Marine genomics最新文献

{"title":"Complete genome sequence of Halomonas alkaliantarctica MSP3 isolated from marine sediment, Jeju Island","authors":"Minji Kim,&nbsp;Soo-Je Park","doi":"10.1016/j.margen.2023.101046","DOIUrl":"10.1016/j.margen.2023.101046","url":null,"abstract":"<div><p>As a moderate halophilic-heterotrophic bacterium, <em>Halomonas alkaliantarctica</em> MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes (61 tRNA and 18 rRNA). According to the genome annotation, it was revealed that the strain MSP3 harbors genes encoding for urease and urea transporters, which play a crucial role in the process of urea degradation and utilization. In addition, it is noteworthy that the MSP3 strain possesses genes encoding for both cytochrome <em>c</em> oxidase and cytochrome <em>bd</em> oxidase, thereby conferring upon it the ability to adapt to various levels of oxygen (oxic to microoxic) and to execute denitrification processes in the absence of oxygen. Moreover, it was observed that strain MSP3 had genes for the glyoxylate cycle, which is an alternative pathway to the TCA cycle. Furthermore, it was observed that the MSP3 strain exhibited the ability to thrive across a diverse spectrum of NaCl concentrations, ranging from 2% to 10% (<em>w</em>/<em>v</em>). Collectively, strain MSP3 may possess an advantage over competitors within the marine ecosystem, particularly in conditions where carbon substrates are restricted. The genomic-based assumption could potentially be substantiated by the presence of a multitude of transporter genes within the genome.</p></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":"10041771","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}

{"title":"Genomic analysis of Marinomonas algicola SM1966T reveals its role in marine sulfur cycling","authors":"Min Zhang ,&nbsp;Xiao-Di Wang ,&nbsp;Yue Lin ,&nbsp;Shu-Yan Wang ,&nbsp;Shan Zhang ,&nbsp;Jin Cheng ,&nbsp;Mei-Ling Sun ,&nbsp;Peng Wang ,&nbsp;Hui-Hui Fu ,&nbsp;Chun-Yang Li ,&nbsp;Nan Zhang","doi":"10.1016/j.margen.2023.101043","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101043","url":null,"abstract":"<div><p>Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling, which is mainly produced by marine phytoplankton and macroalgae. <em>Marinomonas algicola</em> SM1966^T, a Gram-negative, aerobic and rod-shaped bacterium, was isolated from the surface of <em>Ulva pertusa</em> (Chlorophyta) algal sample collected off the coastal areas of Rongcheng, China. Here, we report the complete genome sequence of strain SM1966^T and its genomic characteristics to utilize DMSP, which may be produced by <em>Ulva pertusa.</em> The genome of strain SM1966^T contains one circular chromosome (4.3 Mbp) and one circular plasmid (149,271 bp). Genomic analysis showed that strain SM1966^T possesses a set of genes involved in DMSP transport, DMSP cleavage and the catabolism of acrylate, one product of DMSP cleavage. The results indicated that strain SM1966^T has the capacity to utilize DMSP and produce dimethyl sulfide (DMS), a volatile infochemical with important roles in global sulfur cycling. This study provides genetic insights into DMSP catabolism by algae-associated bacteria.</p></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":"49855077","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}

{"title":"Complete genome sequence of Streptomyces sp. HNA39, a new cyclizidine producer isolated from a South China Sea sediment","authors":"Suzhen Li ,&nbsp;Yong-Jun Jiang ,&nbsp;Zhongjun Ma ,&nbsp;Nan Wang","doi":"10.1016/j.margen.2023.101033","DOIUrl":"10.1016/j.margen.2023.101033","url":null,"abstract":"<div><p><em>Streptomyces</em> sp. HNA39 is a promising candidate for the production of antineoplastic metabolites screened from a collection of 448 actinomycetes derived from coastal sediments. The complete genome sequence of HNA39 comprises a 7,351,753-bp linear chromosome with a GC content of 71.94%. Whole genome analysis reveals the presence of 29 putative biosynthetic gene clusters (BGCs) encoding secondary metabolites. Among them, a type I PKS BGC shows an 82% similarity with the cyclizidine (CLD) BGC identified from <em>Streptomyces</em> NCIB 11649. LC-MS profiles further supported the production of new CLD congeners. Bafilomycins were also found produced in abundance, corresponding to another type I PKS BGC highly homologous to that of bafilomycin B1 from <em>S. lohii</em>. CLDs are indolizidine alkaloids consisting a fused five- and six-membered ring system with an intriguing cyclopropane terminal linked by a <em>trans</em>-dienic chain. The cyclization mechanism of the cylopropyl ring, one of its pharmacophores, is still unknown. Genome sequencing of the new CLD producer and subsequent comparative analysis of their gene clusters would further our understanding of the chemistry behind cyclopropane formation.</p></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":"10041770","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}

{"title":"Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223T, isolated from bathypelagic seawater","authors":"Jin-Cheng Rong,&nbsp;Li Sheng,&nbsp;Li-Hua Jiang,&nbsp;Mao-Li Yi,&nbsp;Jin-Ying Wu,&nbsp;Qi Zhao","doi":"10.1016/j.margen.2023.101031","DOIUrl":"https://doi.org/10.1016/j.margen.2023.101031","url":null,"abstract":"<div><p>During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus <em>Hyphococcus</em>. The type strain, <em>Hyphococcus flavus</em> MCCC 1K03223^T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223^T is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of <em>H. flavus</em> revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.</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":"49855181","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}

{"title":"Shotgun metagenomic analysis of bacterial symbionts associated with “Chromodoris quadricolor” mantle","authors":"Engy Mahmoud,&nbsp;Amro Hanora,&nbsp;Salah Abdalla,&nbsp;Ali A. Abdelrahman Ahmed,&nbsp;Samira Zakeer","doi":"10.1016/j.margen.2023.101030","DOIUrl":"10.1016/j.margen.2023.101030","url":null,"abstract":"<div><p>Nudibranchs are colorful marine invertebrates having a diverse group of understudied animals. Recently, some nudibranch members have acquired some attention while others still have not. <em>Chromodoris quadricolor</em> is a member of the Red Sea nudibranch, which did not have the chance to get significant attention. Unlike various invertebrates, it lacks a shell suggesting that it must defend itself in other ways. Therefore, in the present study, we were concerned about the mantle-associated bacterial communities. Being essential partners of this dorid nudibranch system, we investigated their taxonomic and functional profiles. We performed a whole metagenomic shotgun approach for the mantle bacterial cells after a differential pelleting procedure. In this procedure, we separated most of the prokaryotic cells from the eukaryotic host cells. Our findings showed that the mantle-body part holds a diverse group of bacterial species relating mainly to <em>Proteobacteria</em> and <em>Tenericutes</em> phyla. There were novel findings regarding the bacterial members associated with the nudibranch mollusks group. Various species were not previously recorded as bacterial symbionts with nudibranchs. Those members were <em>Bathymodiolus brooksi thiotrophic gill symbiont</em> (23.2%), <em>Mycoplasma marinum</em> (7.4%), <em>Mycoplasma todarodis</em> (5%), <em>and Solemya velum gill symbiont</em> (2.6%). The presence of these bacterial species assumed a nutritional role to the host. However, some of these species were present in a high abundance, suggesting their important symbiosis with <em>Chromodoris quadricolor</em>. In addition, exploring the bacterial ability to produce valuable products resulted in the prediction of 2088 biosynthetic gene clusters (BGCs). We identified different gene cluster classes. Polyketide BGC class was the most represented. Others were related to fatty acid BGCs, RiPP, saccharide, terpene, and NRP BGC classes. Prediction of the activity of these gene clusters resulted in, mainly, an antibacterial activity. In addition, different antimicrobial secondary metabolites were also detected. These secondary metabolites are considered key components regulating the bacterial species interactions in their ecosystem. This suggested the significant contribution of these bacterial symbionts to protect the nudibranch host against predators and pathogens. Globally, it is the first detailed study concerned with both the taxonomic diversity and functional potentials of the bacterial symbionts associated with <em>Chromodoris quadricolor</em> mantle.</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":"9348792","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}

{"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,&nbsp;Chuan-Lei Suo,&nbsp;Xiao-Mei Geng,&nbsp;Chun-Yang Li,&nbsp;Hui-Hui Fu,&nbsp;Yi Zhang,&nbsp;Peng Wang,&nbsp;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}

{"title":"ROS-dependent cell death of Heterosigma akashiwo induced by algicidal bacterium Hahella sp. KA22","authors":"Qun Lin ,&nbsp;Jiarong Feng ,&nbsp;Zhong Hu ,&nbsp;Runlin Cai ,&nbsp;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}

{"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 ,&nbsp;Yong Guo ,&nbsp;Mahoko Taguchi ,&nbsp;Shigeru Chohnan ,&nbsp;Tomoyasu Nishizawa ,&nbsp;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}

{"title":"Complete genome of Mycolicibacterium phocaicum RL-HY01, a PAEs-degrading marine bacterial strain isolated from Zhanjiang Bay, China","authors":"Yuduan Ou ,&nbsp;John L. Zhou ,&nbsp;Yang Jia ,&nbsp;Mei Liang ,&nbsp;Hanqiao Hu ,&nbsp;Lei Ren","doi":"10.1016/j.margen.2023.101019","DOIUrl":"10.1016/j.margen.2023.101019","url":null,"abstract":"<div><p><em>Mycolicibacterium phocaicum</em> RL-HY01, a marine bacterial strain with the capability to degrade phthalic acid esters (PAEs), was isolated from Zhanjiang Bay, China. Here, the complete genome sequence of strain RL-HY01 was presented. The genome of strain RL-HY01 contains one circular chromosome of 6,064,759 bp with a G + C content of 66.93 mol%. The genome contains 5681 predicted protein-encoding genes, 57 tRNA genes, and 6 rRNA genes. Genes and gene clusters potentially involved in the metabolism of PAEs were further identified. The genome <em>Mycolicibacterium phocaicum</em> RL-HY01 will be helpful for advancing our understanding of the fate of PAEs in marine ecosystem.</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":"9356798","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}

{"title":"Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source","authors":"Ting Hu ,&nbsp;Yin-Xin Zeng ,&nbsp;Yi-He Zhang ,&nbsp;Yu Du ,&nbsp;Wei Han ,&nbsp;Hui-Rong Li ,&nbsp;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}