Marine genomics最新文献_第6页

Complete genome sequence of Bacillus cereus 2-6A, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Pacific Ocean 从太平洋深海热液沉积物中分离的海洋产胞外多糖的蜡样芽孢杆菌2-6A的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-06-01 DOI: 10.1016/j.margen.2023.101029

Xuan Zou, Chuan-Lei Suo, Xiao-Mei Geng, Chun-Yang Li, Hui-Hui Fu, Yi Zhang, Peng Wang, Mei-Ling Sun

{"title":"Complete genome sequence of Bacillus cereus 2-6A, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Pacific Ocean","authors":"Xuan Zou, Chuan-Lei Suo, Xiao-Mei Geng, Chun-Yang Li, Hui-Hui Fu, Yi Zhang, Peng Wang, Mei-Ling Sun","doi":"10.1016/j.margen.2023.101029","DOIUrl":"10.1016/j.margen.2023.101029","url":null,"abstract":"<div><p><em>Bacillus cereus</em> 2-6A, was isolated from the sediments in the hydrothermal area of the Pacific Ocean with a water depth of 2628 m. In this study, we report the whole genome sequence of strain 2-6A and analyze that to understand its metabolic capacities and biosynthesis potential of natural products. The genome of strain 2-6A consists of a circular chromosome of 5,191,018 bp with a GC content of 35.3 mol% and two plasmids of 234,719 bp and 411,441 bp, respectively. Genomic data mining reveals that strain 2-6A has several gene clusters involved in exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) production and complex polysaccharides degradation. It also possesses a variety of genes for allowing strain 2-6A to cope with osmotic stress, oxidative stress, heat shock, cold shock and heavy metal stress, which could play a vital role in the adaptability of the strain to hydrothermal environments. Gene clusters for secondary metabolite production, such as lasso peptide and siderophore, are also predicted. Therefore, genome sequencing and data mining provide insights into the molecular mechanisms of <em>Bacillus</em> in adapting to hydrothermal deep ocean environments and can facilitate further experimental exploration.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9356795","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

ROS-dependent cell death of Heterosigma akashiwo induced by algicidal bacterium Hahella sp. KA22 灭藻菌Hahella sp. KA22诱导赤石异食虫ros依赖性细胞死亡

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-06-01 DOI: 10.1016/j.margen.2023.101027

Qun Lin , Jiarong Feng , Zhong Hu , Runlin Cai , Hui Wang

{"title":"ROS-dependent cell death of Heterosigma akashiwo induced by algicidal bacterium Hahella sp. KA22","authors":"Qun Lin , Jiarong Feng , Zhong Hu , Runlin Cai , Hui Wang","doi":"10.1016/j.margen.2023.101027","DOIUrl":"10.1016/j.margen.2023.101027","url":null,"abstract":"<div><p>Marine algicidal bacteria and their metabolites are considered to be one of the most effective strategies to mitigate the harmful algal blooms (HABs). The bacterium <em>Hahella</em> sp. KA22 has previously been confirmed to have strong algicidal activity against the HABs causing microalgae, <em>Heterosigma akashiwo</em>. In this study, the molecular mechanism of microalgae cell death was detected. The results showed that the cell growth rate and photosynthetic efficiency were inhibited with addition of algicidal strain KA22, while the accumulation of reactive oxygen species (ROS) and oxidative damage in <em>H. akashiwo</em> cells increased. A total of 2056 unigenes were recognized to be differentially expressed in transcriptome sequences. In particular, the transcriptional levels of light-harvesting pigments and structural proteins in the oxygen-evolving-complex were continuously down-regulated, corresponding to the significant reduction of photosynthetic efficiency and the accumulation of ROS. Furthermore, glutamate dehydrogenase was significantly up-regulated in abundance. Meanwhile, calcium-dependent protein kinases were also detected with significant changes. Collectively, algicidal stress caused the suppressed electron transfer in chloroplast and impaired detoxification of intracellular oxidants by glutathione, which may subsequently result in multiple cell regulation and metabolic responses and ultimately lead to the ROS-dependent cell death of <em>H. akashiwo</em>.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9724742","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

Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench 日本海沟渤索半岛深海沉积物中分离的一种嗜冷菌PS1M3的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-06-01 DOI: 10.1016/j.margen.2023.101028

Yoshihito Nikaidou , Yong Guo , Mahoko Taguchi , Shigeru Chohnan , Tomoyasu Nishizawa , Yasurou Kurusu

{"title":"Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench","authors":"Yoshihito Nikaidou , Yong Guo , Mahoko Taguchi , Shigeru Chohnan , Tomoyasu Nishizawa , Yasurou Kurusu","doi":"10.1016/j.margen.2023.101028","DOIUrl":"10.1016/j.margen.2023.101028","url":null,"abstract":"<div><p>Herein, we report the complete genome sequence of <em>Pseudoalteromonas</em> sp. PS1M3 (= NCBI <span>87791</span><svg><path></path></svg>), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs. The genome of PS1M3 had a total size of 4,351,630 bp, an average GC content of 39.9%, and contained a total of 3811 predicted protein coding sequences, 28 rRNAs, and 100 tRNAs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was utilized to annotate the genes and KofamKOALA within KEGG assigned a gene cluster involved in glycogen biosynthesis and metabolic pathways with regard to heavy metal resistance (copper; <em>cop</em> and mercury; <em>mer</em>), indicating that PS1M3 can potentially use a stored glycogen as an energy source under oligotrophic environment and cope with multi-heavy metal contamination. To assess available genome relatedness indices, whole-genome average nucleotide identity analysis was examined using the complete genome sequences of <em>Pseudoalteromonas</em> spp., showing that 67.29–97.40% sequence similarity with PS1M3. This study may be useful in understanding the roles of a psychrotrophic <em>Pseudoalteromonas</em> in cold deep-sea sediment adaptation mechanisms.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9356797","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 Mycolicibacterium phocaicum RL-HY01, a PAEs-degrading marine bacterial strain isolated from Zhanjiang Bay, China 湛江湾paes降解海洋菌株phocaicum分枝杆菌RL-HY01的全基因组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-06-01 DOI: 10.1016/j.margen.2023.101019

Yuduan Ou , John L. Zhou , Yang Jia , Mei Liang , Hanqiao Hu , Lei Ren

引用次数: 0

Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source 以二甲基磺酰丙酸(DMSP)为唯一碳源生长的新型海洋假单胞菌BSw22131的全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-04-01 DOI: 10.1016/j.margen.2023.101016

Ting Hu , Yin-Xin Zeng , Yi-He Zhang , Yu Du , Wei Han , Hui-Rong Li , Wei Luo

{"title":"Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source","authors":"Ting Hu , Yin-Xin Zeng , Yi-He Zhang , Yu Du , Wei Han , Hui-Rong Li , Wei Luo","doi":"10.1016/j.margen.2023.101016","DOIUrl":"10.1016/j.margen.2023.101016","url":null,"abstract":"<div><p>Members of the genus <em>Pseudomonas</em> have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, <em>Pseudomonas</em> sp. BSw22131, was isolated from seawater in Kongsfjorden, Svalbard. The bacterium can grow with algae-derived dimethylsulfoniopropionate (DMSP) as the sole carbon source. Here, we sequenced the complete genome of strain BSw22131, which contained a single circular chromosome of 5,739,290 (G + C content of 58.23 mol%) without any plasmids. A total of 5362 protein-coding genes, 65 tRNA genes, and 16 rRNA genes were obtained. Genome sequence analysis revealed that strain BSw22131 was not only a potential novel species of the genus <em>Pseudomonas</em> but also different from <em>Pseudomonas</em> sp. DMSP-1 that was isolated from the same habitat and also utilized DMSP as the sole carbon source for growth. The results can be helpful for understanding the catabolism of the genus <em>Pseudomonas</em> in sulfur cycling in the Arctic fjord ecosystem.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9097574","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

Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites 挖掘四色变色藓共生体以合成新的次生代谢物

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-04-01 DOI: 10.1016/j.margen.2023.101017

Esraa Elsaeed , Shymaa Enany , Samar Solyman , Mohamed Shohayeb , Amro Hanora

{"title":"Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites","authors":"Esraa Elsaeed , Shymaa Enany , Samar Solyman , Mohamed Shohayeb , Amro Hanora","doi":"10.1016/j.margen.2023.101017","DOIUrl":"10.1016/j.margen.2023.101017","url":null,"abstract":"<div><p>Many secondary metabolites with medicinal potential are produced by various animals, plants, and microorganisms. Because marine creatures have a greater proportion of unexplored biodiversity than their terrestrial counterparts, they have emerged as a key research focus for the discovery of natural product drugs. Several studies have revealed that bacteria isolated from <em>Chromodoris quadricolor</em> (<em>C. quadricolor)</em> have antibiotic and anticancer properties. In this study, meta-transcriptomics and meta-proteimic analysis were combined to identify biosynthetic gene clusters (BGCs) in the symbiotic bacteria of the <em>C. quadricolor</em> mantle. Symbiotic bacteria were separated from the host by differential pelleting, and then total RNA was extracted, purified, and sequenced. Meta-transcriptomic analysis was done using different natural product mining tools to identify biosynthetic transcript clusters (BTCs). Furthermore, proteins were extracted from the same cells and then analyzed by LC-MS. A meta-proteomic analysis was performed to find proteins that are translated from BCGs. Finally, only 227 proteins have been translated from 40,742 BTCs. The majority of these clusters were polyketide synthases (PKSs) with antibacterial activity. Ten novel potential metabolic clusters with the ability to produce antibiotics have been identified in Novosphingobium and Microbacteriaceae, including members of the ribosomal synthesized and post-translationally modified peptides (RiPPs), polyketide synthases, and others. We realized that using a meta-proteomic approach to identify BGCs that have already been translated makes it easier to concentrate on BGCs that are utilized by bacteria. The symbiotic bacteria associated with <em>C. quadricolor</em> could be a source of novel antibiotics.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9082877","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

Complete genome analysis of Bacillus subtilis TY-1 reveals its biocontrol potential against tobacco bacterial wilt 枯草芽孢杆菌TY-1的全基因组分析揭示了其对烟草青枯病的生物防治潜力

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-04-01 DOI: 10.1016/j.margen.2023.101018

Yin Tian , Shunhua Ji , Enren Zhang , Yiqiang Chen , Guangxin Xu , Xi Chen , Jianqiang Fan , Xixiang Tang

引用次数: 3

Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism 海洋微生物sp. C6131的基因组分析揭示了其参与几丁质代谢的遗传潜力

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101007

Yan-Ru Dang, Xiao-Yu Zhang, Sha-Sha Liu, Ping-Yi Li, Xue-Bing Ren, Qi-Long Qin

{"title":"Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism","authors":"Yan-Ru Dang, Xiao-Yu Zhang, Sha-Sha Liu, Ping-Yi Li, Xue-Bing Ren, Qi-Long Qin","doi":"10.1016/j.margen.2022.101007","DOIUrl":"10.1016/j.margen.2022.101007","url":null,"abstract":"<div><p><em>Marinimicrobium</em> sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases. Chitin is the most abundant polysaccharide in the ocean. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. The genomic information of strain C6131 revealed its genetic potential involved in chitin metabolism. The strain C6131 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. The genomic sequence of <em>Marinimicrobium</em> sp. C6131 could provide fundamental information for future studies on chitin degradation, and help to improve our understanding of the chitin degradation process in deep-sea environments.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10571439","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

Transcriptome assemblies of two deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata from West Pacific seamount, Godin Guyot 西太平洋海山两种深海八栖珊瑚Calyptrophora lyra和Chrysogorgia stellata的转录组组合

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101006

Taewoo Ryu , Sung-Jin Hwang , Seonock Woo

引用次数: 1

The complete genome sequence of Pseudomonas chengduensis BC1815 for genome mining of PET degrading enzymes 成都假单胞菌BC1815的全基因组序列，用于PET降解酶的基因组挖掘

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101008

Zhengguang Shi , Xue Yu , Jingjing Duan , Wenbin Guo

引用次数: 2