Marine genomics最新文献

Pseudoalteromonas is a widely distributed bacterial genus that is associated with marine algae. However, there is still limited knowledge about their bacteriophage. In this study, we reported the isolation of a novel lytic bacteriophage that infects Pseudoalteromonas marina. Transmission electron microscopy revealed that PS_L5 had an icosahedral head of 52.6 ± 2 nm and a non-contractile tail with length of 96.5 ± 2 nm. The genome sequence of this phage was 34, 257 bp and had a GC content of 40.75%. Furthermore, this genome contained 61 predicted open reading frames (ORFs), which involved in various functions such as phage structure, packaging, DNA metabolism, host lysis and other additional functions. Additionally, the phylogenetic analysis based on major capsid protein showed that the phage PS_L5 was closely related to five other Pseudoalteromonas phages, namely PHS3, PHS21, AL, SL25 and Pq0 which also possessed the non-contractile long tail. This study provided the fundamental insights into the evolutionary dynamics of Pseudoalteromonas phages and the interaction between phage and host.

Polaribacter huanghezhanensis KCTC 32516^T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516^T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.

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 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.

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. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238 Mb, scaffold N50 of 0. 238 Mb and GC level of 40%. Gene annotation, combining ab initio and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (H. laevigata, H. rubra, H. discus hannai and H. rufescens) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that H. midae is closely related to the Australian Greenlip (H. laevigata) and Blacklip (H. rubra). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.

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. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood–Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.

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. In addition, it is noteworthy that the MSP3 strain possesses genes encoding for both cytochrome c oxidase and cytochrome bd oxidase, thereby conferring upon it the ability to adapt to various levels of oxygen (oxic to microoxic) and to execute denitrification processes in the absence of oxygen. Moreover, it was observed that strain MSP3 had genes for the glyoxylate cycle, which is an alternative pathway to the TCA cycle. Furthermore, it was observed that the MSP3 strain exhibited the ability to thrive across a diverse spectrum of NaCl concentrations, ranging from 2% to 10% (w/v). Collectively, strain MSP3 may possess an advantage over competitors within the marine ecosystem, particularly in conditions where carbon substrates are restricted. The genomic-based assumption could potentially be substantiated by the presence of a multitude of transporter genes within the genome.

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 SM1966^T, 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 SM1966^T and its genomic characteristics to utilize DMSP, which may be produced by Ulva pertusa. The genome of strain SM1966^T contains one circular chromosome (4.3 Mbp) and one circular plasmid (149,271 bp). Genomic analysis showed that strain SM1966^T possesses a set of genes involved in DMSP transport, DMSP cleavage and the catabolism of acrylate, one product of DMSP cleavage. The results indicated that strain SM1966^T has the capacity to utilize DMSP and produce dimethyl sulfide (DMS), a volatile infochemical with important roles in global sulfur cycling. This study provides genetic insights into DMSP catabolism by algae-associated bacteria.

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. LC-MS profiles further supported the production of new CLD congeners. Bafilomycins were also found produced in abundance, corresponding to another type I PKS BGC highly homologous to that of bafilomycin B1 from S. lohii. CLDs are indolizidine alkaloids consisting a fused five- and six-membered ring system with an intriguing cyclopropane terminal linked by a trans-dienic chain. The cyclization mechanism of the cylopropyl ring, one of its pharmacophores, is still unknown. Genome sequencing of the new CLD producer and subsequent comparative analysis of their gene clusters would further our understanding of the chemistry behind cyclopropane formation.

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 1K03223^T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223^T 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. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of H. flavus revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.

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. We performed a whole metagenomic shotgun approach for the mantle bacterial cells after a differential pelleting procedure. In this procedure, we separated most of the prokaryotic cells from the eukaryotic host cells. Our findings showed that the mantle-body part holds a diverse group of bacterial species relating mainly to Proteobacteria and Tenericutes phyla. There were novel findings regarding the bacterial members associated with the nudibranch mollusks group. Various species were not previously recorded as bacterial symbionts with nudibranchs. Those members were Bathymodiolus brooksi thiotrophic gill symbiont (23.2%), Mycoplasma marinum (7.4%), Mycoplasma todarodis (5%), and Solemya velum gill symbiont (2.6%). The presence of these bacterial species assumed a nutritional role to the host. However, some of these species were present in a high abundance, suggesting their important symbiosis with Chromodoris quadricolor. In addition, exploring the bacterial ability to produce valuable products resulted in the prediction of 2088 biosynthetic gene clusters (BGCs). We identified different gene cluster classes. Polyketide BGC class was the most represented. Others were related to fatty acid BGCs, RiPP, saccharide, terpene, and NRP BGC classes. Prediction of the activity of these gene clusters resulted in, mainly, an antibacterial activity. In addition, different antimicrobial secondary metabolites were also detected. These secondary metabolites are considered key components regulating the bacterial species interactions in their ecosystem. This suggested the significant contribution of these bacterial symbionts to protect the nudibranch host against predators and pathogens. Globally, it is the first detailed study concerned with both the taxonomic diversity and functional potentials of the bacterial symbionts associated with Chromodoris quadricolor mantle.