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

Abstract

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 that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling during the first 10 hours. Freshwater shock dramatically remodeled the transcriptome, with ~50% of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in cell growth and osmolyte production, and strong induction of specific stress defense genes. Transcripts largely returned to baseline levels within 4-10 hours, 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..

Resolving marine–freshwater transitions by diatoms through a fog of discordant gene trees

“…Given the length of time that has elapsed since the two major freshwater transitions occurred, the probability that shared ancestral polymorphisms persist decreases and the probability that lineage-specific adaptive mutations arise increases (Suh et al 2015; Zou and Zhang 2015; Mendes et al 2016). A large number of genes and pathways have been implicated in the response to low salinity (Nakov et al 2020; Downey et al 2022; Pinseel et al 2022), so an adaptive allele in one of the many possible target genes might have made it possible simply to survive in freshwaters initially. In the tens of millions of years since then, any hemiplasious alleles were most likely overwritten in the extant freshwater descendents, leaving a shared ancestral phenotype (e.g., enhanced transport of sodium ions) as the only remaining evidence of the hemiplasy.…”

“…The divergent evolutionary outcomes also suggest a greater role for homoplasy over hemiplasy. The genus Cyclotella includes freshwater, secondarily marine, and generalist euryhaline species that can tolerate a wide range of salinities (Guillard and Ryther 1962; Nakov et al 2020; Downey et al 2022). Similarly, most freshwater transitions at the tips of the tree (Fig.…”

“…Nevertheless, we found that a substantial set of the putatively hemiplasious genes identified here are involved in acclimation to low salinity conditions in one of the species in our analysis, S. marinoi (Pinseel et al 2022), suggesting a possible role for hemiplasy in freshwater adaptation. In addition, adaptation to low or changing salinity may be linked to modifications of gene expression (Bussard et al 2017; Nakov et al 2020; Downey et al 2022; Pinseel et al 2022), codon usage (Prabha et al 2017), nucleotide substitution rates (Mitterboeck et al 2016), transposable element activity (Yuan et al 2018), epigenetic responses (Artemov et al 2017), and epistatic interactions (Stern et al 2022). The genomic resources and phylogenetic framework presented here represent an important advance towards identifying the genes and processes underpinning freshwater adaptation by diatoms.…”

“…The vast differences between marine and freshwaters result in strong selective pressures on freshwater colonists. Low salinity provokes a broad range of physiological and metabolic responses in diatoms (Nakov et al 2020; Downey et al 2022; Pinseel et al 2022), but the current genetic architectures of freshwater adaptation reflect tens of millions of years of optimization and change since the earliest transitions. As a result, it may be difficult to identify specific alleles—whatever the process that generated them—that currently allow these diatoms to thrive in freshwaters.…”

The role of plastic and evolvedDNAmethylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus)

“…However, an important caveat is that fish in the RU study were acclimated to salinity environments for only four days before testing, so it is possible that methylation changes in some CpGs are due to short‐term acute stress that could differ from the methylation responses that would be observed under long‐term rearing conditions. Short versus long‐term exposure to environmental change has been shown to result in distinct transcriptomic patterns in fish and other aquatic species (Downey et al, 2022; Logan & Buckley, 2015). Further studies that compare short and long‐term methylation responses in ancestral versus novel environments will be helpful for a more comprehensive understanding of the role of epigenetic plasticity in adaptation.…”