Pub Date : 2024-11-20DOI: 10.1016/j.margen.2024.101161
Meixue Pan , Wenbin Guo , Jingjing Duan
Stenotrophomonas sp. P2112, isolated from a marine sediment sample of the Pacific Ocean, can grow in mineral medium with polyvinyl chloride (PVC) plastic as sole carbon source. Here, we present the complete genome of Stenotrophomonas sp. P2112, which will facilitate the genome mining of PVC degrading enzymes. The total length of the sequenced genome consists of 4,382,508 bases, with mean G + C content of 66.61%. A total of 4024 coding genes including 73 tRNAs and 13 rRNAs were predicted in the genome. Some potential PVC degrading enzymes including monooxygenase and peroxidases were found in this genome.
{"title":"The complete genome sequence of Stenotrophomonas sp. P2112 for genome mining of polyvinyl chloride degrading enzymes","authors":"Meixue Pan , Wenbin Guo , Jingjing Duan","doi":"10.1016/j.margen.2024.101161","DOIUrl":"10.1016/j.margen.2024.101161","url":null,"abstract":"<div><div><em>Stenotrophomonas</em> sp. P2112, isolated from a marine sediment sample of the Pacific Ocean, can grow in mineral medium with polyvinyl chloride (PVC) plastic as sole carbon source. Here, we present the complete genome of <em>Stenotrophomonas</em> sp. P2112, which will facilitate the genome mining of PVC degrading enzymes. The total length of the sequenced genome consists of 4,382,508 bases, with mean G + C content of 66.61%. A total of 4024 coding genes including 73 tRNAs and 13 rRNAs were predicted in the genome. Some potential PVC degrading enzymes including monooxygenase and peroxidases were found in this genome.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101161"},"PeriodicalIF":1.3,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700541","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}
Pub Date : 2024-11-12DOI: 10.1016/j.margen.2024.101159
Jiayi Chu , Yonglian Ye , Yue-Hong Wu
The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion–Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0–8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0–6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.
{"title":"A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis","authors":"Jiayi Chu , Yonglian Ye , Yue-Hong Wu","doi":"10.1016/j.margen.2024.101159","DOIUrl":"10.1016/j.margen.2024.101159","url":null,"abstract":"<div><div>The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion–Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0–8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0–6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101159"},"PeriodicalIF":1.3,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623283","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}
Pub Date : 2024-11-09DOI: 10.1016/j.margen.2024.101158
Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang
Chitin, the most abundant polysaccharide in the ocean, is a kind of high molecular weight organic matter formed by N-acetyl-D-glucosamine (GlcNAc) via β-1,4-glucoside linkage. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. Pseudoalteromonas sp. M58, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M58 and its genomic characteristics to degrade chitin. The genome of strain M58 contains two circular chromosomes (3,348,672 bp and 723,540 bp, respectively). Genomic analysis showed that strain M58 contained a set of genes involved in chitin degradation, indicating that it possesses the potential ability to degrade chitin. This study provides novel insights into chitin degradation by marine microorganisms.
{"title":"Genomic analysis of Pseudoalteromonas sp. M58 reveals its role in chitin biodegradation","authors":"Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang","doi":"10.1016/j.margen.2024.101158","DOIUrl":"10.1016/j.margen.2024.101158","url":null,"abstract":"<div><div>Chitin, the most abundant polysaccharide in the ocean, is a kind of high molecular weight organic matter formed by <em>N</em>-acetyl-D-glucosamine (GlcNAc) via β-1,4-glucoside linkage. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. <em>Pseudoalteromonas</em> sp. M58, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M58 and its genomic characteristics to degrade chitin. The genome of strain M58 contains two circular chromosomes (3,348,672 bp and 723,540 bp, respectively). Genomic analysis showed that strain M58 contained a set of genes involved in chitin degradation, indicating that it possesses the potential ability to degrade chitin. This study provides novel insights into chitin degradation by marine microorganisms.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101158"},"PeriodicalIF":1.3,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142662895","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}
Pub Date : 2024-11-04DOI: 10.1016/j.margen.2024.101151
Zeping He , Lian Yuan , Haoran Li , Lihua Peng , Xiao Liang , Jin-Long Yang
Bacteria of the genus Sulfitobacter are widely distributed across various marine environments and play a vital role in the sulfur cycle. Sulfitobacter pontiacus 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 S. pontiacus 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. S. pontiacus 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 S. pontiacus may provide valuable insights into elucidating the ecological significance of the sulfur cycle and assessing its impact on marine invertebrate settlement.
{"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":"79 ","pages":"Article 101151"},"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}
Pub Date : 2024-11-02DOI: 10.1016/j.margen.2024.101150
Hai-Xia Zhu , Zhi-Gang Tang , Shi-Ning Cai , Jun-Hui Cheng , Peng Wang , Mei-Ling Sun
Vreelandella 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 Vreelandella adapting to the deep-sea hydrothermal environment, and provide a basis for further experimental exploration.
{"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":"79 ","pages":"Article 101150"},"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}
Pub Date : 2024-10-18DOI: 10.1016/j.margen.2024.101149
Kyuin Hwang , Hanna Choe , Kyung Mo Kim
Members of the genus Arenibacter 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. Arenibacter antarcticus KCTC 52924T 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.
{"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":"78 ","pages":"Article 101149"},"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}
Pub Date : 2024-10-10DOI: 10.1016/j.margen.2024.101147
Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang
Bacteria of the genus Shewanella in the class Gammaproteobacteria are widely distributed in marine environments. Shewanella 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.
{"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":"78 ","pages":"Article 101147"},"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}
Pub Date : 2024-10-10DOI: 10.1016/j.margen.2024.101148
Yadan Deng , Yunjin Zhu , Jiaxuan He , Xin Yin , Qian Li , Zhengxing Chen , Bingshu Wang , Li Zheng
{"title":"Complete genome analysis of deep-sea hydrothermal sulfur-oxidizing bacterium Sulfitobacter sp. TCYB15 associated with mussel Bathymodiolus marisindicus and insights into its habitat adaptation","authors":"Yadan Deng , Yunjin Zhu , Jiaxuan He , Xin Yin , Qian Li , Zhengxing Chen , Bingshu Wang , Li Zheng","doi":"10.1016/j.margen.2024.101148","DOIUrl":"10.1016/j.margen.2024.101148","url":null,"abstract":"","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"78 ","pages":"Article 101148"},"PeriodicalIF":1.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400701","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}
Pub Date : 2024-09-06DOI: 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
Streptomyces FIM95-F1, an actinomycete originating from mangroves of Quanzhou bay, exhibits the capability to produce the antifungal antibiotic scopafungin. Here, the complete genome of Streptomyces 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 Streptomyces 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.
{"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":"78 ","pages":"Article 101146"},"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}
Pub Date : 2024-08-29DOI: 10.1016/j.margen.2024.101145
Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang
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. Rhodopirellula sp. P2, a novel marine bacterium of the phylum Planctomycetota, 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 Rhodopirellula 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 Planctomycetota, and also facilitate the exploitation of Planctomycetota and enzyme resources to utilize fucoidan. This study provides genetic insights into fucoidan catabolism by Planctomycetota, expanding our understanding of fucoidan-degrading microbial groups.
{"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":"78 ","pages":"Article 101145"},"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}
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