Genomics. A genome for the environment

QSAR assessment of aquatic toxicity potential of diverse agrochemicals

The fast-increasing number of commercially produced chemicals challenges the experimental ecotoxicity assessment methods, which are costly, time-consuming, and dependent on the sacrifice of animals. In this regard, Quantitative Structure-Property/Activity Relationships (QSPR/QSAR) have led the way in developing ecotoxicity assessment models. In this study, QSAR models have been developed using the pEC50 values of 82 diverse agrochemicals or agro-molecules against a planktonic crustacean Daphnia magna with easily interpretable 2D descriptors. Moreover, a link among octanol-water partition coefficient (KOW), bio-concentration factor (BCF), and critical body residue (CBR) has been addressed, and their imputation for the prediction of the toxicity endpoint (EC50) has been done with an objective of the advanced exploration of several ecotoxicological parameters for toxic chemicals. The developed partial least squares (PLS) models were validated rigorously and proved to be robust, sound, and immensely well-predictive. The final Daphnia toxicity model derived from experimental derived properties along with computed descriptors emerged better in statistical quality and predictivity than those obtained solely from computed descriptors. Additionally, the pEC50 and other important properties (log KOW, log BCF, and log CBR) for a set of external agro-molecules, not employed in model development, were predicted to show the predictive ability of the models.

Synergistic toxic mechanisms of microplastics and triclosan via multixenobiotic resistance (MXR) inhibition-mediated autophagy in the freshwater water flea Daphnia magna

Since a mixed state of environmental contaminants, including microplastics (MPs), heavy metals, pharmaceuticals, and personal care products (PPCPs), exists in aquatic ecosystems, it is necessary to evaluate not only the adverse effects of exposure to a single stressor but to combined stressors. In this study, we exposed the freshwater water flea Daphnia magna to 2 μm MPs and triclosan (TCS), one of PPCPs, for 48 h to investigate the synergistic toxic consequences of simultaneous exposure to both pollutants. We measured in vivo endpoints, antioxidant responses, multixenobiotic resistance (MXR) activity, and autophagy-related protein expression via the PI3K/Akt/mTOR and MAPK signaling pathways. While MPs single exposure did not show toxic effects in water fleas, simultaneous exposure to TCS and MPs was associated with significantly greater deleterious effects in the form of increased mortality and alterations in antioxidant enzymatic activities compared with water fleas exposed to TCS alone. In addition, MXR inhibition was confirmed by measurement of the expression of P-glycoproteins and multidrug-resistance proteins in MPs-exposed groups, which led to the accumulation of TCS. Overall, these results suggest that simultaneous exposure to MPs and TCS resulted in higher TCS accumulation via MXR inhibition, leading to synergistic toxic effects such as autophagy in D. magna.

Acute toxicity, oxidative stress, and apoptosis due to short-term triclosan exposure and multi- and transgenerational effects on in vivo endpoints, antioxidant defense, and DNA damage response in the freshwater water flea Daphnia magna

In this study, we measured the acute toxicity of triclosan (TCS) in neonate and adult Daphnia magna water fleas. The median lethal concentrations were 184.689 and 349.511 μg/L, respectively. Oxidative stress induced by TCS was analyzed based on changes in reactive oxygen species (ROS) content and antioxidant enzymatic activities in D. magna. Based on these endpoints, TCS concentrations of 50 and 100 μg/L induced oxidative stress. However, several apoptosis-mediated proteins showed TCS-induced oxidative-stress damage in response to 25 μg/L, indicating that apoptotic proteins were the most sensitive mediators. We also evaluated the multi- and transgenerational effects of TCS on D. magna over three generations in terms of various in vivo endpoints, DNA damage responses, and biochemical reactions. The transgenerational group exposed to TCS exhibited greater negative impacts on antioxidant responses, DNA fragmentation status, and biological endpoints compared with the multigenerational exposure group, leading to decreased reproductive rates and higher ROS content. The transcriptional expression levels of glutathione S-transferase genes in the transgenerational exposure group were upregulated compared to those in the multigenerational group but were fully recovered in F2 offspring. Our findings provide an in-depth understanding of the adaptive effects of multigenerational exposure to TCS.

Short- and long-term single and combined effects of microplastics and chromium on the freshwater water flea Daphnia magna

In this study, we investigated the individual and combined effects of microplastics (MPs) and chromium (Cr) on the freshwater water flea Daphnia magna by measuring mortality, bioaccumulation, antioxidative response, multixenobiotic resistance activity, and sestrin-related mitochondrial biogenesis in short-term assays and in vivo endpoints including reproduction and adult survival rate in long-term assays. Exposure to MPs, Cr, and their combination caused significant deleterious effects and acute toxicity in D. magna. Alterations in oxidative stress occurred in the groups treated with MPs and Cr alone and together. However, upon co-exposure to MPs, the Cr concentration, measured by inductively coupled plasma optical emission spectroscopy, decreased, suggesting that MPs and Cr interact with each other. Based on enzymatic activities, we noted a decrease in MP egestion via inhibition of P-glycoprotein activity in the MP-exposed groups, and multidrug resistance-associated protein activity increased in some of the MP-exposed animals depending on Cr concentration. On the other hand, MP exposure seemed to lead to mitochondrial transcription dysfunction induced by Cr via sestrin-related mitochondrial biogenesis. Overall, these results indicate that co-exposure to MPs and Cr causes acute toxicity in D. magna but lacks the chronic toxicity (21 days) and mitochondrial dysfunction caused by Cr exposure alone.

Daphnia as a versatile model system in ecology and evolution

Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.

G protein-coupled receptors (GPCRs) in rotifers and cladocerans: Potential applications in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology

The G protein-coupled receptor (GPCR) superfamily plays a fundamental role in both sensory functions and the regulation of homeostasis, and is highly conserved across the eukaryote taxa. Its functional diversity is related to a conserved seven-transmembrane core and invariant set of intracellular signaling mechanisms. The interplay between these properties is key to the evolutionary success of GPCR. As this superfamily originated from a common ancestor, GPCR genes have evolved via lineage-specific duplications through the process of adaptation. Here we summarized information on GPCR gene families in rotifers and cladocerans based on their evolutionary position in aquatic invertebrates and their potential application in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology. Phylogenetic analyses were conducted to examine the evolutionary significance of GPCR gene families and to provide structural insight on their role in aquatic invertebrates. In particular, most GPCR gene families have undergone sporadic evolutionary processes, but some GPCRs are highly conserved across species despite the dynamics of GPCR evolution. Overall, this review provides a better understanding of GPCR evolution in aquatic invertebrates and expand our knowledge of the potential application of these receptors in various fields.

Genome-wide identification of 194 G protein-coupled receptor (GPCR) genes from the water flea Daphnia magna

In crustaceans, G protein-coupled receptors (GPCRs) are the largest transmembrane receptor family and function by mediating various environmental stimuli in cells. Understanding GPCR signaling is crucial to better understanding of crustacean endocrinology. GPCRs evolved from early eukaryotes, and genome-wide identification of GPCRs in a particular taxon can provide insight into evolutionary tendencies and adaptive strategies of GPCR response to environmental stimuli. Here, we identified 194 full-length GPCR genes in the water flea Daphnia magna that can be divided into five distinct classes (A, B, C, F, and other). A strong orthologous relationship for amine, neuropeptide, and opsin receptors was found in the phylogenetic comparison of D. magna GPCRs to those of humans and two well-known insects (Drosophila melanogaster and Solenopsis invicta). Our results based on phylogenetic relationships suggest that most GPCRs subfamilies have undergone sporadic evolutionary processes for adaptation to environmental pressures. Despite the dynamics of GPCR evolution, some GPCRs are highly conserved between species. This study provides a better understanding of the evolution of GPCRs and expands our knowledge of the potential physiological mechanisms in D. magna in response to various environmental stimuli.

Emerging trends in nanoparticle toxicity and the significance of using Daphnia as a model organism

Nanoparticle production is on the rise due to its many uses in the burgeoning nanotechnology industry. Although nanoparticles have growing applications, there is great concern over their environmental impact due to their inevitable release into the environment. With uncertainty of environmental concentration and risk to aquatic organisms, the microcrustacean Daphnia spp. has emerged as an important freshwater model organism for risk assessment of nanoparticles because of its biological properties, including parthenogenetic reproduction; small size and short generation time; wide range of endpoints for ecotoxicological studies; known genome, useful for providing mechanistic information; and high sensitivity to environmental contaminants and other stressors. In this review, we (1) highlight the advantages of using Daphnia as an experimental model organism for nanotoxicity studies, (2) summarize the impacts of nanoparticle physicochemical characteristics on toxicity in relation to Daphnia, and (3) summarize the effects of nanoparticles (including nanoplastics) on Daphnia as well as mechanisms of toxicity, and (4) highlight research uncertainties and recommend future directions necessary to develop a deeper understanding of the fate and toxicity of nanoparticles and for the development of safer and more sustainable nanotechnology.

Pollution induces epigenetic effects that are stably transmitted across multiple generations

It has been hypothesized that the effects of pollutants on phenotypes can be passed to subsequent generations through epigenetic inheritance, affecting populations long after the removal of a pollutant. But there is still little evidence that pollutants can induce persistent epigenetic effects in animals. Here, we show that low doses of commonly used pollutants induce genome‐wide differences in cytosine methylation in the freshwater crustacean Daphnia pulex. Uniclonal populations were either continually exposed to pollutants or switched to clean water, and methylation was compared to control populations that did not experience pollutant exposure. Although some direct changes to methylation were only present in the continually exposed populations, others were present in both the continually exposed and switched to clean water treatments, suggesting that these modifications had persisted for 7 months (>15 generations). We also identified modifications that were only present in the populations that had switched to clean water, indicating a long‐term legacy of pollutant exposure distinct from the persistent effects. Pollutant‐induced differential methylation tended to occur at sites that were highly methylated in controls. Modifications that were observed in both continually and switched treatments were highly methylated in controls and showed reduced methylation in the treatments. On the other hand, modifications found just in the switched treatment tended to have lower levels of methylation in the controls and showed increase methylation in the switched treatment. In a second experiment, we confirmed that sublethal doses of the same pollutants generate effects on life histories for at least three generations following the removal of the pollutant. Our results demonstrate that even low doses of pollutants can induce transgenerational epigenetic effects that are stably transmitted over many generations. Persistent effects are likely to influence phenotypic development, which could contribute to the rapid adaptation, or extinction, of populations confronted by anthropogenic stressors.

Evolution of tolerance to chlorpyrifos causes cross-tolerance to another organophosphate and a carbamate, but reduces tolerance to a neonicotinoid and a pharmaceutical

Exposure to pesticides is a major stressor in freshwater ecosystems. While populations can evolve tolerance to pesticides and thereby ensure their persistence in contaminated environments, this may have important consequences for their sensitivity to other pollutants. Indeed, tolerance to one pollutant may both increase (as a cost of tolerance) or decrease (cross-tolerance) the sensitivity to other pollutants. Despite the increasing concern of pharmaceuticals in waterbodies, no patterns of pesticide-induced (cross-)tolerance have been studied. We conducted 48 h acute toxicity assays with a range of concentrations of different pollutants to determine how the evolution of tolerance to the insecticide chlorpyrifos affects the sensitivity to other pesticides and a pharmaceutical in the water flea Daphnia magna, a keystone zooplankton species in aquatic food webs. We capitalized on an experimental evolution trial with chlorpyrifos, hence could unambiguously identify any patterns in increased tolerance or sensitivity to the other pollutants as a direct result of the evolution of tolerance to chlorpyrifos. We found that evolution of tolerance to chlorpyrifos conferred cross-tolerance to another organophosphate, namely malathion (mean change in EC_50,48h: factor 3.1), and to the carbamate carbaryl (factor 1.7), confirming that a shared mode of action favours the evolution of cross-tolerance. While the evolution of tolerance to chlorpyrifos did not affect the sensitivity to the pyrethroid esfenvalerate, it increased the sensitivity to the neonicotinoid imidacloprid as shown by the decrease in EC_50,48h (factor 0.6). Notably, we demonstrated for the first time that the evolution of tolerance to a pesticide increased the sensitivity to a pharmaceutical, namely fluoxetine (decrease in EC_50,48h with factor 0.7), thereby identifying an overlooked cost of tolerance to a pesticide. Given the increasing exposure to pesticides and pharmaceuticals, our results highlight that considering cross-tolerance and costs of tolerance is crucial in risk assessment of both pesticides and pharmaceuticals in aquatic ecosystems.

Combined exposure to microplastics and zinc produces sex-specific responses in the water flea Daphnia magna

Microplastics are ubiquitous environmental pollutants and a great threat to the aquatic environment. Due to their small size (ranging from 1 µm to 5 mm), microplastics be easily ingested by a wide range of organisms and can serve as a vector for various contaminants. In this study, additive or possible synergistic effects of microplastics and zinc were demonstrated through sex-specific alterations in behavior, redox status, and modulation of detoxification-related genes in Daphnia magna, with males being more sensitive than females with stronger modulations of antioxidant responses, particularly on glutathione S-transferases expressions. Furthermore, we demonstrated microplastics may act as vectors for metals (Zn²⁺) in the aquatic environment in D. magna, with reduced bio-concentration of the total Zn concentration, inducing greater toxicity. Our findings demonstrated synergistic toxicity of the heavy metal Zn and microplastics and could contribute to greater understanding of sex-specific effects of microplastics in aquatic organisms.

Model Systems in Ecology, Evolution, and Behavior: A Call for Diversity in Our Model Systems and Discipline

AbstractEcologists and evolutionary biologists are fascinated by life's variation but also seek to understand phenomena and mechanisms that apply broadly across taxa. Model systems can help us extract generalities from amid all the wondrous diversity, but only if we choose and develop them carefully, use them wisely, and have a range of model systems from which to choose. In this introduction to the Special Feature on Model Systems in Ecology, Evolution, and Behavior (EEB), we begin by grappling with the question, What is a model system? We then explore where our model systems come from, in terms of the skills and other attributes required to develop them and the historical biases that influence traditional model systems in EEB. We emphasize the importance of communities of scientists in the success of model systems-narrow scientific communities can restrict the model organisms themselves. We also consider how our discipline was built around one type of "model scientist"-a history still reflected in the field. This lack of diversity in EEB is unjust and also narrows the field's perspective, including by restricting the questions asked and talents used to answer them. Increasing diversity, equity, and inclusion will require acting at many levels, including structural changes. Diversity in EEB, in both model systems and the scientists who use them, strengthens our discipline.

The genome of the marine water flea Diaphanosoma celebensis: Identification of phase I, II, and III detoxification genes and potential applications in marine molecular ecotoxicology

To assemble the genome of the marine water flea Diaphanosoma celebensis, a sentinel model for marine environmental monitoring, we constructed a high-quality genome using PromethION and HiSeq 2500 platforms. The total length of the assembled genome was 100.08 Mb, with N50 = 2.56 Mb (benchmarking universal single-copy orthologs, 96.9%) and consisted of 179 scaffolds. A total of 15,427 genes were annotated, and orthologous gene clusters in D. celebensis were analyzed and compared with those of the cladocerans Daphnia magna and Daphnia pulex. In addition, phase I, II, and III detoxification gene families of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette were fully identified and revealed lineage-specific gene loss and/or expansion, suggesting that the evolution of detoxification gene families likely modulates fitness and susceptibility in response to environmental stressors. The study improves our understanding of the detoxification-related gene system and should contribute to future studies of molecular ecotoxicology in cladoceran species and their responses to emerging pollutants.

Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna

This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.

Knowing the Enemy: Inducible Defences in Freshwater Zooplankton

Phenotypic plasticity in defensive traits is an appropriate mechanism to cope with the variable hazard of a frequently changing predator spectrum. In the animal kingdom these so-called inducible defences cover the entire taxonomic range from protozoans to vertebrates. The inducible defensive traits range from behaviour, morphology, and life-history adaptations to the activation of specific immune systems in vertebrates. Inducible defences in prey species play important roles in the dynamics and functioning of food webs. Freshwater zooplankton show the most prominent examples of inducible defences triggered by chemical cues, so-called kairomones, released by predatory invertebrates and fish. The objective of this review is to highlight recent progress in research on inducible defences in freshwater zooplankton concerning behaviour, morphology, and life-history, as well as difficulties of studies conducted in a multipredator set up. Furthermore, we outline costs associated with the defences and discuss difficulties as well as the progress made in characterizing defence-inducing cues. Finally, we aim to indicate further possible routes in this field of research and provide a comprehensive table of inducible defences with respect to both prey and predator species.

Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics

The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.

The Mercury-Tolerant Microbiota of the Zooplankton Daphnia Aids in Host Survival and Maintains Fecundity under Mercury Stress

Many aquatic organisms can thrive in polluted environments by having the genetic capability to withstand suboptimal conditions. However, the contributions of microbiomes under these stressful environments are poorly understood. We investigated whether a mercury-tolerant microbiota can extend its phenotype to its host by ameliorating host survival and fecundity under mercury-stress. We isolated microbiota members from various clones of Daphnia magna, screened for the mercury-biotransforming merA gene, and determined their mercury tolerance levels. We then introduced the mercury-tolerant microbiota, Pseudomonas-10, to axenic D. magna and quantified its merA gene expression, mercury reduction capability, and measured its impact on host survival and fecundity. The expression of the merA gene was up-regulated in Pseudomonas-10, both in isolation and in host-association with mercury exposure. Pseudomonas-10 is also capable of significantly reducing mercury concentration in the medium. Notably, mercury-exposed daphnids containing only Pseudomonas-10 exhibited higher survival and fecundity than mercury-exposed daphnids supplemented with parental microbiome. Our study showed that zooplankton, such as Daphnia, naturally harbor microbiome members that are eco-responsive and tolerant to mercury exposure and can aid in host survival and maintain host fecundity in a mercury-contaminated environment. This study further demonstrates that under stressful environmental conditions, the fitness of the host can depend on the genotype and the phenotype of its microbiome.

Ageing differently: Sex-dependent ageing rates in Daphnia magna

Ageing is defined as the gradual decline of normal physiological functions in a time-dependent manner. Significant progress has been made in characterising the regulatory processes involved in the mechanisms of ageing which would have been hindered without the use of model organisms. Use of alternative model organisms greatly diversifies our understanding of different factors underpinning the ageing process and the potential translation for human application. Unique characteristics make Daphnia an attractive model organism for research into mechanisms underlying ageing, such as transparent body, short generation time, well-characterised methylome, regenerative capabilities and available naturally occurring ecotypes. Most interestingly, genetically identical female and male Daphnia have evolved different average lifespans, providing a unique opportunity for understanding the underlying mechanisms of ageing and regulation of lifespan. Investigating sex differences in longevity could provide insight into principal mechanisms of ageing and lifespan regulation. In this study we provide evidence in support of establishing genetically identical female and male Daphnia as unique and valuable resources for research into mechanisms of ageing and begin to delineate the mechanisms involved in sex differences in lifespan. We identify significant differences between genders in physiological markers such as lifespan, growth rate, heart rate and swimming speed in addition to molecular markers such as lipid peroxidation product accumulation, thiol content decline and age-dependent decline in DNA damage repair efficiency. Overall, our data indicates that investigating sex differences in longevity in the clonal organism Daphnia under controlled laboratory conditions can provide insight into principal mechanisms of ageing and lifespan regulation.

The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology

The water flea Daphnia magna is a small planktonic cladoceran. D. magna has been used as a model species for ecotoxicology, as it is sensitive to environmental stressors and environmental changes. Since Daphnia is affected by culture environment and each population/strain has its own ecological and genetic characteristics, its population/strain-based genome information is useful for environmental genomic studies. In this study, we assembled and characterized the genome of D. magna. Using a high-density genetic map of D. magna xinb3, the draft genome was integrated to 10 linkage groups (LGs). The total length of the integrated genome was about 123 Mb with N50 = 10.1 Mb, and the number of scaffolds was 4193 including 10 LGs. A total of 15,721 genes were annotated after manual curation. Orthologous genes were characterized in the genome and compared with other genomes of Daphnia. In addition, we identified defense related genes such as cytochrome P450 (CYP) genes, glutathione S-transferase (GST) genes, and ATP-binding cassette (ABC) genes from the assembled D. magna genome for its potential use in molecular ecotoxicological studies in the freshwater environment. This genomic resource will be helpful to study for a better understanding on molecular mechanism in response to various pollutants.

Carbonyl reductase sniffer from the model organism daphnia: Cloning, substrate determination and inhibitory sensitivity

Carbonyl reductases (CRs) represent a fundamental enzymatic defense mechanism against oxidative stress. While commonly two carbonyl reductases (CBR1 and CBR3) are found in mammalian genomes, invertebrate model organisms like Drosophila melanogaster express no CR but a functional homolog to human CBR1, termed sniffer. The importance of sniffer could be demonstrated in D. melanogaster where it protected against age-dependent neurodegeneration. Interestingly, the microcrustacean Daphnia harbors four copies of the CR gene (CR1, CR2, CR3, CR4) in addition to one sniffer gene. Due to this unique equipment Daphnia is an ideal model organism to investigate the function of sniffer. Recombinant sniffer from D. magna und D. pules were produced in E. coli, purified by Ni-affinity chromatography and tested with a variety of aliphatic and aromatic diketones, reactive aldehydes and precursors of advanced glycation end products (AGE). The highest catalytic activities were determined for sniffer from D. pulex with the aromatic dicarbonyls 9,10-phenanthrenequinone (k_cat/K_m = 2.6 s^-1 x μM^-1) and isatin (k_cat/K_m = 1.5 s^-1 x μM^-1). While sniffer from D. magna displayed preference for the same two substances, the respective catalytic activities were noticeably lower. Kinetic constants with aliphatic diketones were generally lower than those with aromatic dicarbonyls for both sniffer enzymes. The best aliphatic diketone as substrate for sniffer from D. magna and D. pulex was hexane-3,4-dione with k_cat/K_m = 0.23 s^-1 μM^-1 and k_cat/K_m = 0.35 s^-1 μM^-1, respectively. Poor or no detectable activity of the two sniffer enzymes was seen with the aliphatic diketones 2,5-hexanedione and 3,5-heptanedione, the aldehydes butanal, hexanal, decanal, crotonaldehyde, acrolein, trans-2-hexenal, and the AGE precursors glyoxal, methylglyoxal, furfural and glyceraldehyde, indicating no physiological function in the metabolism of short-chain aldehydes. Substrate inhibition for both sniffer enzymes was observed with the quinone substrates 1,4-naphthoquinone and 2-methyl-1,4-benzoquinone. From a variety of pesticides endosulfan turned out as an effective inhibitor of the sniffer enzymes (Ki = 9.2 μM for sniffer from D. magna, Ki = 12.0 μM for sniffer from D. pulex). In conclusion, the present results on sniffer from the protein superfamily of the short-chain dehydrogenases/reductases (SDR) in Daphnia ssp. complement earlier studies on carbonyl reductases in the same species and indicate that Daphnia is an interesting model to study the overall response to carbonyl stress.

Draft Genome Sequence of "Candidatus Spirobacillus cienkowskii," a Pathogen of Freshwater Daphnia Species, Reconstructed from Hemolymph Metagenomic Reads

We report here the near-complete genome sequence of “Candidatus Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.

We report here the near-complete genome sequence of “Candidatus Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.

Metabolite changes behind faster growth and less reproduction of Daphnia similis exposed to low-dose silver nanoparticles

With increasing presence of silver nanoparticles (AgNPs) into the environment, the chronic and low-dose effects of AgNPs are of vital concern. This study evaluated chronic physiological effects of AgNPs on Daphnia similis, which were exposed to two ambient encountered concentrations (0.02 and 1 ppb) of AgNPs for 21 days. It was observed that the low-dose AgNPs stimulated a significant increase in average length/dry mass, but inhibited reproduction compared to control specimens. Non-targeted metabolomics based on liquid chromatography-quadrupole-time of flight-mass spectrometry (LC-QTOFMS-MS) and gas chromatograph-quadrupole time of flight mass spectrometry (GC-QTOF-MS) were utilized to elucidate the underlying molecular mechanisms of these responses. Forty one metabolites were identified, including 18 significantly-changed metabolites, suggesting up regulation in protein digestion and absorption (amino acids, such as isoleucine, tryptophan, lysine, leucine, valine, aspartic acid, threonine, tyrosine) and down regulation of lipid related metabolism (fatty acids, such as arachidonic acid, stearidonic acid, linoelaidic acid and eicosapentaenoic acid) were key events in these responses. The increase in these amino acid contents explains the accelerated growth of D. similis from the metabolic pathway of aminoacyl-tRNA biosynthesis. Down regulation of fatty acid contents corresponds to the observed drop in the reproduction rate considering the fatty acid biological enzymatic reaction pathways. Significant changes in metabolites provided a renewed mechanistic understanding of low concentration chronic toxicity of AgNP toxicity on D. similis.

Carbonyl reductases from Daphnia are regulated by redox cycling compounds

Oxidative stress is a major source of reactive carbonyl compounds that can damage cellular macromolecules, leading to so-called carbonyl stress. Aside from endogenously formed carbonyls, including highly reactive short-chain aldehydes and diketones, air pollutants derived from diesel exhaust like 9,10-phenanthrenequinone (PQ) can amplify oxidative stress by redox cycling, causing tissue damage. Carbonyl reductases (CRs), which are inducible in response to ROS, represent a fundamental enzymatic defense mechanism against oxidative stress. While commonly two carbonyl reductases (CBR1 and CBR3) are found in mammalian genomes, invertebrate model organisms like Drosophila melanogaster express no CR but a functional homolog to human CBR1, termed sniffer. The microcrustacean Daphnia is an ideal model organism to investigate the function of CRs because of its unique equipment with even four copies of the CR gene (CR1, CR2, CR3, CR4) in addition to one sniffer gene. Cloning and catalytic characterization of two carbonyl reductases CR1 and CR3 from D. magna and D. pulex arenata revealed that both proteins reductively metabolize aromatic dicarbonyls (e.g., menadione, PQ) and aliphatic α-diketones (e.g., 2,3-hexanedione), while sugar-derived aldehydes (methylglyoxal, glyoxal) and lipid peroxidation products such as acrolein and butanal were poor substrates, indicating no physiological function in the metabolism of short-chain aldehydes. Treatment of D. magna with redox cyclers like menadione and the pesticide paraquat led to an upregulation of CR1 and CR3 mRNA, suggesting a role in oxidative stress defense. Further studies are needed to investigate their potential to serve as novel biomarkers for oxidative stress in Daphnia.

Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray

Background

Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D. magna.

Results

Up to 93% of the existing 41,317 D. magna gene models showed differential transcription patterns across the developmental stages of D. magna, 59% of which were functionally annotated. Embryos showed the highest number of unique transcribed genes, mainly related to DNA, RNA, and ribosome biogenesis, likely related to cellular proliferation and morphogenesis of the several body organs. Adult females showed an enrichment of transcripts for genes involved in reproductive processes. These female-specific transcripts were essentially absent in males, whose transcriptome was enriched in specific genes of male sexual differentiation genes, like doublesex.

Conclusion

Our results define major characteristics of transcriptional programs involved in the life-cycle, differentiate males and females, and show that large scale gene-transcription data collected in whole animals can be used to identify genes involved in specific biological and biochemical processes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4725-7) contains supplementary material, which is available to authorized users.

Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

The basic helix-loop-helix (bHLH) proteins represent a key group of transcription factors implicated in numerous eukaryotic developmental and signal transduction processes. Characterization of bHLHs from model species such as humans, fruit flies, nematodes and plants have yielded important information on their functions and evolutionary origin. However, relatively little is known about bHLHs in non-model organisms despite the availability of a vast number of high-throughput sequencing datasets, enabling previously intractable genome-wide and cross-species analyses to be now performed. We extensively searched for bHLHs in 126 crustacean species represented across major Crustacea taxa and identified 3777 putative bHLH orthologues. We have also included seven whole-genome datasets representative of major arthropod lineages to obtain a more accurate prediction of the full bHLH gene complement. With focus on important food crop species from Decapoda, we further defined higher-order groupings and have successfully recapitulated previous observations in other animals. Importantly, we also observed evidence for lineage-specific bHLH expansions in two basal crustaceans (branchiopod and copepod), suggesting a mode of evolution through gene duplication as an adaptation to changing environments. In-depth analysis on bHLH-PAS members confirms the phenomenon coined as 'modular evolution' (independently evolved domains) typically seen in multidomain proteins. With the amphipod Parhyale hawaiensis as the exception, our analyses have focused on crustacean transcriptome datasets. Hence, there is a clear requirement for future analyses on whole-genome sequences to overcome potential limitations associated with transcriptome mining. Nonetheless, the present work will serve as a key resource for future mechanistic and biochemical studies on bHLHs in economically important crustacean food crop species.

Adequacy of planctomycetes as supplementary food source for Daphnia magna

The nutritional quality of daphnids diet can influence their growth, reproduction and survival. In aquatic ecosystems, bacteria can contribute significantly to Daphnia diet by supporting, for instances, their high needs for phosphorus. The laboratory feeding of the model organisms Daphnia spp. is algal based, but should be improved to allow their better performance. The aim of this study was to evaluate the potential of two planctomycetes, Gemmata obscuriglobus and Rhodopirellula rubra, from exponential and stationary growth phases as alternative or supplementary food source for Daphnia magna. The actinobacterium Arthrobacter sp. was used for comparison. The feeding with only bacteria showed the inefficacy of both planctomycetes and actinobacteria as the only food source. However, when used in supplement to Raphidocelis subcapitata, a decrease in the age of first reproduction, a significant increase in reproductive output, in somatic growth and in rate of population increase was found for the highest cell densities of bacteria tested. The typical pink coloration of these bacteria present in daphnids body and eggs confirmed bacterial absorption and metabolization of their pigment. Planctomycetes yielded better results than the actinobacteria Arthrobacter but G. obscuriglobus that possesses sterols did not induce a better performance comparatively to R. rubra. No relation could be established between the feeding treatments that allowed improvement of Daphnia performance and the different kind of Daphnia' Fatty Acid Methyl Esters. The use of sonication to separate planctomycetal cells before feeding the daphnids proved to be efficient. We confirmed that R. subcapitata supplemented by bacteria allows a better growth performance of D. magna.

Temperature and food quantity effects on the harpacticoid copepod Nitocra spinipes: Combining in vivo bioassays with population modeling

The harpacticoid copepod Nitocra spinipes has become a popular model species for toxicity testing over the past few decades. However, the combined influence of temperature and food shortage, two climate change-related stressors, has never been assessed in this species. Consequently, effects of three temperatures (15, 20 and 25°C) and six food regimes (between 0 and 5 × 10⁵ algal cells/mL) on the life cycle of N. spinipes were examined in this study. Similarly to other copepod species, development times and brood sizes decreased with rising temperatures. Mortality was lowest in the 20°C temperature setup, indicating a close-by temperature optimum for this species. Decreasing food concentrations led to increased development times, higher mortality and a reduction in brood size. A sex ratio shift toward more females per male was observed for increasing temperatures, while no significant relationship with food concentration was found. Temperature and food functions for each endpoint were integrated into an existing individual-based population model for N. spinipes which in the future may serve as an extrapolation tool in environmental risk assessment. The model was able to accurately reproduce the experimental data in subsequent verification simulations. We suggest that temperature, food shortage, and potentially other climate change-related stressors should be considered in environmental risk assessment of chemicals to account for non-optimal exposure conditions that may occur in the field. Furthermore, we advocate combining in vivo bioassays with population modeling as a cost effective higher tier approach to assess such considerations.

TALEN-mediated knock-in via non-homologous end joining in the crustacean Daphnia magna

Transcription activator-like effector nucleases (TALENs) are versatile tools that enable the insertion of DNA into different organisms. Here, we confirmed TALEN-mediated knock-in via non-homologous end joining in the crustacean Daphnia magna, a model organism for ecological and toxicological genomics. We tested two different TALENs, ey1 TALEN and ey2 TALEN, both of which target the eyeless locus. The donor DNA plasmid, harbouring the H2B-GFP reporter gene, was designed to contain both TALEN target sites and was co-injected with each TALEN mRNA into eggs. The ey1 TALEN and ey2 TALEN constructs both resulted in H2B-GFP expression in Daphnia with a germline transmission efficiency of 3%. Of the three transgenic animals generated, two had donor DNA at the targeted genomic site, which suggested concurrent cleavage of the injected plasmid DNA and genome DNA. The availability of such tools that are capable of targeted knock-in of foreign genes will be extremely useful for advancing the knowledge of gene function and contribute to an increased understanding of functional genomics in Daphnia.

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna

BACKGROUND

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome.

RESULTS

A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates.

CONCLUSIONS

Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation

Background

Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia.

Results

Here we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods.

Conclusions

This research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel functional annotation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2998-2) contains supplementary material, which is available to authorized users.

Inducible Defenses with a "Twist": Daphnia barbata Abandons Bilateral Symmetry in Response to an Ancient Predator

Predation is one of the most important drivers of natural selection. In consequence a huge variety of anti-predator defenses have evolved in prey species. Under unpredictable and temporally variable predation pressure, the evolution of phenotypically plastic defensive traits is favored. These “inducible defenses”, range from changes in behavior, life history, physiology to morphology and can be found in almost all taxa from bacteria to vertebrates. An important group of model organisms in ecological, evolutionary and environmental research, water fleas of the genus Daphnia (Crustacea: Cladocera), are well known for their ability to respond to predators with an enormous variety of inducible morphological defenses. Here we report on the “twist”, a body torsion, as a so far unrecognized inducible morphological defense in Daphnia, expressed by Daphnia barbata exposed to the predatory tadpole shrimp Triops cancriformis. This defense is realized by a twisted carapace with the helmet and the tail spine deviating from the body axis into opposing directions, resulting in a complete abolishment of bilateral symmetry. The twisted morphotype should considerably interfere with the feeding apparatus of the predator, contributing to the effectiveness of the array of defensive traits in D. barbata. As such this study does not only describe a completely novel inducible defense in the genus Daphnia but also presents the first report of a free living Bilateria to flexibly respond to predation risk by abandoning bilateral symmetry.

Temperature-dependent benefits of bacterial exposure in embryonic development of Daphnia magna resting eggs

The environments in which animals develop and evolve are profoundly shaped by bacteria, which affect animals both indirectly through their roles in biogeochemical processes and also through direct antagonistic or beneficial interactions. The outcomes of these activities can differ according to environmental context. In a series of laboratory experiments with diapausing eggs of the water flea Daphnia magna, we manipulated two environmental parameters, temperature and presence of bacteria, and examined their effect on development. At elevated temperatures (≥26 °C), resting eggs developing without live bacteria had reduced hatching success and correspondingly higher rates of severe morphological abnormalities compared to eggs with bacteria in their environment. The beneficial effect of bacteria was strongly reduced at 20 °C. Neither temperature nor presence of bacteria affected directly developing parthenogenetic eggs. The mechanistic basis of this effect of bacteria on development is unclear, but these results highlight the complex interplay of biotic and abiotic factors influencing animal development after diapause.

A Population Biology Perspective on the Stepwise Infection Process of the Bacterial Pathogen Pasteuria ramosa in Daphnia

The infection process of many diseases can be divided into series of steps, each one required to successfully complete the parasite's life and transmission cycle. This approach often reveals that the complex phenomenon of infection is composed of a series of more simple mechanisms. Here we demonstrate that a population biology approach, which takes into consideration the natural genetic and environmental variation at each step, can greatly aid our understanding of the evolutionary processes shaping disease traits. We focus in this review on the biology of the bacterial parasite Pasteuria ramosa and its aquatic crustacean host Daphnia, a model system for the evolutionary ecology of infectious disease. Our analysis reveals tremendous differences in the degree to which the environment, host genetics, parasite genetics and their interactions contribute to the expression of disease traits at each of seven different steps. This allows us to predict which steps may respond most readily to selection and which steps are evolutionarily constrained by an absence of variation. We show that the ability of Pasteuria to attach to the host's cuticle (attachment step) stands out as being strongly influenced by the interaction of host and parasite genotypes, but not by environmental factors, making it the prime candidate for coevolutionary interactions. Furthermore, the stepwise approach helps us understanding the evolution of resistance, virulence and host ranges. The population biological approach introduced here is a versatile tool that can be easily transferred to other systems of infectious disease.

Ecology, Virulence, and Phylogeny of Blastulidium paedophthorum, a Widespread Brood Parasite of Daphnia spp

Parasitism is now recognized as a major factor impacting the ecology and evolution of plankton, including Daphnia. Parasites that attack the developing embryos of daphniids, known as brood parasites, were first described in the early 1900s but have received relatively little study. Here, we link previous morphological descriptions of the oomycete brood parasite Blastulidium paedophthorum with information on its phylogenetic placement, ecology, and virulence. Based on the morphology and phylogenetic relationship with other members of the Leptomitales, we show that a brood parasite observed in daphniids in the Midwestern United States is B. paedophthorum. We used morphology, DNA sequences, and laboratory infection experiments to show that B. paedophthorum is a multihost parasite that can be transmitted between species and genera. A field survey of six hosts in 15 lakes revealed that B. paedophthorum is common in all six host taxa (present on 38.3% of our host species-lake-sampling date combinations; the maximum infection prevalences were 8.7% of the population and 20% of the asexual adult female population). Although B. paedophthorum was observed in all 15 lakes, presence and infection prevalence varied among lakes. Infection with B. paedophthorum did not reduce host life span but significantly impacted host fecundity. Theory predicts that parasites that affect host fecundity without affecting host life span should have the strongest impact on host population dynamics. Based on its virulence and commonness in natural populations and on the central role of daphniids in freshwater food webs, we predict that B. paedophthorum will influence daphniid ecology and evolution, as well as the larger food web.

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.

Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold

Maturation is a critical developmental process, and the age and size at which it occurs have important fitness consequences. Although maturation is remarkably variable, certain mechanisms, including a minimum size or state threshold, are proposed to underlie the process across a broad diversity of taxa. Recent evidence suggests that thresholds may themselves be developmentally plastic, and in the crustacean Daphnia pulex it is unclear whether maturation follows a threshold or is a gradual process more akin to a rate. Changes in gene expression across four instars before and during maturation were compared in a cDNA microarray experiment. Developmental stage was treated statistically both as a discontinuous and as a continuous variable, to determine whether genes showed gradual or discrete changes in expression. The continuous analysis identified a greater number of genes with significant differential expression (45) than the discontinuous analysis (11). The majority of genes, including those coding for histones, factors relating to transcription and cell cycle processes, and a putative developmental hormone showed continuous increases or decreases in expression from the first to the fourth instars that were studied, suggestive of a prolonged and gradual maturation process. Three genes coding for a fused vitellogenin/superoxide dismutase showed increases in expression following the second instar and coincided with the posited maturation threshold, but even their expression increased in a continuous fashion.

An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits

Background

Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories.

Results

Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures.

Conclusions

The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1033) contains supplementary material, which is available to authorized users.

Longevity of Daphnia and the attenuation of stress responses by melatonin

Background

The widespread occurrence of melatonin in prokaryotes as well as eukaryotes indicates that this indoleamine is considerably old. This high evolutionary age has led to the development of diverse functions of melatonin in different organisms, such as the detoxification of reactive oxygen species and anti-stress effects. In insects, i.e. Drosophila, the addition of melatonin has also been shown to increase the life span of this arthropod, probably by reducing age-related increasing oxidative stress.

Although the presence of melatonin was recently found to exist in the ecological and toxicological model organism Daphnia, its function in this cladoceran has thus far not been addressed. Therefore, we challenged Daphnia with three different stressors in order to investigate potential stress-response attenuating effects of melatonin. i) Female and male daphnids were exposed to melatonin in a longevity experiment, ii) Daphnia were confronted with stress signals from the invertebrate predator Chaoborus sp., and iii) Daphnia were grown in high densities, i.e. under crowding-stress conditions.

Results

In our experiments we were able to show that longevity of daphnids was not affected by melatonin. Therefore, age-related increasing oxidative stress was probably not compensated by added melatonin. However, melatonin significantly attenuated Daphnia’s response to acute predator stress, i.e. the formation of neckteeth which decrease the ability of the gape-limited predator Chaoborus sp. to handle their prey. In addition, melatonin decreased the extent of crowding-related production of resting eggs of Daphnia.

Conclusions

Our results confirm the effect of melatonin on inhibition of stress-signal responses of Daphnia. Until now, only a single study demonstrated melatonin effects on behavioral responses due to vertebrate kairomones, whereas we clearly show a more general effect of melatonin: i) on morphological predator defense induced by an invertebrate kairomone and ii) on life history characteristics transmitted by chemical cues from conspecifics. Therefore, we could generally confirm that melatonin plays a role in the attenuation of responses to different stressors in Daphnia.

Daphnia longicephala neuropeptides: morphological description of crustacean cardioactive peptide (CCAP) and periviscerokinins in the Ctenodaphnia central nervous system

The publication of the Daphnia genome has driven research in this ecologically relevant model organism in many directions. However, information on this organism's physiology and the relevant controlling factors is limited. In this regard, especially neuropeptides are important biochemical regulators that control a variety of cellular processes, which in combination influence physiological conditions and allow the adaptation of the internal physiological state to external conditions. Thus, neuropeptides are prime in understanding an organism's physiology. We here aimed to detect and describe the distribution of evolutionary conserved neuropeptides including the crustacean cardioactive peptide (CCAP) and peptides of the family periviscerokinins (PVKs) in the central nervous system and the periphery of the Daphnia longicephala head region. We were able to identify a large pair of CCAP immunoreactive cells within central nervous system. In addition, in the periphery we found CCAP immunoreactive cells in the epidermis of the head with processes indicating cuticular secretion. Furthermore, we were able to identify and describe a complex neuronal circuit of PVK neuropeptides in the central nervous system. The data obtained in this study will provide important background information for future investigations aiming to unravel the cellular, neuronal and physiological pathways in a highly adaptive organism such as Daphnia.

Water fleas require microbiota for survival, growth and reproduction

Microbiota have diverse roles in the functioning of their hosts; experiments using model organisms have enabled investigations into these functions. In the model crustacean Daphnia, little knowledge exists about the effect of microbiota on host well being. We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts. We tested Daphnia coming from both lab-reared parthenogenetic eggs of a single genotype and from genetically diverse field-collected resting eggs. We showed that bacteria-free hosts are smaller, less fecund and have higher mortality than those with microbiota. We also manipulated the association by exposing bacteria-free Daphnia to a single bacterial strain of Aeromonas sp., and to laboratory environmental bacteria. These experiments further demonstrated that the Daphnia-microbiota system is amenable to manipulation under various experimental conditions. The results of this study have implications for studies of D. magna in ecotoxicology, ecology and environmental genomics.

Endocrinology: advances through omics and related technologies

The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.

Development and staging of the water flea Daphnia magna (Straus, 1820; Cladocera, Daphniidae) based on morphological landmarks

Background

Crustaceans of the genus Daphnia are one of the oldest model organisms in ecotoxicology, ecology and evolutionary biology. The publication of the Daphnia pulex genome has facilitated the development of genetic tools to answer long-standing questions in these research fields (Science 331: 555-561, 2011). A particular focus is laid on understanding the genetic basis of the striking ability of daphnids to change their phenotype in response to environmental stressors. Furthermore, Daphnia have recently been developed into crustacean model organisms for EvoDevo research, contributing to the ongoing attempt to resolve arthropod phylogeny. These problems require the comparative analyses of gene expression and functional data, which in turn require a standardized developmental staging system for Daphnia.

Results

Here we provide a detailed staging system of the embryonic development of Daphnia magna based on morphological landmarks. The staging system does not rely on developmental hours and is therefore suitable for functional and ecological experiments, which often cause developmental delays in affected embryos and thus shifts in time reference points. We provide a detailed description of each stage and include schematic drawings of all stages showing relevant morphological landmarks in order to facilitate the application of this staging scheme.

Conclusion

We present here a staging system for Daphnia magna, which is based on morphological landmarks. The staging system can be adopted for other daphnids with minor variations since the sequence of development is highly conserved during early stages and only minor heterochronic shifts occur in late embryonic stages.

Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog-dependent

Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1-mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species.

Effects of deltamethrin (pyrethroid insecticide) on growth, reproduction, embryonic development and sex differentiation in two strains of Daphnia magna (Crustacea, Cladocera)

Acute and different chronic ecotoxic effects of deltamethrin have been investigated on two strains (coming from two different laboratories) of Daphnia magna. The effective concentrations immobilizing 50% of daphnids (EC50s) after 24 h and 48 h were 9.40 and 0.32 μg L(-1), 8.86 and 0.63 μg L(-1) for first strain (strain 1) and second strain (strain 2), respectively. Thus, there was an increase of deltamethrin ecotoxicity with time of exposure as confirmed by chronic studies. After 21 days of exposure to deltamethrin, daphnids have showed significant effects on survival at deltamethrin concentrations of 0.16 μg L(-1) and 0.31 μg L(-1) for strains 1 and 2, respectively. Eleven other endpoints were examined: body length, population growth rate and various reproductive parameters (days to first brood, number of broods, number of cumulative molts and number of neonates), embryotoxicity and appearance of males. IC10 values related to the number of juveniles per live adult were 11 and 46 ng L(-1) for strains 1 and 2, respectively. Furthermore, an increase in embryo deformities was observed at the highest concentrations tested for both strains. Following deltamethrin exposure, undeveloped second antennae, curved or unextended shell spines, and curved post abdomen spines were observed in live neonates. The production of male juveniles was only registered with strain 1 at 0.16 μg L(-1). Results suggest that deltamethrin could act as an endocrine disruptor in D. magna as it interferes with sex determination and development abnormality but there is a difference in sensitivity between the two tested strains.

The hypergenome in inheritance and development

Both theory and experimentation suggest that during development, the DNA of multicellular organisms, recognized as graced with a lifelong intrinsic stability, is instead target of several modifications (point mutations, larger structural variations, epigenetic marks) and partner of complex interactions with non-DNA moieties (RNAs and proteins). Some of these modifications probably affect a fraction of the genome larger than standard point mutations and are more likely to respond to environmental cues. Thus, the traditional concepts of gene and genome need revision: the structure serving as depository of the overall bioinformation of the cell is more dynamic and less homogeneous than allowed for by the Central Dogma, since in addition to DNA, it includes also RNA and proteins. Each of the individual contributors as well as their stoichiometry undergo modifications. Compared to the traditional unidimensional and static genome, the resulting dynamic aggregate could be more competent to cope with different regulatory requirements: its structural variations may respond to unscheduled macro- and microenvironmental stresses as well as to scheduled genetic programs. A detailed assessment of these variations in time and space should provide a basis for a deeper comprehension of the phenotypic changes punctuating the organism's physio-pathological development, aging and transgenerational transmission. The variations of such information storage-delivery system may interest also the germ cells: the inheritance of parental traits and hence their evolutionary transmission would be affected. For the structure featuring all these properties, we propose the term 'hypergenome' to underscore the dynamic composition of a complex nucleoprotein responsive to both unpredictable environmental stimuli and internal built-in programs.