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2,078 results for “soil data”
Raw data for the submitted manuscript: The Effect of Clay Type on the Toxicity of Carbendazim and Imidacloprid to the Earthworm Eisenia andrei in Artificial Soils
<p>Raw data obtained from toxicity tests with the earthworm <em>Eisenia </em><em>andrei </em>exposed for 56 days to carbendazim and imidacloprid in artificial soils created with kaolin and bentonite clay. Tests were performed following OECD guideline 222. The file includes data on earthworm starting and ending weights, survival, and reproduction.</p>
Data-driven Soil Moisture Sensing with mmWave Radar
<p>This is a mmWave radar soil moisture dataset, which includes two different environments, specifically two conference rooms with different layouts. In Environment 1, soil with 20 different moisture levels was collected, ranging from 6.20% to 43.82%, with an interval of approximately 2%.In the bin file names, the first number after "data" represents the soil moisture level, labeled as 1 to 20, with moisture levels of 6.20%, 8.30%, 10.80%, 12.60%, 14.44%, 16.14%, 18.96%, 19.70%, 23.34%, 25.24%, 26.24%, 28.90%, 31.10%, 32.46%, 33.80%, 36.44%, 38.20%, 40.56%, 42.68%, and 43.82%, respectively.In the bin file names, the second number after "data" represents the height of the radar development board above the soil surface, measured in centimeters, specifically 16 cm, 20 cm, and 24 cm. The data was collected using the IWR1843 radar board, with 1 transmitting antenna and 4 receiving antennas. Each bin file contains 128 radar frames, with each frame consisting of 32 chirps, and each chirp containing 384 sampling points.</p> <p>In Environment 2, soil with 20 different moisture levels was collected, ranging from10.0% to 48.0%, with an interval of 2%.In the bin file names, the first number after "data" represents the soil moisture level, labeled as 1 to 20, with moisture levels of 10.0%, 12.0%, 14.0%, 16.0%, 18.0%, 20.0%, 22.0%, 24.0%, 26.0%, 28.0%, 30.0%, 32.0%, 34.0%, 36.0%, 38.0%, 40.0%, 42.0%, 44.0%, 46.0%, and 48.0%, respectively.In the bin file name, the second number after 'data' indicates the environment: 0 represents a static environment, and 1 represents a dynamic environment, where there is human movement.In the bin file name, 'train' and 'test' after 'data' represent the training and testing data, which were collected in two separate sessions.The data was collected using the IWR1843 radar board, which has 3 transmitting antennas and 4 receiving antennas. Each bin file contains 64 radar frames, with each frame consisting of 96 chirps, and each chirp containing 384 sampling points.</p>
Data-driven Soil Moisture Sensing with mmWave Radar In Environment 2
<p>This is a millimeter-wave radar soil moisture dataset, which includes soil samples with 20 different moisture levels, ranging from 10.0% to 48.0% with approximately 2% intervals.In the bin file names, the first number after "data" represents the soil moisture level, labeled as 1 to 20, with moisture levels of 10.0%, 12.0%, 14.0%, 16.0%, 18.0%, 20.0%, 22.0%, 24.0%, 26.0%, 28.0%, 30.0%, 32.0%, 34.0%, 36.0%, 38.0%, 40.0%, 42.0%, 44.0%, 46.0%, and 48.0%, respectively.In the bin file name, the second number after 'data' indicates the environment: 0 represents a static environment, and 1 represents a dynamic environment, where there is human movement.In the bin file name, 'train' and 'test' after 'data' represent the training and testing data, which were collected in two separate sessions.The data was collected using the IWR1843 radar board, which has 3 transmitting antennas and 4 receiving antennas. Each bin file contains 64 radar frames, with each frame consisting of 96 chirps, and each chirp containing 384 sampling points.</p>
Data and R code used in Hennecke et al. "Plant species richness and the root economics space drive soil fungal communities"
<p>To investigate how plant diversity and root traits relate to soil fungal communities, in 2021 we collected trait data from plots in the Jena Experiment (https://the-jena-experiment.de; funded by the DFG FOR 5000) and characterized fungal communities by sequencing, respiration and lipid fatty acid quantification. </p>
Processed data for Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria
<p>Processed/source data for the manuscript Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling <em>Listeria</em>.</p>
Observed soil water retention and soil hydraulic conductivity data and fits to those data by RIAfitter and KRIAfitter
<p>Weber soils SWRC.7z: zipped file with the Windows folders that hold all input and output data related to fitting the RIA parameterization (de Rooij, 2022, 2024a) to soil water retention data of 13 soils.</p> <p>Weber soils UHCC.7z: the zipped folder structure with fits of several models (de Rooij, 2024b, c) for the unsaturated hydraulic conductivity for the same 13 soils as the other file. The fitting code (KRIAfitter) used the fitted parameters of the other file plus soil hydraulic conductivity data to produce the fits.</p> <p>Both files contain Excel files that process the input and output of all fits.</p> <p>The soils are taken from Weber et al. (2019). The support of T.K.D. Weber in providing the data is gratefully acknowledged,</p> <p>N.B. The output format may differ somewhat from that reported in the User Manual of de Rooij (2024c) because the fits were used to improve details of the code and the way information is provided in the output files. These variations do not affect the parameter fitting process.</p> <p>References</p> <p>de Rooij, G. H.: Technical note: A sigmoidal soil water retention curve without asymptote that is robust when dry-range data are unreliable, Hydrol. Earth Syst. Sci., 26, 5849–5858, doi: 10.5194/hess-26-5849-2022, 2022.</p> <p>de Rooij, G.: Fitting the parameters of the RIA parameterization of the soil water retention curve (2.0), Zenodo [code], doi: 10.5281/zenodo.6491978, 2024a.</p> <p><br>de Rooij, G. H.: Averaging or adding domain conductivities to calculate the unsaturated soil hydraulic conductivity, Vadose Zone J., e20329, doi: 10.1002/vzj2.20329, 2024b.</p> <p><br>de Rooij, G.: Fitting the junction model and other models for the unsaturated hydraulic conductivity curve: KRIAfitter, Zenodo [code], doi: 10.5281/zenodo.14047942, 2024c.</p> <p><br>Weber, T. K. D., Durner, W., Streck, T., and Diamantopoulos, E.: A modular framework for modeling unsaturated soil hydraulic properties over the full moisture range, Water Resour. Res., 55, 4994-5011, doi: 10.1029/2018WR024584, 2019.</p> <p> </p>
Data from: Non-linear responses of soil nematode community composition to increasing aridity
Aim: Increasing aridity under global change is predicted to have a profound impact on the structure and functioning of terrestrial ecosystems, yet we have poor understanding of how belowground communities respond. In order to understand the longer-term responses of different trophic levels in the soil food web to increasing aridity, we investigated the abundance, richness and community similarity of the soil nematode community along a 3200-km aridity gradient. Location: A transect across semi-arid and arid grasslands in Northern China, where the aridity ranges from 0.43 to 0.97. Time period: July and August 2012. Major taxa studied: Soil-borne Nematoda. Methods: We used Generalized Additive (Mixed) Models to analyze the abundance, richness and community similarity patterns of soil nematodes. We used Structural Equation Modelling (SEM) to disentangle the direct and indirect environmental drivers (aridity, soil and plant variables) of the nematode community. Results: The abundance, richness and similarity of nematode communities declined non-linearly with increasing aridity. The most pronounced decline in nematode richness and community similarity occurred under arid conditions (aridity > 0.80). However, the shape of response to aridity differed among nematode feeding groups. Under arid conditions, the abundance and richness of bacterial feeders were less sensitive to changes in aridity than fungal feeders. The SEM analysis revealed that nematode community responses to aridity were not mediated via changes in plant and soil variables, but rather were directly affected by aridity. Main conclusions: Our results show that in mesic grasslands increasing aridity primarily caused decline in nematode abundance, whereas increasing aridity in xeric grasslands led to loss of nematode diversity. The non-linear responses of nematodes to aridity could result in non-linear shifts in ecosystem functioning as well, because soil nematodes operate at various trophic levels in the soil food web, thereby influencing the performance of plants, soil biodiversity and biogeochemical cycling.
Data from: Desiccation and rehydration of mosses greatly increases resource fluxes that alter soil carbon and nitrogen cycling
1. Mosses often have positive effects on soil carbon and nitrogen cycling, but we know little about how environmentally determined cycles of desiccation and rehydration in mosses influence these processes. 2. In this context, we compared carbon and nitrogen in throughfall after precipitation passed through eight moss species that were either hydrated continuously or desiccated and rehydrated. Also, the throughfall of four moss species was added to soil and used to determine the net effect of carbon and nitrogen added in moss throughfall on soil CO2 and N2O efflux. 3. Depending on the species, desiccated-rehydrated (rehydrated) mosses lost 2-31 times more carbon in throughfall than mosses that were continuously hydrated (hydrated). Hydrated mosses lost little to no detectable nitrogen; whereas most rehydrated mosses lost some nitrogen in throughfall. Throughfall from both hydrated and rehydrated mosses generated higher CO2 and N2O efflux than water treated soils, but rehydrated moss throughfall promoted larger N2O efflux than hydrated moss throughfall. Throughfall from hydrated mosses caused net negative changes in soil carbon and had very little effect on soil nitrogen, whereas throughfall from rehydrated mosses generated positive changes in soil carbon and nitrogen. 4. Synthesis. Our results indicate that resources lost from desiccated mosses during rehydration influence soil carbon and nitrogen transformations and may be important drivers of carbon and nitrogen cycling and storage in ecosystems.
Data from: Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land
Stable isotope composition of plants and soil animals in abandoned arable land <p>Dataset provides raw data on stable isotope composition of C and N of plants and soil meso- and macrofauna. Dominating animal groups were collected in arable fallow systems 3 and 14-16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a non-legume herb (Taraxacum officinale) and a grass (Bromus sterilis). More information can be found in the associated paper.</p>
Data from: Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes
<p class="AbstractSummary">Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analyzed polymorphic loci from the perennial crop <i>Medicago sativa </i>(alfalfa or lucerne) and the annual legume model species <i>M. truncatula </i>to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial <i>Medicago</i> species.</p> <p class="AbstractSummary">We identified a set of candidate genes of environmental adaptation associated with environmental gradients along the distribution of the two <i>Medicago</i> species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses.</p> <p>Hundreds of GEA candidate genes were species-specific, of these, 13.4% (<i>M. sativa</i>) and 24% (<i>M. truncatula</i>) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in Gene Ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis.</p> <p class="AbstractSummary">Our results point to the existence of a molecular basis of adaptation to abiotic stress in <i>Medicago</i> determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.</p>
FIGURE 5 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 5: Rhagidial organs I in dorsal (A, D) and lateral (B, E) views and rhagidial organs II in latero-dorsal view (C, F) of Brevipalpia minima (A-C) and Hammenia macrostella (D-F). Insert of famulus in C. Scale bar = 100 µm.
FIGURE 1 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 1: Dorsal aspect of different soil Rhagidiidae. A – Brevipalpia minima Zacharda, 1980; B – Coccorhagidia clavifrons (Canestrini, 1886); C – Hammenia macrostella Zacharda, 1980; D – Parallelorhagidia evansi (Strandtmann and Prasse, 1976); E – Crassocheles virgo Zacharda, 1980 (from Zacharda 1980).
FIGURE 4 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 4: Brevipalpia minima Zacharda, 1980: A – dorsum, B – venter, C – trichobothrium, D – palp, E – tarsus I in lateral aspect, F – chelicera, G – subcapitulum, H – rhagidial organ I (from Zacharda 1980).
FIGURE 7 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 7: Legs III and IV in antiaxial (A, B) and paraxial (C, D) views of Brevipalpia minima (A-B) and Hammenia macrostella (C-D). Insert showing the microsculpture in B and D. Scale bar = 100 µm.
FIGURE 6 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 6: Hammenia macrostella Zacharda, 1980: A – dorsum, B – venter, C – trichobothrium, D – palp, E – chelicera, F – subcapitulum, G – tarsus I in lateral aspect, H – rhagidial organ I (from Zacharda 1980).
Data for: Plant diversity effects on herbivory are related to soil biodiversity and plant chemistry
<p><span>Insect herbivory is a key process in ecosystem functioning. While theory predicts that plant diversity modulates herbivory, the mechanistic links remain unclear. We postulated that the plant metabolome mechanistically links plant diversity and herbivory.</span></p> <p>In late summer and in spring, we assessed individual plant aboveground herbivory rates and metabolomes of seven plant species in experimental plant communities varying in plant species diversity and resource acquisition strategies. In the same communities, we also measured plant individual biomass as well as soil microbial and nematode community composition.</p> <p>Herbivory rates decreased with increasing plant species richness. Path modelling revealed that plant species richness and community resource acquisition strategy correlated with soil community composition. In particular, changes in nematode community composition were related to plant metabolome composition and thereby herbivory rates.</p> <p><span>These results suggest that soil community composition plays an important role in reducing herbivory rates with increasing plant diversity by changing plant metabolomes.</span></p>
Data from: Volatile fatty acid concentration, soil pH and soil texture during anaerobic soil conditions affect germination of Athelia (Sclerotium) rolfsii sclerotia
<p>Anaerobic growth chamber trials were conducted to evaluate effects of VFA and VFA concentration, and interactions with soil pH and soil texture, on <i>A. rolfsii</i> sclerotia germination. In the first objective, sclerotia were exposed to 4, 8, or 16 mmol/kg soil of acetic or <i>n</i>-butyric acids in sandy soil; soil pH was buffered to 5, 6, or 7. In the second objective, sclerotia in sandy or sandy loam soil were exposed to 4 or 16 mmol VFA/kg soil at soil pH 5 or 6. VFAs are probable important factors in <i>A. rolfsii </i>suppression<i> </i>due to ASD treatment in many soil environments, and activity is dependent on VFA concentration, soil solution pH, and soil texture.</p>
Data for manuscript "Prominent Role of Sulfate Reduction in Robust Sulfur Retention in Subtropical Soil"
<p>Data for manuscript "Prominent Role of Sulfate Reduction in Robust Sulfur Retention in Subtropical Soil" submitted to Geophysical Research Letters</p>
Data for: Soil microbes alter competition between native and invasive plants
<p>Invasive plants can alter soil microbial communities and generate positive plant-soil feedbacks that facilitate their performance, but the magnitude and direction of feedbacks may change with novel conditions under climate change. We assessed how potential soil legacy effects of plant invasion and simulated drought influenced plant performance and competition in the longleaf pine ecosystem.</p> <p>We collected soil from a four-year factorial invasion (cogongrass, <i>Imperata cylindrica</i>) by drought (simulated with rainout shelters) field experiment and used it as live or sterilized soil inoculum in a greenhouse experiment that included two native foundation species, longleaf pine (<i>Pinus palustris</i>) and wiregrass (<i>Aristida stricta</i>), and cogongrass, grown individually or in competition.</p> <p>There was no evidence of biotic soil legacy effects of invasion or drought for any plant species, but microbes played a significant role in competition. When plants were grown alone, the invader had 12% greater biomass in live soil than sterile soil but both native species had 25% less biomass in live soil. When grown in competition, these effects were reversed for cogongrass (37% smaller in live soil) and pine (17% larger in live soil). In competition, the three species grown in sterile soil produced similar amounts of biomass, whereas live soil created a competitive hierarchy where pine was more competitive than wiregrass and cogongrass.</p> <p>Synthesis: These results emphasize the importance of soil biota in native plant restoration because, although the invader was highly successful when grown alone, plant-microbe interactions influenced the outcome of competition between native and invasive species by promoting native longleaf pine. There was little evidence that invasive cogongrass inhibited native plants via biotic soil legacies, instead, results suggested that plant-soil interactions can be highly resilient to global change such that the biotic legacy of invasion and drought may not promote or inhibit invasion.</p>
Data in support to the manuscript: Testing a novel sensor design to jointly measure cosmic-ray neutrons, muons and gamma rays for non-invasive soil moisture estimation by Gianessi et al. (2024)
<p>The files contain data presented and discussed in the manuscript: Testing a novel sensor design to jointly measure cosmic-ray neutrons, muons and gamma rays for non-invasive soil moisture estimation by Gianessi et al. (2024).</p> <div> <div>Gianessi, Stefano, Matteo Polo, Luca Stevanato, Marcello Lunardon, Till Francke, Sascha E. Oswald, Hami Said Ahmed, et al. “Testing a Novel Sensor Design to Jointly Measure Cosmic-Ray Neutrons, Muons and Gamma Rays for Non-Invasive Soil Moisture Estimation.” <em>Geoscientific Instrumentation, Methods and Data Systems</em> 13, no. 1 (January 16, 2024): 9–25. <a href="https://doi.org/10.5194/gi-13-9-2024">https://doi.org/10.5194/gi-13-9-2024</a>.</div> </div> <p> </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.
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DANDI Archive for NWB datasets
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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.