A THREE DOMAIN RATHER THAN FIVE KINGDOM CLASSIFICATION In 1987

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). INTRODUCING THE HIDDEN WORLD OF THE PROKARYOTES One of the most significant developments in microbiology has been the discovery of many new bacterial species that are so unique that taxonomists have accorded them the rank of new phyla and even kingdoms. The collective scientific name for these organisms is “Prokaryote,” meaning a cell characterized by the lack of a distinct membrane-bound nucleus. (In contrast, cells whose chromosomes are contained within a membrane-bound nucleus are termed eukaryotes.) Far more commonly prokaryotes are given the generic term “bacteria. ” They are found throughout the entire planetary ecosystem including niches where eukaryotic species are rare or absent (e.g. the ocean depths, the planet’s subsurface, thermal and polar environments, and oxygen-free environments). This wide ecological range reflects their vast metabolic capabilities that allow different prokaryotic species to inhabit different environments. Prokaryotes also occur in great abundance. A recent analysis suggested that the total number of living prokaryotic cells is 4 6 x 1030 composed of 1.2 x 1029 cells in the ocean, 2.6 x 1029 cells in soil, and 0.25 2.4 x 1030 cells within the Earth’s subsurface (Whitman et al 1998). An alternative way to appreciate these figures is that even while accounting for the idea that a prokaryote cell is typically about 10,000fold smaller in volume than a eukaryotic cell, the total amount of prokaryote biomass is still approximately 10,000 times greater than the amount of human biomass currently living on Earth. Because of these large numbers, their metabolic capabilities, and their ubiquity, prokaryotes play an essential function in the planet’s biochemical processes including decomposition in soil, the provision of atmospheric components, nitrogen fixation, and photosynthesis. Despite this significance, we have as yet only a very poor description of living prokaryotic species, and perhaps for obvious reasons, surveys of biodiversity often overlook bacteria. There are severe technical limitations among the traditional census-gathering methods of microscopy and bacteriology. Most species are indistinguishable under the microscope, and it has long been observed that only a fraction of the bacteria observed under the microscope can be successfully cultivated in the laboratory. Compounding this, those prokaryotic species that readily adapt to ABOUT THE AUTHORS. James O. McInerney and Richard Powell are university lecturers whose research groups are interested in bioinformatics and molecular microbial ecology respectively. For several years, the two groups have combined their interests in a research study of uncultured marine bacteria. Under their supervision, Marice Malarkey and Martina E. Wernecke have recently successfully completed their postgraduate studies using molecular techniques to analyze uncultured Archaea in Irish coastal waters.