Archaea: very diverse, often different but never bad?
Christa Schleper is Professor and Head of the Department of Genetics in Ecology at the University of Vienna. Her research combines microbial physiology, genetics and metagenomics and is now focused primarily on anaerobic ammoniaoxidizing Archaea and on the study of genetic elements in Sulfolobus. This is the second Current Opinions in Microbiology volume dedicated to the Archaea. Comparing the reviews published here with those published in December 2005 underlines the impressive progress made in several areas of on-going archaeal research (evolution and phylogenetics, metabolic diversity and pathway biochemistry, transcription, cell cycle and pyrrolysine studies) and identifies areas in which archaeal research has more recently expanded (anaerobic methane and aerobic ammonia oxidations, CRISPR, tRNAs, cell surface structures, viruses and symbiotic interactions). The impacts of rapid genome sequencing, metagenomics and microbial cultivation techniques, all much expanded since 2005, are also very apparent. Perhaps most notably, they have documented the presence of Archaea in almost all natural environments, and confirmed that Archaea contribute substantially to the global carbon and nitrogen cycles, in both marine and terrestrial ecosystems. The accumulation of microbial genome sequences has also fully established that the Archaea and Bacteria constitute fundamentally different evolutionary Domains [1]. As a taxon, the term prokaryote is therefore seriously questioned [2] but, with no nuclear membrane, Archaea and Bacteria may share features not found in Eukarya. For example, translation can be tightly coupled with transcription and, although transmitted horizontally, adaptive immunity CRISPR systems (see below) may exist only in Archaea and Bacteria. Prokaryote is also still used sometimes as a synonym for Bacteria, ignoring the Archaea, and many of the 2005 reviews addressed this with features described as being (or not being) bacterial-like or eukaryal-like. Evolutionary relationships are often still noted, but the reviews now published definitively describe archaeal features and functions. A reader must therefore recognize the diversity of the Archaea; an archaeal feature is not necessarily present in all Archaea, just as not all Bacteria are Gram-negative.