Haemoglobin-mediated response to hyper-thermal stress in the keystone species Daphnia magna

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high-throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

Environmental Stress and the Morphology of Daphnia pulex

AbstractMorphological variation is sometimes used as an indicator of environmental stress in animals. Here, we assessed how multiple morphological traits covaried in Daphnia pulex exposed to five common forms of environmental stress (high temperature, presence of predator cues, high salinity, low food abundance, and low Ca). We measured animal body length, body width, head width, eyespot diameter, and tail spine length along with mass in animals of five different ages (3, 6, 9, 12, and 15 d). There were strong allometric relationships among all morphological traits in reference animals and strong univariate effects of environmental stress on body mass and body length. We found that environmental stressors altered bivariate relationships between select pairwise combinations of morphological traits, with effects being dependent on animal age. Multivariate analyses further revealed high connectivity among body size-related traits but that eyespot diameter and tail spine length were less tightly associated with body size. Animals exposed to natural lake water with and without supplemental food also varied in morphology, with body size differences being suggestive of starvation and other unknown nutritional deficiencies. Yet our results demonstrate that the scaling of body morphological traits of Daphnia pulex is largely invariant with possible context-dependent plasticity in eye size and tail spine lengths. The strong coordination of traits indicates tight molecular coordination of body size during development despite strong and varied environmental stress.

Genome-wide identification of fatty acid synthesis genes, fatty acid profiles, and life parameters in two freshwater water flea Daphnia magna strains

The freshwater water flea Daphnia magna is a planktonic animal belonging to the Cladocera. To evaluate differences between two D. magna strains (KIT and NIES) in terms of life parameters and fatty acid profiles, we examined several endpoints. In the D. magna KIT strain, the numbers of total and cumulative offspring were lower at 23 °C and higher at 14 °C than in the D. magna NIES strain. However, at 14 °C, the D. magna KIT strain showed an increased lifespan. Although the n-3/n-6 polyunsaturated fatty acids (PUFA) ratio was always decreased at a low temperature, the PUFA ratio in the KIT strain had a higher value on day 3 than the NIES strain, which gave it higher adaptability to low temperature. In addition, we identified the elongation of very long chain fatty acids (elovl) and fatty acid desaturase (fad) genes, which are involved in fatty acid biosynthesis pathways, in the genomes of both D. magna KIT and NIES. The Elovl and Fad genes in both D. magna strains were highly conserved, including tandem duplicated Elovl 1/7 genes. This study provides new information about the molecular basis for the difference in temperature sensitivity between two strains of D. magna.

Historical exposure to chemicals reduces tolerance to novel chemical stress in Daphnia (waterflea)

Until the last few decades, anthropogenic chemicals used in most production processes have not been comprehensively assessed for their risk and impact on wildlife and humans. They are transported globally and usually end up in the environment as unintentional pollutants, causing long‐term adverse effects. Modern toxicology practices typically use acute toxicity tests of unrealistic concentrations of chemicals to determine their safe use, missing pathological effects arising from long‐term exposures to environmentally relevant concentrations. Here, we study the transgenerational effect of environmentally relevant concentrations of five chemicals on the priority list of international regulatory frameworks on the keystone species Daphnia magna. We expose Daphnia genotypes resurrected from the sedimentary archive of a lake with a known history of chemical pollution to the five chemicals to understand how historical exposure to chemicals influences adaptive responses to novel chemical stress. We measure within‐ and transgenerational plasticity in fitness‐linked life history traits following exposure of “experienced” and “naive” genotypes to novel chemical stress. As the revived Daphnia originate from the same genetic pool sampled at different times in the past, we are able to quantify the long‐term evolutionary impact of chemical pollution by studying genome‐wide diversity and identifying functional pathways affected by historical chemical stress. Our results suggest that historical exposure to chemical stress causes reduced genome‐wide diversity, leading to lower cross‐generational tolerance to novel chemical stress. Lower tolerance is underpinned by reduced gene diversity at detoxification, catabolism and endocrine genes in experienced genotypes. We show that these genes sit within pathways that are conserved and potential chemical targets in other species, including humans.

Elevated temperature alleviates benzophenone-3 toxicity in Daphnia magna

Water temperature rises due to thermal discharge and global warming and the potential resulting impacts on the ecotoxicity of emerging chemicals are a growing concern. Benzophenone-3 (BP-3) is an ultraviolet filter added to personal care and plastic products, which is detected at highest concentrations during the hot summer season. This study aimed to investigate the effect of elevated temperature on acute (48 h) and chronic (21 d) BP-3 toxicity in Daphnia magna. Neonates (<24 h) acclimated at 28 °C showed much lower acute toxicity (EC₅₀ = 3.91 and 2.69 mg L^-1 at 20 and 28 °C, respectively) than those acclimated at 20 °C (EC₅₀ = 2.96 and 2.04 mg L^-1 at 20 and 28 °C, respectively). The body length, embryonic development, and the number of offspring in D. magna offspring exposed to BP-3 for 21 d were significantly decreased after exposure to 0.8 mg L^-1 BP-3 at 20 °C. However, these adverse effects of BP-3 in D. magna were significantly ameliorated at 28 °C. Under these conditions, stress response genes such as Hb (hemoglobin), Hsp70 (heat shock protein), Cyp4 (cytochrome P450), and GST (glutathione-S-transferase) were significantly upregulated. These findings suggest that elevated temperature activated stress responses in D. magna, leading to enhanced protection against BP-3 toxicity. This study will contribute to a better understanding of the ecotoxicological impacts of toxic chemicals on aquatic organisms at elevated temperature.

Generational sensitivity alteration in Chironomus yoshimatsui to carbamate and pharmaceutical chemicals and the effect on Catalase, CYP450, and hemoglobin gene transcription

To ascertain the tolerance mechanisms of aquatic organisms to artificial chemicals, intergenerational sensitivity changes of Chironomus yoshimatsui to a carbamate pesticide (pirimicarb) and pharmaceutical chemical (diazepam) were investigated. The larvae (<48-h-old) in each generation were exposed to both chemicals for 48 h and then the surviving chironomids were cultured until the fifth generation (F0-F4) without chemical addition. The 48-h 50% effective concentration (EC₅₀) value of chironomids was determined for each generation. In the pirimicarb treatment group, the EC₅₀ values significantly increased in F3 and F4, and those in the diazepam treatment group slightly increased. Catalase, Cytochrome P450 and hemoglobin (Hb) mRNA levels were monitored to see whether these were related to the trans-generational sensitivity. Although the generalized linear model results showed that the sensitivity to diazepam was slightly increased in the diazepam treatment, we could not find any mRNA levels related to sensitivity alteration. In contrast, the model approach showed that the chironomids exposed to pirimicarb trans-generationally became tolerant with increasing Hb mRNA levels. Therefore, they might decrease their chemical stress by modifying Hb gene transcription.

Breaking free from thermodynamic constraints: thermal acclimation and metabolic compensation in a freshwater zooplankton species

Respiration rates of ectothermic organisms are affected by environmental temperatures, and sustainable metabolism at high temperatures sometimes limits heat tolerance. Organisms are hypothesized to exhibit acclimatory metabolic compensation effects, decelerating their metabolic processes below Arrhenius expectations based on temperature alone. We tested the hypothesis that either heritable or plastic heat tolerance differences can be explained by metabolic compensation in the eurythermal freshwater zooplankton crustacean Daphnia magna We measured respiration rates in a ramp-up experiment over a range of assay temperatures (5-37°C) in eight genotypes of D. magna representing a range of previously reported acute heat tolerances and, at a narrower range of temperatures (10-35°C), in D. magna with different acclimation history (either 10 or 25°C). We discovered no difference in temperature-specific respiration rates between heat-tolerant and heat-sensitive genotypes. In contrast, we observed acclimation-specific compensatory differences in respiration rates at both extremes of the temperature range studied. Notably, there was a deceleration of oxygen consumption at higher temperature in 25°C-acclimated D. magna relative to their 10°C-acclimated counterparts, observed in active animals, a pattern corroborated by similar changes in filtering rate and, partly, by changes in mitochondrial membrane potential. A recovery experiment indicated that the reduction of respiration was not caused by irreversible damage during exposure to a sublethal temperature. Response time necessary to acquire the respiratory adjustment to high temperature was lower than for low temperature, indicating that metabolic compensation at lower temperatures requires slower, possibly structural changes.

Linking multiple biomarker responses in Daphnia magna under thermal stress

Temperature is an important abiotic variable that greatly influences the performance of aquatic ectotherms, especially under current anthropogenic global warming and thermal discharges. The aim of the present study was to evaluate thermal stress (20 °C vs 28 °C) in Daphnia magna over 21 d, focusing on the linkage among molecular and biochemical biomarker responses. Thermal stress significantly increased the levels of reactive oxygen species (ROS) and lipid peroxidation, especially in the 3-d short-term exposure treatment. This change in the ROS level was also correlated with mitochondrial membrane damage. These findings suggest that oxidative stress is the major pathway for thermally-induced toxicity of D. magna. Additionally, the expression levels of genes related to hypoxia (Hb), development (Vtg1), and sex determination (Dsx1-α, Dsx1-β, and Dsx2) were greatly increased by elevated temperature in a time-dependent manner. The cellular energy allocation was markedly decreased at the elevated temperature in the 3-d exposure treatment, mainly due to carbohydrates consumption for survival (oxidative stress defense). The present study showed that linking multiples biomarker responses are crucial for understanding the underlying mechanism of thermal stress on D. magna.

Daphnia magna modifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference

Caloric restriction (CR) produces clear phenotypic effects within and between generations of the model crustacean Daphnia magna. We have previously established that micro-RNAs and cytosine methylation change in response to CR in this organism, and we demonstrate here that CR has a dramatic effect on gene expression. Over 6,000 genes were differentially expressed between CR and well-fed D. magna, with a bias towards up-regulation of genes under caloric restriction. We identified a highly expressed haemoglobin gene that responds to CR by changing isoform proportions. Specifically, a transcript containing three haem-binding erythrocruorin domains was strongly down-regulated under CR in favour of transcripts containing fewer or no such domains. This change in the haemoglobin mix is similar to the response to hypoxia in Daphnia, which is mediated through the transcription factor hypoxia-inducible factor 1, and ultimately the mTOR signalling pathway. This is the first report of a role for haemoglobin in the response to CR. We also observed high absolute expression of superoxide dismutase (SOD) in normally fed individuals, which contrasts with observations of high SOD levels under CR in other taxa. However, key differentially expressed genes, like SOD, were not targeted by differentially expressed micro-RNAs. Whether the link between haemoglobin and CR occurs in other organisms, or is related to the aquatic lifestyle, remains to be tested. It suggests that one response to CR may be to simply transport less oxygen and lower respiration.

Eco-Corona vs Protein Corona: Effects of Humic Substances on Corona Formation and Nanoplastic Particle Toxicity in Daphnia magna

Despite many studies on the toxicity of nanoplastic particles (NPPs) to aquatic invertebrates, the effects of ecological constituents such as humic substances (HSs) are often neglected. In our study, Daphnia magna was used to evaluate the effects of three HSs, natural organic matter (NOM), fulvic acid (FA), and humic acid (HA), on NPP toxicity and corona formation. Acute toxicities of NPPs were reduced by all HSs at environmentally relevant concentrations. NPPs elicited the upregulation of all genes related to detoxification, oxidative stress, and endocrine activity after 7 days of exposure. The presence of NOM or HA resulted in the mitigation of gene expression, whereas significantly higher upregulation of all of the genes was observed with FA. The presence of FA led to increased protein adsorption on NPPs in D. magna culture medium (eco-corona, EC) and homogenates (protein corona, PC), while there was less adsorption in the presence of HA. The highly abundant proteins identified in EC are involved in immune defense, cell maintenance, and antipredator response, while those in PC are responsible for lipid transport, antioxidant effects, and estrogen mediation. Our findings revealed the key influence of HSs on the toxicity of NPPs and provide an analytical and conceptual foundation for future study.

Hemoglobin in Arthropods-Daphnia as a Model

Hemoglobin is the respiratory protein of many arthropods, enhancing the oxygen transport capacity of the hemolymph. One example, that has been subject of extensive studies, is the hemoglobin of the crustacean genus Daphnia. Here the characteristics of this oxygen binding protein are reviewed. The genetic structure is the result of repeated duplication events in the evolution, leading to a variety of di-domain isoforms. Adjustments to environmental changes thus result from differential expression of these paralogs. The biochemical properties, including spectral characteristics, concentration ranges, molecular mass of monomers and native oligomers, are compared. Structural differences between isoforms can be correlated to functional properties of oxygen binding characteristics. The mechanism of hemoglobin induction via hypoxia-inducible factor 1 allows the response to altered oxygen and temperature conditions. Changes of the hemoglobin suite in quantity and functional quality can be linked to their benefits for the animals' physiological performance. However, there is a large inter- and intra-specific variability of this induction potential. The consequences of altered hemoglobin characteristics for the animals' success within their habitat are discussed.

Transgenerational response to early spring warming in Daphnia

Temperature and photoperiod regulate key fitness traits in plants and animals. However, with temperature increase due to global warming, temperature cue thresholds are experienced at shorter photoperiods, disrupting the optimal seasonal timing of physiological, developmental and reproductive events in many species. Understanding the mechanisms of adaptation to the asynchrony between temperature and photoperiod is key to inform our understanding of how species will respond to global warming. Here, we studied the transgenerational mechanisms of responses of the cyclical parthenogen Daphnia magna to different photoperiod lengths co-occurring with warm temperature thereby assessing the impact of earlier spring warming on its fitness. Daphnia uses temperature and photoperiod cues to time dormancy, and to switch between sexual and asexual reproduction. Daphnia life cycle offers the opportunity to measure the relative contribution of plastic and genetic responses to environmental change across generations and over evolutionary time. We use transgenerational common garden experiments on three populations 'resurrected' from a biological archive experiencing temperature increase over five decades. Our results suggest that response to early spring warming evolved underpinned by a complex interaction between plastic and genetic mechanisms while a positive maternal contribution at matching environments between parental and offspring generation was also observed.

Predictability of the impact of multiple stressors on the keystone species Daphnia

Eutrophication and climate change are two of the most pressing environmental issues affecting up to 50% of aquatic ecosystems worldwide. Mitigation strategies to reduce the impact of environmental change are complicated by inherent difficulties of predicting the long-term impact of multiple stressors on natural populations. Here, we investigated the impact of temperature, food levels and carbamate insecticides, in isolation and in combination, on current and historical populations of the freshwater grazer Daphnia. We used common garden and competition experiments on historical and modern populations of D. magna ‘resurrected’ from a lake with known history of anthropogenic eutrophication and documented increase in ambient temperature over time. We found that these populations response dramatically differed between single and multiple stressors. Whereas warming alone induced similar responses among populations, warming combined with insecticides or food limitation resulted in significantly lower fitness in the population historically exposed to pesticides. These results suggest that the negative effect of historical pesticide exposure is magnified in the presence of warming, supporting the hypothesis of synergism between chemical pollution and other stressors.

Automated measurement of upper thermal limits in small aquatic animals

We present a method for automating the measurement of upper thermal limits in small aquatic organisms. Upper thermal limits are frequently defined by the cessation of movement at high temperature, with measurement being performed by manual observation. Consequently, estimates of upper thermal limits may be subject to error and bias, both within and among observers. Our method utilises video-based tracking software to record the movement of individuals when exposed to high, lethal temperatures. We develop an algorithm in the R computing language that can objectively identify the loss of locomotory function from tracking data. Using independent experimental data, we validate our approach by demonstrating the expected response in upper thermal limits to acclimation temperature.

Thermal evolution offsets the elevated toxicity of a contaminant under warming: A resurrection study in Daphnia magna

Synergistic interactions between temperature and contaminants are a major challenge for ecological risk assessment, especially under global warming. While thermal evolution may increase the ability to deal with warming, it is unknown whether it may also affect the ability to deal with the many contaminants that are more toxic at higher temperatures. We investigated how evolution of genetic adaptation to warming affected the interactions between warming and a novel stressor: zinc oxide nanoparticles (nZnO) in a natural population of Daphnia magna using resurrection ecology. We hatched resting eggs from two D. magna subpopulations (old: 1955-1965, recent: 1995-2005) from the sediment of a lake that experienced an increase in average temperature and in recurrence of heat waves but was never exposed to industrial waste. In the old "ancestral" subpopulation, exposure to a sublethal concentration of nZnO decreased the intrinsic growth rate, metabolic activity, and energy reserves at 24°C but not at 20°C, indicating a synergism between warming and nZnO. In contrast, these synergistic effects disappeared in the recent "derived" subpopulation that evolved a lower sensitivity to nZnO at 24°C, which indicates that thermal evolution could offset the elevated toxicity of nZnO under warming. This evolution of reduced sensitivity to nZnO under warming could not be explained by changes in the total internal zinc accumulation but was partially associated with the evolution of the expression of a key metal detoxification gene under warming. Our results suggest that the increased sensitivity to the sublethal concentration of nZnO under the predicted 4°C warming by the end of this century may be counteracted by thermal evolution in this D. magna population. Our results illustrate the importance of evolution to warming in shaping the responses to another anthropogenic stressor, here a contaminant. More general, genetic adaptation to an environmental stressor may ensure that synergistic effects between contaminants and this environmental stressor will not be present anymore.

Haemoglobin-mediated response to hyper-thermal stress in the keystone species Daphnia magna

Anthropogenic global warming has become a major geological and environmental force driving drastic changes in natural ecosystems. Due to the high thermal conductivity of water and the effects of temperature on metabolic processes, freshwater ecosystems are among the most impacted by these changes. The ability to tolerate changes in temperature may determine species long-term survival and fitness. Therefore, it is critical to identify coping mechanisms to thermal and hyper-thermal stress in aquatic organisms. A central regulatory element compensating for changes in oxygen supply and ambient temperature is the respiratory protein haemoglobin (Hb). Here, we quantify Hb plastic and evolutionary response in Daphnia magna subpopulations resurrected from the sedimentary archive of a lake with known history of increase in average temperature and recurrence of heat waves. By measuring constitutive changes in crude Hb protein content among subpopulations, we assessed evolution of the Hb gene family in response to temperature increase. To quantify the contribution of plasticity in the response of this gene family to hyper-thermal stress, we quantified changes in Hb content in all subpopulations under hyper-thermal stress as compared to nonstressful temperature. Further, we tested competitive abilities of genotypes as a function of their Hb content, constitutive and induced. We found that Hb-rich genotypes have superior competitive abilities as compared to Hb-poor genotypes under hyper-thermal stress after a period of acclimation. These findings suggest that whereas long-term adjustment to higher occurrence of heat waves may require a combination of plasticity and genetic adaptation, plasticity is most likely the coping mechanism to hyper-thermal stress in the short term. Our study suggests that with higher occurrence of heat waves, Hb-rich genotypes may be favoured with potential long-term impact on population genetic diversity.

Evolutionary aspects of resurrection ecology: Progress, scope, and applications-An overview

This perspective provides an overview to the Special Issue on Resurrection Ecology (RE). It summarizes the contributions to this Special Issue, and provides background information and future prospects for the use of RE in both basic and applied evolutionary studies.