Marine genomics最新文献_第4页

Complete genome sequence of pectin-degrading Flavobacteriaceae bacterium GSB9 果胶降解黄杆菌科细菌GSB9的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101047

Binna Lee , Jeong Ah. Kim , Yunjon Han, Jae Jun Song, Jong Hyun Choi, Ji Young Kang

引用次数: 0

Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent 深海热液喷口分离的厌氧内孢子形成细菌Tepidibacter sp. SWIR-1的基因组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101049

Xue-Gong Li , Jie Dai , Wei-Jia Zhang , Ai-Jun Jiang , Deng-Hui Li , Long-Fei Wu

{"title":"Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent","authors":"Xue-Gong Li , Jie Dai , Wei-Jia Zhang , Ai-Jun Jiang , Deng-Hui Li , Long-Fei Wu","doi":"10.1016/j.margen.2023.101049","DOIUrl":"10.1016/j.margen.2023.101049","url":null,"abstract":"<div>Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C content and a circular plasmid comprising 38,843 nucleotides with 29.46% G + C content. In total, 3861 protein coding genes, 104 tRNA genes and 46 rRNA genes were obtained. SWIR-1 genome contains numerous genes related to sporulation and germination. Compared with the other three Tepidibacter species, SWIR-1 contained more spore germination receptor proteins. In addition, SWIR-1 contained more genes involved in chemotaxis and two-component systems than other Tepidibacter species. These results indicated that SWIR-1 has developed versatile adaptability to the Southwest Indian Ridge hydrothermal vent environment. The genome of strain SWIR-1 will be helpful for further understanding adaptive strategies used by bacteria dwelling in the deep-sea hydrothermal vent environments of different oceans.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10083543","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}

引用次数: 0

Isolation and genome sequencing of a novel lytic Pseudoalteromonas phage SL20 新型假互生单胞菌噬菌体SL20的分离及基因组测序

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101048

Huifang Li , Jie Gao , Shiyun Ma , Rongda Xiao , Xing Zhou , Wanting Feng , Siyu Zhao , Jiaqi Luo , Di Zhang

引用次数: 1

Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea 从南海红树林沉积物中分离出的一种桔黄色溶脂菌Rossellomorea sp. DA94的全基因组

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101059

Qun-Jian Yin , Hong-Zhi Tang , Fang-Chao Zhu , Xin Liu , Yong-Ze Xing , Li-Chang Tang , Xue-Gong Li

{"title":"Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea","authors":"Qun-Jian Yin , Hong-Zhi Tang , Fang-Chao Zhu , Xin Liu , Yong-Ze Xing , Li-Chang Tang , Xue-Gong Li","doi":"10.1016/j.margen.2023.101059","DOIUrl":"10.1016/j.margen.2023.101059","url":null,"abstract":"<div>Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains. Less CAZymes were organized more PULs, indicating highly efficiently polysaccharides utilization in Rossellomorea. Meanwhile, PUL0459, PUL0460 and PUL0316 related to agar degradation, and exolytic beta-agarase GH50, endo-type beta-agarase GH86 and arylsulfatase were identified in the genome of strain DA94. We verified that strain DA94 can degrade agar to form a bright clear zone around the bacterial colonies in the laboratory. Moreover, the carotenoid biosynthetic pathways were proposed, which may be responsible for orange-pigment of Rossellomorea sp. DA94. This study represents a thorough genomic characterization of CAZymes repertoire and carotenoid biosynthetic pathways of Rossellomorea, provides insight into diversity of related enzymes and their potential biotechnological applications.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10083545","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}

引用次数: 0

Genomic analysis of a marine alphaproteobacterium Sagittula sp. strain MA-2 that carried eight plasmids 携带8个质粒的海洋矢状α变形菌MA-2的基因组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-09-27 DOI: 10.1016/j.margen.2023.101070

Mayuko Abe, Robert A. Kanaly, Jiro F. Mori

{"title":"Genomic analysis of a marine alphaproteobacterium Sagittula sp. strain MA-2 that carried eight plasmids","authors":"Mayuko Abe, Robert A. Kanaly, Jiro F. Mori","doi":"10.1016/j.margen.2023.101070","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101070","url":null,"abstract":"<div>Bacteria that belong to the family Roseobacteraceae in the Alphaproteobacteria class are widely distributed in marine environments with remarkable physiological diversity, which is considered to be attributed to their genomic plasticity. In this study, a novel isolate of the genus Sagittula within Roseobacteraceae, strain MA-2, was obtained from a coastal marine bacterial consortium enriched with aromatic hydrocarbons, and its complete genome was sequenced. The genome with a total size of 5.69 Mbp was revealed to consist of a 4.67-Mbp circular chromosome and eight circular plasmids ranging in size from 19.5 to 361.5 kbp. Further analyses of functional genes in the strain MA-2 genome identified homologous genes responsible for the biotransformation of gentisic acid, which were located on one of its plasmids and were not found in genomes of other Sagittula strains available from databases. This suggested that strain MA-2 had acquired these genes via horizontal gene transfers that enabled them to degrade and utilize gentisic acid as a growth substrate. This study provided the second complete genome sequence of the genus Sagittula and supports the hypothesis that acquisition of ecologically relevant genes in extrachromosomal replicons allows Roseobacteraceae to be highly adaptable to diverse lifestyles.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49886265","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}

引用次数: 0

Characterization and genomic analysis of a novel Pseudoalteromonas phage PS_L5 假互交单胞菌噬菌体PS_L5的鉴定与基因组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-09-14 DOI: 10.1016/j.margen.2023.101069

Xing Zhou , Jie Gao , Rongda Xiao , Yifan Qiao , Yuang Zhu , Di Zhang , Xinyu Zhang , Huifang Li , Juntian Xu

{"title":"Characterization and genomic analysis of a novel Pseudoalteromonas phage PS_L5","authors":"Xing Zhou , Jie Gao , Rongda Xiao , Yifan Qiao , Yuang Zhu , Di Zhang , Xinyu Zhang , Huifang Li , Juntian Xu","doi":"10.1016/j.margen.2023.101069","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101069","url":null,"abstract":"<div>Pseudoalteromonas is a widely distributed bacterial genus that is associated with marine algae. However, there is still limited knowledge about their bacteriophage. In this study, we reported the isolation of a novel lytic bacteriophage that infects Pseudoalteromonas marina. Transmission electron microscopy revealed that PS_L5 had an icosahedral head of 52.6 ± 2 nm and a non-contractile tail with length of 96.5 ± 2 nm. The genome sequence of this phage was 34, 257 bp and had a GC content of 40.75%. Furthermore, this genome contained 61 predicted open reading frames (ORFs), which involved in various functions such as phage structure, packaging, DNA metabolism, host lysis and other additional functions. Additionally, the phylogenetic analysis based on major capsid protein showed that the phage PS_L5 was closely related to five other Pseudoalteromonas phages, namely PHS3, PHS21, AL, SL25 and Pq0 which also possessed the non-contractile long tail. This study provided the fundamental insights into the evolutionary dynamics of Pseudoalteromonas phages and the interaction between phage and host.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49886266","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}

引用次数: 0

Complete genome of Polaribacter huanghezhanensis KCTC 32516T isolated from glaciomarine fjord sediment of Svalbard 从斯瓦尔巴冰川海峡湾沉积物中分离的黄河山北极杆菌KCTC 32516T的全基因组

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-08-30 DOI: 10.1016/j.margen.2023.101068

Kyuin Hwang , Hanna Choe , Kyung Mo Kim

{"title":"Complete genome of Polaribacter huanghezhanensis KCTC 32516T isolated from glaciomarine fjord sediment of Svalbard","authors":"Kyuin Hwang , Hanna Choe , Kyung Mo Kim","doi":"10.1016/j.margen.2023.101068","DOIUrl":"10.1016/j.margen.2023.101068","url":null,"abstract":"<div>Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48142737","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}

引用次数: 0

Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community 埃及红海海绵Theonella sp.相关微生物群落的宏基因组和宏转录组研究

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-08-01 DOI: 10.1016/j.margen.2023.101032

Manar El Samak , Samira Zakeer , Amro Hanora , Samar M. Solyman

{"title":"Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community","authors":"Manar El Samak , Samira Zakeer , Amro Hanora , Samar M. Solyman","doi":"10.1016/j.margen.2023.101032","DOIUrl":"10.1016/j.margen.2023.101032","url":null,"abstract":"<div>Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9673955","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}

引用次数: 2

A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance 第一个对鲍鱼进化和经济重要性特征具有基因组见解的midae halotis基因组序列的注释

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-08-01 DOI: 10.1016/j.margen.2023.101044

Thendo S. Tshilate , Edson Ishengoma , Clint Rhode

{"title":"A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance","authors":"Thendo S. Tshilate , Edson Ishengoma , Clint Rhode","doi":"10.1016/j.margen.2023.101044","DOIUrl":"10.1016/j.margen.2023.101044","url":null,"abstract":"<div>Haliotis midae or “perlemoen” is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in minimising the pressure on the wild populations. Here, the draft genome of H. midae has been sequenced, assembled, and annotated. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238 Mb, scaffold N50 of 0. 238 Mb and GC level of 40%. Gene annotation, combining ab initio and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (H. laevigata, H. rubra, H. discus hannai and H. rufescens) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that H. midae is closely related to the Australian Greenlip (H. laevigata) and Blacklip (H. rubra). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9737332","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}

引用次数: 0

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean 西南印度洋深海沉积物中碳固定微生物及其碳固定途径的宏基因组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-08-01 DOI: 10.1016/j.margen.2023.101045

Xiao-Lan Yue , Lin Xu , Li Cui , Ge-Yi Fu , Xue-Wei Xu

{"title":"Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean","authors":"Xiao-Lan Yue , Lin Xu , Li Cui , Ge-Yi Fu , Xue-Wei Xu","doi":"10.1016/j.margen.2023.101045","DOIUrl":"10.1016/j.margen.2023.101045","url":null,"abstract":"<div>Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood–Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058442","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}

引用次数: 1