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

Impact of short-term elevated temperature stress on winter-acclimated individuals of the marine gastropod Crepidula fornicata

The intertidal zone is an especially stressful thermal habitat, typically exposing residents to air temperatures for up to 6 h at a time, twice daily. Tolerance to elevated temperatures has been particularly well-studied for a variety of intertidal species, especially with regard to upper thermal limits during summers. However, in recent years, as climates have been changing around the world, temperate zone intertidal organisms have sometimes been exposed to periods of unusually high air temperatures during the winter. The present study sought to examine the impact of elevated temperatures on survival and clearance rates of winter-acclimated intertidal individuals of the sedentary marine suspension-feeding gastropod Crepidula fornicata. Individuals were collected intertidally from Nahant, Massachusetts from late January to early April each year for 5 years, maintained in the laboratory at the acclimation temperature of 6 °C, and exposed in the laboratory for 3 h to temperatures as high as 37 °C in seawater either once or twice, 24 h apart. Although mean clearance rates were substantially reduced for at least the next 12-24 h after individuals were returned to the 6 °C control condition following exposures to elevated temperatures as low as 21-26 °C, we saw little mortality even following two 3 h exposures to 35 °C, or single exposures to 37 °C. Mortality was substantial, however, in one experiment following a double exposure to 37 °C. Smaller individuals (~5-12 mm in shell length) were somewhat more sensitive to the thermal stress than adults were. Intertidal members of C. fornicata in Massachusetts seem well-prepared to deal with the increasing range of winter air temperatures associated with the global climate confusion predicted for future years. Additional studies will be required to understand the physiological and biochemical mechanisms used by winter-acclimated individuals of this species to tolerate such periodic substantial temperature increases of 29-31 °C.

Genetic compensation rather than genetic assimilation drives the evolution of plasticity in response to mild warming across latitudes in a damselfly

Global warming is causing plastic and evolutionary changes in the phenotypes of ectotherms. Yet, we have limited knowledge on how the interplay between plasticity and evolution shapes thermal responses and underlying gene expression patterns. We assessed thermal reaction norm patterns across the transcriptome and identified associated molecular pathways in northern and southern populations of the damselfly Ischnura elegans. Larvae were reared in a common garden experiment at the mean summer water temperatures experienced at the northern (20°C) and southern (24°C) latitudes. This allowed a space-for-time substitution where the current gene expression levels at 24°C in southern larvae are a proxy for the expected responses of northern larvae under gradual thermal evolution to the predicted 4°C warming. Most differentially expressed genes showed fixed differences across temperatures between latitudes, suggesting that thermal genetic adaptation will mainly evolve through changes in constitutive gene expression. Northern populations also frequently showed plastic responses in gene expression to mild warming, while southern populations were much less responsive to temperature. Thermal responsive genes in northern populations showed to a large extent a pattern of genetic compensation, namely gene expression that was induced at 24°C in northern populations remained at a lower constant level in southern populations, and were associated with metabolic and translation pathways. There was instead little evidence for genetic assimilation of an initial plastic response to mild warming. Our data therefore suggest that genetic compensation rather than genetic assimilation may drive the evolution of plasticity in response to mild warming in this damselfly species.

Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation

Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.

Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies

Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.

Adaptations to the mudflat: Insights from physiological and transcriptional responses to thermal stress in a burrowing bivalve Sinonovacula constricta

Understanding physiological adaptations of organisms to temperature changes that characterize their habitat is the first step in predicting the putative effects of global climate change on population dynamics. Mudflats are an important part of the intertidal zone and experience extreme and fluctuating temperatures. Therein, species would be potentially susceptible to global warming. The present study explored physiological adaptations of burrowing species to life in an intertidal mudflat by analyzing the potential operative temperatures in the mudflat, and assessing cardiac performance and the transcriptional response to thermal stress by a typical burrowing bivalve, the razor clam Sinonovacula constricta in different thermal environments, mimicking conditions during low tides. Clams showed higher thermal sublethal limits in mud with overlying air than in mud with overlying water, indicating an adaptation to rapidly changing ambient temperatures and thermal environments during emersion. This sublethal limit was far above the maximum operative temperature in the actual habitat site and suggests a potential buffer zone to ensure survival under unexpected high temperatures, that could occur with global warming. In response to high temperature, S. constricta exhibited the common heat stress response by up-regulating expression of the Bcl2-associated athanogene 3 (BAG3) and heat shock proteins to cope with the adverse effects of high temperature on protein homeostasis. Increased expression of key genes, including molybdenum cofactor synthesis 3 (MOCS3), oligoribonuclease (REX2), and NFκappaB inhibitor alpha (NFIA) may further remit the effect of thermal stress during the emersion period and delay a situation where clams reach their thermal sublethal limit, thereby helping to endure high temperature during low tide. These results clearly illustrate significant adaptations of a burrowing bivalve to life in intertidal mudflats at both physiological and molecular levels and can provide insights into potential physiological or evolutionary responses that could aid survival of mudflat species in a changing global climate.

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain

Predation risk induces broad behavioral and physiological responses that have traditionally been considered acute and transitory. However, prolonged or frequent exposure to predators and the sensory cues of their presence they broadcast to the environment impact long-term prey physiology and demographics. Though several studies have assessed acute and chronic stress responses in varied taxa, these attempts have often involved a priori expectations of the molecular pathways involved in physiological responses, such as glucocorticoid pathways and neurohormone production in vertebrates. While relatively little is known about physiological and molecular predator-induced stress in insects, many dramatic insect defensive behaviors have evolved to combat selection by predators. For instance, several moth families, such as Noctuidae, include members equipped with tympanic organs that allow the perception of ultrasonic bat calls and facilitate predation avoidance by eliciting evasive aerial flight maneuvers. In this study, we exposed adult male fall armyworm (Spodoptera frugiperda) moths to recorded ultrasonic bat foraging and attack calls for a prolonged period and constructed a de novo transcriptome based on brain tissue from predator cue-exposed relative to control moths kept in silence. Differential expression analysis revealed that 290 transcripts were highly up- or down-regulated among treatment tissues, with many annotating to noteworthy proteins, including a heat shock protein and an antioxidant enzyme involved in cellular stress. Though nearly 50% of differentially expressed transcripts were unannotated, those that were are implied in a broad range of cellular functions within the insect brain, including neurotransmitter metabolism, ionotropic receptor expression, mitochondrial metabolism, heat shock protein activity, antioxidant enzyme activity, actin cytoskeleton dynamics, chromatin binding, methylation, axonal guidance, cilia development, and several signaling pathways. The five most significantly overrepresented Gene Ontology terms included chromatin binding, macromolecular complex binding, glutamate synthase activity, glutamate metabolic process, and glutamate biosynthetic process. As a first assessment of transcriptional responses to ecologically relevant auditory predator cues in the brain of moth prey, this study lays the foundation for examining the influence of these differentially expressed transcripts on insect behavior, physiology, and life history within the framework of predation risk, as observed in ultrasound-sensitive Lepidoptera and other 'eared' insects.

Transcriptomic responses to predator kairomones in embryos of the aquatic snail Radix balthica

The ability of organisms to respond to predation threat by exhibiting induced defenses is well documented, but studies on the potential mechanistic basis for such responses are scarce. Here, we examine the transcriptomic response to predator kairomones of two functionally distinct developmental stages in embryos of the aquatic snail Radix balthica: E8-the stage at which a range-finding trial indicated that kairomone-induced accelerated growth and development first occurred; and E9-the stage at which embryos switched from ciliary- to crawling-driven locomotion. We tested whether expression profiles were influenced by kairomones and whether this influence varied between stages. We also identified potential candidate genes for investigating mechanisms underpinning induced responses. There were 6,741 differentially expressed transcripts between developmental stages, compared to just five in response to predator kairomones. However, on examination of functional enrichment in the transcripts responding to predator kairomones and adopting a less stringent significance threshold, 206 transcripts were identified relating to muscle function, growth, and development, with this response being greater at the later E9 stage. Furthermore, these transcripts included putative annotations for genes identified as responding to predator kairomones in other taxa, including C1q, lectin, and actin domains. Globally, transcript expression appeared reduced in response to predator kairomones and we hypothesize that this might be a result of metabolic suppression, as has been reported in other taxa in response to predation threat.

Transcriptome sequencing and differential gene expression analysis of the schistosome-transmitting snail Oncomelania hupensis inhabiting hilly and marshland regions

The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology. All paired-end reads were assembled into contigs from which 34,760 unigenes were predicted. Based on single nucleotide polymorphisms, principal component analysis and neighbor-joining clustering revealed two distinct clusters of hilly and marshland snails. Analysis of expression changes between environments showed that upregulated genes relating to immunity and development were enriched in hilly snails, while those associated with reproduction were over-represented in marshland snails. Eight differentially expressed genes between the two types of snails were validated by qRT-PCR. Our study identified candidate genes that could be targets for future functional studies, and provided a link between expression profiling and ecological adaptation of the snail that may have implications for schistosomiasis control.

Merging elemental and macronutrient approaches for a comprehensive study of energy and nutrient flows

Global warming and predation risk can have important impacts on animal physiology and life histories that can have consequences for ecosystem function. Zhang et al. () recently tested the separate and interactive effects of warming and predation risk on the body composition of Daphnia magna. By measuring both the elemental and biochemical composition of individuals, they showed that D. magna body elemental composition responded opposite to theoretical predictions and previous studies but that these changes were explained by adaptive life-history shifts in allocation to protein in eggs versus body lipid reserves. Photograph by Joachim Mergeay. Zhang, C., Jansen, M., De Meester, L. & Stoks, R. (2016) Energy storage and fecundity explain deviations from ecological stoichiometry predictions under global warming and size-selective predation. Journal of Animal Ecology 85, 1431-1441. Understanding the mechanisms through which energy and nutrients flow through ecosystems is critical to predicting and mitigating the consequences of climate change and other ecological disturbances. Ecological stoichiometry and nutritional geometry, using data on elements and macromolecules, respectively, have independently made major contributions towards this goal. Zhang et al. () provide data demonstrating that these two major frameworks can provide complementary insight into the consequences of global warming and predation risk for the physiology and life-history traits of a key aquatic herbivore, Daphnia magna. This study should catalyse further work to unite these two parallel and complementary frameworks.

De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome

The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.

Early Caregiving and Human Biobehavioral Development: A Comparative Physiology Approach

A large and growing body of evidence demonstrates associations between quality of the early caregiving environment and risk for stress-related illness across the lifespan. The recent research examining associations between early caregiving environments and subsequent development is reviewed, with particular attention to early programming and subsequent malleability of systems underlying stress responsivity. A developmental comparative physiology model is suggested; one in which postnatal programming and phenotypic plasticity act in concert as mechanisms underlying the persisting effects of early care environments for biobehavioral outcomes.

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.