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2,078 results for “soil data”
Data from: Changes in plant, soil and microbes in a typical steppe from simulated grazing: explaining potential change in soil carbon
Grazing can directly or indirectly influence carbon (C) inputs, turnover, and retention in grassland soil. However, relative to the plant response to grazing, belowground biota and process responses are more complex and often do not correlate with the aboveground responses. Ungulate grazing involves three mechanisms - defoliation (removal of plant shoot tissue), dung and urine return, and trampling. An evaluation of the relative roles of these mechanisms and their combinations in grazing can explain the causes of changes in grassland, thereby explaining the soil carbon sequestration in a steppe ecosystem. In this study, we examined the changes in plants attributes, soil abiotic characteristics, and the soil microbial community in response to mowing (M), dung and urine addition (DU), simulated trampling (T), and their combinations by conducting a 3-year experiment in a steppe ecosystem in Inner Mongolia, China. Most of the variation in the grazing effects on grassland was explained by defoliation through decreased plant production and soil respiration and altered vegetation composition. Dung and urine return was second to defoliation in explaining grazing effects on grassland, and lead to increasing plant C inputs to the soil, while simultaneously potential loss of soil C due to the increase of the abundance of bacteria and soil respiration, eventually accelerated soil C cycling. An interaction between defoliation and trampling on microbial growth was observed in our study: trampling increased the abundance of total bacteria, fungi, and AMF only in the no-mowing plots. Trampling led to plant allocation to the belowground tissues and increased the abundance of fungi and AMF, which is critical for soil carbon sequestration, and trampling with defoliation further decreased the abundance of soil microbes, which may decelerate soil C cycling and increase its retention time. These results indicate that defoliation and dung and urine return play major roles in explaining grazing effects on grassland systems, including plant, soil, and microbe parameters examined, but the trampling effects and the interaction between defoliation and trampling are the two key factors that contribute to explaining the overall effects of grazing on soil carbon sequestration in a typical steppe ecosystem in Inner Mongolia.
Data from: Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant
1. Pathogens can accumulate on invasive plants over time, which could lead to population declines. The time required for these dynamics to occur is unknown and seldom addressed. Furthermore, no study has assessed plant-soil feedback while characterising plant pathogen and mutualist root fungal communities in the context of invasion time. 2. We used a plant-soil feedback study and 454 pyrosequencing to investigate pathogen accumulation over 100 years on a highly invasive plant in eastern North America that shows localised declines, Vincetoxicum rossicum (Apocynaceae). 3. We collected soil from five sites representing each of four invasion periods of V. rossicum across Ontario, Canada (old, ~100 years; intermediate, 50-60 years; young, <12 years; and uninvaded), and grew V. rossicum in these soils in a glasshouse study. Our hypothesis was that plants grown in soils invaded for longer periods of time would experience less positive feedbacks compared to those grown in more recently invaded or uninvaded soils. We collected roots of V. rossicum from the invasion periods and performed 454 pyrosequencing targeting fungi. We hypothesised that the abundance and richness of fungi that are known plant pathogens would be higher in roots from older invasions compared to more recent invasions. 4. Contrasting with our hypothesis, V. rossicum experienced overall growth promotion due to soil biota, regardless of invasion period. Vincetoxicum rossicum roots were colonised by a large number of fungal taxa, including many known plant pathogens or mutualistic arbuscular mycorrhizal fungi. However, we found no evidence of pathogen accumulation in older invaded sites in terms of species composition, richness or abundance. 5. Synthesis: Our consistent results in the glasshouse and the field highlight the strength of combining high-throughput sequencing data with plant-soil feedback experiments. We showed that the roots of Vincetoxicum rossicum (Apocynaceae) were colonised by many fungal taxa, but found no evidence for changes in plant growth or accumulation of fungal pathogens with longer invasion time. High pathogen loads may not lead to concurrent declines in invasive plants. Plant invasions, as demonstrated by V. rossicum, may be unpredictable in their ability to accumulate pathogens capable of leading to population declines.
Data from: Disentangling the 'brown world' faecal-detritus interaction web: dung beetle effects on soil microbial properties
Many ecosystem services are sustained by the combined action of microscopic and macroscopic organisms, and shaped by interactions between the two. However, studies tend to focus on only one of these two components. We combined the two by investigating the impact of macrofauna on microbial community composition and functioning in the context of a major ecosystem process: the decomposition of dung. We compared bacterial communities of pasture soil and experimental dung pats inhabited by one (Aphodius), two (Aphodius and Geotrupes), or no dung beetle genera. Overall, we found distinct microbial communities in soil and dung samples, and that the communities converged over the course of the experiment. Characterising the soil microbial communities underlying the dung pats revealed a significant interactive effect between the microflora and macrofauna, where the diversity and composition of microbial communities was significantly affected by the presence or absence of dung beetles. The specific identity of the beetles had no detectable impact, but the microbial evenness was lower in the presence of both Aphodius and Geotrupes than in the presence of Aphodius alone. Differences in microbial community composition were associated with differences in substrate usage as measured by Ecoplates. Moreover, microbial communities with similar compositions showed more similar substrate usage. Our study suggests that the presence of macrofauna (dung beetles) will modify the microflora (bacteria) of both dung pats and pasture soil, including community diversity and functioning. In particular, the presence of dung beetles promotes the transfer of bacteria across the soil–dung interface, resulting in increased similarity in community structure and functioning. The results demonstrate that to understand how microbes contribute to the ecosystem process of dung decomposition, there is a need to understand their interactions with larger co-occurring fauna.
Data from: Light regulates tropical symbiotic nitrogen fixation more strongly than soil nitrogen
Nitrogen limits primary production in almost every biome on Earth1,2. Symbiotic nitrogen fixation, conducted by certain angiosperms and their endosymbiotic bacteria, is the largest potential natural source of new nitrogen into the biosphere3, influencing global primary production, carbon sequestration and element cycling. Because symbiotic nitrogen fixation represents an alternative to soil nitrogen uptake, much of the work on symbiotic nitrogen fixation regulation has focused on soil nitrogen availability4,5,6,7,8. However, because symbiotic nitrogen fixation is an energetically expensive process9, light availability to the plant may also regulate symbiotic nitrogen fixation rates10,11. Despite the importance of symbiotic nitrogen fixation to biosphere functioning, the environmental factors that most strongly regulate this process remain unresolved. Here we show that light regulates symbiotic nitrogen fixation more strongly than does soil nitrogen and that light mediates the response of symbiotic nitrogen fixation to soil nitrogen availability. In a shadehouse experiment, low light levels (comparable with forest understories) completely shut down symbiotic nitrogen fixation, whereas soil nitrogen levels that far exceeded plant demand did not fully downregulate symbiotic nitrogen fixation at high light. For in situ forest seedlings, light was a notable predictor of symbiotic nitrogen fixation activity, but soil-extractable nitrogen was not. Light as a primary regulator of symbiotic nitrogen fixation is a departure from decades of focus on soil nitrogen availability. This shift in our understanding of symbiotic nitrogen fixation regulation can resolve a long-standing biogeochemical paradox12, and it will improve our ability to predict how symbiotic nitrogen fixation will fuel the global forest carbon sink and respond to human alteration of the global nitrogen cycle.
Data from: Reducing soil erosion by improving community functional diversity in semi-arid grasslands
1. Great efforts have been made to control soil erosion by restoring plant communities in degraded ecosystems world-wide. However, soil erosion has not been substantially reduced mainly because current restoration strategies lead to large areas of mono-specific vegetation, which are inefficient in reducing soil erosion because of their simple canopy and root structure. Therefore, an advanced understanding of how community functional composition affects soil erosion processes, as well as an improved restoration scheme to reduce soil erosion, is urgently needed. 2. We investigated the effect of community functional composition on soil erosion in restored semi-arid grasslands on the Loess Plateau of China. Community functional composition of 16 restored grasslands was quantified by community-weighted mean (CWM) and functional diversity (FD) trait values, which were calculated from nine plant functional traits of thirteen locally dominant plant species. Species richness and evenness were also measured. Soil erosion rates were measured using standard erosion plots. The multimodel inference approach was used to estimate the direction and the relative importance of these biodiversity indices in reducing soil erosion. 3. A robust and strong negative effect of functional divergence (FDiv) on soil erosion was found. The prevalence of particular trait combinations can also decrease soil erosion. The greatest control over soil erosion was exerted when the community mean root diameter was small and the root tensile strength was great. 4. Synthesis and applications: These findings imply that community functional diversity plays an important role in reducing soil erosion in semi-arid restored grasslands. This means that current restoration strategies can be greatly improved by incorporating community functional diversity into restoration design. We propose a trait-based restoration framework for reducing soil erosion, termed 'SSM' (Screening–Simulating–Maintaining). SSM aims to translate the target of community functional diversity into community assemblages that can be manipulated by practitioners. Based on this framework, a comprehensive procedure, highlighting functional diversity as the primary concern in determining optimal community assemblages, was developed to meet the pressing need for more effective restoration strategies to reduce soil erosion.
Data from: Active sound production of scarab beetle larvae opens up new possibilities for species-specific pest monitoring in soils
Root-feeding Scarabaeidae larvae can pose a serious threat to agricultural and forest ecosystems, but many details of larval ecology are still unknown. We developed an acoustic data analysis method based on active sound production by larvae (i.e. stridulations) for gaining new insights into larval ecology. In a laboratory study, third instar larvae of the Common Cockchafer (Melolontha melolontha) (n = 38) and the Forest Cockchafer (M. hippocastani) (n = 15) kept in soil-filled containers were acoustically monitored for 5 min each, resulting in the first known stridulation recordings for each species. Subsequent continuous monitoring of three M. hippocastani larvae over several hours showed that a single larva could stridulate more than 70 times per hour, and stridulation rates increased drastically with increasing larval abundance. The new fractal dimension-based data analysis method automatically detected audio sections with stridulations and provided a semi-quantitative estimate of stridulation activity. It is the first data analysis method specifically targeting Scarabaeidae larvae stridulations in soils, enabling for the first time non-invasive species-specific pest monitoring.
Data from: Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States
Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.
Data from: Asymmetric effects of grazing intensity on macroelements and microelements in grassland soil and plants in Inner Mongolia
<p>Grazing is a traditional grassland management technique and greatly alters ecosystem nutrient cycling. The effects of grazing intensity on the nutrient dynamics of soil and plants in grassland ecosystems remain uncertain, especially among microelements. A two-year field grazing experiment was conducted in a typical grassland with four grazing intensities (ungrazed control, light, moderate, and heavy grazing) in Inner Mongolia, China. Nutrient concentration was assessed in soil and three dominant plant species (<i>Stipa krylovii</i>, <i>Leyums chinensis</i>, and <i>Cleistogenes squarrosa</i>). Assessed quantities included four macroelements (carbon (C), nitrogen (N), phosphorus (P), and magnesium (Mg)) and four microelements (copper (Cu), iron (Fe), manganese (Mn), and zinc (Zn)). Soil total C, total N, total P, available N, and available P concentrations significantly increased with grazing intensity but soil Mg, Cu, Fe, Mn, Zn concentrations had no significant response. Plant C concentration decreased but plant N, P, Mg, Cu, Fe, Mn, and Zn concentrations significantly increased with grazing intensity. In soil, macroelement dynamics (i.e., C, N, and P) exhibited higher sensitivity with grazing intensity, conversely in plants, microelements were more sensitive. This result indicates macroelements and microelements in soil and plants had asymmetric responses with grazing intensity. The slopes of nutrient linear regression in <i>C. squarrosa</i> were higher than that of <i>S. krylovii</i> and <i>L. chinensis</i>, indicating that <i>C. squarrosa</i> had higher nutrient acquisition capacity and responded more rapidly to heavy grazing. These findings indicate that short-term heavy grazing accelerates nutrient cycling of the soil-plant system in grassland ecosystems, elucidate the multiple nutrient dynamics of soil and plants with grazing intensity, and emphasize the important function of microelements in plant adaptation in grazing management.</p>
Data from: Soil dynamics in forest restoration: a data set for temperate and tropical regions
<p>Restoring forest ecosystems has become a global priority. Yet, soil dynamics is still poorly assessed among restoration studies and lacks knowledge on how soil is affected by forest restoration process. Here, we compile information on soil dynamics in forest restoration based on soil physical, chemical and biological attributes in temperate and tropical forest regions. It encompasses 50 scientific papers across 17 different countries and contains 1,469 quantitative information of soil attributes between reference (e.g., old-growth forest) and restored ecosystems (e.g. forests in their initial or secondary stage of succession) within the same study. To be selected, studies had to be conducted in forest ecosystems, to include multiple sampling sites (replicates) in both restored and reference ecosystems, and to encompass quantitative data of soil attributes for both reference and restored ecosystems.</p> <p>We recorded in each study the following information: (i) study year; (ii) country; (iii) forest region (tropical or temperate); (iv) latitude; (v) longitude; (vi) soil class; (vii) past disturbance; (viii) restoration strategy (active or passive); (ix) restoration age; (x) soil attribute type (physical, chemical or biological); (xi) soil attribute; (xii) soil attribute unit; (xiii) soil sampling (procedures); (xiv) date of sampling; (xv) soil depth sampled; (xvi) soil analysis; (xvii) quantitative values of soil attributes for both restored and reference ecosystems; (xviii) type of variation (standard error ou deviation) for both restored and reference ecosystems; and (xix) quantitative values of the variation for both restored and reference ecosystems. These were the most common data available in the selected studies.</p> <p>This extensive database on the extent soil physical, chemical and biological attributes differ between reference and restored ecosystems can fill part of the existing gap on both soil science and forest restoration in terms of: (i) which are the critical soil attributes to be monitored during forest restoration? and (ii) how do environmental factors affect soil attributes in forest restoration? The data will be made available to the scientific community for further analyses on both soil science and forest restoration. Soil information gap during the forest restoration process and its general patterns can be addressed using this data set.</p>
Data from: An inventory of the foliar, soil, and dung arthropod communities in pastures of the Southeastern United States
<p>Grassland systems constitute a significant portion of the land area in the U.S. and as a result harbors significant arthropod biodiversity. During this time of biodiversity loss around the world, bioinventories of ecologically important habitats serve as important indicators for the effectiveness of conservation efforts. We conducted a bioinventory of the foliar, soil, and dung arthropod communities in 10 cattle pastures located in the southeastern U.S. during the 2018 grazing season. In sum, 126,251 arthropod specimens were collected. From the foliar community, 13 arthropod orders were observed, with the greatest species richness found in Hymenoptera, Diptera, and Hemiptera. The soil-dwelling arthropod community contained 18 orders. The three orders comprising the highest species richness were Coleoptera, Diptera, and Hymenoptera. Lastly, 12 arthropod orders were collected from cattle dung, with the greatest species richness found in Coleoptera, Diptera, and Hymenoptera. Herbivores were the most abundant functional guild found in the foliar community, and predators were most abundant in the soil and dung communities. Arthropod pests constituted a small portion of the pasture arthropod communities, with 1.01%, 0.34%, and 0.46% pests found in the foliar, soil, and dung communities, respectively. While bioinventories demand considerable time, energy, and resources to accomplish, the information from these inventories has many uses for conservation efforts, land management recommendations, and the direction of climate change science.</p>
FIGURE 3 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 3: Prodorsum of Brevipalpia minima and Hammenia macrostella. Scale bar = 25 µm.
FIGURE 2 in From Parataxonomy To Molecular Data: The Case Of Rhagidiidae (Acari) From Belgian Soils
FIGURE 2: Brevipalpia minima and Hammenia macrostella in ventral view. Scale bar = 50 µm.
Data from: Monitoring soil moisture at the catchment scale – A novel approach combining antecedent precipitation index and radar-derived rainfall data
<p>Knowledge about soil moisture is important for event-based rainfall-runoff models but monitoring conditions at the catchment scale is not a trivial task. Soil moisture is highly variable in space and time, particularly in dry climates with seasonal and spatially heterogeneous rainfall. Point measurements are difficult to upscale, and remotely sensed (RS) data often lack in spatial or temporal resolution for local or regional studies. Longer latency periods – the time required before data becomes available – of some RS data make them less applicable to time-sensitive analyses such as flash flood forecasting. This study evaluated a novel approach for estimating catchment-scale volumetric soil moisture using an antecedent precipitation index (API) -based model. The model was trained and tested using in-situ soil moisture measurements collected during a 3-month field sampling campaign in a 142 km<sup>2</sup><span><span><span><span><span><span><span><span><span> study area in central New Mexico. The calibrated model was applied at the catchment scale to produce soil moisture grids from radar-derived rainfall estimates. Model performance, resolution and latency were compared to satellite-based soil moisture estimates. Benefits of the proposed new method include high spatial resolution (1 × 1 km or less depending on the precipitation data source) and high prediction accuracy (root mean square errors 0.014–0.018 m</span></span></span></span></span></span></span></span></span><sup>3</sup><span><span><span><span><span><span><span><span><span>/m</span></span></span></span></span></span></span></span></span><sup>3</sup><span><span><span><span><span><span><span><span><span>). Given the short latency period for radar-derived rainfall data, the method has potential for use in operational flood risk assessment and forecasting.</span></span></span></span></span></span></span></span></span></p>
INMET data - "Intensification of heatwaves by soil moisture–atmosphere coupling in Southeast Brazil"
<p>Time series of Daily Maximum Temperature values from two meteorological stations from INMET (Brazilian National Institute of Meteorology) located in São Paulo and Curitiba.</p>
Data for: Plant-soil biota interactions explain shifts in plant community composition under global change
<p>1. Plant-soil biota interactions play a crucial role in the assembly of plant communities and the maintenance of plant species diversity. However, few studies have tested how the effect of soil biota on plant species and communities depend on environmental context and whether shifts in plant community composition caused by environmental change are associated with variation in plant-soil biota interactions. 2. We combined a field experiment in a Tibetan alpine meadow and a greenhouse experiment with factorial combinations of nitrogen (N) enrichment and warming to examine the role of plant-soil biota interactions in plant community dynamics. 3. The results showed that plant relative abundances were negatively correlated with the net effects of soil biota on plant growth but only under ambient field conditions. Warming and N-enrichment alleviated the negative soil biota effects in the greenhouse, and changed plant community composition and reduced species diversity in the field. Importantly, changes in soil biota effects on plant growth were positively correlated with changes in plant relative abundances caused by warming and N-enrichment in field. In a parallel field experiment, the diversity of mycorrhizal fungi increased while the diversity of fungal pathogens remained unchanged under warming and N-enrichment, indicating that soil biodiversity may play a critical role in plant responses to environmental change. 4. This study empirically demonstrates that altered plant-soil biota interactions explain shifts in plant community composition under global change, providing new insights into the mechanisms of diversity loss in a changing world.</p>
Dataset for effects of shear zone thickness in root-reinforced soils: Fallow P X-ray CT scans and digital volume correlation data
<p>Dataset for effects of shear zone thickness in root-reinforced soils: Fallow P X-ray CT scans and digital volume correlation data</p>
Dataset for effects of shear zone thickness in root-reinforced soils: Gorse A X-ray CT scans and digital volume correlation data
<p>Dataset for effects of shear zone thickness in root-reinforced soils: Gorse A X-ray CT scans and digital volume correlation data</p>
Dataset for effects of shear zone thickness in root-reinforced soils: Willow C X-ray CT scans and digital volume correlation data
<p>Dataset for effects of shear zone thickness in root-reinforced soils: Willow C X-ray CT scans and digital volume correlation data</p>
Dataset for effects of shear zone thickness in root-reinforced soils: Gorse G X-ray CT scans and digital volume correlation data
<p>Dataset for effects of shear zone thickness in root-reinforced soils: Gorse G X-ray CT scans and digital volume correlation data</p>
Dataset for effects of shear zone thickness in root-reinforced soils: Fallow D X-ray CT scans and digital volume correlation data
<p>Dataset for effects of shear zone thickness in root-reinforced soils: Fallow D X-ray CT scans and digital volume correlation data</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.