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Measurement of Fuel load (organic biomass) Quantities of Organic Soils, Understory Plants and Trees at Sites within the Bonanza Creek LTER Regional Site Network in Interior Alaska, 2019
This dataset contains fuel load measurements for a subset of the BNZ LTER's RSN sites (n = 28). The data for each site separted by 16 fuel types (or plant functional types) including organic soil layers (fibric, mesic), vascular understory (evergreen shrub, short deciduous shrub, graminoid, forb, tall deciduous shrub, tree seedling/sapling, dead-downed wood), nonvascular understory (feather moss, Sphagnum moss, colonizer moss, lichen) and trees (evergreen tree, deciduous tree).
Effects of nutrients and organic carbon on the relative proportion of primary producers (microalgae) and heterotrophic decomposers (bacteria and fungi) during aquatic biofilm development in boreal peatland located near Fairbanks Alaska - 2018
1. Producer-decomposer interactions within aquatic biofilms can range from mutualistic associations to competition depending on available resources. The outcomes of such interactions have implications for biogeochemical cycling, and as such, may be especially important in northern peatlands, which are a global carbon sink and are expected to experience changes in resource availability with climate change. The purpose of this study was to evaluate the effects of nutrients and organic carbon on the relative proportion of primary producers (microalgae) and heterotrophic decomposers (bacteria and fungi) during aquatic biofilm development in a boreal peatland. Given that decomposers are often better competitors for nutrients than primary producers in aquatic ecosystems, we predicted that labile carbon subsidies would shift the biofilm composition towards heterotrophy owing to the ability of decomposers to outcompete primary producers for available nutrients in the absence of carbon limitation. 2. We manipulated nutrients (nitrate and phosphate) and organic carbon (glucose) in a full factorial design using nutrient-diffusing substrates in an Alaskan fen. 3. Heterotrophic bacteria were limited by organic carbon and algae were limited by inorganic nutrients. However, the outcomes of competitive interactions depended on background nutrient levels. Heterotrophic bacteria were able to outcompete algae for available nutrients when organic carbon was elevated and nutrient levels remained low, but not when organic carbon and nutrients were both elevated through enrichment. 4. Fungal biomass was significantly lower in the presence of glucose alone, possibly owing to antagonistic interactions with heterotrophic bacteria. In contrast to bacteria, fungi were stimulated along with algae following nutrient enrichment. 5. The decoupling of algae and heterotrophic bacteria in the presence of glucose alone shifted the biofilm trophic status towards heterotrophy. This effect was overturned
Particulate organic carbon and nitrogen measurements at selected depths in the water column in the CCE region since 2006 - 2024 (ongoing).
Water column bottle samples at multiple depths are taken during CCE Process cruises (since 2006, ongoing) at various CTD stations, filtered, and stored at -20°C. Measurements of particulate organic carbon (POC) and nitrogen (PON) are performed onshore in the lab where samples are acidified, dried and analyzed by high-temperature combustion. The sample and tin capsule react with oxygen and combust at 1000°C, and the sample is broken down, thus converting organic carbon to CO2 and reducing nitrogen oxides to N2 gas. Both gases are measured by thermal conductivity. Samples analyzed within the CCE constrain the mean C:N ratio of small particulates and by difference relative to measured living biomass, the biomass of suspended detritus.
Total dissolved organic carbon and nitrogen measurements at selected depths in the water column from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Water column bottle samples at multiple depths are taken during CCE Process cruises (since 2006, ongoing) at various CTD stations, and measurements of total organic carbon (TOC) and total nitrogen (TN) are performed onshore in the lab. TOC includes both dissolved and particulate organic carbon (DOC and POC, respectively). TN includes particulate and dissolved organic nitrogen as well as dissolved inorganic nitrogen species. In open ocean waters, POC is subtracted from TOC, and likely provides an accurate estimate of DOC because particles are typically small and homogeneously distributed in the sample. In coastal waters, and at stations where relatively high chlorophyll concentrations are present, the TOC measurement is not easily converted to DOC by subtracting POC values. Experience has shown that particles in these regions are large and inhomogeneously distributed. Therefore, samples collected in the CCE are reported as TOC and TN, expressed as micromoles of carbon (nitrogen) per liter of sea water.
Total dissolved organic carbon measurements at standard depths in the water column from nine CalCOFI cruises, 2008-2017.
Water column bottle samples at multiple depths are taken during CalCOFI cruises (since 2006, ongoing) at various CTD stations, and measurements of total organic carbon (TOC) are performed onshore in the lab. TOC includes both dissolved and particulate organic carbon (DOC and POC, respectively). In open ocean waters, POC is subtracted from TOC, and likely provides an accurate estimate of DOC because particles are typically small and homogeneously distributed in the sample. In coastal waters, and at stations where relatively high chlorophyll concentrations are present, the TOC measurement is not easily converted to DOC by subtracting POC values. Experience has shown that particles in these regions are large and inhomogeneously distributed. Therefore, samples collected in the CCE are reported as TOC, expressed as micromoles of carbon per liter of sea water.
Station data of passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE-CalCOFI Augmented cruises in the California Current System, 2012 - October 2020.
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system (these are not samples from bottles!) during CalCOFI cruises while on station. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence. ALF data are merged with CTD and bottle data that were collected by the CalCOFI group.
Continuous passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE-CalCOFI Augmented cruises in the California Current System, 2012 - 2020
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system during CalCOFI cruises. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence.
Continuous passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE process cruises in the California Current System, 2012 - 2019 (ongoing).
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system during CCE process cruises. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence.
Particulate organic carbon and nitrogen measurements at selected depths in the water column from CalCOFI-CCE Augmented cruises in the California Current System, 2004 - November 2022
Water column bottle samples at multiple depths are taken during CalCOFI cruises (since 2004, ongoing) at various CTD stations, filtered, and stored at -20°C. Measurements of particulate organic carbon (POC) and nitrogen (PON) are performed onshore in the lab where samples are acidified, dried and analyzed by high-temperature combustion. The sample and tin capsule react with oxygen and combust at 1000°C, and the sample is broken down, thus converting organic carbon to CO2 and reducing nitrogen oxides to N2 gas. Both gases are measured by thermal conductivity. Samples analyzed within the CCE constrain the mean C:N ratio of small particulates and by difference relative to measured living biomass, the biomass of suspended detritus.
Primary production estimates from 14C uptake (in situ), determined by the incorporation of inorganic carbon into particulate organic carbon (POC) due to photosynthesis at selected light levels from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Primary productivity samples of seawater are taken each day shortly before noon on the CTD rosette up-cast during the CCE Process crusies (since 2006, ongoing). Light penetration below the surface is estimated from the Secchi disk depth. Niskin bottles from depths with ambient light intensities corresponding to light levels simulated by on-deck incubators are identified and sampled. Primary production is estimated from 14C uptake using this simulated in situ technique (followed by filtering) by which the assimilation of dissolved inorganic carbon by phytoplankton yields a measure (in µg/L/day) of the rate of photosynthetic primary production (particulate organic carbon, POC) at selected light levels in the euphotic zone within the CCE study area.
Soils Organic Matter: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Dissolved organic carbon (doc) in stream water at watersheds 7, 14, and 27 at the Coweeta Hydrologic Laboratory, Otto, North Carolina, USA.
Dissolved organic carbon (DOC) plays a critical role in stream ecosystem processes. This study seeks to examine long-term patterns in DOC concentration in stream water resulting from climatic variation and associated with recovery form clear-cutting. Watershed 7 was clear-cut in 1977 as part of a multi-investigator study examining the response of both the terrestrial and aquatic communities to commercial clear-cutting.
Forest Floor Mass, Organic Matter and Chemistry in Watershed 5 at the Hubbard Brook Experimental Forest, 1982 Pre-Harvest Collection
Watershed 5 was surveyed in 1982 and clearcut in 1983. A pre-cut forest floor survey was done in 1982. This data set includes organic matter mass, thickness and trace metals for samples collected in the summer of 1982 as two separate collections, one in July and one in August. 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.
Heliconia fluid and organic matter analyses
Mineral concentrations of Heliconia bract fluid and organic matter accumulated in the bracts. Data collected during a study of the invertebrates in Heliconia bract fluid. 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.
Dissolved organic carbon (DOC) concentrations in glacial meltwater streams, McMurdo Dry Valleys, Antarctica (1990-2023, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, a systematic aqueous geochemical sampling program has been undertaken. A series of terrestrial water samples have been collected and analyzed for dissolved organic carbon levels. This dataset shows concentrations of dissolved organic carbon found in various streams of the McMurdo Dry Valleys.
Dissolved organic carbon (DOC) concentrations in discrete water column samples collected from lakes in the McMurdo Dry Valleys, Antarctica (1993-2022, ongoing)
The McMurdo Long Term Ecological Research (LTER) project monitors patterns of organic material transport in perennial ice-capped lakes. This data set addresses this core area of research and quantifies dissolved organic carbon concentrations at specific depths in McMurdo Dry Valley lakes.
The photooxidation of dissolved organic matter in surface waters analyzed by Fourier-transform ion cyclotron resonance mass spectrometry.
Dissolved organic matter (DOM) plays an important role in carbon cycling in natural waters. The processing of DOM in these waters can occur via photooxidation, or interaction with sunlight. This processing can lead to the production of CO2, and also the alteration of organic compounds that make up DOM. It is likely that the extent of photooxidation is at least partially determined by the chemical composition of DOM. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize the dissolved organic matter at the molecular level for all water samples, both before and after light exposure to better understand the photooxidation of DOM. Chemical formulas were assigned to mass to generated mass to charge ratios using a custom script in R, resulting in a list of chemical formula assignments for each DOM sample, at multiple light exposure time points.
Geum and Kobresia soil inorganic and organic property data for Saddle and North of Tvan, 1993.
This study was initiated to examine bulk density and organic matter content differences between soils where Geum (Acomastylis) rossii and Kobresia myosuroides were present. A subset of samples were also measured for total C, N, and P. Paired plots were randomly selected in locations where Kobresia and Geum populations were adjacent to one another. Soil samples were collected from 35 plots, 22 and 13 of which had southerly and northerly aspects, respectively. Soil cores were removed with 3.5-cm interior diameter PVC pipe that was driven into the tundra by use of a rubber mallet. The minimum depth of individual cores was 9 cm, and these depths were recorded at the time of removal (15 July, 19 July, 22 July, and 9 August 1993).
Krummholz island soil inorganic and organic property data for East of Tvan, 1995 - 1996.
Previous work has shown that passage of Engelmann spruce (Picea engelmannii) and subalpine fir (Abies lasiocarpa) tree islands across tundra lowers the soil carbon and nitrogen storage capacity of the top 15cm of soil (A horizon) (Pauker and Seastedt 1996). This study shows that levels of KCl extractable ammonium and percent organic matter were also significantly higher in the A horizon of undisturbed tundra sites compared with soils underneath or immediately adjacent to (windward or leeward) the krummholz. The response of soil KCl extractable NO3- also showed this trend but was not statistically significant. Holtmeier and Broll (1992) suggested that the depletion of organics and nutrients following the passage of tree island may be associated with a reduced clay content. We analyzed a subsample of these soils for cation exchange capacity (CEC) and texture. We did not find significantly lower clay content in soils under or adjacent to krummholz compared with those from undisturbed tundra. In fact, percent clay was greater in krummholz and windward sites than in tundra sites. The percent clay of windward sites was significantly greater in windward soils than either krummholz or tundra soils. Clearly, depletion of organics following the passage of tree islands does not appear to be associated with a depleted clay content. We found that CEC was very highly significantly correlated with percent organic content (using percent organic data only from the subset of soils on which CEC was measured). Therefore, the CEC content of these soils would appear to be strongly associated with the organic content but not with the clay content. Percent soil moisture was significantly higher directly underneath the krummholz compared with the other sites. There was no effect of treatment on pH. We also investigated whether the organic matter lost in association with krummholz colonization (i.e. 1m from the tree) was replenished as tundra vegetation recolonized in the wake of the tree is
Soil inorganic and organic property data for subalpine forest, treeline, and alpine zone, 1999.
This study was initiated to examine the nitrogen content of three montane soils: subalpine, treeline and alpine; and to determine if the differences in soil nitrogen content were attributed to plant community and elevation. Soil organic matter, soil carbon, bulk density, pH and soil moisture were also measured for each site. Soil samples were collected from 64 total plots [22 subalpine,15 treeline and 27 alpine sites]. The subalpine site plots included aspen, fir, lodgepole, spruce and meadow vegetation cover. The treeline site plots included fir, spruce and meadow vegetation cover. The alpine site plots included dry meadow and mesic meadow fertilization (control, N, P, NP) plots. Soil cores were removed with 3.5-cm interior diameter PVC pipe that was driven into the soil by use of a rubber mallet. The minimum depth of individual cores was 10 cm. Cores were taken at each site three times over the period between 29 June 1999 and 29 July 1999.
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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.
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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.