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102 results for “soil conditioning”
data sets for the article Short‑term impact of crop diversifcation on soil carbon fuxes and balance in rainfed and irrigated woody cropping systems under semiarid Mediterranean conditions
<p>Diversifcation practices such as intercropping in woody cropping systems have recently been proposed as a promising management strategy for addressing problems related to soil degradation, climate change mitigation and food security. In this study, we assess the impact of several diversifcation practices in diferent management regimes on the main carbon fuxes regulating the soil carbon balance under semiarid Mediterranean conditions.</p>
Pseudomonas veronii Tn-seq analysis of soil and liquid growth conditions
<p>Readme file content</p> <p>The files stored here contain the following material as supplementary and source data for the manuscript in submission</p> <p>Fitness-conditional genes for soil adaptation in the bioaugmentation agent Pseudomonas veronii 1YdBTEX2</p> <p>Marian Morales, Vladimir Sentchilo, Nicolas Carraro, Senka Causevic, Dominique Vuarambon & Jan R. van der Meer</p> <p>Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland</p> <p><br> %%%%%%%<br> Folder Tn-seq<br> %%%%%%</p> <p>This folder has the scripts, procedures, raw and intermediate data of the Pseudomonas veronii tn-seq libraries Lib1 and Lib2, at time 0 and incubated in liquid, sand or silt microcosms for up to 51 generations of growth.</p> <p>Subfolders are organized to the steps in the analysis, from the initial experimental design, to the sequence mapping, read cleaning, normalization procedures, essentiality analysis, paired (liq-soil) analysis, gene group plots and the COG-KEGG category analysis.</p> <p>Scripts are text-readable for MATLAB, vs 2021b; or BASH-UNIX slurm command line tools. Data files are either .mat (MATLAB readable) or .xlsx (for the major summary steps).</p> <p>Individual procedures and steps are described in Word documents, which then point to scripts in the script folder, output and the data formats.</p> <p>%%%%%%%<br> Community diversity data<br> %%%%%%</p> <p>This folder has the raw fastq- files of the sample reads of the T1 incubated sand or silt-Tn5 library replicates. Four replicates in total, two sequencing data sets which were combined.</p> <p>Folder also has the meta data as to the sample descriptions, and the OTU-taxa output file from Qiime2 analysis.</p> <p> </p>
Impact of Schistosomiasis, Soil-Transmitted Helminthiasis and Anaemia on preschool and school-age children's health condition: post treatment predictive mapping in Benin Republic.
<p>This dataset provides information about the epidemiology of schistosomiasis, soil transmitted helminthiasis and anemia alongside malnutrition among preschool and school age children in Ouake and Bembereke districts of donga and borgou departments in Benin republic.</p>
Data from: Pyrophilic plants respond to post-fire soil conditions in a frequently burned longleaf pine savanna
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Data from: Soils from cold and snowy temperate deciduous forests release more nitrogen and phosphorus after soil freeze–thaw cycles than soils from warmer, snow-poor conditions
<p>Effects of global warming are most pronounced in winter. A reduction in snow cover due to warmer atmospheric temperature in formerly cold ecosystems, however, could counteract an increase in soil temperature by reduction of insulation. Thus, soil freeze-thaw cycles (FTC) might increase in frequency and magnitude with warming, potentially leading to a disturbance of the soil biota and release of nutrients.</p> <p>Here, we assessed how soil freeze-thaw magnitude and frequency affect short-term release of nutrients in temperate deciduous forest soils by conducting a three factorial gradient experiment with ex-situ soil samples in climate chambers. The fully-crossed experiment included soils from forests dominated by <i>Fagus sylvatica</i> (European beech) that originate from different winter climate (mean coldest month temperature range ΔT > 4 K), a range of FTC magnitudes from no (T = 4.0 °C) to strong (T = -11.3 °C) soil frost, and a range of FTC frequencies (f = 0–7). We hypothesized that higher FTC magnitude and frequency, respectively, will increase the release of nutrients. Furthermore, soils from cold climates with historically stable winter soil temperatures due to deep snow cover will be more responsive to FTC than soils from warmer, more fluctuating winter soil climates.</p> <p>FTC magnitude and, to a lesser extent, also FTC frequency resulted in increased nitrate, ammonium, and phosphate release almost exclusively in soils from cold, snow-rich sites. The hierarchical regression analyses of our three-factorial gradient experiment revealed that the effects of climatic origin (mean minimum winter temperature) followed a sigmoidal curve for all studied nutrients and was modulated either by FTC magnitude (phosphate) or by FTC magnitude and frequency (nitrate, ammonium) in complex two- and, for all studied nutrients, in threefold interactions of the environmental drivers. Compared to initial concentrations, soluble nutrients were predicted to increase to 250 % for nitrate (up to 16 µg NO<sub>3</sub>-N kg<sup>-1</sup>DM), to 110 % for ammonium (up to 60 µg NH<sub>4</sub>-N kg<sup>-1</sup>DM), and to 400 % for phosphate (2.2 µg PO<sub>4</sub>-P kg<sup>-1</sup>DM) at the coldest site for strongest magnitude and highest frequency. Soils from warmer sites showed little nutrient release and were largely unaffected by the FTC treatments except for above-average nitrate release at the warmest sites in response to extremely cold FTC magnitude.</p> <p>We suggest that currently warmer forest soils have historically already passed the point of high responsiveness to winter climate change, displaying some form of adaptation either in the soil biotic composition or in labile nutrient sources. Our data suggests that previously cold sites, which will lose their protective snow cover during climate change, are most vulnerable to increasing FTC frequency and magnitude, resulting in strong shifts in nitrogen and phosphorus release. In nutrient poor European beech forests of the studied Pleistocene lowlands, nutrients released over winter may be leached out, inducing reduced plant growth rates in the following growing season.</p> <p>Here, we provide the raw data of a three-factorial regression experiment and the R-Code used in the hierarchical regression analysis of this raw data in Kreyling et al.: Soils from cold and snowy temperate deciduous forests release more nitrogen and phosphorus after soil freeze-thaw cycles than soils from warmer, snow-poor conditions.</p>
δ15N of nitric oxide produced under aerobic or anaerobic conditions from seven soils and their associated N isotope fractionations
<p>Measuring the nitrogen isotope compositions (δ<sup>15</sup>N) of nitric oxide (NO) from different sources helps to quantify the relative contributions of atmospheric NO<sub>x</sub>. Soil is one of the most important sources of atmospheric NO<sub>x</sub>, but only limited measurements on the δ<sup>15</sup>N of soil emitted NO exist, hampering our ability to partition sources to air pollution. Here we conducted soil incubations to measure the δ<sup>15</sup>N-NO under defined aerobic or anaerobic conditions, favoring either nitrification or denitrification. Soils were collected from seven sites spanning three ecosystems in northern China (two agricultural, two forest, and three grassland sites). We found that the δ<sup>15</sup>N-NO and their associated N isotope fractionations were significant different between anaerobic and aerobic conditions in seven soils. Under aerobic condition, the δ<sup>15</sup>N-NO ranged from -62‰ to -50‰ (averaged -56 ± 4‰), being significantly more negative (by 23‰) than those under anaerobic condition (-45‰ to -23‰, averaged -33 ± 7‰). The apparent N isotope fractionation for NO production under aerobic condition (<sup>15</sup><em>ε</em><sub>aerobic</sub> = 61 ± 3‰) was significantly higher (by 26‰) than under anaerobic condition (<sup>15</sup><em>ε</em><sub>anaerobic</sub> = 35 ± 6‰), with a small variability among ecosystem types. Our study demonstrates that the δ<sup>15</sup>N-NO from different soils are very different from fuel combustions (mainly from 0 to +20‰), supporting that measuring <sup>15</sup>N is a useful tool to partition the contributions of soil NO to atmospheric NO<sub>x</sub>. Our results also imply δ<sup>15</sup>N-NO produced by nitrification and denitrification distinctly different, as these two processes are dominant processes producing NO under aerobic and anaerobic conditions, respectively.</p>
Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions
<p>There is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance.<strong> </strong>Two ecotypes of <em>Imperata cylindrica</em> produce F1 hybrids. The early flowering type (E-type) in wet habitats has larger internal gas spaces (aerenchyma) than the common type (C-type) in dry habitats. This study evaluated the relationships between the habitat utilisation, aerenchyma plasticity, and growth of <em>I. cylindrica</em> accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions.</p> <p>Aerenchyma formation was examined in the leaf midribs, rhizomes, and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in the leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes. Their vegetative growth performance was also quantified.</p> <p>In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation of aerenchyma formation in the rhizomes than their parental ecotypes. In the common garden experiments, the F1 hybrids showed high plasticity of aerenchyma formation in the rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively.</p> <p>The results demonstrate that the F1 hybrids of <em>I. cylindrica</em> exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.</p>
Dataset for: Phosphorus mobilization from intact soil monoliths flooded under simulated summer versus spring snowmelt with intermittent freeze-thaw conditions
<p>Enhanced phosphorus (P) release from flooded, anaerobic soils have been extensively studied under summer temperatures, but not under cold temperatures with intermittent freeze-thaw events. We investigated the temperature and freeze/ thaw effects during flooding on the release of P to floodwater from soil monoliths (15-cm depth) collected from eight agricultural fields in Manitoba. Soil monoliths were flooded with reverse osmosis water and incubated for 56 d under simulated summer flooding (SSF, 22±1 ℃), or snowmelt flooding with intermittent freeze thaw (IFT, 4±1 ℃ with intermittent freezing) in triplicates. Redox potential (Eh), pore water and floodwater dissolved reactive P (DRP) concentrations, pH and concentrations of Ca, Mg, Fe and Mn were determined weekly. In seven soils, Eh decreased rapidly with days after flooding (DAF) under SSF to values < 200 mV, but not under IFT. Pore water and floodwater DRP concentrations significantly increased with DAF in all soils under SSF, and in seven soils under IFT. While DRP concentrations were consistently greater under SSF than IFT in four soils, other soils had similar concentrations at certain DAFs. Significant relationships between ion concentrations and redox status , that fitted both IFT and SSF data in most soils, suggests that similar redox-driven mechanisms are responsible for the P release; however, less P is released under IFT than SSF, since soils were not severely reduced under IFT. Substantial P release in a few soils under IFT, appeared to be unrelated to redox status, suggesting other P release mechanisms that are not redox driven.</p>
Initial soil conditions outweigh management in a cool-season dairy farm's carbon sequestration potential
<p>Data used in the manuscript "Initial soil conditions outweigh management in a cool-season dairy farm’s carbon sequestration potential" (<a href="http://dx.doi.org/10.1016/j.scitotenv.2021.152195">10.1016/j.scitotenv.2021.152195</a>)</p> <p> </p> <p>Soil samples, gas fluxes, and biomass samples measured at the Organic Dairy Research Farm at the University of New Hampshire. Soil samples were in two sets, a spatially explicit set from 0 - 15 cm depth, and less spatially explicit samples taken at 10 cm increments. Soils were sampled for soil carbon and nitrogen content. Gas fluxes were measured using the chamber method with carbon dioxide and nitrous oxide gases measured on gas chromatographs with the change over time used to measure the gas flux rates. Forage biomass was measured by collecting biomass in 1 m2 plots. Please see the manuscript for more details on sampling.</p>
Light condition experienced by parent plants influences the response of offspring to light via both parental effects and soil legacy effects
<p>1. Environmental conditions experienced by parent plants can influence offspring performance through parental effects induced by DNA methylation. The offspring can also be influenced by environmental conditions experienced by their parents via soil legacy effects due to plant-mediated changes in the composition of soil microbes. These two effects are likely to act simultaneously, but empirical evidence for combined effects is limited.</p> <p>2. We conducted a two-phase experiment with five genotypes of a clonal plant <em>Hydrocotyle vulgaris</em>. In the first phase, we grew parent plants of each genotype under two light conditions (ambient vs. shade) and two DNA demethylation treatments (treated with water vs. 5-azacytidine). We then collected soils and clonal offspring for each genotype from each of these four treatments and measured soil (a)biotic properties. In the second phase, we grew the offspring from each of the four treatments in the four different soils, under the two light conditions.</p> <p>3. When grown under ambient light condition and in soil from ambient parents, offspring produced by ambient parents grew larger than offspring produced by shaded parents when the parents were treated with water. This difference was smaller when the parents were treated with 5-azacytidine, and disappeared when the offspring were grown in soil from shaded parents. The growth difference was also observed when the offspring were grown under shaded condition and in soil from shaded parents. However, this difference was greater when the parents were treated with 5-azacytidine, and disappeared when the offspring were grown in soil from ambient parents. Moreover, offspring growth was associated with fungal composition and total phosphorus of the soil in which the parents had grown.</p> <p>4. Our results show, for the first time, that light condition experienced by parents can influence offspring responses to light through both parental effects and soil legacies. The parental effects were mediated by changes in DNA methylation and the soil legacies were due to plant-mediated changes in a combination of soil biotic and abiotic properties. These impacts may eventually influence the ecological and evolutionary trajectories of clonal plant populations.</p>
Hydrothermal conditions determine soil potential net N mineralization rates in arid and semi-arid grasslands
<p>Soil net nitrogen (N) mineralization is a key biogeochemical process influencing plant available N and net primary productivity (NPP) in terrestrial ecosystems. However, the spatial variations and controlling factors of soil net N mineralization (RPNM) in arid and semi-arid grasslands are less studied and unclear. In this study, we investigated the soil RPNM by performing a laboratory incubation experiment. Soil samples were collected from 30 sites in three east-west transects on the Inner Mongolia Plateau (MP), Loess Plateau (LP), and Tibetan Plateau (TP) along a 3,200 km arid and semi-arid grassland gradient, with each transect containing three different grassland types (meadow steppe, typical steppe, and desert steppe, respectively). Results showed that the average RPNM values ranged from -0.37 to 1.29 mg N kg–1 d–1, with a significantly lower RPNM found in the desert steppe (0.08 ± 0.01 mg N kg–1 d–1) compared with those in the meadow steppe (0.30 ± 0.03 mg N kg–1 d–1) and in the typical steppe (0.33 ± 0.03 mg N kg–1 d–1) in the MP and LP transects (p < 0.05). This difference could be explained by variations in climatic and soil factors, such as hydrothermal index (HT), the soil pH, soil organic matter (SOM) and precipitation. However, no significant differences in RPNM were found among different grassland types in the TP transect, possibly due to the similarly low microbial activity, as indicated by the MBC values. Across all three grassland transects, HT, SOM, and microbial variables were the major factors controlling RPNM, which together explained 20.7% of the variation in RPNM. Further SEM analysis indicated HT was an integral predictor of RPNM, directly or indirectly via SOM, under different conditions of precipitation and temperature. Our findings provide field evidence and parameters for biogeochemical cycling to better predict future N transformation processes under changing precipitation and temperature regimes across a wide range of arid and semi-arid grassland ecosystems.</p>
Soil properties and crop yield in fruit orchards under Mediterranean conditions in terms of intercropping, tillage and fertilizer type
<p>This data set contains a data-mining performed to assess the impact of intercropping, tillage and fertilizer type on soil and crop yield in fruit orchards under Mediterranean conditions by a further meta-analysis of the data. </p> <p>These data correspond to the open-access article "The impact of intercropping, tillage and fertilizer type on soil and crop yield in fruit orchards under Mediterranean conditions: A meta-analysis of field studies" published in Agricultural Systems. (<a href="https://doi.org/10.1016/j.agsy.2019.102736">https://doi.org/10.1016/j.agsy.2019.102736</a>), funded by he European Commission Horizon 2020 project Diverfarming [grant agreement 728003]. Raúl Zornoza acknowledges the financial support from the Spanish Ministry of Science, Innovation and Universities through the “Ramón y Cajal” Program [RYC-2015-18758].. </p> <p> </p>
Effect of Environmental Weathering on Biodegradation of Biodegradable Plastic Mulch Films under Ambient Soil and Composting Conditions
<p>Plastic mulch films contribute to better crop production. Concerns for lack of sustainable disposal methods for conventional polyethylene (PE) mulch led to development of biodegradable plastic mulches (BDMs) that can be soil-incorporated or composted after use. Environmental weathering of BDMs during crop growth reduces their mechanical strength and alters the molecular structure of their polymeric components. However, the impact of weathering on BDMs' biodegradability is not fully understood. The biodegradability of agriculturally weathered and unweathered BDMs in soil and compost was compared using standardized laboratory tests (ASTM D5988 and D5338) using four BDMs (experimental polylactic acid and polyhydroxyalkanoate-based film [PLA/PHA] and three commercially available polybutyrate [PBAT]-based BDMs). In soil, biodegradation of weathered PLA/PHA was greater than its unweathered counterpart. For PBAT-based BDMs, the extent of biodegradation varied. A decrease of the weight-averaged molecular weight (M<sub>w</sub>) of PBAT and PLA and thermostability of PLA, PHA, PBAT, and starch components was observed during biodegradation in the soil. The proportion of the minor components PHA and starch decreased during biodegradation, indicating preferential utilization of PHA over PLA and starch over PBAT by microbes. Bacterial abundance was significantly higher than fungal abundance in soil and was more prominent in soil adjacent to weathered than unweathered BDM treatments. Under composting conditions, unweathered PBAT-enriched mulches yielded higher CO<sub>2</sub> evolution than their weathered counterpart. Together, these results suggest that environmental weathering enhances biodegradation of BDMs and mulch's polymeric constituents also influence the microbial degradation, more so for bacterial than fungal communities.</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: Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards
<p>Soil tillage or herbicide applications are commonly us<span>ed in agriculture for weed control. These measures may also represent a disturbance for soil microbial communities and their functions. However, the generality of response patterns of microbial communities and functions to disturbance have rarely been studied at large geographical scales. We investigated how a soil disturbance gradient (low, intermediate, high), realized by either tillage or herbicide application, affects diversity and composition of soil bacterial and fungal communities as well as soil functions in vineyards across five European countries. Microbial alpha-diversity metrics responded to soil disturbance sporadically, but inconsistently across countries. Increasing soil disturbance changed soil microbial community composition at the European level. However, the effects of soil disturbance on the variation of microbial communities were smaller compared to the effects of location and soil covariates. Microbial respiration was consistently impaired by soil disturbance, while effects on decomposition of organic substrates were inconsistent and showed positive and negative responses depending on the respective country. </span><span>Therefore, we conclude that it is difficult to extrapolate results from one locality to others because microbial communities and environmental conditions vary strongly over larger geographical scales.</span><span> </span></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>
Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition
<p><span>The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1,550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil, and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.</span></p>
δ15N of nitric oxide produced under aerobic or anaerobic conditions from seven soils and their associated N isotope fractionations
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Effect of Environmental Weathering on Biodegradation of Biodegradable Plastic Mulch Films under Ambient Soil and Composting Conditions
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Data from: Volatile fatty acid concentration, soil pH and soil texture during anaerobic soil conditions affect germination of Athelia (Sclerotium) rolfsii sclerotia
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