Applied Microbiology

Tools in Environmental Microbiology

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of Metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Metagenomics is the study of the collective genomes of the members of a microbial community. It involves cloning and analysing the genomes without culturing the organisms in the community, thereby offering the opportunity to describe the planet’s diverse microbial inhabitants, many of which cannot yet be cultured.

Metagenomics analysis involves isolating DNA from an environmental sample, cloning the DNA into a suitable vector, transforming the clones into a host bacterium, and screening the resulting transformants. The clones can be screened for phylogenetic markers or “anchors,” such as 16S rRNA and recA, or for other conserved genes by hybridization or multiplex PCR (136) or for expression of specific traits, such as enzyme activity or antibiotic production, or they can be sequenced randomly. Each approach has strengths and limitations; together these approaches have enriched our understanding of the uncultured world, providing insight into groups of prokaryotes that are otherwise entirely unknown.