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388 results for “organic matter”
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.
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.
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.
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.
Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.
In this dataset, we used a controlled flow-through reactor (FTR) experiment to test the role of nitrate as an electron acceptor, and its effect on organic matter decomposition and the associated microbial community in salt marsh sediments. Organic matter decomposition significantly increased in response to nitrate, even at sediment depths typically considered resistant to decomposition. The use of isotope tracers suggests this pattern was largely driven by stimulated denitrification. Nitrate addition also significantly altered the microbial community and decreased alpha diversity, selecting for taxa belonging to groups known to reduce nitrate and oxidize more complex forms of organic matter. Fourier Transform-Infrared Spectroscopy further supported these results, suggesting that nitrate facilitated decomposition of complex organic matter compounds into more bioavailable forms. Taken together, these results suggest the existence of organic matter pools that only become accessible with nitrate and would otherwise remain stabilized in the sediment. The existence of such pools could have important implications for carbon storage, since greater decomposition rates as N loading increases may result in less overall burial of organic-rich sediment. Given the extent of nitrogen loading along our coastlines, it is imperative that we better understand the resilience of salt marsh systems to nutrient enrichment, especially if we hope to rely on salt marshes, and other blue carbon systems, for long-term carbon storage.
Fiddler crab impacts from observational study 2020-21: Aboveground & diatom biomass, plant height, percent N, burrow & mussel density, belowground biomass, and organic matter
The fiddler crab, Minuca pugnax, expanded its range into the Gulf of Maine recently and was first observed in the Plum Island Estuary in 2014. In 2020 and 2021, we investigated the impact of this burrowing crab on benthic microalgal biomass, sediment properties and the above- and belowground biomass of the cordgrass, Spartina alterniflora. To accomplish this, we conducted a control-impact study in plots with and without fiddler crabs in three marshes in the PIE-LTER: Sawyer, Clubhead, and Metcalf. In its historical range (i.e., south of Cape Cod), M. pugnax, enhances Spartina aboveground biomass. In contrast, we found that, on average, when fiddler crabs were present, aboveground biomass was 40% lower in the PIE-LTER. We also found that belowground biomass was 30% lower and benthic microalgal biomass was 45% lower when fiddler crabs were present, which is in line with our expectations. Because fiddler crabs reduced the biomass of foundational primary producers in its expanded range, our results imply that M. pugnax can influence other saltmarsh functions such as carbon storage and accretion as they expand north. More broadly, our results suggest that as species expand or shift their range with climate change, not only can they have profound impacts in their new ranges, but that those impacts can be the inverse of what is seen in their historical ranges.
Shear Stress, Biomass, Bulk Density, Organic Matter on the Bank of the York River, VA 2018
This dataset includes data used to assess marsh vulnerability to sea-level rise by quantifying marsh erodibility along a salinity gradient in the York River in southeastern Virginia. We measured the erodibility of marshes along a salinity gradient in the York River, a tributary of the Chesapeake Bay (Virginia, USA). We chose five marshes along the York River salinity gradient for this study. Salinity decreases upriver from 18 ppt at the Goodwin Islands to 0 ppt at the Pamunkey Indian Reservation. Within these overall sites, we chose sampling locations along tidal creeks 5-10 m wide, with marsh widths beyond 20 meters and consistent elevations across all study sites. We collected samples from both the tidal channel marsh edge and from the marsh interior. Edge sites were located between the tidal channel and any levee (1 m from edge), while interior sites were located at a measured distance of 10-12 m away from the edge site. All field work was done in July-August 2018, except for the collection of cores for belowground biomass at the Sweet Hall Marsh and Pamunkey Indian Reservation marsh edge sites (September 2018) and elevation profiles of the Pamunkey Indian Reservation (March 2020). Data tables are: 1) shear strength, 2) aboveground biomass, 3) belowground biomass, 4) LOI (loss on ignition), 5) kinematic GPS data along the transects and 6) averages for each station of variables in tables 1, 3 and 4.
Dataset: Bacterioplankton metabolism of phytoplankton lysates across a cyclone-anticyclone eddy dipole impacts the cycling of semi-labile organic matter in the photic zone
<p>This dataset contains both field data and the results of dilution batch-culture bioassay experiments characterizing bacterioplankton usage of ambient and added dissolved organic matter across a cyclone to anticyclone spatial transect in the North Pacific Subtropical Gyre. Field data include total organic carbon, total nitrogen, bacterioplankton cell abundances, ammonia monooxygenase subunit A gene concentrations, and 16S rRNA gene amplicons. Experimental data include time-resolved changes in total organic carbon, nitrogen species, and bacterioplankton cell abundances.</p>
Data for: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)
<p>Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4–11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.</p>
FIG. 5 in Trophic position of some Late Devonian-Carboniferous (Mississippian) conodonts revealed on carbon organic matter isotope signatures: a case study of the East European basin
FIG. 5. — δ13Cdistribution along the facies profile plotted for dominating taxa (latest Famennian-middle Tournaisian; Kamenka River section org
FIG. 3 in Trophic position of some Late Devonian-Carboniferous (Mississippian) conodonts revealed on carbon organic matter isotope signatures: a case study of the East European basin
FIG. 3. — Distribution of δ13Cvalues among conodonts having different morphological types of P1 elements. Scale bar: 0.1 mm. org
FIG. 2 in Trophic position of some Late Devonian-Carboniferous (Mississippian) conodonts revealed on carbon organic matter isotope signatures: a case study of the East European basin
FIG. 2. — Lithology, biostratigraphy, and facies distribution of the Kamenka River section (Pechora Craton). Legend: 1, limestone; 2, clayey limestone; 3, clay; 4, cherty nodules; 5, flat lamination; 6, wavy lamination.
FIG. 1 in Trophic position of some Late Devonian-Carboniferous (Mississippian) conodonts revealed on carbon organic matter isotope signatures: a case study of the East European basin
FIG. 1. — Localization of the sites under consideration: A, Generalized map of Eastern Europe; rectangles mark the localities: 1, Pechora Craton; 2, Voronezh Anteclise (Kamenka Quarry and Russkiy Brod Quarry sections); 3, Ilmen Lake region (Chudovo section, Syas River section, Ilmen Lake borehole 8, Ilmen Lake section); 4, Chimbulat Quarry. B, Map of Pechora Craton; C, Scheme of outcrops' position in the Kozhva River basin.
Data for: Dissolved organic matter (DOM) offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera
<div> <div> <div> <div> <p>Diazotrophs provide a significant reactive nitrogen source in the ocean. Increased warming and stratification may decrease nutrient availability in the future, forcing microbial communities to use dissolved organic matter (DOM). Not depending on reactive nitrogen availability, diazotrophs may be "winners" in a nutrient depleted ocean. However, their ability to exploit DOM may influence this success. We exposed cultures of the widespread <em>Crocosphaera</em> to low (26°C, pH 8.1), moderate (28°C, pH 8.0), and extreme (30°C, pH 7.9) climate change scenarios, under control or DOM-amended conditions. Growth was suboptimal in the low and extreme treatments, and favoured in the moderate treatment. DOM was preferred as a carbon source regardless of the treatment, and promoted N<sub>2</sub> fixation in extreme conditions. This was reflected in the increased expression of photosynthesis genes to obtain energy. DOM provides <em>Crocosphaera</em> with a key ecological advantage, possibly dictating diazotroph-derived nitrogen inputs in the future ocean.</p> </div> </div> </div> </div>
Sorption of Colored vs Noncolored Organic Matter by Tidal Marsh Soils
<p>Supplemental Files for Biogeosciences article:<br>Sorption of Colored vs Noncolored Organic Matter by Tidal Marsh Soils<br>Patrick J Neale, J Patrick Megonigal, Maria Tzortziou, Elizabeth A Canuel, Christina R. Pondell, Hannah K. Morrissette</p> <p>Contents:</p> <p>Plots of measured DOC in incubation solutions vs absorption coefficient at 355 nm (a355), showing linear regression line and equation. Equation slope is the inverse of the specific absorbance of colored dissolved organic carbon (CDOC) and intercept is the background level of non-colored dissolved organic carbon (NCDOC). See table 1 of Neale et al. (2023) for listing of all slopes, intercepts and r2.</p> <p>Labels - KM - Kirkpatrick Marsh (GCREW)<br> JugBay - Jug Bay<br> Task - Taskinas Marsh<br> Wach - Wachapreague Marsh</p> <p>00, 10, 20, 35 - incubation salinities</p> <p>Pre - Pre-incubation - measurements on standard solutions at the start of the incubations<br>Post - Post-incubation - measurements on filtrate after the incubation</p> <p>V2 - Plots for Pre were updated. v1 plots were incorrect for Pre</p>
Chemical, optical, and oxidizing properties of three kinds of water-soluble organic matter in PM2.5 from biomass and coal combustion in rural areas in Northwest China
<p>this data set is about the molecular carbon content, light absorption, infrared spectra, and oxidation activity in PM2.5</p>
Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function
<p>Two datasets supporting the publication, "Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function" in Global Change Biology.</p> <p><strong>DATA S1 </strong>Detailed metadata for sampled glacier-fed streams, including sample date and time, GPS coordinates, elevation, physical streamwater measurements, glacier characteristics, nutrient chemistry, and a column indicating samples used in metagenomics analyses.</p> <p><strong>DATA S2 </strong>Full patch-level dataset of extracellular enzyme activities (nmol h<sup>-1</sup> g<sup>-1</sup> DM sediment) and chlorophyll <em>a </em>(µg chlorophyll <em>a</em> g<sup>-1</sup> DM).</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)
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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.
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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.