title: Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.
abstract: Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.
authors.affiliation: Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
authors.forename: C B
authors.initials: CB
authors.lastname: Walker
authors.forename: J R
authors.initials: JR
authors.lastname: de la Torre
authors.forename: M G
authors.initials: MG
authors.lastname: Klotz
authors.forename: H
authors.initials: H
authors.lastname: Urakawa
authors.forename: N
authors.initials: N
authors.lastname: Pinel
authors.forename: D J
authors.initials: DJ
authors.lastname: Arp
authors.forename: C
authors.initials: C
authors.lastname: Brochier-Armanet
authors.forename: P S G
authors.initials: PS
authors.lastname: Chain
authors.forename: P P
authors.initials: PP
authors.lastname: Chan
authors.forename: A
authors.initials: A
authors.lastname: Gollabgir
authors.forename: J
authors.initials: J
authors.lastname: Hemp
authors.forename: M
authors.initials: M
authors.lastname: Hügler
authors.forename: E A
authors.initials: EA
authors.lastname: Karr
authors.forename: M
authors.initials: M
authors.lastname: Könneke
authors.forename: M
authors.initials: M
authors.lastname: Shin
authors.forename: T J
authors.initials: TJ
authors.lastname: Lawton
authors.forename: T
authors.initials: T
authors.lastname: Lowe
authors.forename: W
authors.initials: W
authors.lastname: Martens-Habbena
authors.forename: L A
authors.initials: LA
authors.lastname: Sayavedra-Soto
authors.forename: D
authors.initials: D
authors.lastname: Lang
authors.forename: S M
authors.initials: SM
authors.lastname: Sievert
authors.forename: A C
authors.initials: AC
authors.lastname: Rosenzweig
authors.forename: G
authors.initials: G
authors.lastname: Manning
authors.forename: D A
authors.initials: DA
authors.lastname: Stahl
mesh_terms: D000599:Amino Acids, Diamino / Q000096:biosynthesis; D000641:Ammonia / Q000378:metabolism; D052818:Autotrophic Processes / Q000235:genetics*; D002455:Cell Division / Q000235:genetics; D019615:Crenarchaeota / Q000166:cytology / Q000235:genetics*; D004579:Electron Transport / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D020745:Genome, Archaeal / Q000235:genetics*; D038622:Internationality; D054892:Metagenome / Q000235:genetics; D009584:Nitrogen / Q000378:metabolism*; D010084:Oxidation-Reduction; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D000599:Amino Acids, Diamino; D022661:RNA, Untranslated; C121557:hydroxyectoine; D000641:Ammonia; D009584:Nitrogen