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Fall 2000 soil organic content survey -- ash-free dry weight analysis for soil samples from 10 GCE LTER sampling sites
Soil core samples were collected from the permanent plots at 10 GCE LTER sampling sites in October, 2000, to survey the fractional organic content in marsh sediments. Surveys will be conducted annually to assess changes in soil organic content in response to environmental factors documented by other GCE monitoring efforts.
Soil salinity and organic content at GCE-LTER vegetation monitoring plots in October 2009
Soil samples were collected in conjunction with Fall 2009 plant monitoring at half of the permanent vegetation monitoring plots in the creekbank and midmarsh zones at 10 GCE study sites. Pore-water salinity was determined by analysis of supernatant salinity in dried soil samples hydrated with a measured volume of deionized water. Organic content was measured gravimetrically by comparing ash-free dry weight and total weight of soil samples.
Soil salinity and organic content at GCE-LTER vegetation monitoring plots in October 2011
Soil samples were collected in conjunction with Fall 2011 plant monitoring at half of the permanent vegetation monitoring plots in the creekbank and midmarsh zones at 10 GCE study sites. Pore-water salinity was determined by analysis of supernatant salinity in dried soil samples hydrated with a measured volume of deionized water. Organic content was measured gravimetrically by comparing ash-free dry weight and total weight of soil samples.
Organic components of decomposing hardwood boles at the Hubbard Brook Experimental Forest, 1990-2016
In 1990-1991 segments of boles from felled sugar maple (Acer saccharum), yellow birch (Betula alleghaniensis) and American beech (Fagus grandifolia) trees were placed in the field to study the rate of decomposition and nutrient loss (or gain) over time. The segments incubated in the field, ranging from 0.5-1.3 meters in length, were paired with fresh segments from the same trees. The fresh segments were taken to the lab shortly after felling, dried, weighed and subsampled. Fresh samples of wood and bark were collected separately. Incubated bole segments were collected in 1993 (T1), 1997 (T2), 2001 (T3), 2007 (T4) and 2015/2016 (T5). The whole bole segments were transported to the lab, measured, dried and weighed to determine mass loss. Subsamples of the bole wood and bark were collected for chemical analysis, including cross-polarization with magic-angle spinning (CPMAS) 13C NMR. Chemical analyses were conducted concurrently on the fresh (T0) and incubated samples. This data package includes the unprocessed NMR data, phased spectra, and integrated (spectral area) data in chemical shift regions that correspond to key structural groups. This data set includes data for T1, T3, T4, and T5 samples and their paired T0 fresh samples. Samples from T2 were measured for mass, but inadvertently discarded prior to chemical analysis. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
WAT05 Soil organic matter response to thirty years of increased precipitation at Konza Prairie
This dataset contains carbon and nitrogen concentrations and stocks in total soil organic matter and its fractions from the Konza Prairie Irrigation Transect Experiment. The dataset also includes pyrogenic organic matter C and N, as well as microbial amino sugars and root quality measurements. Data are availble for irrigated and control plots. Total pyrogenic and unburned soil organic matter C and N are availble for both the upland and lowland positions at 0-5, 5-15, and 15-30cm depth increments. Fraction and root data are avaible at both landscape positions, but for only the 0-5cm and 5-15cm depths and 0-5 and 5-30cm depths, respectively. Amino sugar data are only available for the lowland plots for the 0-5 and 5-15cm depths.
StreamFRE: Benthic Organic Matter in Prieta Stream
Measurements of benthic organic matter (BOM) in Prieta Stream, as part of the Stream Flow Reduction Experiment (StreamFRE). Background: StreamFRE started in October 2016 with the goal of assessing the effects of droughts on stream ecosystems. The project is designed to assess the effect of flow reduction, the main effect of droughts on streams. We collected pre-manipulation data from October 2016 to September 2017, when Hurricanes Irma and Maria hit Puerto Rico. The project became a hurricane impact assessment from September 2017 to early 2022, when the flow reduction is scheduled to start. BOM is measured using corer samplers in pools and Surber samplers in riffles. Samples are collected monthly as part of our macroinvertebrate sampling. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Soil organic matter dynamics in the tabonuco forest, a plantation and a secondary forest in Guzman
In this project we try to find out the relationship between the primary production and the soil organic carbon fractions. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Sediment and organic matter fluxes from the Stream Channel Aeolian Transect (SCAT), McMurdo Dry Valleys, Antarctica (2019-2023, ongoing)
The Stream Channel Aeolian Transect (SCAT) project was established by the McMurdo Dry Valleys LTER during the 2018-2019 austral summer to quantify the seasonal sediment and organic matter flux into stream channels in Fryxell Basin, Taylor Valley, Antarctica. Data collection began in 2019, with annual measurements of total sediment, ash-free dry mass (AFDM), and associated fluxes of sediment and organic matter analyzed each year. The initial SCAT array was installed along Von Guerard Stream during the 2018-2019 austral summer. It consists of six transects, each with eight collectors spanning the length of Von Guerard Stream, with three placed at the down-valley edge of the stream channel, two in the wetted margins, and three at the up-valley edge. In 2022, additional transects were established in Green Creek and Aiken Creek, each with four collectors placed in the wetted margins. These ongoing data collections provide critical insights into aeolian sediment and organic matter dynamics, highlighting their influence on stream channel processes in the McMurdo Dry Valleys.
Particulate organic carbon (POC) and nitrogen (PON) concentrations in discrete water column samples collected from lakes in the McMurdo Dry Valleys, Antarctica (1993-2024, ongoing)
An important part of the McMurdo Long Term Ecological Research (LTER) is evaluating carbon and nitrogen budgets in perennial ice-covered lakes. This dataset addresses this core area of research and quantifies the particulate organic carbon (POC) and nitrogen (PON) found at specific depths in lakes across the McMurdo Dry Valleys of Antarctica.
Stables isotopes of organisms along a transect from the Greenwood Creek outfall pipe to the Ipswich River, Ipswich, MA, Plum Island Ecosystems LTER
Organisms, plants and animals, were collected along a transect in Greenwood Creek, Ipswich, MA from the Ipswich sewage treatment plant outfall pipe to the mouth of Greenwood Creek on the Ipswich River. Tissue from the organisms was analysed for del 13C and del 15N to determine if the treatment plant effluent del 15N signal could be detected in the biota of Greenwood Creek.
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 YSI EXO2 sonde 15-minute interval water quality measurements of water column temperature, salinity, oxygen, pH, algae, fluorescent dissolved organic matter, turbidity, and depth at four sites in the Plum Island Estuary in year 2023.
Four YSI EXO2 water quality sondes were deployed from May 2023 to October 2023 at four sites in the Plum Island Estuary. One was at the mouth of the sound at the Ipswich Bay Yacht Club, one in the Rowley River, and two in the Parker River. The sondes measured water column temperature, salinity, oxygen, pH, algae, organic matter, turbidity, and depth in 15-minute intervals.
PIE LTER YSI EXO2 sonde 15-minute interval water quality measurements of water column temperature, salinity, oxygen, pH, algae, fluorescent dissolved organic matter, turbidity, and depth at four sites in the Plum Island Estuary in year 2024.
Four YSI EXO2 water quality sondes were deployed from April 2024 to October 2024 at four sites in the Plum Island Estuary. One was at the mouth of the sound at the Ipswich Bay Yacht Club, one in the Rowley River, and two in the Parker River. The sondes measured water column temperature, salinity, oxygen, pH, algae, organic matter, turbidity, and depth in 15-minute intervals.
PIE LTER YSI EXO2 sonde 15-minute interval water quality measurements of water column temperature, salinity, oxygen, pH, algae, fluorescent dissolved organic matter, turbidity, and depth at four sites in the Plum Island Estuary in year 2025.
Four YSI EXO2 water quality sondes were deployed from May 2025 to November 2025 at four sites in the Plum Island Estuary. One was at the mouth of the sound at the Ipswich Bay Yacht Club, one in the Rowley River, and two in the Parker River. The sondes measured water column temperature, salinity, oxygen, pH, algae, organic matter, turbidity, and depth in 15-minute intervals.
SBC LTER: OCEAN: Particulate Organic Matter Content and Composition of Stream, Estuarine, and Marine Sediments
An unprecedented five-year drought in California, coupled with conditions of anomalously low ocean productivity and the prospect of one of the strongest El Niño periods on record with above average rainfall were the impetus for this RAPID award, which seeks to test specific hypotheses pertaining to the origin, distribution, processing, and bioavailability of terrestrial organic matter in coastal marine sediments and their potential for serving as a reservoir of nitrogen storage to fuel nearshore primary production during periods when nitrate concentrations are low. The goals of the research were to: (1) measure bulk properties and biomarker tracers of particulate organic matter (POM) in stream water and in coastal marine sediments at SBC LTER and other reef sites differing in exposure to terrestrial runoff prior to and following large storm events, (2) determine the bioavailability of dissolved organic matter (DOM) released from POM in marine sediments following large runoff events, and (3) measure changes in concentrations of dissolved inorganic and organic nitrogen in pore water of marine sediments near to and distant from stream mouths in the Santa Barbara Channel. Samples were analyzed for organic matter content using a loss-on-ignition combustion method, and samples were also analyzed for organic carbon and nitrogen content and isotopes using a stable isotope mass spectrometer interfaced with an elemental analyzer. Subsamples were shipped to the laboratory of Marc Lucotte at the University of Québec, Montréal for analysis of lignin content using the cupric oxidation method.
SBC LTER: Santa Cruz Island: Abundance and Biomass of Benthic Organisms (food resource collection)
These data describe the abundance of benthic organisms as determined by random quadrat scrapings. These data represent the availability of food resources for fish at various depths, and are part of a long term investigation of temporal patterns in reef community composition. The sampling locations in this dataset include three sites along the north shore of Santa Cruz Island. Data collection began in 1982 and this dataset is updated annually.
Long-term dynamics of soil organic matter and aboveground net primary production in a Chihuahuan Desert Grassland at the Sevilleta National Wildlife Refuge, New Mexico (1989-2014)
Drylands contain a third of the organic carbon stored in global soils; however, the long-term dynamics of soil organic carbon and soil organic matter (SOM) in drylands remain poorly understood relative to dynamics of the vegetation carbon pool. We examined long-term patterns in SOM against both climate and prescribed fire in a Chihuahuan Desert grassland in central New Mexico, USA. SOM was measured each spring and fall for 25 years (1989–2014) in unburned desert grassland and from 2003 to 2014 following a prescribed fire. SOM concentration from 0-20 cm depth did not show a clear long-term trend but fluctuated seasonally at both burned and unburned sites, ranging from a minimum of 0.9% to a maximum of 3.3%. SOM concentration declined nonlinearly in wet seasons and peaked in dry seasons. These results not only contrast with the positive relationships between aboveground net primary production and precipitation for this region, but also with previous reports of greater SOM in wetter sites across drylands globally, suggesting that space is not a good substitute for time in predicting the dynamics of dryland SOM. We suggest that declines in SOM in wet periods are caused by increased soil respiration, runoff, leaching, and soil erosion. In addition to tracking natural variability in climate, SOM concentration also decreased by 14% following prescribed fire, a response that magnified over time and has persisted for nearly a decade due to the slow recovery of primary production. Our results document the surprisingly dynamic nature of soil organic matter and its high sensitivity to climate and fire in this dryland ecosystem.
Enzymes from the BRENDA and CAZy databases annotated with organism growth temperatures and predicted Topt
<p>This repo is an updated version of repo <strong>Gang Li, & Martin KM Engqvist. (2019). Enzymes from the BRENDA database annotated with organism growth temperatures and predicted <em>T</em><sub>opt</sub> (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.2539114. </strong></p> <p>Experimental as well as predicted organism growth temperatures were used to annotate enzymes from the BRENDA database (doi: 10.1093/nar/gky1048, https://www.brenda-enzymes.org) version 2018.2 (July 2018) and CAZy database (http://www.cazy.org/). </p> <p>An updated machine learning model was applied to predict the optimal functional temperature of enzymes from BRENDA and CAZy. </p> <p>There are four files in this repo:</p> <p>1. 'annotated_brenda.tsv' is a tab-seperated file that contains the annotated enzymes from BRENDA. There are 9 columns in the file: index column; "ec", EC number; "uniprot_id", protein id in Uniprot database; "domain", the domain of life (superkingdom), either Archaea, Bacteria, or Eukarya; "organism", species name; "ogt", optimal growth temperature of the organism; "ogt_note", whether the experimental or predicted ogt is used; "topt", the optimal functional temperature of the enzyme; "topt_note", whether the experimental or predicted topt is used.</p> <p>2. 'annotated_cazy.tsv' is a tab-seperated file that contains the annotated enzymes from CAZy. There are 12 columns in the file: index column; "family", CAZy family id; "genbank", genbank id; "Protein Name", the protein name from CAZy database; "ec", EC number; "organism", strain name; "uniprot_id", protein id in Uniprot database; "PDB/3D", structure id in PDB database; "ogt", optimal growth temperature of the organism; "ogt_note", whether the experimental or predicted ogt is used; "topt", the optimal functional temperature of the enzyme; "topt_note", whether the experimental or predicted topt is used.</p> <p>3. 'brenda.sql', which is a SQLite3 database version of 'annotated_brenda.tsv', with an additional column of enzyme sequences.</p> <p>4. 'cazy.sql', which is a SQLite3 database version of 'annotated_cazy.tsv'', with an additional column of enzyme sequences.</p> <p>The SQLite3 databases are for the Tome tool (<a href="https://github.com/EngqvistLab/Tome">https://github.com/EngqvistLab/Tome</a>), version 2.0.</p>
Italy Southern Regions organic waste stream, Agricultural, Forest and Municipal Solid Waste, years 2018 and 2030
<p>Southern Italy regions agricultural residues (straw, pruning) quantification, years 2018 and 2030</p> <p>Souther Italy regions above ground annual forest increment, 2018 and 2030 technical and environmental contraints</p> <p>Souther Italy regions Municipal Solid Waste separation 2018, and 2030 minimum target EU waste Directive 2018/851</p>
Carbon emissions and economic assessment of farm operations under different tillage practices in organic rainfed almond orchards under semiarid Mediterranean conditions
<p>This dataset corresponds to yield, price and fuel consumption from organic rainfed almond orchards in SE Spain under different diversification and tillage practices. The objective is to carry out an integrated environmental (focused on the CO<sub>2</sub> emissions) and economic assessment of farm operations under different diversification and tillage practices through a cradle-to-farm gate life cycle assessment (LCA) based on these data.</p> <p>These data correspond to the open-access article " Carbon emissions and economic assessment of farm operations under different tillage practices in organic rainfed almond orchards under semiarid Mediterranean conditions" published in Scientia Horticulturae. (https://doi.org/10.1016/j.scienta.2019.108978), funded by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003].</p>
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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)
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.