Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

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.

Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.

A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for the first time. The type strain, KORDI 51-2(T), was isolated from seawater of Chuuk lagoon located in a tropical area. Although it belonged to a clade exclusively comprised of extremely halotolerant strains by phylogenetic analyses, R. lacunae is known to be incapable of growth at high salt concentration over 10%. Here we report the main features of the genome of R. lacunae strain KORDI 51-2(T). The genome of R. lacunae contains a gene cluster for phosphonate utilization encoding three transporters, one regulator and eight C-P lyase subunits.

Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment.

Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play important roles in the global nitrogen and carbon cycles. We here present a high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, which was found to dominate an ammonia-oxidizing enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a significant number of nonoverlapping genes (ca. 30%), similarities of this strain to "Candidatus Nitrosopumilus maritimus" were revealed by core genes for archaeal ammonia oxidation and carbon fixation, G+C content, and extensive synteny conservation.

Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample.

A bacterial strain (B2-7(T)) capable of degrading a wide range of polycyclic aromatic hydrocarbon compounds (2-4 rings) was isolated from a water sample taken from Botan Oil Port in Xiamen, China. The isolate was Gram-negative, short-rod-shaped, aerobic, non-motile and formed yellow-pigmented colonies on LB medium. Cells of strain B2-7(T) were catalase-positive and oxidase-negative. Optimal growth of strain B2-7(T) was observed at pH 7.0, at 26 °C and in 0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B2-7(T) grouped with members of the genus Sphingomonas and it showed 16S rRNA gene sequence similarity of 95.40 % to Sphingomonas yunnanensis YIM 003(T). The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. Q-10 and sym-homospermidine were the predominant ubiquinone and polyamine components, respectively. The major fatty acids were C(18:1)ω7c (67.2 %), C(14:0) 2-OH (10.0 %) and C(16:0) (9.6 %). The G+C content of the genomic DNA was 61.8 mol%. Based on phenotypic properties, and phylogenetic and genomic data, strain B2-7(T) represents a novel species of the genus Sphingomonas within the class Alphaproteobacteria, for which the name Sphingomonas polyaromaticivorans sp. nov. is proposed. The type strain is B2-7(T) ( = KCCM 42951(T) = JCM 16711(T)).