Transcriptome profiles link environmental variation and physiological response of Mytilus californianus between Pacific tides

Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress

Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.

Elevated aerial temperature modulates digestive enzyme activities in Mytilus californianus

The marine intertidal mussel Mytilus californianus aggregates to form beds along the Pacific shores of North America. As a sessile organism it must cope with fluctuations in temperature during low-tide aerial exposure, which elevates maintenance costs and negatively affects its overall energy budget. The function of its digestive gland is to release enzymes that break apart ingested polymers for subsequent nutrient absorption. The effects of elevated aerial warming acclimation on the functioning of digestive gland enzymes are not well studied. In this study we asked whether digestive gland carbohydases and proteases could be overstimulated in warm condition to possibly mitigate the costs related to the heat-shock response. We compared mussels acclimated to a + 9 °C heat-shock during daily low-tide aerial exposure to mussels acclimated to isothermal tidal conditions in a simulated intertidal system. The results showed fairly consistent activities of cellulase, trypsin, and amino-peptidase across tidal variation and between thermal treatments; however, amylase activity was lower in warmed versus cool mussels across low and high-tide. We also observed the expression of heat-shock genes in gill tissue during warm tidal conditions, suggestive that moderate temperatures during aerial exposure can induce a stress response.

Interactions Between Temperature Variability and Reproductive Physiology Across Traits in an Intertidal Crab

Thermal extremes alter population processes, which can result in part from temperature-induced movement at different spatial and temporal scales. Thermal thresholds for animal movement likely change based on underlying thermal physiology and life-history stage, a topic that requires greater study. The intertidal porcelain crab Petrolisthes cinctipes currently experiences temperatures that can reach near-lethal levels in the high-intertidal zone at low tide. However, the thermal thresholds that trigger migration to cooler microhabitats, and the extent to which crabs move in response to temperature, remain unknown. Moreover, the influence of reproductive status on these thresholds is rarely investigated. We integrated demographic, molecular, behavioral, and physiological measurements to determine if behavioral thermal limits varied due to reproductive state. Demographic data showed a trend for gravid, egg bearing, crabs to appear more often under rocks in the cooler intertidal zone where crab density is highest. In situ expression of 31 genes related to stress, metabolism, and growth in the field differed significantly based on intertidal elevation, with mid-intertidal crabs expressing the gene for the reproductive yolk protein vitellogenin (vg) earlier in the season. Furthermore, VG protein levels were shown to increase with density for female hemolymph. Testing for temperatures that elicit movement revealed that gravid females engage in heat avoidance behavior at lower temperatures (i.e., have a lower voluntary thermal maximum, VTmax) than non-gravid females. VTmax was positively correlated with the temperature of peak firing rate for distal afferent nerve fibers in the walking leg, a physiological relationship that could correspond to the mechanistic underpinning for temperature dependent movement. The vulnerability of marine organisms to global change is predicated by their ability to utilize and integrate physiological and behavioral strategies in response to temperature to maximize survival and reproduction. Interactions between fine-scale temperature variation and reproductive biology can have important consequences for the ecology of species, and is likely to influence how populations respond to ongoing climate change.

Transcriptome analysis reveals acclimation responses of pearl oysters to marine heatwaves

Marine heatwaves (MHWs) are weather-timescale extreme events in the oceans and can have devastating effects on marine bivalves and ecosystems they support, with considerable socio-economic consequences. Yet, the extent to which marine bivalves have the capacity to acclimate and adapt to MHWs remains unknown. Understanding molecular responses to MHWs is imperative to develop strategies for conservation of ecologically and economically important marine organisms. Here, using RNA-Seq, we investigate how various MHWs scenarios elicit molecular changes in threatened and vulnerable pearl oysters, Pinctada maxima (Jameson). Acute exposure of MHWs - mimicked by rapid increases of seawater temperature from 24 °C to 28 °C and 32 °C, respectively - significantly affected the expression levels of metabolic and immune-related genes, with thermal stress-responsive genes especially like HSP20, HSP70 and HSP90 being remarkably up-regulated. Following repeat exposure to MHWs, encouragingly, pearl oysters exhibited evident acclimation responses, as best exemplified by significantly lowered expression levels of key stress-responsive genes involved in metabolism and immunity in comparison to those observed during acute exposure. Findings of the present study provide a better understanding of molecular processes underpinning the acclimation and adaptation of marine bivalves to MHWs in the context of climate change.

Negative carry-over effects on larval thermal tolerances across a natural thermal gradient

Under climate change, marine organisms will need to tolerate or adapt to increasing temperatures to persist. The ability of populations to cope with thermal stress may be influenced by conditions experienced by parents, by both genetic changes and transgenerational phenotypic plasticity through epigenetics or maternal provisioning. In organisms with complex life cycles, larval stages are particularly vulnerable to stress. Positive parental carry-over effects occur if more stressful parental environments yield more tolerant offspring while the opposite pattern leads to negative carry-over effects. This study evaluated the role of parental effects in determining larval thermal tolerances for the intertidal mussel, Mytilus californianus. We tested whether thermal environments across a natural gradient (shoreline elevation) impacted mussel temperature tolerances. Lethal thermal limits were compared for field-collected adults and their larvae. We observed parental effects across one generation, in which adult mussels exposed to warmer habitats yielded less tolerant offspring. Interestingly, although parental environments influenced offspring tolerances, we found no clear effects of habitat conditions on adult phenotypes (tolerances). We found indicators of trade-offs in energy investment, with higher reproductive condition and larger egg diameters in low stress environments. These results suggest that parental effects are negative, leading to possible adverse effects of thermal stress on the next generation.

Comparative Transcriptome and DNA Methylation Analysis of Phenotypic Plasticity in the Pacific Abalone (Haliotis discus hannai)

Phenotypic plasticity is an adaptive mechanism used by organisms to cope with environmental fluctuations. Pacific abalone (Haliotis discus hannai) are large-scale farmed in the temperate area of northern China and in the warmer waters of southern China. RNA-seq and comparative transcriptomic analysis here were performed to determine if the northern and southern populations have evolved divergent plasticity and if functional differences are associated with protein synthesis and growth-related biological progress. The DNA methylation (5mC) landscape of H. discus hannai from the two populations using whole genomic bisulfite sequencing (WGBS), exhibited different epigenetic patterns. The southern population had significant genomic hypo-methylation that may have resulted from long-term acclimation to heat stress. Combining 790 differentially expressed genes (DEGs) and 7635 differentially methylated genes (DMGs), we found that methylation within the gene body might be important in predicting abalone gene expression. Genes related to growth, development, transduction, and apoptosis may be regulated by methylation and could explain the phenotypic divergence of H. discus hannai. Our findings not only emphasize the significant roles of adaptive plasticity in the acclimation of H. discus hannai to high temperatures but also provide a new understanding of the epigenetic mechanism underlying the phenotypic plasticity in adaptation to climate change for marine organisms.

Resilience in Greenland intertidal Mytilus: The hidden stress defense

The Arctic is experiencing particularly rapid rates of warming, consequently invasive boreal species are now able to survive the less extreme Arctic winter temperatures. Whilst persistence of intertidal and terrestrial species in the Arctic is primarily determined by their ability to tolerate the freezing winters, air temperatures in the Arctic summer can reach 36 °C in the intertidal, which is beyond the upper thermal limits of many marine species. This is normally lethal for the conspicuous ecosystem engineer Mytilus edulis. Transcriptomic analyses were undertaken on both in situ collected and experimentally warmed animals to understand whether M. edulis is able to tolerate these very high summer temperatures. Surprisingly there was no significant enrichment for Gene Ontology terms (GO) when comparing the inner and outer fjord intertidal animals with outer fjord subtidal (control) animals, representing animals collected at 27 °C, 19 °C and 3 °C respectively. This lack of differentiation indicated a wide acclimation ability in this species. Conversely, significant enrichment for processes such as signal transduction, cytoskeleton and cellular protein modification was identified in the expression profiles of the 22 °C and 32 °C experimentally heated animals. This difference in gene expression between in situ collected and experimentally warmed animals was almost certainly due to the former being acclimated to a fluctuating, but predictable, temperature regime, which has increased their thermal tolerances. Interestingly, there was no evidence for enrichment of the classical cellular stress response in any of the animals sampled. Identification of a massive expansion of the HSPA12 heat shock protein 70 kDa gene family presented the possibility of these genes acting as intertidal regulators underpinning thermal resilience. This expansion has resulted in a modified cellular stress response, as an evolutionary adaptation to the rigour of the invasive intertidal life style. Thus, M. edulis appear to have considerable capacity to withstand the current rates of Arctic warming, and the very large attendant thermal variation.

DNA methylation mediates differentiation in thermal responses of Pacific oyster (Crassostrea gigas) derived from different tidal levels

Epigenetic mechanisms such as DNA methylation have the potential to affect organism acclimatization and adaptation to environmental changes by influencing their phenotypic plasticity; however, little is known about the role of methylation in the adaptive phenotypic divergence of marine invertebrates. Therefore, in this study, a typical intertidal species, the Pacific oyster (Crassostrea gigas), was selected to investigate the epigenetic mechanism of phenotypic plasticity in marine invertebrates. Intertidal and subtidal oysters subjected to one-generation common garden experiments and exhibited phenotypic divergence were used. The methylation landscape of both groups of oysters was investigated under temperate and high temperature. The two tidal oysters exhibited divergent methylation patterns, regardless of the temperature, which was mainly original environment-induced. Intertidal samples exhibited significant hypomethylation and more plasticity of methylation in response to heat shock, while subtidal samples showed hypermethylation and less plasticity. Combined with RNA-seq data, a positive relationship between methylation and expression in gene bodies was detected on a genome-wide scale. In addition, approximately 11% and 7% of differentially expressed genes showed significant methylation variation under high temperatures in intertidal and subtidal samples, respectively. Genes related to apoptosis and organism development may be regulated by methylation in response to high temperature in intertidal oysters, whereas oxidation-reduction and ion homeostasis-related genes were involved in subtidal oysters. The results also suggest that DNA methylation mediates phenotypic divergence in oysters adapting to different environments. This study provides new insight into the epigenetic mechanisms underlying phenotypic plasticity in adaptation to rapid climate change in marine organisms.

Modulated Expression and Activities of Ruditapes philippinarum Enzymes After Oxidative Stress Induced by Aerial Exposure and Reimmersion

Ruditapes philippinarum, is an economically and scientifically important bivalve mollusk. Its tolerance of aerial exposure has long been considered an important trait for its survival under acute environmental stress. In this study, the effects of air exposure at high and low temperatures (28 and 4°C) on the survival, antioxidant and metabolic enzyme activities, and the expression of antioxidant and immune-related genes in R. philippinarum were investigated. The activities of antioxidant and metabolic enzymes [superoxide dismutase (SOD), α-amylase, and proline hydroxylase (PHD)] were significantly affected by aerial exposure and reimmersion (reoxygenation) at both low (4°C) and high (28°C) temperatures. Moreover, the mRNA expression of α-amylase, SOD, and C-type lectin was also examined, which reveals these genes were significantly affected by aerial exposure challenge. In addition, the effects of aerial exposure and reimmersion on survival rate were calculated to evaluate the recovery capacity of Manila clam after aerial exposure at high and low temperatures. All individuals survived under low temperature aerial exposure for 24 h and reimmersion for 120 h. However, individuals died after reimmersion for 12 h following high temperature aerial exposure, and mortality peak occurred at 48 h. These data indicate that long-term aerial exposure during the transportation of clams should be in a low temperature environment. This study demonstrates that enzyme expression and activities linked to the stress response increase during the aerial exposure of R. philippinarum and provide useful information for future work on the molecular basis of tolerance of aerial exposure stress.

Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: potential HIF and NF-κB crosstalk in immune responses in clam

Background

Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophication and resulting hypoxia. As a filter-feeding organism living in the seafloor sediment, Ruditapes philippinarum represents an excellent “sentinel” species to assess the quality of marine environment. In order to gain insight into the molecular response and acclimatization mechanisms to hypoxia stress in marine invertebrates, we examined hypoxia-induced changes in immune-related gene expression and gene pathways involved in hypoxia regulation of R. philippinarum.

Results

We investigated the response of the Manila clam R. philippinarum to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and time course qPCR analysis. A total of 75 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, and cell proliferation/apoptosis. Fourteen hypoxia responsive genes were validated significantly up/down regulated at different time 0, 2, 5, and 8 d in gills of R. philippinarum in hypoxia challenged group. Functional enrichment analysis revealed the HIF signaling pathway and NF-κB signaling pathway play pivotal roles in hypoxia tolerance and resistance in R. philippinarum.

Conclusion

The HIF signaling pathway and NF-κB signaling pathway play a critical role in hypoxia tolerance and resistance in Manila clam. The immune and defense related genes and pathways obtained here gain a fundamental understanding of the hypoxia stress in marine bivalves and provide important insights into the physiological acclimation, immune response and defense activity under hypoxia challenge. The reduced metabolism is a consequence of counterbalancing investments in immune defense against other physiological processes.

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones

Fine-scale adaptive evolution is always constrained by strong gene flow at vertical level in marine organisms. Rapid environmental fluctuations and phenotypic plasticity through optimization of fitness-related traits in organisms play important roles in shaping intraspecific divergence. The coastal systems experience strong variations in multiple abiotic environmental factors, especially the temperature. We used a typical intertidal species, Pacific oyster (Crassostrea gigas), to investigate the interaction between plasticity and adaptive evolution. We collected intertidal and subtidal oysters from two ecological niches and carried out common garden experiments for one generation. We identified fine-scale vertical adaptive divergence between intertidal and subtidal F1 progeny at both sites, based on different hierarchical phenotypes, including morphological, physiological, and molecular traits. We further quantified the global plasticity to thermal stress through transcriptomic analysis. The intertidal oysters exhibited slow growth rate. However, they showed high survival and metabolic rates under heat stress, indicating vertically fine-scale phenotypic adaptive mechanisms and evolutionary trade-offs between growth and thermal tolerance. Transcriptomic analysis confirmed that the intertidal oysters have evolved high plasticity. The genes were classified into three types: evolutionarily divergent, concordantly plastic, and adaptive plastic genes. The evolved divergence between intertidal and subtidal oysters for these gene sets showed a significant positive correlation with plastic changes of subtidal populations in response to high temperature. Furthermore, the intertidal oysters exhibited delayed large-scale increase in expressional plasticity than that in subtidal counterparts. The same direction between plasticity and selection suggests that the oysters have evolved adaptive plasticity. This implies that adaptive plasticity facilitates the oyster to adapt to severe intertidal zones. The oysters exposed to strong environmental variability are thermal tolerant and have high adaptive potential to face the current global warming. Our findings will not only provide new insights into the significant role of plasticity in adaptive evolution that can be extended to other marine invertebrates, but also provide basic information for oyster resources conservation and reef reestablishment.

RNA-Seq analysis of differentially expressed genes in the grand jackknife clam Solen grandis under aerial exposure

Aerial exposure tolerance has been long considered as an important trait for the life survival under acute environmental stress. In this study, we utilized RNA-seq-based transcriptomic profiling to characterize the molecular responses of grand jackknife clam in response to aerial exposure. This assembly yielded 190,856 unigenes with an average length of 1147 bp, a minimum length of 201 bp, and a maximum length of 51,869 bp, with an N50 length of 1875 bp. After differential expression analysis, a total of 1344 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, immune alteration, and apoptosis. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under aerial exposure stress. All these pathways could be assigned to the following biological functions in the aerial exposure tolerant Solen grandis: signaling, transporter activity, macromolecular complex, cellular component organization or biogenesis, and molecular transducer activity. This study highlighted candidate genes linked to stress response during aerial exposure and provide a useful resource for further work on gills tissue or for selection of aerial exposure tolerant phenotypes.

The role of stochastic thermal environments in modulating the thermal physiology of an intertidal limpet, Lottia digitalis

Much of our understanding of the thermal physiology of intertidal organisms comes from experiments with animals acclimated under constant conditions and exposed to a single heat stress. In nature, however, the thermal environment is more complex. Aerial exposure and the unpredictable nature of thermal stress during low tides may be critical factors in defining the thermal physiology of intertidal organisms. In the fingered limpet, Lottia digitalis, we investigated whether upper temperature tolerance and thermal sensitivity were influenced by the pattern of fluctuation with which thermal stress was applied. Specifically, we examined whether there was a differential response (measured as cardiac performance) to repeated heat stress of a constant and predictable magnitude compared with heat stress applied in a stochastic and unpredictable nature. We also investigated differences in cellular metabolism and damage following immersion for insights into biochemical mechanisms of tolerance. Upper temperature tolerance increased with aerial exposure, but no significant differences were found between predictable treatments of varying magnitudes (13°C versus 24°C versus 32°C). Significant differences in thermal tolerance were found between unpredictable trials with different heating patterns. There were no significant differences among treatments in basal citrate synthase activity, glycogen content, oxidative stress or antioxidants. Our results suggest that aerial exposure and recent thermal history, paired with relief from high low-tide temperatures, are important factors modulating the capacity of limpets to deal with thermal stress.

High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response

Ruditapes philippinarum, is an economically important marine bivalve species. The ability to cope with low salinity stress is quite important for the survival of aquatic species under natural conditions. In this study, the transcriptional response of the Manila clam to low salinity stress was characterized using RNA sequencing. The transcriptomes of a low salinity-treatment group (FRp1, FRp2), which survived under low salinity stress, and control group (SRp1, SRp2), which was not subjected to low salinity stress, were sequenced with the Illumina HiSeq platform. A total of 196,578 unigenes were generated. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under low salinity stress. All these pathways could be assigned to the following biological functions in the low salinity tolerant Manila clam: signal response to low salinity stress, antioxidant response, intracellular free amino acid transport and metabolism, energy production and conversion, cell signaling pathways, and regulation of ionic content and cell volume. In summary, this is the first study using high-throughput sequencing to identify gene targets that could explain osmotic regulation mechanisms under salinity stress in R. philippinarum.

Physiological performance of the intertidal Manila clam (Ruditapes philippinarum) to long-term daily rhythms of air exposure

Intertidal organisms, especially the sessile species, often experience long-term periodic air exposure during their lives. Learning the biochemical and physiological responses of intertidal organisms to long-term periodic air exposure and the relationship to duration of air exposure provides insight into adaptation to this variably stressful environment. We studied the Manila clam, Ruditapes philippinarum, an important species in world aquaculture, as a model to evaluate survival, growth, lipid composition, oxygen consumption, oxidative damage, and antioxidant enzyme activity in relation to the duration of air exposure in a long-term (60 days) laboratory study of varying durations of periodic emersion and re-immersion. Our results show: (1) clams undergoing a longer period of air exposure had lower survival and growth compared to those given a shorter exposure, (2) levels of oxidative damage and activities of antioxidant enzymes were higher in all air exposure treatments, but did not increase with duration of air exposure, and (3) the content of docosahexaenoic acid increased with duration of air exposure. Our results can largely be interpreted in the context of the energy expenditure by the clams caused by aerobic metabolism during the daily cycle of emersion and re-immersion and the roles of docosahexaenoic acid against oxidative stress.

The environmentally tuned transcriptomes of Mytilus mussels

Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography.

2-DE Mapping of the Blue Mussel Gill Proteome: The Usual Suspects Revisited

The Blue Mussel (Mytilus edulis, L. 1758) is an ecologically important and commercially relevant bivalve. Because of its ability to bioconcentrate xenobiotics, it is also a widespread sentinel species for environmental pollution, which has been used in ecotoxicological studies for biomarker assessment. Consequently, numerous proteomics studies have been carried out in various research contexts using mussels of the genus Mytilus, which intended to improve our understanding of complex physiological processes related to reproduction, adaptation to physical stressors or shell formation and for biomarker discovery. Differential-display 2-DE proteomics relies on an extensive knowledge of the proteome with as many proteoforms identified as possible. To this end, extensive characterization of proteins was performed in order to increase our knowledge of the Mytilus gill proteome. On average, 700 spots were detected on 2-DE gels by colloidal blue staining, of which 122 different, non-redundant proteins comprising 203 proteoforms could be identified by tandem mass spectrometry. These proteins could be attributed to four major categories: (i) “metabolism”, including antioxidant defence and degradation of xenobiotics; (ii) “genetic information processing”, comprising transcription and translation as well as folding, sorting, repair and degradation; (iii) “cellular processes”, such as cell motility, transport and catabolism; (iv) “environmental information processing”, including signal transduction and signalling molecules and interaction. The role of cytoskeleton proteins, energetic metabolism, chaperones/stress proteins, protein trafficking and the proteasome are discussed in the light of the exigencies of the intertidal environment, leading to an enhanced stress response, as well as the structural and physiological particularities of the bivalve gill tissue.

Does zebra mussel (Dreissena polymorpha) represent the freshwater counterpart of Mytilus in ecotoxicological studies? A critical review

One of the fundamentals in the ecotoxicological studies is the need of data comparison, which can be easily reached with the help of a standardized biological model. In this context, any biological model has been still proposed for the biomonitoring and risk evaluation of freshwaters until now. The aim of this review is to illustrate the ecotoxicological studies carried out with the zebra mussel Dreissena polymorpha in order to suggest this bivalve species as possible reference organism for inland waters. In detail,we showed its application in biomonitoring, as well as for the evaluation of adverse effects induced by several pollutants, using both in vitro and in vivo experiments. We discussed the advantages by the use of D. polymorpha for ecotoxicological studies, but also the possible limitations due to its invasive nature.

Thermal stress and predation risk trigger distinct transcriptomic responses in the intertidal snail Nucella lapillus

Thermal stress and predation risk have profound effects on rocky shore organisms, triggering changes in their feeding behaviour, morphology and metabolism. Studies of thermal stress have shown that underpinning such changes in several intertidal species are specific shifts in gene and protein expression (e.g. upregulation of heat-shock proteins). But relatively few studies have examined genetic responses to predation risk. Here, we use next-generation RNA sequencing (RNA-seq) to examine the transcriptomic (mRNA) response of the snail Nucella lapillus to thermal stress and predation risk. We found that like other intertidal species, N. lapillus displays a pronounced genetic response to thermal stress by upregulating many heat-shock proteins and other molecular chaperones. In contrast, the presence of a crab predator (Carcinus maenas) triggered few significant changes in gene expression in our experiment, and this response showed no significant overlap with the snail's response to thermal stress. These different gene expression profiles suggest that thermal stress and predation risk could pose distinct and potentially additive challenges for N. lapillus and that genetic responses to biotic stresses such as predation risk might be more complex and less uniform across species than genetic responses to abiotic stresses such as thermal stress.

A selection of reference genes and early-warning mRNA biomarkers for environmental monitoring using Mytilus spp. as sentinel species

mRNA biomarkers are promising tools for environmental health assessment and reference genes are needed to perform relevant qPCR analyses in tissue samples of sentinel species. In the present study, potential reference genes and mRNA biomarkers were tested in the gills and digestive glands of native and caged mussels (Mytilus spp.) exposed to harbor pollution. Results highlighted the difficulty to find stable reference genes in wild, non-model species and suggested the use of normalization indices instead of single genes as they exhibit a higher stability. Several target genes were found differentially expressed between mussel groups, especially in gills where cyp32, π-gst and CuZn-sod mRNA levels could be biomarker candidates. Multivariate analyses confirmed the ability of mRNA levels to highlight site-effects and suggested the use of several combined markers instead of individual ones. These findings support the use of qPCR technology and mRNA levels as early-warning biomarkers in marine monitoring programs.

A skellam model to identify differential patterns of gene expression induced by environmental signals

Background

RNA-seq, based on deep-sequencing techniques, has been widely employed to precisely measure levels of transcripts and their isoforms expressed under different conditions. However, robust statistical tools used to analyze these complex datasets are lacking. By grouping genes with similar expression profiles across treatments, cluster analysis provides insight into gene functions and networks that have become increasingly important.

Results

We proposed and verified a cluster algorithm based on a skellam model for grouping genes into distinct groups based on the pattern of gene expression in response to changing conditions or in different tissues. This algorithm capitalizes on the skellam distribution to capture the count property of RNA-seq data and clusters genes in different environments. A two-stage hierarchical expectation-maximization (EM) algorithm was implemented to estimate the optimal number of groups and mean expression levels of each group across two environments. A procedure was formulated to test whether and how a given group shows a plastic response to environmental changes. The model was used to analyze an RNA-seq dataset measured from reciprocal crosses of early Arabidopsis thaliana embryos that respond differently based on the extent of maternal and paternal genome contributions, from which genes associated with maternal and paternal contributions were identified. Simulation studies were also performed to validate the statistical behavior of the model.

Conclusions

This model is a useful tool for clustering gene expression data by RNA-seq, thus facilitating our understanding of gene functions and networks.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers

Background

The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy.

Results

Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function.

Conclusions

We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.

Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.

A complex life cycle in a warming planet: gene expression in thermally stressed sponges

Sponges are abundant, diverse and functionally important components of aquatic biotopes with crucial associations for many reef fish and invertebrates. Sponges have strict temperature optima, and mass mortality events have occurred after unusually high temperatures. To assess how sponges may adapt to thermal stress associated with a changing climate, we applied gene expression profiling to both stages of their bipartite life cycles. Adult Rhopaloeides odorabile are highly sensitive to thermal stress (32 °C), yet their larvae can withstand temperatures up to 36 °C. Here, we reveal the molecular mechanisms that underpin these contrasting thermal tolerances, which may provide sponges with a means to successfully disperse into cooler waters. Heat shock protein 70 was induced by increasing temperature in adult sponges, and genes involved in important biological functions including cytoskeleton rearrangement, signal transduction, protein synthesis/degradation, oxidative stress and detoxification were all negatively correlated with temperature. Conversely, gene expression in larvae was not significantly affected until 36 °C when a stress response involving extremely rapid activation of heat shock proteins occurred. This study provides the first transcriptomic assessment of thermal stress on both life history stages of a marine invertebrate facilitating better predictions of the long-term consequences of climate change for sponge population dynamics.

DNA damage and transcriptional changes in the gills of mytilus galloprovincialis exposed to nanomolar doses of combined metal salts (Cd, Cu, Hg)

Aiming at an integrated and mechanistic view of the early biological effects of selected metals in the marine sentinel organism Mytilus galloprovincialis, we exposed mussels for 48 hours to 50, 100 and 200 nM solutions of equimolar Cd, Cu and Hg salts and measured cytological and molecular biomarkers in parallel. Focusing on the mussel gills, first target of toxic water contaminants and actively proliferating tissue, we detected significant dose-related increases of cells with micronuclei and other nuclear abnormalities in the treated mussels, with differences in the bioconcentration of the three metals determined in the mussel flesh by atomic absorption spectrometry. Gene expression profiles, determined in the same individual gills in parallel, revealed some transcriptional changes at the 50 nM dose, and substantial increases of differentially expressed genes at the 100 and 200 nM doses, with roughly similar amounts of up- and down-regulated genes. The functional annotation of gill transcripts with consistent expression trends and significantly altered at least in one dose point disclosed the complexity of the induced cell response. The most evident transcriptional changes concerned protein synthesis and turnover, ion homeostasis, cell cycle regulation and apoptosis, and intracellular trafficking (transcript sequences denoting heat shock proteins, metal binding thioneins, sequestosome 1 and proteasome subunits, and GADD45 exemplify up-regulated genes while transcript sequences denoting actin, tubulins and the apoptosis inhibitor 1 exemplify down-regulated genes). Overall, nanomolar doses of co-occurring free metal ions have induced significant structural and functional changes in the mussel gills: the intensity of response to the stimulus measured in laboratory supports the additional validation of molecular markers of metal exposure to be used in Mussel Watch programs.

Transcriptomic responses to salinity stress in the Pacific oyster Crassostrea gigas

BACKGROUND

Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas is considered to be tolerant to relative low salinity. The genes that regulate C. gigas responses to osmotic stress were monitored using the next-generation sequencing of whole transcriptome with samples taken from gills. By RNAseq technology, transcript catalogs of up- and down-regulated genes were generated from the oysters exposed to low and optimal salinity seawater.

METHODOLOGY/PRINCIPAL FINDINGS

Through Illumina sequencing, we reported 1665 up-regulated transcripts and 1815 down-regulated transcripts. A total of 45771 protein-coding contigs were identified from two groups based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes that changed expression significantly were highly represented in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlighted genes related to osmoregulation, signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytoskeleton and cell cycle.

CONCLUSIONS/SIGNIFICANCE

Through more than 1.5 million sequence reads and the expression data of the two libraries, the study provided some useful insights into signal transduction pathways in oysters and offered a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will not only provide a better understanding of the molecular mechanisms about the response to osmotic stress of the oysters, but also facilitate research into biological processes to find underlying physiological adaptations to hypoosmotic shock for marine invertebrates.