Pearl Farming Micro-Nanoplastics Affect Oyster Physiology and Pearl Quality.

Pearl farming is crucial for the economy of French Polynesia. However, rearing structures contribute significantly to plastic waste, and the widespread contamination of pearl farming lagoons by microplastics has raised concerns about risks to the pearl industry. This study aimed to evaluate the effects of micro-nanoplastics (MNPs, 0.4-200 µm) on the pearl oyster (Pinctada margaritifera) over a 5-month pearl production cycle by closely mimicking ecological scenarios. MNPs were produced from weathered plastic pearl farming gear and tested at environmentally relevant concentrations (0.025 and 1 µg L-1) to decipher biological and functional responses through integrative approaches. The significant findings highlighted the impacts of MNPs on oyster physiology and pearl quality, even at remarkably low concentrations. Exposure to MNPs induced changes in energy metabolism, predominantly driven by reduced assimilation efficiency of microalgae, leading to an alteration in gene expression patterns. A distinct gene expression module exhibited a strong correlation with physiological parameters affected by MNP conditions, identifying key genes as potential environmental indicators of nutritional-MNP stress in cultured oysters. The alteration in pearl biomineralization, evidenced by thinner aragonite crystals and the presence of abnormal biomineral concretions, known as keshi pearls, raises concerns about the potential long-term impact on the Polynesian pearl industry.

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.

Long dsRNAs promote an anti-viral response in Pacific oyster hampering ostreid herpesvirus 1 replication.

Double-stranded RNA (dsRNA)-mediated genetic interference (RNAi) is a widely used reverse genetic tool for determining the loss-of-function phenotype of a gene. Here, the possible induction of an immune response by long dsRNA was tested in a marine bivalve (Crassostrea gigas), as well as the specific role of the subunit 2 of the nuclear factor κB inhibitor (IκB2). This gene is a candidate of particular interest for functional investigations in the context of oyster mass mortality events, as Cg-IκB2 mRNA levels exhibited significant variation depending on the amount of ostreid herpesvirus 1 (OsHV-1) DNA detected. In the present study, dsRNAs targeting Cg-IκB2 and green fluorescent protein genes were injected in vivo into oysters before being challenged by OsHV-1. Survival appeared close to 100% in both dsRNA-injected conditions associated with a low detection of viral DNA and a low expression of a panel of 39 OsHV-1 genes as compared with infected control. Long dsRNA molecules, both Cg-IκB2- and GFP-dsRNA, may have induced an anti-viral state controlling the OsHV-1 replication and precluding the understanding of the specific role of Cg-IκB2 Immune-related genes including Cg-IκB1, Cg-Rel1, Cg-IFI44, Cg-PKR and Cg-IAP appeared activated in the dsRNA-injected condition, potentially hampering viral replication and thus conferring a better resistance to OsHV-1 infection. We revealed that long dsRNA-mediated genetic interference triggered an anti-viral state in the oyster, emphasizing the need for new reverse genetics tools for assessing immune gene function and avoiding off-target effects in bivalves.

Colonization of Polystyrene Microparticles by Vibrio crassostreae: Light and Electron Microscopic Investigation.

Microplastics collected at sea harbor a high diversity of microorganisms, including some Vibrio genus members, raising questions about the role of microplastics as a novel ecological niche for potentially pathogenic microorganisms. In the present study, we investigated the adhesion dynamics of Vibrio crassostreae on polystyrene microparticles (micro-PS) using electronic and fluorescence microscopy techniques. Micro-PS were incubated with bacteria in different media (Zobell culture medium and artificial seawater) with or without natural marine aggregates. The highest percentage of colonized particles (38-100%) was observed in Zobell culture medium, which may be related to nutrient availability for production of pili and exopolysaccharide adhesion structures. A longer bacterial attachment (6 days) was observed on irregular micro-PS compared to smooth particles (<10 h), but complete decolonization of all particles eventually occurred. The presence of natural marine agreggates around micro-PS led to substantial and perennial colonization featuring monospecific biofilms at the surface of the aggregates. These exploratory results suggest that V. crassostreae may be a secondary colonizer of micro-PS, requiring a multispecies community to form a durable adhesion phenotype. Temporal assessment of microbial colonization on microplastics at sea using imaging and omics approaches are further indicated to better understand the microplastics colonization dynamics and species assemblages.

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

BACKGROUND: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. DESCRIPTION: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. CONCLUSIONS: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

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

BACKGROUND: Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe. METHODS: To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60). RESULTS: A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several transcripts differentially expressed between the Danish and French progenies, for which additive genetic basis is suspected (showing intermediate expression levels in hybrids, and therefore additivity). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism, known to be implicated in coordinated control and success of reproduction. CONCLUSIONS: Observed differences suggest that adaptation of invasive populations might have occurred during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, gamete quality and fertility.

Disruption of amylase genes by RNA interference affects reproduction in the Pacific oyster Crassostrea gigas.

Feeding strategies and digestive capacities can have important implications for variation in energetic pathways associated with ecological and economically important traits, such as growth or reproduction in bivalve species. Here, we investigated the role of amylase in the digestive processes of Crassostrea gigas, using in vivo RNA interference. This approach also allowed us to investigate the relationship between energy intake by feeding and gametogenesis in oysters. Double-stranded (ds)RNA designed to target the two α-amylase genes A and B was injected in vivo into the visceral mass of oysters at two doses. These treatments caused significant reductions in mean mRNA levels of the amylase genes: -50.7% and -59% mRNA A, and -71.9% and -70.6% mRNA B in 15 and 75 µg dsRNA-injected oysters, respectively, relative to controls. Interestingly, reproductive knock-down phenotypes were observed for both sexes at 48 days post-injection, with a significant reduction of the gonad area (-22.5% relative to controls) and germ cell under-proliferation revealed by histology. In response to the higher dose of dsRNA, we also observed reductions in amylase activity (-53%) and absorption efficiency (-5%). Based on these data, dynamic energy budget modeling showed that the limitation of energy intake by feeding that was induced by injection of amylase dsRNA was insufficient to affect gonadic development at the level observed in the present study. This finding suggests that other driving mechanisms, such as endogenous hormonal modulation, might significantly change energy allocation to reproduction, and increase the maintenance rate in oysters in response to dsRNA injection.

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes.

BACKGROUND: Black pearl farming is based on culture of the blacklip pearl oyster Pinctada margaritifera (Mollusca, lophotrochozoa), a protandrous hermaphrodite species. At first maturation, all individuals are males. The female sex appears progressively from two years old, which represents a limitation for broodstock conditioning for aquaculture production. In marine mollusks displaying hermaphroditic features, data on sexual determinism and differentiation, including the molecular sex determining cascade, are scarce. To increase genomic resources and identify the molecular mechanisms whereby gene expression may act in the sexual dimorphism of P. margaritifera, we performed gonad transcriptome analysis. RESULTS: The gonad transcriptome of P. margaritifera was sequenced from several gonadic samples of males and females at different development stages, using a Next-Generation-Sequencing method and RNAseq technology. After Illumina sequencing, assembly and annotation, we obtained 70,147 contigs of which 62.2% shared homologies with existing protein sequences, and 9% showed functional annotation with Gene Ontology terms. Differential expression analysis identified 1,993 differentially expressed contigs between the different categories of gonads. Clustering methods of samples revealed that the sex explained most of the variation in gonad gene expression. K-means clustering of differentially expressed contigs showed 815 and 574 contigs were more expressed in male and female gonads, respectively. The analysis of these contigs revealed the presence of known specific genes coding for proteins involved in sex determinism and/or differentiation, such as dmrt and fem-1 like for males, or foxl2 and vitellogenin for females. The specific gene expression profiles of pmarg-fem1-like, pmarg-dmrt and pmarg-foxl2 in different reproductive stages (undetermined, sexual inversion and regression) suggest that these three genes are potentially involved in the sperm-oocyte switch in P. margaritifera. CONCLUSIONS: The study provides a new transcriptomic tool to study reproduction in hermaphroditic marine mollusks. It identifies sex differentiation and potential sex determining genes in P. margaritifera, a protandrous hermaphrodite species.

Sex-specific regulation of AMP-activated protein kinase (AMPK) in the Pacific oyster Crassostrea gigas.

The hermaphrodite Pacific oyster Crassostrea gigas displays a high energy allocation to reproduction. We studied the expression of AMP-activated protein kinase (AMPK) during gametogenesis in the gonad and characterized the mRNA sequences of the AMPK subunits: the AMPK alpha mRNA sequence was previously characterized; we identified AMPK beta, AMPK gamma, and mRNAs of putative AMPK-related targets following bioinformatics mining on existing genomic resources. We analyzed the mRNA expression of the AMPK alpha, beta, and gamma subunits in the gonads of male and female oysters through a reproductive cycle, and we quantified the mRNA expression of genes belonging to fatty acid and glucose metabolism. AMPK alpha mRNA levels were more abundant in males at the first stage of gametogenesis, when mitotic activity and the differentiation of germinal cells occur, and were always more abundant in males than in females. Some targets of fatty acid and glucose metabolism appeared to be correlated with the expression of AMPK subunits at the mRNA level. We then analyzed the sex-specific AMPK activity by measuring the phosphorylation of the catalytic AMPK alpha protein and its expression at the protein level. Both the amount of AMPK alpha protein and threonine 172 phosphorylation appeared to be almost totally inhibited in mature female gonads at stage 3, at the time when accumulation of reserves in oocytes was promoted, while it remained at a high level in mature spermatozoa. Its activation might play a sex-dependent role in the management of energy during gametogenesis in oyster.

Additives in polypropylene and polylactic acid food packaging: Chemical analysis and bioassays provide complementary tools for risk assessment.

Plastic food packaging represents 40 % of the plastic production worldwide and belongs to the 10 most commonly found items in aquatic environments. They are characterized by high additives contents with >4000 formulations available on the market. Thus they can release their constitutive chemicals (i.e. additives) into the surrounding environment, contributing to chemical pollution in aquatic systems and to contamination of marine organism up to the point of questioning the health of the consumer. In this context, the chemical and toxicological profiles of two types of polypropylene (PP) and polylactic acid (PLA) food packaging were investigated, using in vitro bioassays and target gas chromatography mass spectrometry analyses. Plastic additives quantification was performed both on the raw materials, and on the material leachates after 5 days of lixiviation in filtered natural seawater. The results showed that all samples (raw materials and leachates) contained additive compounds (e.g. phthalates plasticizers, phosphorous flame retardants, antioxidants and UV-stabilizers). Differences in the number and concentration of additives between polymers and suppliers were also pointed out, indicating that the chemical signature cannot be generalized to a polymer and is rather product dependent. Nevertheless, no significant toxic effects was observed upon exposure to the leachates in two short-term bioassays targeting baseline toxicity (Microtox® test) and Pacific oyster Crassostrea gigas fertilization success and embryo-larval development. Overall, this study demonstrates that both petrochemical and bio-based food containers contain harmful additives and that it is not possible to predict material toxicity solely based on chemical analysis. Additionally, it highlights the complexity to assess and comprehend the additive content of plastic packaging due to the variability of their composition, suggesting that more transparency in polymer formulations is required to properly address the risk associated with such materials during their use and end of life.

On the horns of a dilemma: Evaluation of synthetic and natural textile microfibre effects on the physiology of the pacific oyster Crassostrea gigas.

Fast fashion and our daily use of fibrous materials cause a massive release of microfibres (MF) into the oceans. Although MF pollution is commonly linked to plastics, the vast majority of collected MF are made from natural materials (e.g. cellulose). We investigated the effects of 96-h exposure to natural (wool, cotton, organic cotton) and synthetic (acrylic, nylon, polyester) textile MF and their associated chemical additives on the capacity of Pacific oysters Crassostrea gigas to ingest MF and the effects of MF and their leachates on key molecular and cellular endpoints. Digestive and glycolytic enzyme activities and immune and detoxification responses were determined at cellular (haemocyte viability, ROS production, ABC pump activity) and molecular (Ikb1, Ikb2, caspase 1 and EcSOD expression) levels, considering environmentally relevant (10 MF L-1) and worst-case scenarios (10 000 MF L-1). Ingestion of natural MF perturbed oyster digestive and immune functions, but synthetic MF had few effects, supposedly related with fibers weaving rather than the material itself. No concentration effects were found, suggesting that an environmental dose of MF is sufficient to trigger these responses. Leachate exposure had minimal effects on oyster physiology. These results suggest that the manufacture of the fibres and their characteristics could be the major factors of MF toxicity and stress the need to consider both natural and synthetic particles and their leachates to thoroughly evaluate the impact of anthropogenic debris. Environmental Implication. Microfibres (MF) are omnipresent in the world oceans with around 2 million tons released every year, resulting in their ingestion by a wide array of marine organisms. In the ocean, a domination of natural MF- representing more than 80% of collected fibres-over synthetic ones was observed. Despite MF pervasiveness, research on their impact on marine organisms, is still in its infancy. The current study aims to investigate the effects of environmental concentrations of both synthetic and natural textile MF and their associated leachates on a model filter feeder.

Discussion about suitable applications for biodegradable plastics regarding their sources, uses and end of life.

This opinion paper offers a scientific view on the current debate of the place of biodegradable plastics as part of the solution to deal with the growing plastic pollution in the world's soil, aquatic, and marine compartments. Based on the current scientific literature, we focus on the current limits to prove plastic biodegradability and to assess the toxicity of commercially used biobased and biodegradable plastics in natural environments. We also discuss the relevance of biodegradable plastics for selected applications with respect to their use and end of life. In particular, we underlined that there is no universal biodegradability of plastics in any ecosystem, that considering the environment as a waste treatment system is not acceptable, and that the use of compostable plastics requires adaptation of existing organic waste collection and treatment channels.

A critical review on the evaluation of toxicity and ecological risk assessment of plastics in the marine environment.

The increasing production of plastics together with the insufficient waste management has led to massive pollution by plastic debris in the marine environment. Contrary to other known pollutants, plastic has the potential to induce three types of toxic effects: physical (e.g intestinal injuries), chemical (e.g leaching of toxic additives) and biological (e.g transfer of pathogenic microorganisms). This critical review questions our capability to give an effective ecological risk assessment, based on an ever-growing number of scientific articles in the last two decades acknowledging toxic effects at all levels of biological integration, from the molecular to the population level. Numerous biases in terms of concentration, size, shape, composition and microbial colonization revealed how toxicity and ecotoxicity tests are still not adapted to this peculiar pollutant. Suggestions to improve the relevance of plastic toxicity studies and standards are disclosed with a view to support future appropriate legislation.

Intertidal limits shape covariation between metabolic plasticity, oxidative stress and telomere dynamics in Pacific oyster (Crassostrea gigas).

In intertidal zones, species such as sessile shellfish exhibit extended phenotypic plasticity to face rapid environmental changes, but whether frequent exposure to intertidal limits of the distribution range impose physiological costs for the animal remains elusive. Here, we explored how phenotypic plasticity varied along foreshore range at multiple organization levels, from molecular to cellular and whole organism acclimatization, in the Pacific oyster (Crassostrea gigas). We exposed 7-month-old individuals for up to 16 months to three foreshore levels covering the vertical range for this species, representing 20, 50 and 80% of the time spent submerged monthly. Individuals at the upper range limit produced energy more efficiently, as seen by steeper metabolic reactive norms and unaltered ATP levels despite reduced mitochondrial density. By spending most of their time emerged, oysters mounted an antioxidant shielding concomitant with lower levels of pro-oxidant proteins and postponed age-related telomere attrition. Instead, individuals exposed at the lower limit range near subtidal conditions showed lower energy efficiencies, greater oxidative stress and shorter telomere length. These results unraveled the extended acclimatization strategies and the physiological costs of living too fast in subtidal conditions for an intertidal species.

Chemical effects of different types of rubber-based products on early life stages of Pacific oyster, Crassostrea gigas.

Rubber products and debris with specific chemical signatures can release their constitutive compounds into the surrounding environment. We investigated the chemical toxicity of different types of new and used rubber products (tires, crumb rubber granulates, aquaculture rubber bands) on early life stages of a model marine organism, Pacific oyster Crassostrea gigas. Leachates obtained from used products were generally less toxic than those from new ones. Leachates from new products induced embryotoxicity at different concentrations: oyster-farming rubber bands (lowest observed effect concentration, LOEC = 1 g L-1) and crumb rubber granulates (LOEC = 1 g L-1) > tires (LOEC = 10 g L-1). Moreover, new oyster-farming rubber bands induced spermiotoxicity at 10 g L-1 (-29% survival) resulting in decreased oyster reproductive output (-17% fertilization yield). Targeted chemical analyses revealed some compounds (2 mineral contaminants, 15 PAHs, 2 PCBs) in leachates, which may have played a role. Rubber used in marine aquaculture (rubber bands) or present at sea as waste (tire, crumb rubber granulates) therefore release hazardous chemical molecules under realistic conditions, which may affect oyster development. Aquaculture development work is necessary to improve practices for eco-safety, as efforts to limit the contamination of marine environments by terrestrial rubber debris.

Cryogrinding and sieving techniques as challenges towards producing controlled size range microplastics for relevant ecotoxicological tests.

The impact of microplastics (MP) has attracted much attention from the scientific community and many laboratory assessments have been made of their effects on aquatic organisms. To produce MP from real environmental plastic waste, which would enable more realistic experiments, we used plastic pearl farming equipment from French Polynesian lagoons. Here, the pearl oyster Pinctada margaritifera could encounter MP coming from their breakdown in its surrounding environment. We tested an established method based on mechanical cryogenic grinding and liquid sieving. Our desired size range was 20-60 µm, corresponding to the optimal particle size ingested by P. margaritifera. The protocol was effective, generating MP particles of 20-60 µm (∼17,000-28,000 MP µg-1), but also produced too many smaller particles. The peak in the desired size range was thus flattened by the many small particles <3 µm (∼82,000-333,000 MP µg-1; 53-70% of total analysed particles), visible at the limit of Coulter counter analysis (cut-off point: 2 µm). Laser diffraction analysis (cut-off point: 0.4 µm) provided greater detail, showing that ∼80-90% of the total analysed particles were <1 µm. Diverging particle size distributions between those expected based on sieving range and those really observed, highlight the need to perform fine-scaled particle size distribution analyses to avoid underestimating the number of small micro- and nanoplastics (MNP) and to obtain an exact estimation of the fractions produced. Size and microstructure characterization by scanning electron microscopy suggested spontaneous particle self-assembly into crystal superstructures, which is the supposed cause of the divergence we observed. Overall, our results emphasize that particle self-assembly is a technical hurdle requiring further work and highlight the specific need to finely characterize the size distribution of MNP used in ecotoxicological experiments to avoid overestimating effects.

Tire rubber chemicals reduce juvenile oyster (Crassostrea gigas) filtration and respiration under experimental conditions.

Tires can release a large number of chemical compounds that are potentially hazardous for aquatic organisms. An ecophysiological system was used to do high-frequency monitoring of individual clearance, respiration rates, and absorption efficiency of juvenile oysters (8 months old) gradually exposed to four concentrations of tire leachates (equivalent masses: 0, 1, 10, and 100 µg tire mL-1). Leachates significantly reduced clearance (52 %) and respiration (16 %) rates from 1 µg mL-1, while no effect was observed on the absorption efficiency. These results suggest that tire leachates affect oyster gills, which are the organ of respiration and food retention as well as the first barrier against contaminants. Calculations of scope for growth suggested a disruption of the energy balance with a significant reduction of 57 %. Because energy balance directs whole-organism functions (e.g., growth, reproductive outputs), the present study calls for an investigation of the long-term consequences of chemicals released by tires.

Harsh intertidal environment enhances metabolism and immunity in oyster (Crassostrea gigas) spat.

The Pacific oyster Crassostrea gigas is established in the marine intertidal zone, experiencing rapid and highly dynamic environmental changes throughout the tidal cycle. Depending on the bathymetry, oysters face oxygen deprivation, lack of nutrients, and high changes in temperature during alternation of the cycles of emersion/immersion. Here we showed that intertidal oysters at a bathymetry level of 3 and 5 m delayed by ten days the onset of mortality associated with Pacific Oyster Mortality Syndrome (POMS) as compared to subtidal oysters. Intertidal oysters presented a lower growth but similar energetic reserves to subtidal oysters but induced proteomic changes indicative of a boost in metabolism, inflammation, and innate immunity that may have improved their resistance during infection with the Ostreid herpes virus. Our work highlights that intertidal harsh environmental conditions modify host-pathogen interaction and improve oyster health. This study opens new perspectives on oyster farming for mitigation strategies based on tidal height.

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns.

BACKGROUND: Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. RESULTS: In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. CONCLUSIONS: This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.