Marine genomics最新文献

{"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 ,&nbsp;Ruilin Fan ,&nbsp;Chen Han ,&nbsp;Yue Dong ,&nbsp;Qinzeng Xu ,&nbsp;Sudong Xia ,&nbsp;Chenlin Liu ,&nbsp;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^T. Furthermore, an Average Nucleotide Identity (ANI) value of &lt;77.3 % confirms its designation as a novel species within the genus <em>Sphingosinithalassobacter</em>. Unlike <em>Sphingosinithalassobacter portus</em> FM6^T, 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}

{"title":"Complete genome sequence of Cytobacillus sp. BC1816 for genome mining of polystyrene degrading enzymes","authors":"Zhen Zhang ,&nbsp;Yanbin Tong ,&nbsp;Rongyong Zhang ,&nbsp;Wei Bai ,&nbsp;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}

{"title":"Genomic analysis of Paracoccus homiensis HT-F reveals its role in marine sulfur cycling","authors":"Wen-Jing Zhu,&nbsp;Dan Liu,&nbsp;Buke Zhang,&nbsp;Hou-Qi Wang,&nbsp;Peng Wang,&nbsp;Chen Wang,&nbsp;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}

{"title":"Complete genome of Thalassotalea piscium NK451B, an Antarctic bacterium with abundant extracellular proteases","authors":"Jia-Yi Song ,&nbsp;Zi-Ying Li ,&nbsp;Xiao-Hui Yang ,&nbsp;Jin-Rong Wei ,&nbsp;Kang Li ,&nbsp;Yi Zhang","doi":"10.1016/j.margen.2025.101216","DOIUrl":"10.1016/j.margen.2025.101216","url":null,"abstract":"<div><div><em>Thalassotalea piscium</em> 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 <em>Thalassotalea piscium</em> NK451B and enhance our understanding of its ecological role in Antarctic marine environments.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101216"},"PeriodicalIF":1.5,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933539","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}

{"title":"Genomic analysis of Pseudoalteromonas sp. SD03 reveals its potential in chitin hydrolysis","authors":"Yu-Xuan Jiang,&nbsp;Wen-Yue Xu,&nbsp;Hui Liu,&nbsp;Si-Qi Lin,&nbsp;Sha-Sha Liu,&nbsp;Xi-Ying Zhang,&nbsp;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}

{"title":"Genomic analysis of Caballeronia sp. DA-9 reveals its role in glutathione metabolism","authors":"Jun Li ,&nbsp;Kun Liang ,&nbsp;Ya Ma ,&nbsp;Nan Zhang","doi":"10.1016/j.margen.2025.101214","DOIUrl":"10.1016/j.margen.2025.101214","url":null,"abstract":"<div><div>Glutathione (GSH) is a well-known tripeptide composed of glutamic acid, cysteine and glycine. It plays critical roles in maintaining the redox homeostasis of cells and in cell cycle regulation, apoptosis, immunological defense, and pathological abnormalities. <em>Caballeronia</em> sp. DA-9, a Gram-negative and aerobic bacterium, was isolated from the sediment collected from the Weddell Sea. Here, we report the complete genome sequence of strain DA-9 and its genomic characteristics to synthesize and catabolize GSH. The genome of strain DA-9 contains three circular chromosomes and two plasmids. Genomic analysis showed that strain DA-9 contained a set of genes involved in GSH metabolism, indicating that it possesses the potential ability to synthesize and catabolize GSH. This study provides novel insights into GSH metabolism by marine microorganisms.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"83 ","pages":"Article 101214"},"PeriodicalIF":1.5,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144912106","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}

{"title":"Complete genome sequence of Lysinibacillus sp. WB86, a potential antimicrobial lanthipeptides producer","authors":"Huai-Ying Sun ,&nbsp;Ji-Xiang Xin ,&nbsp;Gen Li ,&nbsp;Zhen-Yi Zhou ,&nbsp;Xin Li ,&nbsp;Hong Wang ,&nbsp;Qun-Jian Yin ,&nbsp;Bin Wei","doi":"10.1016/j.margen.2025.101204","DOIUrl":"10.1016/j.margen.2025.101204","url":null,"abstract":"<div><div><em>Lysinibacillus</em> sp. WB86 was isolated from a cold seep in the South China Sea, and its complete genome was sequenced using Oxford Nanopore Technologies (ONT). The genome consists of a single circular chromosome spanning 4,537,071 bp, with a G + C content of 37 %. FastANI analysis revealed a 99.38 % average nucleotide identity (ANI) with <em>Lysinibacillus sphaericus</em> A1, confirming its classification as a strain of <em>L. sphaericus</em>. Genome annotation identified 4397 protein-coding genes, along with 111 tRNAs and 34 rRNAs. Functional categorization using the COG database assigned 84.6 % of the protein-coding genes to specific roles, with the majority involved in transcription, amino acid transport and metabolism, translation and ribosomal biogenesis, and replication, recombination, and repair. Additionally, antiSMASH-based analysis uncovered eight biosynthetic gene clusters (BGCs), only one of which exhibited high similarity (&gt;50 %) to known BGCs. This cluster was predicted to encode novel antimicrobial lanthipeptides, suggesting potential biotechnological applications.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101204"},"PeriodicalIF":1.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779565","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}

{"title":"Complete genome sequence of Pseudoalteromonas lipolytica M7NS11, a chitinolytic bacterium isolated from the New Britain Trench","authors":"Bin Jin ,&nbsp;Xiao Liang ,&nbsp;Xiaoyu Wang ,&nbsp;Li-Hua Peng ,&nbsp;Jin-Long Yang","doi":"10.1016/j.margen.2025.101203","DOIUrl":"10.1016/j.margen.2025.101203","url":null,"abstract":"<div><div><em>Pseudoalteromonas</em>, recognized as one of chitin decomposers in marine environments, plays a pivotal role in global carbon and nitrogen cycling. This study reports the whole genome sequence of bacterium M7NS11, which was isolated from deep-sea sediments of the New Britain Trench. Genomic analysis revealed two circular elements: a 3,607,764-bp chromosomal structure (41.79 % GC) and an 899,258-bp plasmid structure (40.87 % GC). Whole-genome analysis revealed that this strain possesses 9 genes encoding chitinases and 1 gene encoding lytic polysaccharide monooxygenase (LPMO), indicating that the strain may efficiently degrade chitin through synergistic interactions between chitinases and LPMO to acquire essential nutrients. Additionally, it contains four genes (<em>amgK</em>, <em>glmU</em>, <em>murA</em>, and <em>murB</em>), encoding enzymes which could utilize chitin degradation products to synthesize peptidoglycan, a major component of cell wall. The analysis of the complete genome of <em>P. lipolytica</em> M7NS11 provides new insights into the role of <em>Pseudoalteromonas</em> in deep-sea material cycling, and underscores the potential of <em>P. lipolytica</em> M7NS11 as a valuable resource for isolating efficient chitinases.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101203"},"PeriodicalIF":1.3,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144713441","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}

{"title":"Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds","authors":"Serena Federico ,&nbsp;Roberta Esposito ,&nbsp;Maria De Rosa ,&nbsp;Michele Sonnessa ,&nbsp;Sofia Reddel ,&nbsp;Gaia Laurenzi ,&nbsp;Marco Bertolino ,&nbsp;Marco Giovine ,&nbsp;Marina Pozzolini ,&nbsp;Valerio Zupo ,&nbsp;Maria Costantini","doi":"10.1016/j.margen.2025.101202","DOIUrl":"10.1016/j.margen.2025.101202","url":null,"abstract":"<div><div>Marine sponges host a range of microorganisms and among them, bacteria represent a significant part of their biomass. Furthermore, bacteria are promising sources of natural products to be applied in various fields. Often the study their biotechnological potential is relented by low grow rates. For this reason, such cultivation-independent approaches, as metagenomics tools applied to sponges is obtaining wide success. For the first time, here we aimed at having an almost complete information about taxonomic and functional diversity of bacteria associated to three sponges, <em>Agelas oroides</em>, <em>Haliclona</em> (<em>Halichoclona</em>) <em>vansoesti</em> and <em>Geodia cydonium</em>, previously reported as candidate sources of bioactive compounds for pharmacological, nutraceutical and cosmeceutical purposes. Comparative metagenomic analyses were applied, sequencing DNA from the three sponges by ONT GridION X5 Mk1 sequencer. Our findings revealed for all the analyzed sponges the presence of genes/enzymes responsible for the synthesis of vitamins, fatty acids, antioxidant glutathione, terpenes, steroids and carotenoids. Consequently, we demonstrated the three sponges under analysis and their associated microorganisms could be considered good candidates for the isolation and identification of bioactive compounds for biotechnological application in the field of pharmacology, nutraceuticals and cosmeceuticals as well as environmental biotechnologies. Overall, metagenomic data represent a useful tool exploitable to sustainably develop bioactive products.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101202"},"PeriodicalIF":1.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144672176","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}

{"title":"Complete genome sequence of Vibrio sinus, a potential contributor to collagen degradation","authors":"Dingyong Huang ,&nbsp;Wanjia Tong ,&nbsp;Jinfeng Wang ,&nbsp;Jianjia Wang ,&nbsp;Yan Zhuang ,&nbsp;Peng Tian ,&nbsp;Xiaolei Wang","doi":"10.1016/j.margen.2025.101201","DOIUrl":"10.1016/j.margen.2025.101201","url":null,"abstract":"<div><div>Collagenase is an enzyme that has been shown to be highly effective in the degradation of both native triple-helical collagen and its denatured form (<em>e.g.</em>, gelatin). As a virulence factor secreted by pathogenic bacteria (<em>Clostridium histolyticum</em>, <em>Vibrio</em>, <em>Bacillus cereus</em>), this efficacy is attributed to the unique ability of the enzyme to hydrolyze Gly-X-Y bonds within thermally stable fibrillar structures. A highly efficient gelatin degrading strain, <em>Vibrio sinus</em> S4M6^T, was isolated from the surface seawater collected in Dongshan Bay (Fujian, PR China), but the key genes involved in gelatin degradation remain unknown. Here, we report the complete genome sequence of <em>Vibrio sinus</em> S4M6^T and its collagen degrading genes. The genome of strain S4M6^T consists of two circular chromosomes, with a total chromosome length of 4.78 Mbp and a GC content of 43.4 %. Genomic analysis revealed that strain S4M6^T encodes a collagenase gene involved in collagen degradation. This study provides a genetic insight of collagen degradation in marine <em>Vibrio</em> species.</div></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"82 ","pages":"Article 101201"},"PeriodicalIF":1.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578852","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}