Pub Date : 2025-02-18DOI: 10.1016/j.margen.2025.101182
André Gomes-dos-Santos , André M. Machado , Francisco Baldó , Juan Carlos Arronte , L. Filipe C. Castro , David Barros-García
The genus Notacanthus comprises worldwide distributed bathypelagic deep-sea fish species. Despite several interesting ecological traits and their interesting phylogenetic position as relatives of eels, no transcriptomic, genomic, or proteomic resources are currently available. Here, we present a brain and eye transcriptome for two different notacanthid species: the shortfin spiny eel Notacanthus bonaparte (Risso, 1840) and N. arrontei (Bañón et al., 2024). Functional annotation of the transcripts is also provided. These novel datasets will be valuable for future studies on notacanthid fish and the deep-sea bathypelagic fish community.
{"title":"A “light in the darkness”: First transcriptomic data from deep-sea spiny eels (Notacanthus, Notacanthiformes)","authors":"André Gomes-dos-Santos , André M. Machado , Francisco Baldó , Juan Carlos Arronte , L. Filipe C. Castro , David Barros-García","doi":"10.1016/j.margen.2025.101182","DOIUrl":"10.1016/j.margen.2025.101182","url":null,"abstract":"<div><div>The genus <em>Notacanthus</em> comprises worldwide distributed bathypelagic deep-sea fish species. Despite several interesting ecological traits and their interesting phylogenetic position as relatives of eels, no transcriptomic, genomic, or proteomic resources are currently available. Here, we present a brain and eye transcriptome for two different notacanthid species: the shortfin spiny eel <em>Notacanthus bonaparte</em> (Risso, 1840) and <em>N. arrontei</em> (<span><span>Bañón et al., 2024</span></span>). Functional annotation of the transcripts is also provided. These novel datasets will be valuable for future studies on notacanthid fish and the deep-sea bathypelagic fish community.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101182"},"PeriodicalIF":1.3,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-12DOI: 10.1016/j.margen.2025.101181
Fei-Fei Li , Zhen-Kun Li , Ming-Chen Wang , Jia-Rong Liu , Na Wang , Zhi-Qing Wang , Yu-Zhong Zhang , Hui-Hui Fu
Dimethylsulfoniopropionate (DMSP) is an important organosulfur compound, with key roles in global carbon and sulfur cycling, stress tolerance, chemotaxis, and, potentially, climate regulation. The strain Vibrio sp. D3 was isolated from the surface seawater samples in Qingdao coastal area, which could grow on DMSP as sole carbon source. Here, we report the complete genome sequence of strain D3 and analyzed its genomic characteristics related to the sulfur metabolism, especially DMSP. The genome of strain D3 contains two circular chromosomes of total 5,104,020 bp with a mean GC content of 44.87 %. DMSP transporter gene bccT and acryloy-CoA reductase gene acuI, which is essential in DMSP cleavage, are identified in the genome of Vibrio sp. D3. Potential DMSP demethylase gene dmdA (26.07 %, amino acid sequence identity) and DMSP lyase gene dddX (26.32 %, amino acid sequence identity) are predicted in the genome of strain D3, whose functions need further experimental verification. Vibrio sp. D3 also contains L-Met gamma-lyase (MegL) to generate MeSH from L-Met and complete assimilatory sulfate reduction pathway. Together, the genome of strain D3 reveals the possible DMSP catabolic pathways and supports its role in sulfur cycling.
{"title":"Genomic analysis of Vibrio sp. D3 reveals its role in marine sulfur cycling","authors":"Fei-Fei Li , Zhen-Kun Li , Ming-Chen Wang , Jia-Rong Liu , Na Wang , Zhi-Qing Wang , Yu-Zhong Zhang , Hui-Hui Fu","doi":"10.1016/j.margen.2025.101181","DOIUrl":"10.1016/j.margen.2025.101181","url":null,"abstract":"<div><div>Dimethylsulfoniopropionate (DMSP) is an important organosulfur compound, with key roles in global carbon and sulfur cycling, stress tolerance, chemotaxis, and, potentially, climate regulation. The strain <em>Vibrio</em> sp. D3 was isolated from the surface seawater samples in Qingdao coastal area, which could grow on DMSP as sole carbon source. Here, we report the complete genome sequence of strain D3 and analyzed its genomic characteristics related to the sulfur metabolism, especially DMSP. The genome of strain D3 contains two circular chromosomes of total 5,104,020 bp with a mean GC content of 44.87 %. DMSP transporter gene <em>bccT</em> and acryloy-CoA reductase gene <em>acuI</em>, which is essential in DMSP cleavage, are identified in the genome of <em>Vibrio</em> sp. D3. Potential DMSP demethylase gene <em>dmdA</em> (26.07 %, amino acid sequence identity) and DMSP lyase gene <em>dddX</em> (26.32 %, amino acid sequence identity) are predicted in the genome of strain D3, whose functions need further experimental verification. <em>Vibrio</em> sp. D3 also contains <sub><em>L</em></sub>-Met gamma-lyase (MegL) to generate MeSH from <sub><em>L</em></sub>-Met and complete assimilatory sulfate reduction pathway. Together, the genome of strain D3 reveals the possible DMSP catabolic pathways and supports its role in sulfur cycling.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101181"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387294","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 : 2025-02-12DOI: 10.1016/j.margen.2025.101179
Dan Liu, Tie-Ji Gu, Hou-Qi Wang, Ze-Kun Liu, Meng-Qi Wang, Jing-Li Lü, Xin-Yi Wang, Peng Wang, Chen Wang
D-amino acids are generally supposed to be unique metabolites existing only in bacteria. They can not only modify the bacterial cell wall and promote plant growth, but also participate in the immune regulation of mammals, which is of great significance in nature. Vreelandella piezotolerans V23, a Gram-negative and aerobic bacterium, was isolated from coastal seawater of the Yellow Sea, China. Here, we report the genome of strain V23 and its genomic characteristics to utilize D-amino acids. The genome of strain V23 consists of a single circular chromosome with a size of 3,926,051 bp and a GC content of 58.11 %. Genomic analysis revealed that strain V23 possessed various genes responsible for D-amino acids metabolism and a pathway of synthesizing peptidoglycan from D-amino acids. The results indicated that strain V23 has the capacity to utilize D-amino acids. And strain V23 has been confirmed to be able to grow up with different D-amino acids as the sole nitrogen source. This study also enhances our understanding of the physiological and metabolic characteristics, interspecific diversity of strains of Vreelandella genus, and provides a crucial foundation for further investigation of D-amino acids metabolism.
{"title":"Genomics analysis of Vreelandella piezotolerans V23 reveals its role in D-amino acids metabolism","authors":"Dan Liu, Tie-Ji Gu, Hou-Qi Wang, Ze-Kun Liu, Meng-Qi Wang, Jing-Li Lü, Xin-Yi Wang, Peng Wang, Chen Wang","doi":"10.1016/j.margen.2025.101179","DOIUrl":"10.1016/j.margen.2025.101179","url":null,"abstract":"<div><div>D-amino acids are generally supposed to be unique metabolites existing only in bacteria. They can not only modify the bacterial cell wall and promote plant growth, but also participate in the immune regulation of mammals, which is of great significance in nature. <em>Vreelandella piezotolerans</em> V23, a Gram-negative and aerobic bacterium, was isolated from coastal seawater of the Yellow Sea, China. Here, we report the genome of strain V23 and its genomic characteristics to utilize D-amino acids. The genome of strain V23 consists of a single circular chromosome with a size of 3,926,051 bp and a GC content of 58.11 %. Genomic analysis revealed that strain V23 possessed various genes responsible for D-amino acids metabolism and a pathway of synthesizing peptidoglycan from D-amino acids. The results indicated that strain V23 has the capacity to utilize D-amino acids. And strain V23 has been confirmed to be able to grow up with different D-amino acids as the sole nitrogen source. This study also enhances our understanding of the physiological and metabolic characteristics, interspecific diversity of strains of <em>Vreelandella</em> genus, and provides a crucial foundation for further investigation of D-amino acids metabolism.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101179"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143395373","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 : 2025-02-12DOI: 10.1016/j.margen.2025.101180
Meng-Ru Wang, Yuke Zhang, Zheng-Jun Li
Polyhydroxyalkanoate (PHA) is a promising polyester with superior properties including biodegradability, biocompatibility, and biorenewability. Marinobacterium sediminicola CGMCC 1.7287T, isolated from marine sediment in the East China Sea, has been found capable of producing PHA using volatile fatty acids as cost-effective substrates. Here, we report the genomic characteristics of M. sediminicola CGMCC 1.7287T, which possesses a circular chromosome of 3,554,135 bp with a GC content of 56.10 %. Gene annotation analysis revealed that the bacterium harbors enzymes involved in volatile fatty acids utilization, PHA synthesis, and ectoine accumulation. The presence of genes associated with ectoine synthesis suggests that this bacterium has stress resistance and cellular protection mechanism to adapt to saline environments. The genomic features provide important references for further genetic engineering of marine bacteria to effectively utilize volatile fatty acids for PHA production and enhance stress tolerance through ectoine accumulation.
{"title":"Genomic insights into Marinobacterium sediminicola CGMCC 1.7287T: A polyhydroxyalkanoate-producing bacterium isolated from marine sediment","authors":"Meng-Ru Wang, Yuke Zhang, Zheng-Jun Li","doi":"10.1016/j.margen.2025.101180","DOIUrl":"10.1016/j.margen.2025.101180","url":null,"abstract":"<div><div>Polyhydroxyalkanoate (PHA) is a promising polyester with superior properties including biodegradability, biocompatibility, and biorenewability. <em>Marinobacterium sediminicola</em> CGMCC 1.7287<sup>T</sup>, isolated from marine sediment in the East China Sea, has been found capable of producing PHA using volatile fatty acids as cost-effective substrates. Here, we report the genomic characteristics of <em>M. sediminicola</em> CGMCC 1.7287<sup>T</sup>, which possesses a circular chromosome of 3,554,135 bp with a GC content of 56.10 %. Gene annotation analysis revealed that the bacterium harbors enzymes involved in volatile fatty acids utilization, PHA synthesis, and ectoine accumulation. The presence of genes associated with ectoine synthesis suggests that this bacterium has stress resistance and cellular protection mechanism to adapt to saline environments. The genomic features provide important references for further genetic engineering of marine bacteria to effectively utilize volatile fatty acids for PHA production and enhance stress tolerance through ectoine accumulation.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101180"},"PeriodicalIF":1.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387889","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 : 2025-01-31DOI: 10.1016/j.margen.2025.101178
Liyan Liu , Hai Shi , Zihua Guo , Xiaotong Zhang , Xueqi Li , Xiao-Hua Zhang , Yunhui Zhang
Dimethylsulfide (DMS) is a volatile organic compound that influences climate change and plays a key role in the global sulfur cycle and chemotaxis. Marine bacteria can produce DMS from dimethylsulfoniopropionate (DMSP) and other sulfur precursors. A highly efficient DMS-producing strain, Marinobacter flavimaris ZYH30, was isolated from the surface sediment of the South China Sea, but the key genes involved in DMS production in its genome remain unknown. Here, we reported the complete genome sequence of M. flavimaris ZYH30 and its genomic potential in DMS cycling. The genome of M. flavimaris ZYH30 consists of a circular chromosome with a length of 4,631,282 bp and its GC content is 57.26 %. Genomic analysis showed that strain ZYH30 possesses a set of genes involved in DMS cycling, including a DMSP lyase DddL. In addition, M. flavimaris ZYH30 contained a mddH gene involved in hydrogen sulfide (H2S) and methanethiol (MeSH) dependent DMS production pathways. This study provides genetic insights into the DMS production processes and sulfur cycling in marine sediment bacteria.
{"title":"Genomic analysis of Marinobacter flavimaris ZYH30 reveals its role in marine dimethylsulfide cycling","authors":"Liyan Liu , Hai Shi , Zihua Guo , Xiaotong Zhang , Xueqi Li , Xiao-Hua Zhang , Yunhui Zhang","doi":"10.1016/j.margen.2025.101178","DOIUrl":"10.1016/j.margen.2025.101178","url":null,"abstract":"<div><div>Dimethylsulfide (DMS) is a volatile organic compound that influences climate change and plays a key role in the global sulfur cycle and chemotaxis. Marine bacteria can produce DMS from dimethylsulfoniopropionate (DMSP) and other sulfur precursors. A highly efficient DMS-producing strain, <em>Marinobacter flavimaris</em> ZYH30, was isolated from the surface sediment of the South China Sea, but the key genes involved in DMS production in its genome remain unknown. Here, we reported the complete genome sequence of <em>M. flavimaris</em> ZYH30 and its genomic potential in DMS cycling. The genome of <em>M. flavimaris</em> ZYH30 consists of a circular chromosome with a length of 4,631,282 bp and its GC content is 57.26 %. Genomic analysis showed that strain ZYH30 possesses a set of genes involved in DMS cycling, including a DMSP lyase DddL. In addition, <em>M. flavimaris</em> ZYH30 contained a <em>mddH</em> gene involved in hydrogen sulfide (H<sub>2</sub>S) and methanethiol (MeSH) dependent DMS production pathways. This study provides genetic insights into the DMS production processes and sulfur cycling in marine sediment bacteria.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101178"},"PeriodicalIF":1.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158637","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 : 2025-01-25DOI: 10.1016/j.margen.2025.101168
Shi-Ning Cai , Hai-Xia Zhu , Zhi-Gang Tang , Xue-Yun Geng , Mei-Ling Sun
As a consequence of marine eutrophication, there has been an exponential growth of Ulva prolifera, culminating in the yearly emergence of a massive green tide along the shores of Qingdao. This phenomenon exerts a detrimental impact on the marine ecosystem. As reported, the expression level of Alteromonas enzymes involved in U. prolifera polysaccharides degradation is increased during the green tide outbreak period, potentially accelerating the breakdown of U. prolifera biomass. This enhanced degradation could facilitate the transition to the waning phase of the green tide event. In this study, strain Alteromonas marina OM2201 was isolated from seawater samples taken during an U. prolifera bloom in the coastal waters of Qingdao. Its genome contains a ring chromosome and two plasmids. The length of the circular chromosome was 4,489,073 bp with GC content of 44.21 mol%, and the length of plasmid 1 was 233,636 bp with GC content of 42.24 mol%, and the length of plasmid 2 was 5594 bp with GC content of 39.61 mol%. Genomic analysis showed that Alteromonas marina OM2201 contained a variety of ulvan lyase genes, indicating that it could promote the degradation of U. prolifera polysaccharides. This genetic makeup potentially enables the strain to expedite the decomposition of U. prolifera biomass. Therefore, this study broadens our understanding of the Alteromonas bacteria that can degrade U. prolifera polysaccharides during the outbreak period.
{"title":"Complete genome sequence of Alteromonas marina OM2201, a marine bacterium degrading Ulva prolifera polysaccharides isolated from surface of the Yellow Sea","authors":"Shi-Ning Cai , Hai-Xia Zhu , Zhi-Gang Tang , Xue-Yun Geng , Mei-Ling Sun","doi":"10.1016/j.margen.2025.101168","DOIUrl":"10.1016/j.margen.2025.101168","url":null,"abstract":"<div><div>As a consequence of marine eutrophication, there has been an exponential growth of <em>Ulva prolifera</em>, culminating in the yearly emergence of a massive green tide along the shores of Qingdao. This phenomenon exerts a detrimental impact on the marine ecosystem. As reported, the expression level of <em>Alteromonas</em> enzymes involved in <em>U. prolifera</em> polysaccharides degradation is increased during the green tide outbreak period, potentially accelerating the breakdown of <em>U. prolifera</em> biomass. This enhanced degradation could facilitate the transition to the waning phase of the green tide event. In this study, strain <em>Alteromonas marina</em> OM2201 was isolated from seawater samples taken during an <em>U. prolifera</em> bloom in the coastal waters of Qingdao. Its genome contains a ring chromosome and two plasmids. The length of the circular chromosome was 4,489,073 bp with GC content of 44.21 mol%, and the length of plasmid 1 was 233,636 bp with GC content of 42.24 mol%, and the length of plasmid 2 was 5594 bp with GC content of 39.61 mol%. Genomic analysis showed that <em>Alteromonas marina</em> OM2201 contained a variety of ulvan lyase genes, indicating that it could promote the degradation of <em>U. prolifera</em> polysaccharides. This genetic makeup potentially enables the strain to expedite the decomposition of <em>U. prolifera</em> biomass. Therefore, this study broadens our understanding of the <em>Alteromonas</em> bacteria that can degrade <em>U. prolifera</em> polysaccharides during the outbreak period.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101168"},"PeriodicalIF":1.3,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158638","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 : 2025-01-23DOI: 10.1016/j.margen.2025.101166
Liyun Liang , Songyang Li , Zengpeng Li , Mingliang Chen
We isolated a novel bacterial strain Acinetobacter sp. P1332 from the pufferfish Takifugu oblongus in the southeastern coast of Fujian Province, China. This strain has been identified as a potent producer of the neurotoxin tetrodotoxin (TTX). In this study, we present the complete genome sequence of Acinetobacter sp. P1332, which is a crucial advancement in identifying the genetic factors involved in TTX biosynthesis. The genome spans 4,017,868 base pairs and has a mean G + C content of 41.3 %. It encodes 3944 genes, along with 90 tRNAs and 21 rRNAs. This detailed genomic information provides an essential resource for further research into the biosynthetic pathways of TTX and its applications in biotechnology and toxinology.
{"title":"The complete genome sequence of Acinetobacter sp. P1332, a tetrodotoxin-producing bacteria","authors":"Liyun Liang , Songyang Li , Zengpeng Li , Mingliang Chen","doi":"10.1016/j.margen.2025.101166","DOIUrl":"10.1016/j.margen.2025.101166","url":null,"abstract":"<div><div>We isolated a novel bacterial strain <em>Acinetobacter</em> sp. P1332 from the pufferfish <em>Takifugu oblongus</em> in the southeastern coast of Fujian Province, China. This strain has been identified as a potent producer of the neurotoxin tetrodotoxin (TTX). In this study, we present the complete genome sequence of <em>Acinetobacter</em> sp. P1332, which is a crucial advancement in identifying the genetic factors involved in TTX biosynthesis. The genome spans 4,017,868 base pairs and has a mean G + C content of 41.3 %. It encodes 3944 genes, along with 90 tRNAs and 21 rRNAs. This detailed genomic information provides an essential resource for further research into the biosynthetic pathways of TTX and its applications in biotechnology and toxinology.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101166"},"PeriodicalIF":1.3,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158640","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 : 2025-01-22DOI: 10.1016/j.margen.2025.101167
Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang
Betaine is a zwitterionic compatible compound, which is widely distributed in nature and can be found in a variety of microorganisms. It plays key roles in osmotic protection and one‑carbon metabolism. Sulfitobacter sp. PM12, a Gram-negative and aerobic bacterium, was isolated from the deep-sea samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain PM12 and its genomic characteristics to synthesize and catabolize betaine. The genome of strain PM12 contains one circular chromosome (3,009,717 bp) and seven circular plasmids. Genomic analysis showed that strain PM12 contained a set of genes involved in betaine biosynthesis and biodegradation, indicating that it possesses the ability to metabolize betaine. This study enlarges our understanding of the betaine metabolism driven by bacteria in the ocean, and reveals the potential strategy of the strain PM12 to adapt the extreme environments of the Mariana Trench.
{"title":"Genomic analysis of Sulfitobacter sp. PM12 reveals its role in betaine metabolism","authors":"Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang","doi":"10.1016/j.margen.2025.101167","DOIUrl":"10.1016/j.margen.2025.101167","url":null,"abstract":"<div><div>Betaine is a zwitterionic compatible compound, which is widely distributed in nature and can be found in a variety of microorganisms. It plays key roles in osmotic protection and one‑carbon metabolism. <em>Sulfitobacter</em> sp. PM12, a Gram-negative and aerobic bacterium, was isolated from the deep-sea samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain PM12 and its genomic characteristics to synthesize and catabolize betaine. The genome of strain PM12 contains one circular chromosome (3,009,717 bp) and seven circular plasmids. Genomic analysis showed that strain PM12 contained a set of genes involved in betaine biosynthesis and biodegradation, indicating that it possesses the ability to metabolize betaine. This study enlarges our understanding of the betaine metabolism driven by bacteria in the ocean, and reveals the potential strategy of the strain PM12 to adapt the extreme environments of the Mariana Trench.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"80 ","pages":"Article 101167"},"PeriodicalIF":1.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143158639","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 : 2025-01-16DOI: 10.1016/j.margen.2025.101165
Yu-Qi Zhang , Qi Yuan , Ji-Qing Liu , Xiao-Chen Liang , Jing-Ping Wang , Wen-Xin Jiang , Ping-Yi Li
Marine bacteria play important roles in the degradation and recycling of algal polysaccharides. However, the marine bacteria involved in fucoidan degradation and their degradation pathways remain poorly understood. Here, we report the complete genome sequence of Isoptericola halotolerans SM2308, isolated from a brown algal sample collected from an intertidal zone of the Yellow Sea in China. The genome of strain SM2308 consists of a single circular chromosome of 4,011,455 bp with a high GC content of 72.70 %. Strain SM2308 exhibited rapid growth on fucoidan as the sole carbon source, indicating its capacity to degrade fucoidan. Gene annotation and metabolic pathway analyses showed that strain SM2308 possesses a complete pathway for utilizing fucoidan, including the extracellular breakdown of polymeric fucoidan into smaller fucooligosaccharides/fucose by fucoidanases, the transmembrane transport of fucooligosaccharides/fucose into the cytoplasm by an ABC transporter, and the intracellular fucose catabolism via a non-phosphorylative pathway. This represents the first genome of an actinobacterium from the order Micrococcales with fucoidan-degrading ability. The genome of Isoptericola halotolerans SM2308 provides insights into the role of actinobacteria in the biogeochemical cycling of fucoidan in marine ecosystems.
{"title":"Genomic analysis of Isoptericola halotolerans SM2308 reveals its potential involved in fucoidan degradation","authors":"Yu-Qi Zhang , Qi Yuan , Ji-Qing Liu , Xiao-Chen Liang , Jing-Ping Wang , Wen-Xin Jiang , Ping-Yi Li","doi":"10.1016/j.margen.2025.101165","DOIUrl":"10.1016/j.margen.2025.101165","url":null,"abstract":"<div><div>Marine bacteria play important roles in the degradation and recycling of algal polysaccharides. However, the marine bacteria involved in fucoidan degradation and their degradation pathways remain poorly understood. Here, we report the complete genome sequence of <em>Isoptericola halotolerans</em> SM2308, isolated from a brown algal sample collected from an intertidal zone of the Yellow Sea in China. The genome of strain SM2308 consists of a single circular chromosome of 4,011,455 bp with a high GC content of 72.70 %. Strain SM2308 exhibited rapid growth on fucoidan as the sole carbon source, indicating its capacity to degrade fucoidan. Gene annotation and metabolic pathway analyses showed that strain SM2308 possesses a complete pathway for utilizing fucoidan, including the extracellular breakdown of polymeric fucoidan into smaller fucooligosaccharides/fucose by fucoidanases, the transmembrane transport of fucooligosaccharides/fucose into the cytoplasm by an ABC transporter, and the intracellular fucose catabolism via a non-phosphorylative pathway. This represents the first genome of an actinobacterium from the order Micrococcales with fucoidan-degrading ability. The genome of <em>Isoptericola halotolerans</em> SM2308 provides insights into the role of actinobacteria in the biogeochemical cycling of fucoidan in marine ecosystems.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"79 ","pages":"Article 101165"},"PeriodicalIF":1.3,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008063","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 : 2024-12-11DOI: 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}
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