title: Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean.
abstract: Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613; asantoro@umces.edu.
authors.forename: Alyson E
authors.initials: AE
authors.lastname: Santoro
authors.affiliation: Microbial and Environmental Genomics and.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Informatics Group, J. Craig Venter Institute, San Diego, CA 92037;
authors.forename: R Alex
authors.initials: RA
authors.lastname: Richter
authors.affiliation: Microbial and Environmental Genomics and Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA 92110; and.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Craig
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613;
authors.forename: Paul
authors.initials: P
authors.lastname: Carini
authors.affiliation: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: McIlvin
authors.affiliation: Informatics Group, J. Craig Venter Institute, San Diego, CA 92037;
authors.forename: Youngik
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613;
authors.forename: William D
authors.initials: WD
authors.lastname: Orsi
authors.affiliation: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Moran
authors.affiliation: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543.
authors.forename: Mak A
authors.initials: MA
authors.lastname: Saito
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism; D019843:Archaeal Proteins / Q000096:biosynthesis / Q000235:genetics; D019848:Gene Expression Regulation, Archaeal / Q000502:physiology*; D056186:Metagenomics; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D020543:Proteome / Q000096:biosynthesis / Q000235:genetics; D040901:Proteomics; D014871:Water Microbiology
chemical_list: D019843:Archaeal Proteins; D020543:Proteome
keywords: archaea; genome streamlining; marine metagenomics; nitrification