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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 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 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 52924T 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 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 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
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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 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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引用次数: 0
Genomic analysis of Rhodopirellula sp. P2 reveals its role in fucoidan degradation Rhodopirellula sp. P2 的基因组分析揭示了其在褐藻糖胶降解中的作用
IF 1.3 4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2024-08-29 DOI: 10.1016/j.margen.2024.101145
Chen Wang, Dan Liu, Hou-qi Wang, Yu-zhong Zhang, Peng Wang

Fucoidan, the main polysaccharide in various species of brown seaweed, has a high annual production. It is an important source of marine organic carbon and exhibits diverse biological activities and significant application potential. Rhodopirellula sp. P2, a novel marine bacterium of the phylum Planctomycetota, was isolated from intertidal algae samples collected from the Weihai coast, the Yellow Sea, China. The strain P2 is a Gram-negative, aerobic, and pear-shaped bacterium. Here, we report the complete genome sequence of Rhodopirellula sp. P2. The genome of strain P2 consists of a single circular chromosome with 7,291,416 bp and a GC content of 57.38 %, including 5462 protein-coding genes, 2 rRNA genes, and 48 tRNA genes. Genomic analysis revealed that strain P2 possessed 173 CAZymes and 106 sulfatases, indicating that strain P2 has the potential ability to utilize multiple polysaccharides, especially hydrolyze fucoidan to fucose. The genome of strain P2 also encodes a gene cluster related to bacterial microcompartment, suggesting the ability of strain P2 to metabolize fucose. These results enhance the understanding of the diversity and ecological functions of Planctomycetota, and also facilitate the exploitation of Planctomycetota and enzyme resources to utilize fucoidan. This study provides genetic insights into fucoidan catabolism by Planctomycetota, expanding our understanding of fucoidan-degrading microbial groups.

褐藻糖胶是各种褐藻中的主要多糖,年产量很高。它是海洋有机碳的重要来源,具有多种生物活性和巨大的应用潜力。从中国黄海威海沿岸采集的潮间带藻类样品中分离到了一种新型海洋细菌,即 Planctomycetota 门的 Rhodopirellula sp.菌株 P2 是一种革兰氏阴性、需氧的梨形细菌。我们在此报告 Rhodopirellula sp.菌株P2的基因组由一条单环染色体组成,长度为7,291,416 bp,GC含量为57.38%,包括5462个蛋白编码基因、2个rRNA基因和48个tRNA基因。基因组分析表明,菌株 P2 拥有 173 种 CAZymes 和 106 种硫酸酯酶,表明菌株 P2 具有利用多种多糖的潜在能力,特别是能将褐藻糖胶水解为岩藻糖。菌株P2的基因组还编码了一个与细菌微室相关的基因簇,表明菌株P2具有代谢岩藻糖的能力。这些结果加深了人们对 Planctomycetota 的多样性和生态功能的了解,同时也有助于利用 Planctomycetota 和酶资源来利用褐藻糖胶。这项研究为 Planctomycetota 分解褐藻糖胶提供了遗传学见解,拓展了我们对褐藻糖胶降解微生物群的了解。
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引用次数: 0
Complete genome sequence of the 4-hydroxybenzoate-degrading bacterium Gymnodinialimonas sp. 57CJ19, a potential novel species from intertidal sediments 潮间带沉积物中的潜在新物种--4-羟基苯甲酸盐降解细菌Gymnodinialimonas sp.57CJ19的完整基因组序列
IF 1.3 4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2024-07-17 DOI: 10.1016/j.margen.2024.101135
Dong-Hui Li , Ning Zheng , Zhen-Hai Liu , Xiao-Rui Dong , Chen Zhao , Shi-Gan Yan , Bin-Bin Xie

A bacterium Gymnodinialimonas sp. 57CJ19, was isolated from the intertidal sediments of Aoshan Bay, and further assays showed that it has the ability to degrade the antibacterial preservative 4-hydroxybenzoate. The complete genome sequence was sequenced, and phylogenomic analyses indicated that strain 57CJ19 represents a potential novel species in the genus Gymnodinialimonas (family Rhodobacteraceae). Its genome contains a 3,861,607-bp circular chromosome with 61.25% G + C content. Gene prediction revealed 3716 protein-encoding genes, 41 tRNA genes, 3 rrn operons, and 3 non-coding RNA genes. Functional annotation revealed a complete metabolic pathway for 4-hydroxybenzoate. The genome sequence of strain 57CJ19 provides new insights into the potential and underlying genomic basis of aromatic compound pollutant degradation by marine bacteria.

研究人员从鳌山湾潮间带沉积物中分离到一株Gymnodinialimonas sp.57CJ19细菌,进一步检测表明该细菌具有降解抗菌防腐剂4-羟基苯甲酸酯的能力。对其完整的基因组序列进行了测序,系统进化分析表明,57CJ19菌株可能是Gymnodinialimonas属(罗杆菌科)的一个新物种。其基因组包含一个 3,861,607 bp 的环状染色体,G + C 含量为 61.25%。基因预测发现了 3716 个蛋白质编码基因、41 个 tRNA 基因、3 个 rrn 操作子和 3 个非编码 RNA 基因。功能注释揭示了 4-hydroxybenzoate 的完整代谢途径。57CJ19 菌株的基因组序列为了解海洋细菌降解芳香族化合物污染物的潜力和基因组基础提供了新的视角。
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引用次数: 0
The complete genome sequence of the planctomycetotal bacterium Bremerella sp. P1 with abundant genes involved in polysaccharide degradation 含有丰富多糖降解基因的平面菌P1的完整基因组序列
IF 1.3 4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101126
Jia-Xuan Wang, Jing Wang, Ji-Qing Liu, Jian Li, Wen-Xin Jiang, Fei Xu, Ping-Yi Li, Qi-Long Qin, Xiu-Lan Chen, Xi-Ying Zhang

Isolated from intertidal sediment of the Yellow Sea, China, Bremerella sp. P1 putatively represents a novel species within the genus Bremerella of the family Pirellulaceae in the phylum Planctomycetota. The complete genome of strain P1 comprises a single circular chromosome with a size of 6,955,728 bp and a GC content of 55.26%. The genome contains 5772 protein-coding genes, 80 tRNA and 6 rRNA genes. A total of 147 CAZymes and 128 sulfatases have been identified from the genome of strain P1, indicating that the strain has the capability to degrade a wide range of polysaccharides. Moreover, a gene cluster related to bacterial microcompartments (BMCs) formation containing genes encoding the shell proteins and related enzymes to metabolize fucose or rhamnose is also found in the genome of strain P1. The genome of strain P1 represents the second complete one in the genus Bremerella, expanding the understanding of the physiological and metabolic characteristics, interspecies diversity, and ecological functions of the genus.

从中国黄海潮间带沉积物中分离出的 Bremerella sp.菌株 P1 的完整基因组由一条单环染色体组成,大小为 6,955,728 bp,GC 含量为 55.26%。基因组包含 5772 个蛋白质编码基因、80 个 tRNA 和 6 个 rRNA 基因。从菌株 P1 的基因组中共鉴定出 147 种 CAZymes 和 128 种硫酸酯酶,表明该菌株具有降解多种多糖的能力。此外,在菌株 P1 的基因组中还发现了一个与细菌微孔(BMC)形成有关的基因簇,其中含有编码壳蛋白和相关酶的基因,可代谢岩藻糖或鼠李糖。菌株 P1 的基因组是 Bremerella 属中第二个完整的基因组,拓展了对该属的生理和代谢特征、种间多样性和生态功能的认识。
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引用次数: 0
Marine eDNA sampling from submerged surfaces with paint rollers 用油漆辊从水下表面采集海洋 eDNA 样本
IF 1.3 4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2024-06-20 DOI: 10.1016/j.margen.2024.101127
Simon Jarman , Jason B. Alexander , Kathryn L. Dawkins , Sherralee S. Lukehurst , Georgia M. Nester , Shaun Wilkinson , Michael J. Marnane , Justin I. McDonald , Travis S. Elsdon , Euan S. Harvey

Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.

对海洋环境中存在的物种进行环境 DNA(eDNA)分析是目前最有效的生物多样性测量工具。确定和开发尽可能快速、经济、通用和实用的 eDNA 采样方法将提高海洋物种的检测率。eDNA 生物多样性调查的最佳结果来自于采用高水平重复采样的研究,因此任何能使采样更快、更便宜的方法都将提高科学成果。在这项研究中,我们比较了从水下海洋表面采集 eDNA 样本的几种方法的多样性检测:聚氨酯泡沫、尼龙棉签、超细纤维油漆滚筒和沉积物勺。所有方法都能鉴定出不同的物种,研究地点的 eDNA 代表了 250 个多细胞物种。我们发现,对于从水下海洋表面采集 eDNA 样本,广泛使用的小型油漆辊是一种有效、易于获得且经济实惠的方法。这种方法可以在人工采样不可行的情况下,使用加长杆或遥控潜水器对海洋 eDNA 进行采样。
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引用次数: 0
Genome analysis of Salinimicrobium sp. 3283s, a deep-sea bacterium isolated from the sediments of South China Sea, China 从中国南海沉积物中分离的深海细菌 Salinimicrobium sp.
IF 1.9 4区 生物学 Q4 GENETICS & HEREDITY Pub Date : 2024-06-18 DOI: 10.1016/j.margen.2024.101125
Shijie Bai , Kun Shang , Shuqian Zeng , Ziming Huang , Zhuang Han

Salinimicrobium sp. 3283s is an aerobic, golden-yellow pigment-producing, Flavobacteriaceae bacterium isolated from the sediments at the depth of 1751 m in the South China Sea. In this study, we present the complete genome sequence of strain 3283s, which only have a single circular chromosome comprising 3,702,683 bp with 41.41% G + C content and no circular plasmid. In total, 3257 protein coding genes, 45 tRNA, 9 rRNA, and 13 sRNA genes were obtained. In terms of the function of gene annotation, strain 3283s was more different from Salinimicrobium oceani J15B91, which was isolated from the South China Sea at a similar depth, and more similar to a Mariana Trench-derived strain Salinimicrobium profundisediminis MT39, which was closer in phylogenetic taxonomic status, suggesting that strain 3283s possesses a stronger potential to adapt to the deep-sea environment. Furthermore, the high- pressure simulations also confirmed that strain 3283s can grow in both 30 MPa and 60 MPa hydrostatic pressure environments, and that it grows better in 30 MPa hydrostatic pressure environments than in 60 MPa hydrostatic pressure environments. In addition, we found a large number of genes in strain 3283s that can promote better adaptation of the bacteria to the low oxygen and high hydrostatic pressure (HHP) environment of the deep sea, such as biosynthetic enzymes of antioxidant pigments, genes encoding cytochromes with enhanced affinity for oxygen, proteins for adaptation to HHP, and genes encoding TonB-dependent transporters in the absence of flagella.

Salinimicrobium sp. 3283s是一种好氧、产金黄色色素的黄杆菌科细菌,从中国南海1751米深处的沉积物中分离出来。该菌株只有一个由 3,702,683 bp 组成的单环染色体,G+C 含量为 41.41%,没有环状质粒。共获得 3257 个蛋白质编码基因、45 个 tRNA、9 个 rRNA 和 13 个 sRNA 基因。从基因的功能注释来看,3283s菌株与分离自中国南海、深度相近的Salinimicrobium oceani J15B91菌株差异较大,而与马里亚纳海沟来源的Salinimicrobium profundisediminis MT39菌株更为相似,在系统发育分类地位上更为接近,这表明3283s菌株具有更强的适应深海环境的潜力。此外,高压模拟还证实,菌株 3283s 可以在 30 兆帕和 60 兆帕的静水压环境中生长,而且在 30 兆帕静水压环境中的生长情况比在 60 兆帕静水压环境中更好。此外,我们还在 3283s 菌株中发现了大量能促进细菌更好地适应深海低氧和高静水压(HHP)环境的基因,如抗氧化色素的生物合成酶、编码对氧亲和力增强的细胞色素的基因、适应 HHP 的蛋白质以及编码无鞭毛情况下依赖 TonB 的转运体的基因。
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