Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes

Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones

BACKGROUND

Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress.

RESULTS

KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype.

CONCLUSIONS

Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.

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.

Identification of biomarkers and sex differences in the placenta of fetal growth restriction

AIM

Fetal growth restriction (FGR) can lead to short-term and long-term impairments in the fetus. The placenta functions as an exchanger for substance transport, playing a critical role in fetal growth. However, the mechanism from the placental standpoint is still not fully understood. In this study, we aimed to investigate the pathophysiological mechanisms in the placenta that mediated the development of FGR and sex differences.

METHODS

We analyzed the gene expression profiles of GSE100415 containing specific normotensive FGR placental samples and GSE114691 with canonical samples using three different methods, differentially expressed gene analysis, weighted gene co-expression network analysis, and gene set enrichment analysis. Gene enrichment was performed, including the gene ontology and pathway from the Kyoto Encyclopedia of Genes and Genomes. The important process was then validated in pregnant Wistar rats subcutaneously administered dexamethasone (0.2 mg/kg/d) or saline from gestation Day 9 to 21.

RESULTS

Our results revealed little difference between the comparison of normal and normotensive FGR placental samples but confirmed the sex difference. Further analyses of the canonical samples identified the occurrence of vascular dysfunction, which was validated by the calculation of the vascular lumen area, showing that the vascular lumen in the FGR group was more than in the control. We also discovered 17 significantly expressed genes from the involved eigengenes.

CONCLUSION

Our study provides an important theoretical and experimental basis to reevaluate the development of FGR from the placental standpoint and suggests a series of biomarkers for future clinical use.

Differences of functionalized graphene materials on inducing chronic aquatic toxicity through the regulation of DNA damage, metabolism and oxidative stress in Daphnia magna

Graphene can be modified with functional groups when released into the environment. However, very little is known about molecular mechanisms of chronic aquatic toxicity induced by graphene nanomaterials with different surface functional groups. By using RNA sequencing, we investigated the toxic mechanisms of unfunctionalized graphene (u-G), carboxylated graphene (G-COOH), aminated graphene (G-NH₂), hydroxylated graphene (G-OH) and thiolated graphene (G-SH) to Daphnia magna during 21-day exposure. We revealed that alteration of ferritin transcription levels in the "mineral absorption" signaling pathway is a molecular initiating event leading to potential of oxidative stress in Daphnia magna by u-G, while toxic effects of four functionalized graphenes are related to several metabolic pathways including the "protein digestion and absorption" pathway and "carbohydrate digestion and absorption" pathway. The transcription and translation related pathways were inhibited by G-NH₂ and G-OH, which further affected the functions of proteins and normal life activities. Noticeably, detoxifications of graphene and its surface functional derivatives were promoted by increasing the gene expressions related to chitin and glucose metabolism as well as cuticle structure components. These findings demonstrate important mechanistic insights that can potentially be employed for safety assessment of graphene nanomaterials.

In situ boron-doped cellulose-based biochar for effective removal of neonicotinoids: Adsorption mechanism and safety evaluation

Biochar materials have been widely employed for adsorption of pollutants, which necessitates further consideration of their efficiency and safety in environmental remediation. In this study, a porous biochar (AC) was prepared through the combination of hydrothermal carbonization and in situ boron doping activation to effectively adsorb neonicotinoids. The adsorption process was shown to be a spontaneous endothermic physical adsorption process, where the predominant interaction forces between the acetamiprid and AC were electrostatic and hydrophobic interactions. The maximum adsorption capacity was 227.8 mg g^-1for acetamiprid and the safety of AC was verified by simulating the situation where the aquatic organism (D. magna) was exposed to the combined system (AC & neonicotinoids). Interestingly, AC was observed to reduce the acute toxicity of neonicotinoids owing to the reduced bioavailability of acetamiprid in D. magna and the newly generated expression of cytochrome p450. Thus, it enhanced the metabolism and detoxification response in D. magna, which reducing the biological toxicity of acetamiprid. This study not only demonstrates the potential application of AC from a safety perspective, but also provides insight into the combined toxicity caused by biochar after adsorption of pollutants at the genomic level, which fills the gap in related research.

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.

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.

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.

Proteomic changes associated with predator-induced morphological defenses in oysters

Inducible prey defenses occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defenses. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defenses. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with up-regulation of calcium transport proteins that could influence biomineralization. Inducible defenses evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were down-regulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defense response evolved in oysters that co-occur with drills through modification of an existing mechanism.

Coping with antagonistic predation risks: Predator-dependent unique responses are dominant in Ceriodaphnia cornuta

Inducible defences of prey are evolved under diverse and variable predation risks. However, during the co-evolution of prey and multiple predators, the responses of prey to antagonistic predation risks, which may put the prey into a dilemma of responding to predators, remain unclear. Based on antagonistic predation pressure from an invertebrate (Chaoborus larvae) and a vertebrate (Rhodeus ocellatus) predator, we studied the responses of multiple traits and transcriptomes of the freshwater crustacean Ceriodaphnia cornuta under multiple predation risks. Chaoborus predation risk altered the expression of genes encoding cuticle proteins and modulated the biosynthesis of steroid hormones, cutin, suberine, and wax, leading to the development of horns and increase in size at the late developmental stage. Meanwhile, fish predation risk primarily triggered genes encoding ribosomes and those involved in unsaturated fatty acid biosynthesis and cysteine and methionine metabolism, resulting in smaller individual size and earlier reproduction. Inducible responses of both transcriptome and individual traits revealed that predator-dependent unique responses were dominant and the dilemma of antagonistic responses was relatively limited. However, the unique individual traits in response to invertebrate predation could be significantly impaired by vertebrate predation risk, even though the unique responses to different predators were extremely weakly correlated and could be elicited simultaneously. These results indicate that diverse predator-dependent unique responses are favoured by Ceriodaphnia during its co-evolution with multiple predators. Nonetheless, Ceriodaphnia is not a generalist that can fully adopt all predator-dependent unique responses simultaneously under multiple predation risks.

Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity.

Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change.

Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential.

An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts.

We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.

Modular Screening Reveals Driver Induced Additive Mechanisms of Baicalin and Jasminoidin on Cerebral Ischemia Therapy

Combination therapy with increased efficacy and reduced toxicity plays a crucial role in treating complex diseases, such as stroke, but it remains an insurmountable barrier to elucidate the mechanisms of synergistic effects. Here, we present a Driver-induced Modular Screening (DiMS) strategy integrated synergistic module and driver gene identification to elucidate the additive mechanisms of Baicalin (BA) and Jasminoidin (JA) on cerebral ischemia (CI) therapy. Based on anti-ischemia genomic networks BA, JA, and their combination (BJ), we obtained 4, 3, and 9 On-modules of BA, JA, and BJ by modular similarity analysis. Compared with the monotherapy groups, four additive modules (Add-module, BJ_Mod-4, 7, 9, and 13), 15 driver genes of BJ were identified by modular similarity and network control methods, and seven driver proteins (PAQR8, RhoA, EMC10, GGA2, VIPR1, FAM120A, and SEMA3F) were validated by animal experiments. The functional analysis found neuroprotective roles of the Add-modules and driver genes, such as the Neurotrophin signaling pathway and FoxO signaling pathway, which may reflect the additive mechanisms of BJ. Moreover, such a DiMS paradigm provides a new angle to explore the synergistic mechanisms of combination therapy and screen multi-targeted drugs for complex diseases.

Potential differences in chitin synthesis ability cause different sensitivities to diflubenzuron among three strains of Daphnia magna

Ecotoxicity testing of crustaceans using Daphnia magna has been implemented in the chemical management systems of various countries. While the chemical sensitivity of D. magna varies depending on genetically different clonal lineages, the strain used in ecotoxicity tests, including the acute immobilization test (OECD TG202), has not been specified. We hypothesized that comprehensive gene expression profiles could provide useful information on phenotypic differences among strains, including chemical sensitivity. To test this hypothesis, we performed mRNA sequencing on three different strains (NIES, England, and Clone 5) of D. magna under culture conditions. The resulting expression profile of the NIES strain was clearly different compared to the profiles of the other two strains. Gene ontology (GO) enrichment analysis suggested that chitin metabolism was significantly enriched in the NIES strain compared to that in the England strain. Consistent with the GO analysis, evidence of high levels of chitin metabolism in the NIES strain were observed across multiple levels of biological organization, such as expression of chitin synthase genes, chitin content, and chitinase activity, which suggested that the different strains would exhibit different sensitivities to chemicals used to inhibit chitin synthesis. We found that among all strains, the NIES strain was more tolerant to diflubenzuron, a chitin synthesis inhibitor, with a 14-fold difference in the 48 h-EC₅₀ value for the acute immobilization test compared to the England strain. The present study demonstrates that the differences among strains in chitin metabolism may lead to sensitivity difference to diflubenzuron, and serves as a case study of the usefulness of comprehensive gene expression profiles in finding sensitivity differences.

Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.

In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds

BACKGROUND

High-throughput sequencing generates large volumes of biological data that must be interpreted to make meaningful inference on the biological function. Problems arise due to the large number of characteristics p (dimensions) that describe each record [n] in the database. Feature selection using a subset of variables extracted from the large datasets is one of the approaches towards solving this problem.

METHODOLOGY

In this study we analyzed the transcriptome of Glossina morsitans morsitans (Tsetsefly) antennae after exposure to either a repellant (δ-nonalactone) or an attractant (ε-nonalactone). We identified 308 genes that were upregulated or downregulated due to exposure to a repellant (δ-nonalactone) or an attractant (ε-nonalactone) respectively. Weighted gene coexpression network analysis was used to cluster the genes into 12 modules and filter unconnected genes. Discretized and association rule mining was used to find association between genes thereby predicting the putative function of unannotated genes.

RESULTS AND DISCUSSION

Among the significantly expressed chemosensory genes (FDR < 0.05) in response to Ɛ-nonalactone were gustatory receptors (GrIA and Gr28b), ionotrophic receptors (Ir41a and Ir75a), odorant binding proteins (Obp99b, Obp99d, Obp59a and Obp28a) and the odorant receptor (Or67d). Several non-chemosensory genes with no assigned function in the NCBI database were co-expressed with the chemosensory genes. Exposure to a repellent (δ-nonalactone) did not show any significant change between the treatment and control samples. We generated a coexpression network with 276 edges and 130 nodes. Genes CAH3, Ahcy, Ir64a, Or67c, Ir8a and Or67a had node degree values above 11 and therefore could be regarded as the top hub genes in the network. Association rule mining showed a relation between various genes based on their appearance in the same itemsets as consequent and antecedent.

Environmental RNA: A Revolution in Ecological Resolution?

Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

BACKGROUND

Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes.

RESULTS

We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the "Reactome," we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling.

CONCLUSIONS

Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services. Video Abstract.

Effect of chronic UVR exposure on zooplankton molting and growth

Molting is a crucial physiological process in arthropods development, growth, and adult reproduction, where the chitinolytic enzyme chitobiase (CB) and the apoptosis process (caspase-3 activity) play crucial roles. Both molecular endpoints have been observed to be affected by different toxics that may be present in aquatic environments. However, the role of ultraviolet radiation (UVR) in the molting process remains with poor evidence and the possible effect of the previous exposure on F1 generation is unknown. Here, we conducted laboratory experiments with chronic UVR exposure to test the effect on the molting process of Daphnia commutata. Our results showed a clear negative effect of the UVR that affected the molting process with a reduction in individual growth. This trend was also observed in CB and caspase-3 activities. Our results also suggest that the UV dose received by the mother and eggs has an additive effect with the dose received by the offspring. These results imply that the cumulative impact of small UVR doses (2 h per day, daily dose: 2520 J m^-2 of 340 nm) on mothers and eggs (which cannot be discriminated in our experiments) can have an additive or synergistic effect along with the generations through a potential increase in lethal effect. Finally, the observed desynchronization in the molting process by UVR will affect the fitness of individuals and population dynamics.

Insights into the genetic basis of predator-induced response in Daphnia galeata

Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges-these responses comprise morphological, behavioral but also life-history changes. Alteration of life-history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia. However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator-induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator-induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D. galeata. Furthermore, we used an orthology-based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator-induced responses in Daphnia. Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones-mediated life-history changes in other Daphnia species.

Daphnia magna modifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference

Caloric restriction (CR) produces clear phenotypic effects within and between generations of the model crustacean Daphnia magna. We have previously established that micro-RNAs and cytosine methylation change in response to CR in this organism, and we demonstrate here that CR has a dramatic effect on gene expression. Over 6,000 genes were differentially expressed between CR and well-fed D. magna, with a bias towards up-regulation of genes under caloric restriction. We identified a highly expressed haemoglobin gene that responds to CR by changing isoform proportions. Specifically, a transcript containing three haem-binding erythrocruorin domains was strongly down-regulated under CR in favour of transcripts containing fewer or no such domains. This change in the haemoglobin mix is similar to the response to hypoxia in Daphnia, which is mediated through the transcription factor hypoxia-inducible factor 1, and ultimately the mTOR signalling pathway. This is the first report of a role for haemoglobin in the response to CR. We also observed high absolute expression of superoxide dismutase (SOD) in normally fed individuals, which contrasts with observations of high SOD levels under CR in other taxa. However, key differentially expressed genes, like SOD, were not targeted by differentially expressed micro-RNAs. Whether the link between haemoglobin and CR occurs in other organisms, or is related to the aquatic lifestyle, remains to be tested. It suggests that one response to CR may be to simply transport less oxygen and lower respiration.

The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors

Rapid environmental changes impact the global distribution and abundance of species, highlighting the urgency to understand and predict how populations will respond. The analysis of differentially expressed genes has elucidated areas of the genome involved in adaptive divergence to past and present environmental change. Such studies however have been hampered by large numbers of differentially expressed genes and limited knowledge of how these genes work in conjunction with each other. Recent methods (broadly termed "pathway analyses") have emerged that aim to group genes that behave in a coordinated fashion to a factor of interest. These methods aid in functional annotation and uncovering biological pathways, thereby collapsing complex datasets into more manageable units, providing more nuanced understandings of both the organism-level effects of modified gene expression, and the targets of adaptive divergence. Here, we reanalyze a dataset that investigated temperature-induced changes in gene expression in marine-adapted and freshwater-adapted threespine stickleback (Gasterosteus aculeatus), using Weighted Gene Co-expression Network Analysis (WGCNA) with PANTHER Gene Ontology (GO)-Slim overrepresentation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Six modules exhibited a conserved response and six a divergent response between marine and freshwater stickleback when acclimated to 7°C or 22°C. One divergent module showed freshwater-specific response to temperature, and the remaining divergent modules showed differences in height of reaction norms. PPARAa, a transcription factor that regulates fatty acid metabolism and has been implicated in adaptive divergence, was located in a module that had higher expression at 7°C and in freshwater stickleback. This updated methodology revealed patterns that were not found in the original publication. Although such methods hold promise toward predicting population response to environmental stressors, many limitations remain, particularly with regard to module expression representation, database resources, and cross-database integration.

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure

BACKGROUND

Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses.

RESULTS

By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing.

CONCLUSIONS

Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.

Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids

Background

Nutritional quality of phytoplankton is a major determinant of the trophic transfer efficiency at the plant-herbivore interface in freshwater food webs. In particular, the phytoplankton’s content of the essential polyunsaturated omega-3 fatty acid eicosapentaenoic acid (EPA) has been repeatedly shown to limit secondary production in the major zooplankton herbivore genus Daphnia. Despite extensive research efforts on the biological model organism Daphnia, and the availability of several Daphnia genomes, little is known regarding the molecular mechanisms underlying the limitations in Daphnia related to dietary EPA availability.

Results

We used RNA-seq to analyse the transcriptomic response of Daphnia magna which were fed with two different diets — each with or without supplementation of EPA — at two different temperature levels (15 and 20 °C). The transcripts were mapped to the D. magna genome assembly version 2.4, containing 26,646 translations. When D. magna fed on green alga, changing the temperature provoked a differential expression of 2001 transcripts, and in cyanobacteria-fed daphnia, 3385 transcripts were affected. The supplementation of EPA affected 1635 (on the green algal diet), or 175 transcripts (on the cyanobacterial diet), respectively. Combined effects for diet and temperature were also observed (669 for the green algal and 128 transcripts for the cyanobacterial diet). Searching for orthologous genes (COG-analysis) yielded a functional overview of the altered transcriptomes. Cross-matched transcript sets from both feed types were compiled to illuminate core responses to the factors temperature and EPA-supplementation.

Conclusions

Our highly controlled eco-physiological experiments revealed an orchestrated response of genes involved in the transformation and signalling of essential fatty acids, including eicosanoid-signalling pathways with potential immune functions. We provide an overview of downstream-regulated genes, which contribute to enhance growth and reproductive output. We also identified numerous EPA-responsive candidate genes of yet unknown function, which constitute new targets for future studies on the molecular basis of EPA-dependent effects at the freshwater plant-herbivore interface.

Co-expression network analysis identifies gonad- and embryo-associated protein modules in the sentinel species Gammarus fossarum

Next generation sequencing and mass spectrometry technologies have recently expanded the availability of whole transcriptomes and proteomes beyond classical model organisms in molecular biology, even in absence of an annotated genome. However, the fragmented nature of transcriptomic and proteomic data reduces the ability to interpret the data, notably in non-model organisms. Network-based approaches may help extracting important biological information from -omics datasets. The reproductive cycle of the freshwater crustacean Gammarus fossarum.provides an excellent case study to test the relevance of a network analysis in non-model organisms. Here, we illustrated how the use of a co-expression network analysis (based on Weighted Gene Co-expression Network Analysis algorithm, WGCNA) allowed identifying protein modules whose expression profiles described germ cell maturation and embryonic development in the freshwater crustacean Gammarus fossarum. Proteome datasets included testes, ovaries or embryos samples at different maturation or developmental stages, respectively. We identified an embryonic module correlated with mid-developmental stages corresponding to the organogenesis and it was characterized by enrichment in proteins involved in RNA editing and splicing. An ovarian module was enriched in vitellogenin-like proteins and clottable proteins, confirming the diversity of proteins belonging to the large lipid transfer family involved in oocytes maturations in this freshwater amphipod. Moreover, our results found evidence of a fine-tuned regulation between energy production by glycolysis and actin-myosin-dependent events in G. fossarum spermatogenesis. This study illustrates the importance of applying systems biology approaches to emergent animal models to improve the understanding of the molecular mechanisms regulating important physiological events with ecological relevance.

Variation in transcriptional responses to copper exposure across Daphnia pulex lineages

Copper pollution is pervasive in aquatic habitats and is particularly harmful to invertebrates sensitive to environmental changes such as Daphnia pulex. Mechanisms of toxicity and tolerance to copper are not well understood. We used RNA-sequencing to investigate these mechanisms in three genetically distinct D. pulex clonal lineages with different histories of copper exposure. Upregulated genes after copper exposure were enriched with Gene Ontology (GO) categories involved in digestion, molting and growth, whereas downregulated genes after copper exposure were enriched in the metal-regulatory system, immune response and epigenetic modifications. The three D. pulex clones in our study show largely similar transcriptional patterns in response to copper, with only a total of twenty genes differentially expressed in a single clonal lineages. We also detected lower relative expression of some genes known to be important for copper tolerance, metallothionein and glutathione-S-transferase, in a sensitive lineage sampled from an uncontaminated habitat. Daphnia-specific genes (without orthologs outside the genus) and Daphnia-specific duplications (genes duplicated in the Daphnia lineage) were overrepresented in differentially expressed genes, highlighting an important role for newly emerged genes in tolerating environmental stressors. The results indicate that the D. pulex lineages tested in this study generally respond to copper stress using the same major pathways, but that the more resistant clone with previous copper exposure might be better able to regulate key genes. This finding highlights the important nuances in gene expression among clones, shaped by historical exposure and influencing copper tolerance.

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

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

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.

R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics

A challenge of modern ecological genomics is reducing uncertainty surrounding the biological inferences from gene expression. For example, approximately 40% of proteins in eukaryotic model organisms do not contain characterized domains (Gollery et al., 2006). Even proteins of "known function" are typically only characterized in the sense that they have a domain function, but provide no information on their biological role within the cell (e.g., activation, pathways or targets). Yet, as molecular ecologists, a common objective is to elucidate how organisms respond to environmental variation through changes in gene expression, including homoeostatic, acclimatory, and adaptive responses to environmental stressors, a challenge increased by poor protein ecological annotation. Now, in this issue of Molecular Ecology, Orsini et al. (2017) use the quintessential Daphnia system to characterize the differences in stress response in three genotypic backgrounds to common biotic and abiotic stressors found in nature. Using an optimized weighted gene co-expression network analysis, they link genes of unknown function to genes that they co-activate with and enrich for gene ontology. Determining the functional networks of genes that behave in genotype- and treatment-specific responses gives insight into possible pathways and respective ecological roles, helping pave the way for the next generation of transcriptomic studies in molecular ecology.

Comparative Transcriptome Analysis for Understanding Predator-Induced Polyphenism in the Water Flea Daphnia pulex

The crustacean Daphnia pulex is one of the best model organisms for studying inducible defense mechanisms due to their inducible morphology in response to the predator Chaoborus larvae. In this study, multiple developmental stages of D. pulex were exposed to C. flavicans larvae and transcriptome profiles of samples from late embryo to fifth instar were sequenced by the RNA-seq technique to investigate the genetic background underlying inducible defenses. In comparison, differentially expressed genes between defensive and normal morphs were identified, including 908 genes in late embryo, 1383 genes in the first-third (1–3) instar, and 1042 genes in fourth-fifth (4–5) instar. Gene ontology enrichment analysis showed that structural constituents of the cuticle and structural molecule activity genes were prominent up-regulated genes in late embryos. Down-regulated genes in late embryos and 1–3 instar comprised metabolic process, hydrolase activity, and peptidase activity gene classes. Pathway analysis indicated that small molecule neurotransmitter pathways were potentially involved in the development of inducible defenses. The characterization of genes and pathways in multiple developmental stages can improve our understanding of inducible defense responses of D. pulex to predation at the molecular level.

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.