Coastal bivalves are important ecosystem engineers, and identifying critical habitats can enhance conservation outcomes for threated keystone species as well as determining hotspots for invasive species. As early action is more efficient in both conservation and mitigation of species invasions, efficient and reliable tools for mapping and monitoring species over large scales are essential. We assessed the reliability and efficiency of towed video and quadrat sampling for estimating the abundance of three keystone macrofaunal bivalve species. To assess reliability, we compared the measured density based on each of the two methods to the \"true\" density estimated by manually surveying an entire transect. We found that both the video and quadrat method caused underestimation of the density of bivalves, but that the amount of underestimation was comparable, and further that both methods took substantially less time than surveying an entire transect manually. The video method underestimated the abundance of Pacific oysters (Magallana gigas), European flat oysters (Ostrea edulis), and blue mussels (Mytilus spp.) by 23%, 24%, and 16%, respectively. The causes of underestimation for the two oyster species were bivalves grouped in clusters, large amounts of small individuals, and generally higher abundances. While Mytilus spp. were underestimated overall, here observer experience was important, with inexperienced observers overestimating and experienced observers underestimating. Our study found both methods to be reliable and efficient for estimating the abundance of three keystone macrofaunal species, suggesting their potential applicability to other sessile or slow-moving species. We propose that these methods, due to their efficiency, can advance scientific knowledge and enhance conservation outcomes by establishing population baselines, assessing trends over time, and identifying and protecting critical habitats.

We present a genome assembly from an individual Magallana gigas (the Pacific oyster; Mollusca; Bivalvia; Ostreida; Ostreidae). The genome sequence is 564.0 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.23 kilobases in length.

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive success, founder effects, and rapid genetic drift, but is important to retain adaptive potential and avoid inbreeding depression. To support broodstock management and selective breeding in cultured Pacific oysters (Crassostrea (Magallana) gigas), we developed an amplicon panel targeting 592 genomic regions and SNP variants with an average of 50 amplicons per chromosome. Target SNPs were selected based on elevated observed heterozygosity or differentiation in Pacific oyster populations in British Columbia, Canada. The use of the panel for parentage applications was evaluated using multiple generations of oysters from a breeding program on Vancouver Island, Canada (n = 181) and families selected for Ostreid herpesvirus-1 resistance from the Molluscan Broodstock Program in Oregon, USA (n = 136). Population characterization was evaluated using wild, naturalized, farmed, or hatchery oysters sampled throughout the Northern Hemisphere (n = 190). Technical replicates showed high genotype concordance (97.5%; n = 68 replicates). Parentage analysis found suspected pedigree and sample handling errors, demonstrating the panel\'s value for quality control in breeding programs. Suspected null alleles were identified and found to be largely population dependent, suggesting population-specific variation impacting target amplification. Null alleles were identified using existing data without the need for pedigree information, and once they were removed, assignment rates increased to 93.0% and 86.0% of possible assignments in the two breeding program datasets. A pipeline for analyzing the amplicon sequence data from sequencer output, amplitools, is also provided.

The quality of Pacific oyster (Crassostrea gigas) can be affected by many factors during depuration, in which temperature is the major element. In this study, we aim to determine the quality and plasmalogen changes in C. gigas depurated at different temperatures. The quality was significantly affected by temperature, represented by varying survival rate, glycogen content, total antioxidant capacity, alkaline phosphatase activity between control and stressed groups. Targeted MS analysis demonstrated that plasmalogen profile was significantly changed during depuration with PUFA-containing plasmalogen species being most affected by temperature. Proteomics analysis and gene expression assay further verified that plasmalogen metabolism is regulated by temperature, specifically, the plasmalogen synthesis enzyme EPT1 was significantly downregulated by high temperature and four plasmalogen-related genes (GPDH, PEDS, Pex11, and PLD1) were transcriptionally regulated. The positive correlations between the plasmalogen level and quality characteristics suggested plasmalogen could be regarded as a quality indicator of oysters during depuration.

Species in estuaries tend to undergo both cadmium (Cd) and low salinity stress. However, how low salinity affects the Cd toxicity has not been fully understood. Investigating the impacts of low salinity on the dose-response relationships between Cd and biological endpoints has potential to enhance our understanding of the combined effects of low salinity and Cd. In this work, changes in the transcriptomes of Pacific oysters were analyzed following exposure to Cd (5, 20, 80 μg/L Cd2+) under normal (31.4 psu) and low (15.7 psu) salinity conditions, and then the dose-response relationship between Cd and transcriptome was characterized in a high-throughput manner. The benchmark dose (BMD) of gene expression, as a point of departure (POD), was also calculated based on the fitted dose-response model. We found that low salinity treatment significantly influenced the dose-response relationships between Cd and transcripts in oysters indicated by altered dose-response curves. In details, a total of 219 DEGs were commonly fitted to best models under both normal and low salinity conditions. Nearly three quarters of dose-response curves varied with salinity condition. Some monotonic dose-response curves in normal salinity condition even were replaced by nonmonotonic curves in low salinity condition. Low salinity treatment decreased the PODs of differentially expressed genes induced by Cd, suggesting that gene differential expression was more prone to being triggered by Cd in low salinity condition. The changed sensitivity to Cd in low salinity condition should be taken into consideration when using oyster as an indicator to assess the ecological risk of Cd pollution in estuaries.

Comprehending the potential effects of environmental variability on bivalves aquaculture becomes crucial for its sustainability under climate change scenarios, specially in the Humboldt Current System (HCS) where upwelling intensification leading to frequent hypoxia and acidification is expected. In a year-long study, Pacific oysters (Magallana gigas) were monitored at two depths (1.5m, 6.5m) in a bay affected by coastal upwelling. Surface waters exhibited warmer, well-oxygenated conditions and higher chlorophyll-a concentrations, while at depth greater hypoxia and acidification events occur, especially during upwelling. Surface cultured oysters exhibited 60 % larger size and 35% greater weight due to faster growth rate during the initial month of cultivation. The condition index (CI) increases in surface oysters after 10 months, whereas those at the bottom maintain a lower index. Food availability, temperature, and oxygen, correlates with higher growth rates, while pH associates with morphometric variables, indicating that larger oysters tend to develop under higher pH. Increased upwelling generally raises CI, but bottom oysters face stressful conditions such as hypoxia and acidification, resulting in lower performance. However, they acclimate by changing the organic composition of their shells and making them stronger. This study suggests that under intensified upwelling scenario, oysters would grow slowly, resulting in smaller sizes and lower performance, but the challenges may be confronted through complex compensation mechanisms among biomass production and maintenance of the shell structure and function. This poses a significant challenge for the sustainability of the aquaculture industry, emphasizing the need for adaptive strategies to mitigate the effects of climate change.

This study successionally monitored how nano- and micro-sized polystyrene beads (MNPs) influence larval mortality, growth, and attachment behavior of the Pacific oyster Crassostrea gigas related to MNP diameter and concentration. D-shaped larvae were sequentially exposed to three-diameter MNPs (0.55, 3.00, 6.00 µm) at five concentrations (0, 0.1, 1.0, 10, 20 μg/mL), and their mortality, growth stages and attachment were observed daily until they die. In addition, MNP intake and accumulation in larvae at each growth stage were determined using fluorescent beads. Deterioration in larval growth and survival was observed under all the exposure conditions, while significant negative effects on the growth parameters were defined with smaller MNPs at lower concentrations. Fluorescent signals were detected in larval digestive tracts at all except D-shaped larval stage, and on the mantle and foot in pediveligers. Therefore, MNP intake adversely affects larval physiological conditions by the synchronal effects of MNP size and concentration. Our findings highlight the implications of MNP characteristics on Pacific oyster larvae, emphasizing the interplay between size, concentration, and physiological responses, crucial for mitigating nanoparticle pollution in marine ecosystems.

Both genetic and environmental factors affect the morphology of oysters. Molecular identification is currently the primary means of species identification, but it is inconvenient and costly. In this research, we evaluated the effectiveness of geometric morphometric (GM) techniques in distinguishing between two oyster species, Crassostreagigas and C.ariakensis. We used traditional morphometric and GM methods, including principal component analysis (PCA), thin-plate spline analysis (TPS) and canonical variable analysis (CVA), to identify specific features that distinguish the two species. We found that differences in shape can be visualised using GM methods. The Procrustes analysis revealed significant differences in shell morphology between C.gigas and C.ariakensis. The shells of C.ariakensis are more prominent at the widest point and are more scattered and have a greater variety of shapes. The shells of C.gigas are more oval in shape. PCA results indicated that PC1 explained 45.22%, PC2 explained 22.09% and PC3 explained 10.98% of the variation between the two species, which suggests that the main morphological differences are concentrated in these three principal components. Combining the TPS analysis function plots showed that the shell shape of C.ariakensis is mainly elongated and spindle-shaped, whereas the shell shape of C.gigas is more oval. The CVA results showed that the classification rate for the two species reached 100% which means that C.ariakensis and C.gigas have distinct differences in shell morphology and can be completely separated, based on morphological characteristics. Through these methods, a more comprehensive understanding of the morphological characteristics of different oyster populations can be obtained, providing a reference for oyster classification and identification.

Ostreid herpes virus 1 (OsHV-1) has been classified within the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 is the etiological agent of a contagious viral disease of Pacific oysters, C. gigas, affecting also other bivalve species. Mortality rates reported associated with the viral infection vary considerably between sites and countries and depend on the age of affected stocks. A variant called μVar has been reported since 2008 in Europe and other variants in Australia and in New Zealand last decade. These variants are considered as the main causative agents of mass mortality events affecting C. gigas. Presently there is no established cell line that allows for the detection of infectious OsHV-1. In this context, a technique of propidium monoazide (PMA) PCR was developed in order to quantify \"undamaged\" capsids. This methodology is of interest to explore the virus infectivity. Being able to quantify viral particles getting an undamaged capsid (not only an amount of viral DNA) in tissue homogenates prepared from infected oysters or in seawater samples can assist in the definition of a Lethal Dose (LD) 50 and gain information in the experiments conducted to reproduce the viral infection. The main objectives of the present study were (i) the development/optimization of a PMA PCR technique for OsHV-1 detection using the best quantity of PMA and verifying its effectiveness through heat treatment, (ii) the definition of the percentage of undamaged capsids in four different tissue homogenates prepared from infected Pacific oysters and (iii) the approach of a LD50 during experimental viral infection assays on the basis of a number of undamaged capsids. Although the developped PMA PCR technique was unable to determine OsHV-1 infectivity in viral supensions, it could greatly improve interpretation of virus positive results obtained by qPCR. This technique is not intended to replace the quantification of viral DNA by qPCR, but it does make it possible to give a form of biological meaning to the detection of this DNA.

Thioester-containing proteins (TEPs) play a vital role in the innate immune response to biotic and abiotic stresses. In this study, the TEPs in C. gigas were identified, and their gene structure, phylogenetic relationships, collinearity relationships, expression profiles, sequence diversity, and alternative splicing were analyzed. Eight Tep genes were identified in C. gigas genome. Functional analysis and evolutionary relationships indicated a high level of homology to other mollusks TEPs. The transcriptome quantitative analysis results showed that the Tep genes in C. gigas respond to heat stress and Vibrio stress. Alternative splicing analysis revealed four Tep genes (designated A2M_1, CD109_3, CD109_5, complement C3) encode multiple alternative splice variants. Analysis of gene structure and multiple alignments revealed that seven CD109_5 variants are produced through the alternative splicing of the 19th exon, which encodes the highly variable central region. Sequence diversity analysis revealed thirteen missense variants within the 19th exon region of these seven CD109_5 alternative splice variants. Furthermore, the differential alternative splicing analysis showed significant induction of CD109_5, A2M_1 and A2M_2 variants after infection with V. parahaemolyticus. This study explores the Tep genes of C. gigas, providing insights into the molecular mechanisms underlying the involvement of C. gigas TEPs in innate immunity.