ABSTRACT
Microbial ecology encompasses the study of the functional role and the diversity of microorganisms in their environment. This can be expressed in terms of the diversity of microbial species, the genetic potential encoded by the microbially encoded functional genes, and their expressed phenotype as defined by gene expression, protein production and cellular activity (1). Microbial communities are typically extremely complex and exhibit high diversity consisting of thousands of different bacterial species within small environmental samples (2). In addition to the high levels of species diversity, the bacteria that comprise environmental microbial communities may display a panoply of different functional roles. For many years our understanding of the diversity of microorganisms was limited to those organisms that we could physically culture. However, microscopic techniques revealed that these cultured organisms represented only ≤10% of the microorganisms within any given environment (3). The last two decades have seen a revolution in microbial ecology with the application of culture-independent methodologies typically involving analysis of nucleic acids extracted directly from an environmental sample that comprises the genomes of all microorganisms present within that sample. Approaches for isolation of nucleic acids are described in Chapter 1.
