Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage.
Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage.
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酸性矿山排水中典型嗜酸菌嗜酸菌属的代谢和进化研究
DOI：
10.1128/msystems.00867-20
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发表时间：
2020-11-17
期刊：
影响因子：
6.4
通讯作者：
Yin H
中科院分区：
文献类型：
--
作者：
Li L;Liu Z;Zhang M;Meng D;Liu X;Wang P;Li X;Jiang Z;Zhong S;Jiang C;Yin H
极端微生物是在极端环境中茁壮成长的生物，是研究生物适应的关键模型。它们可以为生命的起源和进化提供线索，并提高对元素生物地球化学循环的理解。极端嗜酸菌如嗜酸菌广泛存在于酸性矿山排水系统中，但该属的代谢潜力、生态功能和进化历史仍不清楚。在这里，我们对三个新的嗜酸菌菌株的基因组进行了测序，并对这个极端嗜酸的细菌属进行了比较基因组分析。通过系统发育重建和基因背景比较，我们在嗜酸杆菌基因组中发现了丰富的水平转移基因(HTGs)，这些基因有助于环境适应和代谢能力的扩展。这项研究加深了我们对极端生态位中微生物进化和生物地球化学循环的理解。在此，我们报道了三个新的Acidiphilium基因组，对现有的Acidiphilium物种进行了重新分类，并首次对Acidiphilium进行了比较基因组分析，试图探讨Acidiphilium属的代谢潜力、生态功能和进化历史。在Acidiphilium基因组中，我们发现了丰富的与环境适应和代谢扩张有关的水平转移基因(HTGs)，包括光合作用(PUF，puh)、二氧化碳同化(RBC)、甲烷代谢能力(MMO、mdh、frm)、氮源利用(NAR、Cyn、HMP)、硫化合物利用(SOX、PSR、SQR)以及多重金属和渗透胁迫抗性(cZc、CoP等)。此外，预测的水平基因转移供体存在于嗜酸菌的共生网络中。基因组水平的正选择分析表明，15个基因包含适应性突变，其中大多数是多功能基因，在极端条件下的生存中发挥关键作用。我们认为嗜酸菌起源于温和的环境，并在获得许多基本功能后适应于极端环境，如酸性矿场。极端微生物是在极端环境中茁壮成长的生物，它们是研究生物适应的关键模型。它们可以为生命的起源和进化提供线索，并提高对元素生物地球化学循环的理解。极端嗜酸菌如嗜酸菌广泛存在于酸性矿山排水系统中，但该属的代谢潜力、生态功能和进化历史仍不清楚。在这里，我们对三个新的嗜酸菌菌株的基因组进行了测序，并对这个极端嗜酸的细菌属进行了比较基因组分析。通过系统发育重建和基因背景比较，我们在嗜酸杆菌基因组中发现了丰富的水平转移基因(HTGs)，这些基因有助于环境适应和代谢能力的扩展。这项研究加深了我们对极端生态位中微生物进化和生物地球化学循环的理解。
Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches. Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.
影响因子：
3.7
作者：
San Martin-Uriz P;Mirete S;Alcolea PJ;Gomez MJ;Amils R;Gonzalez-Pastor JE
通讯作者：
Gonzalez-Pastor JE