MicroRNAs are involved in cadmium tolerance in Daphnia pulex

Chronic metal contamination shapes the size structure of Gammarus fossarum populations in French headwater rivers

Assessing the effects of multigenerational exposure of aquatic animal populations to chemical contamination is essential for ecological risk assessment. However, beyond rare examples reporting the sporadic emergence of a toxicological tolerance within populations that persist in contaminated environments, conclusive results are even more limited from field studies when it comes to the alteration of life-history traits. Here, we investigated whether long-term exposure to cadmium (Cd) influences size-related life-history traits (i.e., size at puberty, median adult size, maximum size) in Gammarus fossarum, a keystone species of European stream ecosystems. We studied 13 field populations of G. fossarum (cryptic lineage B) living in headwater rivers located in natural areas scattered at a large geographical scale and exposed to contrasted bioavailable Cd contamination levels due to different local geochemical backgrounds. We achieved a detailed description of the physical and physicochemical conditions of the river reaches investigated. Land-use parameters, hydrological characteristics (flow, slope, river width, flow structure, mosaic of substrates), and physicochemical conditions (temperature, conductivity, dissolved oxygen) were measured. Metallic bioavailable contamination was assessed using a standardized active biomonitoring procedure (Gammarus caging). Based on the field demographic census of the 13 populations, our results demonstrated that chronic Cd contamination significantly influences life-history in the G. fossarum species, with a significant reduction in all size traits of populations (size at puberty, median adult size, maximum size). In addition, we confirmed Cd-tolerance in contaminated populations during exposure tests in the laboratory. Various hypotheses can be then put forward to explain the modification of size-related life-history traits: a direct toxic effect of Cd, a cost of Cd-tolerance, or an adaptive evolution of life-history exposed to toxic pressure.

Transcriptomic analysis reveals interactive effects of polyvinyl chloride microplastics and cadmium on Mytilus galloprovincialis: Insights into non-coding RNA responses and environmental implications

Despite increasing concerns regarding the interactions of microplastic and heavy metal pollution, there is limited knowledge on the molecular responses of marine organisms to these stressors. In this study, we used whole-transcriptome sequencing to investigate the molecular responses of the ecologically and economically important bivalve Mytilus galloprovincialis to individual and combined exposures of environmentally relevant concentrations of PVC microplastics and cadmium (Cd). Our results revealed distinct transcriptional changes in M. galloprovincialis, with significant overlap in the differentially expressed genes between the individual and combined exposure groups. Genes involved in cellular senescence, oxidative stress, and galactose metabolism were differentially expressed. Additionally, key signaling pathways related to apoptosis and drug metabolism were significantly modulated. Notably, the interaction of PVC microplastics and Cd resulted in differential expression of genes involved in drug metabolism and longevity regulating compared to single exposures. This suggests that the interaction between these two stressors may have amplified effects on mussel health. Overall, this comprehensive transcriptomic analysis provides valuable insights into the adaptive and detrimental responses of M. galloprovincialis to PVC microplastics and Cd in the environment.

Acclimation and transgenerational plasticity support increased cadmium tolerance in Gammarus populations exposed to natural metal contamination in headwater streams

Considering long-term population effects of chronic exposure to contaminants remains limited in ecological risk assessment. Field evidence that multigenerational exposure influences organisms' sensitivity is still scarce, and mechanisms have yet to be elucidated in the environmental context. This study focuses on the crustacean Gammarus fossarum, for which an increased tolerance to cadmium (Cd) has previously been reported in a naturally low-contaminated headwater stream. Our objectives were to investigate whether Cd tolerance is a common phenomenon in headwater populations, and to elucidate the nature of the tolerance and its intergenerational transmission. For this, we carried out an in-depth in situ characterization of Cd exposure (gammarids' caging) and levels of tolerance in nine populations on a regional scale, as well as laboratory maintenance and cross-breeding of contaminated and uncontaminated populations. Acute tolerance levels correlate positively with bioavailable Cd contamination levels among streams. The contaminated and non-contaminated populations differ about two-fold in sensitivity to Cd. Tolerance was found in all age classes of contaminated populations, it can be transiently lost during the year, and it was transmissible to offspring. In addition, tolerance levels dropped significantly when organisms were transferred to a Cd-free environment for two months. These organisms also ceased producing tolerant offspring, confirming a non-genetic transmission of Cd tolerance between generations. These findings support that Cd tolerance corresponds to non-genetic acclimation combined with transgenerational plasticity. Moreover, cross-breeding revealed that tolerance transmission to offspring is not limited to maternal effect. We suggest epigenetics as a plausible mechanism for the plasticity of Cd sensitivity observed in the field. Our results therefore highlight the neglected role of plasticity and non-genetic transmission of modified sensitivities during the long-term exposure of natural populations to environmental contamination.

miR-252 targeting temperature receptor CcTRPM to mediate the transition from summer-form to winter-form of Cacopsylla chinensis

Temperature determines the geographical distribution of organisms and affects the outbreak and damage of pests. Insects seasonal polyphenism is a successful strategy adopted by some species to adapt the changeable external environment. Cacopsylla chinensis (Yang & Li) showed two seasonal morphotypes, summer-form and winter-form, with significant differences in morphological characteristics. Low temperature is the key environmental factor to induce its transition from summer-form to winter-form. However, the detailed molecular mechanism remains unknown. Here, we firstly confirmed that low temperature of 10 °C induced the transition from summer-form to winter-form by affecting the cuticle thickness and chitin content. Subsequently, we demonstrated that CcTRPM functions as a temperature receptor to regulate this transition. In addition, miR-252 was identified to mediate the expression of CcTRPM to involve in this morphological transition. Finally, we found CcTre1 and CcCHS1, two rate-limiting enzymes of insect chitin biosyntheis, act as the critical down-stream signal of CcTRPM in mediating this behavioral transition. Taken together, our results revealed that a signal transduction cascade mediates the seasonal polyphenism in C. chinensis. These findings not only lay a solid foundation for fully clarifying the ecological adaptation mechanism of C. chinensis outbreak, but also broaden our understanding about insect polymorphism.

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

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

Altered life history traits and transcripts of molting- and reproduction-related genes by cadmium in Daphnia magna

Cadmium (Cd) is a non-essential element and can be toxic to aquatic organisms at low concentrations. Despite its well-known toxicity to Daphnia magna, the effects of Cd on physiological parameters (heart rate and thoracic limb activity) and molting- and reproduction-related genes are relatively understudied. In this study, D. magna were exposed to 0 (control), 25, 50 and 75 μg L^-1 of Cd for 7 d and 21 d to determine the toxicity of Cd. The results showed that the Cd body burden in D. magna was significantly increased with elevated Cd concentrations, up to 13.4 μg Cd/g dry weight (dw) after exposure to 75 μg L^-1 for 21 d. After 21 d of exposure, the body length and body weight of D. magna were significantly decreased in all Cd treatments compared to the control. The heart rate and thoracic limb activity were reduced by 4.3-11.7 and 5.0-10.3%, respectively. The levels of malondialdehyde (MDA) were increased by ~24-37% and the activity of catalase (CAT) was inhibited by ~50% compared to the control. The reproductive parameters (i.e., size of the first brood, the total number of offspring per female and the number of offspring per brood) were remarkably reduced, causing adverse effects on the population dynamics. In addition, the transcripts of genes (cyp314, cyp18a1, ecra, usp, hr3, cut, cht and cht3) related to the molting of D. magna were altered, whereas the transcripts of genes (vtg1, vtg2 and vmo1) related to reproduction were down-regulated. This study helps better understand the effects of Cd at different biological levels.

Integrated transcriptome analysis of immune-related mRNAs and microRNAs in Macrobrachium rosenbergii infected with Spiroplasma eriocheiris

Macrobrachium rosenbergii (M. rosenbergii), is a major aquaculture species in China and Southeast Asia. However, infection with Spiroplasma eriocheiris (S. eriocheiris) has caused huge economic losses to the cultivation of M. rosenbergii. Currently, there are few reports on the immune response mechanism of M. rosenbergii that are infected with S. eriocheiris. To clarify the immune response mechanism of M. rosenbergii infected with S. eriocheiris, the key immune genes which respond to the infection with the pathogen and the regulation of related microRNAs (miRNAs) on them were identified. In this study, the mRNA and miRNA transcriptome of hepatopancreas of M. rosenbergii at different infection stages were analyzed using high-throughput sequencing and qRT-PCR. In the mRNA transcriptome, 27,703 and 33,402 genes were expressed in healthy and susceptible M. rosenbergii, respectively. By digital gene-expression profiling analysis, 23,929 and 24,325 genes were expressed, and 223 and 373 genes were significantly up-regulated and down-regulated, respectively. A total of 145 key genes related to Toll, IMD, JAK/STAT and MAPK were excavated from the transcriptome. In the miRNA transcriptome, 549 miRNAs (Conserved: 41, PN-type: 83, PC-type: 425) were sequenced, of which 87 were significantly up-regulated and 23 were significantly down-regulated. Among the related immune pathways, there are 259 miRNAs involved in the regulation of target genes in the Toll and IMD pathways, 231 JAK/STAT pathways and 122 MAPK pathways. qRT-PCR differential detection of immune-related miRNAs and mRNAs showed that 22 miRNAs with significant differences (P < 0.05) such as mro-miR-100, PC-mro-3p-27 and PN-mro-miR-316 had corresponding regulatory relationships with 22 important immune genes such as TLR2, TLR3, TLR4, TLR5, MyD88, Pelle and Relish in different stages after infection. In this study, the immune genes and related regulatory miRNAs of M. rosenbergii in response to S. eriocheiris infection were obtained. The results can provide basic data to further reveal the immune defense mechanism of M. rosenbergii against S. eriocheiris infection.

Cadmium promotes apoptosis and inflammation via the circ08409/miR-133a/TGFB2 axis in bovine mammary epithelial cells and mouse mammary gland

Cadmium is a common environmental heavy metal pollutant that can accumulate over long periods of time and cause disease. Thus, analysis of the molecular mechanisms affected by cadmium in the body could be of great significance for the prevention and treatment of cadmium-related diseases. In this study, flow cytometry, immunofluorescence, transmission electron microscopy, H&E (Hematoxylin Eosin) staining and TUNEL (TdT-mediated dUTP Nick-End Labeling) assays were used to verify that cadmium induced apoptosis and immune responses in bovine mammary epithelial cells (BMECs) and in mouse mammary gland. Isolated BMECs cultured with or without cadmium were collected to screen miRNA (microRNA) using high-throughput sequencing. There were 42 differentially-expressed miRNAs among which 27 were upregulated and 15 downregulated including bta-miR-133a, bta-miR-23b-5p, bta-miR-29e, bta-miR-365-5p, bta-miR-615, bta-miR-7, bta-miR-11975, bta-miR-127, and bta-miR-411a. Among those, miR-133a (which can specifically target TGFB2 (Recombinant Transforming Growth Factor Beta 2) was the most significantly downregulated with a fold-change of 5.27 in BMECs cultured with cadmium. Application of the double luciferase reporter system, western blotting, and qRT-PCR (Quantitative Real-time PCR) revealed that circ08409 can directly bind to miR-133a. Experiments demonstrated that circRNA-08409 could adsorb bta-miR-133a. Both circ08409 and TGFB2 significantly increased apoptosis and altered expression level of a series of inflammatory factors in BMECs. In contrast, miR-133a decreased significantly apoptosis and inflammation in the cells. Compared with cultures receiving only cadmium, the miR-133a+cadmium cultures exhibited significant reductions in the occurrence of late apoptosis. Overall, results indicated that circ08409 could relieve the inhibitory effect of miR-133a on TGFB2 expression by combining with miR-133a and subsequently modulating cell proliferation, apoptosis and inflammation. Overall, the data suggested that the circ08409/miR-133a/TGFB2 axis might play a role in mediating the effect of cadmium on BMECs. As such, data provide novel insights into controlling hazards that cadmium could induce in the mammary gland.

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.

Micro RNA (miRNA) Differential Expression and Exposure to Crude-Oil-Related Compounds

This review summarizes studies on miRNA differential regulation related to exposure to crude oil and 20 different crude oil chemicals, such as hydrocarbons, sulphur, nitrogen, and metal- containing compounds. It may be interesting to explore the possibility of using early post-transcriptional regulators as a potential novel exposure biomarker.

Crude oil has been defined as a highly complex mixture of solids, liquids, and gases. Given the toxicological properties of the petroleum components, its extraction and elaboration processes represent high-risk activities for the environment and human health, especially when accidental spills occur. The effects on human health of short-term exposure to petroleum are well known, but chronic exposure effects may variate depending on the exposure type (i.e., work, clean-up activities, or nearby residence).

As only two studies are focused on miRNA differential expression after crude-oil exposure, this review will also analyse the bibliography concerning different crude-oil or Petroleum-Related Compounds (PRC) exposure in Animalia L. kingdom and how it is related to differential miRNA transcript levels. Papers include in vitro, animal, and human studies across the world.

A list of 10 miRNAs (miR-142-5p, miR-126-3p, miR-24-3p, miR-451a, miR-16-5p, miR-28-5p, let-7b-5p, miR-320b, miR-27a-3p and miR-346) was created based on bibliography analysis and hypothesised as a possible “footprint” for crude-oil exposure. miRNA differential regulation can be considered a Big-Data related challenge, so different statistical programs and bioinformatics tools were used to have a better understanding of the biological significate of the most interesting data.

Metal and metallothionein levels in zooplankton in relation to environmental exposure: spatial and temporal variability (Saronikos Gulf, Greece)

Metal and metallothionein (MT) in mixed zooplankton were investigated as means of monitoring metal availability regarding environmental exposure. Spatial and temporal variability of Cd, Cu, Ni, Zn, Fe, Mn and Pb in zooplankton and seawater were studied in Saronikos Gulf (Aegean Sea, Eastern Mediterranean), once every second month during an annual cycle (2011-2012). Particulate organic carbon and chlorophyll α were also measured in seawater samples. Median zooplankton metal concentrations were 0.65, 32.4, 7.1, 864, 1420, 40.2 and 26.8 μg g^-1 dw for Cd, Cu, Ni, Zn, Fe, Mn and Pb, respectively, and 109 μg g^-1 ww for MTs. Metal levels in zooplankton and MTs were higher at sites influenced by human-derived pressures. Additionally, metal concentrations in pelagic fish flesh from the Greek MED-POL data base were used for bioconcentration and biomagnification factors calculation. Bioconcentration from water to zooplankton was higher than metal transfer from either seston to zooplankton or zooplankton to fish.

A novel microRNA and its pfk target control growth length in the freshwater shrimp Neocaridina heteropoda

MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression and play roles in a wide range of physiological processes, including ontogenesis. Herein, we discovered a novel miRNA, novel miR-26, which inhibits translation of the phosphofructokinase (PFK) gene by targeting the 3' untranslated region (UTR) of pfk directly, thereby inhibiting molting and body length growth of the freshwater shrimp Neocaridina heteropoda Lowering expression of pfk by RNA interference (RNAi) led to a longer ecdysis cycle and smaller individuals. This phenotype was mirrored in shrimps injected with novel miR-26 agomirs, but the opposite phenotype occurred in shrimps injected with novel miR-26 antagomirs (i.e. the ecdysis cycle was shortened and body length was increased). After injection of 20-hydroxyecdysone (ecdysone 20E), expression of the novel miR-26 was decreased, while expression of pfk was up-regulated, and the fructose-1,6-diphosphate metabolite of PFK accumulated correspondingly. Furthermore, expression of eIF2 (eukaryotic initiation factor 2) increased under stimulation with fructose-1,6-diphosphate, suggesting that protein synthesis was stimulated during this period. Taken together, our results suggest that the novel miR-26 regulates expression of pfk and thereby mediates the molting and growth of N. heteropoda.

Effects of nanoplastics at predicted environmental concentration on Daphnia pulex after exposure through multiple generations

The biological effects of nanoplastics are a growing concern. However, most studies have focused on exposure to high concentrations or short-term exposure. The potential effects of exposure to low environmental nanoplastic concentrations over the long-term and across multiple generations remain unclear. In the present study, Daphnia pulex was exposed over three 21-day generations to a typical environmental nanoplastic concentration (1 μg/L) and the effects were investigated at physiological (growth and reproduction), gene transcription and enzyme activity levels. Chronic exposure did not affect the survival or body length of D. pulex, whereas the growth rate and reproduction were influenced in the F2 generation. Molecular responses indicated that environmental nanoplastic concentrations can modulate the response of antioxidant defenses, vitellogenin synthesis, development, and energy production in the F0-F1 generations, and prolongation resulted in inhibitory effects on antioxidant responses in F2 individuals. Some recovery was observed in the recovery group, but reproduction and stress defenses were significantly induced. Taken together, these results suggest that D. pulex recovery from chronic exposure to nanoplastic may take several generations, and that nanoplastics have potent long-term toxic effects on D. pulex. The findings highlight the importance of multigenerational and chronic biological evaluations to assess risks of emerging pollution.

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

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

Small RNA Sequencing Reveals Regulatory Roles of MicroRNAs in the Development of Meloidogyne incognita

MicroRNAs (miRNAs) are an extensive class of small regulatory RNAs. Knowing the specific expression and functions of miRNAs during root-knot nematode (RKN) (Meloidogyne incognita) development could provide fundamental information about RKN development as well as a means to design new strategies to control RKN infection, a major problem of many important crops. Employing high throughput deep sequencing, we identified a total of 45 conserved and novel miRNAs from two developmental stages of RKN, eggs and J2 juveniles, during their infection of cotton (Gossypium hirsutum L.). Twenty-one of the miRNAs were differentially expressed between the two stages. Compared with their expression in eggs, two miRNAs were upregulated (miR252 and miRN19), whereas 19 miRNAs were downregulated in J2 juveniles. Nine miRNAs were expressed at high levels, with >1000 reads per mapped million (RPM) sequenced reads in both eggs and J2 juveniles (miR1, miR124, miR2-3p, miR252, miR279, miR57-5p, miR7904, miR87, and miR92). Three miRNAs were only expressed in eggs (miR4738, miRN3, and miRN5). These differentially expressed miRNAs may control RKN development by regulating specific protein-coding genes in pathways associated with RKN growth and development.

Identification and expression of microRNAs in european eels Anguilla anguilla from two natural sites with different pollution levels

MicroRNAs (miRNAs) are a class of small non-coding RNA that control multiple biological processes through negative post-transcriptional regulation of gene expression. Recently a role of miRNAs in the response of aquatic organisms to environmental toxicants emerged. Toxicant-induced changes in miRNA expression might then represent novel biomarkers to evaluate the health status of these organisms. In this study, we aimed to identify the miRNA repertoire in the liver of the European eel Anguilla anguilla and to compare their differential expression between a polluted site located in the Gironde Estuary and a pristine site in Arcachon Bay (France). A total of 299 mature miRNAs were identified. In polluted water, 19 miRNAs were up-regulated and 22 were down-regulated. We predicted that these differentially expressed miRNAs could target 490 genes that were involved in ribosome biogenesis, response to hormones, response to chemical and chromatin modification. Moreover, we observed only few examples (29) of negative correlation between the expression levels of miRNAs and their targets suggesting that, in the system studied, miRNAs might not only regulate gene expression directly by degrading mRNA but also by inhibiting protein translation or by regulating other epigenetic processes. This study is the first example of in situ investigation of the role of miRNAs in the response of a fish species to water quality. Our findings provide new insights into the involvement of epigenetic mechanisms in the response of animals chronically exposed to pollution and pave the way for the utilization of miRNAs in aquatic ecotoxicology.

Potential role for microRNA in facilitating physiological adaptation to hypoxia in the Pacific whiteleg shrimp Litopenaeus vannamei

Hypoxia is one of the most common physiological stressors in shrimp farming. Post-transcriptional regulation by microRNAs has been recognized as a ubiquitous strategy to enable transient phenotypic plasticity and adaptation to stressful environment, but involvement of microRNAs in hypoxia stress response of penaeid shrimp remains elusive. In this study, small RNA sequencing and comparative transcriptomic analysis was conducted to construct a comprehensive microRNA dataset for the whiteleg shrimp Litopenaeus vannamei exposed to hypoxia challenge. A total of 3324 known miRNAs and 8 putative novel miRNAs were identified, providing a valuable resource for future investigation on the functional mechanism of miRNAs in shrimp. Upon hypoxia, 1213 miRNAs showed significant differential expression, and many well-known miRNAs involved in hypoxia tolerance such as miR-210, let-7, miR-143 and miR-101 were identified. Remarkably, the vast majority of these miRNAs were up-regulated, suggesting that up-regulation of miRNAs may represent an effective strategy to inhibit protein translation under stressful hypoxic condition. The differentially expressed miRNAs were potentially targeting a wide variety of genes, including those with essential roles in hypoxia tolerance such as HIF1a and p53. GO and KEGG enrichment analysis further revealed that a broad range of biological processes and metabolic pathways were over-represented. Several GO terms associated with gene transcription and translation and KEGG pathways related to cytoskeleton remodeling, immune defense and signaling transduction were enriched, highlighting the crucial roles of these cellular events in the adaptation to hypoxia. Taken together, our study revealed that the differentially expressed miRNAs may regulate host response to hypoxia by modulating the expression of stress response genes such as HIF1a and p53 and affecting key cellular events involved in hypoxia adaptation. The findings would expand our knowledge of the biochemical and molecular underpinnings of hypoxia response strategies used by penaeid shrimp, and contribute to a better understanding of the molecular mechanisms of hypoxia tolerance in decapod crustaceans.

Reproduction and development of Spodoptera exigua from cadmium and control strains under differentiated cadmium stress

The growth and development of living organisms is programmed in genes, but exogenous factors (e.g. cadmium) may modulate endogenous information. Heavy metals may disturb physiological functions and accumulate in the tissues. The insects under prolonged heavy metal stress show some modifications in their metabolism management. The aim of this study was to compare the reproduction and development between individuals of S. exigua from the strain, exposed over 130 generations to sublethal concentration of cadmium (44 mg Cd/kg dry weight of larval diet), and the individuals from the control strain, both additionally exposed to different concentration of cadmium (22-704 mg Cd/kg dry weight of larval diet). The exposure to various cadmium concentrations in the diet revealed survival difference between the cadmium and the control animals at the larvae stage. The differences between adults were not evident. The telomere length (responsible for the duration of a lifespan) in the cadmium strain was shorter in the females than in the males and the individuals from the control strain. TERF1 gene expression (indirectly responsible for the telomere length) was higher in the individuals from the cadmium strain 24 hrs after eclosion. The significant reduction in the larvae body mass was observed in both strains, when the metal concentration was equal to or higher than 264 mg/kg dry weight of larval diet. The EC50 values (defined as of body mass loss), calculated 48 hours after cadmium exposure of individuals from control and cadmium strains, were respectively 632 and 725 mg Cd/kg dry weight of diet. However, some difference in reproduction (the total number of eggs laid and the oviposition time) between the strains appeared only in the groups fed on the uncontaminated diet. The control females laid almost two times more eggs than those from the cadmium strain, and the control ones had more than two times longer oviposition time than the females from the cadmium strain. The fluctuation was also noted in the size of eggs and the hatching success on the following days when both strains were compared, while the hatching success was higher for the insects from the cadmium strain. In conclusion, the insects from the cadmium strain are more resistant to cadmium contamination, as it is evidenced by the EC50 parameter. However, the females from the cadmium strain start laying eggs statistically later, have shorter telomeres and slightly reduced TERF1 gene expression, but hutching success in the strain is significantly higher when compared with the control individuals.

microRNAs in Macrobrachium olfersii embryos: Identification, their biogenesis components and potential targets

In embryonic development, microRNAs (miRNAs) regulate the complex gene expression associated with the complexity of embryogenesis. Today, few studies have been conducted on the identification of miRNAs and components of miRNA biogenesis on embryonic development in crustaceans, especially in prawns. In this context, the aim of this study was to identify in silico components of miRNA biogenesis, and miRNAs and potential target genes during embryonic development in the prawn Macrobrachium olfersii through small RNAs and transcriptome analyses. Using the miRDeep2 program, we identified 17 miRNA precursors in M. olfersii, which seven (miR-9, miR-10, miR-92, miR-125, miR-305, miR-1175, and miR-2788) were reported in the miRBase database, indicating high evolutionary conservation of these sequences among animals. The other 10 miRNAs of M. olfersii were novel miRNAs and only similar to Macrobrachium niponnense miRNAs, indicating genus-specific miRNAs. In addition, eight key components of miRNA biogenesis (DROSHA, PASHA/DGCR8, XPO5, RAN, DICER, TRBP2, AGO, and PIWI) were identified in M. olfersii embryos unigenes. In the annotation of miRNA targets, 516 genes were similar to known sequences in the GenBank database. Regarding the conserved miRNAs, we verified that they were differentially expressed during embryonic development in M. olfersii. In conclusion, this is the first study that identifies conserved and novel miRNAs in the prawn M. olfersii with some miRNA target genes involved in embryonic development. Our results will allow further studies on the function of these miRNAs and miRNA biogenesis components during embryonic development in M. olfersii and other prawns of commercial interest.

Analysis of the microRNA transcriptome of Daphnia pulex during aging

Daphnia pulex is an important food organism that exhibits a particular mode of reproduction known as cyclical parthenogenesis (asexual) and sexual reproduction. Regulation of the aging process by microRNAs (miRNAs) is a research hotspot in miRNA studies. To investigate a possible role of miRNAs in regulating aging and senescence, we used Illumina HiSeq to sequence two miRNA libraries from 1-day-old (1d) and 25-day-old (25d) D. pulex specimens. In total, we obtained 11,218,097 clean reads and 28,569 unique miRNAs from 1d specimens and 11,819,106 clean reads and 44,709 unique miRNAs from 25d specimens. Bioinformatic analyses was used to identify 1335 differentially expressed miRNAs from known miRNAs, including 127 miRNAs that exhibited statistically significant differences (P < 0.01); 92 miRNAs were upregulated and 35 were downregulated. Quantitative real-time (qRT)-PCR experiments were performed for nine miRNAs from five samples (1d, 5d, 10d, 15d, 20d and 25d) during the aging process, and the sequencing and qRT-PCR data were found to be consistent. Ninety-four miRNAs were predicted to correspond to 2014 target genes in known miRNAs with 4032 target gene sites. Sixteen pathways changed significantly (P < 0.05) at different developmental stages, revealing many important principles of the miRNA regulatory aging network of D. pulex. Overall, the difference in miRNA expression profile during aging of D. pulex forms a basis for further studies aimed at understanding the role of miRNAs in regulating aging, reproductive transformation, senescence, and longevity.

Identification and characterization of microRNAs from the tube foot in the sea urchin Strongylocentrotus intermedius

MicroRNAs (miRNAs) play critical roles in regulating many bio-processes of eukaryotes. The sea urchin Strongylocentrotus intermedius (an important fishery resource) is of great economic importance in Japan, North Korea, Russia, and China. In the current study, miRNAs of tube foot in S. intermedius were firstly identified and characterized. Data in this study can provide more genomic information for the further understanding of the complex regulation network in sea urchins and present a new way for monitoring the health status of cultured sea urchins.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

Changes in metallothionein transcription levels in the mussel Mytilus galloprovincialis exposed to CdTe quantum dots

Quantum dots (QDs) are a class of engineered nanoparticles (ENPs) with several biomedical, industrial and commercial applications. However, their metabolism and detoxification process in aquatic invertebrates and environmental health hazards remain unclear. This study investigate the transcriptional changes of metallothioneins (MTs) isoforms (mt10IIIa and mt20IV) induced by CdTe QDs, in comparison with its dissolved counterpart, in the marine mussel Mytilus galloprovincialis. Mussels were exposed to CdTe QDs and to the same Cd concentration (10 µg Cd L^-1) of dissolved Cd for 14 days and mt transcription levels were measured by real time quantitative PCR (qPCR). Tissue specific mt transcription patterns were observed in mussels exposed to both Cd forms, wherein the gills were a more sensitive organ compared to the digestive gland. No significant changes were observed in mt10IIIa transcription levels in mussels exposed to both Cd forms. In contrast, transcription of mt20IV was tissue and exposure time dependent, with higher mt20IV mRNA levels in mussels exposed to QDs and dissolved Cd when compared to unexposed mussels. Multivariate analysis indicates particle-specific effects after 14 days of exposure and a dual role of MTs in the QD metabolism and in the protection against oxidative stress in mussels exposed to Cd-based ENPs.

Quantitative Shotgun Proteomics Associates Molecular-Level Cadmium Toxicity Responses with Compromised Growth and Reproduction in a Marine Copepod under Multigenerational Exposure

In this study, the copepod Tigriopus japonicus was exposed to different cadmium (Cd) treatments (0, 2.5, 5, 10, and 50 μg/L in seawater) for five generations (F0-F4), followed by a two-generation (F5-F6) recovery period in clean seawater. Six life-history traits (survival, developmental time of nauplius phase, developmental time to maturation, number of clutches, number of nauplii/clutch, and fecundity) were examined for each generation. Metal accumulation was also analyzed for generations F0-F6. Additionally, proteome profiling was performed for the control and 50 μg/L Cd-treated F4 copepods. In F0-F4 copepods, Cd accumulated in a concentration-dependent manner, prolonging the development of the nauplius phase and maturation and reducing the number of nauplii/clutch and fecundity. However, during F5-F6, Cd accumulation decreased rapidly, and significant but subtle effects on growth and reproduction were observed only for the highest metal treatment at F5. Proteomic analysis revealed that Cd treatment had several toxic effects including depressed nutrient absorption, dysfunction in cellular redox homeostasis and metabolism, and oxidative stress, resulting in growth retardation and reproduction limitation in this copepod species. Taken together, our results demonstrate the relationship between molecular toxicity responses and population-level adverse outcomes in T. japonicus under multigenerational Cd exposure.