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Stream Restoration and Flood Impacts in the Kickapoo River Watershed, Wisconsin, 2019
Data were collected from May to November 2019 at five sites on two stream reaches in the Kickapoo River Watershed. Sites include Billings Creek restoration site (BRES), Billings Creek reference site (BREF), Warner Creek upstream site (WUP), Warner Creek middle site (WMD), and Warner Creek downstream (WDN) site. Data were collected by Dr. Caroline Gottschalk Druschke as part of research into the impacts of stream restoration and flooding on Kickapoo River Watershed (WI, USA) streams. Data were collected on methane and carbon dioxide fluxes on all reaches, as well as cross sectional area and soft sediment depth on the restored reach on Billings Creek before and after restoration in July 2019.
Water properties of Arco Lake, Budd Lake, Deming Lake, and Josephine Lake in Itasca State Park from 2006-2009 and 2019-et seq.
Depth profiles of water column chemical and physical properties were assessed with seasonal-scale frequency from four lakes in the Itasca State Park from 2006-2009 and from 2019-et seq. The data was used to assess the mixing status and major geochemical constituents within the lakes. Several parameters were routinely measured with deployable probes at meter or sub-meter resolution at the deepest location in each lake. Water samples were also collected for laboratory analysis. Bathymetry data collected in 2022 is supplied as rasters.
Efficacy and fate of fluridone applications for control of invasive submersed aquatic vegetation in the estuarine environment of the Sacramento-San Joaquin Delta
We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2-5 parts per billion required for SAV control. Monitoring demonstrated these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries.
LAGOS-NE Shallow Lakes: a dataset of lake variables and multi-scaled ecological context variables used to predict and compare trophic status and TP:CHLa relationships between shallow and non-shallow lakes in the Upper Midwest and Northeastern United States.
We conducted a macroscale study of 2,210 shallow lakes (mean depth ≤ 3m or a maximum depth ≤ 5m) in the Upper Midwestern and Northeastern U.S. We asked: What are the patterns and drivers of shallow lake total phosphorus (TP), chlorophyll a (CHLa), and TP–CHLa relationships at the macroscale, how do these differ from those for 4,360 non-shallow lakes, and do results differ by hydrologic connectivity class? To answer this question, we assembled the LAGOS-NE Shallow Lakes dataset described herein, a dataset derived from existing LAGOS-NE, LAGOS-DEPTH, and LAGOS-CLIMATE datasets. Response data variables were the median of available summer (e.g., 15 June to 15 September) values of total phosphorus (TP) and chlorophyll a (CHLa). Predictor variables were assembled at two spatial scales for incorporation into hierarchical models. At the local or lake-specific scale (including the individual lake, its inter-lake watershed [iws] or corresponding HU12 watershed), variables included those representing land use/cover, hydrology, climate, morphometry, and acid deposition. At the regional scale (e.g., HU4 watershed), variables included a smaller set of predictor variables for hydrology and land use/cover. The dataset also includes the unique identifier assigned by LAGOS-NE(lagoslakeid); the latitude and longitude of the study lakes; their maximum and mean depths along with a depth classification of Shallow or non-Shallow; connectivity class (i.e., whether a lake was classified as connected (with inlets and outlets) or unconnected (lacking inlets); and the zone id for the HU4 to which each lake belongs. Along with the database, we provide the R scripts for the hierarchical models predicting TP or CHLa (TPorCHL_predictive_model.R), and the TP—CHLa relationship (TP_CHL_CSI_Model.R) for depth and connectivity subsets of the study lakes.
Influence of soil amendment and crop species on nutrient cycling in a St. Paul urban garden, 2017-2023
An experiment was conducted from 2017-2023 at the University of St. Thomas research garden (Saint Paul, MN) to determine rates of nutrient recycling and loss from compost applied to urban gardens. Thirty-two 4 m2 study plots received one of six different soil amendment treatments, with four different crops growing on each plot. Meteorological data includes hourly measurements of rainfall, solar radiation, temperature and relative humidity, and wind speed and direction, from June 2017-October 2023. Hourly soil moisture measurements were recorded at depths of 10 cm, 20 cm, and 30 cm, from June-December 2021, June-October 2022, and June-October 2023. Annual crop harvest totals from each subplot are reported for 2017-2023. Leachate was collected from lysimeters installed in each of the 132 subplots weekly from June-October of each year (2017-2023), recording total volume. Leachate subsamples were analyzed for NO3-N, NH4-N, and PO4-P. Soil samples were collected at the beginning and end of the growing season in 2017, and every two weeks during the growing season from 2018-2023, and analyzed for pH, organic matter, Bray-1 extractable P, available K, nitrate, and ammonium, at the University of Minnesota Analytical Research Laboratory.
Otsego Lake (NY, USA) high-frequency buoy data 2017-2021
Yokota Lab, SUNY Oneonta BIological Field Station Volunteer Dive Team and Otsego Lake Association has been operating an NSF-funded (award #1624527) automated lake data buoy since 2017. This data set contains Ice-free season data from 2017 to 2021. Additional support for this project has been provided by New York State Water Research Institute, SUNY Oneonta Faculty Research Grant, and NSF awards to the Global Ecological Lake Observatory Network (GLEON.org).Yokota Lab, SUNY Oneonta BIological Field Station Volunteer Dive Team and Otsego Lake Association has been operating an NSF-funded (award #1624527) automated lake data buoy since 2017. This data set contains Ice-free season data from 2017 to 2021. Additional support for this project has been provided by New York State Water Research Institute, SUNY Oneonta Faculty Research Grant, and NSF awards to the Global Ecological Lake Observatory Network (GLEON.org).
2018-2020 Laboratory measurements of inorganic carbon accompanied by sensor data measurements of in situ inorganic carbon from the Upper Clark Fork River (Montana, USA)
These data were collected to support the Upper Clark Fork River restoration monitoring project supported by the US NSF Long Term Research in Environmental Biology (LTREB) and Consortium for Research in Environmental Water Systems (CREWS) programs. The LTREB monitoring project consists of monthly and bi-weekly water quality monitoring across a 215-km river restoration gradient contaminated by historic mining practices to monitor inorganic phosphorus and nitrogen concentrations, biotic standing stocks, heavy metal contamination, organic and inorganic carbon concentrations, and physicochemical parameters. The original analytical intent for these data was to assess the accuracy of calculating the partial pressure of carbon dioxide (pCO2) from electrochemical and spectrophotometric pH along with total alkalinity (AT). These data correspond to two parts: a tank study and a field application. The tank study was a set of controlled laboratory experiments that took place in a well-mixed temperature-controlled tank of freshwater. Data for the tank study are primarily measurements of electrochemical and spectrophotometric pH, AT, electrical conductivity, temperature, and ionic strength. The field application was used to demonstrate the real-world applicability of the tank study results in the Upper Clark Fork River (USGS HUC 17010201) at the Gold Creek site southeast of Missoula, MT, USA. Data from the field application are primarily high frequency measurements of carbon dioxide, pH, temperature, and electrical conductivity. Additional miscellaneous data were collected for quality control. These field data were collected using field deployments of SAMI sensors from Sunburst Sensors (Missoula, Montana, USA). Electrical conductivity data were collected with a HOBO sensor from Onset Computer Corporation (Bourne, Massachusetts, USA).
Standardized NEON organismal data (neonDivData)
To standardize NEON organismal data for major taxonomic groups, we first systematically reviewed NEON’s documentations for each taxonomic group. We then discussed as a group and with NEON staff to decide how to wrangle and standardize NEON organismal data. See Li et al. 2022 for more details. All R code to process NEON data products can be obtained through the R package ‘ecocomDP’. Once the data are in ecocomDP format, we further processed them to convert them into long data frames with code on Github (https://github.com/daijiang/neonDivData/tree/master/data-raw), which is also archived here.
Marcell Experimental Forest 30-minute water table elevation and temperature from transects of wells in the S2 and S6 peatlands, 2018-ongoing
This data publication contains 30-minute water table elevation and temperature data collected along bog to lagg transects within two watersheds at the Marcell Experimental Forest (MEF) in Itasca County, Minnesota. The bog to lagg transects are located on the north and south sides of S2 and S6 peatlands and contain three surface water wells each. The water table elevations provide information to calculate the hydraulic gradients that drive flow to and from the bogs. The collection of these data was funded by the US Department of Energy. The research program at Marcell Experimental Forest is managed by the USDA Forest Service Northern Research Station.
Plumes and Blooms: phytoplankton pigment concentration
The data set provided here is a curated collection of phytoplankton pigment observations collected from the discrete seawater bottle samples by the Plumes and Blooms program (PnB). The curated data set was used to determine the dominant seasonal to multi-decadal patterns and forcings of phytoplankton groups in the Santa Barbara Channel, CA. The data included here encompass the PnB cruises since Nov 2005.
Journey North - Oriole observations by volunteer community scientists across Central and North America (1997-2020)
This data package contains oriole migration data consisting of 14,476 total observational reports from 1997 - 2020 across North and Central America. These data were collected by 7,331 community scientists for Journey North, a crowdsourced participatory science program of the University of Wisconsin-Madison Arboretum. The Journey North Oriole Project is an ongoing study of oriole phenology conducted at broad spatial and temporal scales. Since 1997, community scientists have tracked first arrival dates and breeding and feeding behavior as well as the onset of fall migration and presence of oriole species throughout the winter months in the United States. Focal species are the Baltimore Oriole (Icterus galbula), Bullock’s Oriole (Icterus bullockii), and Orchard Oriole (Icterus spurius fuertesi). Observers also provide estimates of the number of birds sighted. However, observers do not follow standardized methods for counting species observed. Observers do not observe at set times of the day, do not repeat observations regularly, and are not required to provide the length of time during which a specified number of species observed were counted. Therefore, it is recommended that this dataset be analyzed to indicate presence not abundance. Researchers are encouraged to read the rich information provided by volunteers in their comments. These comments provide qualitative information about observational reports. Researchers are also encouraged to refer to submitted photographs that also provide context for observational reports. The Journey North Oriole Project dataset is hosted by the University of Wisconsin-Madison Shared Web Hosting Service.
International Soil Carbon Network version 3 Database (ISCN3)
The ISCN is an international scientific community devoted to the advancement of soil carbon research. The ISCN manages an open-access, community-driven soil carbon database. This is version 3-1 of the ISCN Database, released in December 2015. It gathers 38 separate data set contributions, totaling 67,112 sites with data from 71,198 soil profiles and 431,324 soil layers. For more information about the ISCN, its scientific community and resources, data policies and partner networks visit: http://iscn.fluxdata.org/. For information about processes used to construct the DB: https://iscn.fluxdata.org/data/data-information/.
Flume Erosion Testing Data of Root-Permeated and Organic Matter Amended Soil Samples Using Three Streambank Boundary Conditions.
The data published here is expected to accompany one publicly available dissertation (Chapter 6 of dissertation) and one separate journal publication. Once published and available online, the metadata will be updated with the relevant article information. The journal article/dissertation will have additional information regarding the published datasets and the methods used to collect the data. All data collected from these studies, and the accompanying Acoustic Doppler Profiler MATLAB files, are presented here. Journal Article title: Artificial Roots and Soil Microorganisms Increase Soil Resistance to Fluvial Erosion
Journey North - Common Loon and Ice-Out observations by volunteer community scientists across North America (1997-2020)
This data package contains Common Loon migration and ice melt data consisting of 9,800 total observational reports from 1997 - 2020 across North America. These data were collected by 1,437 community scientists for Journey North, a crowdsourced participatory science program of the University of Wisconsin-Madison Arboretum. The Journey North Loon and Ice-Out Project is an ongoing study of loon and ice melt phenology conducted at broad spatial and temporal scales. Since 1997, community scientists have tracked first arrival dates of Common Loons (Gavia immer) and ice that has melted from bodies of water in the United States. Observers also provide estimates of the number of birds sighted. However, observers do not follow standardized methods for counting species observed. Observers do not observe at set times of the day, do not repeat observations regularly, and are not required to provide the length of time during which a specified number of species observed were counted. Therefore, it is recommended that this dataset be analyzed to indicate presence not abundance. Researchers are encouraged to read the rich information provided by volunteers in their comments. These comments provide qualitative information about observational reports. Researchers are also encouraged to refer to submitted photographs that also provide context for observational reports. The Journey North Common Loon and Ice-Out Project Project dataset is hosted by the University of Wisconsin-Madison Shared Web Hosting Service.
Journey North - Gray Whale observations by volunteer community scientists across the Eastern Pacific Ocean (1997-2020)
This data package contains Gray Whale migration data consisting of 1,546 total observational reports from 1997 - 2020 across the Eastern Pacific Ocean. These data were collected by 163 community scientists for Journey North, a crowdsourced participatory science program of the University of Wisconsin-Madison Arboretum. The Journey North Gray Whale Project is a study of Gray Whale phenology conducted at broad spatial and temporal scales. Since 1997, community scientists have tracked the migration of Gray Whales (Eschrichtius robustus) through the Eastern Pacific Ocean. Observers also provide estimates of the number of whales sighted. However, observers do not follow standardized methods for counting species observed. Observers do not observe at set times of the day, do not repeat observations regularly, and are not required to provide the length of time during which a specified number of species observed were counted. Therefore, it is recommended that this dataset be analyzed to indicate presence not abundance. Researchers are encouraged to read the rich information provided by volunteers in their comments. These comments provide qualitative information about observational reports. Researchers are also encouraged to refer to submitted photographs that also provide context for observational reports. The Journey North Gray Whale Project dataset is hosted by the University of Wisconsin-Madison Shared Web Hosting Service.
Daily water temperature (C) in the Yolo Bypass and Sacramento River, 1998-2019
This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge. The raw YBFMP’s water temperature data was collected by loggers attached to the rotary screw trap (STTD) and Sherwood Harbor (SHR). Logger data ranged from daily means (1998) to a fifteen-minute collection interval (2013-2017 for the Yolo Bypass, 2009-2019 for Sherwood Harbor). A daily mean, maximum, minimum, standard deviation and coefficient of variation in water temperature was produced as well as columns for sample size (n, number of measurements per day), method (data collection or estimation), category, length (number of consecutive missing dates) and site. Daily water temperature data for the full extent of the YBFMP’s fish collection is valuable for a variety of purposes. For example, variation in water temperature during inundation and comparisons between temperatures in the Sacramento River and Yolo Bypass have been used as metrics of habitat complexity and linked to life history diversity in salmon (Goertler et al. 2017).
Marcell Experimental Forest chemistry of surface water draining the S2 catchment, 1986 - ongoing
This data set is a record since 1986 of chemistry for surface water draining the S2 catchment at the Marcell Experimental Forest (MEF) in Itasca County, Minnesota. Unfiltered water is usually collected every one or two weeks as part of the long-term monitoring program of the S2 catchment. Some samples were collected more often for various other studies and are included in this data set. Samples are routinely measured for pH, specific conductivity, anions (chloride, sulfate), cations (calcium, magnesium, potassium, sodium, aluminum, iron, manganese, strontium), silicon, nutrients (ammonium, nitrate+nitrite, soluble reactive phosphorus, total nitrogen, total phosphorus), and total organic carbon. Occasionally, stable water and mercury isotopes as well as concentrations of dissolved organic carbon (DOC), bacterial respiration of dissolved organic matter, biodegradable DOC (BDOC), ferrous and ferric iron, total mercury (filtered or unfiltered), methylmercury (filtered or unfiltered), and lead were measured. Ultraviolet (UV) absorbance, a measure of water color or dissolved organic matter optical properties, was also measured for some samples. More solutes and values will be added as additional metadata are documented (pre-1986 to 1992), water samples are collected and analyzed (concentrations and isotopes), or archived water samples are analyzed for stable water isotopes. The MEF is operated and maintained by the USDA Forest Service, Northern Research Station.
Flume Experiment Testing the Impact of Artificial Streambank Roots on Velocity, Reynold's Shear Stress, and Turbulent Kinetic Energy using an Acoustic Doppler Profiler
The data published here is expected to accompany one publicly available dissertation (Chapter 4 of dissertation) and one separate journal publication. Once published and available online, the metadata will be updated with the relevant article information. The journal article/dissertation will have additional information regarding the published datasets and the methods used to collect the data. All data collected from these studies, and the accompanying Acoustic Doppler Profiler MATLAB files, are presented here. Journal Article title: Impact of Flexible and Rigid Artificial Roots on Stream Hydrodynamics
Directed Outflow Project Lower Trophic Study
The upper San Francisco Bay Estuary and Sacramento San Joaquin Delta is critical habitat for the endemic Delta Smelt (Hypomesus transpacificus), an endangered planktivorous fish with an annual, semi-anadromous life cycle. Freshwater outflow actions during the fall season are hypothesized to improve Delta Smelt habitat and therefore Delta Smelt condition before the spawning life stage. As part of efforts to evaluate the effectiveness of such actions to benefit Delta Smelt populations, various studies were initiated by the U.S. Bureau of Reclamation under the Directed Outflow Project (DOP). One component of the DOP was to evaluate how the Fall X2 freshwater outflow action changed the lower trophic prey available to Delta Smelt. The action is hypothesized to change abiotic and biotic aspects that can benefit Delta Smelt habitat by using freshwater outflow to maintain the position of X2 (defined as the distance in kilometers from the Golden Gate Bridge to the tidally averaged 2 ppt salinity isohaline) at around 70 km during wet or above normal precipitation water years. This moves the low salinity zone (0.5 - 6 ppt) further seaward into Suisun Bay which increases the area of preferred Delta Smelt habitat. Field sampling began the September of 2017 and occurred bi-weekly through the end of November, paired with the U.S. Fish and Wildlife Service Enhanced Delta Smelt Monitoring program. Three random sites were sampled per target region (Suisun Bay, Suisun Marsh, the Lower Sacramento River, the Cache Slough Complex, and the Sacramento Deep Water Ship Channel) per week. Sites were chosen using a Generalized Random Tessellation Stratified design. During 2018, sampling was increased to weekly and in 2019-2020 sampling began in April and ended in November. Sampling occurs for three different habitat types: shoal, channel surface and channel deep at each site depending on the depth of the water column. The shoal habitat is less than 10 feet, channel habitat is greater than 10 f
Intertidal Crab Data in Midcoast Maine: 2018-2024
Invasive species have caused major disruptions to ecosystems worldwide. The European green crab invaded North America in the 1800s and is considered one of the world’s 100 worst invaders by the IUCN. Observations of spatiotemporal green crab population dynamics are essential for predicting and managing the ecological and economic impacts of this harmful invasive species. These data come from a standardized method for assessing green crab population dynamics in the rocky intertidal zone of New England and Atlantic Canada. Data was collected from 10 survey sites located along the coast of Maine from Yarmouth, ME (furthest point south), to Walpole, ME (furthest site north) from January, 2018 to November, 2024. Data was collected following the survey design described in McMahan (2020), using a 1m^2 quadrat to sample rocky intertidal habitat. The resulting data collected using this protocol has a wide range of uses, including to inform ecological research, conservation efforts, mitigation strategies, and fishery development, as well as for educational outreach purposes.
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.