Marine genomics最新文献_第8页

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>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 Hahella sp. KA22 has previously been confirmed to have strong algicidal activity against the HABs causing microalgae, Heterosigma akashiwo. 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 H. akashiwo 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 H. akashiwo.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"69 ","pages":"Article 101027"},"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 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>Members of the genus Pseudomonas have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, Pseudomonas 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 Pseudomonas but also different from Pseudomonas 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 Pseudomonas in sulfur cycling in the Arctic fjord ecosystem.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"68 ","pages":"Article 101016"},"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>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 Chromodoris quadricolor (C. quadricolor) 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 C. quadricolor 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 C. quadricolor could be a source of novel antibiotics.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"68 ","pages":"Article 101017"},"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>Marinimicrobium 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 Marinimicrobium 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.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"67 ","pages":"Article 101007"},"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

Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae 海洋玫瑰杆菌系Ruegeria sp. YS9与5个红藻质粒的全基因组序列分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.100997

Qun-Jian Yin , Fang-Chao Zhu , Hong-Zhi Tang , Xu-Yang Chen , Xin Liu , Li-Chang Tang , Xue-Gong Li

{"title":"Complete genome sequence of marine Roseobacter lineage member Ruegeria sp. YS9 with five plasmids isolated from red algae","authors":"Qun-Jian Yin , Fang-Chao Zhu , Hong-Zhi Tang , Xu-Yang Chen , Xin Liu , Li-Chang Tang , Xue-Gong Li","doi":"10.1016/j.margen.2022.100997","DOIUrl":"10.1016/j.margen.2022.100997","url":null,"abstract":"<div>Ruegeria sp. YS9, an aerobic and chemoheterotrophic bacterium belonging to marine Roseobacter lineage, was a putative new species isolated from red algae Eucheuma okamurai in the South China Sea (Beihai, Guangxi province). The complete genome sequence in strain YS9 comprised one circular chromosome with 3,244,635 bp and five circular plasmids ranging from 38,085 to 748,160 bp, with a total length of 4.30 Mb and average GC content of 58.39%. In total, 4129 CDSs, 52 tRNA genes and 9 rRNA genes were obtained. Genomic analysis of strain YS9 revealed that 85 CAZymes were organized in 147 PUL-associated CAZymes involved in polysaccharides metabolism, which were the highest among its two closely related Ruegeria strains. Numerous PULs related to degradation on the cell wall of algae, especially agar, indicated its major player role in the remineralization of algal-derived carbon. Further, the existence of multiple plasmids provided strain YS9 with distinct advantages to facilitate its rapid environmental adaptation, including polysaccharide metabolism, denitrification, resistance to heavy metal stresses such as copper and cobalt, type IV secretion systems and type IV toxin-antitoxin systems, which were obviously different from the two Ruegeria strains. This study provides evidence for polysaccharide metabolic capacity and functions of five plasmids in strain YS9, broadening our understanding of the ecological roles of bacteria in the environment around red algae and the function patterns of plasmids in marine Roseobacter lineage members for environmental adaptation.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"67 ","pages":"Article 100997"},"PeriodicalIF":1.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10581017","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

De novo transcriptomes for two species of snappers from the Western Atlantic (Lutjanus griseus and Lutjanus synagris) 西大西洋两种鲷鱼(Lutjanus griseus和Lutjanus synagris)的从头转录组分析

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101005

Adam Hallaj , Logan F. Turner , Carolyn A. McArdle, Moisés A. Bernal

引用次数: 0

Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4 红海裸鳃诺卡藻相关细菌的生物活性及dassonvilnocardiopsis RACA-4全基因组序列

IF 1.9 4区生物学

Marine genomics Pub Date : 2023-02-01 DOI: 10.1016/j.margen.2022.101004

Hossam H. Elfeky , Amro Hanora , Samar M. Solyman

{"title":"Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4","authors":"Hossam H. Elfeky , Amro Hanora , Samar M. Solyman","doi":"10.1016/j.margen.2022.101004","DOIUrl":"10.1016/j.margen.2022.101004","url":null,"abstract":"<div>Microorganisms associated with marine invertebrates consider an important source of bioactive products. This study aimed to screen for antimicrobial and anticancer activity of crude extracts of bacteria associated with Red sea nudibranchs and molecular identification of the bioactive isolates using 16Sr RNA sequencing, in addition to whole-genome sequencing of one of the most bioactive bacteria. This study showed that bacteria associated with Red sea nudibranchs are highly bioactive and 16Sr RNA sequencing results showed that two isolates belonged to Firmicutes, and two isolates belonged to Proteobacteria, and Actinobacteria. The whole genome sequence data of the isolated Nocardiopsis RACA4 isolate has an estimated genome length of 6,721,839 bp and the taxonomy showed it belongs to the bacteria Nocardiopsis dassonvillei. The De novo assembly of RACA-4 paired reads using Unicycler v0.4.8 initially yielded 97 contigs with an N50 value of 214,568 bp and L50 value of 10, The resulting assembly was further mapped to the reference genome Nocardiopsis dassonvillei strain NCTC10488 using RagTag software v.2.1.0 and a final genome assembly resulted in 39 contigs and N50 value of 6,726,007 and L50 of 1. Genome mining using anti-smash showed around 9.1% of the genome occupied with genes related to secondary metabolites biosynthesis. A wide variety of secondary metabolites belonging to Polyketides, Terpenes, and nonribosomal peptides were predicted with high degree of similarity to known compounds. Non-characterized clusters were also found which suggest new natural compounds discovered by further studies.</div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":"67 ","pages":"Article 101004"},"PeriodicalIF":1.9,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10627920","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: 4