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2,367 results for “aquatic”
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment quantified in a montane stream in Puerto Rico. (Shrimp/Algae/Can J. Fish Aquat. Sci. (1994))
Effects of biotic (shrimp) and abiotic (discharge) factors on the depositional environment were quantified in a montane stream in Puerto Rico. Electricity was used experimentally to exclude large (approximately >1cm in length) biota without artificially increasing sedimentation as in cage enclosure/exclosure experiments in stream systems. Shrimp (>1cm in length) were excluded from substrata by semicircular fence hooked up to battery-powered fence chargers which emitted continuous pulses of electricity. Unelectrified control substrata had natural high densities of atyid shrimp. Significantly greater masses of total sediment, fine and large organic particles, and algal biovolume occurred in shrimp exclusion treatments relative to controls. Shrimp exclusion treatments experienced slow and steady accumulation of sediments under base flow conditions and a large stepwise increase in sediment following a storm. No measurable sediment accrued in the presence of natural densities of shrimp under base flow conditions. Shrimp rapidly removed sediments that accrued during the storm (440-620 g*m2 dry mass-1), decreasing sediment mass in control treatments to near prestorm levels (5-13 g*m2 dry mass-1) within 30 h. Atyid shrimp can significantly affect the accumulation of organic and inorganic materials on rock substrata in stream pools between high-discharge events. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Aquatic macrophyte, snail, and crayfish abundance and richness data for ten lakes in Vilas County, WI, USA, 1987-2020
Data accompanying the paper Szydlowski et al. "Macrophyte and snail community responses to 30 years of population declines of invasive rusty crayfish (Faxonius rusticus)." Macrophytes and snails were sampled in ten lakes in Vilas County, Wisconsin, USA during summer sampling events in 1987, 2002, 2011, and 2020. Lakes had varying levels of invasion by F. rusticus, which affected measures of macrophytes and snails. Macrophytes were sampled using a point-intercept transect method and snails were sampled using different sampler types which were dependent on substrate. Macrophytes were sampled at 6-14 sites per lake and snails were sampled at 16-31 sites per lake. Crayfish were regularly sampled at either 24 or 36 sites per lake between 1987 and 2020. Overall, this dataset provides abundance and richness data for over 25 species of snails and over 40 species of macrophytes in 10 north temperate lakes.
Measurements of aquatic production and respiration in tidal creeks draining high and low elevation marshes.
Production and respiration measurements of aquatic systems can help to inform calculations of whole system metabolism. These measurements are focused on creeks draining high and low elevation marsh systems to develop a better understanding of connectivity between aquatic production and consumption and coastal salt marshes. Production and respiration were determined by measuring oxygen changes in creek water incubated in light and dark bottles.
Supplementary data: The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.
<p>Supporting information for the article "<strong>The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.</strong>"</p> <p>This provides all the R script and .csv files for each dataset. </p>
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
<p>This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - <em>Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers</em>, <a href="https://www.alpine-space.eu/projects/eco-alpswater/en/home">https://www.alpine-space.eu/projects/eco-alpswater/en/home</a></p> <p>Individual archives include 16S rRNA (cyanobacteria) and 18S rRNA (microalgae) FASTA sequences and associated blastn results obtained from the high throughput sequencing of plankton and biofilm bulk/eDNA samples collected in 2019 in 37 lakes and 22 rivers across the Alpine region. These are supporting files for the paper by Salmaso et al., 2022. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. Science of the Total Environment, in press.</p>
Data on submerged aquatic vegetation and its water environment in Lake Saint-Pierre, Saint Lawrence River, from 2012 to 2016
<p>This dataset is the result of a large collaborative work lead by the GRIL from 2012 to 2015 on a submerged aquatic vegetation meadow located downstream of two agricultural tributaries (Saint-François and Yamaska rivers) in Lake Saint-Pierre, a fluvial lake of the Saint Lawrence River. The data describe plants (as rake biomass and echosounding) and their environment, including water chemistry, current velocity as well as light, temperature and instantaneous meteo. Only echosounding data are available in 2016 and sediments were collected in 2015. Data are organized as a relational database and the GRIL_LSP_database.png provides keys and links between tables as well as data format. Data are in the tables mesure_integree, mesure_spatiale, mesure_verticale, plante_biomass_taxon, plante_recolte, plante_in_situ. The other tables are metadata about spatiotemporal locations and reported measures. Additional data (e.g. zooplankton, sediments) should eventually be made available and associated to this overall GRIL dataset.</p>
Testing a biological mechanism of the insurancehypothesis in experimental aquatic communities - Data Deposit
<p>1.The insurance hypothesis predicts a stabilizing effect of increasing species richness on commu-nity and ecosystem properties. Difference among species’ responses to environmental fluctuationsprovides a general mechanism for the hypothesis. Previous experimental investigations of theinsurance hypothesis have not examined this mechanism directly.</p> <p>2.First, responses to temperature of four protist species were measured in laboratory microcosms.For each species, we measured the response of intrinsic rate of increase (r) and carrying capacity(K) to temperature.</p> <p>3.Next, communities containing pairs of species were exposed to temperature fluctuations. Com-munity biomass varied less when correlation inKbetween species (but notr) was more negative,and this resulted from more negative covariances in population sizes, as predicted. Results werecontingent on species identity, with findings differing between analyses including or not includingcommunities containing one particular species.</p> <p>4.These findings provide the clearest support to date for this mechanism of the insurance hypo-thesis. Biodiversity, in terms of differences in species’ responses to environmental fluctuations (i.e.functional response diversity) stabilizes community dynamics.</p>
Submerged aquatic vegetation and nitrogen retention data from 2012 to 2017 in lake Saint-Pierre, Saint Lawrence River
<p>Here we provide seven datasets that describes plant biomass (2012 to 2016), environmental variables and nitrogen retention time series (2012 to 2016) in a submerged aquatic vegetation (SAV) meadow at the confluence of two agricultural tributaries (Saint-François and Yamaska) with the St. Lawrence River in southern Lake Saint-Pierre.</p> <p>Version 2 adds the dataset 6 and 7.</p> <p>The seven datasets are:</p> <p>1) Growing season (June 21 to September 22) daily environmental variables (water level, water temperature, light, tributaries input, and SAV biomass indicator)</p> <p>2) Mean SAV biomass measured using rake or quadrat samples in the meadow</p> <p>3) Modelled daily nitrate tributary inputs to the SAV bed</p> <p>4) Daily nitrate output to the SAV bed estimated from a sensor</p> <p>5) Daily nitrate budget</p> <p>6) Hourly nitrate output to the SAV bed and signal decomposition from ensemble empirical mode decomposition (EEMD)</p> <p>7) Hourly dissolved oxygen and gas exchange velocities at the SAV bed outflow for 2016</p> <p>Original data comes from Lake Saint-Pierre, either from publicly available government agencies data, from a project led by the Groupe de recherche interuniversitaire en limnologie (GRIL, 2012-2015) and by Morgan Botrel Ph.D. candidate (2016-2017, Université de Montréal) or from Christiane Hudon (ECCC). Data were created for an article on climate-driven variation in nitrogen retention, led by Morgan Botrel and supervisor Roxane Maranger, with Christiane Hudon, James B. Heffernan and Pascale M. Biron (https://doi.org/10.1029/2022WR032678).</p>
EukZoo, an aquatic protistan protein database for meta-omics studies.
<p>This database contain protein sequences of aquatic microbial eukaryotes, or protists. The purpose of this is to make a database that is of reasonable quality to serve as resource for both taxonomy and functional interpretation of metagenomic and metatranscriptomic studies of protists. The source of the sequences were mainly from Marine Microbial Eukaryotes Transcriptome Sequencing Project (MMETSP), and supplemented with various genomes and transcriptomes of organisms that were not a part of MMETSP.</p> <p>To use this database, one has to understand the main function of the three files here.</p> <p>(1) The protein sequences are stored in .faa file. You can build an alignment/search database out of that and search your meta-omics sequences against it. Each sequence in the FASTA file has an ID which always consists of two parts like this: "MMETSP0004_1234567". The text before the first underscore is the source ID of that sequence.</p> <p>(2) Taxonomy information of each source ID are stored in "EukZoo_taxonomy_table_v_0.2.tsv". One can use the information within in conjunction with database search results to assign taxonomy to sequences.</p> <p>(3) KEGG annotation of each sequence are stored in "EukZoo_KEGG_annotation_v_0.2.tsv". One can use the information within in conjunction with database search results to assign KEGG functional annotation (KO ID) to sequences.</p> <p>I also provide scripts to assign taxonomy and KEGG annotation from database search results. You can also find the scripts and explanations on how to use them on the <a href="https://github.com/zxl124/EukZoo-database">EukZoo GitHub page</a>. You will find details on how the database was created and curated on there as well.</p> <p>Please contact me at zhenfeng.liu1@gmail.com if you have any questions or requests. Thank you for your interest in EukZoo.</p>
Checklist of the moss of aquatic and riverside habitats of the Komi Republic (European North-East of Russia)
<p>Представленная информация о мхах водных и прибрежно-водных местообитаний Республики Коми является дополнением к статье Г.В. Железновой, Т.П. Шубиной, Б.Ю. Тетерюка «Анализ флоры мхов водных и прибрежно-водных местообитаний Республики Коми», принятой к публикации в журнале «Известия Коми НЦ УрО РАН» в 2019 г.</p> <p>Список включает 275 таксонов мхов из 103 родов и 37 семейств. Он составлен на основе фактического материала, хранящегося в гербарии Института биологии Коми научного центра Уральского отделения Российской академии наук (SYKO) (УНУ «Научный гербарий SYKO Института биологии Коми НЦ УрО РАН») и литературных сведений (Ruprecht, 1850; Zickendrath, 1895, 1900; Поле, 1915; Кильдюшевский, 1956; Куваев, 1970).</p> <p>Исследованиями были охвачены прибрежные и водные местообитания водотоков и озер Республики Коми. На равнинной территории сборы выполнены в пределах тундры (подзона южной тундры), лесотундры, тайги (подзоны северной и средней тайги), в горах – на Полярном, Приполярном и Северном Урале. Полевые бриологические исследования проводились с использованием маршрутного и стационарного методов.</p> <p>Объем семейств, родов и названия видов приведены в основном согласно списку мхов Восточной Европы и Северной Азии (Check-list…, 2006)</p> <p>The checklist provides information about mosses aquatic and riverside habitats of the Komi Republic. It is a supplement to the article by G. V. Zheleznova, T. P. Shubina, B. Yu. Teteryuk "Analysis of the moss flora of aquatic and riverside habitats of the Komi Republic (European North-East of Russia)", accepted for publication in the journal "Proceedings of the Komi Science Center URD RAS" in 2019.</p> <p>The checklist includes 275 moss taxa from 103 genera and 37 families. It is based on the samples preserved in the Herbarium of the Institute of Biology of the Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences (SYKO) and literary data (Ruprecht, 1850; Zickendrath, 1895, 1900; Pole, 1915; Kildyushevsky, 1956; Kuvaev, 1970). The species names were given according to “Checklist of mosses of East Europe and North Asia” (2006).</p> <p>The mosses were collected in aquatic and riverside habitats of the mountains and plain territories of the Komi Republic. The research covered three parts of the Urals mountain range: the Polar Urals, the Subpolar Urals and the Northern Urals. The plain territory was covered within the southern tundra, forest tundra, northern taiga and middle taiga.</p>
Simulated submerged aquatic vegetation spectral signatures under different water quality conditions using Hydrolight
<p>Reflectance spectra were simulated using the Hydrolight radiative transfer model (Sequoia Scientific, Bellevue, WA) for four different submerged macrophyte species under a range of water quality conditions at two different depths. We used the four-component case-2 model with spectral reflectance of four submerged species, Egeria densa, Ceratophyllum demersum, Cabomba caroliniana, and Stukenia pectinata. These four reflectance spectra were calculated from the median of 10 measurements of the canopies of the representative species placed in clear tap-water made with a handheld ASD FieldSpec Pro spectrometer. Total suspended solids concentration was varied from 1 to 40 g·m<sup>−3</sup>, chlorophyll-a concentration was varied from 0.5 to 50 mg·m<sup>−3</sup>, and colored dissolved organic matter (CDOM) was varied from 0.25 to 3.5 m<sup>−1</sup>. A total of 4,742 spectra were simulated for all four species and a mud substrate at two different depths, 1 m and 5 m, and for optically deep water.</p>
Submerged aquatic vegetation biomass from the Saint Lawrence River (2006-2016) to compare estimation from quadrat-diver technique to rake collection and echosounding
<p>Here we provide 4 datasets that describes 1) the comparison between quadrat and rake collected biomass (QR), 2) the comparison of rake biomass and biovolume, a biomass proxy derived from echosounding (RE), 3) a validation dataset that confronts quadrat measurements to quadrat prediction measured from echosounding using two intercalibration equations (derived from QR and RE datasets), and 4) a whole-system biomass estimation comparing biomass predicted from echosounding and from rake.</p> <p>Original data comes from the Saint Lawrence River, mainly from Lac Saint-Pierre, but for the QR dataset also from Lac Saint-François and Lac Saint-Louis. Data from the QR (2006-2009) and validation dataset (2016) were collected by Christiane Hudon, Environment and Climate Change Canada, while the RE dataset and part of the validation dataset were collected as part of a project led by the Groupe de recherche interuniversitaire en limnologie (GRIL, 2012-2015) and by Morgan Botrel Ph.D. candidate (2016-2017, Université de Montréal). Data were created for an article on a method to estimate SAV biomass, led by Morgan Botrel and supervisor Roxane Maranger, with co-supervisor Christiane Hudon and Pascale Biron.</p> <p>For the second version, the data is more clearly organized in the four categories mentioned above. Additionally, revised prediction equations were applied which modifies results used in the validation and whole-system datasets (dataset 2 and 4). Equations are presented in the associated publication:</p> <p>Botrel, M., C. Hudon, P.M. Biron, R. Maranger. Combining quadrat, rake and echosounding to estimate submerged aquatic vegetation biomass at the ecosystem scale. Limnology & Oceanography: Methods. Accepted (as of 2023/02/08)</p>
Metal and nutrient content from submerged aquatic macrophytes collected from Southern Coeur d'Alene Lake, Idaho (USA) in August 2018.
<p>This repository contains data and R scripts used to produce the analyses reported in the manuscript listed below. See the Readme.txt and metadata.csv files for more explanation. The .R file can be used to unbundle the .tar.gz file via the packrat library. The data and script files are contained in the .tar.gz file. </p> <p>Scofield, B.D., Fields, S.F. & Chess, D.W. Aquatic macrophytes show distinct spatial trends in contaminant metal and nutrient concentrations in Coeur d’Alene Lake, USA. <em>Environ Sci Pollut Res</em> (2023). <a href="https://doi.org/10.1007/s11356-023-27211-x">https://doi.org/10.1007/s11356-023-27211-x</a></p>
Energetic costs increase with faster heating in an aquatic ectotherm: Respirometry data
<p>Using closed chamber respirometry we estimated the aerobic metabolic rate of an aquatic ectotherm, the Atlantic ditch shrimp <em>Palaemonetes varians,</em> under varying thermal conditions. We continuously measured oxygen consumption of shrimp during heating, cooling, and constant temperatures, starting trials at a range of acclimation temperatures and exposing shrimp to a variety of rates of temperature change.</p> <p>Data corrections and associated methodologies are detailed fully in the accompanying manuscript. </p> <p>## Description of the data and file structure</p> <p>Stable temperature trial data found in stable_trials_raw.csv</p> <p>Ramping temperature trial data found in ramping_trials_raw.csv</p> <p>Both datasets include the respirometry data for all temperature trials, with dissolved oxygen concentration corrected for background respiration ("doconc_corr") following the methodology outlined in the associated manuscript. Identification number of the individual is stored under "ID", time from start of trial to end of trial (in minutes) is stored under "time_min" and temperature of the chamber (in degrees Celcius) is stored under "temp_degC".</p>
Supplementary file 1 from: Moliner Cachazo L, Makati K, Chadwick MA, Catford JA, Price BW, Mackay AW, Guiry MD, Murray-Hudson M, Murray-Hudson F (2023) A review of the freshwater diversity in the Okavango Delta and Lake Ngami (Botswana): taxonomic composition, ecology, comparison with similar systems and conservation status. Aquatic Sciences
<p>Dataset with 2,204 freshwater species from the Okavango Delta and Lake Ngami (Botswana), with additional 355 species found in other areas of Botswana that are likely to be present in the study region. The dataset covers the following groups: amphibians, birds, fishes, macroinvertebrates, macrophytes, mammals, reptiles, phytoplankton, and zooplankton. The following information is given for each species: status in the Okavango Delta and Lake Ngami (present/potentially present); conservation status globally, Phylum, Class, Order, Family, Genus, species name, cited synonyms, common name, habitat, presence in high water, presence in low water, ecology, distribution in continental Africa, confirmed locations in the Okavango Delta, site coordinates, references, notes.</p>
NEON Provisional aquatic biology and single aspirated air temperature data 2020-2021
NEON field and taxonomic and abundance data for the periphyton (DP1.20166.001), macroinvertebrate (DP1.20120.001), and zooplankton (DP1.20219.001) collection for all aqatic sites, as well as single aspirated air temperature for 15 sites, were downloaded from the NEON data portal. Provisional data, not included in the 2022 data release, are included in this upload. Data are from all 34 aquatic sites across the network. Data are from NEON sources only. NEON is sponsored by the National Science Foundation (NSF) and operated under a cooperative agreement by Battelle. This material is based in part upon work supported by NSF through the NEON Program. NEON (National Ecological Observatory Network). Periphyton, seston, and phytoplankton collection (DP1.20166.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). Macroinvertebrate collection (DP1.20120.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). Zooplankton collection (DP1.20219.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). (2022e). Single aspirated air temperature (DP1.00002.001). https://data.neonscience.org (accessed March 12, 2022) NEON field and taxonomic and abundance data for the periphyton (DP1.20166.001), macroinvertebrate (DP1.20120.001), and zooplankton (DP1.20219.001) collection were downloaded from the NEON data portal. Provisional data, not included in the 2021 data release, are included in this upload. Data are from all 34 aquatic sites across the network. Data are from NEON sources only. NEON is sponsored by the National Science Foundation (NSF) and operated under cooperative agreement by Battelle. This material is based in part upon work supported by NSF through the NEON Program. NEON (National Ecological Observatory Network). Periphyton, seston, and phytoplankton collection (DP1.20166.001). https://data.neonscience.org (accesse
Temperature Thresholds for Aquatic Species in the Sacramento San-Joaquin Delta
The effects of increasing water temperature on species in the Sacramento San-Joaquin Delta is of growing importance for conservation and resource management; however, species metrics of temperature sensitivity vary across agency groups and can result in varied understanding and predictions of species vulnerability and modeling. Here, we provide a catalogue of key temperature metrics for several species in the Sacramento San Joaquin Delta that may be used as a standard for scientists studying temperature effects and resource management of native and non-native species. The dataset includes both documented physiological thresholds for suboptimal and upper temperature tolerances from metrics such as growth or critical and lethal limits, as well as calculated minimum, maximum and mean temperature values of species catch in the Delta from long-term monitoring surveys from 1954-2022. Species include critical estuarine fishes such as Delta Smelt, Longfin Smelt, Chinook Salmon, and sturgeon, as well as the species they interact with such as invasive fishes and invertebrates, cyanobacteria, and aquatic vegetation. The dataset includes values for different life-stages where possible and references for information. This information can help guide conservation measures and species management needed to lessen the impact stressful temperature conditions.
Decomissioned Site: Arthur Brook's (D01 ARTH) Legacy and Prototype Aquatic invertebrates (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains legacy and prototype NEON aquatic invertebrates from the decommissioned Arthur Brook's site in Worcester County, Massachusets. These samples and specimens were collected using NEON protocol NEON.DP1.20120 and are summarized in NEON Prototype dataset e7d152a1-1181-4c7e-ac75-ae707ffc7299. This data is available here.
Decomissioned Site: Ichawanochaway Creek (D03 ICHA) Legacy and Prototype Aquatic invertebrates (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains legacy and prototype NEON aquatic invertebrates from the decommissioned Ichawanochaway Creek site in Baker County, Georgia. These samples and specimens were collected using NEON protocol NEON.DP1.20120 and are summarized in NEON Prototype dataset 1599af29-fad4-4721-9b09-f8324b672d50. This data is available here.
Dataset from a study of aquatic macrophyte phenology across three sites in the Coeur d'Alene Lake Basin.
This repository includes data on aquatic macrophytes, water temperature, water clarity, and other water quality measures, such as pH, dissolved oxygen, and specific conductance relative to understanding the growth cycle (i.e., phenology) of aquatic plants. The data was generated during a project to study the phenology of macrophytes across the growing season of 2017, in three temperate lakes of the Coeur d’Alene Basin, USA. The project’s aim was to demarcate the timing of initial macrophyte growth, peak biomass, and senescence. The project also sought to compare traditional biomass measures with sonar biovolume (percent water column occupied by vegetation), which is relatively easier to collect. Macrophytes were measured twice per month with biomass collection via rake twirl, sonar biovolume, and species identification. Hourly water temperatures were measured over the course of the growing season at each site in shallow water near the macrophyte collection sites. The hourly water temperature data was used to calculate cumulative growing degree days over the growing season using minimum and maximum growth thresholds for Myriophyllum spicatum. Water temperature was also measured with a multi-parameter sonde at 0.5 meter increments from the water surface to the lake sediment and collected twice per month. Photosynthetically active radiation was measured during these vertical profiles and light extinction was calculated from this data. Water clarity was also measured with a standard black and white 20 centimeter Secchi disk. The data in this repository was originally reported in the following publication: Torso, K., Scofield, B.D. and Chess, D.W., 2020. Variations in aquatic macrophyte phenology across three temperate lakes in the Coeur d’Alene Basin. Aquatic Botany, 162, p.103209. https://doi.org/10.1016/j.aquabot.2020.103209
ScienceDex guides
Understand access before you commit
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.