The ecoresponsive genome of Daphnia pulex

New genes helped acorn barnacles adapt to a sessile lifestyle

Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.

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 cuticle proteome of a planktonic crustacean

The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the D. magna genome. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.

Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.

Antidepressants - The new endocrine disruptors? The case of crustaceans

Antidepressants are high-volume pharmaceuticals that accumulate to concentrations in the μg·L-1 range in surface waters. The release of peptide hormones via neurosecretory cells appears as a natural target for antidepressants. Here I review research that suggests that antidepressants indeed disrupt endocrine signalling in crustaceans, by acting on the synthesis and release of neurohormones, such as crustacean hyperglycaemic hormone, moult inhibiting hormone and pigment dispersing hormone in decapods, as well as methyl farnesoate in Daphnids. Hence, antidepressants can affect hormonal regulation of physiological functions: increase in energy metabolism and activity, lowered ecdysteroid levels, potentially disrupting moult and somatic growth, reducing colour change capacity and compromising camouflage, as well as induction of male sex determination. Several studies further suggest effects of antidepressants on crustacean reproduction, but the hormonal regulation of these effects remains elusive. All things considered, a body of evidence strongly suggests that antidepressants are endocrine disrupting compounds in crustaceans.

RNA-seq analysis reveals changes in mRNA expression during development in Daphnia mitsukuri

Temporal transcriptional variation is a major contributor to functional evolution and the developmental process. Parthenogenetic water fleas of the genus Daphnia (Cladocera) provide an ideal model to characterize gene expression patterns across distinct developmental stages. Herein, we report RNA-seq data for female Daphnia mitsukuri at three developmental stages: the embryo, juvenile (three timepoints) and adult. Comparisons of gene expression patterns among these three developmental stages and weighted gene co-expression network analysis based on expression data across developmental stages identified sets of genes underpinning each of the developmental stages of D. mitsukuri. Specifically, highly expressed genes (HEGs) at the embryonic developmental stage were associated with cell proliferation, ensuring the necessary foundation for subsequent development; HEGs at the juvenile stages were associated with chemosensory perception, visual perception and neurotransmission, allowing individuals to enhance detection of potential environmental risks; HEGs at the adult stage were associated with antioxidative defensive systems, enabling adults to mount an efficient response to perceived environmental risks. Additionally, we found a significant overlap between expanded gene families of Daphnia species and HEGs at the juvenile stages, and these genes were associated with visual perception and neurotransmission. Our work provides a resource of developmental transcriptomes, and comparative analyses that characterize gene expression dynamics throughout development of Daphnia.

Combined effects of spinetoram and Microcystis aeruginosa on Daphnia pulex offspring: Maternal effects and multigenerational implications

The increasing occurrence of harmful algal blooms (HABs) in freshwater ecosystems detrimentally affect global water environments. Zooplankton's role in controlling HABs is hindered by contaminant exposure, necessitating research into combined stressors' ecological impacts. The response of Daphnia, a freshwater keystone species, to environmental stressors can be influenced by its maternal effects. Here, we investigated the combined effects of the world-widely used insecticide spinetoram and non-toxic HABs species Microcystis aeruginosa on the life-history traits of D. pulex offspring produced from different maternal food conditions. Four maternal groups were established, with each group receiving a specific blend of C. vulgaris (Ch) and M. aeruginosa (Ma) in varying proportions: A (100% Ch), B (90% Ch + 10% Ma), C (80% Ch + 20% Ma), and D (70% Ch + 30% Ma). The offspring from the third brood were gathered, and a 21-day experiment was carried out, involving various feeding groups (AA, AD, BA, BB, CA, CC, DA, and DD). Results demonstrated that grazing on M. aeruginosa by D. pulex induced maternal effects on their offspring, with the continuous exposure group showing an enhanced tolerance to M. aeruginosa. This study also unveiled that spinetoram could interfere with the molting of D. pulex, leading to developmental retardation. The Recovery Group exhibited an intriguing phenomenon: under the influence of both concentrations of the pesticide spinetoram (0.18, 0.35 μg L-1), D. pulex produced more offspring. This might be due to a combined strategy of allocating more energy towards reproduction in response to low-quality food and a potential hormetic effect from low concentrations of spinetoram. Assessing the interplay of combined stressors across multiple generations, encompassing harmful algal blooms (HABs) and environmental pollutants, is essential for predicting population responses to evolving environmental conditions. This understanding is vital for the protection and management of aquatic environments and ecosystems.

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.

Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum

In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.

Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events

Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.

Daphnia magna Multigeneration Exposure to Carbendazim: Gene Transcription Responses

The world population is experiencing colossal growth and thus demand for food, leading to an increase in the use of pesticides. Persistent pesticide contamination, such as carbendazim, remains a pressing environmental concern, with potentially long-term impacts on aquatic ecosystems. In the present study, Daphnia magna was exposed to carbendazim (5 µg L-1) for 12 generations, with the aim of assessing gene transcription alterations induced by carbendazim (using a D. magna custom microarray). The results showed that carbendazim caused changes in genes involved in the response to stress, DNA replication/repair, neurotransmission, ATP production, and lipid and carbohydrate metabolism at concentrations already found in the environment. These outcomes support the results of previous studies, in which carbendazim induced genotoxic effects and reproduction impairment (increasing the number of aborted eggs with the decreasing number of neonates produced). The exposure of daphnids to carbendazim did not cause a stable change in gene transcription between generations, with more genes being differentially expressed in the F0 generation than in the F12 generation. This could show some possible daphnid acclimation after 12 generations and is aligned with previous multigenerational studies where few ecotoxicological effects at the individual and populational levels and other subcellular level effects (e.g., biochemical biomarkers) were found.

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.

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

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

No recombination suppression in asexually produced males of Daphnia pulex

Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex, OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-density linkage maps, we find that these males show only slightly and nonsignificantly reduced recombination rates compared to CP males and females. Both meiosis disruption and recombination suppression are therefore sex-limited (or partly so), which speaks against the evolution of OP by disruption of a gene that is essential for meiosis or recombination in both sexes. The findings may be explained by female-limited action of genes that suppress recombination, but previously identified candidate genes are known to be expressed in both sexes. Alternatively, and equally consistent with the data, OP might have evolved through a reuse of the parthenogenesis pathways already present in CP and through their extension to all events of oogenesis. The causal mutations for the CP to OP transition may therefore include mutations in genes involved in oogenesis regulation and may not necessarily be restricted to genes of the "meiosis toolkit." More generally, our study emphasizes that there are many ways to achieve asexuality, and elucidating the possible mechanisms is key to ultimately identify the genes and traits involved.

Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics

While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.

Gene identification and RNAi-silencing of p62/SQSTM1 in the vector Rhodnius prolixus reveals a high degree of sequence conservation but no apparent deficiency-related phenotypes in vitellogenic females

Autophagy and the ubiquitin-proteasome system (UPS) are important cellular mechanisms that coordinate protein degradation essential for proteostasis. P62/SQSTM1 is a receptor cargo protein able to deliver ubiquitinated targets to the proteasome proteolytic complex and/or to the autophagosome. In the insect vector of Chagas disease, Rhodnius prolixus, previous works have shown that the knockdown of different autophagy-related genes (ATGs) and ubiquitin-conjugating enzymes resulted in abnormal oogenesis phenotypes and embryo lethality. Here, we investigate the role of the autophagy/UPS adaptor protein p62 during the oogenesis and reproduction of this vector. We found that R. prolixus presents one isoform of p62 encoded by a non-annotated gene. The predicted protein presents the domain architecture anticipated for p62: PB1 (N-term), ZZ-finger, and UBA (C-term) domains, and phylogenetic analysis showed that this pattern is highly conserved within insects. Using parental RNAi, we found that although p62 is expressed in the ovary, midgut, and fat body of adult females, systemic silencing of this gene did not result in any apparent phenotypes under in-house conditions. The insects' overall levels of blood meal digestion, lifespan, yolk protein production, oviposition, and embryo viability were not altered when compared to controls. Because it is known that autophagy and UPS can undergo compensatory mechanisms, we asked whether the silencing of p62 was triggering adaptative changes in the expression of genes of the autophagy, UPS, and the unfolded protein response (UPR) and found that only ATG1 was slightly up regulated in the ovaries of silenced females. In addition, experiments to further investigate the role of p62 in insects previously silenced for the E1-conjugating enzyme (a condition known to trigger the upregulation of p62), also did not result in any apparent phenotypes in vitellogenic females.

Chromosome-scale genome assembly of the freshwater cladoceran crustacean Chydorus sphaericus: A resource for discovery of genes responsive to ecological challenges

The genus Chydorus Leach 1816 (family Chydoridae) is a diverse and ecologically important taxon within freshwater ecosystems. Despite having been widely used in ecological, evolutionary and eco-toxicological studies, no high-quality genomic resource is available for any member of the genus. Here, we present a high-quality chromosome-level assembly of the C. sphaericus genome by combining 7.40 Gb (∼ 50 × coverage) PacBio reads, 19.28 Gb (∼ 135 × coverage) Illumina paired-end reads, and 34.04 Gb Hi-C reads. Our genome assembly is approximately 151 Mb, with contig and scaffold N50 lengths of 1.09 Mb and 13.70 Mb, respectively. The assembly captured 94.9% of the complete eukaryotic BUSCO. Repetitive elements accounted for 17.6% of the genome, and 13,549 protein-coding genes were predicted (based on transcriptome sequencing data, ab-initio or homology-based prediction), of which 96.4% have been functionally annotated in the NCBI-NR database. We identified 303 gene families specific to C. sphaericus, mainly families enriched in functions related to immune response, visual senses and detoxification. Interestingly, we also found 53 significantly expanded gene families in C. sphaericus, mostly with functions related to detoxification. This high-quality assembly genome will act as a reference genome for C. sphaericus and benefit studies on functional and comparative genomics of Chydorus and other crustaceans.

The stereoselective toxicity of dinotefuran to Daphnia magna: A systematic assessment from reproduction, behavior, oxidative stress and digestive function

Dinotefuran is a promising neonicotinoid insecticide with chiral structure. In the present study, the stereoselective toxicity of dinotefuran to Daphnia magna (D. magna) was studied. The present result showed that S-dinotefuran inhibited the reproduction of D. magna at 5.0 mg/L. However, both R-dinotefuran and S-dinotefuran had no genotoxicity to D. magna. Additionally, neither R-dinotefuran nor S-dinotefuran had negative influences on the motor behavior of D. magna. However, S-dinotefuran inhibited the feeding behavior of D. magna at 5.0 mg/L. Both R-dinotefuran and S-dinotefuran induced oxidative stress effect in D. magna after exposure. R-dinotefuran significantly activated the activities of superoxide dismutase (SOD) and glutathione S-transferase (GST), while S-dinotefuran showed the opposite effect. S-dinotefuran had more obvious activation effect on the acetylcholinesterase (AchE) activity and trypsin activity compared to R-dinotefuran. The transcriptome sequencing results showed that S-dinotefuran induced more DEGs in D. magna, and affected the normal function of ribosome. The DEGs were mainly related to the synthesis and metabolism of biomacromolecules, indicating the binding mode between dinotefuran enantiomer and biomacromolecules were different. Additionally, the present result indicated that the digestive enzyme activity and digestive gene expression levels in D. magna were greatly enhanced to cope with the inhibition of S-dinotefuran on the feeding.

Anti-Aging Effects of Quercetin in Cladocera Simocephalus vetulus Using Proteomics

Quercetin is a flavonoid widely found in food and traditional herbs. In this study, we evaluated the anti-aging effects of quercetin on Simocephalus vetulus (S. vetulus) by assessing lifespan and growth parameters and analyzed the differentially expressed proteins and crucial pathways associated with quercetin activity using proteomics. The results demonstrated that, at a concentration of 1 mg/L, quercetin significantly prolonged the average and maximal lifespans of S. vetulus and increased the net reproduction rate slightly. The proteomics-based analysis revealed 156 differently expressed proteins, with 84 being significantly upregulated and 72 significantly downregulated. The protein functions were identified as being associated with glycometabolism, energy metabolism, and sphingolipid metabolism pathways, and the key enzyme activity and related gene expression, such that of AMPK, supported the importance of these pathways in the anti-aging activity of quercetin. In addition, quercetin was found to regulate the anti-aging-related proteins Lamin A and Klotho directly. Our results increased the understanding of quercetin's anti-aging effects.

The impact of pharmaceutical pollutants on daphnids - A metabolomic approach

Pharmaceuticals have been classified as emerging contaminants in the aquatic ecosystem, mainly due to their increased use and improper disposal. A significant range of pharmaceutical compounds and their metabolites have been globally detected in surface waters and pose detrimental effects to non-target organisms. Monitoring pharmaceutical water pollution relies on the analytical approaches for their detection, however, such approaches are limited by their sensitivity limit and coverage of the wide range pharmaceutical compounds. This lack of realism in risk assessment is bypassed with effect-based methods, which are complemented by chemical screening and impact modelling, and are able to provide mechanistic insight for pollution. Focusing on the freshwater ecosystem, in this study we evaluated the acute effects on daphnids for three distinct groups of pharmaceuticals; antibiotics, estrogens, and a range of commonly encountered environmentally relevant pharmaceutical pollutants. Combining several endpoints such as mortality, biochemical (enzyme activities) and holistic (metabolomics) we discovered distinct patterns in biological responses. In this study, changes in enzymes of metabolism e.g. phosphatases and lipase, as well as the detoxification enzyme, glutathione-S-transferase, were recorded following acute exposure to the selected pharmaceuticals. A targeted analysis of the hydrophilic profile of daphnids revealed mainly the up-regulation of metabolites following metformin, gabapentin, amoxicillin, trimethoprim and β-estradiol. Whereas gemfibrozil, sulfamethoxazole and oestrone exposure resulted in the down-regulation of majority of metabolites.

The Precision Toxicology Initiative

The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distantly related animals. An international consortium is systematically testing the toxicological effects of a diverse set of chemicals on a suite of five model species comprising fruit flies, nematodes, water fleas, and embryos of clawed frogs and zebrafish along with human cell lines. Multiple forms of omics and comparative toxicology data are integrated to map the evolutionary origins of biomolecular interactions, which are predictive of adverse health effects, to major branches of the animal phylogeny. These conserved elements of adverse outcome pathways (AOPs) and their biomarkers are expect to provide mechanistic insight useful for regulating groups of chemicals based on their shared modes of action. PrecisionTox also aims to quantify risk variation within populations by recognizing susceptibility as a heritable trait that varies with genetic diversity. This initiative incorporates legal experts and collaborates with risk managers to address specific needs within European chemicals legislation, including the uptake of new approach methodologies (NAMs) for setting precise regulatory limits on toxic chemicals.

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.

Increasing complexity of opsin expression across stomatopod development

Stomatopods are well studied for their unique visual systems, which can consist of up to 16 different photoreceptor types and 33 opsin proteins expressed in the adults of some species. The light-sensing abilities of larval stomatopods are comparatively less well understood with limited information about the opsin repertoire of these early-life stages. Early work has suggested that larval stomatopods may not possess the extensive light detection abilities found in their adult counterparts. However, recent studies have shown that these larvae may have more complex photosensory systems than previously thought. To examine this idea at the molecular level, we characterized the expression of putative light-absorbing opsins across developmental stages, from embryo to adult, in the stomatopod species Pullosquilla thomassini using transcriptomic methods with a special focus on ecological and physiological transition periods. Opsin expression during the transition from the larval to the adult stage was further characterized in the species Gonodactylaceus falcatus. Opsin transcripts from short, middle, and long wavelength-sensitive clades were found in both species, and analysis of spectral tuning sites suggested differences in absorbance within these clades. This is the first study to document the changes in opsin repertoire across development in stomatopods, providing novel evidence for light detection across the visual spectrum in larvae.

Unexpected Distribution of Chitin and Chitin Synthase across Soft-Bodied Cnidarians

Cnidarians are commonly recognized as sea jellies, corals, or complex colonies such as the Portuguese man-of-war. While some cnidarians possess rigid internal calcareous skeletons (e.g., corals), many are soft-bodied. Intriguingly, genes coding for the chitin-biosynthetic enzyme, chitin synthase (CHS), were recently identified in the model anemone Nematostella vectensis, a species lacking hard structures. Here we report the prevalence and diversity of CHS across Cnidaria and show that cnidarian chitin synthase genes display diverse protein domain organizations. We found that CHS is expressed in cnidarian species and/or developmental stages with no reported chitinous or rigid morphological structures. Chitin affinity histochemistry indicates that chitin is present in soft tissues of some scyphozoan and hydrozoan medusae. To further elucidate the biology of chitin in cnidarian soft tissues, we focused on CHS expression in N. vectensis. Spatial expression data show that three CHS orthologs are differentially expressed in Nematostella embryos and larvae during development, suggesting that chitin has an integral role in the biology of this species. Understanding how a non-bilaterian lineage such as Cnidaria employs chitin may provide new insight into hitherto unknown functions of polysaccharides in animals, as well as their role in the evolution of biological novelty.

Freshwater crustacean exposed to active pharmaceutical ingredients: ecotoxicological effects and mechanisms

Concerns over the ecotoxicological effects of active pharmaceutical ingredients (APIs) on aquatic invertebrates have been raised in the last decade. While numerous studies have reported the toxicity of APIs in invertebrates, no attempt has been made to synthesize and interpret this dataset in terms of different exposure scenarios (acute, chronic, multigenerational), multiple crustacean species, and the toxic mechanisms. In this study, a thorough literature review was performed to summarize the ecotoxicological data of APIs tested on a range of invertebrates. Therapeutic classes including antidepressants, anti-infectives, antineoplastic agents, hormonal contraceptives, immunosuppressants, and neuro-active drugs exhibited higher toxicity to crustaceans than other API groups. The species sensitivity towards APIs exposure is compared in D. magna and other crustacean species. In the case of acute and chronic bioassays, ecotoxicological studies mainly focus on the apical endpoints including growth and reproduction, whereas sex ratio and molting frequency are commonly used for evaluating the substances with endocrine-disrupting properties. The multigenerational and "Omics" studies, primarily transcriptomics and metabolomics, were confined to a few API groups including beta-blocking agents, blood lipid-lowing agents, neuroactive agents, anticancer drugs, and synthetic hormones. We emphasize that in-depth studies on the multigenerational effects and the toxic mechanisms of APIs on the endocrine systems of freshwater crustacean are warranted.

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.

Genome-wide identification glutathione-S-transferase gene superfamily in Daphnia pulex and its transcriptional response to nanoplastics

Glutathione S-transferases (GSTs) are key multifunctional phase II detoxification enzymes involved in the regulation of growth, development, and stress responses. However, the knowledge of GSTs in the model invertebrate organism Daphnia pulex at the genomic level remains limited. In the present study, 35 GST genes were identified in D. pulex (Dp-GST), belonging to eight subfamilies, with the sigma, mu, and delta/epsilon subfamilies constituting approximately 29 %, 20 %, and 20 % of the GST superfamily, respectively. Chromosome tandem duplication of genes within the same subfamily was observed, which may be the main force driving GST expansion in D. pulex. DpGST genes showed different expression patterns in response to nanoplastic exposure for 96 h and 21 days. Some homologous GST genes in D. pulex showed similar expression patterns in response to nanoplastic exposure, likely owing to their unique motifs. For example, motif 9 is found in all delta/epsilon GST genes, whereas motifs 1, 2, 3, 5, and 7 are highly conserved in sigma GST genes. The characterization of D. pulex GSTs extending the knowledge of GST-mediated environmental contaminants, especially nanoplastics.

Characterizing nutritional phenotypes using experimental nutrigenomics: Is there nutrient-specificity to different types of dietary stress?

The ability to directly measure and monitor poor nutrition in individual animals and ecological communities is hampered by methodological limitations. In this study, we use nutrigenomics to identify nutritional biomarkers in a freshwater zooplankter, Daphnia pulex, a ubiquitous primary consumer in lakes and a sentinel of environmental change. We grew animals in six ecologically relevant nutritional treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium and high Cyanobacteria. We extracted RNA for transcriptome sequencing to identify genes that were nutrient responsive and capable of predicting nutritional status with a high degree of accuracy. We selected a list of 125 candidate genes, which were subsequently pruned to 13 predictive potential biomarkers. Using a nearest-neighbour classification algorithm, we demonstrate that these potential biomarkers are capable of classifying our samples into the correct nutritional group with 100% accuracy. The functional annotation of the selected biomarkers revealed some specific nutritional pathways and supported our hypothesis that animal responses to poor nutrition are nutrient specific and not simply different presentations of slow growth or energy limitation. This is a key step in uncovering the causes and consequences of nutritional limitation in animal consumers and their responses to small- and large-scale changes in biogeochemical cycles.

The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex

Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.

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.

In vivo singlet state filtered nuclear magnetic resonance: towards monitoring toxic responses inside living organisms

In line with recent paradigm shifts in toxicity testing, in vivo nuclear magnetic resonance (NMR) is a powerful tool for studying the biological impacts and perturbations caused by toxicants in living organisms. However, despite the excellent molecular insights that can be obtained through this technique, in vivo NMR applications are hampered by considerable experimental challenges such as poor line shape and spectral overlap. Here, we demonstrate the application of singlet-filtered NMR to target specific metabolites and facilitate the study of metabolite fluxes in living Daphnia magna, an aquatic keystone species and model organism. Informed by mathematical simulations and experiments on ex vivo organisms, singlet state NMR is used to monitor the flux of metabolites such as d-glucose and serine in living D. magna, during the environmentally relevant processes of anoxic stress and reduced food availability. Overall, singlet state NMR is shown to have significant future potential for studying metabolic processes in vivo.

QTL study reveals candidate genes underlying host resistance in a Red Queen model system

Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.

The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex

The inheritance of epigenetic marks induced by environmental variation in a previous generation is broadly accepted as a mediator of phenotypic plasticity. Transgenerational effects linking maternal experiences to changes in morphology, gene expression, and life history of successive generations are known across many taxa. While the number of studies linking epigenetic variation to ecological maternal effects is increasing rapidly, few if any attempts have been made to investigate molecular mechanisms governing epigenetic functions in the context of ecologically relevant maternal effects. Daphnia make an ideal model for investigating molecular epigenetic mechanisms and ecological maternal effects because they will reproduce asexually in the lab. Daphnia are also known to have strong maternal effects, involving a variety of traits and environmental variables. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food limitation within and across generations. We found strong evidence of genotypic variation of responses of life history and Dnmt expression to low food diets, both within and across generations. In general, effects of offspring diet were larger than either the direct maternal effect or offspring-maternal environment interactions, but the direction of the maternal effect was usually in the opposite direction of the within-generation effect. For both life history and Dnmt expression, we also found that when offspring had low food, effects of the maternal environment were stronger than when offspring had high food.

RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton

Zooplankton are important eukaryotic constituents of marine ecosystems characterized by limited motility in the water. These metazoans predominantly occupy intermediate trophic levels and energetically link primary producers to higher trophic levels. Through processes including diel vertical migration (DVM) and production of sinking pellets they also contribute to the biological carbon pump which regulates atmospheric CO₂ levels. Despite their prominent role in marine ecosystems, and perhaps, because of their staggering diversity, much remains to be discovered about zooplankton biology. In particular, the circadian clock, which is known to affect important processes such as DVM has been characterized only in a handful of zooplankton species. We present annotated de novo assembled transcriptomes from a diverse, representative cohort of 17 marine zooplankton representing six phyla and eight classes. These transcriptomes represent the first sequencing data for a number of these species. Subsequently, using translated proteomes derived from this data, we demonstrate in silico the presence of orthologs to most core circadian clock proteins from model metazoans in all sequenced species. Our findings, bolstered by sequence searches against publicly available data, indicate that the molecular machinery underpinning endogenous circadian clocks is widespread and potentially well conserved across marine zooplankton taxa.

High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation

Diaphanosoma dubium Manuilova, 1964, is a widespread planktonic water flea in Asian freshwater. Although sharing similar ecological roles with species of Daphnia, studies on D. dubium and its congeners are still few and lacking a genome for the further studies. Here, we assembled a high quality and chromosome level genome of D. dubium by combining long reads sequencing and Hi-C technologies. The total length of assembled genome was 101.8 Mb, with 98.92 Mb (97.2%) anchored into 22 chromosomes. Through comparative genomic analysis, we found the genes, involved in anti-ROS, detoxification, protein digestion, germ cells regulation and protection, underwent expansion in D. dubium. These genes and their expansion helpfully explain its widespread geographical distribution and dominance in eutrophic waters. This study provides insight into the adaptive evolution of D. dubium at genomic perspectives, and the present high quality genomic resource will be a footstone for future omics studies of the species and its congeners.

Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life

The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.

Assembly of a Draft Genome for the Mouse Ectoparasite Myocoptes musculinus

Myocoptes musculinus is a common ectoparasite of wild mice and is occasionally found on research mice. Infestations of research mice are often subclinical but can cause severe dermatitis. Perhaps more importantly, infestations can cause immunologic reactions that may alter research outcomes, and most animal research facilities strive to prevent or eliminate mites from their mouse colonies. M. musculinus infestations are currently detected by using microscopic evaluation of the fur and skin and PCR assays of pelt swabs targeting the rRNA genes of this mite. In our facility, we encountered multiple, false-positive 18S rRNA PCR results from a closed mouse colony. We could not identify the source of the false positives even after performing PCR analysis of other Myocoptes gene targets using assays developed from the few other target genomic sequences available for M. musculinus or Myocoptes japonensis in public databases. This situation highlighted the limited genetic resources available for development of diagnostic tests specific for this ectoparasite. To expand the available genetic resources, we generated a metagenome of M. musculinus derived by sequencing from fur plucks of an infected mouse. We also determined the completeness of this metagenome and compared it with those of related mites.

Daphnia as a model organism to probe biological responses to nanomaterials-from individual to population effects via adverse outcome pathways

The importance of the cladoceran Daphnia as a model organism for ecotoxicity testing has been well-established since the 1980s. Daphnia have been increasingly used in standardised testing of chemicals as they are well characterised and show sensitivity to pollutants, making them an essential indicator species for environmental stress. The mapping of the genomes of D. pulex in 2012 and D. magna in 2017 further consolidated their utility for ecotoxicity testing, including demonstrating the responsiveness of the Daphnia genome to environmental stressors. The short lifecycle and parthenogenetic reproduction make Daphnia useful for assessment of developmental toxicity and adaption to stress. The emergence of nanomaterials (NMs) and their safety assessment has introduced some challenges to the use of standard toxicity tests which were developed for soluble chemicals. NMs have enormous reactive surface areas resulting in dynamic interactions with dissolved organic carbon, proteins and other biomolecules in their surroundings leading to a myriad of physical, chemical, biological, and macromolecular transformations of the NMs and thus changes in their bioavailability to, and impacts on, daphnids. However, NM safety assessments are also driving innovations in our approaches to toxicity testing, for both chemicals and other emerging contaminants such as microplastics (MPs). These advances include establishing more realistic environmental exposures via medium composition tuning including pre-conditioning by the organisms to provide relevant biomolecules as background, development of microfluidics approaches to mimic environmental flow conditions typical in streams, utilisation of field daphnids cultured in the lab to assess adaption and impacts of pre-exposure to pollution gradients, and of course development of mechanistic insights to connect the first encounter with NMs or MPs to an adverse outcome, via the key events in an adverse outcome pathway. Insights into these developments are presented below to inspire further advances and utilisation of these important organisms as part of an overall environmental risk assessment of NMs and MPs impacts, including in mixture exposure scenarios.

Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay

Concentrations at which global gene expression profiles in cells or animals exposed to a test substance start to differ significantly from those of controls have been proposed as an alternative point of departure for use in screening level hazard assessment. The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. Results showed a strong association between the total number of genes for which a concentration response relationship could be derived and the overall variability in the resulting tPOD estimates. We conclude that, for our current assay design and analysis pipeline, tPODs based on fewer than 15 differentially expressed genes are likely to be unreliable for screening and that interindividual variability in gene expression profiles appears to be a more significant driver of tPOD variability than sample size alone. Results represent initial steps toward developing high throughput transcriptomics assays for use in ecological hazard screening.

Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.

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.

The diversity of invertebrate visual opsins spanning Protostomia, Deuterostomia, and Cnidaria

Across eumetazoans, the ability to perceive and respond to visual stimuli is largely mediated by opsins, a family of proteins belonging to the G protein-coupled receptor (GPCR) superclass. Lineage-specific gains and losses led to a striking diversity in the numbers, types, and spectral sensitivities conferred by visual opsin gene expression. Here, we review the diversity of visual opsins and differences in opsin gene expression from well-studied protostome, invertebrate deuterostome, and cnidarian groups. We discuss the functional significance of opsin expression differences and spectral tuning among lineages. In some cases, opsin evolution has been linked to the detection of relevant visual signals, including sexually selected color traits and host plant features. In other instances, variation in opsins has not been directly linked to functional or ecological differences. Overall, the array of opsin expression patterns and sensitivities across invertebrate lineages highlight the diversity of opsins in the eumetazoan ancestor and the labile nature of opsins over evolutionary time.

Degradation of Azithromycin from aqueous solution using Chlorine-ferrous- oxidation: ANN-GA modeling and Daphnia magna biotoxicity test assessment

Azithromycin (AZM), an antibacterial considered one of the most consumed drugs, especially during the period against the Covid 19 pandemic, and it is one of the persistent contaminants that can be released into aquatic ecosystems. The purpose of this study is to determine the efficacy of a Fenton-like process (chlorine/iron) for the degradation of AZM in an aqueous medium by determining the impact of several factors (the initial concentration of (FeSO₄, NaClO, pollutant), and the initial pH) on the degradation rate. The Response Surface Methodology (RSM) based on the Box-Wilson design as well as the Artificial Neural Network (ANN) modeling combined with a genetic algorithm (GA) approaches were used to determine the optimal levels of the selected variables and the optimal rate of degradation. The quadratic model of multi-linear regression developed indicated that the optimal conditions were a concentration of chlorine of 600 μM, the concentration of AZM is 32.8 mg/L, the mass of the catalyst FeSO₄ is 3.5 mg and a pH of 2.5, these optimal values gave a predicted and experimental yield of 64.05% and 70% respectively, the lack of fit test in RSM modeling (F₀ = 3.31 which is inferior to Fcritic (0.05, 10.4) = 5.96) indicates that the true regression function is not linear therefore, the ANN-GA modeling as non-linear regression indicated that the optimal conditions were a concentration of chlorine of 256 μM, the concentration of AZM is 5 mg/L, the mass of the catalyst FeSO₄ is 9.5 mg and a pH of 2.8, these optimal values gave a predicted and experimental yield of 79.69% and close to 80% respectively, Furthermore, biotoxicity tests were conducted to confirm the performance of our process using bio-indicators called daphnia (Daphnia magna), which demonstrated the efficacy of the like-Fenton process after 4 h of degradation.

Crustacean conundrums: a review of opsin diversity and evolution

Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

Daphnia as a Sentinel Species for Environmental Health Protection: A Perspective on Biomonitoring and Bioremediation of Chemical Pollution

Despite available technology and the knowledge that chemical pollution damages human and ecosystem health, chemical pollution remains rampant, ineffectively monitored, rarely prevented, and only occasionally mitigated. We present a framework that helps address current major challenges in the monitoring and assessment of chemical pollution by broadening the use of the sentinel species Daphnia as a diagnostic agent of water pollution. And where prevention has failed, we propose the application of Daphnia as a bioremediation agent to help reduce hazards from chemical mixtures in the environment. By applying "omics" technologies to Daphnia exposed to real-world ambient chemical mixtures, we show improvements at detecting bioactive components of chemical mixtures, determining the potential effects of untested chemicals within mixtures, and identifying targets of toxicity. We also show that using Daphnia strains that naturally adapted to chemical pollution as removal agents of ambient chemical mixtures can sustainably improve environmental health protection. Expanding the use of Daphnia beyond its current applications in regulatory toxicology has the potential to improve both the assessment and the remediation of environmental pollution.

The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia, and short‐term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress‐tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 h of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein‐coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing upregulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia‐by‐habitat of origin or chronic‐by‐acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through upregulation of cuticular proteins and neurotrophins, respectively.

Endocrine-disrupting potential and toxicological effect of para-phenylphenol on Daphnia magna

Several phenol derivatives are suspected endocrine disruptors and have received attention in risk assessment studies for several decades owing to the structural similarity between estrogens and phenolic compounds. We assessed the endocrine disrupting effect of the phenolic compound para-phenylphenol (PPP) through acute tests and evaluating chronic endpoints in an invertebrate model, Daphnia magna. Exposure of D. magna to PPP induced substantial adverse effects, namely, reduced fecundity, slowed growth rate, delayed first brood, and a reduction in neonate size. Furthermore, we investigated the mRNA expression of relevant genes to elucidate the mechanism of endocrine disruption by PPP. Exposure of D. magna to PPP induced the substantial downregulation of genes and markers related to reproduction and development, such as EcR-A, EcR-B, Jhe, and Vtg. Consequently, we demonstrated that PPP has an endocrine disrupting effect on reproduction and development in D. magna.

Morphological and molecular evolution of hadal amphipod’s eggs provides insights into embryogenesis under high hydrostatic pressure

Hadal zones are unique habitats characterized by high hydrostatic pressure (HHP) and scarce food supplies. The ability of eggs of species dwelling in hadal zones to develop into normal embryo under high hydrostatic pressure is an important evolutionary and developmental trait. However, the mechanisms underlying the development of eggs of hadal-dwelling species remain unknown due to the difficulty of sampling ovigerous females. Here, morphological and transcriptome analyses of eggs of the “supergiant” amphipod Alicella gigantea collected from the New Britain Trench were conducted. The morphology of A. gigantea eggs, including size, was assessed and the ultrastructure of the eggshell was investigated by scanning electron microscopy. Transcriptome sequencing and molecular adaptive evolution analysis of A. gigantea eggs showed that, as compared with shallow-water Gammarus species, genes exhibiting accelerated evolution and the positively selected genes were mostly related to pathways associated with “mitosis” and “chitin-based embryonic cuticle biosynthetic process”, suggesting that “normal mitosis maintenance” and “cuticle development and protection” are the two main adaptation strategies for survival of eggs in hadal environments. In addition, the concentration of trimethylamine oxide (TMAO), an important osmotic regulator, was significantly higher in the eggs of hadal amphipods as compared to those of shallow-water species, which might promote the eggs’ adaptation abilities. Morphological identification, evolutionary analysis, and the trimethylamine oxide concentration of A. gigantea eggs will facilitate a comprehensive overview of the piezophilic adaptation of embryos in hadal environments and provide a strategy to analyze embryogenesis under high hydrostatic pressure.