Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan.

ABSTRACT: Psychrobacter sp. strain KH172YL61 is a Gram-negative bacterium isolated from deep-sea sediment in the Nankai Trough in Japan. Here, we report the complete genome sequence of this strain, which has a genome size of 3.19?Mb, with a G+C content of 44.0%.

SUBMITTER: Evans-Yamamoto D

PROVIDER: S-EPMC6473151 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete Genome Sequence of <i>Psychrobacter</i> sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan.

Evans-Yamamoto Daniel D Takeuchi Nao N Masuda Takahiro T Murai Yumi Y Onuma Yasuhide Y Mori Hideto H Masuyama Nanami N Ishiguro Soh S Yachie Nozomu N Arakawa Kazuharu K

Microbiology resource announcements 20190418 16

<i>Psychrobacter</i> sp. strain KH172YL61 is a Gram-negative bacterium isolated from deep-sea sediment in the Nankai Trough in Japan. Here, we report the complete genome sequence of this strain, which has a genome size of 3.19 Mb, with a G+C content of 44.0%. ...[more]

PMID: 31000557

Similar Datasets

Draft Genome Sequence of Alcanivorax sp. Strain KX64203 Isolated from Deep-Sea Sediments of Iheya North, Okinawa Trough.

Project description:This report describes the draft genome sequence of Alcanivorax sp. strain KX64203, isolated from deep-sea sediment samples. The reads generated by an Ion Torrent PGM were assembled into contigs, with a total size of 4.76 Mb. The data will improve our understanding of the strain's function in alkane degradation.

| S-EPMC5000830 | biostudies-literature

Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone.

Project description:Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration of subseafloor microbes. Detection of a diverse array of reductive dehalogenase-homologous (rdhA) genes suggests that subseafloor organohalide-respiring microbial communities may play significant ecological roles in the biogeochemical carbon and halogen cycle in the subseafloor biosphere. We report here the spatial distribution of dehalogenation activity in the Nankai Trough plate-subduction zone of the northwest Pacific off the Kii Peninsula of Japan. Incubation experiments with slurries of sediment collected at various depths and locations showed that degradation of several organohalides tested only occurred in the shallow sedimentary basin, down to 4.7 metres below the seafloor, despite detection of rdhA in the deeper sediments. We studied the phylogenetic diversity of the metabolically active microbes in positive enrichment cultures by extracting RNA, and found that Desulfuromonadales bacteria predominate. In addition, for the isolation of genes involved in the dehalogenation reaction, we performed a substrate-induced gene expression screening on DNA extracted from the enrichment cultures. Diverse DNA fragments were obtained and some of them showed best BLAST hit to known organohalide respirers such as Dehalococcoides, whereas no functionally known dehalogenation-related genes such as rdhA were found, indicating the need to improve the molecular approach to assess functional genes for organohalide respiration.

| S-EPMC3638456 | biostudies-literature

Complete Genome Sequence of Alteromonas sp. Strain I4, Isolated from the Japan Sea.

Project description:A novel strain of Alteromonas, I4, was isolated from a shallow beach of the Japan Sea. Here, we report the complete genome sequence of I4; this strain contains a single circular chromosome (5,133,645 bp; G+C content, 48.4%) and a single circular putative plasmid (123,836 bp; G+C content, 45.1%).

| S-EPMC6872891 | biostudies-literature

Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment.

Project description:Bacillus sp. strain KH172YL63 is a Gram-positive bacterium isolated from the deep-sea floor surface sediment at 3,308 m below sea level in the Nankai Trough in Japan. Here, we report the complete genome sequence of Bacillus sp. strain KH172YL63, which has a genome size of 4,251,700 bp and a G+C content of 44.8%.

| S-EPMC7163022 | biostudies-literature

Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341T, Isolated from Deep-Sea Hydrothermal Sediments.

Project description:We report the genome sequence of Palaeococcus pacificus DY20341(T), isolated from a sediment sample collected from eastern Pacific Ocean hydrothermal fields, which is the first report of a complete genome for a Palaeococcus species. The genome sequence will help to better understand differentiation phylogenetic relationships and evolution of several Thermococcales species.

| S-EPMC4574382 | biostudies-literature

Draft Genome Sequence of Thiobacimonas sp. Strain D13, a Phthalate Ester-Degrading Bacterium Isolated from Deep-Sea Sediments.

Project description:Thiobacimonas sp. strain D13, newly isolated from the sediments of the southeastern Pacific, can effectively degrade phthalate ester. Here, we report the 5.22-Mbp draft genome sequence of this strain, which will provide insights into the molecular mechanisms underlying its degradation ability.

| S-EPMC6588033 | biostudies-literature

Draft Genome Sequence of Salinispora sp. Strain H7-4, Isolated from Deep-Sea Sediments of the Shikoku Basin.

Project description:Salinispora spp. are obligate marine actinomycetes reported mainly from shallow tropical and subtropical marine habitats. In this announcement, we present the isolation and draft genome sequence of Salinispora sp. strain H7-4 of a new 16S rDNA phylotype from deep-sea sediments of the Shikoku Basin.

| S-EPMC7645655 | biostudies-literature

Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater.

Project description:BackgroundSpecial features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host.ResultsA total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHB-4 (PHB-negative mutant).ConclusionsA new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes.

| S-EPMC4326521 | biostudies-literature

Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off Kashima, Japan.

Project description:Altererythrobacter sp. strain B11 is an aromatic monomer-degrading bacterium newly isolated from sediment under the seabed off Kashima, Japan, at a depth of 2,100 m. Here, we report the complete nucleotide sequence of the genome of strain B11.

| S-EPMC5864952 | biostudies-literature