Marine genomics最新文献

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Genomic analysis of Vreelandella sp. F11 reveals its role in alginate utilization 对 Vreelandella sp. F11 的基因组分析揭示了其在海藻酸盐利用中的作用

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-21 DOI: 10.1016/j.margen.2024.101160

Xin-Xiao Qu , Yu-Qi Zhang , Fei-Yu He , Xi-Ying Zhang , Peng Wang , Fei Xu , Yu-Qiang Zhang , Long-Sheng Zhao , Ping-Yi Li , Fang Zhao

Alginate, mainly produced by brown algae, is an important polysaccharide that supports the growth of marine bacteria. Vreelandella sp. F11 is a Gram-negative and aerobic marine bacterium, which was isolated from the brown algae sample collected from the Weihai coast, the Yellow Sea, China. Here, we present the complete genome of strain F11 and its genomic characteristics to utilize alginate. The genome of strain F11 comprises one circular chromosome with 4,840,724 bp and a GC content of 55.04 %. Strain F11 could grow with alginate as the sole carbon source. Genomic analysis revealed that strain F11 contains a gene cluster, encoding the enzymes, transporters and a regulator protein involved in utilizing alginate. Gene annotations suggested that the alginate utilization system of strain F11 is similar to those in Vibrio strains. However, strain F11 does not contain homologs of known KdgF (a key enzyme involved in the metabolism of alginate monomer) and inner membrane transporters of alginate oligomer uptake. The result indicated that strain F11 contains novel KdgF and inner membrane transporter system, which warrants further investigation. These data suggested that Vreelandella strains play a role in alginate utilization in the ocean and lay a foundation for the application of Vreelandella in the conversion of brown algae.

藻酸盐主要由褐藻产生，是支持海洋细菌生长的重要多糖。F11 是一种革兰氏阴性好氧海洋细菌，从中国黄海威海沿岸采集的褐藻样品中分离得到。在此，我们展示了菌株 F11 的完整基因组及其利用海藻酸盐的基因组特征。菌株F11的基因组由一条环状染色体组成，共有4,840,724 bp，GC含量为55.04%。菌株 F11 能以海藻酸盐为唯一碳源生长。基因组分析表明，菌株 F11 含有一个基因簇，编码参与利用海藻酸的酶类、转运体和调节蛋白。基因注释表明，菌株 F11 的藻酸盐利用系统与弧菌菌株相似。然而，菌株 F11 不含已知的 KdgF（参与藻酸盐单体代谢的关键酶）和藻酸盐低聚物吸收内膜转运体的同源物。结果表明，菌株F11含有新型KdgF和内膜转运系统，值得进一步研究。这些数据表明，Vreelandella 菌株在海洋藻酸盐利用中发挥作用，为 Vreelandella 在褐藻转化中的应用奠定了基础。

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引用次数: 0

The complete genome sequence of Stenotrophomonas sp. P2112 for genome mining of polyvinyl chloride degrading enzymes 用于聚氯乙烯降解酶基因组挖掘的 P2112 菌株的完整基因组序列

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-20 DOI: 10.1016/j.margen.2024.101161

Meixue Pan , Wenbin Guo , Jingjing Duan

Stenotrophomonas sp. P2112, isolated from a marine sediment sample of the Pacific Ocean, can grow in mineral medium with polyvinyl chloride (PVC) plastic as sole carbon source. Here, we present the complete genome of Stenotrophomonas sp. P2112, which will facilitate the genome mining of PVC degrading enzymes. The total length of the sequenced genome consists of 4,382,508 bases, with mean G + C content of 66.61%. A total of 4024 coding genes including 73 tRNAs and 13 rRNAs were predicted in the genome. Some potential PVC degrading enzymes including monooxygenase and peroxidases were found in this genome.

从太平洋的海洋沉积物样本中分离出的P2112血吸单胞菌能够在以聚氯乙烯（PVC）塑料为唯一碳源的矿物培养基中生长。在此，我们展示了 P2112 链霉菌的完整基因组，这将有助于对 PVC 降解酶基因组的挖掘。测序的基因组总长度为 4,382,508 碱基，平均 G + C 含量为 66.61%。基因组中共预测了 4024 个编码基因，包括 73 个 tRNA 和 13 个 rRNA。在该基因组中发现了一些潜在的聚氯乙烯降解酶，包括单氧化酶和过氧化物酶。

引用次数: 0

A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis 基于元基因组分析的东太平洋克拉里昂-克利珀顿断裂带微生物金属代谢潜力一瞥。

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-12 DOI: 10.1016/j.margen.2024.101159

Jiayi Chu , Yonglian Ye , Yue-Hong Wu

The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion–Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0–8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0–6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.

分布在深海海底的多金属结核富含锰、铁、铜和稀土元素，极具经济价值。目前，人们对居住在东太平洋克拉里昂-克利珀顿断裂带（CCFZ）的微生物的多样性和代谢潜力知之甚少。本研究从克拉里昂-克利珀顿断裂带采集了表层沉积物（0-8 厘米），每隔 1 厘米分为 8 个部分。通过元基因组测序和分选研究了微生物多样性和金属代谢潜力。金属氧化还原基因和金属转运基因在不同深度也呈现出一定的变化趋势，表层最高，0-6 cm 大致相同，>6 cm 后变化较大。回收的 58 个高、中元基因组（MAGs）经去复制后被归入 14 个细菌门和 1 个古细菌门。阿尔法蛋白菌主要进行铁/锰的氧化和汞的还原，伽马蛋白菌主要进行锰/铜的氧化和铬/汞的还原，甲基米拉比洛他主要进行锰的氧化和砷/铬/汞的还原。在已发现的五个热蛋白菌群 MAGs 中，只有一个有锰氧化基因注释，这表明在底层的这一过程中，热蛋白菌群 MAGs 的作用有限，但可能很重要。通过确定不同深度的微生物多样性和金属代谢潜力，我们的研究加强了对 CCFZ 金属代谢的了解，为进一步分析此类生态系统的金属代谢奠定了基础。

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引用次数: 0

Genomic analysis of Pseudoalteromonas sp. M58 reveals its role in chitin biodegradation 假交替单胞菌 M58 的基因组分析揭示其在几丁质生物降解中的作用

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-09 DOI: 10.1016/j.margen.2024.101158

Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang

Chitin, the most abundant polysaccharide in the ocean, is a kind of high molecular weight organic matter formed by N-acetyl-D-glucosamine (GlcNAc) via β-1,4-glucoside linkage. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. Pseudoalteromonas sp. M58, a Gram-negative and aerobic bacterium, was isolated from the seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M58 and its genomic characteristics to degrade chitin. The genome of strain M58 contains two circular chromosomes (3,348,672 bp and 723,540 bp, respectively). Genomic analysis showed that strain M58 contained a set of genes involved in chitin degradation, indicating that it possesses the potential ability to degrade chitin. This study provides novel insights into chitin degradation by marine microorganisms.

甲壳素是海洋中含量最高的多糖，是由 N-乙酰-D-葡萄糖胺（GlcNAc）通过 β-1,4-葡萄糖苷连接而成的一种高分子量有机物。由海洋细菌驱动的几丁质降解和循环对海洋中碳和氮的生物地球化学循环至关重要。从马里亚纳海沟采集的海水样本中分离出了一种革兰氏阴性好氧菌--假交替单胞菌（Pseudoalteromonas sp.在此，我们报告了菌株 M58 的完整基因组序列及其降解几丁质的基因组特征。菌株 M58 的基因组包含两条环状染色体（分别为 3,348,672 bp 和 723,540 bp）。基因组分析表明，菌株M58含有一组参与几丁质降解的基因，表明它具有降解几丁质的潜在能力。这项研究为海洋微生物降解几丁质提供了新的见解。

引用次数: 0

Complete genome sequence of Sulfitobacter pontiacus WPMT18310, a dimethylsulfoniopropionate (DMSP) degradation bacterium isolated from the Mariana Trench 从马里亚纳海沟分离出的二甲基硫代丙酸酯（DMSP）降解细菌 Sulfitobacter pontiacus WPMT18310 的完整基因组序列

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-04 DOI: 10.1016/j.margen.2024.101151

Zeping He , Lian Yuan , Haoran Li , Lihua Peng , Xiao Liang , Jin-Long Yang

Bacteria of the genus Sulfitobacter are widely distributed across various marine environments and play a vital role in the sulfur cycle. Sulfitobacter pontiacus WPMT18310 was isolated from water samples collected at a depth of 10,890 m in the Mariana Trench. In this study, we report the complete genome of S. pontiacus WPMT18310, which contained 3533 genes and a total length of 3,706,453 base pairs organized within a single chromosome. Additionally, the genome contains four plasmids, suggesting its significant capacity for gene transfer. S. pontiacus WPMT18310 is capable for synthesizing signaling molecules and degrading dimethylsulfoniopropionate (DMSP). The degradation product dimethyl sulfide (DMS) serves as a potential signaling molecule that can induce the settlement of marine invertebrates. This genomic information of S. pontiacus may provide valuable insights into elucidating the ecological significance of the sulfur cycle and assessing its impact on marine invertebrate settlement.

硫杆菌属细菌广泛分布于各种海洋环境中，在硫循环中发挥着重要作用。从马里亚纳海沟 10,890 米深处采集的水样中分离出了庞氏硫杆菌 WPMT18310。在这项研究中，我们报告了庞氏硫杆菌 WPMT18310 的完整基因组，其中包含 3533 个基因，总长度为 3706453 碱基对，由一条染色体组成。此外，该基因组还包含四个质粒，这表明它具有很强的基因转移能力。庞蒂亚克氏菌 WPMT18310 能够合成信号分子和降解二甲基硫代丙酸酯（DMSP）。降解产物二甲基硫醚（DMS）是一种潜在的信号分子，可诱导海洋无脊椎动物定居。庞氏无脊椎动物的基因组信息可为阐明硫循环的生态意义和评估其对海洋无脊椎动物定居的影响提供宝贵的见解。

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引用次数: 0

Complete genome sequence of Vreelandella sp. SM1641, a marine exopolysaccharide-producing bacterium isolated from deep-sea hydrothermal sediment of the Southwest Indian Ocean 从西南印度洋深海热液沉积物中分离出的海洋外多糖生产细菌 Vreelandella sp.

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-02 DOI: 10.1016/j.margen.2024.101150

Hai-Xia Zhu , Zhi-Gang Tang , Shi-Ning Cai , Jun-Hui Cheng , Peng Wang , Mei-Ling Sun

Vreelandella sp. SM1641 was isolated from the hydrothermal vent sediment of the southwest Indian Ocean at a water depth of 2519 m. The complete genome sequence of strain SM1641 was analyzed to understand its metabolic capacities and biosynthesis potential of natural products in this study. The genome of strain SM1641 consists of a circular chromosome and two plasmids. The length of the circular chromosome was 4,731,121 bp with GC content of 54.46 mol%, and the length of plasmid A was 302,095 bp with GC content of 54.95 mol%, and the length of plasmid B was 8857 bp with GC content of 46.31 mol%. Genomic data showed that strain SM1641 had several gene clusters involved in the synthesis of exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs) synthesis. SM1641 also has a variety of genes that respond to osmotic stress, heat shock, cold shock, oxidative stress, and heavy metal stress, which plays a critical role in bacterial adaptation to hydrothermal environments. Therefore, genome sequencing and data mining of strain SM1641 are helpful to further understand the molecular mechanism of Vreelandella adapting to the deep-sea hydrothermal environment, and provide a basis for further experimental exploration.

本研究分析了菌株SM1641的完整基因组序列，以了解其代谢能力和天然产物的生物合成潜力。菌株 SM1641 的基因组由一个环状染色体和两个质粒组成。环状染色体的长度为 4,731,121 bp，GC 含量为 54.46 mol%；质粒 A 的长度为 302,095 bp，GC 含量为 54.95 mol%；质粒 B 的长度为 8857 bp，GC 含量为 46.31 mol%。基因组数据显示，菌株 SM1641 有多个基因簇参与外多糖（EPSs）的合成和聚羟基烷酸酯（PHAs）的合成。此外，SM1641 还具有多种对渗透胁迫、热休克、冷休克、氧化胁迫和重金属胁迫做出反应的基因，这在细菌适应热液环境中起着至关重要的作用。因此，对菌株SM1641进行基因组测序和数据挖掘，有助于进一步了解Vreelandella适应深海热液环境的分子机制，为进一步的实验探索提供依据。

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引用次数: 0

Complete genome and carbohydrate-active enzymes of Arenibacter antarcticus KCTC 52924T isolated from deep sea sediment of Ross Sea, Antarctica 从南极罗斯海深海沉积物中分离出的南极 Arenibacter antarcticus KCTC 52924T 的完整基因组和碳水化合物活性酶

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-10-18 DOI: 10.1016/j.margen.2024.101149

Kyuin Hwang , Hanna Choe , Kyung Mo Kim

Members of the genus Arenibacter were widely distributed in oceanic habitats around the world and have been studied for a variety of useful properties, including antigen deactivation, pollutant degradation, and the production of antimicrobial agents. Arenibacter antarcticus KCTC 52924^T of our interest is an aerobic, non-motile, Gram-negative, psychrotolerant type strain isolated from the deep-sea sediment of Ross Sea, Antarctica. The extreme conditions of this habitat are believed to have diversified the substrate spectrum and range of operational conditions of the enzymes, offering both scientific interest and potential industrial benefits. Here, we obtained the complete genome sequence of this promising strain, which consists of 4,694,007 bp (G + C content of 38.8 %) with a single chromosome, 3917 protein-coding genes, 43 tRNAs, and 3 rRNA operons. The functional annotations of the genome reveal four metabolite biosynthesis clusters and a variety of carbohydrate-active enzymes with potential biotechnological applications. Additionally, several interesting features related to environmental interactions were identified. Therefore, this genome data and its genomic potentials figured out in this study serve as a conner stone in further study aimed at understanding physiology of this strain which may be valuable in biotechnological purpose.

Arenibacter 属的成员广泛分布于世界各地的海洋栖息地，其各种有用的特性已得到研究，包括抗原失活、污染物降解和抗菌剂的生产。我们感兴趣的南极 Arenibacter antarcticus KCTC 52924T 是一种从南极罗斯海深海沉积物中分离出来的需氧、非运动、革兰氏阴性、精神耐受型菌株。这一栖息地的极端条件被认为使酶的底物谱和工作条件范围多样化，从而带来了科学兴趣和潜在的工业效益。在这里，我们获得了这一有潜力的菌株的完整基因组序列，该序列由 4,694,007 bp（G + C 含量为 38.8%）组成，具有单条染色体、3917 个蛋白质编码基因、43 个 tRNA 和 3 个 rRNA 操作子。该基因组的功能注释揭示了四个代谢物生物合成簇和多种具有潜在生物技术应用价值的碳水化合物活性酶。此外，还发现了一些与环境相互作用有关的有趣特征。因此，本研究中发现的基因组数据及其基因组潜力可作为进一步研究的基石，旨在了解该菌株的生理机能，这可能在生物技术方面具有重要价值。

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引用次数: 0

The complete genome sequence of proteases-producing Shewanella sp. H8 isolated from Antarctica 从南极洲分离的产蛋白酶的雪旺氏菌 H8 的完整基因组序列

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101147

Xiao-Hui Yang, Jia-Yi Song, Kang Li, Mei-ling Sun, Hai-Yan Cao, Peng Wang, Yi Zhang

Bacteria of the genus Shewanella in the class Gammaproteobacteria are widely distributed in marine environments. Shewanella sp. H8, was isolated from a red algae sample collected from Nelson Island, Antarctica. Here, we present the complete genome sequence of strain H8, which consists of a single circular chromosome comprising 4,490,743 nucleotides with 40.59 % G + C content without any plasmid. In total, 3983 protein coding genes, 95 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain H8 showed that it contains four cold shock proteins and three fatty acid desaturases and possesses the potential to synthesize hglE-KS, arylpolyene, betalactone and RiPP-like compounds. Through genomic annotation, 91 protease-encoding genes were identified within the genome of strain H8. These proteases are classified into six categories based on their catalytic types. Among these proteases, metalloproteinases and serine proteases are dominant. These proteases may provide carbon and nitrogen sources to H8 by degrading proteins in the environment. This study will provide potential genetic information for the future research and development of cold-adapted proteases.

广谱变形菌类中的雪旺菌属细菌广泛分布于海洋环境中。从南极洲纳尔逊岛采集的红藻样本中分离出了 Shewanella sp.在此，我们展示了菌株 H8 的完整基因组序列，它由一条单环染色体组成，包含 4,490,743 个核苷酸，其中 G + C 含量为 40.59%，不含任何质粒。共获得 3983 个蛋白质编码基因、95 个 tRNA 基因和 25 个 rRNA 基因。菌株 H8 的基因组分析表明，它含有 4 种冷激蛋白和 3 种脂肪酸去饱和酶，并具有合成 hglE-KS、芳基聚烯、betalactone 和 RiPP 类化合物的潜力。通过基因组注释，在菌株 H8 的基因组中发现了 91 个蛋白酶编码基因。根据其催化类型，这些蛋白酶被分为六类。在这些蛋白酶中，金属蛋白酶和丝氨酸蛋白酶占主导地位。这些蛋白酶可通过降解环境中的蛋白质为 H8 提供碳源和氮源。这项研究将为今后研究和开发适应寒冷的蛋白酶提供潜在的遗传信息。

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引用次数: 0

Complete genome analysis of deep-sea hydrothermal sulfur-oxidizing bacterium Sulfitobacter sp. TCYB15 associated with mussel Bathymodiolus marisindicus and insights into its habitat adaptation 与贻贝Bathymodiolus marisindicus相关的深海热液硫氧化细菌Sulfitobacter sp.

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-10-10 DOI: 10.1016/j.margen.2024.101148

Yadan Deng , Yunjin Zhu , Jiaxuan He , Xin Yin , Qian Li , Zhengxing Chen , Bingshu Wang , Li Zheng

引用次数: 0

The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin 可产生抗真菌抗生素 Scopafungin 的海洋放线菌--链霉菌 FIM 95-F1 的完整基因组序列

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-09-06 DOI: 10.1016/j.margen.2024.101146

Peng Fei , Lin Yangjun , Zhuang Yuee , Lin Ping , Liu Chengzhi , Chen Linlin , Jiang Hong , Lian Yunyang , Zhang Wenzhou , Huang Youxia

Streptomyces FIM95-F1, an actinomycete originating from mangroves of Quanzhou bay, exhibits the capability to produce the antifungal antibiotic scopafungin. Here, the complete genome of Streptomyces sp. FIM95-F1 is presented with a GC content of 71.04 %, comprising a 9,718,239-bp linear chromosome, 8236 protein-coding genes, 18 rRNA genes, 64 tRNA genes, 2 prophages, and 58 CRISPR regions. In silico analysis revealed the presence of 42 biosynthetic gene clusters (BGCs), the majority of which demonstrated similarity to both known and novel BGCs responsible for the biosynthesis of previously known and novel bioactive agents of microbial origin. A comprehensive comparison between the scopafungin BGC and niphimycin BGC has indicated a potential shared pathway for the biosynthesis of scopafungin. One of the intriguing findings of this study was the discovery of at least two novel BGCs (namely Cluster 26 and Cluster 32) present within biosynthetic gene clusters. Our findings suggest that Streptomyces sp. FIM95-F1 possesses significant potential in producing a diverse array of both known and novel bioactive compounds, which could be valuable in the field of drug discovery.

泉州湾红树林中的放线菌 FIM95-F1 链霉菌具有生产抗真菌抗生素 Scopafungin 的能力。本文展示了链霉菌 FIM95-F1 的完整基因组，其 GC 含量为 71.04%，包括 9,718,239 bp 的线性染色体、8236 个编码蛋白质的基因、18 个 rRNA 基因、64 个 tRNA 基因、2 个噬菌体和 58 个 CRISPR 区域。硅学分析表明存在 42 个生物合成基因簇（BGC），其中大部分与负责生物合成微生物来源的已知和新型生物活性物质的已知和新型 BGC 相似。通过全面比较东莨菪茵 BGC 和尼泊金霉素 BGC，发现了东莨菪茵生物合成的潜在共享途径。这项研究的一个有趣发现是在生物合成基因簇中发现了至少两个新的 BGC（即簇 26 和簇 32）。我们的研究结果表明，链霉菌 FIM95-F1 具有生产多种已知和新型生物活性化合物的巨大潜力，这在药物发现领域可能很有价值。

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