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16 results for “eastern oyster”
Meta-analysis of ecosystem services associated with oyster restoration on the Eastern and Gulf coasts of the US
We conducted a meta-analysis to systematically quantify the success and uncertainty of oyster reef restoration for a suite of biological, biogeochemical, and physical ecosystem services relative to both degraded and natural reference habitats. We focused on the eastern oyster, Crassostrea virginica. To evaluate whether restored eastern oyster reefs enhance ecosystem services relative to unaltered, degraded habitats and whether restored reefs provide ecosystem services equivalent to reference reefs, we synthesized data and calculated log response ratios for 245 restored-degraded reef pairs and 136 restored-reference reef pairs from 106 publications collected along 3500 km of U.S. Gulf of Mexico and Atlantic coastlines.
Data From: Population-specific responses in eastern oysters exposed to low salinity in the northern Gulf of Mexico
<p>Eastern oysters, <em>Crassostrea virginica</em>, are facing rapid environmental changes in the northern Gulf of Mexico and can respond to these changes via plasticity or evolution. Plastic responses can immediately buffer against environmental changes, although this buffering may impact the organism's ability to evolve in subsequent generations. While plasticity and evolution are not mutually exclusive, the relative contribution and interaction between them remain unclear. In this study, we investigate the roles of plastic and evolved responses to low salinity in <em>C. virginica</em> using a common garden experiment with four populations exposed to two salinities. We use three transcriptomic analyses (edgeR, PERMANOVA, and WGCNA) combined with physiology data to identify the effect of genotype (population), environment (salinity), and genotype-by-environment interaction on both whole organism and molecular phenotypes. We demonstrate that variation in gene expression is mainly driven by population, with relatively small changes in response to salinity. In contrast, the morphology and physiology data reveal that salinity has a larger influence on oyster performance than the population of origin. All analyses lacked signatures of genotype-by-environment interaction, and in contrast to previous studies, we find no evidence for population-specific responses to low salinity. However, individuals from the highest salinity estuary displayed highly divergent gene expression from other populations, which could potentially drive population-specific responses to other stressors. Our findings suggest that C. virginica largely rely on plasticity in physiology to buffer the effects of low salinity, but that these changes in physiology do not rely on large persistent changes in gene expression.</p>
Data From: Population-specific responses in eastern oysters exposed to low salinity in the northern Gulf of Mexico
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Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
<p><b><span>Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (</span><span>Crassostrea virginica</span><span>) exposed to experimental OA over 80 days. Oysters were reared under three experimental </span><span>p</span><span>CO</span><span><span>2</span></span><span> treatments ('control', 580 μatm; 'moderate OA', 1000 μatm; 'high OA', 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced an increase in the pH of the extrapallial fluid (pH</span><span><span>EPF</span></span><span>) relative to the external seawater that peaked at day 9, but then diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from days 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed under OA, the pH</span><span><span>EPF</span></span><span> was significantly correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression.</span><span> </span><span>Gene body methylation, however, was not significantly correlated with the eigengene expression of pH</span><span><span>EPF</span></span><span>-correlated gene clusters. These results suggest that OA induces a subtle response in a large number of genes in </span><span>C. virginica</span><span>, but also indicate that plasticity at the molecular level may be limited. Our study highlights the need to reassess our understanding of tissue-specific molecular responses in marine calcifiers</span><span>, </span><span>as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA. </span></b></p>
Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
<p>1. It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments.</p> <p>2. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters (<i>Crassostrea virginica</i>) from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity.</p> <p>3. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression.</p> <p>4. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments.</p> <p>5. An analysis of CpG observed/expected values (CpG O/E ) across the <i>C. virginica</i> genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation, and higher, and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression.</p> <p>6. Taken together, the differential methylation results suggest that only a small portion of the <i>C. virginica</i> genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.</p>
Morphometrics and nutrient concentration of eastern oysters (Crassostrea virginica) sampled from Chesapeake Bay, USA
<p><span><strong>Acknowledgements</strong></span> Ward Slacum and Olivia Caretti from the Oyster Recovery Partnership for providing the support and resources to compile the initial oyster BMP dataset and maintenance. </p> <p><strong><u>Background Information</u></strong></p> <p>The Chesapeake Bay Program (CBP) approved the use of eastern oyster (<em>Crassostrea virginica</em>) aquaculture as a nitrogen and phosphorus reduction best management practice in December 2016. The CBP decision was based on the recommendations of the Oyster Best Management Practice Expert Panel. The approved BMP report, “Panel Recommendations on the Oyster BMP Nutrient and Suspended Sediment Reduction Effectiveness Determination Decision Framework and Nitrogen and Phosphorus Assimilation in Oyster Tissue Reduction Effectiveness for Oyster Aquaculture Practices” is available here: <a href="https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster_BMP_1st_Report_Final_Approved_2016-12-19.pdf">https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster_BMP_1st_Report_Final_Approved_2016-12-19.pdf</a></p> <p>And a summary fact sheet about the report and the panel’s findings is available here: <a href="https://oysterrecovery.org/wp-content/uploads/June_2018-FINAL-bmp-fact-sheet-1.pdf">https://oysterrecovery.org/wp-content/uploads/June_2018-FINAL-bmp-fact-sheet-1.pdf</a></p> <p>The panel’s recommendations were based on an analysis of two datasets: 1) available literature for eastern oyster tissue nitrogen and phosphorus concentrations (%) across the Northeast region of the United States, and 2) available literature for the relationship between shell height (mm) vs. tissue dry weight (g) for eastern oysters sampled within Chesapeake Bay, USA. The nitrogen and phosphorus concentration datasets were relatively small, and the data were published in the report. The dataset describing the relationship between oyster shell height vs. tissue dry weight was much larger (n = 6,816). The report contains summary statistics and visual representations of the data, but the data themselves were not publicly released.</p> <p>A second report was released by the Oyster Best Management Practice Expert Panel in 2023, with additional analysis of an expanded dataset for the relationship between oyster shell height vs. tissue dry weight (n = 10,786) and a new dataset for the relationship between oyster shell height vs. shell dry weight to support the development of an oyster restoration BMP. The second BMP report, “Nitrogen and Phosphorus Reduction Associated with Harvest of Hatchery-Produced Oysters and Reef Restoration: Assimilation and Enhanced Denitrification” is available here:</p> <p><a href="https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster-BMP-Second-Report_Approved_with_Minutes.pdf">https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster-BMP-Second-Report_Approved_with_Minutes.pdf</a></p> <p>The second report contains summary statistics and visual representations of the data, but the data themselves were not publicly released.</p> <p><strong><em><u>Data Description</u></em></strong></p> <p>This repository contains 77% of the data (n = 8,395) used by the Chesapeake Bay Program’s Oyster Best Management Practice Expert Panel to develop its recommendations for both the 2016 first report and the 2023 second report. Some of the data in this repository were previously published in the peer-reviewed literature as summary statistics, but the raw data were not archived. The remaining data are either not currently available or are published in the gray literature. Two datasets that were used in the Expert Panel analysis are not included in this repository, as the data are unpublished with the data owners intending to publish these data in the future.</p> <p>The repository is organized with individual oyster samples as rows and a combination of numerical and categorical information as columns. Each row/sample in the repository contains data on oyster shell height (mm) and oyster dry weight (g), data source, and sample collection location information. Location information is presented across columns with different levels of spatial resolution. This repository also contains additional information provided by scientists when available, such as nitrogen, carbon, or phosphorus concentration, details about the oyster source and growth conditions, and sampling time (e.g., season/date/year).</p>
Morphometrics and nutrient concentration of farmed eastern oysters (Crassostrea virginica) from the US Northeast Region
<p><strong><u>Acknowledgements</u></strong></p> <p>This work was supported by the NOAA Fisheries Northeast Fisheries Science Center and the NOAA Fisheries Office of Aquaculture. Thanks to Marta Gomez-Chiarri, PG Harris, Mark Luckenbach, and Christine Thompson for sharing data, although these data were not included in the final repository.</p> <p><strong><u>Background Information</u></strong></p> <p>The removal of excess nitrogen from eutrophic environments is an ecosystem service provided by shellfish aquaculture that is well described in the literature (Lindahl et al., 2005; Rose et al., 2014; Petersen et al., 2014; Clements and Comeau, 2019). Nitrogen removal associated with shellfish farms can occur via three mechanisms: the assimilation of nitrogen into tissue and shell, which is removed from the waterbody when animals are harvested; the enhancement of sediment denitrification through biodeposit production on farms; and the long-term burial of biodeposits.</p> <p>A robust calculation of the nitrogen removed at shellfish harvest has been previously published using relatively simple metrics: the nitrogen concentration of tissue/shell, the number and mean size of animals harvested, and a conversion of animal size to tissue and shell dry weight (Reichert-Nguyen et al., 2016; Clements and Comeau, 2019). The quantity of nitrogen removed at shellfish harvest has been previously predicted with high confidence, which has led to the integration of oyster and clam aquaculture into nutrient management programs at the local and estuary scale in the United States (Town of Mashpee, 2015; Reichert-Nguyen et al., 2016; Reitsma et al., 2017).</p> <p>The data in this repository were compiled with the intention of expanding the geographic scope of calculation of nitrogen removal associated with harvested eastern oysters (<em>Crassostrea virginica</em>), and to evaluate variation in this ecosystem service across common cultivation practices and ploidy. Data were obtained from sampling locations across the US from the state of North Carolina north to the state of Maine. Data are included for both diploid and triploid oysters, and for three common styles of cultivation: oysters grown on bottom without the use of aquaculture gear, oysters grown in bottom cages, and oysters grown in floating gear at the sea surface. Data curation was undertaken to obtain a dataset that most closely reflects on-farm conditions as possible. The highest priority was to find data collected from working oyster farms, and a second priority was to identify data collected by scientists who employed common cultivation practices in their research studies. In one state within the region (Rhode Island) we were unable to locate data that fit the previous description, and instead have included data from wild oysters from waterbodies that have oyster farms.</p> <p>This data set was used to support the development of the Aquaculture Nutrient Removal Calculator (ANRC,<a href="https://connect.fisheries.noaa.gov/ANRC/">https://connect.fisheries.noaa.gov/ANRC/</a>), a tool designed for use by both shellfish farmers and managers within the aquaculture permit review process. The ANRC is a publicly available, simple online tool that was developed in direct response to feedback from aquaculture resource managers. The ANRC accurately predicts harvest-based nitrogen removal from an eastern oyster farm located within the geographic range of North Carolina to Maine, USA. We have taken an adaptive management approach to tool development, basing our tool on current best available scientific information, with the intention of maintaining and updating this tool when new information and data become available in the future.</p> <p><strong><u>Data Description</u></strong></p> <p>This repository contains information on morphometrics and nitrogen concentration of tissue and shell for eastern oysters sampled within the US geographic region spanning the states of North Carolina to Maine. Some of the data in this repository (6 of 10 sources) were previously published as summary statistics in the peer-reviewed literature, but the raw data included here were not archived. Three datasets were not previously published in raw or summary form. One dataset is publicly available in a technical report.</p> <p>The repository is organized with individual oysters as rows and numerical/categorical information associated with those oyster samples as columns. Each sample in the repository contains data on oyster shell height (mm), tissue dry weight (g), data source, ploidy, cultivation practice, and location of sample collection. The repository also contains additional information provided by data sources as available, such as shell dry weight, nitrogen, carbon, sampling date, oyster stock, and other morphometric measurements.</p> <p><strong><u>References</u></strong></p> <p>Clements, J.C., Comeau, L.A., 2019. Nitrogen removal potential of shellfish aquaculture harvests in eastern Canada: A comparison of culture methods. Aquaculture Reports 13, 100183.</p> <p>Lindahl, O., Hart, R., Hernroth, B., Kollberg, S., Loo, L.-O., Olrog, L., Rehnstam-Holm, A.-S., Svensson, J., Svensson, S., Syversen, U., 2005. Improving marine water quality by mussel farming - a profitable solution for Swedish society. Ambio 34, 129-136.</p> <p>Petersen, J.K., Hasler, B., Timmermann, K., Nielsen, P., Tørring, D.B., Larsen, M.M., Holmer, M., 2014. Mussels as a tool for mitigation of nutrients in the marine environment. Marine Pollution Bulletin 82, 137-143.</p> <p>Reichert-Nguyen, J., Cornwell, J., Rose, J., Kellogg, L., Luckenbach, M., Bricker, S., Paynter, K., Moore, C., Parker, M., Sanford, L., Wolinski, B., Lacatell, A., Fegley, L., Hudson, K., French, E., Slacum, W., 2016. Panel recommendations on the oyster BMP nutrient and suspended sediment reduction effectiveness determination decision framework and nitrogen and phosphorus assimilation in oyster tissue reduction effectiveness for oyster aquaculture practices, Report to the Chesapeake Bay Program. Available online at <a href="https://www.oysterrecovery.org/wp-content/uploads/2017/01/Oyster-BMP-1st-Report_Final_Approved_2016-12-19.pdf">https://www.oysterrecovery.org/wp-content/uploads/2017/01/Oyster-BMP-1st-Report_Final_Approved_2016-12-19.pdf.</a></p> <p>Reitsma, J., Murphy, D.C., Archer, A.F., York, R.H., 2017. Nitrogen extraction potential of wild and cultured bivalves harvested from nearshore waters of Cape Cod, USA. Marine Pollution Bulletin 116, 175-181.</p> <p>Rose, J.M., Bricker, S.B., Tedesco, M.A., Wikfors, G.H., 2014. A Role for Shellfish Aquaculture in Coastal Nitrogen Management. Environmental Science & Technology 48, 2519-2525.</p> <p>Rose J.M.,, Morse, R., and Schillaci, C. 2024. Development and application of an online tool to quantify nitrogen removal associated with harvest of cultivated eastern oysters. PLoS ONE 19(9): e0310062. https://doi.org/10.1371/journal.pone.0310062</p> <p>Town of Mashpee Sewer Commission, 2015. Comprehensive watershed nitrogen management plan, Town of Mashpee, Available online at http://www.mashpeewaters.com/documents.html.</p>
Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
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Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
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Data from: Lack of genotype-by-environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster, Crassostrea virginica
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Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number
<p>The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters <i>Crassostrea virginica</i>. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large-scale hatchery-based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long-term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine-scale genetic structure and local adaptation in broadcast-spawning marine species and provide novel information for the management of an important fisheries resource.</p>
Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)
Understanding the interaction between phenotypic plasticity and evolutionary processes is important for predicting a species' response to changing environment. Strong recurrent selection each generation may be an important process in highly fecund species with broad dispersal and extensive early mortality. We tested whether selection was associated with spatial divergence in gene expression plasticity for osmoregulation in the eastern oyster (Crassostrea virginica). We collected adult oysters from high and low salinity reefs within a single estuary and after 9 weeks of acclimation at 10 and 30 salinity, measured gene expression in 24 oysters using next-generation RNA sequencing technology. The oysters had significantly different expression (DE) in response to salinity treatments for 7936 (18.9%) transcripts overall, with planned contrasts showing 8× more DE in oysters from the high-salinity reef and 15× more DE between reefs when tested at 10 salinity. The reef-by-treatment interaction was also genomically pervasive (5858 DE transcripts, 13.9%). Inter-reef F ST for transcript SNPs averaged 0.0025 with the top 1% between 0.29 and 0.73. Transcripts containing "outlier" SNPs were significantly enriched for osmoregulatory genes and showed patterns of variation consistent with selection on the low-salinity reef. Both phenotypic plasticity and recurrent selection seem to be important factors determining the realized niche of oysters within estuaries.
Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica
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Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number
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Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)
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Data from: Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.
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