Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification

Transcriptomic reaction norms highlight metabolic depression as a divergence in phenotypic plasticity between oyster species under ocean acidification

Ocean acidification is occurring at a rate unprecedented for millions of years, forcing sessile organisms, such as oysters, to respond in the short term by relying on their phenotypic plasticity. But phenotypic plasticity has limits, tipping points, beyond which species will have to adapt or disappear. These limits could be related to the adaptation of species to different habitat variabilities. Here, we exposed juvenile pearl oysters, Pinctada margaritifera, to a broad pH range and determined the response at the gross physiological, lipidome and transcriptome levels. Thus, we identified its high tolerance with low pH tipping points at pH 7.3-6.8 below which most physiological parameters are impacted. We then compared the transcriptomic reaction norms of the tropical subtidal P. margaritifera with those of an intertidal temperate oyster, Crassostrea gigas, reusing data from a previous study. Despite showing similar tipping points to C. gigas, P. margaritifera exhibits strong mortality and depletion of energy reserves below these tipping points, which is not the case for C. gigas. This divergence relies mainly on the induction of metabolic depression, an adaptation to intertidal habitats in C. gigas but not P. margaritifera. Our method makes it possible to detect divergence in phenotypic plasticity, probably linked to the species' specific life-history strategies related to different habitats, which will determine the survival of species in the face of ongoing global changes. Such an approach is particularly relevant for studying the physiology of species in a world where physiological tipping points will increasingly be exceeded.

Parentage influence on gene expression under acidification revealed through single-embryo sequencing

The dissolution of anthropogenic carbon dioxide (CO2 ) in seawater has altered its carbonate chemistry in the process of ocean acidification (OA). OA affects the viability of marine species. In particular, calcifying organisms and their early planktonic larval stages are considered vulnerable. These organisms often utilize energy reserves for metabolism rather than growth and calcification as supported by bulk RNA-sequencing (RNA-seq) experiments. Yet, transcriptomic profiling of a bulk sample reflects the average gene expression of the population, neglecting the variations between individuals, which forms the basis for natural selection. Here, we used single-embryo RNA-seq on larval sea urchin Heliocidaris crassispina, which is a commercially and ecologically valuable species in East Asia, to document gene expression changes to OA at an individual and family level. Three paternal half-sibs groups were fertilized and exposed to 3 pH conditions (ambient pH 8.0, 7.7 and 7.4) for 12 h prior to sequencing and oxygen consumption assay. The resulting transcriptomic profile of all embryos can be distinguished into four clusters, with differences in gene expressions that govern biomineralization, cell differentiation and patterning, as well as metabolism. While these responses were influenced by pH conditions, the male identities also had an effect. Specifically, a regression model and goodness of fit tests indicated a significant interaction between sire and pH on the probability of embryo membership in different clusters of gene expression. The single-embryo RNA-seq approach is promising in climate stressor research because not only does it highlight potential impacts before phenotypic changes were observed, but it also highlights variations between individuals and lineages, thus enabling a better determination of evolutionary potential.

Direct and latent effects of ocean acidification on the transition of a sea urchin from planktonic larva to benthic juvenile

Ongoing ocean acidification is expected to affect marine organisms and ecosystems. While sea urchins can tolerate a wide range of pH, this comes at a high energetic cost, and early life stages are particularly vulnerable. Information on how ocean acidification affects transitions between life-history stages is scarce. We evaluated the direct and indirect effects of pH (pH_T 8.0, 7.6 and 7.2) on the development and transition between life-history stages of the sea urchin Strongylocentrotusdroebachiensis, from fertilization to early juvenile. Continuous exposure to low pH negatively affected larval mortality and growth. At pH 7.2, formation of the rudiment (the primordial juvenile) was delayed by two days. Larvae raised at pH 8.0 and transferred to 7.2 after competency had mortality rates five to six times lower than those kept at 8.0, indicating that pH also has a direct effect on older, competent larvae. Latent effects were visible on the larvae raised at pH 7.6: they were more successful in settling (45% at day 40 post-fertilization) and metamorphosing (30%) than larvae raised at 8.0 (17 and 1% respectively). These direct and indirect effects of ocean acidification on settlement and metamorphosis have important implications for population survival.

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development

BACKGROUND

The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable wild fishery species. To examine how M. franciscanus responds to its environment on a molecular level, differences in gene expression patterns were observed in embryos raised under combinations of two temperatures (13 °C or 17 °C) and two pCO2 levels (475 μatm or 1050 μatm). These combinations mimic various present-day conditions measured during and between upwelling events in the highly dynamic California Current System with the exception of the 17 °C and 1050 μatm combination, which does not currently occur. However, as ocean warming and acidification continues, warmer temperatures and higher pCO2 conditions are expected to increase in frequency and to occur simultaneously. The transcriptomic responses of the embryos were assessed at two developmental stages (gastrula and prism) in light of previously described plasticity in body size and thermotolerance under these temperature and pCO2 treatments.

RESULTS

Although transcriptomic patterns primarily varied by developmental stage, there were pronounced differences in gene expression as a result of the treatment conditions. Temperature and pCO2 treatments led to the differential expression of genes related to the cellular stress response, transmembrane transport, metabolic processes, and the regulation of gene expression. At each developmental stage, temperature contributed significantly to the observed variance in gene expression, which was also correlated to the phenotypic attributes of the embryos. On the other hand, the transcriptomic response to pCO2 was relatively muted, particularly at the prism stage.

CONCLUSIONS

M. franciscanus exhibited transcriptomic plasticity under different temperatures, indicating their capacity for a molecular-level response that may facilitate red sea urchins facing ocean warming as climate change continues. In contrast, the lack of a robust transcriptomic response, in combination with observations of decreased body size, under elevated pCO2 levels suggest that this species may be negatively affected by ocean acidification. High present-day pCO2 conditions that occur due to coastal upwelling may already be influencing populations of M. franciscanus.

Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma

Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyse gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and much smaller than genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.

Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey

For nearly a decade, the metazoan-focused research community has explored the impacts of ocean acidification (OA) on marine animals, noting that changes in ocean chemistry can impact calcification, metabolism, acid-base regulation, stress response and behavior in organisms that hold high ecological and economic value. Because OA interacts with several key physiological processes in marine organisms, transcriptomics has become a widely-used method to characterize whole organism responses on a molecular level as well as inform mechanisms that explain changes in phenotypes observed in response to OA. In the past decade, there has been a notable rise in studies that examine transcriptomic responses to OA in marine metazoans, and here we attempt to summarize key findings across these studies. We find that organisms vary dramatically in their transcriptomic responses to pH although common patterns are often observed, including shifts in acid-base ion regulation, metabolic processes, calcification and stress response mechanisms. We also see a rise in transcriptomic studies examining organismal response to OA in a multi-stressor context, often reporting synergistic effects of OA and temperature. In addition, there is an increase in studies that use transcriptomics to examine the evolutionary potential of organisms to adapt to OA conditions in the future through population and transgenerational experiments. Overall, the literature reveals complex organismal responses to OA, in which some organisms will face more dramatic consequences than others. This will have wide-reaching impacts on ocean communities and ecosystems as a whole.

Ocean acidification modulates the incorporation of radio-labeled heavy metals in the larvae of the Mediterranean sea urchin Paracentrotus lividus

The marine organisms which inhabit the coastline are exposed to a number of anthropogenic pressures that may interact. For instance, the accumulation of toxic metals present in coastal waters is expected to be modified by ocean acidification through e.g. changes in physiological performance and/or elements availability. Changes in bioaccumulation due to lowering pH are likely to be differently affected depending on the nature (essential vs. non-essential) and speciation of each element. The Mediterranean is of high concern for possible cumulative effects due to strong human influences on the coastline. The aim of this study was to determine the effect of ocean acidification (from pH 8.1 down to -1.0 pH units) on the incorporation kinetics of six trace metals (Mn, Co, Zn, Se, Ag, Cd, Cs) and one radionuclide (²⁴¹Am) in the larvae of an economically- and ecologically-relevant sea urchin of the Mediterranean coastline: Paracentrotus lividus. The radiolabelled metals and radionuclides added in trace concentrations allowed precise tracing of their incorporation in larvae during the first 74 h of their development. Independently of the expected indirect effect of pH on larval size/developmental rates, Paracentrotus lividus larvae exposed to decreasing pHs incorporated significantly more Mn and Ag and slightly less Cd. The incorporation of Co, Cs and ²⁴¹Am was unchanged, and Zn and Se exhibited complex incorporation behaviors. Studies such as this are necessary prerequisites to the implementation of metal toxicity mitigation policies for the future ocean. We discuss possible reasons and mechanisms for the specific effect of pH on each metals.