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Battistuzzi2009chap06.Pdf Archaebacteria Fabia U. Battistuzzia,b,* and S. Blair Hedgesa higher stability to extreme conditions (5). Chemotrophy aDepartment of Biology, 208 Mueller Laboratory, The Pennsylvania is the most widely used metabolism, although photo- State University, University Park, PA 16802-5301, USA; bCurrent trophic members of the Halobacteriaceae can use light address: Center for Evolutionary Functional Genomics, The Biodesign to produce ATP (6). Six families also have the unique Institute, Arizona State University, Tempe, AZ 85287-5301, USA ability of obtaining energy by combining carbon diox- *To whom correspondence should be addressed (Fabia.Battistuzzi@ asu.edu) ide (or other carbon compounds) and hydrogen into methane (5). 7e Superkingdom Archaebacteria, comprising Abstract ~300 species, is subdivided into two recognized phyla, Euryarchaeota and Crenarchaeota (7). Two other phyla The Superkingdom Archaebacteria (~300 species) is divided have been proposed based on environmental sequences into two phyla, Euryarchaeota and Crenarchaeota, with only (Korarchaeota) and environmental sequences plus two other phyla (Korarchaeota and Nanoarchaeota) under one fully sequenced genome (Nanoarchaeota) (8–11) but consideration. Most large-scale phylogenetic analyses have not been o1 cially recognized and their phylogen- agree on a topology that clusters (i) Methanomicrobia, etic position is uncertain. 7 e molecular information Halobacteria, Archaeoglobi, and Thermoplasmata and (ii) Methanobacteria, Methanococci, and Methanopyri. A molecular timetree estimated here shows divergences among classes in the Archean Eon, 3500–2500 million years ago (Ma), and family divergences in the Proterozoic Eon, 2394–829 Ma. The timetree also suggests that methano- genesis had arisen by the mid-Archean (>3500 Ma) and that adaptation to thermoacidophilic environments occurred before 1000 Ma. Extremophiles are common among species in the Superkingdom Archaebacteria (also called “Archaea”, Fig. 1) (1). For example, the species referred to as “Strain 121” can survive temperatures up to 121°C, higher than any other organism (2), and hyperacidophiles are found in the Family 7 ermoplasmataceae, where two species (Picrophilus oshimae and Picrophilus torridus) are the only known organisms capable of living at a pH as low as zero (3, 4). Archaebacteria show many other phenotypes including the unique ability to produce methane (meth- anogenesis). 7 ey have cell wall structures formed either by pseudopeptidoglycan (i.e., a material similar to the Fig. 1 Halobacteria (rod-shaped Halobacterium) from Mono peptidoglycan of eubacteria), polysaccharides, or glyco- Lake, California; mixed sample (upper left); and close-up of a proteins (S-layer) (5), which resemble the single-layer cell (upper right). Methanococci (round-shaped Methanococcus); Cluster of cells (lower left) and close-up of two cells (lower structure (i.e., cell membrane plus cell wall) present in right). Credits: D. J. Patterson, provided by micro*scope (http:// gram-positive eubacteria. Furthermore, archaebacteria microscope.mbl.edu) under creative commons license (upper have a unique cell membrane structure composed of images); and Electron Microscopy Laboratory, University of ether-linked glycerol diethers or tetraethers that confer a California, Berkeley (lower images). F. U. Battistuzzi and S. B. Hedges. Archaebacteria. Pp. 101–105 in e Timetree of Life, S. B. Hedges and S. Kumar, Eds. (Oxford University Press, 2009). HHedges.indbedges.indb 110101 11/28/2009/28/2009 11:25:23:25:23 PPMM 102 THE TIMETREE OF LIFE Archaeoglobaceae (Archaeoglobi) 8 Halobacteriaceae (Halobacteria) 9 Methanosarcinaceae 6 10 Methanospirillaceae Thermoplasmataceae 12 Methanomicrobia 4 Picrophilaceae Methanopyraceae (Methanopyri) Thermoplasmata 5 Methanobacteriaceae (Methanobacteria) 3 7 Methanocaldococcaceae 11 2 Methanococcaceae Thermococcaceae (Thermococci) Methanococci 1 Sulfolobaceae (Thermoprotei) Nanoarchaeum (Nanoarchaeota) Crenarchaeota Euryarchaeota Ea Pa Ma Na Pp Mp Np Pz HD ARCHEAN PROTEROZOIC PH 4000 3000 2000 1000 0 Million years ago Fig. 2 A timetree of archaebacteria. Divergence times are shown in Table 1. Abbreviations: Ea (Eoarchean), HD (Hadean), Ma (Mesoarchean), Mp (Mesoproterozoic), Na (Neoarchean), Np (Neoproterozoic), Pa (Paleoarchean), PH (Phanerozoic), Pp (Paleoproterozoic), and Pz (Paleozoic). available for Korarchaeota is based only on a few tens weaker biases given by a shorter evolutionary history), of environmental sequences (small subunit ribosomal (ii) a lower known taxonomic diversity (e.g., nine vs. 34 RNA, SSU rRNA) as none of the Korarchaeota has been classes for archaebacteria and eubacteria, respectively) successfully cultivated. 7 e sequences available place (7) which could mask contrasting phylogenetic sig- this group before the Euryarchaeota/Crenarchaeota nals, and (iii) speciation events more evenly distributed divergence and show the presence of A ve major clus- throughout time that did not result in rapid adaptive ters within this putative phylum ( 8, 12). On the other radiations (i.e., no or few short internal branches that are hand, the genome of one species of Nanoarchaeota, di1 cult to resolve phylogenetically) (14). While the geo- Nanoarchaeum equitans, has been fully sequenced (13) logic record and molecular clock studies do not support and it is routinely used in multiple-gene phylogenies and the A rst hypothesis (i.e., archaebacteria and their metab- indel analyses (9, 14–18). 7 ese studies show contrasting olisms appear early in Earth’s history), it is not possible topologies for Nanoarchaeota, with some placing it basal to discard either of the other two hypothesis as a pos- to Euryarchaeota and Crenarchaeota (13), others clus- sible cause for the apparently more stable phylogeny of tering it with Crenarchaeota (17, 18), and other studies archaebacteria. clustering it within Euryarchaeota (9, 14, 16). 7 ese dif- Species of Crenarchaeota are placed in six families, ferent phylogenetic positions aB ect the classiA cation of three of which (7 ermoproteaceae, Desulfurococcaceae, this species, which is either being considered a member and Sulfolobaceae) have been used in multiple-gene ana- of a new phylum (i.e., Nanoarchaeota) or a fast-evolving lyses of relationships. 7 ese analyses consistently have lineage of Euryarchaeota (14). found Sulfolobaceae and Desulfurococcaceae as closest 7 e phylogeny of taxa within the Phyla Euryarchaeota relatives to the exclusion of 7 ermoproteaceae, with sig- and Crenarchaeota is mostly stable. 7 ree hypotheses niA cant support (14, 15, 17–19). Within Euryarchaeota, have been proposed to explain this property of archae- topological diB erences are more common depending bacteria that sets them apart from eubacteria: (i) a youn- on the genes and methods used to build the phylogen- ger origin of archaebacteria compared to eubacteria (i.e., etic tree. Gene content studies, for example, show the HHedges.indbedges.indb 110202 11/28/2009/28/2009 11:25:25:25:25 PPMM Archaebacteria 103 Table 1. Divergence times (Ma) and their confi dence/credibility intervals (CI) among archaebacteria. Timetree Estimates Node Time Ref. (19) This study Ref. (32) Time CI Time CI Time 1 4193 – – 4193 4200–4176 – 2 4187 4112 4486–3314 4187 4199–4163 3460 3 3594 – – 3594 3691–3503 – 4 3468 – – 3468 3490–3460 – 5 3313 – – 3313 3388–3232 – 6316030853514–246931603257–3056– 7309331243520–252230933210–2968– 8 2799 2625 3102–2037 2799 2936–2656 – 9 2430 – – 2430 2596–2256 2740 10 2216 – – 2216 2394–2034 – 11 1676 – – 1676 1875–1475 – 12 992 – – 992 1174–829 – Note: Node times in the timetree are from this study. Class Halobacteria as a deep-diverging lineage at the genome-scale analyses with diB erent tree-building meth- base of Euryarchaeota and Crenarchaeota (20, 21) fol- ods (supertrees, ML, Bayesian) (17, 18, 53). lowed by the Class 7 ermoplasmata, either alone or clus- All of the previous evidence points toward the pres- tering with Crenarchaeota. Because both Halobacteria ence of two main clusters within Euryarchaeota: one and 7 ermoplasmata are classiA ed as euryarchaeotes formed by the classes Methanomicrobia, Halobacteria, (22), their phylogenetic position determines the mono- Archaeoglobi, and 7 ermoplasmata, and another or paraphyly of this phylum. Multiple-gene phylog- by the classes Methanococci, Methanobacteria, and enies show Halobacteria as closely related to the Class Methanopyri. 7 ese clusters are the same found in a Methanomicrobia, a derived position that is highly study of sequences from 25 core proteins shared by 218 supported by maximum likelihood (ML), Bayesian, prokaryote species (including archaebacteria and eubac- and supertree phylogenies with diB erent sets of genes teria) (53). In that analysis, all available species with a (14, 17, 18, 23, 53). 7 ermoplasmata, instead, are alter- complete genome were included and a complete matrix natively supported at the base of Euryarchaeota ( 17, of genes and species was constructed. Single gene trees 18) or clustering with Archaeoglobi, Halobacteria, and were manually screened for orthology and vertical Methanomicrobia (14, 23, 53). Only this last position is inheritance (i.e., genes not showing paraphyly of archae- signiA cantly supported by all analyses (Fig. 2). bacteria and eubacteria or signiA cantly supported deep- Recent studies with large data sets have solved the nesting of one class within another). Site homology of issue of the position of the Class Methanopyri. 7 is the multiple sequence alignment was
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