Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
223
datasets available to search
ShareScore release 0.9.0
Dataset results
223 results for “soil functioning”
Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition
Open the record for dataset details and reuse information.
CONUS VPD and soil moisture thresholds for suboptimal vegetation function
Open the record for dataset details and reuse information.
Effects of crop species on soil functions and soil multifunctionality are species-specific
Open the record for dataset details and reuse information.
Data from: Soil functions are amplified along increasing planting densities via nutrient trade-off driven by rhizobacteria in drought-prone environment
Open the record for dataset details and reuse information.
Keystone species affect the relationship between soil microbial diversity and ecosystem function under land use change in subtropical China
Open the record for dataset details and reuse information.
Fear of predators alters herbivore regulation of soil microbial community function
Open the record for dataset details and reuse information.
Functional traits of soil nematodes define their response to nitrogen fertilization
Open the record for dataset details and reuse information.
Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability
Open the record for dataset details and reuse information.
2007 pre-treatment soils pH, nutrients, texture: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).
Soil microbial functions and enzyme activity:BAC: Biodiversity and Climate
Climate changes forecast for our region by GCM???s and shifts in biodiversity and composition each have the potential to alter ecosystem functioning; their interactive effects are unknown. The "BAC" experiment is designed to determine the direct and interactive effects of plant species numbers, plant community composition, temperature, and precipitation on 11 productivity, C and N dynamics, stability, and plant, microbe, and insect species abundances in CDR grassland ecosystems.
In situ soil respirations throughout the 2020 growing season across an N fertilization gradient: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).
Data from: Above-belowground linkages of functionally dissimilar plant communities and soil properties in a grassland experiment
<p>Changes in plant community composition can have long-lasting consequences for ecosystem functioning. However, how the duration of plant growth of functionally distinct grassland plant communities influences abiotic and biotic soil properties and thus ecosystem functions is poorly known. In a field experiment, we established identical experimental subplots in two successive years comprising of fast- or slow-growing grass and forb community mixtures with different forb:grass ratios. After one and two years of plant growth, we measured above- and belowground biomass, soil abiotic characteristics (pH, organic matter, soil nutrients), soil microbial properties (respiration, biomass, community composition), and nematode abundance. Fast- and slow-growing plant communities did not differ in above- and belowground biomass. However, fast-and slow-growing plant communities created distinct soil bacterial communities, whereas soil fungal communities differed most in 100% forb communities compared to other forb:grass ratio mixtures. Moreover, soil nitrate availability was higher after two years of plant growth, whereas the opposite was true for soil ammonium concentrations. Furthermore, total nematodes and especially bacterial-feeding nematodes were more abundant after two years of plant growth. Our results show that plant community composition is a driving factor in soil microbial community assembly and that the duration of plant growth plays a crucial role in the establishment of plant community and functional group composition effects on abiotic and biotic soil ecosystem functioning under natural field conditions.</p>
Data from: Soil functional responses to drought under range-expanding and native plant communities
1. Current climate warming enables plant species and soil organisms to expand their range to higher latitudes and altitudes. At the same time, climate change increases the incidence of extreme weather events such as drought. While it is expected that plants and soil organisms originating from the south are better able to cope with drought, little is known about the consequences of their range shifts on soil functioning under drought events. 2. Here, we test how range-expanding plant species and soil communities may influence soil functioning under drought. We performed a full-factorial outdoor mesocosm experiment with plant communities of range expanders or related natives, with soil inocula from the novel or the original range, with or without summer drought. We measured litter decomposition, carbon mineralization and enzyme activities, substrate-induced respiration, and the relative abundance of soil saprophytic fungi immediately after drought and at 6 and 12 weeks after rewetting. 3. Drought decreased all soil functions regardless of plant and soil origin except one; soil respiration was less reduced in soils of range-expanding plant communities, suggesting stronger resistance to drought. After rewetting, soil functioning responses depended on plant and soil origin. Soils of native plant communities with a history of drought had more litter mass loss and higher relative abundance of saprophytic fungi than soils without drought and soils of range expanders. Functions of soil from range expanders recovered in a more conservative manner than soils of natives, as litter mass loss did not exceed the control rates. At the end of the experiment, after rewetting, most soil functions in mesocosms with drought history did not differ anymore from the control. 4. We conclude that functional consequences of range expanding plants and soil biota may interact with effects of drought, and that these effects are most prominent during the first weeks after rewetting of the soil.
Data from: Choice of resolution by functional trait or taxonomy affects allometric scaling in soil food webs
Belowground organisms often display a shift in their mass-abundance scaling relationships due to environmental factors such as soil chemistry and atmospheric deposition. Here we present new empirical data that show strong differences in allometric scaling according to whether the resolution at the local scale is based on a taxonomic or a functional classification, while only slight differences arise according to soil environmental conditions. For the first time, isometry (an inverse 1∶1 proportion) is recognized in mass-abundance relationships, providing a functional signal for constant biomass distribution in soil biota regardless of discrete trophic levels. Our findings are in contrast to those from aquatic ecosystems, in that higher trophic levels in soil biota are not a direct function of increasing body mass.
Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. The present study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes, involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.
Data from: Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient
The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative effects of grazing-induced disturbance on soil function. Further, our results suggest that most of this effect will be derived from echidnas, with little positive effects due to rabbits. Activities that enhance the habitat for echidnas or reduce rabbit populations are likely to have a positive effect on soil function in these systems.
Data from: Above and belowground responses of four tundra plant functional types to deep soil heating and surface soil fertilization
1.Climate warming is faster in the Arctic than the global average. Nutrient availability in the tundra soil is expected to increase by climate warming through 1) accelerated nutrient mobilization in the surface soil layers, and 2) increased thawing depths during the growing season which increases accessibility of nutrients in the deeper soil layers. Both processes may initiate shifts in tundra vegetation composition. It is important to understand the effects of these two processes on tundra plant functional types. 2.We manipulated soil thawing depth and nutrient availability at a Northeast-Siberian tundra site to investigate their effects on above and belowground responses of four plant functional types (grasses, sedges, deciduous shrubs and evergreen shrubs). Seasonal thawing was accelerated with heating cables at ~15 cm depth without warming the surface soil, whereas nutrient availability was increased in the surface soil by adding slow-release NPK fertilizer at ~5 cm depth. A combination of these two treatments was also included. This is the first field experiment specifically investigating the effects of accelerated thawing in tundra ecosystems. 3.Deep soil heating increased the aboveground biomass of sedges, the deepest-rooted plant functional type in our study, but did not affect biomass of the other plant functional types. In contrast, fertilization increased aboveground biomass of the two dwarf shrub functional types, which both had very shallow root systems. Grasses showed the strongest response to fertilization, both above and belowground. Grasses were deep-rooted, and they showed the highest plasticity in terms of vertical root distribution, as grass root distribution shifted to deep and surface soil in response to deep soil heating and surface soil fertilization, respectively. 4.Synthesis - Our results indicate that increased thawing depth can only benefit deep-rooted sedges, while the shallow-rooted dwarf shrubs as well as flexible-rooted grasses take advantage of increased nutrient availability in the upper soil layers. Our results suggest that grasses have the highest root plasticity, which enables them to be more competitive in rapidly changing environments. We conclude that root vertical distribution strategies are important for vegetation responses to climate-induced increases in soil nutrient availability in Arctic tundra, and that future shifts in vegetation composition will depend on the balance between changes in thawing depth and nutrient availability in the surface soil.
Data from: Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems
Nitrogen (N) losses from intensified agriculture are a major cause of global change, due to nitrate (NO3-) export and the eutrophication of aquatic systems as well as emissions of nitrous oxide (N2O) into the atmosphere. Diversified agroecosystems with legume cover crops couple N and carbon (C) inputs to soil and reduce N pollution, but there is a need to identify controls on legume N2 fixation across ecosystems with variable soil conditions. Here, I tested the hypothesis that N mineralization from turnover of soil organic matter (SOM) regulates legume N2 fixation across 10 farms that spanned a gradient of SOM levels. I separated soil samples into two SOM fractions, based on size and density, which are indicators of soil nutrient cycling and N availability (free particulate organic matter and intra-aggregate particulate organic matter (POM)). This study indicates downregulation of legume N2 fixation in diversified agroecosystems with increasing N availability in intra-aggregate POM and increasing N mineralization. Intercropping the legume with a grass weakened the relationship between N in POM and N2 fixation due to N assimilation by the grass. Further, mean rates of N and C mineralization across sites increased with two seasons of a legume-grass cover crop mixture, which could enhance this stabilizing feedback between soil N availability and N2 fixation over time. These results suggest a potential mechanism for the diversity-ecosystem function relationships measured in long-term studies of agroecosystems, in which regular use of legume cover crops increases total soil organic C and N and reduces the environmental costs of crop production.
Data from: Using greenhouse gas fluxes to define soil functional types
Aim: Soils provide key ecosystem services and directly control ecosystem functions; thus, there is a need to define the reference state of soil functionality. Most common functional classifications are vegetation-centered, such as plant functional types (PFTs), and neglect soil characteristics and processes. We propose Soil Functional Types (SFTs) as a conceptual approach to represent and describe the functionality of soils based on characteristics of their greenhouse gas (GHG) flux dynamics. Methods: We used automated measurements of CO2, CH4 and N2O soil fluxes in a forested area to define SFTs as surface areas with similar GHG dynamics. We performed mixed effects models, and independent cluster analyses of our environmental variables and SFT classifications. Results Unique groupings based on SFTs, but not environmental variables, supported the hypothesis that SFTs provide additional insights on the spatial variability of soil functionality beyond information represented by commonly measured soil parameters (e.g., soil moisture, soil temperature, litter biomass). Conclusions: This approach could complement vegetation-based functional classifications to better represent the broad range of ecosystem functions. A global application of the proposed SFT framework will only be possible if there is a community-wide effort to share data and create a global database of GHG emissions from soils.
Data from: Testing the validity of functional response models using molecular gut content analysis for prey choice in soil predators
Analysis of predator - prey interactions is a core concept of animal ecology, explaining structure and dynamics of animal food webs. Measuring the functional response, i.e. the intake rate of a consumer as a function of prey density, is a powerful method to predict the strength of trophic links and assess motives of prey choice, particularly in arthropod communities. However, due to their reductionist set-up, functional responses, which are based on laboratory feeding experiments, may not display field conditions, possibly leading to skewed results. Here, we tested the validity of functional responses of centipede predators and their prey by comparing them with empirical gut content data from field-collected predators. Our predator - prey system included lithobiid and geophilomorph centipedes, abundant and widespread predators of forest soils and their soil-dwelling prey. First, we calculated the body size-dependent functional responses of centipedes using a published functional response model in which we included natural prey abundances and animal body masses. This allowed us to calculate relative proportions of specific prey taxa in the centipede diet. In a second step, we screened field-collected centipedes for DNA of eight abundant soil-living prey taxa and estimated their body size-dependent proportion of feeding events. We subsequently compared empirical data for each of the eight prey taxa, on proportional feeding events with functional response-derived data on prey proportions expected in the gut, showing that both approaches significantly correlate in five out of eight predator - prey links for lithobiid centipedes but only in one case for geophilomorph centipedes. Our findings suggest that purely allometric functional response models, which are based on predator-prey body size ratios are too simple to explain predator - prey interactions in a complex system such as soil. We therefore stress that specific prey traits, such as defence mechanisms, must be considered for accurate predictions.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.