The dynamic response to hypo-osmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom found in salinities ranging from fully freshwater to fully marine, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypo-osmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling during the first 10 h. Freshwater shock dramatically remodelled the transcriptome, with similar to 50% of the genome differentially expressed in at least one time point. The peak response occurred within 1 h, with strong repression of genes involved in cell growth and osmolyte production, and strong induction of specific stress defence genes. Transcripts largely returned to baseline levels within 4-10 h, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a transcriptomics study of C. cryptica following months-long acclimation to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.