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388 results for “organic matter”
Isotopic data of kelps and particulate organic matter (POM) from relevant studies and estimated contributions of kelps to local consumers
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Mathematical chromatography deciphers the molecular fingerprints of dissolved organic matter
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Data from: Living, dead, and absent trees - How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline?
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Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter
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Data from: Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments
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Data from: Chemodiversity of dissolved organic matter in the Amazon Basin
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Data from: Can above-ground ecosystem services compensate for reduced fertilizer input and soil organic matter in annual crops?
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Reactive oxygen species alter chemical composition and adsorptive fractionation of soil-derived organic matter
This is the data archive for the corresponding publication with the same title (doi: 10.1016/j.geoderma.2020.114805). Reactive oxygen species (ROS), formed during redox fluctuations in iron-rich soils, have been known to stimulate lignin degradation, although not much is known about how they alter soil organic matter (SOM) composition and interaction with mineral surfaces. We conducted a laboratory experiment to see how ROS altered SOM composition and adsorptive fractionation onto Fe-mineral surfaces. We reacted water extracts of SOM with ·OH, produced by the Fenton reaction, and then conducted a sorption experiment of the extracts with goethite to analyze the amount and quality of SOM adsorbed. The Fenton reaction preferentially consumed low-O, mostly aromatic molecules, and new high-O molecules were detected post-Fenton, nearly half of which were carbohydrate-like. Although the amount of C adsorbed did not change after oxidation, the post-Fenton adsorbed molecules were more oxidized. Pre-Fenton adsorption was dominated by aromatic molecules (90%), but post-Fenton, the adsorbed molecules were 75% aromatic and 25% carbohydrate-like. We show that the ·OH radical oxidized SOM and shifted patterns of adsorption to a more oxidized pool. Because adsorption to minerals is thought to stabilize SOM, our results suggest that ROS may alter the availability and stabilization patterns of SOM
Soil organic matter responses to nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Soil organic matter, total nitrogen and pH:Microbial composition and function across an old-field chronosequence
As mediators of biogeochemical cycles, understanding the ecological forces structuring soil microbial communities is of ecosystem-level significance. Due to gradual shifts in plant species composition and litter addition through time, succession can be used as a model to understand how plant communities shape microbial community composition and function in soil. Numerous studies have investigated microbial biomass and diversity along successional gradients, yet few have quantified changes in microbial communities. Using the established successional dynamics experiment at Cedar Creek, principal investigators Lauren C. Cline and Donald R. Zak investigated the influence of plant community composition in structuring microbial community composition and function. Specifically, their research addressed the following questions: 1. Do shifts in saprotrophic microbial communities correlate to changes in plant community composition through successional time? 2. What is the relative influence of soil properties and plant community characteristics in determining microbial community dynamics? Cline and Zak sampled soils from 8 established abandoned agricultural fields (e054), as well as three adjacent forests representing potential late-successional ecosystems, to investigate microbial dynamics using three complementary approaches: targeted sequencing of fungal and bacterial communities, quantitative PCR, and shotgun metagenomics. Further, the characterization of soil properties across the chronosequence will enable us to disentangle the impact of abiotic factors in structuring microbial communities.
Chemical characteristics of the assigned elemental formulas from the FT-ICR MS data of aerosol-derived organic matter simultaneously collected in Beijing, China and Gwangju, Korea in January 2018
<p>In this study, ambient fine particles (PM2.5) were simultaneously collected in two urban cities in China and Korea (Beijing and Gwangju, respectively) in January 2018. Comprehensive compositional analysis of the organic matter (OM) samples, extracted using dichloromethane, was performed on a 15 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an atmospheric pressure photoionization (APPI) interface in positive ion mode. Analysis of the nonpolar and semipolar OM using APPI FT-ICR MS revealed that CHO and CHON accounted for more than 90% of the total intensity of the OM peaks. Higher proportions of CHON compounds were observed during PM2.5 events (i.e., days with abnormally high PM2.5 levels) at both sites than on regular or non-event days. </p>
Atmospheric evolutions and sources of chromophoric organic matters in fine aerosols over Xi'an, Northwest China
<p>From December 31, 2018 to January 21, 2019, semi-continuous atmospheric observations were carried out using the PILS-EEM-TOC and organic carbon (OC) / element carbon (EC) analyzer system, collected the hourly timeseries data and EEM components data. The timeseries data contains organic carbon (OC) /element carbon (EC) / water soluble organic carbon (WSOC), absorbance (Abs), air pollutants, wind speed, relative humidity, solar radiation, source appointment etc. data.</p>
Data-base of dissolved organic matter composition and reactivity in Lake Victoria, the World's largest tropical lake
<p>Data-base of Chlorophyll-a, dissolved organic carbon (DOC) concentration and dissolved organic matter (DOM) composition (stable carbon isotope signatures, absorption and fluorescence properties) obtained from samples collected in Lake Victoria, a large lake in East Africa. Samples were collected in 2018-2019 along a bathymetric gradient (bays to open waters), during three contrasting seasons: long rainy, short rainy and dry, which corresponded to distinctly water column mixing regimes, respectively, stratified, semi-stratified and mixed regimes. Eight DOM components from parallel factor analysis (PARAFAC) were identified based on three-dimensional excitation–emission matrices (EEMs), which were aggregated into three main groups of components (C1, C5 and C7 as microbial humic-like; C2, C3 and C4 as terrestrial humic-like; C6 and C8 as protein-like).</p> <p>Please note that the dataset is attached to the following paper :</p> <p>Deirmendjian, L., Lambert, T., Morana, C. <em>et al.</em> Dissolved organic matter composition and reactivity in Lake Victoria, the world’s largest tropical lake. <em>Biogeochemistry</em> <strong>150, </strong>61–83 (2020). https://doi.org/10.1007/s10533-020-00687-2</p>
Thermodynamics of soil organic matter decomposition in semi-natural oak (Quercus) woodland in southwest Ireland
<p>The evolution of soil terrestrial ecosystems is a subject with difficulties to define their maturity and evolutionary state. In the last century, thermodynamics was one of the options considered by ecologists for that goal. Difficulties in quantifying the thermodynamic parameters needed by the evolutionary theories caused that this subject has been practically locked since the end of the last century. Application of thermodynamics needs reactions and one of the main reactions in soil ecosystems are those involved in the decomposition of the soil organic matter. This paper aims to provide an initial step to study those reactions from a thermodynamic perspective. With that goal in mind, thermal analysis and isothermal calorespirometric measurements were made on soil samples collected at three depths in semi-natural oak woodlands at three different sites in southwest Ireland. It is assumed that the organic matter evolves from a less to a higher mature state as soil depth increases. The maturity state could be chemically defined by the redox state. The proposed methods yield the enthalpy change, Gibbs energy change, and entropy change for the microbial catabolism and combustion reactions of the soil organic matter. The degree of reduction was calculated by the enthalpy changes. Results show the soil organic matter becomes more reduced from the soil organic surface to mineral soils. The top layer is characterized by high carbon content, organic materials with low energy content per Cmole, and fast biodegradation rates. Mineral soils are characterized by low carbon content, organic materials with high energy content per Cmole, and slow biodegradation rates. Values obtained for the entropy change were sensitive to these differences among the different soil layers. These results contribute to unlock the thermodynamics of the soil reactions and to develop the bioenergetics of soil ecosystems.</p>
Dataset for: Short-term temperature history affects mineralization of fresh litter and extant soil organic matter, irrespective of agricultural management
<p>Dataset for the article:</p> <p>Mason-Jones, K., Vrehen, P, Koper, K., Wang, J., van der Putten, W.H., Veen, G.F. 2020. Short-term temperature history affects mineralization of fresh litter and extant soil organic matter, irrespective of agricultural management. Soil Biology and Biochemistry, 150, 107985.</p> <p>Article DOI: 10.1016/j.soilbio.2020.107985</p>
Dataset of manuscript "A stoichiometric approach to estimate sources of mineral-associated soil organic matter"
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Appendix dataset for "Distribution, storage, and factors influencing particulate and mineral-associated organic matter in paddy soils"
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Hydrodynamic-driven changes in the source and composition of sedimentary organic matter via grain size distribution in shallow lakes
<p>Sediment organic matter (SOM) differs in composition and function in different size fractions in relation to material and energy flows. The hydrodynamic effects on a lake's autochthonous (terrestrial plants) and allochthonous (microalgae, aquatic plants and bacteria) inputs and transformation, and the components of SOM are still far from clear. To elucidate the SOM composition as driven by the hydrodynamic conditions associated with sedimentary grain size, we performed an ecosystem-level investigation in the shallow lake Izunuma, Japan, measuring source-specific fatty acids and the current velocity. High organic matter concentrations occurred in the finer fractions. Bacteria were dominant in the <32 µm fraction, microalgae were mainly present in the <32 and 63-125 µm fractions, aquatic plants appeared to be evenly distributed in all size fractions and terrestrial plants mainly comprised the >125 µm fraction. Although the linear correlation between current velocity and sedimentary total organic carbon (TOC) was not statistically significant, the relationship between current velocity frequency and sedimentary TOC was significant. The highest Pearson coefficient occurred at a current velocity of 6 cm/s in sand. The relationship between allochthonous inputs and current velocity frequency was similar to that of TOC. Autochthonous organics had the greatest coefficient with two peaks at 4.5 and 8 cm/s. The threshold for sand resuspension varied with organic sources, while this phenomenon was absent in cohesive mud. Hydrodynamic forces affected the grain size of sediments and drove the gradient distribution of the SOM sources, which should be considered when managing freshwater lakes in light of future climate change.</p>
Figure 1a from: Hambly A, Stedmon C (2018) FluoRAS Sensor - Online organic matter for optimising recirculating aquaculture systems. Research Ideas and Outcomes 4: e23957. https://doi.org/10.3897/rio.4.e23957
Figure 1a An example of a fluorescence EEM "fingerprint" of drinking water. Multivariate modelling of EEM datasets allows the most important areas of the EEM to be identified, and used for simplified online fluorescence sensors. - EMM viewed as a contour plot
Figure 1b from: Hambly A, Stedmon C (2018) FluoRAS Sensor - Online organic matter for optimising recirculating aquaculture systems. Research Ideas and Outcomes 4: e23957. https://doi.org/10.3897/rio.4.e23957
Figure 1b An example of a fluorescence EEM "fingerprint" of drinking water. Multivariate modelling of EEM datasets allows the most important areas of the EEM to be identified, and used for simplified online fluorescence sensors. - EMM viewed as a waterfall plot
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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.