Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

Elucidating responses of the intertidal clam Ruditapes philippinarum to compound extreme oceanic events

Ocean acidification and heatwaves caused by rising CO2 affect bivalves and other coastal organisms. Intertidal bivalves are vital to benthic ecosystems, but their physiological and metabolic responses to compound catastrophic climate events are unknown. Here, we examined Manila clam (Ruditapes philippinarum) responses to low pH and heatwaves. Biochemical and gene expression demonstrated that pH and heatwaves greatly affect physiological energy enzymes and genes expression. In the presence of heatwaves, Manila clams expressed more enzymes and genes involved in physiological energetics regardless of acidity, even more so than in the presence of both. In this study, calcifying organisms' biochemical and molecular reactions are more susceptible to temperature rises than acidity. Acclimation under harsh weather conditions was consistent with thermal stress increase at lower biological organization levels. These substantial temporal biochemical and molecular patterns illuminate clam tipping points. This study helps us understand how compound extreme weather and climate events affect coastal bivalves for future conservation efforts.

Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides

The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Crassostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms.

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

Plastic waste as a global challenge: are biodegradable plastics the answer to the plastic waste problem?

The strength, flexibility and light weight of traditional oil-derived plastics make them ideal materials for a large number of applications, including packaging, medical devices, building, transportation, etc. However, the majority of produced plastics are single-use plastics, which, coupled with a throw-away culture, leads to the accumulation of plastic waste and pollution, as well as the loss of a valuable resource. In this review we discuss the advances and possibilities in the biotransformation and biodegradation of oil-based plastics. We review bio-based and biodegradable polymers and highlight the importance of end-of-life management of biodegradables. Finally, we discuss the role of a circular economy in reducing plastic waste pollution.

Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling

Harmful Algal Blooms are worldwide occurrences that can cause poisoning in human seafood consumers as well as mortality and sublethal effets in wildlife, propagating economic losses. One of the most widespread toxigenic microalgal taxa is the dinoflagellate Genus Alexandrium, that includes species producing neurotoxins referred to as PST (Paralytic Shellfish Toxins). Blooms cause shellfish harvest restrictions to protect human consumers from accumulated toxins. Large inter-individual variability in toxin load within an exposed bivalve population complicates monitoring of shellfish toxicity for ecology and human health regulation. To decipher the physiological pathways involved in the bivalve response to PST, we explored the whole transcriptome of the digestive gland of the Pacific oyster Crassostrea gigas fed experimentally with a toxic Alexandrium minutum culture. The largest differences in transcript abundance were between oysters with contrasting toxin loads (1098 transcripts), rather than between exposed and non-exposed oysters (16 transcripts), emphasizing the importance of toxin load in oyster response to toxic dinoflagellates. Additionally, penalized regressions, innovative in this field, modeled accurately toxin load based upon only 70 transcripts. Transcriptomic differences between oysters with contrasting PST burdens revealed a limited suite of metabolic pathways affected, including ion channels, neuromuscular communication, and digestion, all of which are interconnected and linked to sodium and calcium exchanges. Carbohydrate metabolism, unconsidered previously in studies of harmful algal effects on shellfish, was also highlighted, suggesting energy challenge in oysters with high toxin loads. Associations between toxin load, genotype, and mRNA levels were revealed that open new doors for genetic studies identifying genetically-based low toxin accumulation.

Invasion trajectory of Pacific oysters in the northern Wadden Sea

Invasion trajectories of introduced alien species usually begin with a long establishment phase of low abundance, often followed by exponential expansion and subsequent adjustment phases. We review the first 26 years of feral Pacific oysters Crassostrea gigas around the island of Sylt in the Wadden Sea (North Sea, NE Atlantic), and reveal causal conditions for the invasion phases. Sea-based oyster farming with repeated introductions made establishment of feral oysters almost inevitable. Beds of mussels Mytilus edulis on mud flats offered firm substrate for attachment and ideal growth conditions around low tide level. C. gigas mapped on to the spatial pattern of mussel beds. During the 1990s, cold summers often hampered recruitment and abundances remained low but oyster longevity secured persistence. Since the 2000s, summers were often warmer and recruitment more regular. Young oysters attached to adult oysters and abundances of >1000 m-2 were achieved. However, peak abundance was followed by recruitment failure. The population declined and then was also struck by ice winters causing high mortality. Recovery was fast (>2000 m-2) but then recruitment failed again. We expect adjustment phase will proceed with mean abundance of about 1000 m-2 but density-dependent (e.g., diseases) and density-independent (e.g., weather anomalies) events causing strong fluctuations. With continued global warming, feral C. gigas at the current invasion fronts in British estuaries and Scandinavian fjords may show similar adjustment trajectories as observed in the northern Wadden Sea, and also other marine introductions may follow the invasion trajectory of Pacific oysters.

Marine invasions enter the genomic era: three lessons from the past, and the way forward

The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.

Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura

Chromosomal rearrangements can shape the structure of genetic variation in the genome directly through alteration of genes at breakpoints or indirectly by holding combinations of genetic variants together due to reduced recombination. The third chromosome of Drosophila pseudoobscura is a model system to test hypotheses about how rearrangements are established in populations because its third chromosome is polymorphic for >30 gene arrangements that were generated by a series of overlapping inversion mutations. Circumstantial evidence has suggested that these gene arrangements are selected. Despite the expected homogenizing effects of extensive gene flow, the frequencies of arrangements form gradients or clines in nature, which have been stable since the system was first described >80 years ago. Furthermore, multiple arrangements exist at appreciable frequencies across several ecological niches providing the opportunity for heterokaryotypes to form. In this study, we tested whether genes are differentially expressed among chromosome arrangements in first instar larvae, adult females and males. In addition, we asked whether transcriptional patterns in heterokaryotypes are dominant, semidominant, overdominant, or underdominant. We find evidence for a significant abundance of differentially expressed genes across the inverted regions of the third chromosome, including an enrichment of genes involved in sensory perception for males. We find the majority of loci show additivity in heterokaryotypes. Our results suggest that multiple genes have expression differences among arrangements that were either captured by the original inversion mutation or accumulated after it reached polymorphic frequencies, providing a potential source of genetic variation for selection to act upon. These data suggest that the inversions are favored because of their indirect effect of recombination suppression that has held different combinations of differentially expressed genes together in the various gene arrangement backgrounds.

Oysters and Vibrios as a Model for Disease Dynamics in Wild Animals

Disease dynamics in the wild are influenced by a number of ecological and evolutionary factors not addressed by traditional laboratory-based characterization of pathogens. Here we propose the oyster, Crassostrea gigas, as a model for studying the interaction of the environment, bacterial pathogens, and the host in disease dynamics. We show that an important first step is to ask whether the functional unit of pathogenesis is a bacterial clone, a population, or a consortium in order to assess triggers of disease outbreaks and devise appropriate monitoring tools. Moreover, the development of specific-pathogen-free (SPF) oysters has enabled assessment of the infection process under natural conditions. Finally, recent results show the importance of microbial interactions and host genetics in determining oyster health and disease.

Oyster reproduction is affected by exposure to polystyrene microplastics

Plastics are persistent synthetic polymers that accumulate as waste in the marine environment. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Because filter-feeder organisms ingest MP while feeding, they are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (micro-PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 0.023 mg·L(-1)) for 2 mo during a reproductive cycle. Effects were investigated on ecophysiological parameters; cellular, transcriptomic, and proteomic responses; fecundity; and offspring development. Oysters preferentially ingested the 6-µm micro-PS over the 2-µm-diameter particles. Consumption of microalgae and absorption efficiency were significantly higher in exposed oysters, suggesting compensatory and physical effects on both digestive parameters. After 2 mo, exposed oysters had significant decreases in oocyte number (-38%), diameter (-5%), and sperm velocity (-23%). The D-larval yield and larval development of offspring derived from exposed parents decreased by 41% and 18%, respectively, compared with control offspring. Dynamic energy budget modeling, supported by transcriptomic profiles, suggested a significant shift of energy allocation from reproduction to structural growth, and elevated maintenance costs in exposed oysters, which is thought to be caused by interference with energy uptake. Molecular signatures of endocrine disruption were also revealed, but no endocrine disruptors were found in the biological samples. This study provides evidence that micro-PS cause feeding modifications and reproductive disruption in oysters, with significant impacts on offspring.

Oyster reproduction is affected by exposure to polystyrene microplastics

Plastics are persistent synthetic polymers that accumulate as waste in the marine environment. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Because filter-feeder organisms ingest MP while feeding, they are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (micro-PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 0.023 mg·L(-1)) for 2 mo during a reproductive cycle. Effects were investigated on ecophysiological parameters; cellular, transcriptomic, and proteomic responses; fecundity; and offspring development. Oysters preferentially ingested the 6-µm micro-PS over the 2-µm-diameter particles. Consumption of microalgae and absorption efficiency were significantly higher in exposed oysters, suggesting compensatory and physical effects on both digestive parameters. After 2 mo, exposed oysters had significant decreases in oocyte number (-38%), diameter (-5%), and sperm velocity (-23%). The D-larval yield and larval development of offspring derived from exposed parents decreased by 41% and 18%, respectively, compared with control offspring. Dynamic energy budget modeling, supported by transcriptomic profiles, suggested a significant shift of energy allocation from reproduction to structural growth, and elevated maintenance costs in exposed oysters, which is thought to be caused by interference with energy uptake. Molecular signatures of endocrine disruption were also revealed, but no endocrine disruptors were found in the biological samples. This study provides evidence that micro-PS cause feeding modifications and reproductive disruption in oysters, with significant impacts on offspring.