IntroductionThermophiles and psychrophiles are groups of extremophilic species adapted to thrive in extreme temperature environments, unlike mesophiles, which grow under normal conditions and cannot withstand extreme conditions1,2,3. Thermophiles, commonly found in hot springs, thrive in high-temperature ranging from 55 to 80 °C4,5,6,7, while psychrophiles flourish in cold conditions below 15 °C, such as polar regions and deep-sea habitats8,9. These temperature-adapted species hold immense potential in a sustainable bio-based economy, with applications spanning biotechnology, pharmaceuticals, and environmental industries10,11,12,13.These groups encompass a diverse array of microorganisms, including bacteria, archaea, fungi, and algae, representing varied taxonomic lineages and evolutionary paths14,15. Despite this diversity, species within each group have independently evolved specialized mechanisms to adapt to their unique environments. Some of the abilities of these extraordinary extremophiles to adapt in extreme temperatures have been previously reported. For example, thermophiles have specific protein and DNA stability mechanisms to be able to thrive in high temperatures16,17. They have increased hydrophobic interactions, and salt bridges, and often contain high GC ratios providing additional thermal stability18,19. On the other hand, psychrophiles adapt to cold environments by having different genomic and molecular features. They have flexible enzymes that allow efficient catalytic activity under low temperatures20 and have increased production of cold-shock proteins and antifreeze proteins, which help stabilize the cellular environment21. Moreover, psychrophiles have reduced hydrogen bonding and increased surface hydrophobicity22, which confer activity in cold environments.However, there is a significant knowledge gap in understanding the mechanisms of adaptation, particularly concerning genomic and metabolic characteristics. Given their extensive applications across various industries and research fields, it is crucial to explore the differences in genomic features and metabolic capabilities among these groups of extremophilic species. In this study, we have conducted a comparative analysis of the genomic features and genome-scale metabolic model predictions for 59 species across different environmental groups, including thermophiles, psychrophiles, and mesophiles. This research addresses the knowledge gap in understanding how extremophiles differ from mesophiles in their genomic and metabolic characteristics. Our findings reveal distinct genomic and metabolic characteristics among these groups. Variations were observed in genome length, gene count, genomic G + C content, and metabolic network size. These species exhibit specific codon preferences and distinct amino acid profiles, likely supporting efficient cellular processes, DNA stability, and growth under extreme temperature conditions. These species also display unique metabolic network properties, including variations in import and export reactions and distinct biochemical reactions linked to key metabolic pathways, which may be crucial for adaptation to extreme environments. These findings enhance our molecular understanding of life in extreme environments and offer potential applications in biotechnology and insights into evolutionary biology.ResultsGenomic insights into thermophiles and psychrophilesA comparative analysis of the genomic features of 59 species, from 22 taxonomy phyla, divided into the three environmental groups; thermophiles, psychrophiles, and mesophiles was conducted to explore the intrinsic genomic characteristics required for adaptation to different temperature conditions (list of species is in Supplementary File 1). The results indicate that psychrophiles generally possess significantly larger genomes than thermophiles and mesophiles (Fig. 1a). In contrast, thermophiles exhibit relatively low variation in genome size and have significantly smaller genomes than psychrophiles (Fig. 1a). However, their genome size is not significantly different from mesophiles, which later also show the highest variation in genome length (Fig. 1a). Since the number of genes are positively correlated with genome size, a similar trend was observed for the number of coding sequences (CDS) in thermophiles and psychrophiles (Fig. 1b). Thermophiles had significantly fewer CDS than psychrophiles, with limited variation. We also conducted a comparative analysis of these genomic features across 22 taxonomic phyla and observed considerable variation within these phyla, regardless of their environmental groupings (Supplementary Fig. 1).Fig. 1Genome intrinsic features across thermophiles, psychrophiles, and Mesophiles. A comparative genomic analysis highlights intrinsic features of thermophiles, psychrophiles, and mesophiles, revealing variations in a genome length, b differences in gene content, and c disparities in G + C content at both the genome and coding sequence levels, which underscore compositional biases characteristic of these organisms. d The analysis of codon usage includes (i) the percentage usage of codons and (ii) the identification of specific codons with significantly higher or lower usage in thermophiles and psychrophiles compared to mesophiles. e Differences at the level of amino acid abundance in all three groups of species (i) forming three distinct amino acids groups: one enriched in hydrophilic amino acids, another dominated by hydrophobic amino acids, and a third consisting of a mix of both types, (ii) and revealing amino acids that are significantly more or less abundant in thermophilic and psychrophilic species relative to mesophiles. * represents p value