Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Data from: Effects of tree functional traits on soil respiration in tropical forest plantations

The study covers four plantations stands of Acacia auriculiformis (A), Eucalyptus urophylla (E), Hopea odorata (H), and X. xylocarpa (X) through a sample plot (50 m x 50 m) in each stand from July 2015 until June 2016. Physical and chemical soil properties were collected at two depths (0-15 cm, 15-30 cm) at the beginning of the study (soil_properties_initial.csv). Additional samplings of topsoil pH, bulk density (BD, g cm-3), organic matter (OM, %), total carbon (TC, %), and nitrogen (TN, %) were conducted monthly (mo_yr) at five random locations (soil_properties_month.csv). Soil respiration (SR) was measured at the beginning of each month (mo_yr) at 12 locations (Point) within each species sample plot (Species) for ten hours (h_time) simultaneously with soil temperature (ST, C), air temperature (AT, C), relative humidity (RH), and soil moisture (SM, %) (soil_respiration.csv). The location of each soil respiration measurement point within the sample plots is provided as well (soil_respiration_location.csv). All trees within each sample plot were mapped (X, Y) and their stem basal area (BA_cm2) and height (H) were measured (stand_inventories.csv).

opencc-zeroMar 2023View details →

Data for: Responses of soil phosphorus cycling and bioavailability to plant invasion in river-lake ecotones

The invasion of exotic plants in the river-lake ecotone has seriously affected the nutrient cycling processes in wetland soil. The South American species Alternanthera philoxeroides (Mart.) Griseb. is rapidly invading the river-lake ecotone in subtropical China, and has become the dominant species in the river-lake ecotone. However, there have been few studies on the effects of A. philoxeroides invasion on soil phosphorus (P) cycling and bioavailability in this ecotone. Herein, we measured the bioavailable P fractions, physicochemical properties and nutrient content in the surface soils of the native plant (Zizania latifolia (Griseb.) Turcz and Nelumbo nucifera Gaertn.) communities and the adjacent invasive A. philoxeroides communities in three river-lake ecotones with different nutrient substrates in the subtropical Dongting Lake basin over a three-year period to reveal the effects of A. philoxeroides invasion on the morphology and concentrations of soil bioavailable P. The principal coordinate analysis results showed that A. philoxeroides invasion significantly altered the bioavailable P concentrations in the soil of native plant communities in the different river-lake ecotones, and this effect was not disturbed by the heterogeneity of the soil matrix. However, the effects of invasion into different native plant communities on the fractions of soil bioavailable P were different. Compared with native Z. latifolia and N. nucifera communities, A. philoxeroides invasion increased the concentration of inorganic P by 39.5% and 3.7%, respectively, and the concentration of organic P decreased by 32.7% and 31.9%, respectively. Meanwhile, the invasion promoted P cycling and accumulation in the river-lake ecotone, which resulted in average decreases in the soil N:P and C:P ratios of 7.9% and 12.5%, respectively. These results highlight the impact of exotic plant invasions on nutrient cycling in wetland ecosystems in the river-lake ecotone, and this process may be detrimental to the late recovery of native plants.

opencc-zeroDec 2022View details →

Data from: Climatic water availability mainly drives context-dependency of tree functional diversity effects on soil organic carbon storage in European forests

The interplay of forest stand and environmental factors shape soil organic C (SOC) storage in forest ecosystems but little is known about their relative impacts in different soil layers. Moreover, how environmental factors modulate the impact of stand factors, particularly species mixing, on SOC storage, is largely unexplored. In this study conducted in 21 forest triplets (two-species mixed stand and respective monocultures nearby) distributed in Europe, we tested the hypothesis that stand factors (functional identity and diversity) have stronger effects on topsoil (FF+0-10 cm) C storage than environmental factors (climatic water availability, clay+silt content, oxalate-extractable Al - Alox) but that the opposite occurs in the subsoil (10-40 cm). We also tested the hypothesis that functional diversity improves SOC storage under high climatic water availability, clay+silt contents, Alox. We characterized functional identity as the proportion of broadleaved species (beech and/or oak), and functional diversity as the product of broadleaved and conifer (pine) proportions. The results show that functional identity was the main driver of topsoil C storage while climatic water availability had the largest control on subsoil C storage. Contrary to expectations, functional diversity decreased topsoil C storage under increasing climatic water availability but the opposite was observed in the subsoil. Functional diversity effects on topsoil C increased with increasing clay+silt content, while its effects on subsoil C was negative at increasing Alox content. This suggests that functional diversity effect on SOC storage along environmental gradients depends on the specific environmental factor and the soil depth under consideration.

opencc-zeroApr 2023View details →

Data from: Long-term grazing intensity by reindeer alters the response of the soil micro-food web to simulated climate change in subarctic tundra

Top-down control by nematodes over soil microorganisms – considered stronger over bacteria than fungi - may dampen microbial responses to global changes in tundra. To test whether large grazers alter the responses of belowground trophic networks to global changes, we employed factorial warming and nitrogen fertilization treatments in adjacent sites with different reindeer grazing intensities for the past 50 years. Lightly grazed tundra is dominated by dwarf shrubs and a more fungal-based microbial community, while in heavily grazed tundra, high reindeer densities during autumn migration have induced shift into graminoids and more bacterial-based microbial community. We analysed the soil micro-food web, i.e., the nematode density, trophic structure, and species composition as well as fungal, bacterial and total phospholipid fatty acids (PLFAs) after four growing seasons of warming and fertilization both before and during reindeer migration. We predicted that bacterivore densities are higher and fungivore densities lower under heavy than light grazing (i.e., nematode populations before migration reflect grazing effects via the base of food web), whereas reindeer migration induces negative impact on nematode densities under heavy grazing (i.e., disturbance by trampling is the driving factor). We further predicted that nematodes negate treatment effects on microbial biomass to a stronger extent in the bacterial-based heavily grazed than the fungal-based lightly grazed tundra. Fungivore densities were higher under light than heavy grazing, but nematodes did not respond to trampling. Warming increased fungivores and the fungal PLFAs irrespective of grazing and timing, but under heavy grazing, increased bacterivores while the bacterial PLFAs remained steady. Fertilization increased carnivores and influenced nematode species composition, diversity and maturity interactively with warming. Our data suggest that large grazers affect tundra soil nematodes via bottom-up effects through microbial community composition and biomass, which in turn may alter the strength of their top-down control soil bacteria under climate warming.

opencc-zeroDec 2022View details →

Data from: Transformation from NHx to NOy deposition aggravated China's forest soil acidification

Elevated nitrogen (N) deposition and changes in reduced or oxidized component contribution greatly affect soil acidification. China has experienced a significant transformation of N deposition components from NHx to NOy over the past 40 years, but the effects of component transformation on soil acidification are poorly understood. Therefore, long-term monitoring data and literature on N deposition, combined with the results of isotope experiments, were used to explore the contributions of different N forms on soil acidification in China's forests. Here, all processes related to NHx and NOy, including the transformation to NH4+ and NO3-, and subsequent N cycling in the soil, were considered. We found that N-induced soil acidification in 80% area of China's forests was dominated by NHx deposition, and the other areas (South China) were dominated by NOy deposition in 2010s. From 1980 to 2019, the average contribution of NHx was higher than that of NOy but the latter contribution continued to increase. Meanwhile, the results showed that soil acidification increased with the decrease of the ratio of NHx to NOy (RNHx/NOy), this is mainly because NOy is more easily leached in the form of NO3- than that of NHx under the influence of different plant preferences and soil retention rates, resulting in a higher net proton production of NOy. Our research has powerful implications for policymaking, provides a theoretical basis for formulating different N reduction policies in different regions, and points out that the synergistic effect of RNHx/NOy changes should be considered to alleviate soil acidification.

opencc-zeroMay 2023View details →

CocciEnv qPCR data and accompanying metadata from soil and settled dust in the San Joaquin Valley

Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides. We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.

opencc-zeroMay 2023View details →

Data for: Coupled anaerobic methane oxidation and metal reduction in soil under elevated CO2

Continued current emissions of carbon dioxide (CO2) and methane (CH4) by human activities will increase global atmospheric CO2 and CH4 concentrations and surface temperature significantly. Fields of paddy rice, the most important form of anthropogenic wetlands, account for about 9% of anthropogenic sources of CH4. Elevated atmospheric CO2 may enhance CH4 production in rice paddies, potentially reinforcing the increase in atmospheric CH4. However, what is not known is whether and how elevated CO2 influences CH4 consumption under anoxic soil conditions in rice paddies, as the net emission of CH4 is a balance of methanogenesis and methanotrophy. In this study, we used a long-term free-air CO2 enrichment experiment to examine the impact of elevated CO2 on the transformation of CH4 in a paddy rice agroecosystem. We demonstrate that elevated CO2 substantially increased anaerobic oxidation of methane (AOM) coupled to manganese and/or iron oxides reduction in the calcareous paddy soil. We further show that elevated CO2 may stimulate the growth and metabolism of Candidatus Methanoperedens nitroreducens, which is actively involved in catalyzing AOM when coupled to metal reduction, mainly through enhancing the availability of soil CH4. These findings suggest that a thorough evaluation of climate-carbon cycle feedbacks may need to consider the coupling of methane and metal cycles in natural and agricultural wetlands under future climate change scenarios.

opencc-zeroMay 2023View details →

Data for: Vegetation and soil ecology of threatened Himalayan Trillium habitats in Kashmir, Himalaya

Understanding the vegetation and soil ecology of natural habitats harbouring threatened species is critical in conservation planning and restoration. The present study investigated the vegetation composition and soil physico-chemical attributes of natural habitats of Trillium govanianum – a threatened Himalayan endemic species. We laid 120 quadrats across eight randomly selected sites where the species was growing in the Kashmir Himalaya. We collected the soil samples from these sites and determined soil physico-chemical attributes using standard methods. Across all the sites, we found a total of 57 plant species with dominance of Rosaceae and Ranunculaceae. The IVI results revealed that Fragaria nubicola, Corydalis diphylla, Galium aparine, and Leucanthemum vulgare, were the dominant species in T. govanianum communities. The density, abundance and IVI of 3-leaf vegetative plants was higher than 1-leaf vegetative and 3-leaf reproductive plants across all the study sites. We found that T. govanianum alone forms 23.5 % positive, 0 negative, 76.4% random co-occurrences with other associated species in its community. Our results reveal that the variations in vegetation composition among the sites was influenced by differences in soil properties. Principal component analysis revealed that several soil parameters such as organic carbon, nitrogen, potassium, and sulphur were concentrated in five sites, namely Dara, Drung, Bangus, Gulmarg, and Doodhpathri, which also showed the highest density, frequency, and abundance of T. govanianum. Overall, our study contributes quantitative information on the vegetation and soil ecology of T. govanianum-assemblages, which in turn can help in developing conservation strategies for this threatened species, and its sustainable management and habitat restoration.

opencc-by-4.0May 2023View details →

Data for: The need to decipher plant drought stress along the soil-plant-atmosphere continuum

Dataset and R-Script accompanying the in OIKOS published manuscript: Schweiger et al. (2023) - The need to decipher plant drought stress along the soil-plant-atmosphere continuum Article DOI: 10.1111/oik.10136   All data is provided within one excel file. Please, pay attention to the provided ReadMe sheet for information on the dataset. The R-Script allows to reproduce the presented results with the provided data.

Data from Comparing organic carbon bound to different minerals in wetland and upland soils

Here is the data and drawing code  for "comparing organic carbon bound to different minerals in wetland and upland soils". Mineral binding of organic carbon (OC) is vital for soil organic carbon (SOC) persistence. However, the relative importance of two main types of soil minerals - metal oxides and silicate clay - in SOC protection remains unclear, hampering our ability to predict and protect this important pool of persistent SOC. Here, using sequential dissolution by dithionite and hydrofluoric acid, we quantified OC bound to metal oxides versus silicate clay in soils from contrasting environments (i.e., wetlands and uplands).  We find that metal oxides override silicate clay in SOC protection in both wetlands and uplands, and OC bound to soil minerals (especially metal oxides) constitutes a higher fraction of SOC in wetlands than uplands, suggesting an underappreciated role of mineral protection in wetland SOC preservation. Furthermore, using lignin phenol analysis in tandem, we find that silicate clay dissolution may release an addition of ~23% lignin phenols from soils, potentially providing a means to assess ‘hidden’ lignin in mineral matrices. These findings highlight the important role of different soil minerals in the protection of SOC and its components in contrasting terrestrial environments, and advance our understanding of predicting and protecting this important pool of persistent SOC.

Data for: How do harvesting methods applied in continuous-cover forestry and rotation forest management impact soil carbon storage and degradability in boreal Scots pine forests?

Forest management affects soil carbon (C) storage through forest composition, microclimate and litter inputs. How two major forest management systems, continuous-cover forestry (CCF) and clear-cut-based rotation forest management (RFM), differ in their impact on soil C in boreal forests is still poorly understood, however. We compared their effects on soil organic carbon (SOC) storage and quality in boreal Scots pine (Pinus sylvestris L.) dominated forests in eastern Finland. We tested the hypotheses that (1) colder microclimates and continuous litter inputs will lead to higher SOC stocks in CCF plots than in clear-cuts and (2) the more labile litter in clear-cuts with varying ground vegetation will enhance SOC decomposition rates. We sampled uncut mature forests, clear-cuts, retention-cuts and gap-cuts, in which we analysed SOC concentrations and calculated the stocks. We measured stand characteristics such as diameter-at-breast height, basal area, dominant tree height, and understorey species coverage of the various treatments and modelled the above- and belowground litter inputs based on these parameters. We used laboratory incubation and sequential fractionation of SOC to assess its degradability under standardized conditions. To estimate the decomposition rate in the various environments we incubated cellulose bags in situ. We assessed the impact of microclimate on SOC decomposition, using data from soil-temperature and soil-moisture field measurements. We quantified the microbial biomass C pool, using chloroform fumigation extraction to gain insight on the impact of forest management practice on soil microbes. The SOC concentrations and SOC stocks did not differ significantly between the treatments, despite the presence of a warmer microclimate and lower litter inputs in the clear-cut plots. However, we found differences in the quality of the SOC. Soils in clear-cut sites showed lower proportions of labile SOC compounds than did the other treatments. As hypothesized, the decomposition rates were elevated in clear-cuts, but were equally as high within the canopy gaps on gap-cut stands. Our work highlights that forest management affects the quality, degradability, long-term accumulation and storage of SOC. We conclude that the accumulation of labile compounds in uncut forests and retention-cuts, combined with the decreased decomposition rates, indicate a higher potential for future C accumulation in the soil than in clear-cuts.

Data from: Can the soil seed bank of Rumex obtusifolius in productive grasslands be explained by management and soil properties?

Rumex obtusifolius is a problematic weed in temperate grasslands worldwide as it decreases yield and nutritional value of forage. Because the species can recruit from the seed bank, we determined the effect of management and soil properties on the soil seed bank of R. obtusifolius in intensively managed, permanent grasslands in Switzerland (CH), Slovenia (SI), and United Kingdom (UK). Following a paired case-control design, soil cores were taken from the topsoil of grassland with a high density of R. obtusifolius plants (cases) and from nearby parcels with very low R. obtusifolius density (controls). Data on grassland management, soil nutrients, pH, soil texture, and density of R. obtusifolius plants were also collected. Seeds in the soil were germinated under optimal conditions in a glasshouse. The number of germinated seeds of R. obtusifolius in case parcels was 866 ±152 m-2 (CH, mean ±SE), 628 ±183 m-2 (SI), and 752 ±183 m-2 (UK), with no significant difference among countries. Densities in individual case parcels ranged from 0 up to approximately 3000 seeds m-2 (each country). Control parcels had significantly fewer seeds, with a mean of 51 ±18, 75 ±52, and 98 ±52 seeds m-2 in CH, SI, and UK, respectively, and a range between 0 and up to 1000 seeds m-2. Across countries, variables explaining variation in the soil seed bank of R. obtusifolius in case parcels were soil pH (negative relation), silt content (negative), land-use intensity (negative), and aboveground R. obtusifolius plant density (positive). Because a large soil seed bank can sustain grassland infestation with R. obtusifolius, management strategies to control the species should target the reduction in the density of mature plants, prevention of the species' seed production and dispersal, as well as the regulation of the soil pH to a range optimal for forage production.

Data for: Soil organic carbon contents of collected soil samples from China's black soil region

The long-term use of cropland and cropland reclamation from natural ecosystems led to soil degradation. This study investigated the effect of the long-term use of cropland and cropland reclamation from natural ecosystems on soil organic carbon (SOC) content and density over the past 35 years. Altogether, 2140 topsoil samples (0–20 cm) were collected across Northeast China. Landsat images were acquired from 1985 to 2020 through Google Earth Engine, and the reflectance of each soil sample was extracted from the Landsat image that its time was consistent with sampling. The hybrid model that included two individual SOC prediction models for two clustering regions was built for accurate estimation after k-means clustering. The probability hybrid model, a combination between the hybrid model and classification probabilities of pixels, was introduced to enhance the accuracy of SOC mapping. Cropland reclamation results were extracted from the land cover time series dataset at a 5-year interval. Our study indicated that: (1) Long-term use of cropland led to a 3.07 g kg-1 and 6.71 Mg C ha-1 decrease in SOC content and density, respectively, and the decrease of SOC stock was 0.32 Pg over the past 35 years; (2) Nearly 64% of cropland had a negative change in terms of SOC content from 1985 to 2020; (3) Cropland reclamation track changed from high to low SOC content, and almost no cropland was reclaimed on the 'Black soils' after 2005; (4) Cropland reclamation from wetlands resulted in the highest decrease, and reclamation period of years 31–35 decreased when SOC density and SOC stock were 16.05 Mg C ha-1 and 0.005 Pg, respectively, while reclamation period of years 26–30 from forest witnessed SOC density and stock decreases of 8.33 Mg C ha-1 and 0.01 Pg, respectively. Our research results provide a reference for SOC change in the black soil region of Northeast China and can attract more attention to the area of the protection of 'Black soils' and natural ecosystems.

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

Dryland soil restoration meta-analysis data

This dataset was used to conduct a meta-analysis on soil restoration in global drylands. It includes data collected from published literature on experiments of soil-based restoration in dryland environments. Predictor variables included in this dataset are site aridity and percent soil sand, type of restoration treatment used, whether seeding or revegetating was done, and time since restoration. Response variables include the effect of soil restoration on aggregate stability, bulk density, volumetric water content, soil organic carbon, soil nitrogen, mycorrhizal colonization, and basal respiration. The calculated effect size on each of these variables is represented as the log response ratio.

Supplementary files for "Data-driven estimation of nitric oxide emissions from global soils based on dominant vegetation covers"

In-situ observations collected from publications, data-driven model codes, DNDC simulation files, and the supporting data for all figures of this study are uploaded. In-situ observations included 1,356 observations of soil nitric oxide (NO) emissions from 192 sites, including 1,032 for cropland soils from 70 sites, 114 for grassland soils from 36 sites, and 208 for forest soils from 86 sites. Data-driven models provided three machine learning methods, including random forest (RF), generalized boosted regression model (GBM), and radial basis function (RBF). The DNDC simulation files included simulation files of 51 selected sites.

Data for the manuscript 'Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools'

Data for manuscript The data provided in the present document corresponds to the manuscript: Engedal, T., Magid, J., Hansen, V., Rasmussen, J., Sørensen, H., Jensen, L. S. (2023): Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools. Global Change Biology, in press.   Short abstract In order to investigate the fate of cover crop-derived belowground C as rhizodeposition and, over time, into the distinct soil organic carbon pools of particulate- and mineral-associated organic carbon (POC and MAOC), a column trial was esblished with 0.25 m top soil and 0.25 m sub soil. Four cover crops were grown for 3 months and 14CO2-labelled twice a week. Four out of eight replicate columns were destructively harvested to quantify root C and the carbon lost via rhizodeposition in absolute (qClvR) and relative terms (%ClvR) in bulk soil and rhizosphere soil from top- and subsoil (t1). The other four replicate columns were harvested for undisturbed incubation for one year, before final sampling (t2). Bulk soil from both sampling times were subject to a simple fractionation protocol by size, where particles larger from 50 microns were assigned to POC and smaller than 50 microns assigned to MAOC after dispersion in NaHMP. All fractions were dried, weighed and analyzed for 14C activity as disintegrations per minute (DPM).   Further details Column ID 1-16 refer to columns sampled at t1, while column ID 17-32 refer to columns sampled at t2. Underlying assumptions and detailed descriptions of the different fractions are to be found in the manuscript.

Supplementary Data for "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates"

Supplementary data includes original sample names and locations, raw geochemical and granulometric data, and calculated geochemical data represented as figures for the manuscript titled "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates". All datasets are in the same excel file on separate tabs. All data were processed according to established procedures cited in the manuscript text. All software used is open access: ImageJ, adobe illustrator, and Microsoft excel.

opencc-by-4.0Jul 2023View details →

Data for "Multiple Equilibria and Soil Moisture-Precipitation Feedbacks in Idealized Convection-Permitting Simulations with an Open Hydrological Cycle"

Code, simulation input files, and simulation output data supporting “Multiple Equilibria and Soil Moisture-Precipitation Feedbacks in Idealized Convection-Permitting Simulations with an Open Hydrological Cycle”, under review at JAMES. Enclosed README files provide detailed descriptions of the archive contents.