Marine genomics最新文献_第6页

Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia 蓝贻贝(Mytilus edulis)对急性缺氧的大小和位点特异性转录组反应

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101060

Stephanie Hall , Denise Méthé , Sarah Stewart-Clark , Fraser Clark

{"title":"Size and site specific transcriptomic responses of blue mussel (Mytilus edulis) to acute hypoxia","authors":"Stephanie Hall , Denise Méthé , Sarah Stewart-Clark , Fraser Clark","doi":"10.1016/j.margen.2023.101060","DOIUrl":"10.1016/j.margen.2023.101060","url":null,"abstract":"<div>The Prince Edward Island (PEI) mussel aquaculture industry is being challenged by climate change induced environmental stressors including hypoxic/anoxic episodes, that can impact mussel health and survival. Physiological responses of mussels to hypoxia/anoxia have been studied; however, less is known about how transcriptomic response leads to physiology. The present study examined the transcriptomic response of acute (4 h) hypoxia in blue mussels (Mytilus edulis) from two sites and size classes in PEI, Canada. Overall, major changes in whole-mussel transcriptomics associated with metabolism, cellular organelles/processes and environmental sensing were observed in the first hours of hypoxia exposure. Differences in differentially expressed transcripts were observed between each site and size, indicating that responses to acute hypoxia exposure are highly complex. A size related pattern was observed, with seed size mussels having differential expression of transcripts associated with development, muscle function, and byssal attachment compared to the adults. Adult mussels had higher HSP 90 expression, while HSPs were predominately under-expressed in seed mussels. Seed mussels had significant under-expression of several classes of byssal thread attachment transcripts, indicating a decline in the production of byssal thread or detachment, both which have negative consequences for mussel aquaculture.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"71 ","pages":"Article 101060"},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10079475","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 analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum 硫氧化细菌Thioclava nitratireducens M1-LQ-LJL-11的全基因组分析及其与深海热液喷口Chrysomallon squamiferum的共生关系

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-01 DOI: 10.1016/j.margen.2023.101058

Xin Yin , Xiang Li , Qian Li , Bingshu Wang , Li Zheng

{"title":"Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum","authors":"Xin Yin , Xiang Li , Qian Li , Bingshu Wang , Li Zheng","doi":"10.1016/j.margen.2023.101058","DOIUrl":"10.1016/j.margen.2023.101058","url":null,"abstract":"<div>One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"71 ","pages":"Article 101058"},"PeriodicalIF":1.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10078909","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 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":"71 ","pages":"Article 101049"},"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":"71 ","pages":"Article 101059"},"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":"72 ","pages":"Article 101070"},"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":"72 ","pages":"Article 101069"},"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":"72 ","pages":"Article 101068"},"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":"70 ","pages":"Article 101032"},"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