title: Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota.
abstract: Globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth. Based on 16S rRNA phylogeny, initial assignment of these archaea was to the Crenarchaeota. By contrast, features of the first genome sequence from a member of this group suggested that they belong to a novel phylum, the Thaumarchaeota. Here, we re-investigate the Thaumarchaeota hypothesis by including two newly available genomes, that of the marine ammonia oxidizer Nitrosopumilus maritimus and that of Nitrososphaera gargensis, a representative of another evolutionary lineage within this group predominantly detected in terrestrial environments. Phylogenetic studies based on r-proteins and other core genes, as well as comparative genomics, confirm the assignment of these organisms to a separate phylum and reveal a Thaumarchaeota-specific set of core informational processing genes, as well as potentially ancestral features of the archaea.
authors.affiliation: University of Vienna, Department of Genetics in Ecology, Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Anja
authors.initials: A
authors.lastname: Spang
authors.forename: Roland
authors.initials: R
authors.lastname: Hatzenpichler
authors.forename: Céline
authors.initials: C
authors.lastname: Brochier-Armanet
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.forename: Patrick
authors.initials: P
authors.lastname: Tischler
authors.forename: Eva
authors.initials: E
authors.lastname: Spieck
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Streit
authors.forename: David A
authors.initials: DA
authors.lastname: Stahl
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.forename: Christa
authors.initials: C
authors.lastname: Schleper
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002455:Cell Division / Q000235:genetics; D017124:Conserved Sequence; D019615:Crenarchaeota / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D004264:DNA Topoisomerases, Type I / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019605:Euryarchaeota / Q000145:classification / Q000235:genetics*; D020745:Genome, Archaeal; D010084:Oxidation-Reduction; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D019843:Archaeal Proteins; D004268:DNA-Binding Proteins; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S; D012269:Ribosomal Proteins; D000641:Ammonia; D012321:DNA-Directed RNA Polymerases; D004264:DNA Topoisomerases, Type I