Navigating salt gradients: Transcriptomic strategies of bivalves for surviving salinity stress in aquatic systems

Salinity fluctuations are among the most pervasive abiotic stressors in coastal and estuarine ecosystems, shaping the physiology, distribution, and resilience of bivalves. Over the past decade, more than thirty transcriptomic studies have examined the molecular responses of oysters, clams, and mussels to salinity change. However, the diversity of experimental designs, tissues analysed, and genome annotation quality has limited cross-species synthesis and has hindered the identification of conserved molecular signatures that define the evolutionary transition between different salinity regimes. In this review, we integrate evidence from 32 transcriptomic datasets encompassing 18 bivalve species to identify convergent molecular processes associated with salinity stress. Across taxa, hyposalinity consistently induces antioxidant defences, osmolyte biosynthesis, and chaperone-mediated protein stabilization, while optimal salinity maintains active mitochondrial metabolism, translation, and ion transport. To illustrate these conserved patterns under standardized analysis, we reanalyzed two representative species, Crassostrea gigas and Mercenaria mercenaria, revealing 217 shared Gene Ontology (GO), including antioxidant defence systems, osmolyte metabolic processes (specifically amino acid transport), and chaperone-mediated protein folding, representing a conserved molecular toolkit for hyposaline acclimation. Beyond these biological insights, our results highlight major methodological disparities among studies, including variable biological replication, analytical frameworks, and annotation completeness, which strongly influence DEG counts and functional interpretations. Addressing these sources of technical heterogeneity through standardized comparative frameworks, rigorous reporting of metadata, and improved genomic resources will be essential to fully resolve the molecular architecture of salinity tolerance across the bivalve tree of life. This framework integrates transcriptomic data to reveal divergent adaptive trajectories along a salinity gradient, providing a molecular perspective on the evolutionary colonization of estuarine and freshwater habitats by bivalve lineages. Several bivalve families, including Unionidae, Margaritiferidae, Tridacnidae, and Pharidae, remain markedly underrepresented, particularly in freshwater environments where transcriptomic resources are scarce compared with marine and estuarine taxa. Expanding coverage across these neglected lineages and regions will be essential for building a more comprehensive picture of salinity adaptation.