Pub Date : 2024-12-11DOI: 10.1016/j.margen.2024.101164
Chen Liang , Wei Wang , Jianming Chen
This is the first report of a transcriptome assembly of a newly discovered a new Protocruzia species sampled from the under-sampled area near the Mariana Trench. We sequenced the transcriptome of P. marianaensis using the Illumina Novaseq 6000 platform. De novo assembly and analysis of the coding regions predicted 36,116 unigenes, 74.91 % of which was annotated by public databases. The transcriptome of P. marianaensis will be a valuable resource in studying the ecological and biological characteristics of this new species, which is the first Protocruzia species in deep sea. These data can also help to understand protozoa survival mechanisms in deep-sea habitats and provide essential biological material for investigating unique life phenomena and processes in the deep ocean.
{"title":"First transcriptome assembly of a new ciliate species (Protocruzia marianaensis) isolated from the Mariana Trench area","authors":"Chen Liang , Wei Wang , Jianming Chen","doi":"10.1016/j.margen.2024.101164","DOIUrl":"10.1016/j.margen.2024.101164","url":null,"abstract":"<div><div>This is the first report of a transcriptome assembly of a newly discovered a new <em>Protocruzia</em> species sampled from the under-sampled area near the Mariana Trench. We sequenced the transcriptome of <em>P. marianaensis</em> using the Illumina Novaseq 6000 platform. De novo assembly and analysis of the coding regions predicted 36,116 unigenes, 74.91 % of which was annotated by public databases. The transcriptome of <em>P. marianaensis</em> will be a valuable resource in studying the ecological and biological characteristics of this new species, which is the first <em>Protocruzia</em> species in deep sea. These data can also help to understand protozoa survival mechanisms in deep-sea habitats and provide essential biological material for investigating unique life phenomena and processes in the deep ocean.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101164"},"PeriodicalIF":1.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143039734","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}
Alginate is a natural marine polysaccharide and an important marine organic carbon source, which is mainly produced by marine brown algae. Marinobacter sp. M5B, a Gram-negative and aerobic bacterium, was isolated from the surface seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M5B and its genomic characteristics to synthesize alginate. The genome of strain M5B contains one circular chromosome (4,415,647 bp) with the GC content of 57.14 %. Genomic analysis showed that strain M5B contained a set of genes involved in alginate synthesis, indicating that it possesses the potential ability to synthesis alginate. This study provides novel insights into alginate synthesis by marine microorganisms.
{"title":"Genomic analysis of Marinobacter sp. M5B reveals its role in alginate biosynthesis","authors":"Xiaoyu Si, Zhenhai Liu, Shuxin Cheng, Jingyao Xi, Bingrui Zeng, Meihui Li, Liping Zhu, Shigan Yan, Nan Zhang","doi":"10.1016/j.margen.2024.101163","DOIUrl":"10.1016/j.margen.2024.101163","url":null,"abstract":"<div><div>Alginate is a natural marine polysaccharide and an important marine organic carbon source, which is mainly produced by marine brown algae. <em>Marinobacter</em> sp. M5B, a Gram-negative and aerobic bacterium, was isolated from the surface seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M5B and its genomic characteristics to synthesize alginate. The genome of strain M5B contains one circular chromosome (4,415,647 bp) with the GC content of 57.14 %. Genomic analysis showed that strain M5B contained a set of genes involved in alginate synthesis, indicating that it possesses the potential ability to synthesis alginate. This study provides novel insights into alginate synthesis by marine microorganisms.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101163"},"PeriodicalIF":1.3,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142746576","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 : 2024-11-26DOI: 10.1016/j.margen.2024.101162
Wenzhou Zhang , Minghuang Ling , Kai Zhang , Ruzhen Liu , Xiaomei Huang , Gaili Fan , Hans-Peter Grossart , Fei Peng , Zhuhua Luo
Mangroves, owing to their unique living environment, serve as an important source of natural bioactive compounds. Sarcopodium sp. QM3–1, a marine fungus isolated from mangrove sediments of Quanzhou Bay, exhibited antifungal activity against the plant pathogen Agrobacterium tumefaciens and Magnaporthe oryzae. Whole-genome sequencing of this fungal strain revealed a genome size of 58,356,150 bp with 17,960 protein-coding genes, 539 tRNA genes, and 170 rRNA genes. Functional annotation identified a series of genes involved in the biosynthesis of secondary metabolites, including several gene clusters associated with antimicrobial activity. Notably, twenty of these gene clusters were associated with the synthesis of known bioactive compounds, including terpene, polyketides (PKS), nonribosomal peptides (NRPS), β-lactones, and phosphonates. Our findings suggest that Sarcopodium sp. QM3–1 could be a promising candidate as a biocontrol agent for combating plant pathogens in agricultural fields.
{"title":"Complete genome sequence of the marine mangrove fungus Sarcopodium sp.QM3–1 confirmed its high potential for antimicrobial activity","authors":"Wenzhou Zhang , Minghuang Ling , Kai Zhang , Ruzhen Liu , Xiaomei Huang , Gaili Fan , Hans-Peter Grossart , Fei Peng , Zhuhua Luo","doi":"10.1016/j.margen.2024.101162","DOIUrl":"10.1016/j.margen.2024.101162","url":null,"abstract":"<div><div>Mangroves, owing to their unique living environment, serve as an important source of natural bioactive compounds. <em>Sarcopodium</em> sp. QM3–1, a marine fungus isolated from mangrove sediments of Quanzhou Bay, exhibited antifungal activity against the plant pathogen <em>Agrobacterium tumefaciens</em> and <em>Magnaporthe oryzae</em>. Whole-genome sequencing of this fungal strain revealed a genome size of 58,356,150 bp with 17,960 protein-coding genes, 539 tRNA genes, and 170 rRNA genes. Functional annotation identified a series of genes involved in the biosynthesis of secondary metabolites, including several gene clusters associated with antimicrobial activity. Notably, twenty of these gene clusters were associated with the synthesis of known bioactive compounds, including terpene, polyketides (PKS), nonribosomal peptides (NRPS), β-lactones, and phosphonates. Our findings suggest that <em>Sarcopodium</em> sp. QM3–1 could be a promising candidate as a biocontrol agent for combating plant pathogens in agricultural fields.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101162"},"PeriodicalIF":1.3,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142719761","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 : 2024-11-21DOI: 10.1016/j.margen.2024.101160
Xin-Xiao Qu , Yu-Qi Zhang , Fei-Yu He , Xi-Ying Zhang , Peng Wang , Fei Xu , Yu-Qiang Zhang , Long-Sheng Zhao , Ping-Yi Li , Fang Zhao
Alginate, mainly produced by brown algae, is an important polysaccharide that supports the growth of marine bacteria. Vreelandella sp. F11 is a Gram-negative and aerobic marine bacterium, which was isolated from the brown algae sample collected from the Weihai coast, the Yellow Sea, China. Here, we present the complete genome of strain F11 and its genomic characteristics to utilize alginate. The genome of strain F11 comprises one circular chromosome with 4,840,724 bp and a GC content of 55.04 %. Strain F11 could grow with alginate as the sole carbon source. Genomic analysis revealed that strain F11 contains a gene cluster, encoding the enzymes, transporters and a regulator protein involved in utilizing alginate. Gene annotations suggested that the alginate utilization system of strain F11 is similar to those in Vibrio strains. However, strain F11 does not contain homologs of known KdgF (a key enzyme involved in the metabolism of alginate monomer) and inner membrane transporters of alginate oligomer uptake. The result indicated that strain F11 contains novel KdgF and inner membrane transporter system, which warrants further investigation. These data suggested that Vreelandella strains play a role in alginate utilization in the ocean and lay a foundation for the application of Vreelandella in the conversion of brown algae.
{"title":"Genomic analysis of Vreelandella sp. F11 reveals its role in alginate utilization","authors":"Xin-Xiao Qu , Yu-Qi Zhang , Fei-Yu He , Xi-Ying Zhang , Peng Wang , Fei Xu , Yu-Qiang Zhang , Long-Sheng Zhao , Ping-Yi Li , Fang Zhao","doi":"10.1016/j.margen.2024.101160","DOIUrl":"10.1016/j.margen.2024.101160","url":null,"abstract":"<div><div>Alginate, mainly produced by brown algae, is an important polysaccharide that supports the growth of marine bacteria. <em>Vreelandella</em> sp. F11 is a Gram-negative and aerobic marine bacterium, which was isolated from the brown algae sample collected from the Weihai coast, the Yellow Sea, China. Here, we present the complete genome of strain F11 and its genomic characteristics to utilize alginate. The genome of strain F11 comprises one circular chromosome with 4,840,724 bp and a GC content of 55.04 %. Strain F11 could grow with alginate as the sole carbon source. Genomic analysis revealed that strain F11 contains a gene cluster, encoding the enzymes, transporters and a regulator protein involved in utilizing alginate. Gene annotations suggested that the alginate utilization system of strain F11 is similar to those in <em>Vibrio</em> strains. However, strain F11 does not contain homologs of known KdgF (a key enzyme involved in the metabolism of alginate monomer) and inner membrane transporters of alginate oligomer uptake. The result indicated that strain F11 contains novel KdgF and inner membrane transporter system, which warrants further investigation. These data suggested that <em>Vreelandella</em> strains play a role in alginate utilization in the ocean and lay a foundation for the application of <em>Vreelandella</em> in the conversion of brown algae.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101160"},"PeriodicalIF":1.3,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700542","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 : 2024-11-20DOI: 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}
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