Marine Genomics

Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. Marinomonas algicola SM1966T , a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of Ulva pertusa (Chlorophyta) algal sample collected off the coastal areas of Rongcheng, China. Here, we report the complete genome sequence of strain SM1966T and its genomic characteristics to utilize DMSP, which may be produced by Ulva pertusa...

As a moderate halophilic-heterotrophic bacterium, Halomonas alkaliantarctica MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes (61 tRNA and 18 rRNA). According to the genome annotation, it was revealed that the strain MSP3 harbors genes encoding for urease and urea transporters, which play a crucial role in the process of urea degradation and utilization...

Streptomyces sp. HNA39 is a promising candidate for the production of antineoplastic metabolites screened from a collection of 448 actinomycetes derived from coastal sediments. The complete genome sequence of HNA39 comprises a 7,351,753-bp linear chromosome with a GC content of 71.94%. Whole genome analysis reveals the presence of 29 putative biosynthetic gene clusters (BGCs) encoding secondary metabolites. Among them, a type I PKS BGC shows an 82% similarity with the cyclizidine (CLD) BGC identified from Streptomyces NCIB 11649...

One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA...

Herein, we report the complete genome sequence of Pseudoalteromonas sp. PS1M3 (= NCBI 87791), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs. The genome of PS1M3 had a total size of 4,351,630 bp, an average GC content of 39.9%, and contained a total of 3811 predicted protein coding sequences, 28 rRNAs, and 100 tRNAs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was utilized to annotate the genes and KofamKOALA within KEGG assigned a gene cluster involved in glycogen biosynthesis and metabolic pathways with regard to heavy metal resistance (copper; cop and mercury; mer), indicating that PS1M3 can potentially use a stored glycogen as an energy source under oligotrophic environment and cope with multi-heavy metal contamination...

Bacillus cereus 2-6A, was isolated from the sediments in the hydrothermal area of the Pacific Ocean with a water depth of 2628 m. In this study, we report the whole genome sequence of strain 2-6A and analyze that to understand its metabolic capacities and biosynthesis potential of natural products. The genome of strain 2-6A consists of a circular chromosome of 5,191,018 bp with a GC content of 35.3 mol% and two plasmids of 234,719 bp and 411,441 bp, respectively. Genomic data mining reveals that strain 2-6A has several gene clusters involved in exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) production and complex polysaccharides degradation...

During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus Hyphococcus. The type strain, Hyphococcus flavus MCCC 1K03223T , was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223T is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites...

Mycolicibacterium phocaicum RL-HY01, a marine bacterial strain with the capability to degrade phthalic acid esters (PAEs), was isolated from Zhanjiang Bay, China. Here, the complete genome sequence of strain RL-HY01 was presented. The genome of strain RL-HY01 contains one circular chromosome of 6,064,759 bp with a G + C content of 66.93 mol%. The genome contains 5681 predicted protein-encoding genes, 57 tRNA genes, and 6 rRNA genes. Genes and gene clusters potentially involved in the metabolism of PAEs were further identified...

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential...

Haliotis midae or "perlemoen" is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in minimising the pressure on the wild populations. Here, the draft genome of H. midae has been sequenced, assembled, and annotated...

Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27...

Nudibranchs are colorful marine invertebrates having a diverse group of understudied animals. Recently, some nudibranch members have acquired some attention while others still have not. Chromodoris quadricolor is a member of the Red Sea nudibranch, which did not have the chance to get significant attention. Unlike various invertebrates, it lacks a shell suggesting that it must defend itself in other ways. Therefore, in the present study, we were concerned about the mantle-associated bacterial communities. Being essential partners of this dorid nudibranch system, we investigated their taxonomic and functional profiles...

Bacillus subtilis TY-1 was isolated from 2000 m-deep sea sediments of the Western Pacific Ocean, which was found to exhibit strong antagonistic activity against tobacco bacterial wilt caused by Ralstonia solanacearum. Here, we present the annotated complete genomic sequence of the strain Bacillus subtilis TY-1. The genome consists of a 4,030,869-bp circular chromosome with a G + C content of 43.88%, 86 tRNAs, and 30 rRNAs. Genomic analysis identified a large number of gene clusters involved in the biosynthesis of antibacterial metabolites, including lipopeptides(surfactin, bacillibactin, and fengycin) and polyketides(bacillaene)...

Members of the genus Pseudomonas have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, Pseudomonas sp. BSw22131, was isolated from seawater in Kongsfjorden, Svalbard. The bacterium can grow with algae-derived dimethylsulfoniopropionate (DMSP) as the sole carbon source. Here, we sequenced the complete genome of strain BSw22131, which contained a single circular chromosome of 5,739,290 (G + C content of 58.23 mol%) without any plasmids...

Marine algicidal bacteria and their metabolites are considered to be one of the most effective strategies to mitigate the harmful algal blooms (HABs). The bacterium Hahella sp. KA22 has previously been confirmed to have strong algicidal activity against the HABs causing microalgae, Heterosigma akashiwo. In this study, the molecular mechanism of microalgae cell death was detected. The results showed that the cell growth rate and photosynthetic efficiency were inhibited with addition of algicidal strain KA22, while the accumulation of reactive oxygen species (ROS) and oxidative damage in H...

Many secondary metabolites with medicinal potential are produced by various animals, plants, and microorganisms. Because marine creatures have a greater proportion of unexplored biodiversity than their terrestrial counterparts, they have emerged as a key research focus for the discovery of natural product drugs. Several studies have revealed that bacteria isolated from Chromodoris quadricolor (C. quadricolor) have antibiotic and anticancer properties. In this study, meta-transcriptomics and meta-proteimic analysis were combined to identify biosynthetic gene clusters (BGCs) in the symbiotic bacteria of the C...

Pseudomonas chengduensis BC1815, isolated from a marine sediment sample of the Pacific Ocean, can grow in mineral medium with PET plastic as sole carbon source. Here, we present the complete genome of Pseudomonas chengduensis BC1815, which will facilitate the genome mining of PET degrading enzymes. The total length of the sequenced genome consists of 5,578,440 bases, with mean G + C content of 62.65%. A total of 5150 coding genes including 65 tRNAs and 12 rRNAs were predicted in the genome. Thirteen proteins of esterase, lipase and α/β hydrolase were taken as candidates for PET degrading enzymes, in which eight were membrane bounded and the others were secretory...

Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of 4.30 Mb and average GC content of 58.39%. In total, 4129 CDSs, 52 tRNA genes and 9 rRNA genes were obtained...

Transcriptomes are appropriate resources for studying species that lack sequenced genomes, as they can serve as references for a broad suite of genetic applications, including: phylogenetic assessments, population genomics, and evaluate responses to environmental fluctuations. Here, we present the transcriptomes of two species of marine fishes of commercial and ecological relevance in the Western Atlantic: Lutjanus griseus and L. synagris. This project represents a step forward on developing genomic resources for important species of the Atlantic Ocean...

Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases...