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Cascade Project at North Temperate Lakes LTER: Zooplankton 1984 - 2007
Zooplankton data from 1984-1995. Sampled approximately weekly with two net hauls through the water column (30 cm diameter net, 80 um mesh). There have been 5 zooplankton counters during this period, so species-level identifications (TAX, below) are not as consistent as those for some of the other datasets. To standardize across counters, I have assigned higher-level taxonomic categories for a few "confusing" taxa; these identifications can be found in the column LLTAX, below. Sampling Frequency: varies Number of sites: 5
Cascade Project at North Temperate Lakes LTER: Phytoplankton 1984 - 1995
Data on epilimnetic phytoplankton from 1984-95, determined by light microscopy from pooled Van Dorn samples at 100percent, 50percent, and 25percent of surface irradiance. There have been 4 counters during this period, with the same counter from 1991-95. Standardization among counters is difficult, so I recommend sticking to the 1991-95 data if possible. Cottingham (1996) describes the counting protocols in detail. Sampling Frequency: varies Number of sites: 5
Microbial Community Composition in lakes - Ecological characteristics of the sample at North Temperate Lakes LTER 2002 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by ecological characteristics of the sample allows the user to retrieve sample IDs, sample dates, lake information (region, type, size, depth) and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The data can be filtered by lake name, sample date, lake information (region, type, size, depth), and physical/chemical data (water temperature, clarity, pH, DOC, SUVA, TN, TP, nitrates/nitrites). The output includes links to individual sample records, which contain links to the taxonomic composition of the sample inferred by dynamically matching clones to ARISA fragments in the individual sample
Microbial Community Composition in Lakes - Taxonomic characteristics of the clones at North Temperate Lakes LTER 2000 - 2007
Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).
Biocomplexity at North Temperate Lakes LTER; Coordinated Field Studies: Fish / Crayfish Abundance 2001 - 2004
Abundance data for fish and crayfish collected for Biocomplexity Project; Landscape Context - Coordinated Field Studies http://infotrek.er.usgs.gov/doc/wdnr_biology/Public_Stocking/StateMapHotspotsAllYears.htm - Infomation on fish stocking by Wisconsin Department of Natural Resouces in Biocomplexity Lakes. Sampling Frequency: annually Number of sites: 58
North Temperate Lakes LTER: Phytoplankton - Madison Lakes Area 1995 - current
Phytoplankton samples for the 4 southern Wisconsin LTER lakes (Mendota, Monona, Wingra, Fish) have been collected for analysis by LTER since 1995 (1996 Wingra, Fish) when the southern Wisconsin lakes were added to the North Temperate Lakes LTER project. Samples are collected as a composite whole-water sample and are preserved in gluteraldehyde. Composite sample depths are 0-8 meters for Lake Mendota (to conform to samples collected and analyzed since 1990 for a UW/DNR food web research study), and 0-2 meters for the other three lakes. A tube sampler is used for the 0-8 m Lake Mendota samples; samples for the other lakes are obtained by collecting water at 1-meter intervals using a Kemmerer water sampler and compositing the samples in a bucket. Samples are taken in the deep hole region of each lake at the same time and location as other limnological sampling. Phytoplankton samples are analyzed by PhycoTech, Inc., a private lab specializing in phytoplankton analyses (see data protocol for procedures). Samples for Wingra and Fish lakes are archived but not routinely counted. Permanent slide mounts (3 per sample) are prepared for all analyzed Mendota and Monona samples as well as 6 samples per year for Wingra and Fish; the slide mounts are archived at the University of Wisconsin - Madison Zoology Museum. Phytoplankton are identified to species using an inverted microscope (Utermohl technique) and are reported as natural unit (i.e., colonies, filaments, or single cells) densities per mL, cell densities per mL, and algal biovolume densities per mL. Multiple entries for the same species on the same date may be due to different variants or vegetative states - (e.g., colonial or attached vs. free cell.) Biovolumes for individual cells of each species are determined during the counting procedure by obtaining cell measurements needed to calculate volumes for geometric solids (e.g., cylinders, spheres, truncated cones) corresponding to actual cell shapes. Biovolume concentratio
North Temperate Lakes LTER: Groundwater Levels 1984 - current
Water levels in monitoring wells are measured several times throughout the year. The number of monitored wells has ranged over the study period from 19 to 44 wells. Currently, 37 wells are being monitored 4 - 5 times per year. The wells are scattered throughout the Trout Lake hydrological basin and the data are used to calibrate and test regional groundwater flow models. In addition (see related data set - Groundwater Chemistry), water chemistry is measured annually in a subset of 11 of these wells to characterize regional groundwater chemistry in the Trout Lake area. Sampling Frequency: varies - generally from 4 - 9 times a year Number of sites: 44
Zooplankton community composition and trait data for Green Lakes Valley, 2009 - ongoing.
Starting in 2012 zooplankton sampling at Green Lake 4 was included in the long term monitoring data set at Niwot Ridge. Immediately after the ice has completely melted from the lakes, zooplankton samples are taken once a week for six consecutive weeks at the deepest portion of the lake from an inflatable raft. Zooplankton were sampled at the deepest location of each lake by pulling a conical net (Wisconsin net) vertically through the water column (i.e., vertical tow sample). For each zooplankton sample obtained, adult organisms were identified to species, or lowest taxonomic level (Chydoridae sp. and Bosminidae sp.). Larvae of cladocerans were counted together as neonates; calanoid and cyclopoid copepodites were counted together as nauplii. Individual body lengths of the first 50 -100 (when possible) individuals of each taxon were recorded using a calibrated eyepiece micrometer and means reported.
Individual plant growth and reproduction in the black sand extended growing season experiment for East Knoll, Audubon, Lefty, and Trough sites, 2018 - 2020.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites, each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows and a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot at each site by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to control plots after snow had naturally melted. We used open top warming chambers (OTCs) to increase summer temperature in three subplots within each of the 10 x 40 m plots. This dataset includes measurements of growth and reproduction for Geum plants as well as counts of buds and flowers were counted and recorded for each tagged study plant, within all snow and warming treatments at all sites except Soddie.
Plant species composition for sensor network array, 2017 - ongoing.
Above-ground plant species cover was recorded for vegetation plots in the sensor network, starting in 2017. Cover was measured annually at peak biomass using a 100 point-intercept method.
Time-lapse camera (phenocam) imagery of sensor network plots, 2017 - ongoing.
Images from time-lapse cameras were analyzed to track the greenness curves of 16 plots in the Sensor Network at Niwot Ridge. Images were taken every 30 minutes during daylight hours throughout the growing season. Cameras were angled to view 1m^2 vegetation plots located at each sensor node. Pixels in the portion of the image capturing the vegetation plot were used to calculate the green chromatic coordinate (GCC). The change in GCC over the growing season represents the growth and phenology of the plant communities captured.
Federal sampler data for Saddle and C1, 2016 - ongoing.
We use an aluminum Standard Federal Snow Sampler to measure snow depth and snow water equivalent (SWE). This device, compared to traditional snow pit techniques, provides efficient measurement capabilities that are less disruptive to the snowpack. Manual Federal Sampler measurements provide high accuracy point data to determine the amount of water in the surrounding snowpack. With a high downstream reliance on water within the regional snowpack, our weekly measurements give a time series of SWE throughout the winter season, offering consistent and dependable information for water resource planning and preparation.
Subalpine tree seed availability and germination at Niwot Ridge, 2015 - ongoing.
These data were collected to assess how seed availability and site limitations affect conifer germination across species distributions. Our study focused on areas above alpine treeline where subalpine tree species must migrate to track movement of suitable climate, but we also included sites in the core and at the lower ecotone of subalpine forests. We monitored seed availability and germination of new seedlings for four subalpine tree species from 2015-present at Niwot Ridge, Colorado, USA. Seed availability was collected in 66-95 seed traps in 14-17 sites (6-12 traps per site; see data for count per site), depending on year. In the lab, seeds were counted by species. In the field, new germinants were counted by species 3-5 weeks after snow disappearance (i.e., peak germination) and again in late September from 2015 to 2018 only. Only one census of new germinants was conducted from 2019 to 2023. New germinants from prior years were censused in subsequent summers.
Plant phenology observations in the black sand extended growing season experiment for East Knoll, Audubon, Lefty, and Trough sites, 2018 - 2020.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites, each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows and a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot at each site by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to control plots after snow had naturally melted. We used open top warming chambers (OTCs) to increase summer temperature in three subplots within each of the 10 x 40 m plots. This dataset includes measurements of plant species phenology within all snow and warming treatments at all sites except Soddie.
Temperature data for Green Lake 4 inlet and outlet, 2019 - ongoing
This dataset contains temperature data from two Onset HOBO temperature pendant loggers installed in Green Lake 4’s inlet and outlet from summer 2019. High-resolution water quality data are fundamental to observing rapid ecological responses to meteorology, climate, and other disturbance events. The inlet and outlet temperature data collected here, together with Niwot Ridge’s buoy deployed in Green Lake 4, allow us to understand lake hydrology, water budget, and stratification and mixing dynamics that drive seasonal in-lake processes to understand effects of warming.
Plant species composition in ITEX subplots in black sand extended growing season experiment, 2018 - 2023.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites, each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows and a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot at each site by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to control plots after snow had naturally melted. We used open top warming chambers (OTCs) to increase summer temperature in three subplots within each of the 10 x 40 m plots. This dataset includes measurements of plant species composition within all snow and warming treatments.
Time lapse camera photos for Green Lakes Valley, 2011 - ongoing.
Time lapse photography is a powerful tool to detect seasonal and interannual change in remote locations. In 2008, a time lapse camera was installed at Niwot Ridge, below D1, with a view overlooking Green Lake 4. The resulting photos give a view into the seasonal evolution of ice and snow cover over the Green Lakes Valley.
Water quality, temperature, ash-free dry mass, photosynthetic activate radiation (PAR), and zooplankton data from a warming and DOC subsidy experiment, 2020 - 2021.
This dataset includes chlorophyll-a concentrations, periphyton biomass estimates, water quality measurements, and qualitative observations from a large-scale mesocosm experiment conducted in the Green Lakes Watershed, Colorado. The experiment was designed to test how earlier lake ice-off and increased dissolved organic material (DOM), associated with terrestrial plant encroachment in alpine watersheds, interactively influence aquatic food webs. In fall 2019, twenty 2600L “megacosms” were established at Sandy Corner (3300 m ASL; 40.042289, -105.584006), left to fill with snowmelt, and maintained throughout the 2020 open water season. The experiment followed a 2 × 2 randomized block design manipulating ice-off timing (via black vs. beige tank coloration) and DOM inputs (presence/absence of willow leaf packs), with five replicates per treatment. All tanks were seeded with sediments and zooplankton from both alpine and montane lakes (Green Lake 1 and Green Lake 4), and instrumented with thermistors recording surface and hypolimnion temperature every two hours year-round. Periphyton growth was monitored using clay tiles, sampled across five time points. Chlorophyll-a concentrations were extracted from filtered water samples and analyzed spectrophotometrically. Periphyton biomass was estimated via ash-free dry mass (AFDM) determinations, based on the mass lost on combustion of material scraped from tiles. Water quality was measured 1–2 times weekly using a YSI ProPlus multiprobe and Li-Cor quantum sensor, and snow/ice cover was qualitatively assessed monthly during winter.
Pollinator visitation, flower count, and seed set in Black Sand plots, 2020.
Anthropogenic climate change is altering interactions among numerous species, including plants and pollinators. Plant-pollinator interactions, crucial for the persistence of most plant and many insect species, are threatened by climate change-driven phenological shifts. Phenological mismatches between plants and their pollinators may affect pollination services, and simulations indicated that these mismatches may reduce floral resources available to up to 50% of insect pollinator species. Although alpine plants rely heavily on vegetative reproduction, seedling recruitment and seed dispersal are likely to be important drivers of alpine community structure. Similarly, advanced flowering may expose plants to increased risk of frost damage and shifted soil moisture regimes; phenologically advanced plants will experience these environmental factors differently, which may alter their floral resource production. These effects may be dependent upon topography. Some species of alpine plants on the Niwot Ridge have displayed advanced phenology under treatments of advanced snowmelt (Forrester, 2021). However, little is understood about how these differences in distribution and phenology affect pollinator community composition and plant fecundity. Here we strive to examine how experimentally-induced changes in the timing of flowering and number of flowers produced by plants impact plant-pollinator interactions and seed set. We also ask how topography and the number of flowers interact with early snowmelt to affect pollination rates and the diversity of pollinating insects. Finally, we ask how seed set of Geum rossii is affected by pollinator visitation at different times of the season, under experimentally advanced snowmelt versus unmanipulated snowmelt, and with visitation by different insect taxa. In summer 2020, we found that plots with advanced phenology experienced peaks in pollinator visitation rates and pollinator diversity earlier than plots with unmanipulated snowmelt.
Homogenized, gap-filled, daily air temperature data for Saddle, 1986 - ongoing.
As part of its long-term climate data core collection, the Niwot Ridge LTER has collected daily air temperature at the Saddle site since 1981. The Saddle station is located at 3525 m.a.s.l. and is an important point location to capture local, ambient meteorological conditions for many biological and environmental datasets collected nearby. The location of the Saddle station has also presented challenges to its operation. Freezing temperatures, snow deposition from strong winds following storms, and exposure to lightning are some elements that have disrupted instrument functionality, affected data quality, and made access for research staff difficult over time, especially in winter months. These interruptions have led to missing or faulty data at times and inconsistent data gap-filling. Additionally, a mixture of mechanical hygrothermograph chart and temperature sensors with electronic data loggers have been used since the inception of the Saddle station to measure and record air temperature. Thus, a close inspection of potential influence from instrument turnover and relevant notes from research staff is required for a quality, daily air temperature time series for Saddle. Here we present a quality-controlled, gap-filled, daily time series of maximum, average, minimum, and diurnal air temperatures that accounts for instrument turnover at the Saddle. Methods follow those used to gap-fill long-term daily air temperature at the Niwot Ridge LTER D1 and C1 stations so there is consistency among core collection daily air temperature datasets. Metadata for this data package centralizes the most complete station history for Saddle air temperature and includes notes to data users on aspects and limitations of the dataset to consider when using these data in scientific analyses.
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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)
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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.