Oren 2004

Oren A. 2004. Prokaryote diversity and taxonomy: current status and future challenges. Philosophical Trans. of the Royal Society of London B 359: 623-638.

This author provides an overview of the current understanding of prokaryote diversity and taxonomy, and discusses recent developments and expected future challenges. The prokaryotes include two of the three Domains of life (Bacteria and Archaea), and their importance in global ecosystems includes astronomical numbers of cells and perhaps as much Carbon as all plants.

Species concepts in Prokaryotes are difficult, and tend to be pragmatic rather than based solidly in theory. Current concepts favour the use of DNA-DNA reassociation, with a 70% similarity cut-off for species identification, combined with 16s rDNA sequences and chemo-phenotypic markers. Higher taxonomic levels are based entirely on subjective decisions, as no clear guidelines for delineating genera, families, orders et cetera exist. However, the problem of horizontal gene transmission is mostly ignorable because species concepts are based on whole-genome properties, not the properties of individual genes. Additionally, a kind of taxonomic “do-over” in 1980 erased the problem of synonyms, by publishing a list of 100% of the known described prokaryotic species, with one name each.

Official recognition of a prokaryotic species is based on depositing viable cultures in two countries, which makes it impossible to officially recognize any species that cannot be cultured. The vast majority of predicted “candidatus” species cannot currently be cultured, though some interesting breakthroughs with marine pelagic forms have recently been made.

Prokaryotic diversity can be sampled in nature using mass sequencing of 16s rDNA. This approach leads to the above estimate of huge numbers of uncultured species, but because 16s rDNA is not fully congruent with whole-genome measures of species identification, cannot be used on its own to identify species. The inability of researchers to cultivate more than a few percent of predicted species is known as the “Great Plate Count Anomaly” (Staley and Konopka, 1985). Extreme estimates for total global prokaryotic species diversity run to billions, based on both soil samples and the observation that prokaryote species numbers probably climb steadily over time because they have enormous populations, ready dispersal, rapid reproduction, and excellent survival of adverse conditions. Thus, in prokaryotes speciation is probably easy and extinction is probably hard.

Little is know about prokaryotic biogeography, and questions of endemicity have hardly been asked. However, no species has yet been identified from both the Arctic and Antarctic, suggesting a possibility of endemicity at that scale.

Until recently, it was apparently widely thought that while we knew little about species, we knew a great deal about the contributions of prokaryotes to global nutrient cycles. Recent novel discoveries of widepread and important biogeochemical processes indicates this is not so. It has been suggested that all thermodynamically favourable chemical reactions may be exploited by some organism, somewhere on Earth.

No prokaryote is considered “endangered”, but a few species are on lists for eradiction, such as the causative agent of leprosy. Other species are probably realistically endangered, as they are obligate symbionts of (for example) endangered species of animals and plants.

The author concludes with a call for better understanding of the issues facing microbiologists today, especially the vast, unexplored numbers of species, and the generally poor funding situation for microbiological research. Ongoing developments in molecular technologies suggest great promise for future work.