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6,771 results for “freshwater”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
PIE LTER dissolved nutrient and particulate concentrations of freshwater inputs to the Plum Island estuarine system, Massachusetts, taken approximately monthly.
Multi-year data of water chemistry including nutrient concentrations for various forms of N, P, C, as well as suspended sediments, was determined from monthly grab samples taken at watershed inputs to the Plum Island Sound Estuary. Sampling sites were the Ipswich River (Sylvania Dam, Ipswich, MA), Parker River Dam (Central St, Newbury, MA), Egypt River (Ipswich, MA) Mill River (Newbury, MA), Muddy Run (Ipswich, MA), Little River (Newbury, MA). These nutrient concentrations are then used in conjunction with USGS discharge data (recorded at gages in the Parker River at Byfield, MA and the Ipswich River at Ipswich, MA) to calculate annual nutrient loading to the Plum Island Sound Estuary, coming over each dam. Annual yield is also calculated for both dams. Refer to file WAT-VA-Load for loading data.
Dynamic landscapes of fear and safety alter prey refuge use in freshwater habitats
The non-consumptive effects of predators on prey behavior have been studied in many different systems. However, predator-prey ecology has placed a bulk of emphasis on how fear alters prey behavior, and new studies have begun to shift focus to the importance that safety in the form of refuges has in structuring prey behavioral responses. This project focuses on changes in the safety landscape as well as changes in the fear landscape and how these changes impact crayfish behavior. Using an established bass-crayfish predator prey system, we altered shelter quality and location in relation to the presence of bass odor signals. We measured shelter use by the crayfish in response to this changing landscape.
Global eutrophication and antibiotic resistance genes dataset for "Coupling mechanisms between cyanobacteria and antibiotic resistance genes in freshwater ecosystems"
This dataset compiles global records of cyanobacteria, antibiotic resistance genes (ARGs), and associated water quality parameters to support research on freshwater ecosystem dynamics. It includes 990 metagenomes, 16,648 chlorophyll-a (Chl-a) records, and over 90 documented cases of ARGs–cyanobacteria co-occurrence under comparable spatiotemporal conditions. The dataset covers the years 2000–2024 and provides both raw measurements and harmonized tables for cross-study comparisons. Data were extracted from previously published literature and public repositories, with references to source publications included. This archive is intended to facilitate reproducible analyses, enable large-scale meta-studies, and support further exploration of microbial interactions in freshwater systems.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Data associated with the 2019 Freshwater Oil Spill Remediation Study (FOReSt) assessing the use of enhanced Monitored Natural Recovery (eMNR) and shoreline washing agent (SWA) of diluted bitumen spills conducted in shoreline enclosures at the IISD Experimental Lakes Area, ON, Canada from 2019 to 2020
The following package includes data from the 2019 Freshwater Oil spill Remediation Study (FOReSt) at the IISD Experimental Lakes Area studying the use of enhanced monitored natural recovery (eMNR) and shoreline washing agent (SWA) as a secondary remediation method for diluted bitumen spills in freshwater shoreline enclosures. This package includes data tables on polycyclic aromatic compound chemistry in water and sediments, basic water quality, nutrient chemistry, and tritium chemistry monitored in the experimental and reference enclosures, and lake reference sites over the duration of the study. Data included in this package was first collected and used in the paper by Palace et al., titled Polycyclic aromatic compounds in freshwater ecosystems following non-invasive remediation of controlled diluted bitumen spills: The Freshwater Oil Spill Remediation Study (FOReSt) at the Experimental Lakes Area, Canada.
The 2021 Freshwater Oil Spill Remediation Study (FOReSt), assessing the use of enhanced Monitored Natural Recovery (eMNR) of conventional heavy crude oil spills conducted in freshwater shoreline enclosures at the IISD Experimental Lakes Area, ON, Canada from 2021 to 2022.
The following package includes data from the 2021 Freshwater Oil spill Remediation Study (FOReSt) at the IISD Experimental Lakes Area studying the use of enhanced monitored natural recovery (eMNR) as a secondary remediation method for conventional heavy crude oil spills in freshwater shoreline enclosures. This package includes data tables on polycyclic aromatic compound chemistry in water and sediments, basic water quality, nutrient chemistry monitored in the experimental and reference enclosures, and lake reference sites over the duration of the study. As well as tables detailing enclosure metrics (depth), tritium chemistry, and a treatment key. Data included in this package was first collected and used in the paper by Stanley et al., titled Rapid Chemical Remediation of Freshwater Enclosures Treated with Conventional Heavy Crude Oil Spills Followed by Enhanced Monitored Natural Recovery
Periphyton Nutritonal Data across the freshwater Everglades (FCE): June 2016-Feb 2017
Fatty Acid profiles were obtained for various periphyton sources (food for consumers) accross the freshwater Everglades in June-July 2016, the peak of the wet season, and in January 2017, the peak of the dry season. These data include specific fatty acid markers for each periphyton type (floating mat, benthic mat, epiphyton, and/or filamentous green) collected. Nutritional measurements for various periphyton sources (food for consumers) were also obtained during the same intervals. These measurements include periphyton type (floating mat, benthic mat, epiphyton, and/or filamentous green), periphyton availability (volume, organic content and mineral content), stoichiometric data (TP, C:N, C:P, and N:P), and macronutrient composition (protein, carbohydrate, lipid). These measurements form the basis for the data discussed in the dissertation chapter, "Freshwater herbivores dominate over omnivores in suboptimal habitats because of their ability to exploit low quality resources" by Jessica L Sanchez and Joel C Trexler.
The dataset and model code pertinent to the Everglades Peat Elevation Model (EvPEM): The salinity and inundation mesocosm experiment in freshwater and brackish water sawgrass wetlands in Florida Coastal Everglades (2015-2017).
This is an assembled data and Everglades Peat Elevation Model (EvPEMv1.0) Stella code used to estimate and simulate net ecosystem carbon balance (NECB) and peat elevation change in response to saltwater intrusion and level of inundations. Data from several studies were combined for the estimation of NECB, model parameterization, and calibration (Wilson, 2018; Wilson et al., 2018, 2019; Charles et al., 2019; Servais et al., 2020). The reported data includes aboveground net primary productivity (ANPP), belowground net primary productivity (BNPP), peat elevation change, and decomposition rates that were collected from outdoor laboratory mesocosm experiments conducted at the Florida Bay Interagency Science Center in Key Largo, Florida during 2015-17. The plant-soil monoliths were obtained from a freshwater peat and a brackish water peat marsh located within the Florida Coastal Everglades and transported to the Key Largo facility for the experimental manipulations. In experiments focused on the brackish water marsh, three experiments were carried out reflecting the combined effect of salinity, inundation, and peat exposure to air. The brackish water experiments characterized submerged (SUB), exposed (EXP), and extended depth of exposure of peat surface (EXTEXP) conditions, as we varied water depth relative to the peat surface. Each experiment was subjected to two salinity manipulations: (1) ambient (~10 ppt) porewater salinity (AMB) and (2) elevated (~20 ppt) salinity (SALT). The experimental design included six (2 X 3) treatments: (1) submerged ambient salinity (AMB.SUB), (2) submerged elevated salinity (SALT.SUB.), (3) exposed ambient salinity (AMB.EXP), (4) exposed elevated salinity (SALT.EXP), (5) exposed with extended exposure/dry-down ambient salinity (AMB.EXTEXP), and (6) exposed with extended exposure/dry-down elevated salinity (SALT.EXTEXP). The water level was kept 4 cm above the peat surface for the brackish water SUB treatments. Exposure for the EXP treatment
PFAS, Coliform, and E. coli Data from Freshwater Canals, Brackish Water in Biscayne Bay, and Ocean Salt Water from Miami Beaches, Florida, USA, July 2023
This package contains data on levels of Per- and polyfluoroalkyl substances (PFAS), Coliform, and E. coli from samples collected at 15 water sampling sites in and around Biscayne Bay, Florida on 2023-07-27 as part of the Coastal Ecosystem-Research Experience for Teachers (CE-BIORETS) program. The sites included waterways leading to Biscayne Bay (freshwater canals), Biscayne Bay directly (marine brackish water), and ocean water from Miami beaches (marine salt water). A total of 500 mL of surface water was collected (at approximately 30 cm depth) from each site. Samples were run through a Solid Phase Extraction process (SPE) and then dried using a Nitrogen Evaporator. Extracts were then analyzed by Liquid Chromatography-Triple quadrupole Mass Spectrometry (LC-MS/MS) to determine the quantity of each of the different PFAS (ng/L) present in the sample. The same sites were selected for Coliform and E. coli colony forming units’ detection, and samples were collected at the same time as the PFAS samples. Samples were analyzed by pouring 100 mL of collected water into the wells on a ColiPlate. The 15 plates were incubated for 1 day at 37°C to determine if Coliforms and E. coli were detected. Data collection for this project is complete.
Effect of salt water intrusion on the distribution of invertebrates in a GA tidal freshwater marshes from the GCE Seawater Addition Long-Term Experiment (SALTEx) project.
To characterize the effect of persistent and episodic salt water intrusion on the distribution of common freshwater marsh invertebrates, we monitored the density of adult and juvenile fiddler crabs and snails. Prior to the start of salt water addition treatments, we collected data on the distribution of crabs and snails in all 30 experimental plots (6 replicates of 5 treatments: pressed salt water addition, pulsed salt water addition, fresh water addition, procedural control structure, and control no structure). In each experimental plot, we counted the number of adult and juvenile fiddler crab burrows and snails visible on the marshs surface in a 50cm x 75cm plot (juvenile fiddler crabs were counted in only half of this area) that was positioned in the Northeastern corner of each experimental plot. Initial data was collected in March 2014. A Bentho Torch was used to measure the concentrations of cyanobacteria, diatoms, and green algae on the marsh surface in 2015 and 2016.
Targeted and untargeted LC-MS copepodamide datasets for marine and freshwater copepods
<p>This repository contains the datasets, analysis code and output generated and used in the scientific article titled "Mass spectroscopy reveals compositional differences in copepodamides from limnic and marine copepods" published in Scientific Reports (https://doi.org/10.1038/s41598-024-53247-1)<em>.</em></p> <p>Detailed information about the datasets are available in the README.txt.</p> <p>The source dataset created from the sampling effort, with targeted liquid chromatography coupled mass spectrometry (LC-MS) data, taxonomic information of individual copepods, their length measurements, estimated biomass etc is available in <em><strong>Masterfile_targeted_data_final.xlsx</strong></em>.</p> <p>The source dataset for precursor LC-MS scan data is available in <em><strong>Precursor_data_Deisotoped.xlsx</strong></em>. </p> <p>The resulting analysis data frames (last sheet in each .xlsx file) are available as separate .csv files (<strong>Arnoldt_targeted_analysis_data.csv</strong> & <strong>Arnoldt_targeted_analysis_data.xlsx</strong>). These files are denoted "Supplementary Data. 2" and "Supplementary Data. 1" respectively in the main article. Data files <strong>Chromatography.csv</strong> and <strong>zooplankton_composition_bulk.csv</strong> are used to create chromatograph line plots (Figures 3a & 3b in the article) and one of the supplementary figures (S1), respectively.</p> <p>A R-markdown file (<strong>Arnoldt_R_Code</strong><em><strong>.Rmd</strong></em>) with the code to analyse and visualise all data, and its html-output file (<strong>Arnoldt_R_Code_Output</strong><em><strong>.html</strong></em>) are also available here. The markdown files uses the four csv-files described in the paragraph above to generate all analyses and figures. The output (.html) file is denoted "Supplementary Code" in the main article.</p>
Indicative distribution map for Ecosystem Functional Group F2.2 Small permanent freshwater lakes
<p>This archive contains indicative distribution maps and profiles for <strong>F2.2 Small permanent freshwater lakes</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group F2.1 Large permanent freshwater lakes
<p>This archive contains indicative distribution maps and profiles for <strong>F2.1 Large permanent freshwater lakes</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group F2.4 Freeze-thaw freshwater lakes
<p>This archive contains indicative distribution maps and profiles for <strong>F2.4 Freeze-thaw freshwater lakes</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group F2.5 Ephemeral freshwater lakes
<p>This archive contains indicative distribution maps and profiles for <strong>F2.5 Ephemeral freshwater lakes</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group F2.3 Seasonal freshwater lakes
<p>This archive contains indicative distribution maps and profiles for <strong>F2.3 Seasonal freshwater lakes</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Indicative distribution map for Ecosystem Functional Group F3.4 Freshwater aquafarms
<p>This archive contains indicative distribution maps and profiles for <strong>F3.4 Freshwater aquafarms</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
LTER-Italy freshwater sites map
<p>Map of Italy where the Italian Long-Term Ecological Research (LTER-Italy) freshwater sites are evidenced. The colours of the dots correspond to the freshwater ecosystem (light blue) typologies. The main features of the sites can be found on DEIMS-SDR, the LTER-Europe repository for research sites and datasets (<a href="https://deims.org">https://deims.org</a>).</p>
Datasets and codes for the peer review article "Human and natural impacts on the U.S. freshwater salinization and alkalinization: A machine learning approach"
<p>Ongoing salinization and alkalinization in U.S. rivers have been attributed to inputs of road salt and effects of human-accelerated weathering in previous studies. Salinization poses a severe threat to human and ecosystem health, while human derived alkalinization implies increasing uncertainty in the dynamics of terrestrial sequestration of atmospheric carbon dioxide. A mechanistic understanding of whether and how human activities accelerate weathering and contribute to the geochemical changes in U.S. rivers is lacking. To address this uncertainty, we compiled dissolved sodium (salinity proxy) and alkalinity values along with 32 watershed properties ranging from hydrology, climate, geomorphology, geology, soil chemistry, land use, and land cover for 226 river monitoring sites across the coterminous U.S. Using these data, we built two machine-learning models to predict monthly-aggregated sodium and alkalinity fluxes at these sites. The sodium-prediction model detected human activities (represented by population density and impervious surface area) as major contributors to the salinity of U.S. rivers. In contrast, the alkalinity-prediction model identified natural processes as predominantly contributing to variation in riverine alkalinity flux, including runoff, carbonate sediment or siliciclastic sediment, soil pH and soil moisture. Unlike prior studies, our analysis suggests that the alkalinization in U.S. rivers is largely governed by local climatic and hydrogeological conditions.</p>
ScienceDex guides
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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.