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对新型目“Sysuiplasmatales”的生态作用和进化的基因组见解。

Genomic Insights into the Ecological Role and Evolution of a Novel Order, " Sysuiplasmatales".

机构信息

School of Life Sciences, Sun Yat-sen Universitygrid.12981.33, Guangzhou, People's Republic of China.

State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural Universitygrid.35155.37, Wuhan, People's Republic of China.

出版信息

Appl Environ Microbiol. 2021 Oct 28;87(22):e0106521. doi: 10.1128/AEM.01065-21. Epub 2021 Sep 15.

Abstract

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (" Sysuiplasmatales") in the class from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain , which typically show obligately anaerobic metabolisms. Notably, " Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders and " Gimiplasmatales," " Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that " Sysuiplasmatales," the closely related orders and " Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type HF Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except , , and within do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, ". Sysuiplasmatales," within in extremely acidic mine environments. ". Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between ". Sysuiplasmatales" and closely related lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.

摘要

最近的组学研究为了解来自各种极端环境的新型古菌的代谢潜力、适应和进化提供了宝贵的见解。我们利用基因组解析宏基因组方法,从中国南方两个铜矿的尾矿和酸性矿山排水 (AMD) 沉积物中回收了八个中高质量的宏基因组组装基因组 (MAG),这些 MAG 可能代表了一个新的门(“Sysuiplasmatales”),隶属于 。基于 16S rRNA 基因的分析表明,这些未培养古菌的栖息地范围狭窄,仅限于 AMD 和温泉相关环境。代谢重建表明,它们是兼性厌氧异养生活方式。这可能使古菌能够适应氧气波动,与域内的大多数谱系形成鲜明对比,后者通常表现出严格的厌氧代谢。值得注意的是,“Sysuiplasmatales”可以通过降解脂肪酸、氨基酸代谢和氧化还原无机硫化合物 (RISCs) 来保存能量,这表明它们可能有助于极端矿山环境中的酸生成。与密切相关的门“Gimiplasmatales”和“Ktedonobacteria”不同,“Sysuiplasmatales”没有进行甲烷生成和碳固定的能力。祖先状态重建表明,“Sysuiplasmatales”、密切相关的门“Ktedonobacteria”和“Gimiplasmatales”以及门 SG8-5 和 RBG-16-68-12 起源于一个能够通过细菌型 HF Wood-Ljungdahl 途径 (WLP) 进行碳固定的兼性厌氧祖先。它们的代谢分歧可能归因于不同的进化路径。 地球的极端环境中存在着各种各样的古菌;因此,它们可能在介导生物地球化学过程(如铁和硫循环)方面发挥重要作用。然而,由于大多数古菌多样性是未培养的,我们对古菌生物学和进化的了解仍然有限。例如,在 中,除了 、 和 之外,大多数目级谱系都没有培养代表。在这里,我们报告了在极其酸性的矿山环境中发现和基因组特征化的一个新目,“Sysuiplasmatales”。“Sysuiplasmatales”被推断为兼性厌氧异养菌,可能通过氧化 RISCs 促进酸的生成。“Sysuiplasmatales”与密切相关的谱系之间的生理分歧可能归因于不同的进化路径。这些结果扩展了我们对极端矿山生态系统中古菌的认识。

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