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177 results for “soil dynamics”
Data from:Modelling the spatiotemporal dynamics of soil nitrogen in croplands of Northeast China from 1980 to 2023 using multisource data and machine learning
<p>This dataset include the spatiotemporal distribution and uncertainty of cropland soil total nitrogen content at 0-30, 30-60, 60-100 cm depths in Northeast China from 1980 to 2023. The long-time series of TN were estimated by using an space-time automatic machine learning. The detail information on the products were given below:</p> <p>Period: 1980-2023</p> <p>Spatial resolution: 0.004166667 degree (~500 m)</p> <p>Temporal resolution: 1 year</p> <p>CRS: geographic latitude/longitude (EPSG:4326 - WGS 84 – Geographic)</p> <p>Data format: GeoTIFF</p>
Water table depth dynamics and surface soil moisture content from three Scottish peatland areas (2021-2022)
<p>This compilation of datasets from three monitoring sites on peatland in Scotland includes water table depth dynamics and surface soil moisture content and covers the period 2021-2022. Further data will be added on an annual basis. This is version 2 of the dataset, which corrects a small number of data QC issues (see README).</p>
3D dataset of root soil bacteria dynamics obtained using large field of view light sheet microscope
<p>A tailor made dual-illumination light-sheet system acquired photons scattered from the plant whilst fluorescence emissions were simultaneously captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm<sup>3</sup> in size with as good as 5 µm resolution at a rate of up to one scan every 30 minutes. The dataset shows the dynamics of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time.</p> <p> </p> <p> </p>
Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests
<p><span><span><span><span><span><span><span><span><span><span><span>Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical datasets are required to account for taxon- and context-dependency but relevant research in understudied areas is often compromised by the taxonomic impediment<span><span>. </span></span>We here employed haplotype-level community DNA metabarcoding, enabled by stringent filtering of Amplicon Sequence Variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, Operational Taxonomic Unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented <i>Quercus alnifolia</i> habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterising metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Decipher soil organic carbon dynamics and driving forces across China using machine learning
<p><span><span>The dynamics of soil organic carbon (SOC) play a critical role in modulating global warming. However, the long-term spatiotemporal changes of SOC at large scale and the impacts of driving forces remain unclear. In this study, we investigated the dynamics of SOC in different soil layers across China through the 1980s to 2010s using a machine learning approach and quantified the impacts of the key factors based on factorial simulation experiments. Our results showed that the latest (2000-2014) SOC stock in the first meter soil (SOC<sub>100</sub>) was 80.68 ± 3.49 Pg C, of which 42.6% was stored in the top 20 cm, sequestrating carbon with a rate of 30.80 </span><span>± 12.37</span><span> g C m<sup>-2</sup> yr<sup>-1</sup> since the 1980s. Our experiments focusing on the recent two periods (2000s and 2010s) revealed that climate change exerted the largest relative contributions to SOC dynamics in both layers and warming or drying can result in SOC loss. However, the influence of climate change weakened with soil depth, while the opposite for vegetation growth. </span><span>Relationships between SOC and forest canopy height further confirmed this strengthened impact of vegetation with soil depth, and highlighted the carbon sink function of deep soil in mature forest. Moreover, our estimates suggested that SOC dynamics in 71% of topsoil were controlled by climate change and its coupled influence with environmental variation (CE). Meanwhile CE and the combined influence of climate change and vegetation growth dominated the SOC dynamics in 82.05% of the first meter soil. </span><span>Additionally, the national cropland topsoil organic carbon increased with a rate of 23.6 </span><span>± 7.6 </span><span>g C m<sup>-2</sup> yr<sup>-1</sup> since the 1980s, and the widely applied nitrogenous fertilizer was a key stimulus. </span><span>Overall, our study extended the knowledge about the dynamics of SOC and deepened our understanding about the impacts of the primary factors.</span></span></p>
Plant litter chemistry controls coarse-textured soil carbon dynamics
<p>1. As soils store more carbon (C) than the Earth's atmosphere and terrestrial biomass together, the balance between soil C uptake in the form of soil organic matter and release as CO2 upon its decomposition is a critical determinant in the global C cycle regulating our planet's climate. Although plant litter is the predominant source of C fueling both soil C build-up and losses, the issue of how litter chemistry influences this balance remains unresolved.</p> <p>2. As a contribution to solving that issue, we traced the fate of C during near-complete decomposition of 13C-labelled leaf and root litters from 12 plant species in a coarse-textured soil. We separated the soil organic carbon (SOC) into mineral-associated organic matter (MAOM) and particulate organic matter (POM) pools, and investigated how 14 litter chemical traits affected novel SOC formation and native SOC mineralization (i.e., the priming effect) in these soil fractions.</p> <p>3. We observed an overall net increase in SOC due to the addition of litter, which was stronger for root than for leaf litters. The presumed stable MAOM-C pool underwent both substantial stabilization and mineralization, whereas the presumably less stable POM-C pool showed substantial stabilization and reduced mineralization. Overall, the initial increase in soil C mineralization was fully counterbalanced by a later decrease in native soil C mineralization. POM-C formation as well as MAOM-C formation and mineralization were positively related to the initial litter lignin concentration and negatively to that of the nitrogen leachates, whereas the opposite was observed for POM-C mineralization.</p> <p>4. Synthesis. Our results highlight the importance of litter chemical traits for SOC formation, and stabilization, destabilization, and mineralization. In our coarse-textured soil, the amount of MAOM-C did not change despite large C fluxes through this pool. The litter chemical traits that drove these processes differed from those frequently reported for fine-textured soils far from mineral-associated C saturation. To account for these discrepancies, we propose an integrative perspective in which litter quality and soil texture interactively control soil C fluxes by modulating several SOC stabilization and destabilization mechanisms. Irrespective, our results open new critical perspectives for managing soil C pools globally.</p>
Water table dynamics and surface soil moisture from an experimental peatland restoration area (Forsinard, Scotland, UK), 2017-2022/2023
<p>This dataset is from an experiment aimed to understand the changes in water level and soil moisture dynamics after rewetting of formerly afforested blanket bog areas. Specifically, it was aiming to test whether the water table and soil moisture dynamics in these areas return to those of control areas that had never been drained or afforested. The data span the period of summer 2017- summer 2022/2023, with gaps in individual time series marked with -9999 entries.</p>
Seasonal precipitation distribution determines ecosystem CO₂ and H₂O exchange by regulating spring soil water-salt dynamics in a brackish wetland
<p>The intensification of the global hydrological cycle is anticipated to increase the variability of precipitation patterns. Brackish wetlands respond to changes in precipitation patterns by regulating the absorption and release of CO<sub>2</sub> and H<sub>2</sub>O to maintain the stability of ecosystem functions. However, there is limited understanding of how the inter-seasonal precipitation distribution affects ecosystem CO<sub>2</sub> and H<sub>2</sub>O exchange compared to annual precipitation totals. Here, we conducted four consecutive years of field experiments in a brackish wetland, manipulating the proportion of precipitation across different seasons while maintaining a constant annual precipitation total. We utilized five inter-seasonal precipitation distribution proportions (+73%, +56%, control (CK), -56%, and -73%) to examine the effects of seasonal precipitation distribution (SPD) on ecosystem CO<sub>2</sub> and H<sub>2</sub>O exchange. Our findings revealed that the ecosystem CO<sub>2</sub> and H<sub>2</sub>O fluxes showed a trend of decreasing with the decrease of spring precipitation distribution. Among them, the annual net ecosystem CO<sub>2 </sub>exchange (NEE), evapotranspiration (ET), carbon use efficiency (CUE), and water use efficiency (WUE) were shown to be more sensitive to decrease in spring precipitation distribution and increase in summer and autumn precipitation distribution. This negative asymmetric response pattern suggests that annual ecosystem CO<sub>2</sub> and H<sub>2</sub>O exchange is primarily governed by seasonal precipitation variability, with spring soil water-salt dynamics identified as the key driver. Therefore, this association can be explained by the fact that drought of the early growth stage exacerbates soil salinization and inhibits vegetation colonization and growth, thereby greatly impairing the annual CO<sub>2</sub>-H<sub>2</sub>O exchange capacity of brackish wetlands. Our results emphasized that the spring's extreme precipitation-induced soil water-salt conditions will greatly influence CO<sub>2</sub> and H<sub>2</sub>O exchange in brackish wetlands in the future. These findings are crucial for improving predictions of the carbon sequestration and water-holding capacity of brackish wetlands.</p>
Fiber-optic seismic sensing of vadose zone soil moisture dynamics data sets
<p>CC_daily.h5: Daily cross-correlation functions for common-offset DAS channels.</p> <p>RCC_dv_v_full.csv: Summary of all the measured dv/v from the ballistic surface waves in daily cross-correlation functions.</p>
Dataset from: Transport and water age dynamics in soils: a comparative study of spatially-integrated and spatially-explicit models
<p>This dataset contains high-resolution vegetated lysimeter experimental dataset carried out in EPFL, Lausanne, Switzerland in March-August 2016. The lysimeter is 100 cm long with a diameter of 120 cm. During this experiment, a simultaneous spike injection of five different solutes (2,5-DFBA, 2-TFMBA, 3,4-DFBA, 2,6-DFBA, 3-TFMBA) took place on the 3rd of March 2016 at 14:00 in an hour. The solutes' mass recovery at the bottom of lysimeter was observed for these solutes.</p> <p>This dataset contains three files which are described in the following:</p> <ul> <li>"hydrologic_data.dat" contains the hourly fluxes (precipitation, irrigation, evapotranspiration measured from load cells, and the water draining at the bottom of lysimeter ) in mm/hr between the 19th of Feb-the 1st of Sep 2016.</li> <li>"tracer_data.dat" contains the tracer concentration observed at the bottom of lysimeter in mg/L. These samples are collected at variable frequencies with an approximate average of 1.5 samples per day.</li> <li>"additional_data.dat" informs you on dry mass and soil volume in the lysimeter, vegetation type, and volume of injection per solute.</li> </ul> <p> </p>
Succession of bacteria and archaea within the soil micro-food web shifts soil respiration dynamics
<p>Supplementary Table 5. Overview over abundance changes, taxonomic affiliation, and response type of dominant ASVs under the different treatment combinations. M: maize litter , A: A. buetschlii, + and – signs indicate presence and absence, respectively.</p>
Soil N dynamics in mixed and larch forests in northeastern China
<p>We developed a multiple-indicator approach to evaluate differences in soil N availability across sites and between larch monoculture and mixed stands paired at three sites (Daxinganling, Maoershan, and Qingyuan) in northeastern China. The selected indicators were foliar %N, soil C/N, soil inorganic N, foliar δ<sup>15</sup>N, and δ<sup>15</sup>N of bulk soil, ammonium, and nitrate in the soil profiles.</p>
Supplementary data to: Soil Moisture to Runoff (SM2R) A data-driven model for runoff estimation across poorly gauged Asian water towers based on soil moisture dynamics
<p>This data archive includes simulated monthly runoff anomaly using the Soil Moisture to Runoff model during 1981‒2020 over the representative drainage basin in each water tower. Please see Readme for more data information. For calculation details please see the publication.</p>
Dataset of "Stabilized explicit 𝑢−𝑝𝑤 solution in soil dynamic problems near the undrained-incompressible limit"
<p>Dataset of "Stabilized explicit 𝑢−𝑝𝑤 solution in soil dynamic problems near the undrained-incompressible limit"</p>
Effects of increasing phosphorus rate on microbial dynamics and soil available P under a Lixisol soil in Zimbabwe
<p> Soil phosphorus (P) deficiency is a major challenge to the attainment of food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources in cropping. A greenhouse study was conducted to evaluate the influence of increasing inorganic P fertilizer rates (16, 26 and 36 kg P ha<sup>-1</sup>) on microbial dynamics, soil P pools and maize P uptake. using soils collected from a long-term (16 seasons) maize-monocropped field experiment where organic nutrient resources of different qualty namely <em>Crotalaria juncea</em> (high quality), <em>Calliandra Calothyrus</em> (medium quality), cattle manure ( variable quality), maize stover and <em>Pinus patula</em> sawdust ( both low quality) were applied at 4 t C ha<sup>-1</sup> with 16 kg P ha<sup>-1</sup> at the start of every season, a 3 x 6 factorial experiment was established by adding single super phosphate (8.5% P) as a basal fertilizer. Maize was used as the test crop and the experiment was conducted at Soil Productivity Research Laboratory in Zimbabwe. Using Pokovskays agar medium and serial dilution methods, phsophate-solubilizing microbes were monitored forthnightly from day 1 to 57 after maize planting. Ninetten (19) fungal and forty-two (42) bacterial colonies were identified over the study period, Fungi dominated bacteria on dayone, wth <em>Aspergillus niger</em> showing 20-98% abundance that depended on organic resources quality. Overall, a microbial explosion bulge characterized sucession on day 29 which coincided with a significant (P< 0.05) increase in diversity (H') and soil available P. Increasing P rate to 26 kg ha<sup>-1 </sup>amplified the explosion bulge under medium-high quality resources while under the control the bulge emerged earlier on day 15. <em>Mucor</em> and <em>Bacillus</em> had peak abundance on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P< 0.01) effect on microbial P. Bacteria were more rsponsive to added P than fungi. Increasing P to 36 kg P ha<sup>-1</sup> also stimulated an earlier bulge under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as nitrogen,did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilzier P rates to increase microbial diversity, soil available P and maize growth on sandy soils (Lixisols). Our results suggest the need to recondiser existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha<sup>-1</sup>, for maize production on sandy soils as well develop new fertilizer formulations to intensify crop production in Zimbabwe.</p> <p> </p>
Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM) simulations focused on Eight Mile Lake, Alaska and Imnavait Creek, Alaska [2000-2015]
<p>This set of files store model simulations using the biosphere model Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM), developed to simulate biophysical and biogeochemical interactions between the soil, vegetation and atmosphere. To improve predictions of net carbon releases from thawing permafrost, we tested the sensitivity of a suite of model parameters. We analyzed the responses of ecosystem carbon balances to permafrost thaw by running site-level simulations at two long-term tundra ecological monitoring sites in Alaska: Eight Mile Lake (EML) and Imnavait Creek watershed (IMN). These sites are characterized by similar tussock tundra vegetation but differing soil drainage conditions and climate, IMN consists of well-drained soils, and EML has historically well-drained soils, however permafrost thaw has altered drainage conditions to wetter soils. Simulations were conducted at a 1km resolution, over a 1,000 km2 area (10x10 km square) centered on two long term ecological research sites in Alaska: Eight Mile Lake located in Interior Alaska (63.8900° N, 149.2535° W), and Imnavait creek watershed located on the northern foothills of the Brooks range (68°37′ N, 149°18′ W).</p> <p>Historical simulations are spanning the 2000 to 2015, and forced using climate simulations from the Climate Research Unit, time series 4.0. We ran 1,000 site level simulations for each model variable. The variables that are produced are gross primary productivity (GPP, in gC.m-2.m-1), net ecosystem exchange (NEE, gC.m-2.m-1), ecosystem respiration (RECO, gC/m2/m-1), active layer thickness (ALT, m), soil temperature (TLAYER,°C) at 5, 10, 40 cm depths, soil moisture (LWCLAYER, m-3/m-3) at 5, 10 cm depths, and snow depth (SNOWDEPTH, m), evapotransipiration(EET, mm/m2/time), potential evapotransipiration (PET, mm/m2/time), leaf area index (LAI, m2/m2), organic layer thickness (OLT, m). The data are stored as compiled csv files, with time as the index, and each model sample output stored in the columns. In addition, there is a postprocessing python script to demonstrate the step and workflow used to generate the individual csv files post processed from the raw model outputs stored as netcdfs.</p>
Supplementary material/Organic carbon dynamics in clay soils: impact of management practices on microorganism structure and abundance under semi-arid conditions
<p>Proper management of soil organic matter in arid and semi-arid regions improves organic carbon storage in the soil, helps in compact soil degradation, and mitigates climate change impacts, and preserves ecosystem functionality and sustainability food security. This study aims to provide a better insight into the biogeochemical processes that drive the organic carbon dynamics of saline clay soil in a semi-arid climate. The study is not intended to be exhaustive but contributes to analyzing the relationship between bacterial microflora, physicochemical properties, and organic carbon dynamics as a function of different soil management modes. The monitoring was carried out on three different plots located at the National Institute of Agronomic Research of Algeria. A physicochemical characterization of the soils was performed. A metagenomic study was also conducted to identify bacterial biodiversity using PCR-amplified DNA sequencing. The study results show that the control plot has the highest average organic carbon stock value at 47 Mg ha<sup>-1</sup>. This was followed by the amended plot and the conventional plot, respectively, with 43 Mg ha<sup>-1</sup> and 38 Mg ha<sup>-1</sup>. In the context of this study, organic carbon dynamics would appear to depend on the interaction of several biotic and abiotic factors. Soil management methods would impact the density and diversity of bacterial microflora. This, in turn, affects the soil's physicochemical properties and, more specifically, organic carbon dynamics and storage.</p>
Temporal dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest
<p class="MsoNormal">Fire is a major evolutionary and ecological driver that shapes biodiversity in forests. While above-ground community responses to fire have been well-documented, those below-ground are much less understood. However, below-ground communities, including fungi, play key roles in forests and facilitate the recovery of other organisms after fire. Here, we used internal transcribed spacer (ITS) meta-barcoding data from forests with three different times since fire [short (3 years), medium (13–19 years) and long (>26 years)] to characterize the temporal responses of soil fungal communities across functional groups, ectomycorrhizal exploration strategies and inter-guild associations. Our findings indicate that fire effects on fungal communities are strongest in the short to medium term, with clear distinctions between communities in forests with a short time (3 years) since fire, a medium time (13–19 years) and a long time (>26 years) since fire. Ectomycorrhizal fungi were disproportionately impacted by fire relative to saprotrophs, but the direction of the response varied depending on morphological structures and exploration strategies. For instance, short-distance ectomycorrhizal fungi increased with recent fire, while medium-distance (fringe) ectomycorrhizal fungi decreased. Further, we detected strong, negative inter-guild associations between ectomycorrhizal and saprotrophic fungi but only at medium and long times since fire. Given the functional significance of fungi, the temporal changes in fungal composition, inter-guild associations and functional groups after fire demonstrated in our study may have functional implications that require adaptive management to curtail.</p>
A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil Dataset
<p>This dataset contains the reference solutions used for training the two neural networks in 1-, 2- and 3-D cases for the article:"A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil" by Zeyuan Song and Zheyu Jiang, submitted to the journal Water Resources Research. </p> <p>This dataset which describes the relationship between the pressure head and number of particles used to train two MLPs in D-GRW based solvers consists of three files, i.e., 1-, 2- and 3-D case study. There are two parts, original reference solutions and reference solutions, corresponding to the original solutions generated by coarse mesh solvers and solutions after data augmentation process, respectively.The dataset is generated by GRW based solvers and simulation results (e.g., Celia's finite difference method). Original reference solutions admit GRW proportionality assumption. We initialize the number of particles by multiplying the initial condition and 1E10. </p>
Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics
<p>Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross-kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial-fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterized soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighboring evergreen broadleaf forest. Carbon (C) mineralization combined with five C-degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial-fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial-fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+−N), nitrate nitrogen (NO3−−N), and available phosphorus (AP). Structural equation modeling indicated that the potential cross-kingdom competition, based on the ratio of negative bacterial-fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C-degrading enzymatic activities and C mineralization.</p> <p>Synthesis and applications: Our results highlight the regulatory role of the negative bacterial-fungal association in enhancing the correlation between bacterial diversity and C mineralization. This suggests that promoting short-term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial-fungal negative associations to mediate carbon mineralization in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.