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387 results for “Oysters”
High and Low Tides of Hog Island Bay, Redbank, VA, and Oyster, VA for the Virginia Coast Reserve 2007-2025
This dataset is a summary version of the 12-minute tide data. It records the date, time and level of tides at high and low tide (as indicated by the data). Water temperatures are also recorded.
Oyster and associated fauna counts and lengths from restored and reference reefs in the coastal bays of Virginia, 2005-2019
This dataset has been superceded by Lusk, B., R. Smith, and M.C.N. Castorani. 2024. Oyster fauna lengths, counts, and biomass from restored and reference reefs in Virginia coastal bays, 2005-2023 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/d68de69f29cee5f737313a07f813f245 (Accessed 2024-02-22). which includes additional years and parameters. Oyster and associated reef fauna counts and lengths were sampled at 16 natural reference reefs and 61 restored shell plant reefs located at 18 sites in the Virginia Coast Reserve. Overfishing and disease decimated oyster reefs in the Virginia Coast Reserve in the 1900s. Reference reefs were defined as remnant reefs that naturally recovered in the early 2000s to develop the pronounced vertical structure and multiple oyster size classes that represent the desired endpoint of restoration efforts. Nearly every year since 2003, The Nature Conservancy and Virginia Marine Resource Commission have constructed oyster reefs in intertidal areas in the VCR. To construct the restored reefs, practitioners applied dredged, fossilized oyster shell to intertidal locations chosen for their bottom stability and accessibility (locations lacked oysters prior to construction). Whelk shell supplemented the oyster shell at 9 of the restored reefs.
Tide Data for Hog Island (1991-), Redbank (1992-), Oyster (2007-)
Tide data from VCR/LTER tide stations. It is available as a single large comma-separated-value file (size >50MB) or as individual years. Zip files contain annually-segmented data in two forms. The file tideYY.dat contains the data for year YY in a column format. The file tideYY.csv contains the same data in a comma-delimited format. For several sites and time periods, water temperatures are also recorded. All dates and times are in Eastern Standard Time.
Biological and Physical Monitoring Data of Restored Oyster Reef in Savannah River, Savannah, GA from May 2023 - February 2025
For the purposes of this study, we constructed two oyster reefs in Savannah, GA, USA using standard spat-on-shell restoration methodology. Reefs were constructed 1-2 meters from the marsh edge to reduce wave energy as it approached the shoreline, similar to a breakwater. We then conducted monitoring on the biological function of the reef, including live juvenile oyster coverage, size, and abundance for approximately 18 months. We also quantified the energy flux of waves offshore and onshore of the reef using water pressure measurements to determine the capability of these reefs at reducing wave energy. The oyster reefs in this study decreased wave energy by up to 40% compared to paired, non-reef control sites. Constructed oyster reefs also experienced healthy oyster population growth throughout the study, with live juvenile coverage of 17-40% almost 18 months post-deployment. This study took place in an erosion-prone area due to recreational and commercial boating traffic at the nearby Port of Savannah. Our results indicate that using restored oyster reefs as living shorelines is a technique with high potential for preventing shoreline loss in coastal areas vulnerable to anthropogenically-caused erosion. Restored Reef Site 1: 32.067957°, -80.985005° Control Site 1: 32.0675194°, -80.986369° Restored Reef Site 2: 32.062663°, -80.965147° Control Site 2: 32.063261°, -80.965889°
Survival Data of Strengthened and Non-Strengthened Oysters on Two Restored Reefs in Georgia, USA
The eastern oyster, Crassostrea virginica, is known to respond to chemical cues from their predators by strengthening their shell in defense. The chemical cues homarine and trigonelline, found in the urine of blue crabs, Callinectes sapidus, are two metabolic waste products known to cause this inducible defense in juvenile oysters. We tested whether this shell strengthening defense is beneficial for juvenile oysters in a restored reef setting by inducing oyster spat with chemical cues, placing them onto a restored reef and measuring their survival for 50-100 days. The first reef location is a previously restored reef (approximately 10 years old) with limited physical exposure to wind waves and boat wake. Juvenile oysters were placed at this site in September of 2021 and survival was measured for 49 days. The second reef location is a newly restored oyster reef (less than 1 year old) that acts as a living shoreline, with significant exposure to boat wake and wind waves. Juvenile oysters were protected from predation using mesh wrapping with an opening of 1 square cm and placed at the reef site in April 2023, where survival was monitored for 103 days. Site locations: Reef 1 (dock site) - 31.988948°, -81.024001° Reef 2 (living shoreline reef) - 32.067957°,-80.985005°
Biomass and abiotic variable data in the study of the ecosystem engeneering effect of oysters on Suaeda linearis distribution in Georgia salt marshes (2008-2009)
Oysters are ecosystem engineers in marine ecosystems, but the functions of oyster shell deposits in intertidal salt marshes are not well understood. The annual plant Suaeda linearis is associated with oyster shell deposits in Georgia salt marshes. We hypothesized that oyster shell deposits promoted the distribution of Suaeda linearis by engineering soil conditions unfavorable to dominant salt marsh plants of the region (the shrub Borrichia frutescens, the rush Juncus roemerianus and the grass Spartina alterniflora). We tested this hypothesis using common garden pot experiments and field transplant experiments. Suaeda linearis thrived in Borrichia frutescens stands in the absence of neighbors, but was suppressed by Borrichia frutescens in the with-neighbor treatment, suggesting that Suaeda linearis was excluded from Borrichia frutescens stands by interspecific competition. Suaeda linearis plants all died in Juncus roemerianus and Spartina alterniflora stands, indicating that Suaeda linearis is excluded from these habitats by physical stress (likely water-logging). In contrast, Borrichia frutescens, Juncus roemerianus and Spartina alterniflora all performed poorly in Suaeda linearis stands regardless of neighbor treatments, probably due to physical stresses such as low soil water content and low organic matter content. Thus, oyster shell deposits play an important ecosystem engineering role in influencing salt marsh plant communities by providing a unique niche for Suaeda linearis, which otherwise would be rare or absent in salt marshes in the southeastern US. Since the success of Suaeda linearis is linked to the success of oysters, efforts to protect and restore oyster reefs may also benefit salt marsh plant communities.
Oyster Paleobiology along the South Atlantic Coast of the United States
This dataset includes morphometric data collected from 37,805 oyster shells (Crassostrea virginica) from 15 Late Archaic (ca. 4500-3500 cal. BP) through Mississippian (ca. 1150 – 370 cal. BP) period archaeological sites situated along the South Atlantic Coast of the United States. Variations in oyster size is an important proxy for paleoenvironment and human population pressures. These data are part of a larger project examining oyster ecosystem stability and Native American oyster harvesting practices over the last 5,000 years. Oyster measurements were collected by many undergraduate and graduate students from multiple universities. Carey Garland added to and cleaned the data sheet between August 2018 and May 2019. The dataset was structured to include the Island, site name, time period, and provenience (e.g., unit, level, etc.) associated with each oyster measured. The original oyster database contains sensitive information, such as the specific location of archaeological sites. If a professional archaeologist needs site location information, they can contact the Georgia Archaeological Site File.
Atmospheric pressure on Hog Island, Phillips Creek Marsh and Oyster, VA 2012-2025
Barometric pressure is measured hourly at meteorological stations on the Atlantic Coast of the Delmarva Peninsula. Data is available as a long table that gives the average, minimum and maximum air pressure for each station at each time, or as a table that gives the average values for each of the stations, along with the median value across stations on each line.
Meta-analysis reveals controls on oyster predation 1977-2021
This dataset was created for investigating the patterns and drivers of variation in predation strength on oysters. Predation on oysters has been the subject of intense study because oysters are vital to creating coastal habitat, sustaining biodiversity, and enhancing or stabilizing important ecosystem functions. Understanding how predators affect oyster populations is important given the global decline in oysters and the substantial efforts focused on re-establishment and conservation. Despite widespread losses of oyster reefs, there have been no standardized and integrated quantitative assessments of the influence of predators on oysters. Therefore, this dataset was created by combining the results of 49 peer-reviewed articles reporting 384 experiments on oyster predation. These field and laboratory experiments tested whether the presence of predators affects oyster mortality or recruitment. The combined data was used in a meta-analysis, the results of which are published in the paper titled Meta-analysis reveals controls on oyster predation (Tedford and Castorani 2022), which represents the first quantitative synthesis to show that across a range of environments, predators have strong impacts on oysters.
Data from Bieri Thesis: Evaluating Coastal Protection Benefits of Restored Oyster Reef Designs - 2022
This dataset consists of spreadsheets used in the creation of: "Elizabeth Bieri, Evaluating Coastal Protection Benefits of Restored Oyster Reef Designs. MS Thesis, University of Virginia, Charlottesville, VA. Advisors: Matthew Reidenbach & Patricia Wiberg, 2022" (https://doi.org/10.18130/2b04-wz72). Documentation on methods and types of data are given in the thesis and are not repeated here. There are two .zip files. One contains the original Excel workbooks. The other contains the data from individual sheets within the workbooks as comma-separated-value (.csv) text files. The file listing for the CSV files are: Archive: Bieri_Comma_separated_Value_Files.zip Length Date Time Name --------- ---------- ----- ---- 0 2025-12-15 12:47 Bieri_Comma_separated_Value_Files/ 1787 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/elevation_crests.csv 239 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/elevation_S4.csv 273 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/elevation_S7.csv 652 2025-12-15 12:45 Bieri_Comma_separated_Value_Files/erosionpins_exposed.csv 476 2025-12-15 12:45 Bieri_Comma_separated_Value_Files/erosionpins_exposed_no_reef.csv 102 2025-12-15 12:46 Bieri_Comma_separated_Value_Files/erosionpins_S4.csv 97 2025-12-15 12:46 Bieri_Comma_separated_Value_Files/erosionpins_S7.csv 297 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/grainsize_july.csv 290 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/grainsize_oct.csv 399 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/infauna_om_All.csv 509 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/infauna_om_July2021.csv 507 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/infauna_om_Oct2021.csv 1242 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/infauna_om_Sed_OM.csv 516 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/infauna_om_Sept2020.csv 913981 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/jul2021waveS4.csv 715881 2025-12-15 12:41 Bieri_Comma_separated_Value_Files/jul2021waveS7.csv 5251
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.
Oyster fauna lengths, counts, and biomass from restored and reference reefs in Virginia coastal bays, 2005-2023
Oyster reef fauna counts and lengths were sampled at natural "reference" reefs and restored shell plant reefs located in the Virginia Coast Reserve. Overfishing and disease decimated oyster reefs in the Virginia Coast Reserve in the 1900s. Reference reefs were defined as remnant reefs that naturally recovered in the early 2000s to develop the pronounced vertical structure and multiple oyster size classes that represent the desired endpoint of restoration efforts. Nearly every year since 2003, The Nature Conservancy and Virginia Marine Resource Commission have constructed oyster reefs in intertidal areas in the VCR. To construct the restored reefs, practitioners launched dredged, fossilized oyster shell from barges to intertidal locations chosen for their bottom stability and accessibility (locations lacked oysters prior to construction). Whelk shell supplemented the oyster shell at some of the restored reefs. TNC practitioners monitor select restored and reference reefs annually for adult and spat live oysters, adult and spat box oysters, mud crabs, mud snails, oyster drills, live clams, and mussels.
Audio and Water Movement Data for Oyster Reef and Mudflat Sites on the Coast of Virginia, 2018
Paired marine audio soundscape recordings with concurrent acoustic Doppler velocimeter (ADV) turbulence measurements at three intertidal sites: a natural oyster reef, a restored oyster reef, and a bare mudflat. The objective was to establish the link between oyster reef soundscapes and hydrodynamics, specifically the role that turbulence plays in generating near field pressure waves that may be used as physical cues by oyster larvae when initiating settlement behaviors. Data were collected at three different locations, with water turbulance measurements at rates up to 25Hz concurrent with audio recording.
Oyster recruitment to standardized ceramic tiles on the Virginia Coast in 2018, 2019, and 2021
This dataset contains measurements of Eastern oyster (Crassostrea virginica) recruitment to standardized ceramic tiles deployed across intertidal oyster reef sites in the Virginia Coast Reserve. Recruitment is defined as the number of macroscopic oyster recruits (less than or equal to 25 mm shell height) per square centimeter of tile surface, capturing settlement and early post-settlement survival. Data were collected in 2018, 2019, and 2021 across 9-16 reef sites per year, including both natural and restored reefs. The dataset supports research on spatial and environmental drivers of oyster recruitment and has been validated against natural reef substrate data for comparability.
Data From: The Oyster River Protocol: A multi assembler and kmer approach for de novo transcriptome assembly.
<p>Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a <em>de novo</em> transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at <a href="https://github.com/macmanes-lab/Oyster_River_Protocol">https://github.com/macmanes-lab/Oyster_River_Protocol</a>. Instructions for software installation and use, and other details are available at <a href="http://oyster-river-protocol.rtfd.org/">http://oyster-river-protocol.rtfd.org/</a>.</p>
Oyster Microcystis aeruginosa feeding experiments, Lafayette-Louisiana, 2021-2022
To determine how the presence of the potentially harmful cyanobacteria M. aeruginosa affects oyster feeding, we quantified clearance rates, pseudofeces production, and pseudofeces composition across two feeding experiments conducted with a non-toxic strain. The first experiment consisted of bialgal feeding experiments where single oysters were fed treatments consisting of 1) only M. aeruginosa, 2) only the diatom Thalassiosira pseudonana, or 3) a 50/50 mix of the two species. To quantify effects of M. aeruginosa on oyster feeding under more environmentally relevant conditions — which includes numerous phytoplankton prey options and the presence of inorganic particles — a second feeding experiment was conducted using a natural phytoplankton community collected from a local estuary and oyster habitat. This natural community was then used to create two treatments, 1) an amended treatment where non-toxic M. aeruginosa was added, and 2) a natural treatment where only M. aeruginosa growth medium without cells was added.
Data for Quantifying Ecosystem Services Under Various Oyster Reef Designs
This data provides the basis for comparison of the services provided by reef designs varying in elevation and width located adjacent to an intertidal marsh within a coastal bay of Virginia, USA. We quantified wave attenuation to determine potential coastal protection of the adjacent marsh, and changes to sediment composition and infaunal communities before and after reef construction for three years. After construction we also quantified oyster size and population density to compare high and low elevation reef designs. Data consists of 4 tables: 1) Depths and wave heights, adjacent to the bay and marsh sides of the reef 2) Abundance of organisms 3) Biomass of organisms 4) Sediment organic matter There is also a .zip file containing the original Excel files from which the consolidated tables were extracted.
Microbiological data from studies to optimise depuration of viruses from Pacific oysters (Crassotrea gigas)
<p>Viral contamination of bivalve molluscan shellfish is a recognised cause of foodborne gastroenteritis. Unlike bacterial contaminants, viruses such as norovirus are not easily removed once shellfish become contaminated. Therefore the normal practice of depurating following harvest may not effectively reduce the risk of become ill following consumption of shellfish.</p> <p>As part of the SeafoodTomorrow consortium project (Horizon 2020), studies were undertaken to determine the optimal conditions under which Pacific oysters (Crassostrea gigas) are depurated (purified) following harvest.</p> <p>This dataset includes levels of norovirus, F specific coliphage genogroup II and E. coli found in oysters following several experiments in which depuration conditions were varied.</p>
Data and code to accompany oyster pound biofouling paper
<p>The fouling_for_zenodo folder contains the data and code needed to reproduce the analyses and figures in Krasnow et al. (2025). The other folders contain images of the experimental oysters taken during the measurement process that may be useful in the future.</p> <p>Krasnow, R., Kiffney, T., Coleman, S., Cuddy, R., & Brady, D. (2025). Interacting effects of environment and cultivation method on biofouling of farmed oysters (<em>Crassostrea virginica</em>). <em>Journal of the World Aquaculture Society</em>, <em>56</em>(3), e70012. <a href="https://ruby.science/pubs.html#0">https://doi.org/10.1111/jwas.70012</a></p>
A software for automatic identification of oyster species
<p>The files includes all data and final analysis of the work done in CS8 - oysters, task 8.2, CSTP8.2.2_A new software for automatic identification of oyster species. This includes the data management descriptor document (DataSheet_oyster_image_classification.docx), images used (oyster_classification_images.zip), the code developed (oyster_classification_code_package.zip) and different models evaluated (oyster_classification_models.zip), the genetics data produced (oyster_classification_biometrics and PCR.xlsx) and the project report (C639_ostronklassificering.pdf). The content of the files is described briefely below. The data is used in deliverables D1.2, D1.4, D1.5 and D1.6 in the AquaVitae project.</p> <p>oyster_classification_images.zip</p> <p>The data set contains the images used for training the classification models that are capable of classifying images of oysters as either Ostrea edulis or Magallana gigas. The images are sorted in folders named “train” (training data) and “validation” (validation data) with both folders containing sub-folders called “mg” (images of Magallana gigas) and “oe” (images of Ostrea edulis).</p> <p>oyster_classification_code_package.zip</p> <p>The data set contains the code for training a neural network for classifying oyster species based on images. The code also includes localization of oyster within an image and inference of the classification along with the trained models.</p> <p>oyster_classification_models.zip</p> <p>The data set contains the trained classification models that are capable of classifying images of oysters as either Ostrea edulis or Magallana gigas.</p> <p>oyster_classification_biometrics and PCR.xlsx</p> <p>The data set contains biometric information for a subset of 240 Ostrea edulis, 240 Magallana gigas and 204 oysters of unsure species denotation sampled as a start pool for the image analysis project and for genetic evaluation of species belonging.</p>
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