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387 results for “Oysters”
Data for: ToadFishFinder classifier model v4: A catalog of oyster toadfish (Opsanus tau) calls for machine learning
<p>This data repository contains labeled passive underwater acoustic data used to train and test the machine-learning model of Bohnenstiehl (in prep – 2023), <span>Automated cataloging of oyster toadfish (<em>Opsanus</em> <em>tau</em>) calls using template matching and machine learning</span>. The software accompanying this paper is known as ToadFishFinder, and the classifier model presented in the paper is v4. It consists of more than 10000 labeled toadfish and 10000 labeled other signals. Labeled spectrogram images are provided, along with pressure-corrected waveforms (micro-Pascals) sampled at 24 kHz. Each waveform sample is 1350 ms long. The center 850 ms of these waveform segments represent the portion of the signal used in training and testing the classifier model. Waveform data are provided in multiple formats: 1) MATLAB (.mat) files containing the 'boatwhistle' and 'other' waveforms stored in column format, and 2) individual .wav files, each containing a labeled waveform example. Codes are provided to demonstrate how these .wav files can be read into MATLAB and PYTHON. These labeled data can be used to re-train the ToadFishFinder model or develop alternative classifiers. </p>
Evaluation of different settlement substrates for field-based collection of Ostrea edulis. Spatial variation in oyster spat settlement along the Swedish west coast was also monitored.
<p>Aim: Evaluate different types of settlement substrates for field-based collection of <em>Ostrea edulis</em>. Document spatial variation in settlement of oyster spat on coupelle collectors along the Swedish west coast.</p> <p>Different types of substrates (shells of different species and materials with different structures) were placed in the sea and the survival and number of spat attached to the substrates were evaluated. Growth and species identification (<em>O. edulis</em> versus <em>M. gigas</em>) were documented. Data was collected from the Swedish west coast in 2020.</p>
Developing and testing protocols for fouling treatments on oysters
<p>Aim: Develop protocols for effective fouling treatment on oysters (Ostrea edulis and Magallana gigas) in the lab.</p> <p>Fouling treatments were evaluated using lab trials (in tanks) for evaluation of effects of heat treatment of fouling organisms on oysters. A range of different temperatures and exposure times was evaluated. The data consists of parameters associated with the treatments (temperature) and survival of oysters, survival of fouling organisms. Data originates from the Swedish west coast.</p>
Chromosome-level genome assembly and annotation of the emblematic silver-lipped pearl oyster, Pinctada maxima Jameson, 1901
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Data from: Shifting seagrass-oyster interactions alter species response to ocean warming and acidification
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Data for: ToadFishFinder classifier model v4: A catalog of oyster toadfish (Opsanus tau) calls for machine learning
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Data From: Population-specific responses in eastern oysters exposed to low salinity in the northern Gulf of Mexico
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Oyster patches within 16 different 0.25 km2 regions throughout the Virginia Coast Reserve, 2015
Oyster patches were digitized based on 2015 USGS LiDAR elevation, within 16 different 0.25 km2 regions throughout the VCR.
Size-dependent predation and intraspecific inhibition of an estuarine snail feeding on oysters
<p><span>Predator outbreaks have increased in the past two decades in many ecosystems and are predicted to become more common with climate change. During these outbreaks, predator densities increase rapidly, and can cause large reductions in prey populations or shifts in prey size structure. However, unexpected interactions may occur at high predator densities, necessitating a mechanistic understanding of how increased predator density affects predator-prey dynamics. In the northern Gulf of Mexico, outbreaks of southern oyster drill (<i>Stramonita haemastoma</i>, Linnaeus, 1767) occur during high salinity events, and can greatly reduce eastern oyster (<i>Crassostrea virginica</i>, Gmelin, 1791) populations. A large outbreak of drills occurred from 2013—2015 in Apalachicola Bay, FL which corresponded with an oyster fishery collapse in that bay. To improve our mechanistic understanding of predation during such a high-density outbreak, laboratory experiments based on field observations were used to quantify the prey size selection by drills and the drill functional response, as a function of drill abundance. Drills fed on medium-sized oysters (50-75 mm) more often than small and larger-sized oysters, and often formed aggregations during feeding events. However, despite this aggregative response, there was a negative relationship between per capita feeding rates and drill abundance. Indeed, the Crowley-Martin functional response model had the most parsimonious fit to the data, suggesting that predator-predator inhibition reduced attack rates and increased handling times. Due to an increase in regional drought conditions and water usage in the southeastern United States, drill outbreaks will likely increase in frequency and duration. A greater understanding of how predation rates change with predator densities during outbreaks will improve predictions of oyster mortality, and strengthen the scientific framework for oyster fishery decisions.</span></p>
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>
Destabilizing effects on a classic tri-trophic oyster-reef cascade
<p>How interactions among multiple predators affect the stability of trophic cascades is a topic of special ecological interest. To examine factors affecting the stability of the classic tri-trophic oyster reef cascade within a different context, configurations of three predators, including the Gulf toadfish, Gulf stone crab, and oystershell mud crab, were manipulated together with either oyster shell or limestone gravel substrate within a multiple predator effects (MPE) experiment. Additionally, a complimentary set of trait-mediated-indirect interaction (TMII) experiments examined the inhibition of oyster consumption relative to mud-crab size and top predator identity in the absence of other cues and factors. The classic tri-trophic cascade formed by the toadfish-mud crab-oyster configuration was potentially weakened by several interactions within the MPE experiment. Consumption of oysters and mud crabs by the intraguild stone crab was undeterred by the presence of toadfish. Although mud crab feeding was inhibited in the presence of both toadfish and stone crabs, estimated non-consumptive effects (NCEs) were weaker for stone crabs in the MPE experiment. Consequently, the total effect was destabilizing when all three predator species were together. Inhibition of mud crab feeding was inversely related to direct predation on mud crabs within the MPE experiment. Complimentary TMII experiments revealed greater inhibition of mud crab feeding in response to stone crabs under sparse conditions. TMII experiments also implied that inhibition of mud crab feeding could have largely accounted for NCEs relative to oysters within the MPE experiment, as opposed to interference by other mud crabs or top predators. An inverse relationship between mud crab size and NCE strength in the TMII experiment disclosed another potentially destabilizing influence on the tri-trophic-cascade. Finally, although habitat complexity generally dampened the consumption of oysters across MPE treatments, complex habitat promoted mud crab feeding in the presence of toadfish alone. This study underscores how ecological interactions can mediate trophic cascades and provides some additional insights into the trophic dynamics of oyster reefs for further testing under natural conditions.</p>
Datasets of recordings of electrical activity of substrates colonised by oyster fungi P. ostreatus and P. djamor.
<p>Datasets of recordings of electrical activity of substrates colonised by oyster fungi P. ostreatus and P. djamor.</p>
Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single-nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of <i>Ostrea lurida</i>.
Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)
Functional trait variation within and across populations can strongly influence population, community, and ecosystem processes, but the relative contributions of genetic vs. environmental factors to this variation are often not clear, potentially complicating conservation and restoration efforts. For example, local adaptation, a particular type of genetic by environmental (G*E) interaction in which the fitness of a population in its own habitat is greater than in other habitats, is often invoked in management practices, even in the absence of supporting evidence. Despite increasing attention to the potential for G*E interactions, few studies have tested multiple populations and environments simultaneously, limiting our understanding of the spatial consistency in patterns of adaptive genetic variation. In addition, few studies explicitly differentiate adaptation in response to predation from other biological and environmental factors. We conducted a reciprocal transplant experiment of first-generation eastern oyster (Crassostrea virginica) juveniles from six populations across three field sites spanning 1000 km in the southeastern Atlantic Bight in both the presence and absence of predation to test for G*E variation in this economically valuable and ecologically important species. We documented significant G*E variation in survival and growth, yet there was no evidence for local adaptation. Condition varied across oyster cohorts: Offspring of northern populations had better condition than offspring from the center of our region. Oyster populations in the southeastern Atlantic Bight differ in juvenile survival, growth, and condition, yet offspring from local broodstock do not have higher survival or growth than those from farther away. In the absence of population-specific performance information, oyster restoration and aquaculture may benefit from incorporating multiple populations into their practices.
Data from: Oyster aquaculture impacts Zostera marina epibiont community composition in Akkeshi-ko estuary, Japan
Coastal fisheries are in decline worldwide, and aquaculture has become an increasingly popular way to meet seafood demand. While finfish aquaculture can have substantial adverse effects on coastal ecosystems due mostly to necessary feed inputs, bivalves graze on natural phytoplankton and are often considered for their positive ecosystem services. We conducted two independent studies to investigate the effects of long-line Crassostrea gigas oyster aquaculture on Zostera marina seagrass beds and associated epibiont communities in Akkeshi-ko estuary, Japan. Results from both studies yielded no evidence of an effect of oyster aquaculture on the morphology, density, or biomass of Z. marina, but significant differences were apparent in the epibiont community. Reference seagrass beds located away from aquaculture had higher seagrass epiphyte loads and higher abundances of amphipods. Conversely, seagrass beds below aquaculture lines had higher sessile polychaete biomass and higher isopod abundances. Our results suggest that the presence of oyster aquaculture may have indirect effects on seagrass by changing epibiont community composition and relative abundances of species. One proposed mechanism is that cultured oysters feed on epiphytic diatoms and epiphyte propagules before they can settle on the seagrass, which reduces epiphyte loads and influences subsequent faunal settlement. If carefully implemented and monitored, long-line oyster aquaculture may be a sustainable option to consider as bivalve aquaculture expands to meet global seafood demand, but further work is needed to fully assess and generalize the community-level effects on seagrass epibionts.
Data from: Oyster reefs as carbon sources and sinks
Carbon burial is increasingly valued as a service provided by threatened vegetated coastal habitats. Similarly, shellfish reefs contain significant pools of carbon and are globally endangered, yet considerable uncertainty remains regarding shellfish reefs' role as sources (+) or sinks (−) of atmospheric CO2. While CO2 release is a by-product of carbonate shell production (then burial), shellfish also facilitate atmospheric-CO2 drawdown via filtration and rapid biodeposition of carbon-fixing primary producers. We provide a framework to account for the dual burial of inorganic and organic carbon, and demonstrate that decade-old experimental reefs on intertidal sandflats were net sources of CO2 (7.1 ± 1.2 MgC ha−1 yr−1 (µ ± s.e.)) resulting from predominantly carbonate deposition, whereas shallow subtidal reefs (−1.0 ± 0.4 MgC ha−1 yr−1) and saltmarsh-fringing reefs (−1.3 ± 0.4 MgC ha−1 yr−1) were dominated by organic-carbon-rich sediments and functioned as net carbon sinks (on par with vegetated coastal habitats). These landscape-level differences reflect gradients in shellfish growth, survivorship and shell bioerosion. Notably, down-core carbon concentrations in 100- to 4000-year-old reefs mirrored experimental-reef data, suggesting our results are relevant over centennial to millennial scales, although we note that these natural reefs appeared to function as slight carbon sources (0.5 ± 0.3 MgC ha−1 yr−1). Globally, the historical mining of the top metre of shellfish reefs may have reintroduced more than 400 000 000 Mg of organic carbon into estuaries. Importantly, reef formation and destruction do not have reciprocal, counterbalancing impacts on atmospheric CO2 since excavated organic material may be remineralized while shell may experience continued preservation through reburial. Thus, protection of existing reefs could be considered as one component of climate mitigation programmes focused on the coastal zone.
Old Oyster farm
Sad coast made from dead oyster shells :( GO VEGAN! Scanned by iPhone 8+ Processed by RealityScan https://www.capturingreality.com/ Source: Objaverse 1.0 / Sketchfab
Oyster IPM Data
<p>Data used in:</p> <p>Moore, J. L., Lipcius, R. N., Puckett, B. and Schreiber, S. J. (2016), The demographic consequences of growing older and bigger in oyster populations. Ecol Appl. Accepted Author Manuscript. doi:10.1002/eap.1374</p>
Oyster IPM w/Positive Feedbacks - Metadata
<p>Description of data and code used in: </p> <p>Moore, J.L., Puckett, B., and Schreiber, S.J. Restoration of Eastern oyster populations with positive density dependence. <em>Submitted to Ecological Applications December 2017.</em></p>
[Raw data collection] - Granular skeleton optimisation and influence of the cement paste content in bio-based oyster shell mortar with 100% aggregate replacement
<h1>Raw data collection</h1> <h2>Associated paper information</h2> <p>- Year: 2024 <br>- Journal: Sustainability <br>- DOI/link: https://doi.org/10.3390/su16062297 <br>- Title: Granular skeleton optimisation and influence of the cement paste content in bio-based oyster shell mortar with 100% aggregate replacement <br>- Authors: Ana Cláudia Pinto Dabés Guimarães (1,2), Olivier Nouailletas (3), Céline Perlot (2,3,4) and David Grégoire (1,3,4,*) <br>- Affiliation: <br> (1) Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, LFCR, Anglet, France, <br> (2) Universite de Pau et des Pays de l’Adour, E2S UPPA, SIAME, Anglet, France, <br> (3) Universite de Pau et des Pays de l’Adour, E2S UPPA, ISA BTP, Anglet, France, <br> (4) Institut Universitaire de France, Paris, France, <br> * Correspondence: david.gregoire@univ-pau.fr</p>
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