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Sensor and nutrient data associated with the article Harrison et al. 2020. Prediction of stream nitrogen and phosphorus concentrations from high-frequency sensors using Random Forests Regression
This document describes a dataset used to produce Random Forests Regression models of stream nitrogen and phosphorus concentrations from high-frequency sensor data, as reported in: Harrison, J.W., Lucius, M.A., Farrell, J.L., Eichler, L.W., and Relyea, R.A. 2020. Prediction of stream nitrogen and phosphorus concentrations from high-frequency sensors using Random Forests Regression. Science of the Total Environment: https://doi.org/10.1016/j.scitotenv.2020.143005. The dataset consists of paired values of stream nitrogen and phosphorus concentrations and various high-frequency sensor parameters (water temperature, specific conductance, pH, fluorescent dissolved organic matter, turbidity, hydrostatic pressure, soil moisture) collected during baseflow and storm events from 2018 to 2019 as part of routine monitoring of eleven tributaries of Lake George, New York. This dataset does not include raw data; two levels of processing were performed: (1) erroneous values (extreme or otherwise outlying values with no apparent environmental cause) were removed from the sensor data as part of the routine QA/QC process of the Jefferson Project, and (2) one-hour rolling medians of the raw sensor data were calculated at a 1-minute timestep to maximize pairing of sensor data with nutrient concentrations. The resultant dataset was used to train and test the models presented in Harrison et al. 2020.
Crossing Treeline: Bacterioplankton community composition in alpine and subalpine lakes of the Rocky Mountain southern ecoregion and associated physical and chemical characteristics
This dataset includes lake water samples collected in the summer of 2016 from 16 different mountain lakes in the Rocky mountains in both Rocky Mountain National Park and the Snowy Range of southern Wyoming. Each lake was sampled twice: once in the early summer when hydrologic connections with the surrounding terrestrial environment were high and again in the late summer when hydrologic connections were low. The main goal of the study was to compare communities of bacterioplankton in alpine and subalpine lakes to determine if communities differed across treeline as soil microbes in the surrounding terrestrial environment were. To do so, we collected water samples from the deepest point of each lake, mixed it with a surface water sample and characterized bacterioplankton communities with 16S sequencing technology. Additionally, we wanted to identify abiotic factors that may correlate with community dissimilarity and characterized a suite of chemical attributes for each lake. Lake characteristics reported included surface temperature, soluble reactive phosphorous (SRP), ammonia (NH3+), pH, total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and total dissolved organic carbon (DOC), and chlorophyll a (chl-a).
Temporal transect of moss-associated N2 fixation rates in Anchorage, Fairbanks, and Toolik
This is a dataset coving multiple moss species (Hylocomium splendens, Ptilium crista-castrensis, Pleurozium schreberi, Sphagnum sp., others) and their associated d15N following incubation with 15N2 in June, July, and August over the course of one growing season in 2017. Three sites at each location (Anchorage, Fairbanks, and Toolik Field Station) were sampled. We measured rates of nitrogen fixation using 15N2 incubations in a common garden close to the sites of collection.
Reciprocal transplant of mosses from Arctic tundra to alpine tundra and associated N2 fixation rates
In the summer of 2018, 12 cores were taken at Toolik Field Station. Six of those cores were retransplanted into their home environment, while six we transplanted to Eight Mile Lake. At Eight Mile Lake, the same procedure was followed. One year later, these transplants were revisited and associated N2 fixation rates were measured for Hylocomium splendens, Pleurozium scheberi and Aulacomnium turgidum using 15N2 gas incubations.
Sediment and nutrient deposition and plant-soil phosphorus interactions associated with Hurricane Irma (2017) in mangroves of the Florida Coastal Everglades (FCE LTER), Florida
We quantified how Hurricane Irma influenced soil nutrient pools, vertical accretion, and plant phosphorus (P) uptake after its passage across the Florida Coastal Everglades in September 2017. Mangrove leaf litter data from three years (2008, 2014, 2018) were selected for each site at Shark River estuary to identify species-specific foliar P responses post-Wilma’s impact in 2005 and immediate post-Irma’s impact in 2017. We also monitored porewater SRP concentrations in the Shark River mangrove sites to evaluate the effect of Hurricane Irma on soil chemistry. The data in this data package were used in the following paper: Castañeda-Moya, E., V.H. Rivera-Monroy, R.M. Chambers, X. Zhao, L. Lamb-Wotton, A. Gorsky, E.E. Gaiser, T.G. Troxler, J.S. Kominoski, and M. Hiatt. 2020. Hurricanes fertilize mangrove forests in the Gulf of Mexico (Florida Everglades, USA). PNAS. In Press.
Periphyton Abundance and Structural Traits, Diatom Taxa Relative Abundance, and Associated Environmental Data from Samples Collected from the Greater Everglades, Florida, USA from September 2005 - ongoing
This data package contains benthic algae (periphyton) and environmental data collected annually during the wet season between 2005 and 2021 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan (CERP MAP) intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units (LSU) and each year, random coordinates are 'drawn' within each PSU and one draw is visited in each sampleable PSU. Sampled periphyton is processed for aggregate structural traits (i.e., biomass, chlorophyll-a, organic content, and phosphorus concentration) and for diatom taxa. For diatoms, slides are prepared, and at least 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental and spatial data for each sampled draw. In addition to the CERP MAP data, this dataset also includes data on the same variables collected from up to 21 primary sampling units in the Broward County Water Preserve Area beginning in 2020. The data in this package replace and supersede those in package knb-lter-fce.1210 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1210).
Integrated measurements of soil micro-invertebrate abundance and associated physicochemical properties from the McMurdo Dry Valleys, Antarctica (1993–2022)
This data package compiles three decades (1993–2022) of soil micro-invertebrate abundance data and associated physicochemical measurements collected as part of the McMurdo Dry Valleys Long Term Ecological Research (MCM LTER) project in Antarctica. Variables include soil micro-invertebrate counts and species richness, along with associated soil physicochemical properties, including gravimetric moisture content, pH, electrical conductivity, soil organic carbon, ammonium, and nitrate. Data originate from both long-term core monitoring efforts and targeted opportunistic sampling campaigns across multiple valleys, including Arena, Beacon, Pearse, Taylor, Victoria, and Wright Valleys. Sampling locations span a range of geomorphic and ecological settings, providing broad spatial and temporal coverage of soil conditions across the Dry Valleys ecosystem. Data were curated to represent the most comprehensive and spatially diverse records available while minimizing sampling bias across years and study types. These integrated measurements provide a valuable resource for understanding the drivers of soil micro-invertebrate abundance and habitat suitability and serve as a foundation for future analyses of long-term ecological change and species distribution modeling in polar desert soils.
Limno run codes, dates, and locations associated with vertical lake profile data collected in the McMurdo Dry Valleys, Antarctica (1991-2025, ongoing)
This data package provides a summary of "limno runs" performed each season in lakes located throughout the McMurdo Dry Valleys of Antarctica as part of the McMurdo Dry Valleys Long Term Ecological Research program. Each limno run is identified by unique code that allows one to compile a complete set of limnological data from a particular lake and location at specific time points. There are usually two or three limno runs performed per lake per austral summer field season, although the number of runs may vary by lake and by season depending on site access, site conditions, and other external factors.
MCR LTER: Coral Reef Resilience: North Shore Herbivorous Fish Counts, Habitat Associations, and Substrate, 2010
These data describe the species abundance, size distributions, and habitat associations of roving herbivorous fishes (fishes belonging to the families, Acanthuridae, Scaridae, and Siganidae) found in different habitats in the lagoon and forereef on the north shore of Moorea. Adult fishes and large juveniles were counted (and their size estimated) by a SCUBA diver or snorkeler on thirty-four 50 m by 5 m wide transects. After counting large fishes, the entire transect was swam a second time, with the diver looking exclusively for small juvenile fishes on a 1 m swath. In addition to recording the species identity and estimated size of each juvenile encountered, the diver also recorded the particular microhabitat each individual or group of individuals was associated with. Finally, to quantify the relative availability of different types of microhabitat, the diver conducted point contacts where the primary benthic substrate was identified at regular (1 m) intervals on the same transect. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Fecal glucocorticoid metabolite levels of American pika (Ochotona princeps) and habitat characteristics of their associated territories found in rock glaciers adjacent to Niwot Ridge and within Rocky Mountain National Park, 2018 - 2019.
To understand whether stress-associated hormones vary with metrics of habitat quality, we measured fecal glucocorticoid metabolite (FGM) levels in the American pika (Ochotona princeps), a small mammal with well-defined habitat (talus), that can vary in quality depending on the presence of rock ice features (RIFs). In 2018, we sampled pika scat from two types of RIFs: “active” rock glaciers thought to harbor subsurface ice recently, and “fossil” rock glaciers considered long devoid of subsurface ice (as classified by Janke 2005, 2007). Specifically, fecal pellets were collected from pika territories located in rock glaciers within eight sites along the Front Range of Colorado: four in Rocky Mountain National Park (2 active, 2 fossil) and four adjacent to Niwot Ridge (2 active, 2 fossil) (pika_fecal_glu_rg.aw.csv). To account for possible seasonal variation in pika FGM, scat samples were collected in the alpine spring and fall. To understand other influences of habitat quality on FGMs, we also measured fine-scale habitat differences between rock glaciers in 2019, including talus depth, clast size, and land cover metrics related to forage (pika_fecal_habitat_rg.aw.csv).
Skin-blubber biopsy samples and associated demographic data collected from cetaceans encountered along the Western Antarctic Peninsula (WAP), 2010 – 2024
Baleen whale populations in the Southern Ocean are recovering after intense commercial whaling in the 20th century. Along the Western Antarctic Peninsula (WAP), this recovery is occurring in one of the planet's most rapidly changing marine ecosystems. Understanding how climate-driven changes influence the population dynamics of whales in this region is critical for understanding what conservation and management actions must be prioritized to maintain the structure and function of this marine ecosystem. To begin understanding the dynamics of whale recovery under continued environmental change, we need to study these whales' demography and population dynamics. As part of our annual sampling surveys for cetaceans along the WAP through the PAL LTER program, we actively collect remote non-lethal skin-blubber biopsy samples and have developed one of the most extensive tissue archives in the Southern Ocean. With these samples, we conduct a series of demographic and physiological measurements. Using the skin portion of the biopsy sample, we isolate nuclear and mitochondrial DNA (mtDNA) to develop a DNA profile for each sample, including genetic sex, a microsatellite genotype, and a mtDNA haplotype. These profiles are used to compare sex ratios of the population, determine individual recaptures through genotype analysis, and better understand population mixing. Using the blubber portion of the biopsy sample, we isolate endocrine markers (e.g., progesterone and cortisol) to monitor population pregnancy rates and stress levels. This data represents some of the first non-lethal quantitative observations of the demography and population dynamics of recovering whale populations in the Antarctic and provides a critical reference point for future work as the Antarctic climate continues to change and populations continue to recover from whaling.
Nassarius obsoletus (Ilyanassa obsoleta) density measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Nassarius obsoletus (Ilyanassa obsoletus) length and biomass measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016.
Nassarius obsoletus (Ilyanassa obsoleta) length and biomass measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Nassarius obsoletus (Ilyanassa obsoleta) length and biomass measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2014 and at Clubhead Creek in 2005 and from 2009 till 2014.
Mummichog (Fundulus heteroclitus) counts and gut content analysis from lift trap transect collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The lift traps were used to capture mummichogs accessing the high marsh platform. Mummichogs were collected to study the effect of marsh-edge geomorphology on mummichog distribution and foraging. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
Mummichog (Fundulus heteroclitus) gut content analysis from Breder trap transect collections in tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and eat invertebrate prey, coupling the high marsh and aquatic creek food webs by gathering energy produced on the high marsh and making it available to the aquatic food web. Changes in the geomorphology of saltmarsh creek edges greatly influence the survival, biomass, and resource use of mummichog populations. Here we use gut content analysis assess the diet of mummichog on the high marsh platform during a flooding spring-cycle tide in July 2018 across 3 PIE creeks known to present different geomorphologic patterns in their low marsh zones. These data allow us to quantify the amount of terrestrial invertebrate prey mummichog consume on a single flooding tide and determine the impact altered low marsh geomorphology has on the trophic relationships in PIE food webs. These mummichog were captured in Breder traps; information about the consumer communities captured in these traps was recorded separately (LTE-TIDE-BrederTrap-Demographics). These data were included in part of the study “Habitat decoupling via saltmarsh creek geomorphology alters connection between spatially-coupled food webs” (Lesser et al. 2020) and were a portion of an MBL REU project.
Demographics of high marsh consumers from Breder trap transect collections in tidal creeks associated with long term fertilization experiments, Rowley, MA
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and eat invertebrate prey, coupling the high marsh and aquatic creek food webs by gathering energy produced on the high marsh and making it available to the aquatic food web. Changes in the geomorphology of saltmarsh creek edges greatly influence the survival, biomass, and resource use of mummichog populations. Here, we capture animals using Breder traps to quantify the communities accessing the high marsh at night during one of these high tides in July 2018 across 3 PIE creeks known to present different geomorphologic patterns in their low marsh zones. These data can be used for the assessment of the impact of low marsh geomorphology on consumer communities in PIE marshes. Mummichog captured in these Breder traps were further analyzed for gut content (LTE-TIDE-BrederTrap-GutContents). These data were included in part of the study “Habitat decoupling via saltmarsh creek geomorphology alters connection between spatially-coupled food webs” (Lesser et al. 2020) and were a portion of an MBL REU project.
Mummichog (Fundulus heteroclitus) caloric value analysis from various collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and eat invertebrate prey, coupling the high marsh and aquatic creek food webs by gathering energy produced on the high marsh and making it available to the aquatic food web. Changes in the geomorphology of saltmarsh creek edges greatly influence the survival, biomass, and resource use of mummichog populations. Here, we use bomb calorimetry to assess individual mummichog caloric content per gram of biomass at 4 PIE creeks known to present different geomorphologic patterns in their low marsh zones. These data can be used for the assessment of the impact of low marsh geomorphology on mummichog caloric content and energy production in PIE food webs. These data were included as part of two studies “Habitat decoupling via saltmarsh creek geomorphology alters connection between spatially-coupled food webs” (Lesser et al. 2020) and “Cross-habitat access modifies the ‘trophic relay’ in New England saltmarsh ecosystems” (Lesser et al. 2021).
Invert species counts and density along transects on the high marsh along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and consume invertebrate prey. Invertebrate surveys were conducted before and after spring tides that flooded the high marsh area to determine the effect of mummichog predation that occurs on the high marsh during the flood events and to assess the impact of low marsh geomorphology on top-down control by mummichog. These data were included in part of the study "Cross-habitat access modifies the ‘trophic relay’ in New England saltmarsh ecosystems” (Lesser et al. 2021) as well as a part of a NEU Three Seas Master's thesis.
Stable isotope values for organisms collected in the Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
To assess differences in trophic relationships and enerygy transfer related to long term fertilization of tidal creeks (TIDE Project: https://thetideproject.org/), organisms including primary producers, invertebrates, and fish were sampled and analyzed for stable isotopes of nitrogen (δ14N) , carbon (δ13C), and sulfur (δ34S). Collections were made during summers from 2000-2018 from reference and nutrient-enriched branches of 4 tidal creeks.
PIE LTER measurements of water column depth at 15 minute intervals in the Parker River near Rt 1A bridge, Newbury, MA, year 2000. Water depths are relative to the sonde pressure transducer and not associated with a datum.
PIE LTER, year 2000,15 minute readings of water column depth in the lower Parker River Estuary at Fernalds Marina bulkhead off Rt. 1A., Newbury, MA. Water depths are relative to the sonde pressure transducer and not associated with a datum.
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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.