Identification of pathways, gene networks, and paralogous gene families in Daphnia pulex responding to exposure to the toxic cyanobacterium Microcystis aeruginosa

Changes in population fitness and gene co-expression networks reveal the boosted impact of toxic cyanobacteria on Daphnia magna through microplastic exposure

The concomitant prevalence of toxic cyanobacteria blooms and plastic pollution in aquatic ecosystems is emerging as a pressing global water pollution dilemma. While toxic cyanobacteria and microplastics (MPs) can each independently exert significant impacts on aquatic biota, the magnitude and trajectory of the combined interactions remains rudimentary. In this study, we evaluated how MPs influences cyanobacterial stress on keystone grazer Daphnia, focusing on population, individual, biochemical and toxicogenomic signatures. We found that toxic Microcystis (TM) adversely affected the fitness of Daphnia populations (intrinsic rate of population increase), and these adverse effects were amplified in the presence of MPs. Through detailed observation, it was ascertained that MPs promoted the ingestion of TM, culminating in enhanced microcystin bioaccumulation. Using the Eco-Evo model, we found that there was potential absence of correlation between the MPs toxicity and the effect size of MPs on the TM. Utilizing gene set enrichment analysis (GSEA), we further identified a marked suppression of molecular pathways and entities crucial to individual growth and development in the TM-MPs consortium compared to exposure to TM alone. The present study provides important insights about the influence of MPs on cyanobacteria toxicity and the prediction the risk of harmful algal blooms in aquatic ecosystems.

Maternal effects in the model system Daphnia: the ecological past meets the epigenetic future

Maternal effects have been shown to play influential roles in many evolutionary and ecological processes. However, understanding how environmental stimuli induce within-generation responses that transverse across generations remains elusive, particularly when attempting to segregate confounding effects from offspring genotypes. This review synthesizes literature regarding resource- and predation-driven maternal effects in the model system Daphnia, detailing how the maternal generation responds to the environmental stimuli and the maternal effects seen in the offspring generation(s). Our goal is to demonstrate the value of Daphnia as a model system by showing how general principles of maternal effects emerge from studies on this system. By integrating the results across different types of biotic drivers of maternal effects, we identified broadly applicable shared characteristics: 1. Many, but not all, maternal effects involve offspring size, influencing resistance to starvation, infection, predation, and toxins. 2. Maternal effects manifest more strongly when the offspring's environment is poor. 3. Strong within-generation responses are typically associated with strong across-generation responses. 4. The timing of the maternal stress matters and can raise or lower the magnitude of the effect on the offspring's phenotype. 5. Embryonic exposure effects could be mistaken for maternal effects. We outline questions to prioritize for future research and discuss the possibilities for integration of ecologically relevant studies of maternal effects in natural populations with the molecular mechanisms that make them possible, specifically by addressing genetic variation and incorporating information on epigenetics. These small crustaceans can unravel how and why non-genetic information gets passed to future generations.

p38 MAPK determines the sensitivity of the aquatic keystone species Moina macrocopa to toxic Microcystis: Insights into potential biomarker applications

Harmful cyanobacterial blooms, particularly those caused by Microcystis species, pose significant ecological threats to freshwater environments by negatively impacting zooplankton populations, essential components of aquatic food webs. Understanding the molecular mechanisms underlying zooplankton responses to these toxic blooms is crucial for assessing and mitigating these impacts. The mitogen-activated protein kinase (MAPK) pathway, known for its critical role in stress response signaling, offers a promising area of study to elucidate these mechanisms. However, the specific involvement of MAPK in zooplankton responses to cyanobacterial stress remains unclear. In this study, we identify and characterize the p38 MAPK gene (MmMAPK) from the zooplankton Moina macrocopa. The gene contains conserved structural elements typical of MAPKs, including a Thr-Gly-Tyr (TGY) motif and a substrate-binding site, Ala-Thr-Arg-Trp (ATRW), indicating its potential functional relevance in stress signaling pathways. Expression analysis reveals a significant upregulation of MmMAPK in M. macrocopa upon exposure to toxic Microcystis, suggesting its role in mediating the organism's stress response. Furthermore, RNA interference (RNAi) experiments demonstrate that knockdown of MmMAPK results in reduced survival and decreased body size, particularly under cyanobacterial stress, underscoring its importance in maintaining stress sensitivity. These findings provide new insights into the molecular mechanisms by which M. macrocopa responds to harmful algal blooms and highlight the potential of MmMAPK as a biomarker for ecological risk assessment and management of cyanobacterial pollution in freshwater ecosystems.

A short-term exposure to saxitoxin triggers a multitude of deleterious effects in Daphnia magna at levels deemed safe for human health

Harmful algal blooms and the toxins produced during these events are a human and environmental health concern worldwide. Saxitoxin and its derivatives are potent natural aquatic neurotoxins produced by certain freshwater cyanobacteria and marine algae species during these bloom events. Saxitoxins effects on human health are well studied, however its effects on aquatic biota are still largely unexplored. This work aims at evaluating the effects of a pulse acute exposure (24 h) of the model cladoceran Daphnia magna to 30 μg saxitoxin L-1, which corresponds to the safety guideline established by the World Health Organization (WHO) for these toxins in recreational freshwaters. Saxitoxin effects were assessed through a comprehensive array of biochemical (antioxidant enzymes activity and lipid peroxidation), genotoxicity (alkaline comet assay), neurotoxicity (total cholinesterases activity), behavioral (swimming patterns), physiological (feeding rate and heart rate), and epigenetic (total 5-mC DNA methylation) biomarkers. Exposure resulted in decreased feeding rate, heart rate, total cholinesterases activity and catalase activity. Contrarily, other antioxidant enzymes, namely glutathione-S-transferases and selenium-dependent Glutathione peroxidase had their activity increased, together with lipid peroxidation levels. The enhancement of the antioxidant enzymes was not sufficient to prevent oxidative damage, as underpinned by lipid peroxidation enhancement. Accordingly, average DNA damage level was significantly increased in STX-exposed daphnids. Total DNA 5-mC level was significantly decreased in exposed organisms. Results showed that even a short-term exposure to saxitoxin causes significant effects on critical molecular and cellular pathways and modulates swimming patterns in D. magna individuals. This study highlights sub-lethal effects caused by saxitoxin in D. magna, suggesting that these toxins may represent a marked challenge to their thriving even at a concentration deemed safe for humans by the WHO.

MicroRNA miR-210 Modulates the Water Flea Daphnia magna Response to Cyanobacterial Toxicity

As a key form of post-transcriptional regulation, microRNAs (miRNAs) regulate gene expression by binding to target mRNAs, leading to mRNA decay or translational repression. Recently, the role of miRNAs in the response of aquatic organisms to environmental stressors has emerged. Daphnia, widely distributed cladocerans, play a crucial role in aquatic ecosystems. Cyanobacterial blooms often cause Daphnia populations to decrease, thereby disrupting ecosystem functionality and water quality. However, the post-transcriptional mechanisms behind Daphnia's response to toxic cyanobacteria are insufficiently understood. This study investigated the role of miR-210, a multifunctional miRNA involved in stress response and toxicity pathways, and its target genes (MLH3, CDHR5, and HYOU1) in two Daphnia magna clones exposed to toxic Microcystis aeruginosa. Results showed that M. aeruginosa inhibited somatic growth rates, led to microcystin accumulation, caused abnormal ultrastructural alterations in the digestive tract, and induced DNA damage in both clones. Notably, exposure significantly increased miR-210 expression and decreased the expression of its target genes compared with the controls. We identified miR-210s regulation on clonal-tolerance variations in D. magna to M. aeruginosa, emphasizing miRNAs' contribution to adaptive responses. Our work uncovered a novel post-transcriptional mechanism of cyanobacterial impact on zooplankton and provided essential insights for assessing cyanobacterial toxicity risks.

Exploring the Sublethal Impacts of Cu and Zn on Daphnia magna: a transcriptomic perspective

Metal contamination of aquatic environments remains a major concern due to their persistence. The water flea Daphnia magna is an important model species for metal toxicity studies and water quality assessment. However, most research has focused on physiological endpoints such as mortality, growth, and reproduction in laboratory settings, as well as neglected toxicogenomic responses. Copper (Cu) and zinc (Zn) are essential trace elements that play crucial roles in many biological processes, including iron metabolism, connective tissue formation, neurotransmitter synthesis, DNA synthesis, and immune function. Excess amounts of these metals result in deviations from homeostasis and may induce toxic responses. In this study, we analyzed Daphnia magna transcriptomic responses to IC5 levels of Cu (120 µg/L) and Zn (300 µg/L) in environmental water obtained from a pristine lake with adjusted water hardness (150 mg/L CaCO3). The study was carried out to gain insights into the Cu and Zn regulated stress response mechanisms in Daphnia magna at transcriptome level. A total of 2,688 and 3,080 genes were found to be differentially expressed (DEG) between the control and Cu and the control and Zn, respectively. There were 1,793 differentially expressed genes in common for both Cu and Zn, whereas the number of unique DEGs for Cu and Zn were 895 and 1,287, respectively. Gene ontology and KEGG pathways enrichment were carried out to identify the molecular functions and biological processes affected by metal exposures. In addition to well-known biomarkers, novel targets for metal toxicity screening at the genomic level were identified.

Mechanisms of harmful effects of Microcystis aeruginosa on a brackish water organism Moina mongolica based on physiological and transcriptomic responses

To investigate the detrimental impacts of cyanobacterial bloom, specifically Microcystis aeruginosa, on brackish water ecosystems, the study used Moina mongolica, a cladoceran species, as the test organism. In a chronic toxicology experiment, the survival and reproductive rates of M. mongolica were assessed under M. aeruginosa stress. It was observed that the survival rate of M. mongolica fed with M. aeruginosa significantly decreased with time and their reproduction rate dropped to zero, while the control group remained maintained stable and normal reproduction. To further explore the underlying molecular mechanisms of the effects of M. aeruginosa on M. mongolica, we conducted a transcriptomic analysis on newly hatched M. mongolica cultured under different food conditions for 24 h. The results revealed significant expression differences in 572 genes, with 233 genes significantly up-regulated and 339 genes significantly down-regulated. Functional analysis of these differentially expressed genes identified six categories of physiological functional changes, including nutrition and metabolism, oxidative phosphorylation, neuroimmunology, cuticle and molting, reproduction, and programmed cell death. Based on these findings, we outlined the basic mechanisms of microcystin toxicity. The discovery provides critical insights into the mechanisms of Microcystis toxicity on organisms and explores the response mechanisms of cladocerans under the stress of Microcystis.

Biotests in Cyanobacterial Toxicity Assessment-Efficient Enough or Not?

Cyanobacteria are a diverse group of organisms known for producing highly potent cyanotoxins that pose a threat to human, animal, and environmental health. These toxins have varying chemical structures and toxicity mechanisms and several toxin classes can be present simultaneously, making it difficult to assess their toxic effects using physico-chemical methods, even when the producing organism and its abundance are identified. To address these challenges, alternative organisms among aquatic vertebrates and invertebrates are being explored as more assays evolve and diverge from the initially established and routinely used mouse bioassay. However, detecting cyanotoxins in complex environmental samples and characterizing their toxic modes of action remain major challenges. This review provides a systematic overview of the use of some of these alternative models and their responses to harmful cyanobacterial metabolites. It also assesses the general usefulness, sensitivity, and efficiency of these models in investigating the mechanisms of cyanotoxicity expressed at different levels of biological organization. From the reported findings, it is clear that cyanotoxin testing requires a multi-level approach. While studying changes at the whole-organism level is essential, as the complexities of whole organisms are still beyond the reach of in vitro methodologies, understanding cyanotoxicity at the molecular and biochemical levels is necessary for meaningful toxicity evaluations. Further research is needed to refine and optimize bioassays for cyanotoxicity testing, which includes developing standardized protocols and identifying novel model organisms for improved understanding of the mechanisms with fewer ethical concerns. In vitro models and computational modeling can complement vertebrate bioassays and reduce animal use, leading to better risk assessment and characterization of cyanotoxins.

Changes in key life-history traits and transcriptome regulations of marine rotifer Brachionus plicatilis in eliminating harmful algae Phaeocystis

Rotifers have great potential in controlling the harmful algae Phaeocystis blooms that frequently occur in coastal waters. To evaluate the effects of harmful algae on the key life-history traits of rotifer in eliminating Phaeocystis and reveal the underlying mechanism of these effects, we fed Brachionus plicatilis with Chlorella vulgaris and Phaeocystis globosa respectively, recorded the key life-history traits, and conducted transcriptomic analysis. Results showed that the rotifers feeding on P. globosa significantly decreased total offspring but obviously prolonged lifespan compared to those feeding on C. vulgaris, indicating that there was a trade-off between the reproduction and lifespan of rotifers feeding on algae with different nutrient contents. Nevertheless, rotifers can completely eliminate the population of P. globosa. The changes in the reproduction and lifespan of rotifers are highly correlated with algal key nutrition and the expression of some related genes. Transcriptomic analysis showed that the changes in the key life history traits of rotifers feeding on harmful algae are determined by regulating the expression of some key genes involved in the pathways of carbohydrate digestion and absorption, glycolysis, gluconeogenesis, unsaturated fatty acid biosynthesis, and environmental stress. Understanding the trade-off of the key life history traits of zooplankton in eliminating harmful algae from the underlying mechanism helps improve their application for controlling harmful algae.

Negative Effects of Cyanotoxins and Adaptative Responses of Daphnia

The plethora of cyanobacterial toxins are an enormous threat to whole ecosystems and humans. Due to eutrophication and increases in lake temperatures from global warming, changes in the distribution of cyanobacterial toxins and selection of few highly toxic species/ strains are likely. Globally, one of the most important grazers that controls cyanobacterial blooms is Daphnia, a freshwater model organism in ecology and (eco)toxicology. Daphnia-cyanobacteria interactions have been studied extensively, often focusing on the interference of filamentous cyanobacteria with Daphnia's filtering apparatus, or on different nutritional constraints (the lack of essential amino acids or lipids) and grazer toxicity. For a long time, this toxicity only referred to microcystins. Currently, the focus shifts toward other deleterious cyanotoxins. Still, less than 10% of the total scientific output deals with cyanotoxins that are not microcystins; although these other cyanotoxins can occur just as frequently and at similar concentrations as microcystins in surface water. This review discusses the effects of different cyanobacterial toxins (hepatotoxins, digestive inhibitors, neurotoxins, and cytotoxins) on Daphnia and provides an elaborate and up-to-date overview of specific responses and adaptations of Daphnia. Furthermore, scenarios of what we can expect for the future of Daphnia-cyanobacteria interactions are described by comprising anthropogenic threats that might further increase toxin stress in Daphnia.

Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species

Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.

Draft genomes for one Microcystis-resistant and one Microcystis-sensitive strain of the water flea, Daphnia pulicaria

Daphnia species are well-suited for studying local adaptation and evolutionary responses to stress(ors) including those caused by algal blooms. Algal blooms, characterized by an overgrowth (bloom) of cyanobacteria, are detrimental to the health of aquatic and terrestrial members of freshwater ecosystems. Some strains of Daphnia pulicaria have demonstrated resistance to toxic algae and the ability to mitigate toxic algal blooms. Understanding the genetic mechanism associated with this toxin resistance requires adequate genomic resources. Using whole-genome sequence data mapped to the Daphnia pulex reference genome (PA42), we present reference-guided draft assemblies from one tolerant and one sensitive strain of D. pulicaria, Wintergreen-6 (WI-6), and Bassett-411 (BA-411), respectively. Assessment of the draft assemblies reveal low contamination levels, and high levels (95%) of genic content. Reference scaffolds had coverage breadths of 98.9-99.4%, and average depths of 33X and 29X for BA-411 and WI-6, respectively. Within, we discuss caveats and suggestions for improving these draft assemblies. These genomic resources are presented with a goal of contributing to the resources necessary to understand the genetic mechanisms and associations of toxic prey resistance observed in this species.

Molecular mechanisms of zooplanktonic toxicity in the okadaic acid-producing dinoflagellate Prorocentrum lima

Prorocentrum lima is a dinoflagellate that forms hazardous blooms and produces okadaic acid (OA), leading to adverse environmental consequences associated with the declines of zooplankton populations. However, little is known about the toxic effects and molecular mechanisms of P. lima or OA on zooplankton. Here, their toxic effects were investigated using the brine shrimp Artemia salina. Acute exposure of A. salina to P. lima resulted in lethality at concentrations 100-fold lower than densities observed during blooms. The first comprehensive results from global transcriptomic and metabolomic analyses in A. salina showed up-regulated mRNA expression of antioxidant enzymes and reduced non-enzyme antioxidants, indicating general detoxification responses to oxidative stress after exposure to P. lima. The significantly up-regulated mRNA expression of proteasome, spliceosome, and ribosome, as well as the increased fatty acid oxidation and oxidative phosphorylation suggested the proteolysis of damaged proteins and induction of energy expenditure. Exposure to OA increased catabolism of chitin, which may further disrupt the molting and reproduction activities of A. salina. Our data shed new insights on the molecular responses and toxicity mechanisms of A. salina to P. lima or OA. The simple zooplankton model integrated with omic methods provides a sensitive assessment approach for studying hazardous algae.

Toxic Microcystis aeruginosa alters the resource allocation in Daphnia mitsukuri responding to fish predation cues

Many prey organisms adaptively respond to predation risk by inducible defenses with underlying tradeoffs in resource allocation. Cyanobacterial blooms expose zooplankton to poor food conditions, affecting the herbivores' fitness. Given the interferences on resources allocation and life history traits, poor-quality cyanobacteria are predicted to affect the adaptive predator-induced responses in zooplankton. Here, we exposed two clones (i.e., clones SH and ZJ) of the cladoceran Daphnia mitsukuri to different combinations of fish predation cues and diets containing toxic Microcystis aeruginosa (0%-30%). D. mitsukuri matured at a small size and had elongated relative tail spine as adaptive responses to fish cues. Despite the comparable tail spine defense, fish cue-induced changes in growth and reproduction in the clone SH were more pronounced than those in the clone ZJ under no M. aeruginosa. Animals accumulated microcystin in the whole body with increasing abundance of M. aeruginosa. However, the inducible enhanced tail spine allometry was not affected, resulting in unchanged tail spine defense by Daphnia under all M. aeruginosa treatments. By contrast, M. aeruginosa remarkably decreased the adaptive maturation size and the offspring number in all animals. However, the inducible reproductive effort tended to increase or remain unchanged depending on clones associated with the constant or decreased responses of the somatic growth effort under increasing M. aeruginosa. Our results suggested that toxic M. aeruginosa did not alter the resource allocation to antipredator morphological defense but affected the somatic growth and reproduction in D. mitsukuri under fish cues. The present study highlights the different effects of toxic cyanobacteria on adaptive predator-induced responses in zooplankton, promoting the understanding for the morphological defense-mediated predator-prey interactions in eutrophic environments.

New insights on the effects of ionic liquid structural changes at the gene expression level: Molecular mechanisms of toxicity in Daphnia magna

Knowledge on the molecular basis of ionic liquids' (ILs) ecotoxicity is critical for the development of these designer solvents as their structure can be engineered to simultaneously meet functionality performance and environmental safety. The molecular effects of ILs were investigated by using RNA-sequencing following Daphnia magna exposure to imidazolium- and cholinium-based ILs: 1-ethyl-3-methylimidazolium chloride ([C₂mim]Cl), 1-dodecyl-3-methylimidazolium chloride ([C₁₂mim]Cl) and cholinium chloride ([Chol]Cl)-; the selection allowing to compare different families and cation alkyl chains. ILs shared mechanisms of toxicity focusing e.g. cellular membrane and cytoskeleton, oxidative stress, energy production, protein biosynthesis, DNA damage, disease initiation. [C₂mim]Cl and [C₁₂mim]Cl were the least and the most toxic ILs at the transcriptional level, denoting the role of the alkyl chain as a driver of ILs toxicity. Also, it was reinforced that [Chol]Cl is not devoid of environmental hazardous potential regardless of its argued biological compatibility. Unique gene expression signatures could also be identified for each IL, enlightening specific mechanisms of toxicity.

Cell free Microcystis aeruginosa spent medium affects Daphnia magna survival and stress response

Primary consumers in freshwater ecosystems, such as the zooplankton organism Daphnia magna, are highly affected by cyanobacteria, both as they may use it as a food source but also by cyanobacterial metabolites present in the water. Here, we investigate the impacts of cyanobacterial metabolites focussing on the environmental realistic scenario of the naturally released mixture without crushing cyanobacterial cells or their uptake as food. Therefore, D. magna were exposed to two concentrations of cell free cyanobacterial spent medium from Microcystis aeruginosa PCC 7806 to represent higher and lower ecologically-relevant concentrations of cyanobacterial metabolites. Including microcystin-LR, 11 metabolites have been detected of which 5 were quantified. Hypothesising concentration and time dependent negative impact, survival, gene expression marking digestion and metabolism, oxidative stress response, cell cycle and molting as well as activities of detoxification and antioxidant enzymes were followed for 7 days. D. magna suffered from oxidative stress as both catalase and glutathione S-transferase enzyme activities significantly decreased, suggesting enzyme exhaustibility after 3 and 7 days. Moreover, gene-expressions of the 4 stress markers (glutathione S-transferase, glutathione peroxidase, catalase and thioredoxin) were merely downregulated after 7 days of exposure. Energy allocation (expression of glyceraldehyde-3-phosphate dehydrogenase) was increased after 3 days but decreased as well after 7 days exposure. Cell cycle was impacted time dependently but differently by the two concentrations, along with an increasing downregulation of myosin heavy chain responsible for cell arrangement and muscular movements. Deregulation of nuclear hormone receptor genes indicate that D. magna hormonal steering including molting seemed impaired despite no detection of microviridin J in the extracts. As a consequence of all those responses and presumably of more than investigated molecular and physiological changes, D. magna survival was impaired over time, in a concentration dependent manner. Our results confirm that besides microcystin-LR, other secondary metabolites contribute to negative impact on D. magna survival and stress response.

Toward Disentangling the Multiple Nutritional Constraints Imposed by Planktothrix: The Significance of Harmful Secondary Metabolites and Sterol Limitation

The harmful bloom-forming cyanobacterium Planktothrix is commonly considered to be nutritionally inadequate for zooplankton grazers, resulting in limited top-down control. However, interactions between Planktothrix and zooplankton grazers are poorly understood. The food quality of Planktothrix is potentially constrained by morphological properties (i.e., filament formation), the production of harmful secondary metabolites, and a deficiency in essential lipids (i.e., primarily sterols). Here, we investigated the relative significance of toxin production (microcystins, carboxypeptidase A inhibitors, protease inhibitors) and sterol limitation for the performance of Daphnia feeding on one Planktothrix rubescens and one P. agardhii wild-type/microcystin knock-out mutant pair. Our data suggest that the poor food quality of both Planktothrix spp. is due to deleterious effects mediated by various harmful secondary metabolites and that the impact of sterol limitation is partially or completely superimposed by toxicity. The significance of the different factors seems to depend on the metabolite profile of the considered Planktothrix strain and the Daphnia clone that is used for the experiments. The toxin-responsive gene expression (transporter genes, gpx, and trypsin) and enzyme activity patterns revealed strain-specific food quality constraints and that Daphnia is capable of modulating its physiological responses according to the ingested Planktothrix strain. Future studies need to consider that Planktothrix-grazer interactions are simultaneously modulated by multiple factors to improve our understanding of top-down influences on Planktothrix bloom formation.

Acute and chronic effects of polystyrene microplastics on juvenile and adult Daphnia magna

We investigate the distribution and effects of polystyrene microplastic (MP) particles in exposure experiments with the ecotoxicology model organism Daphnia magna. The aim was to investigate the short and long-term toxicity of MP at different concentrations. To achieve this goal, the effects of 6 μm commercially available polystyrene beads on two different life-stages of D. magna: < 24 h old juveniles and 9 days old adults was assessed. The following end points in test animals were measured: (1) survival, (2) growth, (3) individual and population fecundity, (4) age at maturation and (5) body size of newborn offspring. These response variables were followed in two acute and two chronic experiments. The acute experiments showed that MP is not acutely toxic to D. magna within 48 h, but cause added mortality within 120 h. The juveniles were about 50% more sensitive than the adults tested. In life-cycle experiments testing chronic exposure to MP, again, animals exposed as juveniles at relatively high concentrations, i.e. > 30 μg ml^-1 showed higher sensitivity. We observed slightly increased mortality, reduced growth and stimulation of early reproduction at the cost of later reproduction. Animals exposed after reaching adulthood did not show increased mortality and showed a stimulation response with higher reproductive rates than the control group. However, both the growth rate of mother animals and the body size of newborn declined with increasing dose of MP. We conclude that these effects indicate a role of MP in mechanical interaction/interference with the animal on the level of feeding (clogging filtering functions), digestion (gut filled with plastic particles), and/or other animal behavior. The study also illustrates how MP with slow break-down rates may accumulate in the environment and enter the food-chain as obstructing non-food particles in filter-feeding organisms.

Genome-Wide Stress Responses to Copper and Arsenic in a Field Population of Daphnia

Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level. We studied population level responses to two heavy metals, copper and arsenic, and their binary mixture across time. Transcriptomic patterns identified significantly regulated gene families and genes at the population level including cuticle proteins and resilins. Furthermore, some of these differentially regulated gene families, such as cuticle proteins, were also significantly enriched for genetic variations including SNPs and MNPs. In general, genetic variation was observed in specific gene families, many of which are known to be involved in stress response. Overall, our results indicate that molecular stress responses can be identified within natural populations and that linking molecular mechanisms with genetic variation at the population level could contribute significantly to adverse outcome frameworks.

The transcriptome of the marine calanoid copepod Temora longicornis under heat stress and recovery

Understanding the impacts of global change in zooplankton communities is crucial, as alterations in the zooplankton communities can affect entire marine ecosystems. Despite the economic and ecological importance of the calanoid copepod Temora longicornis in the Belgian part of the North Sea, molecular data is still very limited for this species. Using HiSeq Illumina sequencing, we sequenced the whole transcriptome of T. longicornis, after being exposed to realistic temperatures of 14 and 17 °C. After both an acute (1 day) and a more sustained (5 days) thermal exposure to 17 °C, we investigated gene expression differences with animals exposed to 14 °C, which may be critical for the thermal acclimation and resilience of this copepod species. We also studied the possibility of a short term stress recovery of a heat shock. A total of 179,569 transcripts were yielded, of which 44,985 putative ORF transcripts were identified. These transcripts were subsequently annotated into roughly 22,000 genes based on known sequences using Gene Ontology (GO) and KEGG databases. Temora only showed a mild response to both the temperature and the duration of the exposure. We found that the expression of 27 transcripts varied significantly with an increase in temperature of 3 °C, of which eight transcripts were differentially expressed after acute exposure only. Gene set enrichment analysis revealed that, overall, T. longicornis was more impacted by a sustained thermal exposure, rather than an immediate (acute) exposure, with two times as many enriched GO terms in the sustained treatment. We also identified several general stress responses independent of exposure time, such as modified protein synthesis, energy mobilisation, cuticle and chaperone proteins. Finally, we highlighted candidate genes of a possible recovery from heat exposure, identifying similar terms as those enriched in the heat treatments, i.e. related to for example energy metabolism, cuticle genes and extracellular matrix. The data presented in this study provides the first transcriptome available for T. longicornis which can be used for future genomic studies.

Timing of maternal exposure to toxic cyanobacteria and offspring fitness in Daphnia magna: Implications for the evolution of anticipatory maternal effects

Organisms that regularly encounter stressful environments are expected to use cues to develop an appropriate phenotype. Water fleas (Daphnia spp.) are exposed to toxic cyanobacteria during seasonal algal blooms, which reduce growth and reproductive investment. Because generation time is typically shorter than the exposure to cyanobacteria, maternal effects provide information about the local conditions subsequent generations will experience. Here, we evaluate if maternal effects in response to microcystin, a toxin produced by cyanobacteria, represent an inheritance system evolved to transmit information in Daphnia magna. We exposed mothers as juveniles and/or as adults, and tested the offspring's fitness in toxic and non-toxic environments. Maternal exposure until reproduction reduced offspring fitness, both in the presence and in the absence of toxic cyanobacteria. However, this effect was accompanied by a small positive fitness effect, relative to offspring from unexposed mothers, in the presence of toxic cyanobacteria. This effect was mainly elicited in response to maternal exposure to toxic cyanobacteria early in life and less so during reproduction. None of these effects were explained by changes in egg size. A meta-analysis using our and others' experiments suggests that the adaptive value of maternal effects to cyanobacteria exposure is weak at best. We suggest that the beneficial maternal effect in our study is an example of phenotypic accommodation spanning generations, rather than a mechanism evolved to transmit information about cyanobacteria presence between generations.

Transcriptomic Analysis Reveals the Pathways Associated with Resisting and Degrading Microcystin in Ochromonas

Toxic Microcystis bloom is a tough environment problem worldwide. Microcystin is highly toxic and is an easily accumulated secondary metabolite of toxic Microcystis that threatens water safety. Biodegradation of microcystin by protozoan grazing is a promising and efficient biological method, but the mechanism in this process is still unclear. The present study aimed to identify potential pathways involved in resisting and degrading microcystin in flagellates through transcriptomic analyses. A total of 999 unigenes were significantly differentially expressed between treatments with flagellates Ochromonas fed on microcystin-producing Microcystis and microcystin-free Microcystis. These dysregulated genes were strongly associated with translation, carbohydrate metabolism, phagosome, and energy metabolism. Upregulated genes encoding peroxiredoxin, serine/threonine-protein phosphatase, glutathione S-transferase (GST), HSP70, and O-GlcNAc transferase were involved in resisting microcystin. In addition, genes encoding cathepsin and GST and genes related to inducing reactive oxygen species (ROS) were all upregulated, which highly probably linked with degrading microcystin in flagellates. The results of this study provided a better understanding of transcriptomic responses of flagellates to toxic Microcystis as well as highlighted a potential mechanism of biodegrading microcystin by flagellate Ochromonas, which served as a strong theoretical support for control of toxic microalgae by protozoans.

Effect of β-adrenergic receptor agents on cardiac structure and function and whole-body gene expression in Daphnia magna

Propranolol (PRO), a human β-AR (β-adrenergic receptor) antagonist, is considered to result in specific effects in a non-target species, D. magna, based on our previous studies. The present study investigated the effects of β-AR agents, including an antagonist and agonist using pharmacologically relevant endpoints as well as a more holistic gene expression approach to reveal the impacts and potential mode of actions (MOAs) in the model non-target species. Results show that the responses in cardiac endpoints and gene expression in D. magna are partially similar but distinguishable from the observations in different organisms. No effect was observed on heart size growth in PRO and isoprenaline (ISO) exposure. The contraction capacity of the heart was decreased in ISO exposure, and the heart rate was decreased in PRO exposure. Time-series exposures showed different magnitudes of effect on heart rate and gene expression dependent on the type of chemical exposure. Significant enrichment of gene families involved in protein metabolism and biotransformation was observed within the differentially expressed genes, and we also observed differential expression in juvenile hormone-inducible proteins in ISO and PRO exposure, which is suspected of having endocrine disruption potential. Taken together, deviation between the effects of PRO and ISO in D. magna and other organisms suggests dissimilarity in MOAs or attributes of target bio-molecules between species. Additionally, PRO and ISO may act as endocrine disruptors based on the gene expression observation. Results in the present study confirm that it is challenging to predict ecological impact of active pharmaceutical ingredients (APIs) based on the available data acquired through human-focused studies. Furthermore, the present study provided unique data and a case study on the impact of APIs in a non-target organism.

Deciphering the Combined Effects of Environmental Stressors on Gene Transcription: A Conceptual Approach

The use of classical mixture toxicity models to predict the combined effects of environmental stressors based on toxicogenomics (OMICS) data is still in its infancy. Although several studies have made attempts to implement mixture modeling in OMICS analysis to understand the low-dose interactions of stressors, it is not clear how interactions occur at the molecular level and how results generated from such approaches can be better used to inform future studies and cumulative hazard assessment of multiple stressors. The present work was therefore conducted to propose a conceptual approach for combined effect assessment using global gene expression data, as illustrated by a case study on assessment of combined effects of gamma radiation and depleted uranium (DU) on Atlantic salmon ( Salmo salar). Implementation of the independent action (IA) model in reanalysis of a previously published microarray gene expression dataset was performed to describe gene expression patterns of combined effects and identify key gene sets and pathways that were relevant for understanding the interactive effects of these stressors. By using this approach, 3120 differentially expressed genes (DEGs) were found to display additive effects, whereas 279 (273 synergistic, 6 antagonistic) were found to deviate from additivity. Functional analysis further revealed that multiple toxicity pathways, such as oxidative stress responses, cell cycle regulation, lipid metabolism, and immune responses were enriched by DEGs showing synergistic gene expression. A key toxicity pathway of DNA damage leading to enhanced tumorigenesis signaling is highlighted and discussed in detail as an example of how to take advantage of the approach. Furthermore, a conceptual workflow describing the integration of combined effect modeling, OMICS analysis, and bioinformatics is proposed. The present study presents a conceptual framework for utilizing OMICS data in combined effect assessment and may provide novel strategies for dealing with data analysis and interpretation of molecular responses of multiple stressors.

Gene Coexpression Networks Drive and Predict Reproductive Effects in Daphnia in Response to Environmental Disturbances

Increasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene coexpression networks and generalized additive models to predict effects on reproduction in the aquatic microcrustacean Daphnia. We developed models to predict effects on reproduction upon exposure to different cyanobacteria, different insecticides and binary mixtures of cyanobacteria and insecticides. Models developed specifically for groups of stressors (e.g., either cyanobacteria or insecticides) performed better than general models developed on all data. Furthermore, models developed using in silico generated mixture gene expression profiles from single stressor data were able to better predict effects on reproduction compared to models derived from the mixture exposures themselves. Our results highlight the potential of gene expression data to quantify effects of complex exposures at higher level organismal effects without prior mechanistic knowledge or complex exposure data.

Multigenerational Effects of the Antibiotic Tetracycline on Transcriptional Responses of Daphnia magna and Its Relationship to Higher Levels of Biological Organizations

Given the risk of environmental pollution by pharmaceutical compounds and the effects of these compounds on exposed ecosystems, ecologically relevant and realistic assessments are required. However, many studies have been mostly focused on individual responses in a single generation exposed to one-effect concentrations. Here, transcriptional responses of the crustacean Daphnia magna to the antibiotic tetracycline across multiple generations and effect concentrations were investigated. The results demonstrated that tetracycline induced different transcriptional responses of daphnids that were dependent on dose and generation. For example, reproduction-related expressed sequence tags (ESTs), including vitellogenin, were distinctly related to the dose-dependent tetracycline exposure, whereas multigenerational exposure induced significant change of molting-related ESTs such as cuticle protein. A total of 65 ESTs were shared in all contrasts, suggesting a conserved mechanism of tetracycline toxicity regardless of exposure concentration or time. Most of them were associated with general stress responses including translation, protein and carbohydrate metabolism, and oxidative phosphorylation. In addition, effects across the dose-response curve showed higher correlative connections among transcriptional, physiological, and individual responses than multigenerational effects. In the multigenerational exposure, the connectivity between adjacent generations decreased with increasing generation number. The results clearly highlight that exposure concentration and time trigger different mechanisms and functions, providing further evidence that multigenerational and dose-response effects cannot be neglected in environmental risk assessment.

Complementary mechanisms for neurotoxin resistance in a copepod

Toxin resistance is a recurring evolutionary response by predators feeding on toxic prey. These adaptations impact physiological interaction and community ecology. Mechanisms for resistance vary depending on the predator and the nature of the toxin. Potent neurotoxins like tetrodotoxin (TTX) and saxitoxin (STX) that are highly toxic to humans and other vertebrates, target conserved voltage-gated sodium channels (Na_V) of nerve and muscle, causing paralysis. The copepod Calanus finmarchicus consumes the STX-producing dinoflagellate, Alexandrium fundyense with no effect on survival. Using transcriptomic approaches to search for the mechanism that confers resistance in C. finmarchicus, we identified splice variants of Na_Vs that were predicted to be toxin resistant. These were co-expressed with putatively non-resistant form in all developmental stages. However its expression was unresponsive to toxin challenge nor was there any up-regulation of genes involved in multi-xenobiotic resistance (MXR) or detoxification (phases I or II). Instead, adults consistently regulated genes encoding digestive enzymes, possibly to complement channel resistance by limiting toxin assimilation via the digestive process. The nauplii, which were more susceptible to STX, did not regulate these enzymes. This study demonstrates how deep-sequencing technology can elucidate multiple mechanisms of toxin resistance concurrently, revealing the linkages between molecular/cellular adaptations and the ecology of an organism.

Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.

Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids

Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the microcrustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.

An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity

Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L^-1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L^-1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L^-1 MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a wider range of biological pathways, compared with pure MC-LR, and even 1 μg L^-1 MC-LR potentially induces a health risk for aquatic organisms.

Glutathione S-Transferase Regulation in Calanus finmarchicus Feeding on the Toxic Dinoflagellate Alexandrium fundyense

The effect of the dinoflagellate, Alexandrium fundyense, on relative expression of glutathione S-transferase (GST) transcripts was examined in the copepod Calanus finmarchicus. Adult females were fed for 5-days on one of three experimental diets: control (100% Rhodomonas spp.), low dose of A. fundyense (25% by volume, 75% Rhodomonas spp.), and high dose (100% A. fundyense). Relative expression of three GST genes was measured using RT-qPCR on days 0.5, 1, 2 and 5 in two independent experiments. Differential regulation was found for the Delta and the Sigma GSTs between 0.5 to 2 days, but not on day 5 in both experiments. The third GST, a microsomal, was not differentially expressed in either treatment or day. RT-qPCR results from the two experiments were similar, even though experimental females were collected from the Gulf of Maine on different dates and their reproductive output differed. In the second experiment, expression of 39 GSTs was determined on days 2 and 5 using RNA-Seq. Global gene expression analyses agreed with the RT-qPCR results. Furthermore, the RNA-Seq measurements indicated that only four GSTs were differentially expressed under the experimental conditions, and the response was small in amplitude. In summary, the A. fundyense diet led to a rapid and transient response in C. finmarchicus in three cytosolic GSTs, while a fourth GST (Omega I) was significantly up-regulated on day 5. Although there was some regulation of GSTs in response the toxic dinoflagellate, the tolerance to A. fundyense by C. finmarchicus is not dependent on the long-term up-regulation of specific GSTs.

Stress-responsive expression of a glutathione S-transferase (delta) gene in waterflea Daphnia magna challenged by microcystin-producing and microcystin-free Microcystis aeruginosa

Harmful cyanobacterial blooms resulting from eutrophication and global warming have emerged as a worldwide environmental concern. Some zooplankton populations, including Daphnia, have been shown to adapt locally to microcystin-producing Microcystis. Previous in vitro experiments indicate that glutathione-S-transferase (GST) may act as the first step of detoxification in Daphnia by conjugating microcystins (MCs) with glutathione. The GST family is categorized into many classes, and different classes present distinct responses to MC detoxification. To date, however, the molecular mechanism of single class GST participation in buffering the toxic effects of MCs in Daphnia remains poorly known. In this study, a full-length delta-GST cDNA of Daphnia magna (Dm-dGST) was isolated and characterized through bioinformatics. Differential gene expression studies revealed that short-term exposure to microcystin-producing (MP) Microcystis aeruginosa increased Dm-dGST transcript levels. By contrast, long-term exposure to MP or microcystin-free (MF) M. aeruginosa decreased Dm-dGST transcript levels. Together with changes in three other antioxidation biomarkers (catalase, CuZn- and Mn-superoxide dismutase), it is concluded that Dm-dGST can potentially biotransform MCs to reduce their toxicity. The present study highlights the importance of Dm-dGST in response to MC toxicity and may thus facilitate future research on the molecular mechanisms of MC tolerance in zooplankton under an increasing eutrophic world.

Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense

In the Gulf of Maine, the copepod Calanus finmarchicus co-occurs with the neurotoxin-producing dinoflagellate, Alexandrium fundyense. The copepod is resistant to this toxic alga, but little is known about other effects. Gene expression profiles were used to investigate the physiological response of females feeding for two and five days on a control diet or a diet containing either a low or a high dose of A. fundyense. The physiological responses to the two experimental diets were similar, but changed between the time points. At 5-days the response was characterized by down-regulated genes involved in energy metabolism. Detoxification was not a major component of the response. Instead, genes involved in digestion were consistently regulated, suggesting that food assimilation may have been affected. Thus, predicted increases in the frequency of blooms of A. fundyense could affect C. finmarchicus populations by changing the individuals' energy budget and reducing their ability to build lipid reserves.

Changes in iTRAQ-Based Proteomic Profiling of the Cladoceran Daphnia magna Exposed to Microcystin-Producing and Microcystin-Free Microcystis aeruginosa

Global warming and increased nutrient fluxes cause cyanobacterial blooms in freshwater ecosystems. These phenomena have increased the concern for human health and ecosystem services. The mass occurrences of toxic cyanobacteria strongly affect freshwater zooplankton communities, especially the unselective filter feeder Daphnia. However, the molecular mechanisms of cyanobacterial toxicity remain poorly understood. This study is the first to combine the established body growth rate (BGR), which is an indicator of life-history fitness, with differential peptide labeling (iTRAQ)-based proteomics in Daphnia magna influenced by microcystin-producing (MP) and microcystin-free (MF) Microcystis aeruginosa. A significant decrease in BGR was detected when D. magna was exposed to MP or MF M. aeruginosa. Conducting iTRAQ proteomic analyses, we successfully identified and quantified 211 proteins with significant changes in expression. A cluster of orthologous groups revealed that M. aeruginosa-affected differential proteins were strongly associated with lipid, carbohydrate, amino acid, and energy metabolism. These parameters could potentially explain the reduced fitness based on the cost of the substance metabolism.

Effects of two copper compounds on Microcystis aeruginosa cell density, membrane integrity, and microcystin release

Microcystin release following Microcystis aeruginosa cell lysis after copper-based algaecide treatment is often cited as a concern leading to restricted use of algaecide in restoration of natural water resources. To examine this concern, bench-scale experiments were conducted to study responses of M. aeruginosa to 8-day copper exposures as copper sulfate and copper-ethanolamine (Cu-EA). M. aeruginosa UTEX 2385 was cultured in BG11 medium to cell density of 10(6)cells/mL with total and extracellular microcystin of 93 and 53μg/L, respectively. Exposures of copper concentration ranged from 40 to 1000μgCu/L. Cell membrane integrity was indicated by erythrosine B. In the end of experiment, total microcystin and cell density in untreated control (313μg/L and 10(7)cells/mL) was 3.3 and 10 times greater than pretreatment value, respectively. Minimum amount of copper required to reduce M. aeruginosa population within 8 days was 160μgCu/L as copper sulfate and 80μgCu/L as Cu-EA, where total and extracellular microcystin concentrations (47 and 44μg/L for copper sulfate; 56 and 44μg/L for Cu-EA) were degraded with degradation rate coefficient 0.1 day(-1) and were less than pretreatment values. Given a copper concentration at 80µgCu/L as Cu-EA, M. aeruginosa cells were intact and less microcystin were released compared to treatments at 160-1000µgCu/L, where lysed cells and relatively greater microcystin release were observed. Based on the laboratory results, a minimum amount of copper required for reducing M. aeruginosa population could decrease total microcystin concentration and not compromise cells and minimize microcystin release.

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

Background

Predator-induced defences are a prominent example of phenotypic plasticity found from single-celled organisms to vertebrates. The water flea Daphnia pulex is a very convenient ecological genomic model for studying predator-induced defences as it exhibits substantial morphological changes under predation risk. Most importantly, however, genetically identical clones can be transcriptionally profiled under both control and predation risk conditions and be compared due to the availability of the sequenced reference genome. Earlier gene expression analyses of candidate genes as well as a tiled genomic microarray expression experiment have provided insights into some genes involved in predator-induced phenotypic plasticity. Here we performed the first RNA-Seq analysis to identify genes that were differentially expressed in defended vs. undefended D. pulex specimens in order to explore the genetic mechanisms underlying predator-induced defences at a qualitatively novel level.

Results

We report 230 differentially expressed genes (158 up- and 72 down-regulated) identified in at least two of three different assembly approaches. Several of the differentially regulated genes belong to families of paralogous genes. The most prominent classes amongst the up-regulated genes include cuticle genes, zinc-metalloproteinases and vitellogenin genes. Furthermore, several genes from this group code for proteins recruited in chromatin-reorganization or regulation of the cell cycle (cyclins). Down-regulated gene classes include C-type lectins, proteins involved in lipogenesis, and other families, some of which encode proteins with no known molecular function.

Conclusions

The RNA-Seq transcriptome data presented in this study provide important insights into gene regulatory patterns underlying predator-induced defences. In particular, we characterized different effector genes and gene families found to be regulated in Daphnia in response to the presence of an invertebrate predator. These effector genes are mostly in agreement with expectations based on observed phenotypic changes including morphological alterations, i.e., expression of proteins involved in formation of protective structures and in cuticle strengthening, as well as proteins required for resource re-allocation. Our findings identify key genetic pathways associated with anti-predator defences.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-015-0109-x) contains supplementary material, which is available to authorized users.

Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia

Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.

Differential transcriptomic responses of ancient and modern Daphnia genotypes to phosphorus supply

Little is known about the role of transcriptomic changes in driving phenotypic evolution in natural populations, particularly in response to anthropogenic environmental change. Previous analyses of Daphnia genotypes separated by centuries of evolution in a lake using methods in resurrection ecology revealed striking genetic and phenotypic shifts that were highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven nutrient enrichment (i.e. eutrophication). Here, we compared the transcriptomes of two ancient (~700-year-old) and two modern (~10-year-old) genotypes in historic (low P) and contemporary (high P) environmental conditions using microarrays. We found considerable transcriptomic variation between 'ancient' and 'modern' genotypes in both treatments, with stressful (low P) conditions eliciting differential expression (DE) of a larger number of genes. Further, more genes were DE between 'ancient' and 'modern' genotypes than within these groups. Expression patterns of individual genes differed greatly among genotypes, suggesting that different transcriptomic responses can result in similar phenotypes. While this confounded patterns between 'ancient' and 'modern' genotypes at the gene level, patterns were discernible at the functional level: annotation of DE genes revealed particular enrichment of genes involved in metabolic pathways in response to P-treatments. Analyses of gene families suggested significant DE in pathways already known to be important in dealing with P-limitation in Daphnia as well as in other organisms. Such observations on genotypes of a single natural population, separated by hundreds of years of evolution in contrasting environmental conditions before and during anthropogenic environmental changes, highlight the important role of transcriptional mechanisms in the evolutionary responses of populations.

Arginine kinase in the cladoceran Daphnia magna: cDNA sequencing and expression is associated with resistance to toxic Microcystis

Nutrient loading derived from anthropogenic activities into lakes have increased the frequency, severity and duration of toxic cyanobacterial blooms around the world. Although herbivorous zooplankton are generally considered to be unable to control toxic cyanobacteria, populations of some zooplankton, including Daphnia, have been shown to locally adapt to toxic cyanobacteria and suppress cyanobacterial bloom formation. However, little is known about the physiology of zooplankton behind this phenomenon. One possible explanation is that some zooplankton may induce more tolerance by elevating energy production, thereby adding more energy allocation to detoxification expenditure. It is assumed that arginine kinase (AK) serves as a core in temporal and spatial adenosine triphosphate (ATP) buffering in cells with high fluctuating energy requirements. To test this hypothesis, we studied the energetic response of a single Daphnia magna clone exposed to a toxic strain of Microcystis aeruginosa, PCC7806. Arginine kinase of D. magna (Dm-AK) was successfully cloned. An ATP-gua PtransN domain which was described as a guanidine substrate specificity domain and an ATP-gua Ptrans domain which was responsible for binding ATP were both identified in the Dm-AK. Phylogenetic analysis of AKs in a range of arthropod taxa suggested that Dm-AK was as dissimilar to other crustaceans as it was to insects. Dm-AK transcript level and ATP content in the presence of M. aeruginosa were significantly lower than those in the control diet containing only the nutritious chlorophyte, Scenedesmus obliquus, whereas the two parameters in the neonates whose mothers had been previously exposed to M. aeruginosa were significantly higher than those of mothers fed with pure S. obliquus. These findings suggest that Dm-AK might play an essential role in the coupling of energy production and utilization and the tolerance of D. magna to toxic cyanobacteria.

Deciphering the genetic basis of microcystin tolerance

BACKGROUND

Cyanobacteria constitute a serious threat to freshwater ecosystems by producing toxic secondary metabolites, e.g. microcystins. These microcystins have been shown to harm livestock, pets and humans and to affect ecosystem service and functioning. Cyanobacterial blooms are increasing worldwide in intensity and frequency due to eutrophication and global warming. However, Daphnia, the main grazer of planktonic algae and cyanobacteria, has been shown to be able to suppress bloom-forming cyanobacteria and to adapt to cyanobacteria that produce microcystins. Since Daphnia's genome was published only recently, it is now possible to elucidate the underlying molecular mechanisms of microcystin tolerance of Daphnia.

RESULTS

Daphnia magna was fed with either a cyanobacterial strain that produces microcystins or its genetically engineered microcystin knock-out mutant. Thus, it was possible to distinguish between effects due to the ingestion of cyanobacteria and effects caused specifically by microcystins. By using RNAseq the differentially expressed genes between the different treatments were analyzed and affected KOG-categories were calculated. Here we show that the expression of transporter genes in Daphnia was regulated as a specific response to microcystins. Subsequent qPCR and dietary supplementation with pure microcystin confirmed that the regulation of transporter gene expression was correlated with the tolerance of several Daphnia clones.

CONCLUSIONS

Here, we were able to identify new candidate genes that specifically respond to microcystins by separating cyanobacterial effects from microcystin effects. The involvement of these candidate genes in tolerance to microcystins was validated by correlating the difference in transporter gene expression with clonal tolerance. Thus, the prevention of microcystin uptake most probably constitutes a key mechanism in the development of tolerance and adaptation of Daphnia. With the availability of clear candidate genes, future investigations examining the process of local adaptation of Daphnia populations to microcystins are now possible.

Ecotoxicity of binary mixtures of Microcystis aeruginosa and insecticides to Daphnia pulex

In aquatic ecosystems, mixtures of chemical and natural stressors can occur which may significantly complicate risk assessment approaches. Here, we show that effects of binary combinations of four different insecticides and Microcystis aeruginosa, a toxic cyanobacteria, on Daphnia pulex exhibited distinct interaction patterns. Combinations with chlorpyrifos and tetradifon caused non-interactive effects, tebufenpyrad caused an antagonistic interaction and fenoyxcarb yielded patterns that depended on the reference model used (i.e. synergistic with independent action, additive with concentration addition). Our results demonstrate that interactive effects cannot be generalised across different insecticides, not even for those targeting the same biological pathway (i.e. tebufenpyrad and tetradifon both target oxidative phosphorylation). Also, the concentration addition reference model provided conservative predictions of effects in all investigated combinations for risk assessment. These predictions could, in absence of a full mechanistic understanding, provide a meaningful solution for managing water quality in systems impacted by both insecticides and cyanobacterial blooms.

Genome-wide transcription profiles reveal genotype-dependent responses of biological pathways and gene-families in Daphnia exposed to single and mixed stressors

The present study investigated the possibilities and limitations of implementing a genome-wide transcription-based approach that takes into account genetic and environmental variation to better understand the response of natural populations to stressors. When exposing two different Daphnia pulex genotypes (a cadmium-sensitive and a cadmium-tolerant one) to cadmium, the toxic cyanobacteria Microcystis aeruginosa, and their mixture, we found that observations at the transcriptomic level do not always explain observations at a higher level (growth, reproduction). For example, although cadmium elicited an adverse effect at the organismal level, almost no genes were differentially expressed after cadmium exposure. In addition, we identified oxidative stress and polyunsaturated fatty acid metabolism-related pathways, as well as trypsin and neurexin IV gene-families as candidates for the underlying causes of genotypic differences in tolerance to Microcystis. Furthermore, the whole-genome transcriptomic data of a stressor mixture allowed a better understanding of mixture responses by evaluating interactions between two stressors at the gene-expression level against the independent action baseline model. This approach has indicated that ubiquinone pathway and the MAPK serine-threonine protein kinase and collagens gene-families were enriched with genes showing an interactive effect in expression response to exposure to the mixture of the stressors, while transcription and translation-related pathways and gene-families were mostly related with genotypic differences in interactive responses to this mixture. Collectively, our results indicate that the methods we employed may improve further characterization of the possibilities and limitations of transcriptomics approaches in the adverse outcome pathway framework and in predictions of multistressor effects on natural populations.

An investigation of the inter-clonal variation of the interactive effects of cadmium and Microcystis aeruginosa on the reproductive performance of Daphnia magna

Interactive effects between chemical and natural stressors as well as genetically determined variation in stress tolerance among individuals may complicate risk assessment and management of chemical pollutants in natural ecosystems. Although genetic variation in tolerance to single stressors has been described extensively, genetic variation in interactive effects between two stressors has only rarely been investigated. Here, we examined the interactive effects between a chemical stressor (Cd) and a natural stressor (the cyanobacteria Microcystis aeruginosa) on the reproduction of Daphnia magna in 20 genetically different clones using a full-factorial experimental design and with the independent action model of joint stressor action as the reference theoretical framework. Across all clones, the reduction of 21-day reproduction compared to the control treatment (no Cd, no M. aeruginosa) ranged from -10% to 98% following Cd exposure alone, from 44% to 89% for Microcystis exposure alone, and from 61% to 98% after exposure to Cd+Microcystis combined. Three-way ANOVA on log-transformed reproduction data of all clones together did not detect a statistically significant Cd×Microcystis interaction term (F-test, p=0.11), meaning that on average both stressors do not interact in inhibiting reproductive performance of D. magna. This finding contrasted expectations based on some known shared mechanisms of toxicity of Cd and Microcystis and therefore cautions against making predictions of interactive chemical+natural stressor effects from incomplete knowledge on affected biological processes and pathways. Further, still based on three-way ANOVA, we did not find statistically significant clone×Cd×Microcystis interaction when data for all clones were analyzed together (F-test, p=0.07), suggesting no inter-clonal variation of the interactive effect between Cd and Microcystis. However, when the same data were quantitatively analyzed on a clone-by-clone scale, we found a relatively wide range of deviations between observed and IA-model-predicted reproduction in combined Cd+Microcystis treatments (both in direction and magnitude), suggesting some biological significance of inter-clonal variation of interactive effects. In one of the twenty clones this deviation was statistically significant (two-way ANOVA, F-test, p=0.005), indicating an interactive Cd×Microcystis effect in this clone. Together, these two observations caution against the extrapolation of conclusions about mixed stressor data obtained with single clones to the level of the entire species and to the level of natural, genetically diverse populations.

Combined exposure to cyanobacteria and carbaryl results in antagonistic effects on the reproduction of Daphnia pulex

In aquatic ecosystems, Daphnia are exposed to a wide variety of natural and chemical stressors that can cause interactive effects resulting in an increased impact on aquatic ecosystems. The authors therefore investigated the interactive effects of harmful cyanobacteria (cyanoHABs) with carbaryl in Daphnia pulex, because cyanobacteria have become an important concern for aquatic ecosystems. Daphnia were exposed for 21 d to 4 selected cyanobacteria (Aphanizomenon sp., Cylindrospermopsis raciborskii, Microcystis aeruginosa, and Oscillatoria sp), carbaryl, and all binary combinations of carbaryl and each individual cyanobacterium. Results were analyzed with both the independent action and the concentration addition model. The estimated median effect concentration (EC50) for carbaryl was comparable between the experiments, ranging from 2.28 µg/L to 5.94 µg/L. The EC50 for cyanobacteria ranged from 13.45% of the total diet ratio for Microcystis to 66.69% of the diet ratio for Oscillatoria. In combination with carbaryl, the response of Daphnia to 3 of the 4 cyanobacteria demonstrated antagonistic deviation patterns (p < 0.05). Exposure to combinations of carbaryl and Cylindrospermopsis did not result in statistically significant deviations from both reference models. The results may have important implications for pesticide risk assessment, underlining the impact of interactive effects on aquatic organisms. Based on these results, the authors suggest that both the independent action and the concentration addition model can serve as a protective approach in risk assessment of carbaryl in the presence of cyanobacterial blooms.

Identification of metabolic pathways in Daphnia magna explaining hormetic effects of selective serotonin reuptake inhibitors and 4-nonylphenol using transcriptomic and phenotypic responses

The molecular mechanisms explaining hormetic effects of selective serotonin reuptake inhibitors (SSRIs) and 4-nonylphenol in Daphnia magna reproduction were studied in juveniles and adults. Transcriptome analyses showed changes in mRNA levels for 1796 genes in juveniles and 1214 genes in adults (out of 15000 total probes) exposed to two SSRIs (fluoxetine and fluvoxamine) or to 4-nonylphenol. Functional annotation of affected genes was improved by assuming the annotations of putatively homologous Drosophila genes. Self-organizing map analysis and partial least-square regression coupled with selectivity ratio procedures analyses allowed to define groups of genes with specific responses to the different treatments. Differentially expressed genes were analyzed for functional enrichment using Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes databases. Serotonin metabolism, neuronal developmental processes, and carbohydrates and lipid metabolism functional categories appeared as selectively affected by SSRI treatment, whereas 4-nonylphenol deregulated genes from the carbohydrate metabolism and the ecdysone regulatory pathway. These changes in functional and metabolic pathways are consistent with previously reported SSRIs and 4-nonylphenol hormetic effects in D. magna, including a decrease in reserve carbohydrates and an increase in respiratory metabolism.