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 degrees 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 omega 7c (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)).National Natural Science Foundation of China [40976069, 40930847, 30710103908

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

Features of binned contigs for genomes of thaumarchaeota, epsilon- and gammaproteobacteria (≥ 5 Kb contigs).

<p>ND, not detected.</p

Principal component analysis of oligonucleotide frequencies in assembled contigs from two archaeal enrichment cultures

<p>(A) AR culture, and (B) SJ culture. Reference genomes are shown as larger circles. The total number of contigs for each group (<i>Gammaproteobacteria</i>, <i>Epsilonproteobacteria,</i> and <i>Thaumarchaeota</i>), total length, mean length, and GC content range are also indicated. The contig types and published genomes are as follows: orange, <i>Gammaproteobacteria</i>; yellow, <i>Thaumarchaeota</i>; green, <i>Epsilonproteobacteria</i>; light green, assembled contigs including viral coding sequences; gray, not identified; red, <i>Ca</i>. “Cenarchaum symbiosum” A (CsymA); fuchsia, <i>Ca</i>. “C. symbiosum” B (CsymB); lime, <i>Nitrosopumilus maritimus</i> SCM1 (Nmar); blue, <i>Ca</i>. “Nitrosoarchaeum koreensis” MY1 (MY1); cyan, <i>Ca</i>. “Nitrosoarchaeum limnia” (Nlim); violet, <i>Ca</i>. “Nitrososphaera gargensis” (Ngar); teal, <i>Sulfurovum</i> sp. NBC37-1 (Sul); and purple, <i>Thiomicrospira crunogena</i> XCL-2 (Tcr).</p

Comparison of the <i>Ca</i>. “Nitrosopumilus sediminis” AR2 genomic region containing genes for urea utilization with those of <i>Ca</i>. “Cenarchaeum symbiosum” and environmental metagenomes.

<p><i>Ca</i>. “N. sediminis” AR2 genome is central, with the <i>Ca</i>. “C. symbiosum”, <i>Ca</i>. “Nitrososphaera gargensis”, and environmental metagenomic regions above and below, respectively. Homologous genes are connected with shaded regions, and the shaded color indicates the percent identity as determined by TBLASTX.</p