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223 results for “soil functions”
Figure 3 in Does logging affect soil biodiversity and its functions? A review
Figure 3. Worldwide distribution of logging studies included in this review. The bar chart represents the number of articles in each country (■).
Figure 1 in Does logging affect soil biodiversity and its functions? A review
Figure 1. General overview of this synthesis review. Silvicultural practices, which can affect soil biodiversity and ecosystem functioning driven by soil organisms, can be categorized into two main aspects: (a) alterations in tree strata and understory vegetation, as silvicultural practices often lead to the simplification of tree strata and bring about changes in the composition of understory vegetation. It is important to note that logging equipment also involves the utilization of temporary roads, trails, and log collection points as integral components of this practice, and (b) technology and infrastructure: the incorporation of technology and the development of infrastructure play a crucial role in shaping the effects of silvicultural practices on soil organisms and the overall functionality of ecosystems.
Figure 1 in Building a global database of soil microbial biomass and function: a call for collaboration
Figure 1. Sampling locations and underrepresented environmental conditions in the dataset as of 19 November, 2019. For each pixel, we measured the percentage of environmental conditions (e.g. climate, soil characteristics, topographic information, vegetation indices) captured by the current dataset. Hot deserts, tropical rainforests and sub-Arctic regions are the least represented.
Figure 3 in Impact of dike age on biodiversity and functional composition of soil macrofaunal communities in poplar forests in a reclaimed coastal area
Figure 3. PCoA ordinal configuration of soil macrofaunal communities from different habitats by Euclidean distance similarity index. In the code of the samples, the prefix means the code of the habitat, and the suffix means the number of the sample.
Figure 2 in Impact of dike age on biodiversity and functional composition of soil macrofaunal communities in poplar forests in a reclaimed coastal area
Figure 2. One-way ANOVA of taxonomic richness and abundance (A) and Margalef 's richness index R and Shannon– Weaver diversity index H' (B) across different habitats (mean ± SE). Means with different scripts are significantly different by Dunnett's T3 test (A) and LSD test (B), α = 0.05.
Drivers of plant diversity, community composition, functional traits and soil processes along an alpine gradient in the central Chilean Andes
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Data collected for: The contrasted impacts of grasshoppers on soil microbial activities in function of ecosystem productivity and herbivore diet
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Agricultural plastic pollution reduces soil function even under best management practices
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Data from: Impact of plant functional group and species removals on soil and plant nitrogen and phosphorus across a retrogressive chronosequence
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Plant and soil organic matter responses to ten years of nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Global soil saturated hydraulic conductivity map using random forest in a Covariate-based GeoTransfer Functions (CoGTF) framework at 1 km resolution
<p>The global Ksat map at 1 km resolution was developed by harnessing the technological advances in machine learning and availability of remotely sensed surrogate information such as terrain, climate, vegetation, and soil covariates. We merge concepts of predictive soil mapping with a large data set of Ksat measurements and local information (soil, vegetation, climate) into covariate-based “Geo Transfer Functions'' (CoGTFs) to generate global estimates of Ksat values (to highlight the impact of Geo-referenced covariates including various remote sensing maps, we use the term Geotransfer function GTF and not pedotransfer function PTF; in the latter case, typically only soil properties are used to estimate Ksat).</p> <p>The Ksat dataset is provided in GeoTIFF format. A total of 4 files that represent different soil depths (0, 30, 60, and 100 cm) are provided. The Ksat values are log-transformed (log10 Ksat) and cm/day was selected as a standardized unit.</p> <p>The Global Ksat training dataset used for this study is available here:<br> <a href="https://doi.org/10.5281/zenodo.3752721">https://doi.org/10.5281/zenodo.3752721</a></p> <p>The R code used for this study is available here:<br> <a href="https://github.com/ETHZ-repositories/Ksat_mapping_2020">https://github.com/ETHZ-repositories/Ksat_mapping_2020</a></p> <p>For more details / to cite this dataset please use:</p> <ul> <li>Gupta, S., Lehmann, P., Bonetti, S., Papritz, A., and Or, D., (2020): <strong>Global prediction of soil saturated hydraulic conductivity using random forest in a Covariate-based Geo Transfer Functions (CoGTF) framework</strong>. Journal of Advances in Modeling Earth Systems,<strong> </strong>13(4), e2020MS002242. https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020MS002242</li> </ul> <p>Other datasets related to this project:</p> <p>The Global vG training dataset is available here:</p> <p><a href="https://doi.org/10.5281/zenodo.5547338">10.5281/zenodo.5547338</a></p> <p>Examples of using this dataset to generate van Genuchten parameters maps can be found in <a href="https://doi.org/10.5281/zenodo.6343570">10.5281/zenodo.6343570</a>.</p> <p>The study was supported by ETH Zurich (Grant ETH-18 18-1). We would like to thank Zhongwang Wei, Samuel Bickel and Simone Fatichi (ETH Zurich) for insightful discussions.</p> <p> </p> <p> </p>
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.
Ecoregional patterns of protist communities in mineral and organic soils: assembly processes, functional traits and diversity of testate amoebae in Northern Eurasia
<p>TA_Traits.csv file includes trait data for testate amoebae. TA_Abundance.csv file includes environmental variables (soil type and region) and relative abundance data of testate amoebae.</p>
Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability
<p>Though not often examined together, both plant-soil feedbacks (PSFs) and functional traits have important influences on plant community dynamics and could interact. For example, seedling functional traits could impact seedling survivorship responses to soils cultured by conspecific versus heterospecific adults. Furthermore, levels of functional traits could vary with soil culturing source. In addition, these relationships might shift with light availability, which can affect trait values, microbe abundance, and whether mycorrhizal colonization is mutualistic or parasitic to seedlings.</p> <p>To determine the extent to which functional traits mediate PSFs via seedling survival, we conducted a field experiment. We planted seedlings of four temperate tree species across a gradient of light availability and into soil cores collected beneath conspecific (sterilized and live) and heterospecific adults. We monitored seedling survival twice per week over one growing season, and we randomly selected subsets of seedlings to measure mycorrhizal colonization and phenolics, lignin, and NSC levels at three weeks.</p> <p>Though evidence for PSFs was limited, <em>Acer saccharum</em> seedlings exhibited positive PSFs (i.e., higher survival in conspecific than heterospecific soils). In addition, soil microbes had a negative effect on <em>A. saccharum</em> and <em>Prunus serotina</em> seedling survival, with reduced survival in live versus sterilized conspecific soil. In general, we found higher trait values (measured amounts of a given trait) in conspecific than heterospecific soils and higher light availability. Additionally, <em>A. saccharum</em> survival increased with higher levels of phenolics, which were higher in conspecific soils and high light.<em> Quercus alba</em> survival decreased with higher AMF colonization.</p> <p>We demonstrate that functional trait values in seedlings as young as three weeks vary in response to soil source and light availability. Moreover, seedling survivorship was associated with trait values for two species, despite both drought and heavy rainfall during the growing season that may have obscured survivorship-trait relationships. These results suggest that seedling traits could have an important role in mediating the effects of local soil source and light levels on seedling survivorship and thus plant traits could have an important role in PSFs.</p>
Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
<p>Pesticides can have unintentional effects on non-target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a 3-year study, how vegetation control (by herbicide application) and soil copper content (from long-term copper-based fungicide application), affect biodiversity and the community structure of soil bacteria, fungi and protists and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45% respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape must were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas , whereas in vineyards with herbicide application it was only 20%. Synthesis and applications: Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration), but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade-off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.</p>
Changes in community-weighted trait mean, functional diversity, soil chemical properties and temperature along an elevational gradient in Tenerife, Canary Islands
<p>This dataset comprises community-weighted trait means and functional diversity of leaf traits, chemical soil properties and temperature recorded in roadside (disturbed) and interior (less disturbed) plots, along an elevational gradient of 2,300 m in Tenerife, Canary Islands. The leaf traits measured were specific leaf area (SLA), nitrogen, nitrogen to phosphorus ratio, leaf dry matter content (LDMC) and carbon to phosphorus ratio. The soil chemical properties measured were pH, nitrogen, nitrogen to phosphorus ratio, carbon to phosphorus ratio, calcium, potassium, magnesium and cation exchange capacity. Also the scores of the three first axes derived from a PCA analysis including the soil chemical properties are included. The temperature variables consist of bioclimatic variables Bio10 (mean temperature of the warmest quarter) and Bio11 (mean temperature of the coldest quarter). This dataset has been used for the analysis presented in Ratier Backes et al. (2021).</p>
Global maps of soil water characteristics parameters developed using the random forest in a Covariate-based GeoTransfer Functions (CoGTF) framework at 1 km resolution
<p>The global soil water characteristics parameters (<em>α, n, θ<sub>r</sub>, and θ<sub>s</sub></em>) maps based on van Genuchten (vG) model at 1 km resolution was developed by harnessing the technological advances in machine learning and availability of remotely sensed surrogate information such as terrain, climate, vegetation, and soil covariates. We merge concepts of predictive soil mapping with a large data set of vG parameters and local information (soil, vegetation, climate) into "Covariate-based GeoTransfer Functions'' (CoGTFs) to generate global estimates of vG parameters (to highlight the impact of Geo-referenced covariates including various remote sensing maps, we use the term Geotransfer Function GTF and not pedotransfer function PTF; in the latter case, typically only soil properties are used to predict vG parameters).</p> <p>The vG parameters (<em>α, n, θ<sub>r</sub>, and θ<sub>s</sub></em>) dataset is provided in GeoTIFF format. A total of 16 files that represent different soil depths (0, 30, 60, and 100 cm) are provided for each parameter.</p> <table> <caption>Description of vG parameters and their units</caption> <tbody> <tr> <td>vG Parameters</td> <td>Description</td> <td>units</td> </tr> <tr> <td><em>α</em></td> <td>Inverse air entry pressure</td> <td>Log<sub>10</sub><em>α (m<sup>-1</sup>)</em></td> </tr> <tr> <td><em>n</em></td> <td>Shape parameter</td> <td>Log<sub>10</sub><em>n </em>(dimensionless)</td> </tr> <tr> <td><em>θ<sub>r</sub></em></td> <td>Residual water content</td> <td>m<sup>3</sup>/m<sup>3</sup></td> </tr> <tr> <td><em>θ<sub>s</sub></em></td> <td>Saturated water content</td> <td>m<sup>3</sup>/m<sup>3</sup></td> </tr> </tbody> </table> <p> </p> <p>The Global vG training dataset used for this study is available here:</p> <p><a href="https://doi.org/10.5281/zenodo.5547338">10.5281/zenodo.5547338</a></p> <p>For more details / to cite this dataset please use:</p> <ul> <li>Gupta, S., Papritz, A., Lehmann, P., Hengl, T., Bonetti, S., & Or, D. (2022). Global Mapping of Soil Water Characteristics Parameters—Fusing Curated Data with Machine Learning and Environmental Covariates. <strong><em>Remote Sensing</em></strong>, <em>14</em>(8), 1947.</li> </ul> <p>The study was supported by ETH Zurich (Grant ETH-18 18-1). We thank Zhongwang Wei, Associate professor at Sun Yat-Sen University, for helping to collect the datasets and for insightful discussions. We would like to thank Andrea Carmintai, Professor at ETH Zurich, for the insightful discussions.</p>
Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project
<p>Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.</p>
CONUS VPD and soil moisture thresholds for suboptimal vegetation function
<p class="MsoNormal"><span>The dataset contains minimum and maximum vapor pressure deficit (VPD) and soil moisture parameters that define the range of suboptimal vegetation function (i.e., between uninhibited photosynthesis and complete shutdown). </span>The ranges were estimated using the Dynamic Canopy Biophysical Properties model (DCBP; Lowman & Barros 2018), which consists of a phenology forecasting model based on the growing season index (GSI), which provides a unitless measure of the potential phenologic state of vegetation based on the concurrent meteorological conditions (Jolly et al. 2005).</p>
Widespread variation in functional trait-vital rate relationships in tropical tree seedlings across a precipitation and soil phosphorus gradient
<p>A fundamental assumption of functional ecology is that functional traits are related to interspecific variation in performance. However, the relationship between functional traits and performance is often weak or uncertain, especially for plants. A potential explanation for this inconsistency is that the relationship between functional traits and vital rates (e.g., growth and mortality) is dependent on local environmental conditions, which would lead to variation in trait-rate relationships across environmental gradients. In this study, we examined trait-rate relationships for six functional traits (seed mass, wood density, maximum height, leaf mass per area, leaf area, and leaf dry matter content) using long-term data on seedling growth and survival of woody plant species from eight forest sites spanning a pronounced precipitation and soil phosphorus gradient in central Panama. For all traits considered except for leaf mass per area-mortality, leaf mass per area-growth, and leaf area-mortality relationships, we found widespread variation in the strength of trait-rate relationships across sites. For some traits, trait-rate relationships showed no overall trend but displayed wide site-to-site variation. In a small subset of cases, variation in trait-rate relationships was explained by soil phosphorus availability. Our results demonstrate that environmental gradients have the potential to influence how functional traits are related to growth and mortality rates, though much variation remains to be explained. Accounting for site-to-site variation may help resolve a fundamental issue in trait-based ecology – that traits are often weakly related to performance – and improve the utility of functional traits for explaining key ecological and evolutionary processes.</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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.