. This field has a broad range of applications in the areas of biodiversity, systems biology and biotechnology (Handelsman et al. 2002). As most microbial communities in soil, sediment or aquatic environments are highly complex, consisting of hundreds oreven thousands of species of which only a few have been cultured, the approaches collectively described as metagenomics, community genomics or environmental genomics have been developed to help to unlock this thus far hidden diversity. Metagenomics is therefore the application of modern genomic tools used to analyze the collective genomes of whole microbial communities (the metagenome) in an environmental sample, thereby bypassing the need for isolation or cultivation (Béjà et al. 2000; Riesenfeld et al. 2004b). Even though the tip of the microbial ice-berg has barely been scratched, this approach is rapidly increasing our knowledge of microbial genetic and functional diversity through gene/pathway discovery either by sequencing or activity-based screening strategies (Handelsman 2005).