title: Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.
abstract: The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.
authors.affiliation: Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Lebedeva
authors.forename: Roland
authors.initials: R
authors.lastname: Hatzenpichler
authors.forename: Eric
authors.initials: E
authors.lastname: Pelletier
authors.forename: Nathalie
authors.initials: N
authors.lastname: Schuster
authors.forename: Sandra
authors.initials: S
authors.lastname: Hauzmayer
authors.forename: Aleksandr
authors.initials: A
authors.lastname: Bulaev
authors.forename: Nadezhda V
authors.initials: NV
authors.lastname: Grigor'eva
authors.forename: Alexander
authors.initials: A
authors.lastname: Galushko
authors.forename: Markus
authors.initials: M
authors.lastname: Schmid
authors.forename: Marton
authors.initials: M
authors.lastname: Palatinszky
authors.forename: Denis
authors.initials: D
authors.lastname: Le Paslier
authors.forename: Holger
authors.initials: H
authors.lastname: Daims
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification* / Q000166:cytology / Q000235:genetics* / Q000648:ultrastructure; D001483:Base Sequence; D001692:Biological Transport / Q000235:genetics; D002244:Carbon / Q000378:metabolism; D002455:Cell Division; D002633:Chemotaxis; D017753:Ecosystem; D005407:Flagella / Q000378:metabolism; D020745:Genome, Archaeal / Q000235:genetics*; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012426:Russia
chemical_list: D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D002244:Carbon; D000641:Ammonia