Pub Date : 2026-01-19DOI: 10.1016/j.margen.2026.101233
Chen-Xi Li , Min Zhang , Meng-Xue Yu , Qing-Yu Dong , Yu Wang , Yu-Fei Ding , Shu-Yan Wang , Jin Cheng , Jing-Yu Zhang , Chun-Yang Li
Dimethylsulfoniopropionate (DMSP) is one of the most important organic sulfur compounds in the ocean and plays a key role in polar carbon and sulfur cycles. Sulfitobacter sp. M13, a Gram-negative and aerobic bacterium, was isolated from the melting sea ice in the central Arctic Ocean. Here, we report the complete genome sequence of strain M13 and its genomic characteristics to catabolize DMSP. The genome of strain M13 contains one circular chromosome (3,987,975 bp) and five circular plasmids. Genomic analysis showed that strain M13 contained genes encoding DMSP lyases and the downstream enzymes involved in the DMSP cleavage pathway, indicating that it possesses the potential ability to participate in DMSP metabolism. These findings enhance our understanding of the global sulfur cycling driven by bacteria and reveal the potential strategy of the strain M13 to adapt the extreme environments of Arctic Ocean.
{"title":"Genomic analysis of Sulfitobacter sp. M13 reveals its role in dimethylsulfoniopropionate (DMSP) metabolism","authors":"Chen-Xi Li , Min Zhang , Meng-Xue Yu , Qing-Yu Dong , Yu Wang , Yu-Fei Ding , Shu-Yan Wang , Jin Cheng , Jing-Yu Zhang , Chun-Yang Li","doi":"10.1016/j.margen.2026.101233","DOIUrl":"10.1016/j.margen.2026.101233","url":null,"abstract":"<div><div>Dimethylsulfoniopropionate (DMSP) is one of the most important organic sulfur compounds in the ocean and plays a key role in polar carbon and sulfur cycles. <em>Sulfitobacter</em> sp. M13, a Gram-negative and aerobic bacterium, was isolated from the melting sea ice in the central Arctic Ocean. Here, we report the complete genome sequence of strain M13 and its genomic characteristics to catabolize DMSP. The genome of strain M13 contains one circular chromosome (3,987,975 bp) and five circular plasmids. Genomic analysis showed that strain M13 contained genes encoding DMSP lyases and the downstream enzymes involved in the DMSP cleavage pathway, indicating that it possesses the potential ability to participate in DMSP metabolism. These findings enhance our understanding of the global sulfur cycling driven by bacteria and reveal the potential strategy of the strain M13 to adapt the extreme environments of Arctic Ocean.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"85 ","pages":"Article 101233"},"PeriodicalIF":1.5,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024740","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}
Freshwater crayfish are an ecological keystone species and flagship organisms for endangered aquatic habitats, yet they face population declines driven by anthropogenic activity. The Hardin crayfish (Faxonius wrighti), endemic to the middle Tennessee River basin, is particularly vulnerable due to habitat degradation from sedimentation, altered flow, and agricultural runoff. Establishing genomic resources for species of conservation concern, such as F. wrighti, is essential for understanding the molecular mechanisms underlying physiological responses to environmental stressors. In this study, RNA-Seq was performed on 11 F. wrighti individuals, using hepatopancreas, gill, and abdominal muscle tissues to generate a comprehensive, multi-tissue transcriptome. De novo assembly using Trinity yielded 91,808 unigenes, with 45.3 % annotated in major databases such as GO, KEGG, and NR. Differential gene expression analysis revealed strong tissue-specific expression, with stress-response pathways highly enriched in hepatopancreas and gill tissues. Notable among these were cytochrome P450 metabolism and Na+/K+-ATPase regulation, key pathways associated with responses to chemical stress and osmotic changes, respectively. This multi-tissue transcriptome represents the first genomic resource for the diverse genus Faxonius, offering a foundational resource for future studies of population-level adaptation and response to environmental stressors. More broadly, these findings also highlight the value of tissue-specific transcriptomics in non-model crayfish species and add to the limited genomic data available for endangered crayfish species.
{"title":"In-depth transcriptome analysis of the Hardin crayfish, Faxonius wrighti","authors":"Holly Gothard , Carla Hurt , Mostafa Rahnama , Jorge L. Pérez-Moreno","doi":"10.1016/j.margen.2026.101232","DOIUrl":"10.1016/j.margen.2026.101232","url":null,"abstract":"<div><div>Freshwater crayfish are an ecological keystone species and flagship organisms for endangered aquatic habitats, yet they face population declines driven by anthropogenic activity. The Hardin crayfish (<em>Faxonius wrighti</em>), endemic to the middle Tennessee River basin, is particularly vulnerable due to habitat degradation from sedimentation, altered flow, and agricultural runoff. Establishing genomic resources for species of conservation concern, such as <em>F. wrighti</em>, is essential for understanding the molecular mechanisms underlying physiological responses to environmental stressors. In this study, RNA-Seq was performed on 11 <em>F. wrighti</em> individuals, using hepatopancreas, gill, and abdominal muscle tissues to generate a comprehensive, multi-tissue transcriptome. <em>De novo</em> assembly using Trinity yielded 91,808 unigenes, with 45.3 % annotated in major databases such as GO, KEGG, and NR. Differential gene expression analysis revealed strong tissue-specific expression, with stress-response pathways highly enriched in hepatopancreas and gill tissues. Notable among these were cytochrome P450 metabolism and Na<sup>+</sup>/K<sup>+</sup>-ATPase regulation, key pathways associated with responses to chemical stress and osmotic changes, respectively. This multi-tissue transcriptome represents the first genomic resource for the diverse genus <em>Faxonius</em>, offering a foundational resource for future studies of population-level adaptation and response to environmental stressors. More broadly, these findings also highlight the value of tissue-specific transcriptomics in non-model crayfish species and add to the limited genomic data available for endangered crayfish species.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"85 ","pages":"Article 101232"},"PeriodicalIF":1.5,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950222","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 : 2025-09-30DOI: 10.1016/j.margen.2025.101220
Renato Barbosa Ferraz , Elsa Froufe , L. Filipe C. Castro , Manuel Nande , Karine Vasconcelos Costa , Raimundo de Jesus Tavares Diniz Neto , Óscar Monroig , André Gomes-dos-Santos
Brycon amazonicus (Spix & Agassiz, 1829), commonly known as matrinxã, is a widely distributed Amazonian native fish species with significant aquacultural importance, being the second most produced native fish in Brazil. Despite its economic relevance, omics resources are scarce, limiting advances in aquaculture and nutrition research. Here, we present the first comprehensive transcriptome for the species, generated using RNA-seq data from three tissues, i.e., liver, kidney, and gill. Our analysis yielded a high-quality transcriptome assembly, with 65,454 transcripts, a N50 of 1959 bp, and 34,548 functionally annotated protein-coding genes. To explore lipid metabolism, we identified key genes involved in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), namely the orthologues of the fatty acyl desaturase fads2 and the elongases elovl2 and elovl5. Comparative evolutionary and structural analyses revealed that B. amazonicus shares conserved features with other Amazonian fish, reinforcing its capacity for LC-PUFA biosynthesis. Overall, the results represent a significant advance in the genetic knowledge of this Brazilian emblematic fish, providing a valuable resource for future studies and ultimately helping to promote more sustainable fish farming practices.
{"title":"Multi-tissue transcriptome of Brycon amazonicus (Spix & Agassiz, 1829): insights into lipid metabolism in an Amazonian fish","authors":"Renato Barbosa Ferraz , Elsa Froufe , L. Filipe C. Castro , Manuel Nande , Karine Vasconcelos Costa , Raimundo de Jesus Tavares Diniz Neto , Óscar Monroig , André Gomes-dos-Santos","doi":"10.1016/j.margen.2025.101220","DOIUrl":"10.1016/j.margen.2025.101220","url":null,"abstract":"<div><div><em>Brycon amazonicus</em> (Spix & Agassiz, 1829), commonly known as <em>matrinxã</em>, is a widely distributed Amazonian native fish species with significant aquacultural importance, being the second most produced native fish in Brazil. Despite its economic relevance, <em>omics</em> resources are scarce, limiting advances in aquaculture and nutrition research. Here, we present the first comprehensive transcriptome for the species, generated using RNA-seq data from three tissues, i.e., liver, kidney, and gill. Our analysis yielded a high-quality transcriptome assembly, with 65,454 transcripts, a N50 of 1959 bp, and 34,548 functionally annotated protein-coding genes. To explore lipid metabolism, we identified key genes involved in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), namely the orthologues of the fatty acyl desaturase <em>fads2</em> and the elongases e<em>lovl2</em> and <em>elovl5</em>. Comparative evolutionary and structural analyses revealed that <em>B. amazonicus</em> shares conserved features with other Amazonian fish, reinforcing its capacity for LC-PUFA biosynthesis. Overall, the results represent a significant advance in the genetic knowledge of this Brazilian emblematic fish, providing a valuable resource for future studies and ultimately helping to promote more sustainable fish farming practices.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101220"},"PeriodicalIF":1.5,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145267214","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 : 2025-09-30DOI: 10.1016/j.margen.2025.101221
Qun-Jian Yin , Meng-Yu Liu , Li-Chang Tang , Peng-Fei Zheng , Xin Liu , Hong-Zhi Tang
Vibrio fluvialis QY27, isolated from 2,500 m deep seawater in the South China Sea, was previously shown to tolerate high pressure via trimethylamine-N-oxide metabolism. However, the comprehensive adaptive mechanisms underlying its adaptation to the deep-sea environment remained poorly understood. To better understand its deep-sea adaptation, we conducted genomic and functional analyses. The complete genome comprises two circular chromosomes (4.78 Mb, 49.99 % GC), encoding 4,265 proteins, 108 tRNAs, and 31 rRNAs. Phylogenetically, QY27 shares 98.51 % ANI with V. fluvialis ATCC33809 and possesses a unique set of accessory and rare genes, reflecting significant genomic plasticity. Key adaptive features of QY27 is underpinned by key systems for essential resource acquisition: a multifaceted iron uptake system (vibriobactin, Feo, Efe), diverse terminal oxidases (bd, cbb₃, aa₃, bo₃) for aerobic flexibility, and integrated nitrogen metabolism pathways (TMAO respiration via torCAD/YZ and assimilatory nitrate reduction via napAB-nirBD). These integrated systems create a synergistic network, enabling QY27 to overcome high pressure, oxygen limitation, and nutrient scarcity in the deep sea. This study provides systematic insights into the metabolic adaptation of a non-piezophilic Vibrio fluvialis, advancing our understanding of microbial ecological adaptation and evolutionary in extreme environments.
{"title":"Genomic analysis of Vibrio fluvialis QY27 related to its deep-sea environment adaptation","authors":"Qun-Jian Yin , Meng-Yu Liu , Li-Chang Tang , Peng-Fei Zheng , Xin Liu , Hong-Zhi Tang","doi":"10.1016/j.margen.2025.101221","DOIUrl":"10.1016/j.margen.2025.101221","url":null,"abstract":"<div><div><em>Vibrio fluvialis</em> QY27, isolated from 2,500 m deep seawater in the South China Sea, was previously shown to tolerate high pressure via trimethylamine-N-oxide metabolism. However, the comprehensive adaptive mechanisms underlying its adaptation to the deep-sea environment remained poorly understood. To better understand its deep-sea adaptation, we conducted genomic and functional analyses. The complete genome comprises two circular chromosomes (4.78 Mb, 49.99 % GC), encoding 4,265 proteins, 108 tRNAs, and 31 rRNAs. Phylogenetically, QY27 shares 98.51 % ANI with <em>V. fluvialis</em> ATCC33809 and possesses a unique set of accessory and rare genes, reflecting significant genomic plasticity. Key adaptive features of QY27 is underpinned by key systems for essential resource acquisition: a multifaceted iron uptake system (vibriobactin, Feo, Efe), diverse terminal oxidases (bd, cbb₃, aa₃, bo₃) for aerobic flexibility, and integrated nitrogen metabolism pathways (TMAO respiration via <em>torCAD/YZ</em> and assimilatory nitrate reduction via <em>napAB-nirBD</em>). These integrated systems create a synergistic network, enabling QY27 to overcome high pressure, oxygen limitation, and nutrient scarcity in the deep sea. This study provides systematic insights into the metabolic adaptation of a non-piezophilic <em>Vibrio fluvialis</em>, advancing our understanding of microbial ecological adaptation and evolutionary in extreme environments.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101221"},"PeriodicalIF":1.5,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145324131","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 : 2025-09-30DOI: 10.1016/j.margen.2025.101222
Nasser Al-Siyabi, Aliya Al-Ansari, Antoine O.H.C. Leduc, Nallusamy Sivakumar
A marine bacterium of the family Flavobacteriaceae, Tenacibaculum mesophilum strain M-16, was isolated from the seawater of Qantab Bay, Sea of Oman. The genome sequence of T. mesophilum strain M-16 was analyzed for its metabolic and zeaxanthin biosynthetic potential. The genome of strain M-16 contains one circular chromosome and is 3,074,487 bp long and has a GC content of 32.7 %. The genome contains 3064 coding genes, 55 tRNAs, and 15 rRNAs. Genome mining revealed the presence of three biosynthetic gene clusters (BGCs), which included a BGC for terpenes associated with carotenoid biosynthesis. Key enzymes in the zeaxanthin biosynthesis pathway, such as phytoene synthase (crtB) phytoene desaturase (crtI), lycopene cyclase (crtY), and β-carotene hydroxylase (crtZ), were identified. This study provides insights into the secondary metabolism of T. mesophilum and its potential applications in marine biotechnology.
{"title":"Complete genome sequence of Tenacibaculum mesophilum strain M-16, a marine bacterium from the sea of Oman with potential for zeaxanthin biosynthesis","authors":"Nasser Al-Siyabi, Aliya Al-Ansari, Antoine O.H.C. Leduc, Nallusamy Sivakumar","doi":"10.1016/j.margen.2025.101222","DOIUrl":"10.1016/j.margen.2025.101222","url":null,"abstract":"<div><div>A marine bacterium of the family <em>Flavobacteriaceae</em>, <em>Tenacibaculum mesophilum</em> strain M-16, was isolated from the seawater of Qantab Bay, Sea of Oman. The genome sequence of <em>T. mesophilum</em> strain M-16 was analyzed for its metabolic and zeaxanthin biosynthetic potential. The genome of strain M-16 contains one circular chromosome and is 3,074,487 bp long and has a GC content of 32.7 %. The genome contains 3064 coding genes, 55 tRNAs, and 15 rRNAs. Genome mining revealed the presence of three biosynthetic gene clusters (BGCs), which included a BGC for terpenes associated with carotenoid biosynthesis. Key enzymes in the zeaxanthin biosynthesis pathway, such as phytoene synthase (<em>crtB</em>) phytoene desaturase (<em>crtI</em>), lycopene cyclase (<em>crtY</em>), and β-carotene hydroxylase (<em>crtZ</em>), were identified. This study provides insights into the secondary metabolism of <em>T. mesophilum</em> and its potential applications in marine biotechnology.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101222"},"PeriodicalIF":1.5,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145474059","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 : 2025-09-26DOI: 10.1016/j.margen.2025.101218
Han Wu , Ruilin Fan , Chen Han , Yue Dong , Qinzeng Xu , Sudong Xia , Chenlin Liu , Peiqing He
The genus Sphingosinithalassobacter comprises marine bacteria species, that notable for their versatile metabolic capabilities. However, their specific roles in nitrogen transformation pathways are largely unexplored. In this study, we present the complete genome sequencing and comprehensive analysis of Sphingosinithalassobacter sp. LHW66–3, a novel strain isolated from Atlantic hydrothermal sulfides. The strain possesses a 3.23 Mb circular chromosome with a GC content of 66.84 % and encodes 3140 predicted protein-coding genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed the highest similarity (97.09 %) to Sphingosinithalassobacter portus FM6T. Furthermore, an Average Nucleotide Identity (ANI) value of <77.3 % confirms its designation as a novel species within the genus Sphingosinithalassobacter. Unlike Sphingosinithalassobacter portus FM6T, which possesses hcaD, mhpA, and pcaC genes for aromatic compound degradation, strain LHW66–3 was found to harbor a complete assimilatory nitrate reduction pathway. This pathway includes NasA (nitrate reductase) and NirD and NirB (nitrite reductase), facilitating the conversion of nitrate to ammonium. Additionally, GlnD displays the ability to senses cellular nitrogen status through glutamine availability, regulating P-II proteins (GlnK and GlnB) and the NtrB-NtrC two-component system to modulate external ammonium uptake. Furthermore, the strain shows the potential to utilizes AmtB to import ammonium, which is assimilated via the GS-GOGAT pathway: GlnA synthesizes glutamine, and GltBD converts it to glutamate. This study expands our understanding of nitrogen utilization by Sphingosinithalassobacter sp. LHW66–3 in hydrothermal environments. Furthermore, its complete assimilatory nitrate reduction pathway highlights the applied potential for nitrogen removal in intensive aquaculture systems.
Sphingosinithalassobacter属由海洋细菌种类组成，以其多种代谢能力而闻名。然而，它们在氮转化途径中的具体作用在很大程度上尚未被探索。本研究对大西洋热液硫化物中分离的Sphingosinithalassobacter sp. LHW66-3进行了全基因组测序和综合分析。该菌株拥有一条3.23 Mb的环状染色体，GC含量为66.84%，可编码3140个预测蛋白编码基因。基于16S rRNA基因序列的系统发育分析显示，该菌株与Sphingosinithalassobacter portus FM6T的相似性最高（97.09%）。此外，77.3%的平均核苷酸同一性（ANI）值证实它是Sphingosinithalassobacter属的新种。与Sphingosinithalassobacter portus FM6T不同，菌株LHW66-3具有完整的同化硝酸盐还原途径，而FM6T具有hcaD、mhpA和pcaC降解芳香族化合物的基因。该途径包括NasA（硝酸还原酶）和NirD和NirB（亚硝酸盐还原酶），促进硝酸盐转化为铵。此外，GlnD通过谷氨酰胺可用性感知细胞氮状态，调节P-II蛋白（GlnK和GlnB）和NtrB-NtrC双组分系统调节外部铵吸收。此外，该菌株显示出利用AmtB进口铵的潜力，铵通过GS-GOGAT途径被同化：GlnA合成谷氨酰胺，GltBD将其转化为谷氨酸。本研究扩大了我们对Sphingosinithalassobacter sp. LHW66-3在热液环境中对氮的利用的认识。此外，其完整的同化硝酸还原途径突出了在集约化水产养殖系统中除氮的应用潜力。
{"title":"Complete genome sequencing and analysis revealing assimilatory nitrate reduction pathway of a novel Sphingosinithalassobacter species isolated from the Atlantic hydrothermal sulfides","authors":"Han Wu , Ruilin Fan , Chen Han , Yue Dong , Qinzeng Xu , Sudong Xia , Chenlin Liu , Peiqing He","doi":"10.1016/j.margen.2025.101218","DOIUrl":"10.1016/j.margen.2025.101218","url":null,"abstract":"<div><div>The genus <em>Sphingosinithalassobacter</em> comprises marine bacteria species, that notable for their versatile metabolic capabilities. However, their specific roles in nitrogen transformation pathways are largely unexplored. In this study, we present the complete genome sequencing and comprehensive analysis of <em>Sphingosinithalassobacter</em> sp. LHW66–3, a novel strain isolated from Atlantic hydrothermal sulfides. The strain possesses a 3.23 Mb circular chromosome with a GC content of 66.84 % and encodes 3140 predicted protein-coding genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed the highest similarity (97.09 %) to <em>Sphingosinithalassobacter portus</em> FM6<sup>T</sup>. Furthermore, an Average Nucleotide Identity (ANI) value of <77.3 % confirms its designation as a novel species within the genus <em>Sphingosinithalassobacter</em>. Unlike <em>Sphingosinithalassobacter portus</em> FM6<sup>T</sup>, which possesses <em>hcaD</em>, <em>mhpA</em>, and <em>pcaC</em> genes for aromatic compound degradation, strain LHW66–3 was found to harbor a complete assimilatory nitrate reduction pathway. This pathway includes NasA (nitrate reductase) and NirD and NirB (nitrite reductase), facilitating the conversion of nitrate to ammonium. Additionally, GlnD displays the ability to senses cellular nitrogen status through glutamine availability, regulating P-II proteins (GlnK and GlnB) and the NtrB-NtrC two-component system to modulate external ammonium uptake. Furthermore, the strain shows the potential to utilizes AmtB to import ammonium, which is assimilated via the GS-GOGAT pathway: GlnA synthesizes glutamine, and GltBD converts it to glutamate. This study expands our understanding of nitrogen utilization by <em>Sphingosinithalassobacter</em> sp. LHW66–3 in hydrothermal environments. Furthermore, its complete assimilatory nitrate reduction pathway highlights the applied potential for nitrogen removal in intensive aquaculture systems.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101218"},"PeriodicalIF":1.5,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155062","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}
Isolated from a Pacific Ocean marine sediment sample, Cytobacillus sp. BC1816 may thrive in mineral media that contains polystyrene (PS) plastic as its only carbon source. Here, we present the complete genome of Cytobacillus sp. BC1816, which will facilitate the genome mining of PS degrading enzymes. The sequenced genome has a mean G + C content of 41.43 % and a total length of 5,343,034 base nucleotides. The genome was predicted to include 5367 coding genes, including 107 tRNAs and 36 rRNAs. This genome contained several putative PS-degrading enzymes, such as peroxidases and cytochrome P450s.
{"title":"Complete genome sequence of Cytobacillus sp. BC1816 for genome mining of polystyrene degrading enzymes","authors":"Zhen Zhang , Yanbin Tong , Rongyong Zhang , Wei Bai , Wenbin Guo","doi":"10.1016/j.margen.2025.101219","DOIUrl":"10.1016/j.margen.2025.101219","url":null,"abstract":"<div><div>Isolated from a Pacific Ocean marine sediment sample, <em>Cytobacillus</em> sp. BC1816 may thrive in mineral media that contains polystyrene (PS) plastic as its only carbon source. Here, we present the complete genome of <em>Cytobacillus</em> sp. BC1816, which will facilitate the genome mining of PS degrading enzymes. The sequenced genome has a mean G + C content of 41.43 % and a total length of 5,343,034 base nucleotides. The genome was predicted to include 5367 coding genes, including 107 tRNAs and 36 rRNAs. This genome contained several putative PS-degrading enzymes, such as peroxidases and cytochrome P450s.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101219"},"PeriodicalIF":1.5,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145105997","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 : 2025-09-05DOI: 10.1016/j.margen.2025.101217
Wen-Jing Zhu, Dan Liu, Buke Zhang, Hou-Qi Wang, Peng Wang, Chen Wang, Mei-Ling Sun
Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound produced by various marine organisms and plays a central role in global sulfur and carbon cycling through microbial catabolism. In this study, we present the complete genome sequence and functional annotation of Paracoccus homiensis HT-F, a marine bacterium isolated from intertidal algae of the Yellow Sea, China. The genome comprises a 2,714,952 bp circular chromosome with a GC content of 63.87 %, along with five plasmids ranging from 25,274 bp to 391,451 bp in size, yielding a total genome size of 3.33 Mb. We analyzed the potential of Paracoccus homiensis HT-F for DMSP metabolism based on genome annotation and homology-based analysis. The genome encodes key enzymes involved in both the cleavage and demethylation pathways of DMSP catabolism, as well as transporters and downstream acrylate-processing enzymes. Collectively, the genomic analysis of Paracoccus homiensis HT-F provides insights into the role of Paracoccus bacteria in DMSP-mediated marine sulfur cycling.
{"title":"Genomic analysis of Paracoccus homiensis HT-F reveals its role in marine sulfur cycling","authors":"Wen-Jing Zhu, Dan Liu, Buke Zhang, Hou-Qi Wang, Peng Wang, Chen Wang, Mei-Ling Sun","doi":"10.1016/j.margen.2025.101217","DOIUrl":"10.1016/j.margen.2025.101217","url":null,"abstract":"<div><div>Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound produced by various marine organisms and plays a central role in global sulfur and carbon cycling through microbial catabolism. In this study, we present the complete genome sequence and functional annotation of <em>Paracoccus homiensis</em> HT-F, a marine bacterium isolated from intertidal algae of the Yellow Sea, China. The genome comprises a 2,714,952 bp circular chromosome with a GC content of 63.87 %, along with five plasmids ranging from 25,274 bp to 391,451 bp in size, yielding a total genome size of 3.33 Mb. We analyzed the potential of <em>Paracoccus homiensis</em> HT-F for DMSP metabolism based on genome annotation and homology-based analysis. The genome encodes key enzymes involved in both the cleavage and demethylation pathways of DMSP catabolism, as well as transporters and downstream acrylate-processing enzymes. Collectively, the genomic analysis of <em>Paracoccus homiensis</em> HT-F provides insights into the role of <em>Paracoccus</em> bacteria in DMSP-mediated marine sulfur cycling.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101217"},"PeriodicalIF":1.5,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144997246","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 : 2025-09-03DOI: 10.1016/j.margen.2025.101216
Jia-Yi Song , Zi-Ying Li , Xiao-Hui Yang , Jin-Rong Wei , Kang Li , Yi Zhang
Thalassotalea piscium NK451B is a cold-adapted marine bacterium isolated from Antarctic red algae, exhibiting remarkable extracellular proteolytic activity against gelatin, casein, and collagen. In this study, we present the complete genome sequence of strain NK451B, which consists of a single circular chromosome of 4,233,832 bp with a G + C content of 36.79 % and no plasmid. Genome annotation revealed 3776 predicted protein-coding genes, 67 tRNA genes, and 16 rRNA genes. Functional analysis using the MEROPS database identified 73 putative protease-encoding genes, including 50 predicted intracellular proteases and 23 predicted extracellular proteases based on signal peptide analysis. These proteases are classified into five categories based on their catalytic types, with metalloproteinases and serine proteases being the most prevalent. These enzymes are presumed to contribute to the strain's adaptation by enabling the degradation of environmental proteins as sources of carbon and nitrogen. Overall, the genomic insights highlight the biotechnological potential of Thalassotalea piscium NK451B and enhance our understanding of its ecological role in Antarctic marine environments.
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Pseudoalteromonas sp. SD03, a marine bacterium capable of chitin degradation, was isolated from Antarctic surface water. Here, the genome of strain SD03 was sequenced and the chitin metabolic pathways were constructed. The genome of strain SD03 contained two circular chromosomes and one plasmid totaling 4,326,719 bp with a G + C content of 40.27%. A total of 4005 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction confirmed that strain SD03 possessed intact gene clusters for the hydrolytic chitin degradation pathway. Chitin represents the predominant polysaccharide in marine ecosystems. The degradation and recycling of chitin, mediated by marine bacteria, underpin critical biogeochemical cycling processes of carbon and nitrogen in marine environments. The genomic information of strain SD03 revealed its genetic potential involved in chitin metabolism. The strain SD03 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. These findings provide genomic insights into the biogeochemical cycling of marine chitin in polar environments.
从南极地表水中分离到一种能降解几丁质的海洋细菌假互生单胞菌sp. SD03。本研究对菌株SD03的基因组进行了测序，并构建了几丁质代谢途径。菌株SD03基因组包含2条环状染色体和1个质粒，总长度为4,326,719 bp， G + C含量为40.27%。共预测4005个蛋白编码序列。基因注释和代谢途径重建证实菌株SD03具有完整的水解几丁质降解途径基因簇。几丁质是海洋生态系统中主要的多糖。海洋细菌介导的几丁质降解和再循环是海洋环境中关键的碳氮生物地球化学循环过程的基础。菌株SD03的基因组信息揭示了其参与几丁质代谢的遗传潜力。菌株SD03能够以胶体几丁质为唯一碳源生长，说明这些基因可能在几丁质降解和利用中起作用。这些发现为极地环境中海洋几丁质的生物地球化学循环提供了基因组学的见解。
{"title":"Genomic analysis of Pseudoalteromonas sp. SD03 reveals its potential in chitin hydrolysis","authors":"Yu-Xuan Jiang, Wen-Yue Xu, Hui Liu, Si-Qi Lin, Sha-Sha Liu, Xi-Ying Zhang, Yan-Ru Dang","doi":"10.1016/j.margen.2025.101215","DOIUrl":"10.1016/j.margen.2025.101215","url":null,"abstract":"<div><div><em>Pseudoalteromonas</em> sp. SD03, a marine bacterium capable of chitin degradation, was isolated from Antarctic surface water. Here, the genome of strain SD03 was sequenced and the chitin metabolic pathways were constructed. The genome of strain SD03 contained two circular chromosomes and one plasmid totaling 4,326,719 bp with a G + C content of 40.27%. A total of 4005 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction confirmed that strain SD03 possessed intact gene clusters for the hydrolytic chitin degradation pathway. Chitin represents the predominant polysaccharide in marine ecosystems. The degradation and recycling of chitin, mediated by marine bacteria, underpin critical biogeochemical cycling processes of carbon and nitrogen in marine environments. The genomic information of strain SD03 revealed its genetic potential involved in chitin metabolism. The strain SD03 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. These findings provide genomic insights into the biogeochemical cycling of marine chitin in polar environments.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101215"},"PeriodicalIF":1.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926429","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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