Evolutionary patterns of archaea predominant in acidic environment

Environmental Microbiome

Research

Mikhail M. Yakimov¹  Aleksei A. Korzhenkov²  Stepan V. Toshchakov²  Rafael Bargiela³  Peter N. Golyshin³  Owen A. McIntosh³  Olga V. Golyshina³ 

[1] Institute of Polar Sciences, CNR, Messina, Italy;Kurchatov Center for Genome Research, NRC Kurchatov Institute, Moscow, Russia;School of Natural Sciences and Centre for Environmental Biotechnology, Bangor University, Bangor, UK;

关键词: Acid mine drainage (AMD);    Mine-impacted environments;    Parys Mountain;    Acidophilic archaea;    Thermoplasmatales;    Microbial dark matter;   

DOI  :  10.1186/s40793-023-00518-5

 received in 2023-04-19, accepted in 2023-07-12,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundArchaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called “alphabet-plasmas”, and collectively dubbed “E-plasma”, were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.ResultsTheir genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the “E-plasma” in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of “E-plasma”, which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.ConclusionsThis study has analysed the metagenome-assembled genome of “E-plasma”, which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.

【 授权许可】

CC BY   
© The Author(s) 2023

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