# The environmental adaptation of acidophilic archaea: promotion of horizontal gene transfer by genomic islands

## TL;DR

This study explores how acid-loving archaea adapt to harsh environments through horizontal gene transfer, focusing on genomic islands and their role in survival.

## Contribution

The study identifies and analyzes 176 genomic islands in acidophilic archaea, revealing their structural and functional roles in environmental adaptation.

## Key findings

- Genomic islands in acidophilic archaea show random size and distribution, with lower GC content compared to the genome average.
- tRNAs with stem-loop structures are commonly found at GI ends, suggesting integration near tRNA sites.
- Genomic islands often carry genes related to genetic processes, metabolism, and toxin-antitoxin systems, aiding adaptation to acidic environments.

## Abstract

Acid mine drainage (AMD) is an extremely acidic leachate highly contaminated with metal ions, yet it harbors a significantly high abundance of archaea. Genomic islands (GIs), as one of the productions of horizontal gene transfer (HGT), play an important role in the environmental adaptation and evolutionary processes of archaea. However, the distribution, structure, and function of GI within the genomes of archaea remain poorly understood. In this study, through the bioinformatic analysis of archaea in AMD, including Ferroplasma acidiphilum ZJ isolated from laboratory and 25 acidophilic archaea collected from NCBI database, 176 GIs were predicted and annotated. Furthermore, we analyzed their structural features and provided insights into the role of HGT in environmental adaptation. The size and distribution of GIs in the genomes were found to be random. In the majority of GIs, the GC content was lower than the average GC content of the strain genome, suggesting that GIs were typically looped out of the genomes with poor stability and transferred into those with higher stability. tRNAs with classical stem-loop secondary structures have been found at the ends of several GIs, suggesting that GIs frequently integrate near tRNAs. In contrast to functional genes directly involved in cellular life processes, GIs were more likely to carry genes related to genetic information and metabolism. Several GIs were identified to carry genes involved in iron oxidation, mercury reduction, and various toxin-antitoxin systems, which enhance the adaptability of the strains to highly acidic environments.

The online version contains supplementary material available at 10.1186/s12864-025-11875-5.