Evolutionary mechanisms underpinning fitness response to multiple stressors in Daphnia

History of exposure to copper influences transgenerational gene expression responses in Daphnia magna

The establishment of transgenerational effects following chemical exposure is a powerful phenomenon, capable of modulating ecosystem health beyond exposure periods. This study assessed the transgenerational effects occurring due to copper exposure in the invertebrate D. magna at the transcriptional level, while evaluating the role of exposure history on such responses. Thus, daphnids acclimated for several generations in a copper vs. clean medium were then exposed for one generation (F0) to this metal, and monitored for the following non-exposed generations (F1, F2 and F3). Organisms differing in exposure histories showed remarkably different transcriptional profiles at the F0, with naïve organisms being more profoundly affected. These trends were confirmed for F3 treatments, which presented different transcriptional patterns for genes involved in detoxification, oxidative stress, DNA damage repair, circadian clock functioning and epigenetic regulation. Furthermore, regardless of exposure history, a great number of histone modifier genes were always found transcriptionally altered, thus suggesting the involvement of histone modifications in the response of Daphnia to metal exposure. Lastly, remarkably distinct transgenerational transcriptional responses were found between naïve and non-naïve organisms, thereby highlighting the influence of exposure history on gene expression and confirming the capacity of metals to determine transgenerational transcriptional effects across non-exposed generations.

Zooplankton vulnerability to glyphosate exacerbated by global change

Anthropogenic activities generate a severe footprint at a global scale. Intensive agriculture is a global change driver that affects aquatic systems due to the discharge of pollutants. This situation can be modified or aggravated by other aspects, such as the disturbance history and other global change factors. Following our study line, it is necessary to evaluate how the disturbance history combined with temperature changes can affect the functioning of aquatic systems. The objectives of this study were divided into two phases. The objectives of phase 1 were to induce vulnerability in Daphnia magna populations through a disturbance history based on sublethal glyphosate concentration exposure under different temperature conditions (20 °C and 25 °C). In phase 2, vulnerability was assessed through the exposure to subsequent stressors (starvation, increased salinity and paracetamol) combined with changes in temperature. During the glyphosate exposure period in phase 1, differences were observed in the D. magna populations with respect to temperature, with lower abundance at 25 °C than at 20 °C. However, no differences were observed in abundance regarding glyphosate treatment. The results obtained in phase 2 with the new stressors combined with temperature changes in both directions, revealed stronger effects in vulnerable populations than in control populations. In addition, the temperature changes modulated the effects in the starvation and increased salinity tests. Agrochemical sublethal concentrations induce vulnerability in D. magna populations and inflicted temperature changes can act as a modulating factor for this vulnerability, showing the complexity in assessing the responses under the multiple scenarios associated with global 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.

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome

Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.

Sublethal exposure to agrochemicals impairs zooplankton ability to face future global change challenges

Intensive agriculture is characterized by the application of multiple stressors that damage aquatic systems. Currently, ecotoxicological evaluations are considered insufficient to understand the environmental risks of stressor mixtures and their consequences in ecosystems. In addition, future global change scenarios could alter the predicted effects of agrochemicals in aquatic systems based on single exposures, making it necessary to consider the history of environmental disturbances that may result in vulnerability to subsequent environmental changes. The objectives of this study were to induce disturbance histories by exposure to sublethal glyphosate concentrations in microcosms and to assess whether this disturbance results in vulnerable populations using Daphnia magna as the target species. Populations were considered vulnerable if their sensitivity to new stressors (inanition, temperature and salinity) was higher than that of undisturbed populations. To induce disturbance history, microcosm aquatic communities (two cladocerans and one microalgae) were exposed to two glyphosate sublethal concentrations (below the No Observed Effect Concentration, NOEC values for D. magna, 0.1 and 1 mg L^-1) in microcosms under controlled conditions in a culture chamber for 48 days. After this period, no significant differences were observed with respect to the control microcosms in the selected parameters (cladoceran abundance, microalgae cell abundance, microalgae colony formation, pH and dissolved oxygen). To test vulnerability, our target D. magna populations, which were previously exposed to different glyphosate treatments, were subjected to inanition, elevated temperature and salinity. Our results showed that D. magna populations with disturbance history performed worse in all the scenarios compared to the populations from undisturbed conditions. These results underscore the need to study how environmental disturbance history influences population responses to new and future stressors. Moreover, our findings raise concern regarding the sublethal effects of pesticides on aquatic populations.

Thermal stress and mutation accumulation increase heat shock protein expression in Daphnia

Understanding the short- and long-term consequences of climate change is a major challenge in biology. For aquatic organisms, temperature changes and drought can lead to thermal stress and habitat loss, both of which can ultimately lead to higher mutation rates. Here, we examine the effect of high temperature and mutation accumulation on gene expression at two loci from the heat shock protein (HSP) gene family, HSP60 and HSP90. HSPs have been posited to serve as 'mutational capacitors' given their role as molecular chaperones involved in protein folding and degradation, thus buffering against a wide range of cellular stress and destabilization. We assayed changes in HSP expression across 5 genotypes of Daphnia magna, a sentinel species in ecology and environmental biology, with and without acute exposure to thermal stress and accumulated mutations. Across genotypes, HSP expression increased ~ 6× in response to heat and ~ 4× with mutation accumulation, individually. Both factors simultaneously (lineages with high mutation loads exposed to high heat) increased gene expression ~ 23×-much more than that predicted by an additive model. Our results corroborate suggestions that HSPs can buffer against not only the effects of heat, but also mutations-a combination of factors both likely to increase in a warming world.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-022-10209-1.

Increased food availability reducing the harmful effects of microplastics strongly depends on the size of microplastics

Shallow lakes and ponds, providing essential ecological and environmental services, are simultaneously disrupted by various pollutants of emerging concern (PECs). As a group of PECs, microplastics (MPs) ubiquitously found in freshwater are toxic to a huge variety of organisms. However, the consequence of secondary factors such as food quantity determining MPs toxicity, and the corresponding water safety risks await assessment is still poorly understood. Accordingly, we investigated how MPs across three particle sizes (10, 1 and 0.07 µm) interacted with food abundance to affect survival, reproduction and population performance in the waterflea Daphnia magna. Across multiple population traits, we found that MPs toxicity on Daphnia population performance was attenuated by higher food quantity, but this attenuation size was strongly dependent on MPs size. Path analysis results showed population growth rate was mainly constrained by reduced survival rather than fecundity. Furthermore, the additive null model revealed that the interactive effects of food abundance and MPs were predominately recognized as synergism and trait dependency. The present findings underscore the importance of considering the complexity of interactions that can occur in the wild, when assessing the effects of plastics pollution on population dynamics of the basic trophic level in lakes and ponds.

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.