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738 results for “estuaries”
Github Repository for: European green crab predation in a Washington State estuary revealed with DNA metabarcoding
<p><strong>Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (2024).<em> </em>Invasive European green crab (<em>Carcinus maenas</em>) predation in a Washington State estuary revealed with DNA metabarcoding. DOI:10.1371/journal.pone.0302518<em><br></em></strong></p> <p>Github release v1.1 of the repository for Fisher et al. 2024, "European green crab predation in a Washington State estuary revealed with DNA metabarcoding." For the most updated repository, see: <a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc">github.com/mfisher5/Green-crab-dDNA</a></p> <p>Contains the code and minimum dataset necessary to replicate study findings.</p> <p> </p> <p>---</p> <p>Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (<em>Carcinus maenas</em>), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (<em>Hemigrapsus oregonensis</em>) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (<em>Crangon franciscorum</em>) and the Pacific staghorn sculpin (<em>Leptocottus armatus</em>) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.</p>
Dataset: Osmoregulation and hypoxia tolerance in the cenote isopod Creaseriella anops: Insights into its distribution in Karst Subterranean Estuaries
<p>This data set contains the information supporting the research article "Osmoregulation and hypoxia tolerance in the cenote isopod Creaseriella anops: Insights into its distribution in Karst Subterranean Estuaries" </p> <p>It contains Respirometry, indicators of cellular damage and Antioxidant system, critical temperatures, and Temperature induced metabolic rates of the isopod Creaseriella anops, and endemic species of the Karst Subterranean Estuaries from the Yucatan Peninsula Mexico.</p>
Fig. 5 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 5. Weight-length relationship (a) and the regular (b) and polyphasic (c) distribution of the proportional residuals in Anableps anableps males collected at the mouth of the Maracanã River, Pará State.
Fig. 9 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 9. Number of eggs/embryos (a) and ovarian weight (b) relative to body size (standard length) recorded in Anableps anableps females from the mouth of the Maracanã River, Pará.
Fig. 11 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 11. Proportion of sexually mature Anableps anableps females by body size (standard length) collected in the mouth of the Maracanã River, Pará State.
Fig. 3 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 3. Between-sexes variation in (a) standard length and (b) weight in Anableps anableps from the Maracanã River, Pará State.
Fig. 7 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 7. Proportion of Anableps anableps females by stage of gonadal maturity in the mouth of the Maracanã River, Pará Sttate.
Fig. 4 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 4. Weight-length relationship (a) and the distribution of the proportional residuals (b) in Anableps anableps females collected at the mouth of the Maracanã River, Pará State.
Fig. 2 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 2. Monthly variation in the sex ratio (females to males) of Anableps anableps in the mouth of the Maracanã River, Pará State.
Fig. 1 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 1. Study area showing the Maracanã River and the collecting locality (white circle) in the Brazilian state of Pará.
Fig. 8 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 8. Monthly variation in the gonadosomatic index (GSI) in Anableps anableps females collected at the mouth of the Maracanã River, Pará State.
Fig. 10 in Reproductive characteristics and the weight-length relationship in Anableps anableps (Linnaeus, 1758) (Cyprinodontiformes: Anablepidae) from the Amazon Estuary
Fig. 10. Embryo length (a) and weight (b) in relation to the number of stage V embryos in Anableps anableps from the Maracanã River, Pará State.
Fig. 2 in Distribution Of Trematodes Cryptokotyle (Trematoda, Heterophyidae), In Fish Of The Family Gobiidae In The Estuary Waters And The Black Sea In Southern Ukraine
Fig. 2. Metacercariae of trematodes of Heterophyidae familyon the body surface and fins of N. fluviatialis.
Fig. 3 in Distribution Of Trematodes Cryptokotyle (Trematoda, Heterophyidae), In Fish Of The Family Gobiidae In The Estuary Waters And The Black Sea In Southern Ukraine
Fig. 3. Part of small intestines of duckling at autopsy. Visible trematodes C. jejunain mucus and on mucosal surfaces.
Fig. 5 in Infection Of Predatory Fish With Larvae Of Eustrongylides Excisus (Nematoda, Dioctophymatidae) In The Delta Of The Dnipro River And The Dnipro-Buh Estuary In Southern Ukraine
Fig. 5. Anterior end of the body of E. еxcisus larva from pike. Arrows show two circles of papillae. x400 magniFIcatoin.
Methane fluxes from four elevation zones in a St. Lawrence Estuary salt marsh
<p>Dataset used in <a href="https://iopscience.iop.org/article/10.1088/2752-664X/ac706a/meta">Spartina alterniflora has the highest methane emissions in a St. Lawrence estuary salt marsh - IOPscience</a>.</p> <p>The dataset contains methane fluxes calculated from gas measurements taken over a 40 or 60 minute period using a dark static chamber method. Methane fluxes were measured at six locations in four elevation zones of a northern salt marsh on the St. Lawrence River estuary at La Pocatière, Quebec (47°22'24.7"N 70°03'26.3"W). Additional environmental data was collected including carbon dioxide fluxes, extractable soil nitrate, extractable soil ammonium, extractable soil dissolved organic carbon, extractable soil total dissolved nitrogen, salinity, temperature, water table depth, soil total organic carbon, soil total nitrogen, soil organic carbon to nitrogen ratio and bulk density. Soil cores were collected from 0-15 cm and used for extractable nutrient analysis, bulk density and soil organic carbon and nitrogen analysis. The work was carried out with funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement 838296, a NSERC Discovery Grant and a Natural Environment Research Council grant number (NE/T012323/1). This dataset is used in a publication entitled <em>Spartina alterniflora</em> has the highest methane emissions in a St. Lawrence Estuary salt marsh in Environmental Research: Ecology (https://doi.org/10.1088/2752- 664X/ac706a), which also contains more details on fieldsite and methodology.</p> <p>Gas samples were collected from dark, static chambers (18L, 26 cm diameter), which were placed onto pre-inserted collars in the vegetated zones (inserted to 2.5 cm, 3 days prior to sampling) or placed directly onto the mudflat. The chambers were insulated and fitted with fans and venting tubes. Gas samples were collected on the 23rd August 2020 from all sites, soil cores were collected between the 24-25th August 2020 and the 19-20th September 2020. Soil samples were collected at 0-15 cm using a 2.5 cm diameter dutch gouge corer.</p> <p>Soil temperature was measured at 10 cm depth using a soil thermometer, (°C, DeltaTrak 11050, Pleasanton, USA), salinity was measured in the laboratory using a portable ATC refractometer. Water table depth was measured using a PVC piezometer, a plastic pipe with tubing was inserted into the piezometer and blown into to determine water table depth through bubbling sound (cm). Soil cores were dried at 60 °C to constant weight and the dry weight over core volume used to calculate bulk density (g cm-3), soil was finely ground and analysed for total organic carbon and total nitrogen (%) using an Elemental Analyser (ThermoFinnigan Flash EA 1112 CN analyser, Carlo Erba, Milan, Italy) with an accuracy of ±5 % for N and ±1 % for C, and a limit of 171 detection of 0.05 % for both N and C. Extractable nitrate+nitrite (assumed to be nitrate) were analysed in soil extractant (2M KCl, 5:1 of extractant to soil) using a microplate reader and methods in Sims et al., 1995 (<a href="https://doi.org/10.1080/00103629509369298">https://doi.org/10.1080/00103629509369298</a>) with a limit of detection of 0.1 ppm and accuracy of ±5%. Extractable dissolved organic carbon and total dissolved nitrogen were analysed in soil extractant (ultrapure water 18.2 MΩ, 5:1 of extractant to soil) on a TOC/TDN analyser (TOC VCSn + TMN-1, Shimadzu, Kyoto, Japan), with a 50 mg C l -1 standard resulting in an accuracy and precision of 3.0 and ±4.4 mg l-1, respectively. CH4 and CO2 concentrations were measured in the gas samples using a gas chromatograph (GC-14, Shimadzu, Kyoto, Japan) fitted with a flame ionisation detector, CO2 was methanised to CH4 before analysis. Standards of CH4 (5.1 ppm) and CO2 (5000 ppm) resulted in an accuracy and precision of 6.6±1.5 and 0.4 ppm, and 5324±324 and 78 ppm, respectively, for CH4 and CO2. Changes in gas concentration over time were converted to fluxes using a linear regression of the linear portion fo the flux and if fluxes were below the minimum detectable concentration difference (see <a href="https://doi.org/10.1002/2017JG003783">https://doi.org/10.1002/2017JG003783</a>), they were set to zero. Results from the experiments were entered into an Excel spreadsheet for ingestion into the Zenodo data repository.</p>
Microbial relationships in the Skidaway River Estuary (GA, USA)
<p>This release includes all files needed to reproduce analysis of 16S and 18S amplicon datasets for the following manuscript: Anderson, S.R., M. Chisholm, and E.L. Harvey. Estuarine microbial networks and relationships vary between environmentally distinct communities. Files are also available on GitHub (<a href="https://github.com/sra34/SkIO-network">https://github.com/sra34/SkIO-network</a>). </p> <p>Included are QIIME 2 (.qza) files representing ASV count tables, taxonomy tables, representative sequences, and rooted tree files for each marker gene region. Associated metadata files are also included (e.g., Sampleinfo_16S.txt), as is the main network file (created in <a href="https://cytoscape.org/">Cytoscape</a>).</p> <p>Taxonomy was assigned to sequences using QIIME 2-formatted reference databases for 16S (SILVA; v.138.1) and 18S (PR2; v.4.12). Reference database files (.qza) are provided: </p> <ul> <li>silva-138-99-tax.qza </li> <li>silva-138-99-seqs.qza </li> <li>pr2_4.12.0_18S_tax.qza </li> <li>pr2_4.12.0_18S_seqs.qza </li> </ul> <p> Raw FASTQ sequence data are available in NCBI SRA under BioProject ID's PRJNA575563 (18S) and PRJNA680039 (16S).</p>
Model outputs of Wei et al. (2022): "Salt intrusion as a function of estuary length in periodically weakly stratified estuaries", published in Geophysical research Letters.
<p>The .mat file includes all model data used in the study "Salt intrusion as a function of estuary length in periodically weakly stratified estuaries", published in Geophyscial Research Letters, 2022. The .txt file contains description of all physical variables contained in the .mat file.</p>
Stable Water Isotopes and Nutrients in the Changjiang (Yangtze River) Estuary and adjacent East China Sea shelf in Winter
<p>The dataset presented here includes the temperature, salinity, stable water isotopes, and nutrients of seawater from the Changjiang Estuary and adjacent East China Sea shelf in March 2013. </p>
Count data, spatial data, environmental data - Dee Estuary Waders 1970-2020
<p>Combined raw ecological field data, WeBS data, and environmental data used to investigate the spatio-temporal drivers of wader community on the Dee estuary (UK).</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.