Marine genomics最新文献

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Genomic analysis of Marinobacter flavimaris ZYH30 reveals its role in marine dimethylsulfide cycling

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2025-01-31 DOI: 10.1016/j.margen.2025.101178

Liyan Liu , Hai Shi , Zihua Guo , Xiaotong Zhang , Xueqi Li , Xiao-Hua Zhang , Yunhui Zhang

Dimethylsulfide (DMS) is a volatile organic compound that influences climate change and plays a key role in the global sulfur cycle and chemotaxis. Marine bacteria can produce DMS from dimethylsulfoniopropionate (DMSP) and other sulfur precursors. A highly efficient DMS-producing strain, Marinobacter flavimaris ZYH30, was isolated from the surface sediment of the South China Sea, but the key genes involved in DMS production in its genome remain unknown. Here, we reported the complete genome sequence of M. flavimaris ZYH30 and its genomic potential in DMS cycling. The genome of M. flavimaris ZYH30 consists of a circular chromosome with a length of 4,631,282 bp and its GC content is 57.26 %. Genomic analysis showed that strain ZYH30 possesses a set of genes involved in DMS cycling, including a DMSP lyase DddL. In addition, M. flavimaris ZYH30 contained a mddH gene involved in hydrogen sulfide (H₂S) and methanethiol (MeSH) dependent DMS production pathways. This study provides genetic insights into the DMS production processes and sulfur cycling in marine sediment bacteria.

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引用次数: 0

Complete genome sequence of Alteromonas marina OM2201, a marine bacterium degrading Ulva prolifera polysaccharides isolated from surface of the Yellow Sea

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2025-01-25 DOI: 10.1016/j.margen.2025.101168

Shi-Ning Cai , Hai-Xia Zhu , Zhi-Gang Tang , Xue-Yun Geng , Mei-Ling Sun

As a consequence of marine eutrophication, there has been an exponential growth of Ulva prolifera, culminating in the yearly emergence of a massive green tide along the shores of Qingdao. This phenomenon exerts a detrimental impact on the marine ecosystem. As reported, the expression level of Alteromonas enzymes involved in U. prolifera polysaccharides degradation is increased during the green tide outbreak period, potentially accelerating the breakdown of U. prolifera biomass. This enhanced degradation could facilitate the transition to the waning phase of the green tide event. In this study, strain Alteromonas marina OM2201 was isolated from seawater samples taken during an U. prolifera bloom in the coastal waters of Qingdao. Its genome contains a ring chromosome and two plasmids. The length of the circular chromosome was 4,489,073 bp with GC content of 44.21 mol%, and the length of plasmid 1 was 233,636 bp with GC content of 42.24 mol%, and the length of plasmid 2 was 5594 bp with GC content of 39.61 mol%. Genomic analysis showed that Alteromonas marina OM2201 contained a variety of ulvan lyase genes, indicating that it could promote the degradation of U. prolifera polysaccharides. This genetic makeup potentially enables the strain to expedite the decomposition of U. prolifera biomass. Therefore, this study broadens our understanding of the Alteromonas bacteria that can degrade U. prolifera polysaccharides during the outbreak period.

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引用次数: 0

The complete genome sequence of Acinetobacter sp. P1332, a tetrodotoxin-producing bacteria

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2025-01-23 DOI: 10.1016/j.margen.2025.101166

Liyun Liang , Songyang Li , Zengpeng Li , Mingliang Chen

We isolated a novel bacterial strain Acinetobacter sp. P1332 from the pufferfish Takifugu oblongus in the southeastern coast of Fujian Province, China. This strain has been identified as a potent producer of the neurotoxin tetrodotoxin (TTX). In this study, we present the complete genome sequence of Acinetobacter sp. P1332, which is a crucial advancement in identifying the genetic factors involved in TTX biosynthesis. The genome spans 4,017,868 base pairs and has a mean G + C content of 41.3 %. It encodes 3944 genes, along with 90 tRNAs and 21 rRNAs. This detailed genomic information provides an essential resource for further research into the biosynthetic pathways of TTX and its applications in biotechnology and toxinology.

引用次数: 0

Genomic analysis of Sulfitobacter sp. PM12 reveals its role in betaine metabolism

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2025-01-22 DOI: 10.1016/j.margen.2025.101167

Jun Li , Ya Ma , Ronghua Zhang , Nan Zhang

Betaine is a zwitterionic compatible compound, which is widely distributed in nature and can be found in a variety of microorganisms. It plays key roles in osmotic protection and one‑carbon metabolism. Sulfitobacter sp. PM12, a Gram-negative and aerobic bacterium, was isolated from the deep-sea samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain PM12 and its genomic characteristics to synthesize and catabolize betaine. The genome of strain PM12 contains one circular chromosome (3,009,717 bp) and seven circular plasmids. Genomic analysis showed that strain PM12 contained a set of genes involved in betaine biosynthesis and biodegradation, indicating that it possesses the ability to metabolize betaine. This study enlarges our understanding of the betaine metabolism driven by bacteria in the ocean, and reveals the potential strategy of the strain PM12 to adapt the extreme environments of the Mariana Trench.

引用次数: 0

Genomic analysis of Isoptericola halotolerans SM2308 reveals its potential involved in fucoidan degradation 对耐盐异翼菌SM2308的基因组分析揭示了其参与褐藻糖聚糖降解的潜力。

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2025-01-16 DOI: 10.1016/j.margen.2025.101165

Yu-Qi Zhang , Qi Yuan , Ji-Qing Liu , Xiao-Chen Liang , Jing-Ping Wang , Wen-Xin Jiang , Ping-Yi Li

Marine bacteria play important roles in the degradation and recycling of algal polysaccharides. However, the marine bacteria involved in fucoidan degradation and their degradation pathways remain poorly understood. Here, we report the complete genome sequence of Isoptericola halotolerans SM2308, isolated from a brown algal sample collected from an intertidal zone of the Yellow Sea in China. The genome of strain SM2308 consists of a single circular chromosome of 4,011,455 bp with a high GC content of 72.70 %. Strain SM2308 exhibited rapid growth on fucoidan as the sole carbon source, indicating its capacity to degrade fucoidan. Gene annotation and metabolic pathway analyses showed that strain SM2308 possesses a complete pathway for utilizing fucoidan, including the extracellular breakdown of polymeric fucoidan into smaller fucooligosaccharides/fucose by fucoidanases, the transmembrane transport of fucooligosaccharides/fucose into the cytoplasm by an ABC transporter, and the intracellular fucose catabolism via a non-phosphorylative pathway. This represents the first genome of an actinobacterium from the order Micrococcales with fucoidan-degrading ability. The genome of Isoptericola halotolerans SM2308 provides insights into the role of actinobacteria in the biogeochemical cycling of fucoidan in marine ecosystems.

海洋细菌在海藻多糖的降解和循环利用中起着重要作用。然而，参与岩藻聚糖降解的海洋细菌及其降解途径仍然知之甚少。本文报道了从黄海潮间带褐藻样品中分离到的耐盐异翼藻SM2308的全基因组序列。菌株SM2308基因组由一条长4,011,455 bp的单圆形染色体组成，GC含量高达72.70%。菌株SM2308以褐藻聚糖为唯一碳源生长迅速，表明其具有降解褐藻聚糖的能力。基因注释和代谢途径分析表明，菌株SM2308具有完整的岩藻聚糖利用途径，包括通过岩藻聚糖酶将聚合岩藻聚糖胞外分解为更小的岩藻聚糖/焦块，通过ABC转运体将岩藻聚糖/焦块跨膜转运到细胞质中，以及通过非磷酸化途径将细胞内焦块分解代谢。这代表了微球菌目放线菌中第一个具有岩藻胶降解能力的基因组。Isoptericola halotolerans SM2308的基因组揭示了放线菌在海洋生态系统岩藻聚糖生物地球化学循环中的作用。

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引用次数: 0

First transcriptome assembly of a new ciliate species (Protocruzia marianaensis) isolated from the Mariana Trench area

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-12-11 DOI: 10.1016/j.margen.2024.101164

Chen Liang , Wei Wang , Jianming Chen

This is the first report of a transcriptome assembly of a newly discovered a new Protocruzia species sampled from the under-sampled area near the Mariana Trench. We sequenced the transcriptome of P. marianaensis using the Illumina Novaseq 6000 platform. De novo assembly and analysis of the coding regions predicted 36,116 unigenes, 74.91 % of which was annotated by public databases. The transcriptome of P. marianaensis will be a valuable resource in studying the ecological and biological characteristics of this new species, which is the first Protocruzia species in deep sea. These data can also help to understand protozoa survival mechanisms in deep-sea habitats and provide essential biological material for investigating unique life phenomena and processes in the deep ocean.

引用次数: 0

Genomic analysis of Marinobacter sp. M5B reveals its role in alginate biosynthesis 海洋杆菌M5B的基因组分析揭示了其在海藻酸盐生物合成中的作用

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-29 DOI: 10.1016/j.margen.2024.101163

Xiaoyu Si, Zhenhai Liu, Shuxin Cheng, Jingyao Xi, Bingrui Zeng, Meihui Li, Liping Zhu, Shigan Yan, Nan Zhang

Alginate is a natural marine polysaccharide and an important marine organic carbon source, which is mainly produced by marine brown algae. Marinobacter sp. M5B, a Gram-negative and aerobic bacterium, was isolated from the surface seawater samples collected from the Mariana Trench. Here, we report the complete genome sequence of strain M5B and its genomic characteristics to synthesize alginate. The genome of strain M5B contains one circular chromosome (4,415,647 bp) with the GC content of 57.14 %. Genomic analysis showed that strain M5B contained a set of genes involved in alginate synthesis, indicating that it possesses the potential ability to synthesis alginate. This study provides novel insights into alginate synthesis by marine microorganisms.

藻酸盐是一种天然的海洋多糖，是重要的海洋有机碳源，主要由海洋褐藻产生。从马里亚纳海沟表层海水样本中分离出革兰氏阴性需氧细菌M5B。本文报道了菌株M5B的全基因组序列及其合成海藻酸盐的基因组特征。菌株M5B基因组包含1条圆形染色体（4,415,647 bp）， GC含量为57.14%。基因组分析表明，菌株M5B含有一组参与海藻酸盐合成的基因，表明其具有潜在的合成海藻酸盐的能力。该研究为海洋微生物合成海藻酸盐提供了新的见解。

引用次数: 0

Complete genome sequence of the marine mangrove fungus Sarcopodium sp.QM3–1 confirmed its high potential for antimicrobial activity 海洋红树林真菌 Sarcopodium sp.QM3-1 的完整基因组序列证实其具有很高的抗菌活性潜力

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Marine genomics

Pub Date : 2024-11-26 DOI: 10.1016/j.margen.2024.101162

Wenzhou Zhang , Minghuang Ling , Kai Zhang , Ruzhen Liu , Xiaomei Huang , Gaili Fan , Hans-Peter Grossart , Fei Peng , Zhuhua Luo

Mangroves, owing to their unique living environment, serve as an important source of natural bioactive compounds. Sarcopodium sp. QM3–1, a marine fungus isolated from mangrove sediments of Quanzhou Bay, exhibited antifungal activity against the plant pathogen Agrobacterium tumefaciens and Magnaporthe oryzae. Whole-genome sequencing of this fungal strain revealed a genome size of 58,356,150 bp with 17,960 protein-coding genes, 539 tRNA genes, and 170 rRNA genes. Functional annotation identified a series of genes involved in the biosynthesis of secondary metabolites, including several gene clusters associated with antimicrobial activity. Notably, twenty of these gene clusters were associated with the synthesis of known bioactive compounds, including terpene, polyketides (PKS), nonribosomal peptides (NRPS), β-lactones, and phosphonates. Our findings suggest that Sarcopodium sp. QM3–1 could be a promising candidate as a biocontrol agent for combating plant pathogens in agricultural fields.

红树林因其独特的生存环境而成为天然生物活性化合物的重要来源。从泉州湾红树林沉积物中分离出的海洋真菌 Sarcopodium sp.QM3-1是一种从泉州湾红树林沉积物中分离出来的海洋真菌，对植物病原体农杆菌和木格氏球菌具有抗真菌活性。该真菌菌株的全基因组测序结果显示，其基因组大小为 58,356,150 bp，包含 17,960 个蛋白编码基因、539 个 tRNA 基因和 170 个 rRNA 基因。功能注释确定了一系列参与次生代谢物生物合成的基因，包括几个与抗菌活性相关的基因簇。值得注意的是，其中 20 个基因簇与已知生物活性化合物的合成有关，包括萜烯、多酮类化合物（PKS）、非核糖体肽（NRPS）、β-内酯和膦酸盐。我们的研究结果表明，马钱子属植物 QM3-1 可能是一种很有前途的植物。QM3-1 有望成为一种生物控制剂，用于对抗农田中的植物病原体。

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引用次数: 0

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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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。

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