Archaea

Just about half a century ago, all prokaryotes, i.e., cells without nucleus, were classified within one kingdom: Monera. However, in the late 1970s, scientists were starting to recognize that this classification system, based predominantly on morphological and metabolic traits, underestimated the vast diversity of prokaryotic life. Around the same time, the pioneering work of Carl Woese and George Fox led to the discovery that prokaryotes were, in fact, composed of two fundamentally different domains of life—the Bacteria and the Archaea (originally referred to as “Eubacteria” and “Archaebacteria,” respectively) [1]. Woese and coworkers used the RNA components of the ribosome to reconstruct the first phylogenetic tree of life based on molecular data [2], which divided cellular organisms into three separate domains of life 230(Figure 21.1A)—the Bacteria, Archaea, and Eukarya, the latter of which comprised all organisms with a true nucleus [2]. At that time, it was suggested that Archaea, in spite of their superficial similarity to Bacteria, may be more closely related to eukaryotes than Bacteria. In fact, they seemed to harbor simplified versions of eukaryotic informational processing machineries (replication, transcription, translation, and cell division), in addition to unique characteristics such as ether-bound isoprenoids rather than ester-bound fatty acid-based lipids (Table 21.1). Subsequent research on Archaea, accompanied by extensive methodological developments in environmental microbiology, sequencing technologies, physiology, cell biology, and phylogenetics, has further changed our view on the diversity of life, the tree topology, as well as the ecological and evolutionary importance of Archaea. In particular, the use of cultivation-independent techniques, such as metagenomics and single-cell genomics, which allow us to obtain genomes of uncultivated organisms directly from environmental samples [3, 4], have been a key element leading to our changed perception of archaeal diversity and distribution. While Archaea have originally been viewed as comprising predominantly “extremophilic” organisms inhabiting environments with high temperature, salinity, and high or low pH, they are now known to be ubiquitous in all environments on Earth, including marine waters and freshwater lakes, sediments, soils (including plant roots), aquifers, and the human microbiome to name a few [5–7]. With their widespread ecological distribution and important metabolic capabilities, Archaea are recognized as key players in a wide variety of biogeochemical processes, including the sulfur, nitrogen, and carbon cycles [8]. For instance, Archaea include the only known organisms able to conserve energy through the anaerobic production or consumption of methane in processes referred to as methanogenesis and anaerobic methane oxidation, respectively. Since methane is an extremely potent greenhouse gas, with a global-warming potential about 25 times greater than carbon dioxide, these Archaea have an essential role in the global carbon budget and consequently climate change [9]. Finally, the study of archaeal phylogenetic diversity and evolution has fundamentally changed our understanding of the eukaryotic cell (see below) [10].