Daphnia as a versatile model system in ecology and evolution

Effects of microplastics on key reproductive and biochemical endpoints of the freshwater microcrustacean Daphnia magna

Human activities have directly impacted the environment, causing significant ecological imbalances. From the different contaminants resulting from human activities, plastics are of major environmental concern. Due to their high use and consequent discharge, plastics tend to accumulate in aquatic environments. There, plastics can form smaller particles (microplastics, MPs), due to fragmentation and weathering, which are more prone to interact with aquatic organisms and cause deleterious effects, including at the basis of different food webs. This study assessed the effects of two microplastics (polyethylene terephthalate, PET; and polypropylene, PP; both of common domestic use) in the freshwater cladoceran species Daphnia magna. Toxic effects were assessed by measuring reproductive traits (first brood and total number of offspring), and activities of biomarkers involved in xenobiotic metabolism (phase I: cytochrome P-450 isoenzymes CYP1A1, 1A2 and 3A4; phase II/conjugation: glutathione S-transferases; and antioxidant defense (catalase)). Both MPs showed a potential to significantly reduce reproductive parameters in D. magna. Furthermore, PET caused a significant increase in some isoenzymes of CYP450 in acutely exposed organisms, but this effect was not observed in chronically exposed animals. Similarly, the activity of the antioxidant defense (CAT) was significantly increased in acutely exposed animals, but not in chronically exposed organisms. This pattern of effects suggests a possible mechanism of long-term adaptation to the presence of the tested MPs. In conclusion, the herein tested MPs have shown the potential to induce deleterious effects on D. magna mainly observed in terms of the reproductive outcomes. Changes at the biochemical level seems transient and are not likely to occur in long term, environmentally exposed crustaceans.

Adverse effects of the 5-alpha-reductase inhibitor finasteride on Daphnia magna: Endocrine system and lipid metabolism disruption

Finasteride, a steroid 5-alpha reductase inhibitor, is commonly used for the treatment of benign prostatic hyperplasia and hair loss. However, despite continued use, its environmental implications have not been thoroughly investigated. Thus, we investigated the acute and chronic adverse impacts of finasteride on Daphnia magna, a crucial planktonic crustacean in freshwater ecosystems selected as bioindicator organism for understanding the ecotoxicological effects. Chronic exposure (for 23 days) to finasteride negatively affected development and reproduction, leading to reduced fecundity, delayed first brood, reduced growth, and reduced neonate size. Additionally, acute exposure (< 24 h) caused decreased expression levels of genes crucial for reproduction and development, especially EcR-A/B (ecdysone receptors), Jhe (juvenile hormone esterase), and Vtg2 (vitellogenin), with oxidative stress-related genes. Untargeted lipidomics/metabolomic analyses revealed lipidomic alteration, including 19 upregulated and 4 downregulated enriched lipid ontology categories, and confirmed downregulation of metabolites. Pathway analysis implicated significant effects on metabolic pathways, including the pentose phosphate pathway, histidine metabolism, beta-alanine metabolism, as well as alanine, aspartate, and glutamate metabolism. This comprehensive study unravels the intricate molecular and metabolic responses of D. magna to finasteride exposure, underscoring the multifaceted impacts of this anti-androgenic compound on a keystone species of freshwater ecosystems. The findings emphasize the importance of understanding the environmental repercussions of widely used pharmaceuticals to protect biodiversity in aquatic ecosystems.

Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp

The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia, the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii, a newly described microsporidian parasite of Daphnia. We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina, as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia-O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources.

IMPORTANCE

The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii. Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.

Zooplankton as a model to study the effects of anthropogenic sounds on aquatic ecosystems

There is a growing interest in the impact of acoustic pollution on aquatic ecosystems. Currently, research has primarily focused on hearing species, particularly fishes and mammals. However, species from lower trophic levels, including many invertebrates, are less studied despite their ecological significance. Among these taxa, studies examining the effects of sound on holozooplankton are extremely rare. This literature review examines the effects of sound on both marine and freshwater zooplankton. It highlights two differences: the few used organisms and the types of sound source. Marine studies focus on the effects of very intense acute sound on copepods, while freshwater studies focus on less intense chronic sound on cladocerans. But, in both, various negative effects are reported. The effects of sound remain largely unknown, although previous studies have shown that zooplankton can detect vibrations using mechanoreceptors. The perception of their environment can be affected by sounds, potentially causing stress. Limited research suggests that sound may affect the physiology, behaviour, and fitness of zooplankton. Following this review, I highlight the potential to use methods from ecology, ecotoxicology, and parasitology to study the effects of sound at the individual level, including changes in physiology, development, survival, and behaviour. Responses to sound, which could alter species interactions and population dynamics, are expected to have larger-scale implications with bottom-up effects, such as changes in food web dynamics and ecosystem functioning. To improve the study of the effect of sound, to better use zooplankton as biological models and as bioindicators, researchers need to better understand how they perceive their acoustic environment. Consequently, an important challenge is the measurement of particle motion to establish useable dose-response relationships and particle motion soundscapes.

Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna

The cladoceran crustacean Daphnia exhibits phenotypic plasticity, a phenomenon that leads to diverse phenotypes from one genome. Alternative usage of gene isoforms has been considered a key gene regulation mechanism for controlling different phenotypes. However, to understand the phenotypic plasticity of Daphnia, gene isoforms have not been comprehensively analyzed. Here we identified 25,654 transcripts derived from the 9710 genes expressed during environmental sex determination of Daphnia magna using the long-read RNA-Seq with PacBio Iso-Seq. We found that 14,924 transcripts were previously unidentified and 5713 genes produced two or more isoforms. By a combination of Illumina short-read RNA-Seq, we detected 824 genes that implemented switching of the highest expressed isoform between females and males. Among the 824 genes, we found isoform switching of an ortholog of CREB-regulated transcription coactivator, a major regulator of carbohydrate metabolism in animals, and a correlation of this switching event with the sexually dimorphic expression of carbohydrate metabolic genes. These results suggest that a comprehensive catalog of isoforms may lead to understanding the molecular basis for environmental sex determination of Daphnia. We also infer the applicability of the full-length isoform analyses to the elucidation of phenotypic plasticity in Daphnia.

The functional role of Daphnia in the host-pathogen interaction of crayfish and the crayfish plague disease agent (Aphanomyces astaci)

Pathogen spores have been recognized as prey with implications for resource dynamics, energy transfer and disease transmission. In aquatic ecosystems, filter-feeders are able to consume such motile forms of pathogens that can cause severe disease in susceptible hosts. The interactions between European crayfish and the crayfish plague pathogen Aphanomyces astaci are of particular conservation interest. In this study, we aim to evaluate the ecological interactions between Ap. astaci, its host Astacus astacus and individuals of the genus Daphnia, filter-feeding planktonic crustaceans. Our focus was on the consumption of the motile zoospores by Daphnia individuals, but we also considered the potential of Daphnia as non-target hosts. We conducted a series of infection and life-history experiments with Ap. astaci, three Daphnia species (D. magna, D. galeata, and D. pulex) and the noble crayfish As. astacus. We did not observe any lethal effects in the infection experiments involving Ap. astaci and Daphnia. Only D. pulex showed differences in some life-history traits. The feeding experiment using the motile zoospores of Ap. astaci as alternative food source or as supplement to different amounts of algal food revealed their nutritional value: D. magna individuals survived, grew, and reproduced on a zoospore diet alone. When zoospores were supplemented to the regular algal diet, all life-history parameters have been significantly improved. However, this successful consumption of zoospores did not result in a reduced mortality of the susceptible crayfish As. astacus during the infection experiment. Nevertheless, the pathogen load of Ap. astaci in the tissues of As. astacus was significantly reduced as a consequence of the feeding activity of Daphnia. Our results indicate that an abundant filter-feeding community can reduce the amount of infective zoospores in the water body and thus be beneficial to susceptible crayfish hosts, potentially acting as a general buffer against zoospore-transmitted diseases in lentic waters.

Enantioselectivity in ecotoxicity of pharmaceuticals, illicit drugs, and industrial persistent pollutants in aquatic and terrestrial environments: A review

At present, there is a serious concern about the alarming number of recalcitrant contaminants that can negatively affect biodiversity threatening the ecological status of marine, estuarine, freshwater, and terrestrial ecosystems (e.g., agricultural soils and forests). Contaminants of emerging concern (CEC) such as pharmaceuticals (PHAR), illicit drugs (ID), industrial persistent pollutants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) and chiral ionic solvents are globally spread and potentially toxic to non-target organisms. More than half of these contaminants are chiral and have been measured at different enantiomeric proportions in diverse ecosystems. Enantiomers can exhibit different toxicodynamics and toxicokinetics, and thus, can cause different toxic effects. Therefore, the enantiomeric distribution in occurrence cannot be neglected as the toxicity and other adverse biological effects are expected to be enantioselective. Hence, this review aims to reinforce the recognition of the stereochemistry in environmental risk assessment (ERA) of chiral CEC and gather up-to-date information about the current knowledge regarding the enantioselectivity in ecotoxicity of PHAR, ID, persistent pollutants (PCBs and PBDEs) and chiral ionic solvents present in freshwater and agricultural soil ecosystems. We performed an online literature search to obtain state-of-the-art research about enantioselective studies available for assessing the impact of these classes of CEC. Ecotoxicity assays have been carried out using organisms belonging to different trophic levels such as microorganisms, plants, invertebrates, and vertebrates, and considering ecologically relevant aquatic and terrestrial species or models organisms recommended by regulatory entities. A battery of ecotoxicity assays was also reported encompassing standard acute toxicity to sub-chronic and chronic assays and different endpoints as biomarkers of toxicity (e.g., biochemical, morphological alterations, reproduction, behavior, etc.). Nevertheless, we call attention to the lack of knowledge about the potential enantioselective toxicity of many PHAR, ID, and several classes of industrial compounds. Additionally, several questions regarding key species, selection of most appropriate toxicological assays and ERA of chiral CEC are addressed and critically discussed.

Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters

Understanding the spatial scales at which organisms can adapt to strong natural and human-induced environmental gradients is important. Salinization is a key threat to biodiversity, ecosystem functioning and the provision of ecosystem services of freshwater systems. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinization. We studied local adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes-a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. More saline bomb crater ponds showed an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show evolutionary adaptation to salinity gradients at different spatial scales, including fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.

Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system

Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.

Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations

Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.

Daphnia magna as a Model Organism to Predict the Teratogenic Effect of Different Compounds

For aquatic ecosystem Daphnia magna is evolving as a model organism to check the teratogenicity of numerous compounds. D. magna can be easily cultured in the laboratory, and the teratogen effect of several compounds can be easily studied. The developmental stages are well studied in D. magna. All the developmental stages are transparent so the defect can be easily accessed. So, the postembryonic developmental changes can be easily studied after the exposure with teratogen. More importantly, D. magna also have a swimming behavioral phenotype. The behavioral defect can be easily accessed after teratogen exposure. The current chapter summarizes numerous protocols associated with embryo and adult staining and adult behavioral assays that can be used to access the teratogenicity of any unknown compound.

Increased virulence due to multiple infection in Daphnia leads to limited growth in 1 of 2 co-infecting microsporidian parasites

Recent outbreaks of various infectious diseases have highlighted the ever-present need to understand the drivers of the outbreak and spread of disease. Although much of the research investigating diseases focuses on single infections, natural systems are dominated by multiple infections. These infections may occur simultaneously, but are often acquired sequentially, which may alter the outcome of infection. Using waterfleas (Daphnia magna) as a model organism, we examined the outcome of sequential and simultaneous multiple infections with 2 microsporidian parasites (Ordospora colligata and Hamiltosporidium tvaerminnensis) in a fully factorial design with 9 treatments and 30 replicates. We found no differences between simultaneous and sequential infections. However, H. tvaerminnensis fitness was impeded by multiple infection due to increased host mortality, which gave H. tvaerminnensis less time to grow. Host fecundity was also reduced across all treatments, but animals infected with O. colligata at a younger age produced the fewest offspring. As H. tvaerminnensis is both horizontally and vertically transmitted, this reduction in offspring may have further reduced H. tvaerminnensis fitness in co-infected treatments. Our findings suggest that in natural populations where both species co-occur, H. tvaerminnensis may evolve to higher levels of virulence following frequent co-infection by O. colligata.

Ultra-low esfenvalerate exposure may disrupt interspecific competition

Field and mesocosm studies repeatedly show that higher tier processes reduce the predictive accuracy of toxicity evaluation and thus their value for pesticide risk assessment. Therefore, understanding the influence of ecological complexity on toxicant effects is crucial to improve realism of aquatic risk assessment. Here we investigate the influence of repeated exposure to ecologically realistic concentrations of esfenvalerate on the two similarly sensitive species Daphnia magna and Culex pipiens in a food limited and highly competitive environment. We show that significant perturbations in population development are only present at 100 ng/L (close to the EC50). In contrast, interspecific competition between species is already reduced at 0.1 ng/L (≤ 3 orders of magnitude below the acute lethal EC50). We conclude that extremely low, environmentally relevant concentrations can disrupt species interactions. This toxicant mediated alteration of competitive balances in ecological communities may be the underlying mechanism for shifts in species distribution at ultra-low pesticide concentrations. A realistic risk assessment should therefore consider these processes in order to predict potential pesticide effects on the structure of communities.

Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna

The fitness of the host is highly influenced by the interplay between the host and its associated microbiota. The flexible nature of these microbiota enables them to respond swiftly to shifts in the environment, which plays a key role in the host's capacity to withstand environmental stresses. To understand the role of the microbiome in host tolerance to hypoxia, one of the most significant chemical changes occurring in water ecosystems due to climate change, we performed a reciprocal gut transplant experiment with the freshwater crustacean Daphnia magna. In a microbiome transplant experiment, two genotypes of germ-free recipients were inoculated with gut microbiota from Daphnia donors of their own genotype or from the other genotype, that had been either pre-exposed to normoxic or hypoxic conditions. We found that D. magna individuals had a higher survival probability in hypoxia if their microbiome had been pre-exposed to hypoxia. The bacterial communities of the recipients changed over time with a reduction in alpha diversity, which was stronger when donors were pre-exposed to a hypoxic environment. While donor genotype had no influence on the long-term survival probability in hypoxia, donor genotypes was the most influential factor of the microbial community 3 days after the transplantation. Our results indicate that microbiome influencing factors mediate host fitness in a hypoxic environment in a time depending way.

UPLC/ESI/MS profiling of red algae Galaxaura rugosa extracts and its activity against malaria mosquito vector, Anopheles pharoensis, with reference to Danio rerio and Daphnia magna as bioindicators

BACKGROUND

Anopheles pharoensis has a major role in transmitting several human diseases, especially malaria, in Egypt?. Controlling Anopheles is considered as an effective strategy to eliminate the spread of malaria worldwide. Galaxaura rugosa is a species of red algae found in tropical to subtropical marine environments. The presence of G. rugosa is indicative of the ecosystem's overall health. The current work aims to investigate UPLC/ESI/MS profile of G. rugosa methanol and petroleum ether extracts and its activity against An. pharoensis and non-target organisms, Danio rerio and Daphnia magna.

METHODS

Galaxaura rugosa specimens have been identified using DNA barcoding for the COI gene and verified as G. rugosa. The UPLC/ESI/MS profiling of G. rugosa collected from Egypt was described. The larvicidal and repellent activities of G. rugosa methanol and petroleum ether extracts against An. pharoensis were evaluated, as well as the toxicity of tested extracts on non-target organisms, Dan. rerio and Dap. magna.

RESULTS

The UPLC/ESI/MS analysis of methanol and petroleum ether extracts led to the tentative identification of 57 compounds belonging to different phytochemical classes, including flavonoids, tannins, phenolic acids, phenyl propanoids. Larval mortality was recorded at 93.33% and 90.67% at 80 and 35 ppm of methanol and petroleum ether extracts, respectively, while pupal mortality recorded 44.44 and 22.48% at 35 and 30 ppm, respectively. Larval duration was recorded at 5.31 and 5.64 days by methanol and petroleum ether extracts at 80 and 35 ppm, respectively. A decrease in acetylcholinesterase (AChE) level and a promotion in Glutathione-S-transferase (GST) level of An. pharoensis 3rd instar larvae were recorded by tested extracts. The petroleum ether extract was more effective against An. pharoensis starved females than methanol extract. Also, tested extracts recorded LC50 of 1988.8, 1365.1, and 11.65, 14.36 µg/mL against Dan. rerio, and Dap. magna, respectively.

CONCLUSIONS

Using red algae derivatives in An. pharoensis control could reduce costs and environmental impact and be harmless to humans and other non-target organisms.

The limits of stress-tolerance for zooplankton resting stages in freshwater ponds

In seasonal environments, many organisms evolve strategies such as diapause to survive stressful periods. Understanding the link between habitat stability and diapause strategy can help predict a population's survival in a changing world. Indeed, resting stages may be an important way freshwater organisms can survive periods of drought or freezing, and as the frequency and extent of drought or freezing vary strongly among habitats and are predicted to change with climate change, it raises questions about how organisms cope with, and survive, environmental stress. Using Daphnia magna as a model system, we tested the ability of resting stages from different populations to cope with stress during diapause. The combination of elevated temperatures and wet conditions during diapause shows to prevent hatching altogether. In contrast, hatching is relatively higher after a dry and warm diapause, but declines with rising temperatures, while time to hatch increases. Resting stages produced by populations from summer-dry habitats perform slightly, but consistently, better at higher temperatures and dryness, supporting the local adaptation hypothesis. A higher trehalose content in resting eggs from summer-dry habitat might explain such pattern. Considering that temperatures and summer droughts are projected to increase in upcoming years, it is fundamental to know how resting stages resist stressful conditions so as to predict and protect the ecological functioning of freshwater ecosystems.

Intraspecific genetic variation is critical to robust toxicological predictions of aquatic contaminants

Environmental risk assessment is a critical tool for protecting aquatic life and its effectiveness is predicated on predicting how natural populations respond to contaminants. Yet, routine toxicity testing typically examines only one genotype, which may render risk assessments inaccurate as populations are most often composed of genetically distinct individuals. To determine the importance of intraspecific variation in the translation of toxicity testing to populations, we quantified the magnitude of genetic variation within 20 Daphnia magna clones derived from one lake using whole genome sequencing and phenotypic assays. We repeated these assays across two exposure levels of microcystins, a cosmopolitan and lethal aquatic contaminant produced by harmful algal blooms. We found considerable intraspecific genetic variation in survival, growth, and reproduction, which was amplified by microcystins exposure. Finally, using simulations we demonstrate that the common practice of employing a single genotype to calculate toxicity tolerance failed to produce an estimate within the 95% confidence interval over half of the time. These results illuminate the importance of incorporating intraspecific genetic variation into toxicity testing to reliably predict how natural populations will respond to aquatic contaminants.

Multigenerational tests on Daphnia spp.: a vision and new perspectives

Multigenerational toxicity testing is a valuable tool for understanding the long-term effects of contaminants on aquatic organisms. This review focuses on the use of multigenerational tests with Daphnia, a widely used model organism in aquatic toxicological studies. The review highlights the importance of studying multiple generations to assess Daphnia spp. reproductive, growth, and physiological responses to various contaminants. We discuss the outcomes of multigenerational tests involving different contaminants, including nanoparticles, pesticides, and pharmaceuticals. The results reveal that multigenerational exposure can lead to transgenerational effects, where the impacts of contaminants are observed in subsequent generations even after the initial exposure has ceased. These transgenerational effects often manifest as reproduction, growth, and development alterations. Furthermore, we emphasize the need for standardized protocols in multigenerational testing to ensure comparability and reproducibility of results across studies. We also discuss the implications of multigenerational testing for ecological risk assessment, as it provides a more realistic representation of the long-term effects of contaminants on populations and ecosystems. Overall, this review highlights the significance of multigenerational tests with Daphnia in advancing our understanding of the ecological impacts of contaminants. Such tests provide valuable insights into the potential risks associated with long-term exposure to pollutants and contribute to the development of effective mitigation strategies for aquatic ecosystems.

Environmental Stress and the Morphology of Daphnia pulex

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

Can long-term salinity acclimation eliminate the inhibitory effect of salinization on anti-predation defense of Daphnia?

Freshwater salinization, due to road salt and other increased anthropogenic activities, has become a significant threat to freshwater organisms. However, whether freshwater salinization affects the response of aquatic organisms to their predators, especially prey that have been acclimated to salinity environments for a long time, remains unclear. In the present study, we investigated the changes in anti-predator defense of Daphnia magna with and without salinity acclimation at five different salinities (0, 0.6, 0.8, 0.10, and 0.12 M). Results showed that freshwater salinization weakened the induced defense response of D. magna, regardless of whether it had undergone long-term salinity acclimation. Specifically, induced defense traits such as smaller body size, higher relative spine length, more relative reproductive output, and smaller body size neonates disappeared at ≥ 0.08 M salinities. In addition, there were no significant differences in most traits of induced defense strength between D. magna with and without salinity acclimation at the same salinity. Importantly, the integrated induced defense response index decreased with increasing salinity. Our study showed that salinity-tolerant organisms do not recover their induced defense at high salinities, underlining the importance of incorporating interspecific interactions when estimating the effects of freshwater salinization on organisms.

Comparison between the gut bacterial community of laboratory cultured and wild Daphnia

The fitness of an organism is often impacted by the composition and biological activity of its associated bacterial community. Many factors, including host genetics, diet, and temperature can influence the bacterial community composition. Furthermore, these factors can differ strongly between natural and laboratory environments. Consequently, several studies have highlighted results from laboratory experiments investigating host-associated bacterial communities to be conflicting with those obtained under field conditions. Here, we compared the Daphnia magna gut bacterial communities in natural host populations with those of laboratory cultured hosts. We further analyzed changes in the gut bacterial communities after transferring hosts from natural populations to the laboratory on the short- and long-term. Results show that, in general, the gut bacterial communities from natural populations differ from those of laboratory cultures and that their composition and diversity changed one hour after being transferred to the laboratory. Over the following 14 days, the composition and diversity changed gradually. On the longer term (after two years of rearing hosts in the laboratory) the composition and diversity of the gut bacterial communities was strongly altered compared to the initial state. Our findings indicate that the gut bacterial communities of Daphnia magna in laboratory experiments is not representative for natural field conditions, and that caution should be taken when interpreting results from laboratory experiments for natural settings.

Marine-montane transitions coupled with gill and genetic convergence in extant crustacean

Marine-terrestrial transition represents an important aspect of organismal evolution that requires numerous morphological and genetic innovations and has been hypothesized to be caused by geological changes. We used talitrid crustaceans with marine-coastal-montane extant species at a global scale to investigate the marine origination and terrestrial adaptation. Using genomic data, we demonstrated that marine ancestors repeatedly colonized montane terrestrial habitats during the Oligocene to Miocene. Biological transitions were well correlated with plate collisions or volcanic island formation, and top-down cladogenesis was observed on the basis of a positive relationship between ancestral habitat elevation and divergence time for montane lineages. We detected convergent variations of convoluted gills and convergent evolution of SMC3 associated with montane transitions. Moreover, using CRISPR-Cas9 mutagenesis, we proposed that SMC3 potentially regulates the development of exites, such as talitrid gills. Our results provide a living model for understanding biological innovations and related genetic regulatory mechanisms associated with marine-terrestrial transitions.

Lipofuscin, amyloids, and lipid peroxidation as potential markers of aging in Daphnia

Accumulation of autofluorescent waste products, amyloids, and products of lipid peroxidation (LPO) are important hallmarks of aging. Until now, these processes have not been documented in Daphnia, a convenient model organism for longevity and senescence studies. We conducted a longitudinal cohort study of autofluorescence and Congo Red (CR) fluorescent staining for amyloids in four clones of D. magna. Additionally, we used a single time point cross-sectional common garden experiment within a single clone in which autofluorescence and BODIPY C11 fluorescence were measured. We observed a robust increase in autofluorescent spots that show diagnostic co-staining by Sudan Black indicating lipofuscin aggregates, particularly in the upper body region. There was also a significant clone-by-age interaction indicating that some genotypes accumulated lipofuscins faster than others. Contrary to predictions, CR fluorescence and lipid peroxidation did not consistently increase with age. CR fluorescence demonstrated a slight non-monotonous relationship with age, achieving the highest values at intermediate ages, possibly due to elimination of physiological heterogeneity in our genetically uniform cohorts. LPO demonstrated a significant ovary status-by-age interaction, decreasing with age when measured in Daphnia with full ovaries (late phase ovarian cycle) and showing no significant trend or slight increase with age when measured during the early phase in the ovarian cycle.

RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex

BACKGROUND

The genus Daphnia switches its reproductive mode from subitaneous egg production to resting egg production in response to environmental stimuli. Although this life history trait is essential for surviving unsuitable environments, the molecular mechanism of resting egg production is little understood. In this study, we examined genes related to induction of resting egg production using two genotypes of panarctic Daphnia pulex, the JPN1 and JPN2 lineages, which differ genetically in the frequency of resting egg production. We reared these genotypes under high and low food levels. At the high food level, individuals of both genotypes continually produced subitaneous eggs, whereas at the low food level, only the JPN2 genotype produced resting eggs. Then, we performed RNA-seq analysis on specimens of three instars, including before and after egg production.

RESULTS

These results showed that expressed genes differed significantly between individuals grown under high and low food levels and among individuals of different instars and genotypes. Among these differentially expressed genes (DEGs), we found 16 that changed expression level before resting egg production. Some of these genes showed high-level expression only before resting egg production and one gene was an ortholog of bubblegum (bgm), which is reportedly up-regulated before diapause in bumblebees. According to gene ontology (GO) enrichment analysis, one GO term annotated as long-chain fatty acid biosynthetic process was enriched among these 16 genes. In addition, GO terms related to glycometabolism were enriched among down-regulated genes of individuals holding resting eggs, compared to those before resting egg production.

CONCLUSIONS

We found candidate genes highly expressed only before resting egg production. Although functions of candidate genes found in this study have not been reported previously in Daphnia, catabolism of long-chain fatty acids and metabolism of glycerates are related to diapause in other organisms. Thus, it is highly probable that candidate genes identified in this study are related to the molecular mechanism regulating resting egg production in Daphnia.

Systemic Alterations of Cancer Cells and Their Boost by Polyploidization: Unicellular Attractor (UCA) Model

Using meta-analyses, we introduce a unicellular attractor (UCA) model integrating essential features of the ‘atavistic reversal’, ‘cancer attractor’, ‘somatic mutation’, ‘genome chaos’, and ‘tissue organization field’ theories. The ‘atavistic reversal’ theory is taken as a keystone. We propose a possible mechanism of this reversal, its refinement called ‘gradual atavism’, and evidence for the ‘serial atavism’ model. We showed the gradual core-to-periphery evolutionary growth of the human interactome resulting in the higher protein interaction density and global interactome centrality in the UC center. In addition, we revealed that UC genes are more actively expressed even in normal cells. The modeling of random walk along protein interaction trajectories demonstrated that random alterations in cellular networks, caused by genetic and epigenetic changes, can result in a further gradual activation of the UC center. These changes can be induced and accelerated by cellular stress that additionally activates UC genes (especially during cell proliferation), because the genes involved in cellular stress response and cell cycle are mostly of UC origin. The functional enrichment analysis showed that cancer cells demonstrate the hyperactivation of energetics and the suppression of multicellular genes involved in communication with the extracellular environment (especially immune surveillance). Collectively, these events can unleash selfish cell behavior aimed at survival at all means. All these changes are boosted by polyploidization. The UCA model may facilitate an understanding of oncogenesis and promote the development of therapeutic strategies.

Molecular Responses of Daphnids to Chronic Exposures to Pharmaceuticals

Pharmaceutical compounds are among several classes of contaminants of emerging concern, such as pesticides, heavy metals and personal care products, all of which are a major concern for aquatic ecosystems. The hazards posed by the presence of pharmaceutical is one which affects both freshwater organisms and human health-via non-target effects and by the contamination of drinking water sources. The molecular and phenotypic alterations of five pharmaceuticals which are commonly present in the aquatic environment were explored in daphnids under chronic exposures. Markers of physiology such as enzyme activities were combined with metabolic perturbations to assess the impact of metformin, diclofenac, gabapentin, carbamazepine and gemfibrozil on daphnids. Enzyme activity of markers of physiology included phosphatases, lipase, peptidase, β-galactosidase, lactate dehydrogenase, glutathione-S-transferase and glutathione reductase activities. Furthermore, targeted LC-MS/MS analysis focusing on glycolysis, the pentose phosphate pathway and the TCA cycle intermediates was performed to assess metabolic alterations. Exposure to pharmaceuticals resulted in the changes in activity for several enzymes of metabolism and the detoxification enzyme glutathione-S-transferase. Metabolic perturbations on key pathways revealed distinct groups and metabolic fingerprints for the different exposures and their mixtures. Chronic exposure to pharmaceuticals at low concentrations revealed significant alterations of metabolic and physiological endpoints.

Differential susceptibility to arsenic in glutathione S-transferase omega 2 (GST-O2)-targeted freshwater water flea Daphnia magna mutants

To examine the role of glutathione S-transferase omega class (GST-O2) genes in the biotransformation and detoxification in Daphnia magna, various responses such as in vivo endpoints, arsenic speciation, enzymatic activities, and gene expression pathways related to arsenic metabolism were investigated in wild-type (WT) and GST-O2-mutant-type (MT) fleas produced by CRISPR/Cas9. Sensitivity to arsenic in MT fleas was higher than in WT fleas. Also, the reduction rate of arsenate (As^V) to arsenite (As^III) in the MT group was significantly lower and led to accumulation of higher arsenic concentrations, resulting in decreased protection against arsenic toxicity. Relative mRNA expression of other GST genes in the GST-O2-targeted MT group generally increased but the enzymatic activity of GST decreased compared with the WT group. Oxidative stress on arsenic exposure was more strongly induced in the MT group compared with the WT group, resulting in a decrease in the ability to defend against toxicity in GST-O2-targeted mutant D. magna. Our results suggest that GST-O2 plays an important role in arsenic biotransformation and detoxification functions in D. magna.

Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics

Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".