Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites

Understanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.

Defining Quality Criteria for Nanoplastic Hazard Evaluation: The Case of Polystyrene Nanoplastics and Aquatic Invertebrate Daphnia spp

Polystyrene nanoparticles are the most investigated type of nanoplastics in environmental hazard studies. It remains unclear whether nanoplastic particles pose a hazard towards aquatic organisms. Thus, it was our aim to investigate whether the existing studies and data provided therein are reliable in terms of data completeness. We used the example of Daphnia spp. studies for the purpose of polystyrene nanoplastic (nanoPS) hazard evaluation. First, a set of quality criteria recently proposed for nanoplastic ecotoxicity studies was applied. These rather general criteria for all types of nanoplastics and different test organisms were then, in the second step, tailored and refined specifically for Daphnia spp. and nanoPS. Finally, a scoring system was established by setting mandatory (high importance) as well as desirable (medium importance) criteria and defining a threshold to pass the evaluation. Among the existing studies on nanoPS ecotoxicity for Daphnia spp. (n = 38), only 18% passed the evaluation for usability in hazard evaluation. The few studies that passed the evaluation did not allow for conclusions on the hazard potential of nanoPS because there was no consensus among the studies. The greatest challenge we identified is in data reporting, as only a few studies presented complete data for hazard evaluation.

Influence of Calcium Resonance-Tuned Low-Frequency Magnetic Fields on Daphnia magna

A biophysical model for calculating the effective parameters of low-frequency magnetic fields was developed by Lednev based on summarized empirical data. According to this model, calcium ions as enzyme cofactors can be the primary target of low-frequency magnetic fields with different parameters tuned to calcium resonance. However, the effects of calcium-resonant combinations of static and alternating magnetic fields that correspond to Lednev's model and differ by order in frequency and intensity were not studied. It does not allow for confidently discussing the primary targets of low-frequency magnetic fields in terms of the magnetic influence on ions-enzyme cofactors. To clarify this issue, we examined the response of freshwater crustaceans Daphnia magna to the impact of combinations of magnetic fields targeted to calcium ions in enzymes according to Lednev's model that differ in order of magnitude. Life-history traits and biochemical parameters were evaluated. Exposure of daphnids to both combinations of magnetic fields led to a long-term delay of the first brood release, an increase in the brood size, a decrease in the number of broods, and the period between broods. The amylolytic activity, proteolytic activity, and sucrase activity significantly decreased in whole-body homogenates of crustaceans in response to both combinations of magnetic fields. The similarity in the sets of revealed effects assumes that different magnetic fields tuned to calcium ions in biomolecules can affect the same primary molecular target. The results suggest that the low-frequency magnetic fields with parameters corresponding to Lednev's model of interaction between biological molecules and ions can remain effective with a significant decrease in the static magnetic background.

Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation

The dynamics of extinction and (re)colonization in habitat patches are characterizing features of dynamic metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, and stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared with the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in younger and also in more isolated subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that evolution is largely driven by genetic drift.

Time between Sequential Exposures to Multiple Stress Turns Antagonism into Synergism

Aquatic communities are exposed to repeated pulses of toxicants and environmental stressors. We hypothesize that the dose, order, and timing of stress events shape the interactions of these communities. For this, we conducted a fully-crossed, four-factorial, multiple stress exposure experiment to study the combined effects of Esfenvalerate and ultraviolet-B (UV-B) radiation related to the exposure timing and order on Daphnia magna. We revealed that initial exposure to low stress doses, independent of the stress type (UV-B or Esfenvalerate), significantly increased the resistance toward the second stressor. This beneficial effect was apparent only when the second stressor was applied immediately after the first stressor (p < 0.01). When the period between stressor applications was extended to 2 days, the antagonism between the two stressors turned into synergism. The stressor interaction could be predicted with an abstract-mechanistic model of the temporal dynamics of the early-stage stress response. With this model, the timing and order of exposures were able to successfully explain interactions observed in all treatments (model-R² = 1.0). We conclude that especially the duration of a break between exposures and the exposure dose have a decisive influence on interactions between toxicants and environmental stressors.

Extending the Bioavailability of Hydrophilic Antioxidants for Metal Ion Detoxification via Crystallization with Polysaccharide Dopamine

Although metal ions, such as silver and gold, have been shown to have strong antimicrobial properties, their potential to have toxic effects on human and environmental health has gained interest with an improved understanding of their mechanisms to promote oxidative stress. Redox control is a major focus of many drug delivery systems and often incorporates an antioxidant as the active pharmaceutical ingredient (API) to neutralize overproduced reactive oxygen species (ROS). Nevertheless, there are still limitations with bioavailability and extended redox control with regard to antioxidant drug delivery. Herein, this study develops a colloidal antioxidant crystal system that dissolves sustainably through polymer stabilization using sodium hyaluronate conjugated with dopamine (HA-dopa). We explore the role of dopamine incorporation into crystal-stabilizing polymers and quantify the balance between drug-polymer interactions and competing polymer-polymer interactions. We propose that this type of analysis is useful in the engineering of and provides insight into the release behavior of polymer-crystal complexes. In developing our crystal complex, N-acetylcysteine (NAC) was used as the model antioxidant to protect against silver ion toxicity. We found that our optimized HA-dopa-stabilized NAC crystals prolong the release time of NAC 5-fold compared to a polymer-free NAC crystal. Therefore, following sublethal exposure to AgNO₃, the extended lifetime of NAC was able to maintain normal intracellular ROS levels, modulate metabolic function, mitigate fluctuations in ATP levels and ATP synthase activity, and preserve contraction frequency in engineered cardiac muscle tissue. Furthermore, the protective effects of the HA-dopa-stabilized NAC crystals were extended to a Daphnia magna model where silver-ion-induced change to both cell-level biochemistry and organ function was alleviated. As such, we propose that the packaging of hydrophilic antioxidants as colloidal crystals drastically extends the lifetime of the API, better maintains ROS homeostasis post metal ion exposure, and therefore preserves both intracellular biochemistry and tissue functionality.

Food quantity and quality shapes reproductive strategies of Daphnia

In freshwater environments, one of the challenges aquatic grazers face are periods of suboptimal food quantity and quality. In a life table experiment, the effects of food quantity (a gradient of algae concentration) and quality (a diet of cyanobacteria) on the life histories and resource allocation strategy in Daphnia magna were tested. Growth‐related traits were similarly affected under different food regimes while the reproductive strategies differed in animals exposed to low food quantity and quality. The per‐clutch investment (clutch volume) did not differ between Daphnia fed with cyanobacteria and underfed mothers, but resources were differently allocated; underfed mothers increased their per‐offspring investment by producing fewer, but larger eggs, whereas cyanobacteria‐fed mothers invested in a greater number of eggs of smaller size. I argue that both strategies of resource allocation (number vs. size of eggs) may be adaptive under the given food regime. The results of the study show that the cyanobacteria diet‐driven fitness losses are comparable to losses caused by food quantity, which is only slightly above the growth capability threshold for Daphnia.

Rapid communication: effects of cadmium exposure on the growth-related genes of Daphnia magna

Few data are available regarding the effects of gene expression on growth in Daphnia magna. The aim of this study was to determine the influence of cadmium (Cd) exposure on global gene transcription and growth-related genes in D. magna using RNASeq generated data. Our results demonstrated that Cd exposure decreased gene expression, but did not adversely affect the expression of growth-related genes, suggesting differential allocation of resources to growth avoids the deleterious effect of the toxicant on this trait.

Multiple Screening of Pesticides Toxicity in Zebrafish and Daphnia Based on Locomotor Activity Alterations

Pesticides are widely used to eradicate insects, weed species, and fungi in agriculture. The half-lives of some pesticides are relatively long and may have the dire potential to induce adverse effects when released into the soil, terrestrial and aquatic systems. To assess the potential adverse effects of pesticide pollution in the aquatic environment, zebrafish (Danio rerio) and Daphnia magna are two excellent animal models because of their transparent bodies, relatively short development processes, and well-established genetic information. Moreover, they are also suitable for performing high-throughput toxicity assays. In this study, we used both zebrafish larvae and water flea daphnia neonates as a model system to explore and compare the potential toxicity by monitoring locomotor activity. Tested animals were exposed to 12 various types of pesticides (three fungicides and 9 insecticides) for 24 h and their corresponding locomotor activities, in terms of distance traveled, burst movement, and rotation were quantified. By adapting principal component analysis (PCA) and hierarchical clustering analysis, we were able to minimize data complexity and compare pesticide toxicity based on locomotor activity for zebrafish and daphnia. Results showed distinct locomotor activity alteration patterns between zebrafish and daphnia towards pesticide exposure. The majority of pesticides tested in this study induced locomotor hypo-activity in daphnia neonates but triggered locomotor hyper-activity in zebrafish larvae. According to our PCA and clustering results, the toxicity for 12 pesticides was grouped into two major groups based on all locomotor activity endpoints collected from both zebrafish and daphnia. In conclusion, all pesticides resulted in swimming alterations in both animal models by either producing hypo-activity, hyperactivity, or other changes in swimming patterns. In addition, zebrafish and daphnia displayed distinct sensitivity and response against different pesticides, and the combinational analysis approach by using a phenomic approach to combine data collected from zebrafish and daphnia provided better resolution for toxicological assessment.

Mycosporine-Like Amino Acids (MAAs) in Zooplankton

Organisms have different adaptations to avoid damage from ultraviolet radiation and one such adaptation is the accumulation of mycosporine-like amino acids (MAAs). These compounds are common in aquatic taxa but a comprehensive review is lacking on their distribution and function in zooplankton. This paper shows that zooplankton MAA concentrations range from non-detectable to ~13 µg mgDW⁻¹. Copepods, rotifers, and krill display a large range of concentrations, whereas cladocerans generally do not contain MAAs. The proposed mechanisms to gain MAAs are via ingestion of MAA-rich food or via symbiotic bacteria providing zooplankton with MAAs. Exposure to UV-radiation increases the concentrations in zooplankton both via increasing MAA concentrations in the phytoplankton food and due to active accumulation. Concentrations are generally low during winter and higher in summer and females seem to deposit MAAs in their eggs. The concentrations of MAAs in zooplankton tend to increase with altitude but only up to a certain altitude suggesting some limitation for the uptake. Shallow and UV-transparent systems tend to have copepods with higher concentrations of MAAs but this has only been shown in a few species. A high MAA concentration has also been shown to lead to lower UV-induced mortality and an overall increased fitness. While there is a lot of information on MAAs in zooplankton we still lack understanding of the potential costs and constraints for accumulation. There is also scarce information in some taxa such as rotifers as well as from systems in tropical, sub(polar) areas as well as in marine systems in general.

[An analytical study of the patterns of the survival curves of experimental objects in model experiments on Daphnia magna.]

The phenomenon of multiphase survival curves found in drosophila is confirmed in experiments on daphnia. Mathematical modeling showed that the multiphase nature of the daphnia survival curves reflects abrupt changes in the intensity of death of crustaceans during the transition from phase to phase. In intact daphnia there is no phase of a sharp increase in mortality observed at an early age in drosophila. It arises as a reaction to weak negative influences, which leads to a sharp decrease in the survival of young individuals. A logical conclusion was made about the readiness for reaction of each experimental individual. The effect was observed in a series of experiments posed in different years. It is proved that in daphnia, the predisposition to reaction persists for an indefinitely large number of generations. It is postulated that this reaction has an epigenetic nature. Previous experimental materials suggest that a reaction of this type is widespread in natural surroundings.

Finding the fish factor

The water flea Daphnia moves to deeper waters to avoid predators when it detects a chemical produced by fish.

5α-cyprinol sulfate, a bile salt from fish, induces diel vertical migration in Daphnia

Prey are under selection to minimize predation losses. In aquatic environments, many prey use chemical cues released by predators, which initiate predator avoidance. A prominent example of behavioral predator-avoidance constitutes diel vertical migration (DVM) in the freshwater microcrustacean Daphnia spp., which is induced by chemical cues (kairomones) released by planktivorous fish. In a bioassay-guided approach using liquid chromatography and mass spectrometry, we identified the kairomone from fish incubation water as 5α-cyprinol sulfate inducing DVM in Daphnia at picomolar concentrations. The role of 5α-cyprinol sulfate in lipid digestion in fish explains why from an evolutionary perspective fish has not stopped releasing 5α-cyprinol sulfate despite the disadvantages for the releaser. The identification of the DVM-inducing kairomone enables investigating its spatial and temporal distribution and the underlying molecular mechanism of its perception. Furthermore, it allows to test if fish-mediated inducible defenses in other aquatic invertebrates are triggered by the same compound.

Sensory Ecology of Predator-Induced Phenotypic Plasticity

Ecological communities are organized in trophic levels that share manifold interactions forming complex food webs. Infochemicals can further modify these interactions, e.g., by inducing defenses in prey. The micro-crustacean Daphnia is able to respond to predator-specific chemical cues indicating an increased predation risk. Daphnia shows plastic responses by adapting its morphology, behavior, and physiology, increasing organism, and population fitness. This stabilizes community structures. This review will describe the progress that has been made in understanding the high degree of plasticity observed in the model crustacean Daphnia. I summarize current knowledge on the processes of predator detection, ranging from the nature of biologically active chemical cues to the underlying neurophysiological mechanisms. With this, I aim to provide a comprehensive overview on the molecular mechanisms of ad hoc environmental phenotypic adaptation. In times of climate change and pollution understanding information transfer in aquatic systems is valuable as it will allow us to predict whether and how community structures are being affected.

Mycoloop: chytrids in aquatic food webs

Parasites are ecologically significant in various ecosystems through their role in shaping food web structure, facilitating energy transfer, and controlling disease. Here in this review, we mainly focus on parasitic chytrids, the dominant parasites in aquatic ecosystems, and explain their roles in aquatic food webs, particularly as prey for zooplankton. Chytrids have a free-living zoosporic stage, during which they actively search for new hosts. Zoospores are excellent food for zooplankton in terms of size, shape, and nutritional quality. In the field, densities of chytrids can be high, ranging from 10(1) to 10(9) spores L(-1). When large inedible phytoplankton species are infected by chytrids, nutrients within host cells are transferred to zooplankton via the zoospores of parasitic chytrids. This new pathway, the "mycoloop," may play an important role in shaping aquatic ecosystems, by altering sinking fluxes or determining system stability. The grazing of zoospores by zooplankton may also suppress outbreaks of parasitic chytrids. A food web model demonstrated that the contribution of the mycoloop to zooplankton production increased with nutrient availability and was also dependent on the stability of the system. Further studies with advanced molecular tools are likely to discover greater chytrid diversity and evidence of additional mycoloops in lakes and oceans.

Light intensity controls anti-predator defences in Daphnia: the suppression of life-history changes

A huge variety of organisms respond to the presence of predators with inducible defences, each of which is associated with costs. Many genotypes have the potential to respond with more than one defence, and it has been argued that it would be maladaptive to exhibit all possible responses at the same time. Here, we test how a well-known anti-fish defence in Daphnia, life-history changes (LHC), is controlled by light. We show that the kairomone-mediated reduction in size at first reproduction is inversely coupled to the light intensity. A similar effect was found for the kairomone-mediated expression of candidate genes in Daphnia. We argue that the light intensity an individual is exposed to determines the degree of LHC, which allows for plastic adjustment to fluctuating environments and simultaneously minimizes the associated costs of multiple alternately deployable defences. It is hypothesized that this allows for a coupling of multiple defences, i.e. LHC and diel vertical migration.

Chronic toxicity of tire and road wear particles to water- and sediment-dwelling organisms

Tire and road wear particles (TRWP) consist of a complex mixture of rubber, and pavement released from tires during use on road surfaces. Subsequent transport of the TRWP into freshwater sediments has raised some concern about the potential adverse effects on aquatic organisms. Previous studies have shown some potential for toxicity for tread particles, however, toxicity studies of TRWP collected from a road simulator system revealed no acute toxicity to green algae, daphnids, or fathead minnows at concentrations up to 10,000 mg/kg under conditions representative of receiving water bodies. In this study, the chronic toxicity of TRWP was evaluated in four aquatic species. Test animals were exposed to whole sediment spiked with TRWP at concentrations up to 10,000 mg/kg sediment or elutriates from spiked sediment. Exposure to TRWP spiked sediment caused mild growth inhibition in Chironomus dilutus but had no adverse effect on growth or reproduction in Hyalella azteca. Exposure to TRWP elutriates resulted in slightly diminished survival in larval Pimephales promelas but had no adverse effect on growth or reproduction in Ceriodaphnia dubia. No other endpoints in these species were affected. These results, together with previous studies demonstrating no acute toxicity of TRWP, indicate that under typical exposure conditions TRWP in sediments pose a low risk of toxicity to aquatic organisms.

Daphnia HR96 is a promiscuous xenobiotic and endobiotic nuclear receptor

Daphnia pulex is the first crustacean to have its genome sequenced. The genome project provides new insight and data into how an aquatic crustacean may respond to environmental stressors, including toxicants. We cloned Daphnia pulex HR96 (DappuHR96), a nuclear receptor orthologous to the CAR/PXR/VDR group of nuclear receptors. In Drosophila melanogaster, (hormone receptor 96) HR96 responds to phenobarbital exposure and has been hypothesized as a toxicant receptor. Therefore, we set up a transactivation assay to test whether DappuHR96 is a promiscuous receptor activated by xenobiotics and endobiotics similar to the constitutive androstane receptor (CAR) and the pregnane X-receptor (PXR). Transactivation assays performed with a GAL4-HR96 chimera demonstrate that HR96 is a promiscuous toxicant receptor activated by a diverse set of chemicals such as pesticides, hormones, and fatty acids. Several environmental toxicants activate HR96 including estradiol, pyriproxyfen, chlorpyrifos, atrazine, and methane arsonate. We also observed repression of HR96 activity by chemicals such as triclosan, androstanol, and fluoxetine. Nearly 50% of the chemicals tested activated or inhibited HR96. Interestingly, unsaturated fatty acids were common activators or inhibitors of HR96 activity, indicating a link between diet and toxicant response. The omega-6 and omega-9 unsaturated fatty acids linoleic and oleic acid activated HR96, but the omega-3 unsaturated fatty acids alpha-linolenic acid and docosahexaenoic acid inhibited HR96, suggesting that these two distinct sets of lipids perform opposing roles in Daphnia physiology. This also provides a putative mechanism by which the ratio of dietary unsaturated fats may affect the ability of an organism to respond to a toxic insult. In summary, HR96 is a promiscuous nuclear receptor activated by numerous endo- and xenobiotics.

The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study, we used a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex is detectable at the genetic level, and if so, whether the genetic patterns seen are consistent with theoretical predictions. We show that there is variation in the genetic structure of these populations in a manner consistent with their investment in sexual reproduction. Populations engaging in a high frequency of sex were in Hardy-Weinberg and gametic phase equilibrium, and showed little genotypic differentiation across sampled years. In contrast, populations with a lower frequency of sex deviated widely from equilibrium, had reduced multilocus clonal diversity, and showed significant temporal genotypic deviation.

Alternative attractors of shallow lakes

Ponds and shallow lakes can be very clear with abundant submerged plants, or very turbid due to a high concentration of phytoplankton and suspended sediment particles. These strongly contrasting ecosystem states have been found to represent alternative attractors with distinct stabilizing feedback mechanisms. In the turbid state, the development of submerged vegetation is prevented by low underwater light levels. The unprotected sediment frequently is resuspended by wave action and by fish searching for food causing a further decrease of transparency. Since there are no plants that could serve as refuges, zooplankton is grazed down by fish to densities insufficient to control algal blooms. In contrast, the clear state in eutrophic shallow lakes is dominated by aquatic macrophytes. The submerged macrophytes prevent sediment resuspension, take up nutrients from the water, and provide a refuge for zooplankton against fish predation. These processes buffer the impacts of increased nutrient loads until they become too high. Consequently, the response of shallow lakes to eutrophication tends to be catastrophic rather than smooth, and various lakes switch back and forth abruptly between a clear and a turbid state repeatedly without obvious external forcing. Importantly, a switch from a turbid to a stable clear state often can be invoked by means of biomanipulation in the form of a temporary reduction of the fish stock.

Inferring Deleterious-Mutation Parameters in Natural Daphnia Populations

Deng and Lynch (1, 2) proposed to characterize deleterious genomic mutations from changes in the mean and genetic variance of fitness traits upon selfing in outcrossing populations. Such observations can be readily acquired in cyclical parthenogens. Selfing and life-table experiments were performed for two such Daphnia populations. A significant inbreeding depression and an increase of genetic variance for all traits analyzed were observed. Deng and Lynch's (2) procedures were employed to estimate the genomic mutation rate (U), mean dominance coefficient (), mean selection coefficient (), and scaled genomic mutational variance (). On average, and (^ indicates an estimate) are 0.84, 0.30, 0.14 and 4.6E-4 respectively. For the true values, the and are lower bounds, and and upper bounds.