Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean
Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean
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DOI：
10.1128/aem.00575-22
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发表时间：
2022-08
影响因子：
4.4
通讯作者：
Jinchang Liang;Jiwen Liu;Xiaolei Wang;Hao Sun;Yulin Zhang;F. Ju;F. Thompson;Xiaohua Zhang
中科院分区：
文献类型：
--
作者：
Jinchang Liang;Jiwen Liu;Xiaolei Wang;Hao Sun;Yulin Zhang;F. Ju;F. Thompson;Xiaohua Zhang
随着深海取样技术的发展，越来越多的深海弧菌菌株被分离出来，但这些富营养化弧菌菌株对深海环境的适应机制尚不清楚。在这里，我们的结果表明，中上层弧菌的基因组经过精简，以适应长期的寡营养环境。摘要 弧菌属具有较高的代谢灵活性和基因组可塑性，广泛分布于海洋从透光层到深海环境中。弧菌基因组特征与环境适应策略之间的关系已在沿海环境中得到广泛研究，但对其在寡营养深海中的生存策略知之甚少。在这项研究中，我们比较了从马里亚纳海沟和雅浦海沟不同水深分离的五种坎贝氏弧菌菌株（包括两种上层菌株和三种深海菌株）的基因组，以确定有利于深海生存的基因组特征。中上层菌株存在基因组精简现象，如基因组尺寸较小、G+C含量较低、基因密度较高，这可能是由于长期生活在寡营养环境中造成的。系统发育结果表明，这5个弧菌菌株根据其收集深度分为两个进化枝。事实上，通过比较基因组学分析，深海分离株含有更多涉及氨基酸代谢和运输、细胞壁/膜/包膜生物发生以及无机离子运输和代谢的基因。通过抗生素和金属抗性基因的注释，深海菌株中存在特定的大环内酯输出基因和更多的亚碲酸盐抗性基因。此外，深海菌株中还富含一些与底物降解相关的基因，例如几丁质酶基因、新支链淀粉酶基因和生物聚合物转运蛋白基因。相比之下，上层菌株具有独特的同化硝酸盐还原能力。这里研究的基因组特征提供了关于弧菌如何通过基因组进化适应深海环境的见解。随着深海取样技术的发展，越来越多的深海弧菌菌株被分离出来，但这些富营养化弧菌菌株对深海环境的适应机制尚不清楚。在这里，我们的结果表明，中上层弧菌的基因组经过精简，以适应长期的寡营养环境。通过系统发育分析，我们发现海洋坎贝氏弧菌菌株的基因组变化与水深有关。我们的数据表明，与抗生素抗性、大分子和难熔底物降解以及稀有离子利用相关的基因增加与V. Campbellii菌株适应深渊环境有关，并且大部分增加的基因是通过水平基因转移获得的。这些发现可能加深我们对海洋细菌对深渊带极端环境的适应策略的理解。
With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. ABSTRACT The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.