Despite our increasing knowledge of the scale of microbial diversity, most microbes observed in natural environments remain uncultivated, their ecology and functional roles are unknown and our understanding of the composition of the natural microbial world is therefore rudimentary. However, modern molecular methods provide an easy way of surveying microbial biodiversity using ribosomal RNA gene sequences retrieved directly from the environment. The most significant finding from the application of such new approaches was the discovery of high numbers of novel archaeal phenotypes. Before, it was considered that Archaea were restricted to specialized "extreme" environments characterized by high temperature, salinity, pH, or strict anoxic. Over the last decade, a ubiquitous distribution of "non-extreme" Archaea in a wide variety of temperate and cold terrestrial and aquatic environments was demonstrated. The results presented in this thesis include the discovery of unexpected and new Archaea in boreal forest soil, freshwater forest lake and temperate estuarine sediment samples. We suggest that Archaea are ecologically much more successful and globally important than previously thought.