2025/10/07 by Monireh Safari, Joseph Butler, Gurjit S. Randhawa +2 · 1 voice
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology
paper · doi:10.1093/nargab/lqaf189
openalex publication_date 2025/10/07 · openalex created_date 2025/12/24 · openalex updated_date 2026/07/29
Extreme environments impose strong mutation and selection pressures that drive distinctive, yet understudied, genomic adaptations in extremophiles. In this study, we identify 15 bacterium-archaeon pairs that exhibit highly similar [Formula: see text]-mer-based genomic signatures despite maximal taxonomic divergence, suggesting that shared environmental conditions can produce convergent, genome-wide sequence patterns that transcend evolutionary distance. To uncover these patterns, we developed a computational pipeline to select a composite genome proxy assembled from noncontiguous subsequences of the genome. Using supervised machine learning on a curated dataset of 693 extremophile microbial genomes, we found that 6-mers and 100 kbp genome proxy lengths provide the best balance between classification accuracy and computational efficiency. Our results provide conclusive evidence of the pervasive nature of [Formula: see text]-mer-based patterns across the genome, and uncover the presence of taxonomic and environmental components that persist across all regions of the genome. The 15 bacterium-archaeon pairs identified by our method as having similar genomic signatures were validated through multiple independent analyses, including 3-mer frequency profile comparisons, phenotypic trait similarity, and geographic co-occurrence data. These complementary validations confirmed that extreme environmental pressures can override traditionally recognized taxonomic components at the whole-genome level. Together, these findings reveal that adaptation to extreme conditions can carry robust, taxonomic domain-spanning imprints on microbial genomes, offering new insight into the relationship between environmental impacts and genome sequence composition convergence.