Bacteria and Archaea: Molecular techniques reveal astonishing diversity

The last decade has produced a significant advance in our appreciation of the diversity of prokaryotic organisms (commonly given the generic term “bacteria”). The need for this improvement was clear as the current list of approximately 5,000 accredited species has long been known to be a major underestimate of living prokaryotic species. The primary reasons for this poor census were 1) the inability to cultivate the vast majority of prokaryotic species in the laboratory and 2) a classification system that inherently required laboratory culture. Fortunately, the impact of DNA-based methods has remarkably improved our knowledge by providing both a new alternative classification system (i.e. phylogenetic classification), and critically, new experimental strategies to identify non-culturable species. The resulting data have not only highlighted the true breath of prokaryotic diversity but have also changed some of our previous views of biological evolution. Phylogenetic analysis of gene sequences retrieved from both cultured and uncultured bacteria has shown that all cellular life can be ordered into three taxa (termed Domains)—Bacteria, Archaea, and Eucarya. Intriguingly, this has resulted in a major taxonomic promotion for the Archaea, which were previously thought to be a series of unusual bacterial species. In addition, the use of DNA-based methods to identify and catalogue non-culturable species has radically improved our knowledge of the diversity found within living prokaryotes. This paper describes our current view of prokaryotic diversity describing the impact over the last decade of DNA-based methods. It is a popular adaptation of a previously published paper (2001).