Marine genomics最新文献_第4页

Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater 温热杆菌科新菌株类型的全基因组分析。11月，与表层海水隔离

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-11-06 DOI: 10.1016/j.margen.2023.101073

Jin-Cheng Rong , Lin-Lin Cui , Xiao-Chen Yang , Mao-Li Yi , Qi Zhao

{"title":"Complete genome analysis of type strain of a novel bacterial family Temperatibacteraceae fam. nov., isolated from surface seawater","authors":"Jin-Cheng Rong , Lin-Lin Cui , Xiao-Chen Yang , Mao-Li Yi , Qi Zhao","doi":"10.1016/j.margen.2023.101073","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101073","url":null,"abstract":"<div>Novel bacterial resources are valuable for studying bacterial taxonomy, bacterial evolution, and genome mining of novel antibiotics, antitumor agents, and immune modulators. In this study, we de novo sequenced the type strain of a novel bacterial family, Temperatibacteraceae fam. Nov., belonging to class Alphaproteobacteria of phylum Pseudomonadota. The type strain, Temperatibacter marinus NBRC 110045T, is mesophilic and was isolated from surface seawater around Muroto city of Japan at a depth of 0.5 m. Here, the sequenced complete genome of strain NBRC 110045T is composed of a circular chromosome of 3,184,799 bp with a mean G + C content of 43.71%. Genome analysis was applied to reveal the genetic basis of its cellular activities. Cellular regulation and signaling was analyzed to infer the regulatory mechanism of its limited growth temperature range. Genomic features of the novel family Temperatibacteraceae may expand our knowledge on environmental adaptation, genetic evolution and natural product discovery of marine bacteria.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91593845","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

The complete genome sequence of Peribacillus sp. R9–11 for genome mining of polystyrene degrading enzymes 为聚苯乙烯降解酶的基因组挖掘提供了芽孢杆菌R9-11的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-20 DOI: 10.1016/j.margen.2023.101072

Xue Yu , Wenbin Guo , Jingjing Duan

引用次数: 0

Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean 西太平洋烟草黑胫病生物防治剂蜡样芽孢杆菌Z4的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-10-13 DOI: 10.1016/j.margen.2023.101071

Shunhua Ji , Yin Tian , Jingjing Li , Guangxin Xu , Yongan Zhang , Shanyi Chen , Yiqiang Chen , Xixiang Tang

{"title":"Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean","authors":"Shunhua Ji , Yin Tian , Jingjing Li , Guangxin Xu , Yongan Zhang , Shanyi Chen , Yiqiang Chen , Xixiang Tang","doi":"10.1016/j.margen.2023.101071","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101071","url":null,"abstract":"<div>Bacillus species have been considered as promising biological control agents due to their excellent antimicrobial ability. Bacillus cereus strain Z4 was isolated from 2000 m deep sea sediments of the Western Pacific Ocean, which possesses significant antifungal activity against Phytophthora nicotianae, the pathogenic fungus of tobacco black shank disease. To reveal the underlying antifungal genetic mechanisms, here, we report the complete genomic sequence of the strain Z4. The genome has one circular chromosome of 5,664,309 bp with a G + C content of 35.31%, 109 tRNAs, and 43 rRNAs. Genomic analysis identified 10 gene clusters related to the biosynthesis of biocontrol active compounds, including bacillibactin, petrobactin, fengycin, and molybdenum cofactor. Meanwhile, 6 gene clusters were responsible for the biosynthesis of metabolites with unknown functions. Strain Z4 also contains a large number of genes encoding carbohydrate-active enzymes and secreted proteins, respectively. The whole genomic analysis of Bacillus cereus Z4 may provide a valuable reference for elucidating its biocontrol mechanism against tobacco black shank.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49886267","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

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":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":"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":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":"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":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