Domain-specific osmoadaptation revealed by metatranscriptomic analysis in hypersaline environments

High-throughput RNA-seq enables the analysis of gene expression in complex, culture-independent microbial communities. In this study, we used this approach to explore the microbial adaptation to salinity changes in hypersaline environments using samples collected from the Santa Pola ponds (Alicante, Spain). Two metatranscriptomic experiments were conducted: (i) salt concentration from 20 to 30%, mimicking summer evaporation, and (ii) dilution from 30 to 25%, simulating rainfall. As a result, these two experiments revealed significant differences in the gene expression of several metabolic pathways and essential processes, revealing different adaptation strategies between Archaea and Bacteria. Under saline concentration, most bacterial taxa, excluding Salinibacter, exhibited higher transcriptional repression compared to Archaea, suggesting an energy conservation response to osmotic stress. In contrast, Archaea maintained metabolic activity, with Haloquadratum showing more gene induction than repression, allowing for osmoadaptation. Conversely, in the dilution experiment, Archaea displayed greater transcriptional plasticity than Bacteria, reflecting their ability to dynamically adapt to fluctuating salinity. Further, metatranscriptomics coupled with the analysis of isoelectric point (pI) distributions revealed a remarkable repression of high-pI predicted proteins under high-salt concentration, particularly in Bacteria, suggesting a selective downregulation of basic proteins in response to osmotic stress and highlighting a potential adaptive mechanism. Overall, these findings underscore domain-specific osmoadaptation strategies to cope with osmotic stress in hypersaline environments.