title: Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.
abstract: Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.
authors.affiliation: Department of Biology, Jeju National University, Jeju, South Korea.
authors.forename: Soo-Je
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain.
authors.forename: Rohit
authors.initials: R
authors.lastname: Ghai
authors.affiliation: Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain.
authors.forename: Ana-Belén
authors.initials: AB
authors.lastname: Martín-Cuadrado
authors.affiliation: Departmento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodríguez-Valera
authors.affiliation: Korean Bioinformation Center, KRIBB, Yuseong-gu, Daejeon, South Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Korea Institute of Ocean Science and Technology, Ansan, South Korea.
authors.forename: KaeKyoung
authors.initials: K
authors.lastname: Kwon
authors.affiliation: Korea Institute of Ocean Science and Technology, Ansan, South Korea.
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Department of Microbiology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Eugene L
authors.initials: EL
authors.lastname: Madsen
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
authors.forename: Sung-Keun
authors.initials: SK
authors.lastname: Rhee
mesh_terms: D000641:Ammonia / Q000378:metabolism; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D020745:Genome, Archaeal; D019015:Geologic Sediments / Q000382:microbiology*; D010084:Oxidation-Reduction; D010802:Phylogeny
chemical_list: D000641:Ammonia