Marine genomics最新文献

Complete genome sequence of Sulfitobacter pontiacus WPMT18310, a dimethylsulfoniopropionate (DMSP) degradation bacterium isolated from the Mariana Trench 从马里亚纳海沟分离出的二甲基硫代丙酸酯（DMSP）降解细菌 Sulfitobacter pontiacus WPMT18310 的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-11-04 DOI: 10.1016/j.margen.2024.101151

Zeping He , Lian Yuan , Haoran Li , Lihua Peng , Xiao Liang , Jin-Long Yang

{"title":"Complete genome sequence of Sulfitobacter pontiacus WPMT18310, a dimethylsulfoniopropionate (DMSP) degradation bacterium isolated from the Mariana Trench","authors":"Zeping He , Lian Yuan , Haoran Li , Lihua Peng , Xiao Liang , Jin-Long Yang","doi":"10.1016/j.margen.2024.101151","DOIUrl":"10.1016/j.margen.2024.101151","url":null,"abstract":"<div><div>Bacteria of the genus <em>Sulfitobacter</em> are widely distributed across various marine environments and play a vital role in the sulfur cycle. <em>Sulfitobacter pontiacus</em> WPMT18310 was isolated from water samples collected at a depth of 10,890 m in the Mariana Trench. In this study, we report the complete genome of <em>S. pontiacus</em> WPMT18310, which contained 3533 genes and a total length of 3,706,453 base pairs organized within a single chromosome. Additionally, the genome contains four plasmids, suggesting its significant capacity for gene transfer. <em>S. pontiacus</em> WPMT18310 is capable for synthesizing signaling molecules and degrading dimethylsulfoniopropionate (DMSP). The degradation product dimethyl sulfide (DMS) serves as a potential signaling molecule that can induce the settlement of marine invertebrates. This genomic information of <em>S. pontiacus</em> may provide valuable insights into elucidating the ecological significance of the sulfur cycle and assessing its impact on marine invertebrate settlement.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142578799","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}

引用次数: 0

Complete genome sequence of Vreelandella sp. SM1641, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Southwest Indian Ocean 从西南印度洋深海热液沉积物中分离出的海洋外多糖生产细菌 Vreelandella sp.

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-11-02 DOI: 10.1016/j.margen.2024.101150

Hai-Xia Zhu , Zhi-Gang Tang , Shi-Ning Cai , Jun-Hui Cheng , Peng Wang , Mei-Ling Sun

{"title":"Complete genome sequence of Vreelandella sp. SM1641, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Southwest Indian Ocean","authors":"Hai-Xia Zhu , Zhi-Gang Tang , Shi-Ning Cai , Jun-Hui Cheng , Peng Wang , Mei-Ling Sun","doi":"10.1016/j.margen.2024.101150","DOIUrl":"10.1016/j.margen.2024.101150","url":null,"abstract":"<div><div><em>Vreelandella</em> sp. SM1641 was isolated from the hydrothermal vent sediment of the southwest Indian Ocean at a water depth of 2519 m. The complete genome sequence of strain SM1641 was analyzed to understand its metabolic capacities and biosynthesis potential of natural products in this study. The genome of strain SM1641 consists of a circular chromosome and two plasmids. The length of the circular chromosome was 4,731,121 bp with GC content of 54.46 mol%, and the length of plasmid A was 302,095 bp with GC content of 54.95 mol%, and the length of plasmid B was 8857 bp with GC content of 46.31 mol%. Genomic data showed that strain SM1641 had several gene clusters involved in the synthesis of exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) synthesis. SM1641 also has a variety of genes that respond to osmotic stress, heat shock, cold shock, oxidative stress, and heavy metal stress, which plays a critical role in bacterial adaptation to hydrothermal environments. Therefore, genome sequencing and data mining of strain SM1641 are helpful to further understand the molecular mechanism of <em>Vreelandella</em> adapting to the deep-sea hydrothermal environment, and provide a basis for further experimental exploration.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572701","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}

引用次数: 0

Complete genome and carbohydrate-active enzymes of Arenibacter antarcticus KCTC 52924T isolated from deep sea sediment of Ross Sea, Antarctica 从南极罗斯海深海沉积物中分离出的南极 Arenibacter antarcticus KCTC 52924T 的完整基因组和碳水化合物活性酶

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-10-18 DOI: 10.1016/j.margen.2024.101149

Kyuin Hwang , Hanna Choe , Kyung Mo Kim

{"title":"Complete genome and carbohydrate-active enzymes of Arenibacter antarcticus KCTC 52924T isolated from deep sea sediment of Ross Sea, Antarctica","authors":"Kyuin Hwang , Hanna Choe , Kyung Mo Kim","doi":"10.1016/j.margen.2024.101149","DOIUrl":"10.1016/j.margen.2024.101149","url":null,"abstract":"<div><div>Members of the genus <em>Arenibacter</em> were widely distributed in oceanic habitats around the world and have been studied for a variety of useful properties, including antigen deactivation, pollutant degradation, and the production of antimicrobial agents. <em>Arenibacter antarcticus</em> KCTC 52924<sup>T</sup> of our interest is an aerobic, non-motile, Gram-negative, psychrotolerant type strain isolated from the deep-sea sediment of Ross Sea, Antarctica. The extreme conditions of this habitat are believed to have diversified the substrate spectrum and range of operational conditions of the enzymes, offering both scientific interest and potential industrial benefits. Here, we obtained the complete genome sequence of this promising strain, which consists of 4,694,007 bp (G + C content of 38.8 %) with a single chromosome, 3917 protein-coding genes, 43 tRNAs, and 3 rRNA operons. The functional annotations of the genome reveal four metabolite biosynthesis clusters and a variety of carbohydrate-active enzymes with potential biotechnological applications. Additionally, several interesting features related to environmental interactions were identified. Therefore, this genome data and its genomic potentials figured out in this study serve as a conner stone in further study aimed at understanding physiology of this strain which may be valuable in biotechnological purpose.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142444652","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}

引用次数: 0

The complete genome sequence of proteases-producing Shewanella sp. H8 isolated from Antarctica 从南极洲分离的产蛋白酶的雪旺氏菌 H8 的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101147

Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang

{"title":"The complete genome sequence of proteases-producing Shewanella sp. H8 isolated from Antarctica","authors":"Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang","doi":"10.1016/j.margen.2024.101147","DOIUrl":"10.1016/j.margen.2024.101147","url":null,"abstract":"<div><div>Bacteria of the genus <em>Shewanella</em> in the class <em>Gammaproteobacteria</em> are widely distributed in marine environments. <em>Shewanella</em> sp. H8, was isolated from a red algae sample collected from Nelson Island, Antarctica. Here, we present the complete genome sequence of strain H8, which consists of a single circular chromosome comprising 4,490,743 nucleotides with 40.59 % G + C content without any plasmid. In total, 3983 protein coding genes, 95 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain H8 showed that it contains four cold shock proteins and three fatty acid desaturases and possesses the potential to synthesize hglE-KS, arylpolyene, betalactone and RiPP-like compounds. Through genomic annotation, 91 protease-encoding genes were identified within the genome of strain H8. These proteases are classified into six categories based on their catalytic types. Among these proteases, metalloproteinases and serine proteases are dominant. These proteases may provide carbon and nitrogen sources to H8 by degrading proteins in the environment. This study will provide potential genetic information for the future research and development of cold-adapted proteases.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142416810","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}

引用次数: 0

Complete genome analysis of deep-sea hydrothermal sulfur-oxidizing bacterium Sulfitobacter sp. TCYB15 associated with mussel Bathymodiolus marisindicus and insights into its habitat adaptation 与贻贝Bathymodiolus marisindicus相关的深海热液硫氧化细菌Sulfitobacter sp.

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101148

Yadan Deng , Yunjin Zhu , Jiaxuan He , Xin Yin , Qian Li , Zhengxing Chen , Bingshu Wang , Li Zheng

引用次数: 0

The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin 可产生抗真菌抗生素 Scopafungin 的海洋放线菌--链霉菌 FIM 95-F1 的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-09-06 DOI: 10.1016/j.margen.2024.101146

Peng Fei , Lin Yangjun , Zhuang Yuee , Lin Ping , Liu Chengzhi , Chen Linlin , Jiang Hong , Lian Yunyang , Zhang Wenzhou , Huang Youxia

{"title":"The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin","authors":"Peng Fei , Lin Yangjun , Zhuang Yuee , Lin Ping , Liu Chengzhi , Chen Linlin , Jiang Hong , Lian Yunyang , Zhang Wenzhou , Huang Youxia","doi":"10.1016/j.margen.2024.101146","DOIUrl":"10.1016/j.margen.2024.101146","url":null,"abstract":"<div><p><em>Streptomyces</em> FIM95-F1, an actinomycete originating from mangroves of Quanzhou bay, exhibits the capability to produce the antifungal antibiotic scopafungin. Here, the complete genome of <em>Streptomyces</em> sp. FIM95-F1 is presented with a GC content of 71.04 %, comprising a 9,718,239-bp linear chromosome, 8236 protein-coding genes, 18 rRNA genes, 64 tRNA genes, 2 prophages, and 58 CRISPR regions. In silico analysis revealed the presence of 42 biosynthetic gene clusters (BGCs), the majority of which demonstrated similarity to both known and novel BGCs responsible for the biosynthesis of previously known and novel bioactive agents of microbial origin. A comprehensive comparison between the scopafungin BGC and niphimycin BGC has indicated a potential shared pathway for the biosynthesis of scopafungin. One of the intriguing findings of this study was the discovery of at least two novel BGCs (namely Cluster 26 and Cluster 32) present within biosynthetic gene clusters. Our findings suggest that <em>Streptomyces</em> sp. FIM95-F1 possesses significant potential in producing a diverse array of both known and novel bioactive compounds, which could be valuable in the field of drug discovery.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147689","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}

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Genomic analysis of Rhodopirellula sp. P2 reveals its role in fucoidan degradation Rhodopirellula sp. P2 的基因组分析揭示了其在褐藻糖胶降解中的作用

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-08-29 DOI: 10.1016/j.margen.2024.101145

Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang

{"title":"Genomic analysis of Rhodopirellula sp. P2 reveals its role in fucoidan degradation","authors":"Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang","doi":"10.1016/j.margen.2024.101145","DOIUrl":"10.1016/j.margen.2024.101145","url":null,"abstract":"<div><p>Fucoidan, the main polysaccharide in various species of brown seaweed, has a high annual production. It is an important source of marine organic carbon and exhibits diverse biological activities and significant application potential. <em>Rhodopirellula</em> sp. P2, a novel marine bacterium of the phylum <em>Planctomycetota</em>, was isolated from intertidal algae samples collected from the Weihai coast, the Yellow Sea, China. The strain P2 is a Gram-negative, aerobic, and pear-shaped bacterium. Here, we report the complete genome sequence of <em>Rhodopirellula</em> sp. P2. The genome of strain P2 consists of a single circular chromosome with 7,291,416 bp and a GC content of 57.38 %, including 5462 protein-coding genes, 2 rRNA genes, and 48 tRNA genes. Genomic analysis revealed that strain P2 possessed 173 CAZymes and 106 sulfatases, indicating that strain P2 has the potential ability to utilize multiple polysaccharides, especially hydrolyze fucoidan to fucose. The genome of strain P2 also encodes a gene cluster related to bacterial microcompartment, suggesting the ability of strain P2 to metabolize fucose. These results enhance the understanding of the diversity and ecological functions of <em>Planctomycetota</em>, and also facilitate the exploitation of <em>Planctomycetota</em> and enzyme resources to utilize fucoidan. This study provides genetic insights into fucoidan catabolism by <em>Planctomycetota</em>, expanding our understanding of fucoidan-degrading microbial groups.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096649","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}

引用次数: 0

Complete genome sequence of the 4-hydroxybenzoate-degrading bacterium Gymnodinialimonas sp. 57CJ19, a potential novel species from intertidal sediments 潮间带沉积物中的潜在新物种--4-羟基苯甲酸盐降解细菌Gymnodinialimonas sp.57CJ19的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-07-17 DOI: 10.1016/j.margen.2024.101135

Dong-Hui Li , Ning Zheng , Zhen-Hai Liu , Xiao-Rui Dong , Chen Zhao , Shi-Gan Yan , Bin-Bin Xie

引用次数: 0

The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation 含有丰富多糖降解基因的平面菌P1的完整基因组序列

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101126

Jia-Xuan Wang, Jing Wang, Ji-Qing Liu, Jian Li, Wen-Xin Jiang, Fei Xu, Ping-Yi Li, Qi-Long Qin, Xiu-Lan Chen, Xi-Ying Zhang

{"title":"The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation","authors":"Jia-Xuan Wang, Jing Wang, Ji-Qing Liu, Jian Li, Wen-Xin Jiang, Fei Xu, Ping-Yi Li, Qi-Long Qin, Xiu-Lan Chen, Xi-Ying Zhang","doi":"10.1016/j.margen.2024.101126","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101126","url":null,"abstract":"<div><p>Isolated from intertidal sediment of the Yellow Sea, China, <em>Bremerella</em> sp. P1 putatively represents a novel species within the genus <em>Bremerella</em> of the family <em>Pirellulaceae</em> in the phylum <em>Planctomycetota</em>. The complete genome of strain P1 comprises a single circular chromosome with a size of 6,955,728 bp and a GC content of 55.26%. The genome contains 5772 protein-coding genes, 80 tRNA and 6 rRNA genes. A total of 147 CAZymes and 128 sulfatases have been identified from the genome of strain P1, indicating that the strain has the capability to degrade a wide range of polysaccharides. Moreover, a gene cluster related to bacterial microcompartments (BMCs) formation containing genes encoding the shell proteins and related enzymes to metabolize fucose or rhamnose is also found in the genome of strain P1. The genome of strain P1 represents the second complete one in the genus <em>Bremerella</em>, expanding the understanding of the physiological and metabolic characteristics, interspecies diversity, and ecological functions of the genus.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434258","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}

引用次数: 0

Marine eDNA sampling from submerged surfaces with paint rollers 用油漆辊从水下表面采集海洋 eDNA 样本

IF 1.3 4区生物学

Marine genomics Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101127

Simon Jarman , Jason B. Alexander , Kathryn L. Dawkins , Sherralee S. Lukehurst , Georgia M. Nester , Shaun Wilkinson , Michael J. Marnane , Justin I. McDonald , Travis S. Elsdon , Euan S. Harvey

{"title":"Marine eDNA sampling from submerged surfaces with paint rollers","authors":"Simon Jarman , Jason B. Alexander , Kathryn L. Dawkins , Sherralee S. Lukehurst , Georgia M. Nester , Shaun Wilkinson , Michael J. Marnane , Justin I. McDonald , Travis S. Elsdon , Euan S. Harvey","doi":"10.1016/j.margen.2024.101127","DOIUrl":"https://doi.org/10.1016/j.margen.2024.101127","url":null,"abstract":"<div><p>Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434767","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}

引用次数: 0