Marine genomics最新文献

{"title":"Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China","authors":"Shijie Bai ,&nbsp;Kun Shang ,&nbsp;Shuqian Zeng ,&nbsp;Ziming Huang ,&nbsp;Zhuang Han","doi":"10.1016/j.margen.2024.101125","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101125","url":null,"abstract":"<div><p><em>Salinimicrobium</em> sp. 3283s is an aerobic, golden-yellow pigment-producing, <em>Flavobacteriaceae</em> bacterium isolated from the sediments at the depth of 1751 m in the South China Sea. In this study, we present the complete genome sequence of strain 3283s, which only have a single circular chromosome comprising 3,702,683 bp with 41.41% G + C content and no circular plasmid. In total, 3257 protein coding genes, 45 tRNA, 9 rRNA, and 13 sRNA genes were obtained. In terms of the function of gene annotation, strain 3283s was more different from <em>Salinimicrobium oceani</em> J15B91, which was isolated from the South China Sea at a similar depth, and more similar to a Mariana Trench-derived strain <em>Salinimicrobium profundisediminis</em> MT39, which was closer in phylogenetic taxonomic status, suggesting that strain 3283s possesses a stronger potential to adapt to the deep-sea environment. Furthermore, the high- pressure simulations also confirmed that strain 3283s can grow in both 30 MPa and 60 MPa hydrostatic pressure environments, and that it grows better in 30 MPa hydrostatic pressure environments than in 60 MPa hydrostatic pressure environments. In addition, we found a large number of genes in strain 3283s that can promote better adaptation of the bacteria to the low oxygen and high hydrostatic pressure (HHP) environment of the deep sea, such as biosynthetic enzymes of antioxidant pigments, genes encoding cytochromes with enhanced affinity for oxygen, proteins for adaptation to HHP, and genes encoding TonB-dependent transporters in the absence of flagella.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141423706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic profiling of biosynthetic potentials of medicinal secondary metabolites for ‘Aliisedimentitalea scapharcae’ KCTC 42119T, isolated from ark shell","authors":"Jin-Cheng Rong ,&nbsp;Lin-Lin Cui ,&nbsp;Na Li ,&nbsp;Mao-Li Yi ,&nbsp;Bo-Tao Huang ,&nbsp;Qi Zhao","doi":"10.1016/j.margen.2024.101124","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101124","url":null,"abstract":"<div><p>Microorganisms living with higher organisms are valuable sources of bioactive substances like antibiotics, which could assist them competing for more and better nutrients or space. Here, we focused on a marine animal-associated bacterium, ‘<em>Aliisedimentitalea scapharcae</em>’ KCTC 42119^T, which was isolated from ark shell collected from Gang-Jin bay of South Korea. We evaluated its biosynthetic potentials of medicinal secondary metabolites by <em>de novo</em> genome sequencing. The complete genome of strain KCTC 42119^T sequenced is 5,083,900 bp and is comprised of one circular chromosome and four circular plasmids. Functional genome analysis by antiSMASH v7.1.0 showed that there are nine biosynthetic gene clusters encoded on the chromosome. The annotated secondary metabolites include antibiotic corynecin, cytoprotective ectoine and antineoplastic ET-743 (Yondelis), which suggested strain KCTC 42119^T possesses potentials to synthesize a series of secondary metabolites of pharmaceutical utility. Genome analysis of ‘<em>A. scapharcae</em>’ also provides more insights into mining bioactive substances from animal-associated microorganisms.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141289753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of Kushneria phosphatilytica YCWA18T reveals the P-solubilizing activity of the genus Kushneria","authors":"Guang-xun Du ,&nbsp;Wen-sheng Yu ,&nbsp;Ji-kun Su ,&nbsp;Guo-chong Liu ,&nbsp;Ping Gao ,&nbsp;Xu-guang Hong ,&nbsp;Ling-yun Qu","doi":"10.1016/j.margen.2024.101123","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101123","url":null,"abstract":"<div><p><em>Kushneria phosphatilytica</em> YCWA18^T (= CGMCC 1.9149^T = NCCB 100306^T) was isolated from sediment collected in a saltern on the eastern coast of Yellow Sea in China. The genome was sequenced and comprised of one circular chromosome with the size of 3,624,619 bp and DNA G + C content of 59.13%. A total of 3267 protein-coding genes, 64 tRNA genes and 12 rRNA genes were obtained. Genomic annotation indicated that the genome of <em>K</em>. <em>phosphatilytica</em> YCWA18^T had 34 genes involved in phosphorus (P) solubilization/metabolism, e.g., <em>gdh</em>, <em>pqq</em>, <em>phoA</em>, <em>phoD</em> and <em>phoX</em>, which products can convert insoluble P-containing compounds to more bio-available dissolved inorganic P. Comparative genomic analysis of <em>Kushneria</em> strains revealed that <em>gdh</em>, <em>pqq</em>, <em>phoA</em>, <em>phoD</em> and <em>phoX</em> were widely distributed in these strains, indicating the genus <em>Kushneria</em> may play an important role in the P cycle. Additionally, a multitude of salt tolerance genes were detected in the genome of <em>K</em>. <em>phosphatilytica</em> YCWA18^T. This study and the genome sequence data will be available for further research and will provide insights into potential biotechnological and agricultural applications of <em>Kushneria</em> strains.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of a novel Pseudomonas sp. IT1137 isolated from Antarctic intertidal sediment showing potential for alkane degradation at low temperatures","authors":"Hui-Yan Ge ,&nbsp;Yi-He Zhang ,&nbsp;Yong-Qiang Hu ,&nbsp;Wei Han ,&nbsp;Yu Du ,&nbsp;Ting Hu ,&nbsp;Yin-Xin Zeng","doi":"10.1016/j.margen.2024.101122","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101122","url":null,"abstract":"<div><p><em>Pseudomonas</em> species are known for their diverse metabolic abilities and broad ecological distribution. They are fundamental components of bacterial communities and perform essential ecological functions in the environment. A psychrotrophic <em>Pseudomonas</em> sp. IT1137 was isolated from intertidal sediment in the coastal region of the Fildes Peninsula, King George Island, Antarctica. The strain contained a circular chromosome of 5,346,697 bp with a G + C content of 61.66 mol% and one plasmid of 4481 bp with a G + C content of 64.61 mol%. A total of 4848 protein-coding genes, 65 tRNA genes and 15 rRNA genes were obtained. Genome sequence analysis revealed that strain IT1137 not only is a potentially novel species of the genus <em>Pseudomonas</em> but also harbors functional genes related to nitrogen, sulfur and phosphorus cycling. In addition, genes involved in alkane degradation, ectoine synthesis and cyclic lipopeptide (CLP) production were detected in the bacterial genome. The results indicate the potential of the strain <em>Pseudomonas</em> sp. IT1137 for biotechnological applications such as bioremediation and secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold coastal environments.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140918691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence analysis of a biosurfactant-producing bacterium Bacillus velezensis L2D39","authors":"Yihan Ding ,&nbsp;Shiping Wei ,&nbsp;Gaiyun Zhang","doi":"10.1016/j.margen.2024.101113","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101113","url":null,"abstract":"<div><p>Biosurfactants are amphipathic molecules with high industrial values owing to their chemical properties and stability under several environmental conditions. They have become attractive microbial products in the emerging biotechnology industry, offering a potential environmentally-friendly alternative to synthetic surfactants. Nowadays, several types of biosurfactants are commercially available for a wide range of applications in healthcare, agriculture, oil extraction and environmental remediation. In this study, a marine bacterium <em>Bacillus velezensis</em> L2D39 with the capability of producing biosurfactants was successfully isolated and characterized. The complete genome sequence of the bacterium <em>B. velezensis</em> L2D39 was obtained using PacBio Sequel HGAP.4, resulting in a sequence consisting of 4,140,042 base pairs with a 46.2 mol% G + C content and containing 4071 protein-coding genes. The presence of gene clusters associated with biosurfactants was confirmed through antiSMASH detection. The analysis of complete genome sequence will provide insight into the potential applications of this bacterium in biotechnological and natural product biosynthesis.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140879644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of Alteromonas sp. M12 isolated from the Mariana Trench reveals its role in dimethylsulfoniopropionate cycling","authors":"Yue Lin ,&nbsp;Min Zhang ,&nbsp;Yu-Xiang Lai ,&nbsp;Teng Liu ,&nbsp;Meng Meng ,&nbsp;Yan Sun ,&nbsp;Yu Wang ,&nbsp;Qing-Yu Dong ,&nbsp;Chen-Xi Li ,&nbsp;Meng-Xue Yu ,&nbsp;Jin Cheng ,&nbsp;Shu-Jun Liu ,&nbsp;Xuan Shao ,&nbsp;Nan Zhang ,&nbsp;Chun-Yang Li","doi":"10.1016/j.margen.2024.101112","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101112","url":null,"abstract":"<div><p>Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in stress tolerance, global carbon and sulfur cycling, and chemotaxis. It is the main precursor of the climate active gas dimethyl sulfide (DMS), which is the greatest natural source of bio‑sulfur transferred from ocean to atmosphere. <em>Alteromonas</em> sp. M12, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench at the depth of 2500 m. Here, we report the complete genome sequence of strain M12 and its genomic characteristics to import and utilize DMSP<em>.</em> The genome of strain M12 contains one circular chromosome (5,012,782 bp) with the GC content of 40.88%. <em>Alteromonas</em> sp. M12 can grow with DMSP as a sole carbon source, and produced DMS with DMSP as a precursor. Genomic analysis showed that strain M12 contained a set of genes involved in the downstream steps of DMSP cleavage, but no known genes encoding DMSP transporters or DMSP lyases. The results indicated that this strain contained novel DMSP transport and cleavage genes in its genome which warrants further investigation. The import of DMSP into cells may be a strategy of strain M12 to adapt the hydrostatic pressure environment in the Mariana Trench, as DMSP can be used as a hydrostatic pressure protectant. This study sheds light on the catabolism of DMSP by deep-sea bacteria.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140879643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequencing of Hortaea werneckii M-3 for identifying polyester polyurethane degrading enzymes","authors":"Minghuang Ling ,&nbsp;Kai Zhang ,&nbsp;Juan Hu ,&nbsp;Xiaomei Huang ,&nbsp;Gaili Fan ,&nbsp;Hans-Peter Grossart ,&nbsp;Zhuhua Luo","doi":"10.1016/j.margen.2024.101111","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101111","url":null,"abstract":"<div><p><em>Hortaea werneckii</em> M-3, a black yeast isolated from the marine sediment of the West Pacific, can utilize polyester polyurethane (PU, Impranil DLN) as a sole carbon source. Here, we present the complete genome of <em>Hortaea werneckii</em> M-3 with the focus on PU degradation enzymes. The total genome size is 38,167,921 bp, consisting of 186 contigs with a N50 length of 651,266 bp and a GC content of 53.06%. Genome annotation analysis predicts a total of 13,462 coding genes, which include 99 tRNAs and 105 rRNAs. Some genes encoding PU degrading enzymes including cutinase and urease are identified in this genome. The genome analysis of <em>Hortaea werneckii</em> M-3 will be helpful for further understanding the degradation mechanism of polyester PU by marine yeasts.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140823283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome analysis of Rossellomorea sp. y25, a deep sea bacterium isolated from the sediments of South China Sea","authors":"Shijie Bai ,&nbsp;Zhaosong Huang ,&nbsp;Xue-Gong Li","doi":"10.1016/j.margen.2024.101110","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101110","url":null,"abstract":"<div><p><em>Rossellomorea</em> sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family <em>Bacillaceae</em>, was isolated from the sediments at the depth of 1829 m in the South China Sea. In this study, we present the complete genome sequences of strain y25, which consisted of only one circular chromosome with 4,633,006 bp and the content of G + C was 41.76%. A total of 4466 CDSs, 106 tRNA, 33 rRNA, and 101 sRNA genes were obtained. Genomic analysis of strain y25 showed that it has the ability to produce antioxidant carotenoids and a large number of heavy metal resistance genes, such as arsenic, cadmium and zinc. In addition, strain y25 contains a prophage that may contribute to host protection against lysis by related <em>Bacillus</em>-like phages. This is the first report of genome-wide information on a bacterium of the genus <em>Rossellomorea</em> isolated from the deep sea, providing insights into how microorganisms of this genus adapt to deep-sea environments.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140645529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic investigation and biomarker discovery for zinc response in oysters Crassostrea gasar","authors":"Clarissa P. Ferreira ,&nbsp;Renato S. Moreira ,&nbsp;Camila L.V. Bastolla ,&nbsp;Miguel Saldaña-Serrano ,&nbsp;Daína Lima ,&nbsp;Carlos H.A.M. Gomes ,&nbsp;Afonso C.D. Bainy ,&nbsp;Karim H. Lüchmann","doi":"10.1016/j.margen.2024.101109","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101109","url":null,"abstract":"<div><p>In an era of unprecedented industrial and agricultural growth, metal contamination in marine environments is a pressing concern. Sentinel organisms such as the mangrove oyster <em>Crassostrea gasar</em> provide valuable insights into these environments' health. However, a comprehensive understanding of the molecular mechanisms underlying their response to metal exposure remains elusive. To address this gap, we reanalyzed the 454-sequencing data of <em>C. gasar</em>, utilizing an array of bioinformatics workflow of CDTA (Combined <em>De Novo</em> Transcriptome Assembly) to generate a more representative assembly. In parallel, <em>C. gasar</em> individuals were exposed to two concentrations of zinc (850 and 4500 μg L⁻¹ Zn) for 48 h to understand their molecular responses. We utilized Trinotate workflow for the 11,684-CDTA unigenes annotation, with most transcripts aligning with the genus <em>Crassostrea</em>. Our analysis indicated that 67.3% of transcript sequences showed homology with Pfam, while 51.4% and 54.5%, respectively had GO and KO terms annotated. We identified potential metal pollution biomarkers, focusing on metal-related genes, such as those related to the GSH biosynthesis (<em>CHAC1</em> and <em>GCLC</em>-like), to zinc transporters (<em>ZNT2</em>-like), and metallothionein (<em>MT</em>-like). The evolutionary conservation of these genes within the <em>Crassostrea</em> genus was assessed through phylogenetic analysis. Further, these genes were evaluated by qPCR in the laboratory exposed oysters. All target genes exhibited significant upregulation upon exposure to Zn at both 850 and 4500 μg L⁻¹, except for <em>GCLC</em>-like, which showed upregulation only at the higher concentration of 4500 μg L⁻¹. This result suggests distinct activation thresholds and complex interactions among these genes in response to varying Zn concentrations. Our study provides insights into the molecular responses of <em>C. gasar</em> to Zn, adding valuable tools for monitoring metal pollution in marine ecosystems using the mangrove oyster as a sentinel organism.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140543986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome analysis of copper resistant bacteria Pseudoalteromonas sp. CuT4–3 isolated from a deep-sea hydrothermal vent","authors":"Bowen Ji ,&nbsp;Tong Yu ,&nbsp;Xiang Zeng","doi":"10.1016/j.margen.2024.101106","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101106","url":null,"abstract":"<div><p><em>Pseudoalteromonas</em> sp. CuT4–3, a copper resistant bacterium, was isolated from deep-sea hydrothermal sulfides on the Southwest Indian Ridge (SWIR), is an aerobic, mesophilic and rod-shaped bacterium belonging to the family <em>Pseudoalteromonadaceae</em> (class <em>Gammaproteobacteria</em>, order <em>Alteromonadales</em>). In this study, we present the complete genome sequence of strain CuT4–3, which consists of a single circular chromosome comprising 3,660,538 nucleotides with 41.05% G + C content and two circular plasmids comprising 792,064 nucleotides with 40.36% G + C content and 65,436 nucleotides with 41.50% G + C content. In total, 4078 protein coding genes, 105 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain CuT4–3 identified numerous genes related to heavy metal resistance (especially copper) and EPS production. The genome of strain CuT4–3 will be helpful for further understanding of its adaptive strategies, particularly its ability to resist heavy metal, in the deep-sea hydrothermal vent environment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140296648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}