Transgenerational acclimation to changes in ocean acidification in marine invertebrates

Transgenerational adaptation to ocean acidification determines the susceptibility of filter-feeding rotifers to nanoplastics

The adaptation of marine organisms to the impending challenges presented by ocean acidification (OA) is essential for their future survival, and mechanisms underlying OA adaptation have been reported in several marine organisms. In the natural environment, however, marine organisms are often exposed to a combination of environmental stressors, and the interactions between adaptive responses have yet to be elucidated. Here, we investigated the susceptibility of filter-feeding rotifers to short-term (ST) and long-term (LT) (≥180 generations) high CO2 conditions coupled with nanoplastic (NPs) exposure (ST+ and LT+). Adaptation of rotifers to elevated CO2 caused differences in ingestion and accumulation of NPs, resulting in a significantly different mode of action on in vivo endpoints between the ST+ and LT+ groups. Moreover, microRNA-mediated epigenetic regulation was strongly correlated with the varied adaptive responses between the ST+ and LT+ groups, revealing novel regulatory targets and pathways. Our results indicate that pre-exposure history to increased CO2 levels is an important factor in the susceptibility of rotifers to NPs.

Epigenetic analytical approaches in ecotoxicological aquatic research

Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.

Effects of one-year exposure to ocean acidification on two species of abalone

Ocean acidification (OA) resulting from the absorption of excess atmospheric CO₂ by the ocean threatens the survival of marine calcareous organisms, including mollusks. This study investigated the effects of OA on adults of two abalone species (Haliotis diversicolor, a subtropical species, and Haliotis discus hannai, a temperate species). Abalone were exposed to three pCO₂ conditions for 1 year (ambient, ~ 880, and ~ 1600 μatm), and parameters, including mortality, physiology, immune system, biochemistry, and carry-over effects, were measured. Survival decreased significantly at ~ 800 μatm pCO₂ for H. diversicolor, while H. discus hannai survival was negatively affected only at a higher OA level (~ 1600 μatm pCO₂). H. diversicolor exhibited depressed metabolic and excretion rates and a higher O:N ratio under OA, indicating a shift to lipids as a metabolism substrate, while these physiological parameters in H. discus hannai were robust to OA. Both abalone failed to compensate for the pH decrease of their internal fluids because of the lowered hemolymph pH under OA. However, the reduced hemolymph pH did not affect total hemocyte counts or tested biomarkers. Additionally, H. discus hannai increased its hemolymph protein content under OA, which could indicate enhanced immunity. Larvae produced by adults exposed to the three pCO₂ levels were cultured in the same pCO₂ conditions and larval deformation and shell length were measured to observe carry-over effects. Enhanced OA tolerance was observed for H. discus hannai exposed under both of the OA treatments, while that was only observed following parental pCO₂ ~ 880 μatm exposure for H. diversicolor. Following pCO₂ ~ 1600 μatm parental exposure, H. diversicolor offspring exhibited higher deformation and lower shell growth in all pCO₂ treatments. In general, H. diversicolor were more susceptible to OA compared with H. discus hannai, suggesting that H. diversicolor could be unable to adapt to acidified oceans in the future.

Review of the toxicity and potential molecular mechanisms of parental or successive exposure to environmental pollutants in the model organism Caenorhabditis elegans

Environmental pollutants such as heavy metals, nano/microparticles, and organic compounds have been detected in a wide range of environmental media, causing long-term exposure in various organisms and even humans through breathing, contacting, ingestion, and other routes. Long-term exposure to environmental pollutants in organisms or humans promotes exposure of offspring to parental and environmental pollutants, and subsequently results in multiple biological defects in the offspring. This review dialectically summarizes and discusses the existing studies using Caenorhabditis elegans (C. elegans) as a model organism to explore the multi/transgenerational toxicity and potential underlying molecular mechanisms induced by environmental pollutants following parental or successive exposure patterns. Parental and successive exposure to environmental pollutants induces various biological defects in C. elegans across multiple generations, including multi/transgenerational developmental toxicity, neurotoxicity, reproductive toxicity, and metabolic disturbances, which may be transmitted to progeny through reactive oxygen species-induced damage, epigenetic mechanisms, insulin/insulin-like growth factor-1 signaling pathway. This review aims to arouse researchers' interest in the multi/transgenerational toxicity of pollutants and hopes to explore the possible long-term effects of environmental pollutants on organisms and even humans, as well as to provide constructive suggestions for the safety and management of emerging alternatives.

Impacts of Low Oxygen on Marine Life: Neglected, but a Crucial Priority for Research

AbstractGlobal ocean O₂ content has varied significantly across the eons, both shaping and being shaped by the evolutionary history of life on planet Earth. Indeed, past O₂ fluctuations have been associated with major extinctions and the reorganization of marine biota. Moreover, its most recent iteration-now anthropogenically driven-represents one of the most prominent challenges for both marine ecosystems and human societies, with ocean deoxygenation being regarded as one of the main drivers of global biodiversity loss. Yet ocean deoxygenation has received far less attention than concurrent environmental variables of marine climate change, namely, ocean warming and acidification, particularly in the field of experimental marine ecology. Together with the lack of consistent criteria defining gradual and acute changes in O₂ content, a general lack of multifactorial studies featuring all three drivers and their interactions prevents an adequate interpretation of the potential effects of extreme and gradual deoxygenation. We present a comprehensive overview of the interplay between O₂ and marine life across space and time and discuss the current knowledge gaps and future steps for deoxygenation research. This work may also contribute to the ongoing call for an integrative perspective on the combined effects of these three drivers of change for marine organisms and ecosystems worldwide.

Paternal hypoxia exposure primes offspring for increased hypoxia resistance

Background

In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia.

Results

We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 6-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that other epigenetic mechanisms are responsible for alterations in gene expression.

Conclusions

Overall, our findings suggest that an epigenetic memory of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01389-x.

Effects of ocean acidification on the biochemistry, physiology and parental transfer of Ampelisca brevicornis (Costa, 1853)

Ocean acidification (OA) has received more attention in the marine research community in recent years than any other topic. Excess carbon dioxide makes the ocean more acidic, threatening marine ecosystems. There has been little research on the impact of OA on crustaceans, particularly on their physiological and potential ecosystem-level consequences. Thus, we investigated the impacts of OA on the physiological and biochemical characteristics of the estuarine amphipod Ampelisca brevicornis. Ovigerous amphipods were harvested from nature and maintained in the laboratory to produce juveniles, which were then further reared to obtain the mature adults (F0) and successive offspring (F1). For this study, four pH treatments (pH 8.1, 7.5, 7.0, and 6.5) mimicking future OA were evaluated to understand the physiological and biochemical effects on the organisms. The findings of this study suggest that A. brevicornis is more vulnerable to OA than was previously established in short-term trials. The survival was significantly reduced as pH decreased over time and a significant interaction between pH and time was observed. Survival was higher in F1 than in F0 juveniles and vice versa in terms of growth. Animal's physiological responses such as growth, burrowing behavior, locomotor activity, swimming speed, ventilation rate and reproductive performance were negatively influenced by acidification. These physiological characteristics can be linked to the oxidative stress induced by global change conditions because excess of free radicals degrade cell functioning, affecting species' biochemical and physiological performance. These alterations may have long-term negative impacts, with ecological consequences. The results of this study provide baseline information regarding the effect of OA on this keystone crustacean that may be useful in simulating the impacts of OA to develop different conceptual models for a better understanding of the consequences and implications of climate change in the future for managing marine ecosystems.

Massive shellfish farming might accelerate coastal acidification: A case study on carbonate system dynamics in a bay scallop (Argopecten irradians) farming area, North Yellow Sea

Seven cruises were carried out in a bay scallop (Argopecten irradians) farming area and its surrounding waters, North Yellow Sea, from March to November 2017 to study the dynamics of the carbonate system and its controlling factors. Results indicated that the studied parameters were highly variability over a range of spatiotemporal scales, comprehensively forced by various physical and biological processes. Mixing effect and scallop calcification played the most important role in the seasonal variation of total alkalinity (TAlk). For dissolved inorganic carbon (DIC), in addition to mixing, air-sea exchange and microbial activity, e.g. photosynthesis and microbial respiration processes, had more important effects on its dynamics. Different from the former, the changes of water pH_T, partial pressure of CO₂ (pCO₂) and aragonite saturation state (Ω_A) were mainly controlled by the combining of the temperature, air-sea exchange, microbial activity and scallop metabolic activities. In addition, the results indicated that massive scallop farming can significantly increase the DIC/TAlk ratio by reducing the TAlk concentration in seawater, thereby reducing the buffering capacity of the carbonate system in seawater especially for Ω_A. Preliminary calculated, ~75.7 and ~45.5 μmol kg^-1 of TAlk were removed from the surface and bottom waters respectively in one scallop cultivating cycle. If these carbonates cannot be replenished in time, it is likely to accelerate the acidification process of coastal waters. This study highlighted the control mechanism of the carbonate system under the influence of bay scallop farming, and provided useful information for revealing the potential link between human activities (shelled-mollusc mariculture) and coastal acidification.

Ecotoxicological epigenetics in invertebrates: Emerging tool for the evaluation of present and past pollution burden

The effect of environmental pollution on epigenetic changes and their heredity in affected organisms is of major concern as such changes can play a significant role in adaptation to changing environmental conditions. Changes of epigenetic marks including DNA methylation, histone modifications, and non-coding RNA's can induce changes in gene transcription leading to physiological long-term changes or even transgenerational inheritance. Such mechanisms have until recently been scarcely studied in invertebrate organisms, mainly focusing on model species including Caenorhabditis elegans and Daphnia magna. However, more data are becoming available, particularly focused on DNA methylation changes caused by anthropogenic pollutants in a wide range of invertebrates. This review examines the literature from field and laboratory studies utilising invertebrate species exposed to environmental pollutants and their effect on DNA methylation. Possible mechanisms of epigenetic modifications and their role on physiology and adaptation as well as the incidence of intergenerational and transgenerational inheritance are discussed. Furthermore, critical research challenges are defined and the way forward is proposed. Future studies should focus on the use of next generation sequencing tools to define invertebrate methylomes under environmental stress in higher resolution, those data should further be linked to gene expression patterns and phenotypes and detailed studies focusing on transgenerational effects are encouraged. Moreover, studies of other epigenetic mechanisms in various invertebrate species, apart from DNA methylation would provide better understanding of interconnected cross-talk between epigenetic marks. Taken together incorporating epigenetic studies in ecotoxicology context presents a promising tool for development of sensitive biomarkers for environmental stress assessment.

Ocean acidification impairs the physiology of symbiotic phyllosoma larvae of the lobster Thenus australiensis and their ability to detect cues from jellyfish

Ocean acidification (OA) can alter the behaviour and physiology of marine fauna and impair their ability to interact with other species, including those in symbiotic and predatory relationships. Phyllosoma larvae of lobsters are symbionts to many invertebrates and often ride and feed on jellyfish, however OA may threaten interactions between phyllosomas and jellyfish. Here, we tested whether OA predicted for surface mid-shelf waters of Great Barrier Reef, Australia, under ∆ pH = -0.1 (pH ~7.9) and ∆pH = -0.3 (pH ~7.7) relative to the present pH (~8.0) (P) impaired the survival, moulting, respiration, and metabolite profiles of phyllosoma larvae of the slipper lobster Thenus australiensis, and the ability of phyllosomas to detect chemical cues of fresh jellyfish tissue. We discovered that OA was detrimental to survival of phyllosomas with only 20% survival under ∆pH = -0.3 compared to 49.2% and 45.3% in the P and ∆pH = -0.1 treatments, respectively. The numbers of phyllosomas that moulted in the P and ∆pH = -0.1 treatments were 40% and 34% higher, respectively, than those in the ∆pH = -0.3 treatment. Respiration rates varied between pH treatments, but were not consistent through time. Respiration rates in the ∆pH = -0.3 and ∆pH = -0.1 treatments were initially 40% and 22% higher, respectively, than in the P treatment on Day 2 and then rates varied to become 26% lower (∆pH = -0.3) and 17% (∆pH = -0.1) higher towards the end of the experiment. Larvae were attracted to jellyfish tissue in treatments P and ∆pH = -0.1 but avoided jellyfish at ∆pH = -0.3. Moreover, OA conditions under ∆pH = -0.1 and ∆pH = -0.3 levels reduced the relative abundances of 22 of the 34 metabolites detected in phyllosomas via Nuclear Magnetic Resonance (NMR) spectroscopy. Our study demonstrates that the physiology and ability to detect jellyfish tissue by phyllosomas of the lobster T. australiensis may be impaired under ∆pH = -0.3 relative to the present conditions, with potential negative consequences for adult populations of this commercially important species.

Parental whole life cycle exposure modulates progeny responses to ocean acidification in slipper limpets

Multigenerational exposure is needed to assess the evolutionary potential of organisms in the rapidly changing seascape. Here, we investigate if there is a transgenerational effect of ocean acidification exposure on a calyptraeid gastropod such that long-term exposure elevates offspring resilience. Larvae from wild type Crepidula onyx adults were reared from hatching until sexual maturity for over 36 months under three pH conditions (pH 7.3, 7.7, and 8.0). While the survivorship, growth, and respiration rate of F₁ larvae were unaffected by acute ocean acidification (OA), long-term and whole life cycle exposure significantly compromised adult survivorship, growth, and reproductive output of the slipper limpets. When kept under low pH throughout their life cycle, only 6% of the F₁ slipper limpets survived pH 7.3 conditions after ~2.5 years and the number of larvae they released was ~10% of those released by the control. However, the F₂ progeny from adults kept under the long-term low pH condition hatched at a comparable size to those in medium and control pH conditions. More importantly, these F₂ progeny from low pH adults outperformed F₂ slipper limpets from control conditions; they had higher larval survivorship and growth, and reduced respiration rate across pH conditions, even at the extreme low pH of 7.0. The intragenerational negative consequences of OA during long-term acclimation highlights potential carryover effects and ontogenetic shifts in stress vulnerability, especially prior to and during reproduction. Yet, the presence of a transgenerational effect implies that this slipper limpet, which has been widely introduced along the West Pacific coasts, has the potential to adapt to rapid acidification.

The genome of the minute marine rotifer Proales similis: Genome-wide identification of 401 G protein-coupled receptor (GPCR) genes

The minute marine rotifer Proales similis is a potential model species for ecotoxicological and ecophysiological studies. Therefore, the provision of whole-genome data for P. similis is an easy way to deepen understanding of the molecular mechanisms involved in response to various environmental stressors. In this research, we assembled the whole-genome sequence (32.7 Mb total, N50 = 2.42 Mb) of P. similis, consisting of 15 contigs with 10,785 annotated genes. To understand the ligand-receptor signaling pathway in rotifers in response to environmental cues, we identified 401 G protein-coupled receptor (GPCR) genes in the P. similis genome and compared them with those from other species. The 401 full-length GPCR genes were classified into five distinct classes: A (363), B (18), C (7), F (2), and other (11). Most GPCR gene families have undergone sporadic evolutionary processes. However, some classes were highly conserved between species. Overall, this result provides new information about GPCR-based signaling pathways and the evolution of GPCRs in the minute rotifer P. similis, and it expands our knowledge of ligand-receptor signaling pathways in response to various environmental cues.

Reproductive toxicities of 1-ethyl-3-methylimidazolium bromide on Caenorhabditis elegans with oscillation between inhibition and stimulation over generations

Ionic liquids (ILs) become emerging pollutants and their toxicities earn increasing attentions. Yet, their effects were seldom explored on reproduction which connects generations and also effects across generations. In the present study, reproductive effects of 1-ethyl-3-methylimidazolium bromide ([C₂mim]Br), one representative IL, were studied on C. elegans with 11 continuously exposed generations (F1 to F11). At 8.20E-5 g/L, the effects on the initial reproduction showed oscillatory changes between stimulation (in F1, F3, F4, F6 and F10) and inhibition (in F2, F5, F7, F8 and F11). At 8.20E-3 g/L, the effects on the reproduction over generations also showed such oscillation despite of different stimulation or inhibition levels, and even opposite influences in F4 and F11. The effects of [C₂mim]Br on the total reproduction also showed the concentration-dependent oscillation between stimulation and inhibition over generations, though they had less alteration frequencies than those on the initial reproduction. Biochemical and molecular indicators were further measured in F1, F4, F7 and F11 to explore potential mechanisms. Results showed that the effects on spermatocyte protein 8 (SPE8) showed positive correlation with those on reproduction while the influences on major sperm protein (MSP) and sperm transmembrane protein 9 (SPE9) showed negative correlation with SPE8. Moreover, the dysregulation on expressions of acs-2 and akt-1 indicated the involvement of glucolipid metabolism. The changes in expressions of set-2, met-2, set-25 and mes-4 demonstrated that the long-term reproductive impacts of [C₂mim]Br over generations also involved histone methylation at H3K4, H3K9 and H3K36, which also connected with the glucolipid metabolism.

Genome-wide identification and transcriptional modulation of histone variants and modification related genes in the low pH-exposed marine rotifer Brachionus koreanus

Histone modification is considered to be a major epigenetic control mechanism. These modifications (e.g. acetylation, phosphorylation, and methylation) may affect the interaction of histones with DNA and/or regulate DNA-based processes (e.g., recombination, repair, replication, and transcription) and chromatin remodeling complexes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify genes undergoing epigenetic control modification in aquatic invertebrates. In this study, we identified whole core histones (70 total genes) and post-translational modification (PTM) histone genes (63 total genes) in the marine rotifer Brachionus koreanus through whole-genome analysis, and annotated them according to the human nomenclature. Notably, upon comparative analysis of cis-regulatory motif sequences, we found that B. koreanus core histone protein structures were similar to those of mammals. Furthermore, to examine the effect of parental low pH stress on the offspring's epigenetic regulation, we investigated the expression of PTM genes in two generations of B. koreanus exposed to low pH conditions. Given that the B. koreanus genome does not possess DNA methyltransferase 1 and 3 genes, we concluded that histone genes could be involved as an important epigenetic mechanism in B. koreanus. Therefore, the histone-associated genes identified in this study could be useful for ecotoxicological studies and facilitate the application of chromatin immunoprecipitation sequencing using high-throughput DNA sequencing based on the genome-wide identification of transcription factor binding sites in rotifers.

Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture

The pH of the global ocean is decreasing due to the absorption of anthropogenically emitted CO₂, causing ocean acidification (OA). OA negatively impacts marine shellfish and threatens the continuing economic viability of molluscan shellfish aquaculture, a global industry valued at more than 19 billion USD. We identify traits linked to growth and lipid regulation that contribute tolerance to OA in abalone aquaculture, with broader implications for adaptation efforts in other shellfish species. We also identify evolved heritable variation for physiological resilience to OA that may be exploited in commercial and restoration aquaculture breeding programs to offset the negative consequences of continuing climate change.

Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusc important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing OA, whereas a captive-raised population sourced from a region of weaker upwelling exhibited significant mortality and vulnerability to OA. This difference was linked to population-specific variation in the maternal provisioning of lipids to offspring, with a positive correlation between lipid concentrations and survival under OA. This relationship also persisted in experiments on second-generation animals, and larval lipid consumption rates varied among paternal crosses, which is consistent with the presence of genetic variation for physiological traits relevant for OA survival. Across experimental trials, growth rates differed among family lineages, and the highest mortality under OA occurred in the fastest growing crosses. Identifying traits that convey resilience to OA is critical to the continued success of abalone and other shellfish production, and these mitigation efforts should be incorporated into breeding programs for commercial and restoration aquaculture.

Multigenerational Mitigating Effects of Ocean Acidification on In Vivo Endpoints, Antioxidant Defense, DNA Damage Response, and Epigenetic Modification in an Asexual Monogonont Rotifer

Ocean acidification (OA) is caused by changes in ocean carbon chemistry due to increased atmospheric pCO₂ and is predicted to have deleterious effects on marine ecosystems. While the potential impacts of OA on many marine species have been studied, the multigenerational effects on asexual organisms remain unknown. We found that low seawater pH induced oxidative stress and DNA damage, decreasing growth rates, fecundity, and lifespans in the parental generation, whereas deleterious effects on in vivo endpoints in F1 and F2 offspring were less evident. The findings suggest that multigenerational adaptive effects play a role in antioxidant abilities and other defense mechanisms. OA-induced DNA damage, including double-strand breaks (DSBs), was fully repaired in F1 offspring of parents exposed to OA for 7 days, indicating that an adaptation mechanism may be the major driving force behind multigenerational adaptive effects. Analysis of epigenetic modification in response to OA involved examination of histone modification of DNA repair genes and a chromatin immunoprecipitation assay, as Bombus koreanus has no methylation pattern for CpG in its genome. We conclude that DSBs, DNA repair, and histone modification play important roles in multigenerational plasticity in response to OA in an asexual monogonont rotifer.

Development of metal adaptation in a tropical marine zooplankton

Tropical marine ecosystems are highly vulnerable to pollution and climate change. It is relatively unknown how tropical species may develop an increased tolerance to these stressors and the cost of adaptations. We addressed these issues by exposing a keystone tropical marine copepod, Pseudodiaptomus annandalei, to copper (Cu) for 7 generations (F1–F7) during three treatments: control, Cu and pCu (the recovery treatment). In F7, we tested the “contaminant-induced climate change sensitivity” hypothesis (TICS) by exposing copepods to Cu and extreme temperature. We tracked fitness and productivity of all generations. In F1, Cu did not affect survival and grazing but decreased nauplii production. In F2-F4, male survival, grazing, and nauplii production were lower in Cu, but recovered in pCu, indicating transgenerational plasticity. Strikingly, in F5-F6 nauplii production of Cu-exposed females increased, and did not recover in pCu. The earlier result suggests an increased Cu tolerance while the latter result revealed its cost. In F7, extreme temperature resulted in more pronounced reductions in grazing, and nauplii production of Cu or pCu than in control, supporting TICS. The results suggest that widespread pollution in tropical regions may result in high vulnerability of species in these regions to climate change.