生物学杂志

生物学杂志 ›› 2025, Vol. 42 ›› Issue (1): 48-.doi: 10.3969/j.issn.2095-1736.2025.01.048

• 研究报告 • 上一篇    下一篇

典型冶金微生物Acidiphilium的比较基因组研究

李　星1， 娄　伟1， 黎亮志2， 尹华群2， 徐习中3， 夏　令4， 孟德龙2   

  1. 1. 湖南省和清环境科技有限公司， 长沙 410221； 2. 中南大学 资源加工与生物工程学院， 长沙 410083；
    3. 湖南桓耀环保科技有限责任公司， 长沙 410300； 4. 武汉理工大学 资源与环境工程学院， 武汉 430070
  • 出版日期:2025-02-18 发布日期:2025-02-12
  • 通讯作者: 孟德龙，博士，副教授，研究方向为环境微生物组学与应用，E-mail:delong.meng@csu.edu.cn
  • 作者简介:李星，硕士，中级工程师，研究方向为环境微生物、资源与环境，E-mail:xingli0803@163.com
  • 基金资助:
    国家重点研发计划项目（2023YFE0114500）； 湖南省自然科学基金项目（2023JJ30658）

Comparative genomics study of the typical bacteria Acidiphilium in biohydrometallurgy system

LI Xing1, LOU Wei1, LI Liangzhi2, YIN Huaqun2, XU Xizhong3, XIA Ling4, MENG Delong2   

  1. 1. Hunan Hikee Environmental Technology Co., Ltd., Changsha 410221, China; 2. School of Minerals Processing
    and Bioengineering, Central South University, Changsha 410083, China; 3. Hunan Huanyao Environmental Protection
    Technology Co., Ltd., Changsha 410300, China; 4. School of Resources and Environmental Engineering,
    Wuhan University of Technology, Wuhan 430070, China
  • Online:2025-02-18 Published:2025-02-12

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摘要： 酸性矿山废水（acid mine drainage, AMD）是一种寡营养、低pH以及富含重金属离子的极端酸性生境。该生境中含有大量的嗜酸、耐酸微生物，是系统中碳、氮和硫等物质循环的主要驱动者。Acidiphilium属菌株为兼性异养微生物，在AMD生境中丰度小于1%,但其与优势物种Acidibacillus经常表现出伴生关系，这说明Acidiphilium属在该系统中可能具有特殊的生态功能。为了探讨Acidiphilium属的生态功能和角色，从极端酸性环境中筛选到Acidiphilium属的菌1株，经16S rDNA和ANI比对，命名为Acidiphilium cryptumAcc2。Acidiphilium cryptumAcc2基因组含有1066个蛋白编码基因，序列总长为4917178 bp，均高于该属其他菌的基因大小。Acidiphilium属泛基因组是开放的，共含有47242个蛋白编码基因，699个蛋白编码基因（1.48%）被鉴定为核心基因，可变基因共有33457个蛋白编码基因，占70.82%，2705个蛋白编码基因是特有基因，占5.73%。其重金属抗性基因的Ka/Ks值95.5%以上均低于1，具有较强的纯化选择。Acidiphilium属基因组中基因之间的流动和交换频率相对其他物种更高，对菌株的进化和环境适应能力具有较大的正向影响。阐明了Acidiphilium属基因组进化和基因水平转移的规律，揭示了其环境适应性进化机制。

关键词: 酸性矿山废水, Acidiphilium, 环境适应机制, 比较基因组学, 基因水平转移

Abstract: Acid mine drainage (AMD) represents a uniquely acidic ecosystem, marked by oligotrophic conditions, a low pH environment, and elevated concentrations of heavy metals. Within this milieu, a diverse array of acidophilic and acid-tolerant microorganisms thrives, playing pivotal roles in the biogeochemical cycling of carbon, nitrogen, sulfur, and various other elements. The complex interplay between heterotrophic and autotrophic microorganisms underscores a significant ecological niche, with theAcidiphiliumgenus, a group of facultative heterotrophic microorganisms constituting a minor proportion (<1%) of the AMD microbial community. Notably, these organisms often engage in symbiotic interactions with prevalent species likeAcidibacillus, suggesting thatAcidiphiliumspecies fulfill unique and crucial ecological functions within the AMD ecosystem. In order to investigate the ecological function ofAcidiphilium, a strain ofAcidiphiliumwas isolated from an extremely acidic environment. It was identified asAcidiphilium cryptumAcc2 after being compared with ANI by 16S rDNA. TheAcidiphilium cryptumAcc2 genome contained 1066 protein-coding genes with a total sequence length of 4917178 bp, all of which were larger than the gene size of other strains in the genus. It was an open genome, containing 47242 protein-coding genes, 699 protein-coding genes (1.48%) were identified as core genes, 33457 protein-coding genes were variable genes (70.82%), and 2705 protein-coding genes were unique genes (5.73%). The Ka/Ks values of heavy metal resistance genes of 95.5% were all lower than 1, which showed strong purification selection. The flow and exchange frequency between genes in the genome of the genusAcidiphiliumwas higher than that of other species, and it had a greater positive impact on the evolution and environmental adaptability of strains. This research shed light on their evolutionary trajectories and gene transfer mechanisms, offering insights into their environmental adaptation mechanism and ecological significance in AMD environments.

Key words: AMD;Acidiphilium, environmental adaptation mechanism, comparative genomics, horizontal gene transfer

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