Comparative Genomic Analysis of Halophiles Reveals New Clues to Their Adaptation Strategies in Hypersaline Environments

Background: Halophiles, which have many potential applications in the biomaterial, bioremediation, and nanotechnology arenas, are microorganisms that live in environments with high salt concentrations. To elucidate the adaptive strategies that allow them to live in such hypersaline environments, the genome sequences of 66 strains of halophiles and non-halophiles (including 27 strains of halophilic bacteria, 24 strains of haloarchaea, and 15 strains of non-halophilic bacteria) were subjected to comparative genomic analysis. Results: The G+C content of the genomic DNA sequence and acidic amino acid composition of the gene product of the haloarchaea were higher than those of both the halophilic and non-halophilic bacteria. In addition, the probability of occurrence and proportion of extra chromosomal genetic elements in the haloarchaea outweighed those of the halophilic and non-halophilic bacteria. Further, proteasome, the mRNA surveillance pathway, and basal transcription factors were present in the haloarchaea but absent in the other two groups of microorganisms. Carotenoid, sesqui-terpenoid, and tri-terpenoid were common in the haloarchaea, but occurred with a relatively low degree of frequency in the halophilic and non-halophilic bacteria. In contrast, some D-amino acids (i.e., D-glutamine, D-glutamate, D-arginine, D-ornithine, and D-alanine) and lipopolysaccharide, fluorobenzoate, limonene, and pinene were widely distributed in both types of bacteria, but absent in the family Halobacteriaceae. Conclusion: Large-scale comparative genomic analysis of the genomes of haloarchaea, halophilic bacteria, and non-halophilic bacteria provided a novel perspective on the strategies that microorganisms adopt to adapt to hypersaline environments. Although both haloarchaea and halophilic bacteria require a high concentration of sodium chloride for growth, they employ different mechanisms of adaptation. Haloarchaea, which contain a significantly high G+C content and proportion of acidic amino acids to with stand their harsh environment, use sun light as an energy resource to balance intracellular and extracellular osmotic pressure, thus allowing them to live in hypersaline environments the same way that non-halophilic bacteria live in more common environments.