Marine genomics最新文献

Erythrobacter sp. JK5, a marine heterotrophic bacterium, was isolated from marine sediment in Jeju island, the Republic of Korea. Here, we report information on the complete genome of strain JK5, including a putative capability for photosynthesis. The genome of JK5 consisted of 3.34 Mbp with 64.2% G + C content, and contained 3210 protein-coding sequences and three rRNA genes. Genomic analysis revealed that strain JK5 might be grown under oxic, microoxic, or anoxic conditions using two types of terminal oxidase (high and low oxygen affinity) or nitrate reductase. The types IV and VI secretion systems presented in strain JK5 genome might reveal a survival advantage against their ecological competitors in the marine environment.

In this paper, we identify some sponge specimens collected in the Faro Lake in Sicily, and belonging to Haliclona (Halicoclona) by using morphological analysis accompanied by molecular analysis through amplification of several molecular markers (18S and 28S rRNA, CO1 and ITS).

The samples are identified as. H. (Halichoclona) vansoesti de Weerdt, de Kluijver & Gómez, 1999, a species native to the Caribbean, and therefore this is the first record of an alien species of the Demospongiae class (Porifera) from the Mediterranean Sea. This presence can be ascribed as results of global change (mainly global warming) that are affecting marine environment.

Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.

Streptomyces malaysiensis HNM0561 is a marine sponge-associated actinomycete with the potential to produce potential anti-androgens against prostate cancer cells, including malaymycin and mccrearamycin E. Here, we present the complete genome sequence of S. malaysiensis HNM0561, which consists of a linear chromosome of 11,656,895 bp and a circular plasmid of 32,797 bp, 9849 protein coding genes, 18 rRNA genes, 66 tRNA genes, and 191 sRNA genes. Genomic annotations revealed that 72.03% of the protein-coding genes were assigned to the COG database, among which the abundant genes were predicted to be involved in transcription, replication, carbohydrate transport and metabolism, and amino acid transport and metabolism. Forty-nine putative secondary metabolite biosynthetic gene clusters were found in the genome. Among them, the potential biosynthetic gene clusters of malaymycin and mccrearamycin E have been described respectively. The complete genome information presented here will enable us to investigate the biosynthetic mechanism of two novel structures of malaymycin and mccrearamycin E and to discover novel secondary metabolites with potential against prostate cancer cell activities.

Turbot (Scophthalmus maximus) is a flatfish, which is not only important in mariculture worldwide with the unique characteristic of body asymmetry, but also as an economically important species in aquaculture. Herein, we performed the first full-length transcriptome sequencing of turbot during the bacterial infection. A total of 307.1 Gb raw reads were obtained and processed with Iso-Seq, generating 187,509 high-quality redundant transcripts with an average length of 3005 base pairs. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis identified 81.5% complete BUSCOs and only 1.7% fragmented BUSCOs, suggesting a transcript structural completeness and functional diversity of this transcriptome. Moreover, the redundant transcripts were collapsed and compared to ENSEMBL reference with Cupcake and SQANTI3. Among 60,476 collapsed transcripts, we identified 12,059 annotated and 1684 novel genes. 42,956 (71.1%) transcripts provided new evidence for splice junctions identification. Furthermore, the untranslated region (UTR) identification was also benefited from the transcriptome. The open read frames prediction was conducted with PASApipeline. 42,118 transcripts were assigned with known function by aligning against Swiss-Prot or functional domain prediction. Taken together, the full-length transcriptome built in this study could provide important resources for immunologic research on turbot.

Southwest Indian Ridge (SWIR) increasingly becomes the hot spot of deep-sea mining and extreme life research. Strategies for future environmental conservation are undoubtedly required which makes investigation of microbial iron metabolisms imperative. Through deep metagenome sequencing, five iron-oxidizing Zetaproteoabacteria metagenome-assembled genomes were recovered from Longqi hydrothermal vent in the SWIR. Phylogenetic analysis revealed that two of the MAGs might represent novel genus in Zetaproteobacteria while other MAGs were related to Mariprofundus. Functional profile suggested that they might be aerobic chemolithoautotrophic species with genes encoding cytochrome c oxidase, iron oxidase cyc2 homologs and carbon fixation CBB pathway. Versatile capabilities of synthesizing diverse amino acids and cofactors were indicated while possession of various metal ion transporters could be vital to heavy metal resistance. Our work has provided more understanding about phylogenetic and functional features of iron-oxidizing Zetaproteobacteria, which might be important to investigate iron biogeochemistry and mineral oxidation in SWIR.

Embryonic development is a complex process involving the co-ordinated onset and integration of multiple morphological features and physiological functions. While the molecular basis of morphological development in embryos is relatively well known for traditional model species, the molecular underpinning of the development of physiological functions is not. Here, we used global gene expression profiling to investigate the transcriptional changes associated with the development of morphological and physiological function in the amphipod crustacean Gammarus chevreuxi. We compared the transcriptomes at three timepoints during the latter half of development, characterised by different stages of the development of heart form and function: 10 days post fertilisation (dpf, Early: no heart structure visible), 15 dpf (Middle: heart present but not fully functional), and 18 dpf (Late: regular heartbeat). Gene expression profiles differed markedly between developmental stages, likely representing a change in the activity of different processes throughout the latter period of G. chevreuxi embryonic development. Differentially expressed genes belonged to one of three distinct clusters based on their expression patterns across development. One of these clusters, which included key genes relating to cardiac contractile machinery and calcium handling, displayed a pattern of sequential up-regulation throughout the developmental period studied. Further analyses of these transcripts could reveal genes that may influence the onset of a regular heartbeat. We also identified morphological and physiological processes that may occur alongside heart development, such as development of digestive caeca and the cuticle. Elucidating the mechanisms underpinning morphological and physiological development of non-model organisms will support improved understanding of conserved mechanisms, addressing the current phylogenetic gap between relatively well known model species.

Genome of Mycetocola spongiae MSC19^T, a novel marine sponge-associated Actinobacteria isolated from the Mariana Trench sponge Cacospongia mycofijiensis, was sequenced. The genome has one circular chromosome of 3,196,754 bp, with an average GC content of 66.43 mol%, and 2887 coding sequences. Gene annotation shows that M. spongiae MSC19^T possesses series of genes related to adaptation to deep-sea environmental stresses including cold shock, heat shock, osmotic stress and oxidative stress. Genes encoding for heavy metal resistance, multidrug resistance and multiple natural product biosynthesis which are crucial for survival in the extreme environment are also detected in the genome. The potentials to synthesize kinds of vitamins and eukaryotic-like proteins indicates the possible nutrient exchange and mutual recognization between M. spongiae MSC19^T and its sponge host. The genome provides insights into the stress resistance and ecological fitness of bacterial symbionts in the deep-sea sponge holobionts.

Thalassospira sp. SW-3-3 is a bacterial strain isolated from deep seawater of the Pacific Ocean at a water depth of 3112 m. It is a Gram-negative, aerobic, and curved rod-shaped bacterium belonging to the family Thalassospiraceae. In this study, we report the complete genome sequence of strain SW-3-3. It has a circular chromosome with a size of 4,764,478 bp and a G + C content of 54.7%. The genome contains 4296 protein-coding genes, 63 tRNA genes, and 12 rRNA genes. Genomic analysis shows that strain SW-3-3 contains genes and catalytic pathways relevant to phthalate metabolism. Phthalates are well-known emerging contaminants that are harmful to environments and human health. They are chemically stable compounds that are widely used in plastic products and are pervasive in our life. With the discharge of plastic pollutants, a huge number of phthalate compounds enter the ocean. The genetic information of strain SW-3-3 suggests that it has the potential to metabolize phthalates. There are 9 key enzymes in the metabolization pathway, and phthalates are finally catalyzed to produce succinyl-CoA which is further degraded through the tricarboxylic acid (TCA) cycle pathway. This genomic analysis will be helpful for further understanding of the applications of strain SW-3-3 in the remediation of phthalate pollution.

Roseivivax marinus strain TCYB24 is a rod-shaped bacterium of Rhodobacteraceae isolated from the gill of deep-sea mussel Bathymodiolus marisindicus which collected from the Tiancheng hydrothermal vent under depth of 2700 m on the southwest Indian ridge. In our previous study, the strain TCYB24 was proved to produce quorum sensing signal of N-Acyl-homoserine lactones (AHLs) and form biofilm. In order to determine its adaptive mechanism against the extreme environment of deep-sea hydrothermal vents, the whole genome was sequenced by high-throughput Illumina tag sequencing. The results show the whole genome consists of one circular chromosome and eight circular plasmids, with a total length of 4.60 Mb (G + C content of 67.4%), 4338 open reading frames, 46 tRNAs and 6 rRNA operons. According to the genome-wide functional annotation, numbers of heavy metal resistance, high pressure and cold adapting related genes were found. In addition, genes about exopolysaccharide (EPS) biosynthesis and secretion and biofilm formation, which facilitate bacteria to resist extreme environments, were identified. Intriguingly, a pair of RaiI/R-type quorum sensing system was discovered firstly in the bacterium isolated from hydrothermal environment. The results may help to understand genetic underpinning of extreme environmental adaptation mechanism of bacteria in deep-sea hydrothermal area.