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2,078 results for “soil data”
Data for A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community
<p>A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community data</p>
Data from: Foliar herbivory creates subtle soil legacy effects that alter future herbivores via changes in plant community biomass allocation
<p>Plants leave legacy effects in the soil they grow in, which can drive important vegetation processes, including productivity, community dynamics and species turnover. Plants at the same time also face continuous pressure posed by insect herbivores. Given the intimate interactions between plants and herbivores in ecosystems, plant identity and herbivory are likely to interactively shape soil legacies. However, the mechanisms that drive such legacy effects on future generations of plants and associated herbivores are little known.<br> In a greenhouse study, we exposed ten common grasses and non-leguminous forbs individually to insect herbivory by two closely related noctuid caterpillars, <i>Mamestra brassicae</i> and <i>Trichoplusia ni</i> (Lepidoptera: Noctuidae) or kept them free of herbivores. We then used the soil legacies created by these plant individuals to grow a plant community composed of all ten plant species in each soil, and exposed these plant communities to <i>M. brassicae</i>. We measured conditioning plant biomass, soil respiration and chemistry of the conditioned soils, as well as individual plant, plant community and herbivore biomass responses.</p> <p>At the end of the conditioning phase, soils with herbivore legacies had higher soil respiration, but only significantly so for <i>M. brassicae</i>. Herbivore legacies had minimal impacts on community productivity. However, path models reveal that herbivore-induced soil legacies affected responding herbivores through changes in plant community shoot: root ratios. Soil legacy effect patterns differed between functional groups. We found strong plant species and functional group-specific effects on soil respiration parameters, which in turn led to plant community shifts in grass: forb biomass ratios. Soil legacies were negative for the growth of plants of the same functional group. </p> <p><strong>Synthesis:</strong><i> </i>We show that insect herbivory, plant species and their functional groups, all incur soil microbial responses that lead to subtle (herbivory) or strong (plants and their functional group) effects in response plant communities and associated polyphagous herbivores. Hence, even though typically ignored, our study emphasizes that legacies of previous insect herbivory in the soil can influence current soil-plant-insect community interactions.</p>
Data from: Plant life history traits rather than soil legacies determine colonisation of soil patches in a multi-species grassland
<p class="MsoNoSpacing">Interactions between plants and soil biota are increasingly shown to play critical roles in plant species co-existence processes. Plant species co-existence is thought to be promoted via biotic legacies that plant species leave behind in the soil after a plant disappears. These soil legacies are hypothesised to supress colonisation success when the preceding plant is of the same species, that is, when a plant species encounters its own, species-specific soil antagonists.</p> <p class="MsoNoSpacing">However, colonisation of vacant spots in plant communities is in the first place determined by the ability of plants to reach such vacant locations. We currently lack an understanding of the explicit role of soil legacy effects and their relative contribution to colonisation processes in plant communities consisting of plant species inherently differing in colonisation ability.</p> <p class="MsoNoSpacing">In experimental, outdoor plant communities consisting of eight grassland species, we tested the effect of five differently conditioned soil patches on plant species colonisation success over three consecutive growing seasons. We found that colonisation success was largely determined by the species' reproductive strategy, lateral spread and growth rate, and not by the plant species that conditioned the soil patch. Fast spreading, clonal plant species reached the soil patches first and initially attained the highest biomass inside the patch. One year later, slower spreading plant species colonised the patch via seedlings. Species with intrinsically high growth rates attained the highest biomass, decreasing biomass of the initial colonisers. While subtle differences between conditioned soil patches did occur, these were not strong enough to overcome the inherent differences in colonisation ability between the various plant species.</p> <p class="MsoNoSpacing"><strong>Synthesis:</strong><em> </em>Our results reject the hypothesis that colonisation of vacant soil patches in plant communities is strongly affected by the legacy that is left behind by the preceding plant species. Instead, plant species life history strategy plays a prominent role, driving sequential plant species replacements. Based on our results and recent accounts in literature we present a conceptual model for local cyclic dynamics in grassland communities, where soil legacy plays a role in affecting the performance of established plant species rather than colonisation of vacant patches.</p>
Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
<p>Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in <em>Mimulus guttatus</em> (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F<sub>IS</sub>) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion that underlies <em>M. guttatus</em> life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.</p>
Data repository for "Climate change increases the severity and duration of soil water stress in the temperate forest of eastern North America"
<p>Dataset provided for publication in Frontiers in Forests and Global Change : "Climate change increases the severity and duration of soil water stress in the temperate forest of eastern North America".</p>
Soil property, microbial abundance, and plant and invertebrate biomass data across a natural soil temperature gradient in Iceland from August 2018
<p><span>This is a dataset of soil physiochemical properties, bacterial and fungal abundance, and above and belowground plant and invertebrate biomass, sampled at 40 plots in the Hengill geothermal valley, Iceland, from 15<sup>th</sup> to 22<sup>nd</sup> August 2018. The plots span a temperature gradient of 10</span><span>-35 °C over the sampling period, and this temperature gradient is consistent over time. The dataset also includes data on the decomposition rate of soil organic matter, which was sampled at 60 plots in the Hengill valley from May to July 2015.</span></p>
Subarctic soil carbon losses after deforestation for agriculture depend on permafrost abundance - study data
<p>Contains the dataset and R code used for the study "Subarctic soil carbon losses after deforestation for agriculture depend on permafrost abundance".</p>
Data from: Decipher soil organic carbon dynamics and driving forces across China using machine learning
<p><span><span>The dynamics of soil organic carbon (SOC) play a critical role in modulating global warming. However, the long-term spatiotemporal changes of SOC at large scale and the impacts of driving forces remain unclear. In this study, we investigated the dynamics of SOC in different soil layers across China through the 1980s to 2010s using a machine learning approach and quantified the impacts of the key factors based on factorial simulation experiments. Our results showed that the latest (2000-2014) SOC stock in the first meter soil (SOC<sub>100</sub>) was 80.68 ± 3.49 Pg C, of which 42.6% was stored in the top 20 cm, sequestrating carbon with a rate of 30.80 </span><span>± 12.37</span><span> g C m<sup>-2</sup> yr<sup>-1</sup> since the 1980s. Our experiments focusing on the recent two periods (2000s and 2010s) revealed that climate change exerted the largest relative contributions to SOC dynamics in both layers and warming or drying can result in SOC loss. However, the influence of climate change weakened with soil depth, while the opposite for vegetation growth. </span><span>Relationships between SOC and forest canopy height further confirmed this strengthened impact of vegetation with soil depth, and highlighted the carbon sink function of deep soil in mature forest. Moreover, our estimates suggested that SOC dynamics in 71% of topsoil were controlled by climate change and its coupled influence with environmental variation (CE). Meanwhile CE and the combined influence of climate change and vegetation growth dominated the SOC dynamics in 82.05% of the first meter soil. </span><span>Additionally, the national cropland topsoil organic carbon increased with a rate of 23.6 </span><span>± 7.6 </span><span>g C m<sup>-2</sup> yr<sup>-1</sup> since the 1980s, and the widely applied nitrogenous fertilizer was a key stimulus. </span><span>Overall, our study extended the knowledge about the dynamics of SOC and deepened our understanding about the impacts of the primary factors.</span></span></p>
Data from: Loamy sand soil approaches organic carbon saturation after 37 years of conservation tillage
<p>This is digital research data corresponding to a published manuscript, Loamy sand soil approaches organic carbon saturation after 37 years of conservation tillage. Conservation tillage is reported to increase soil organic carbon (SOC) and total nitrogen (TN) contents, but long-term (>30 yr) field results quantifying the responses in Coastal Plain Ultisols are sparse. The distribution, accumulation, and topsoil storage of SOC and TN after 37 yr of crop production using conventional (CvT) or conservation tillage (CnT) on a Norfolk loamy sand (fine-loamy, kaolinitic, thermic, Typic Kandiudults) were quantified. Soil samples were collected annually from the 0−5-, 5−10-, and 10−15-cm depth increments beneath corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and cotton (Gossypium hirsutum L.) crops.</p>
A quantitative synthesis of soil microbial effects on plant species coexistence: code and data
<p>This release contains data and code to conduct all analyses in Yan et al. "A quantitative synthesis of soil microbial effects on plant species coexistence".</p>
Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks
<p>The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however, preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial spatial association of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that changes in AM fungal proportional abundance induced by spatial structure in roots of a preferentially allocating host produced positive feedbacks on plant growth, showing that interactions between spatial structure and host choice can determine the direction of plant-soil feedbacks. Our results suggest that symbiont spatial structure within plant roots may act as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with potentially cascading effects on plant-plant interactions.</p>
Data from: Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils
<p><span>Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH<sub>4</sub>) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH<sub>4</sub> oxidation. CH<sub>4</sub> oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH<sub>4 </sub>oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH<sub>4</sub> uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH<sub>4</sub> uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal <em>Ralstonia pickettii</em> associates with CH<sub>4</sub> uptake across soils along with pertinent CH<sub>4</sub> and inorganic N metabolism associated genes. This study highlights the critical relationship between CH<sub>4</sub> and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.</span></p>
Data to support the publication The use of Twitter for knowledge exchange on sustainable soil management
<p>5 farmer semi-structured interviews</p>
Data from: Girth increment changes in response to soil water availability in lowland dipterocarp forest in Borneo: an individualistic time-series analysis
<p><span>Time-series data offer a way of investigating the causes driving ecological processes as phenomena. To test for possible differences in water relations between species of different forest structural guilds at Danum (Sabah, NE Borneo), daily stem girth increments (gthi), of 18 trees across six species were regressed individually on soil moisture potential (SMP) and temperature (TEMP), accounting for temporal autocorrelation (in GLS-arima models), and compared between a wet and a dry period. The best-fitting significant variables were SMP the day before and TEMP the same day. The first resulted in a mix of positive and negative coefficients, the second largely positive ones. An adjustment for dry-period showers was applied. Interactions were stronger in dry than wet period. Negative relationships for overstorey trees can be interpreted in a reversed causal sense: fast transporting stems depleted soil water and lowered SMP. Positive relationships for understorey trees meant they took up most water at high SMP. The unexpected negative relationships for these small trees may have been due to their roots accessing deeper water supplies (if SMP was inversely related to that of the surface layer), and this was influenced by competition with larger neighbour trees. A tree-soil flux dynamics manifold may have been operating. Patterns of mean diurnal girth variation were more consistent among species, and time-series coefficients were negatively related to their maxima. Expected differences in response to SMP in the wet and dry periods did not clearly support a previous hypothesis differentiating drought and non-drought tolerant understorey guilds. Trees within species showed highly individual responses when tree size was standardized. Data on individual root systems and SMP at several depths are needed to get closer to the mechanisms that underlie the tree-soil water phenomena in these tropical forests. Neighborhood stochasticity importantly creates varying local environments experienced by individual trees.</span></p>
Data from: A century of genetic variation inferred from a persistent soil-stored seed bank
Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil-stored seed banks as natural archives, in part because of concerns over non-random attrition and mixed stratification. Here we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records of demographic and population genetic variation. After assembling profiles of the seed bank from radionuclide dated soil cores, we germinated seeds to 'resurrect' cohorts spanning the 20th century. Using microsatellite markers, we assessed genetic diversity and differentiation among depth cohorts, drawing comparisons to extant plants at the study site and in nearby and more distant marshes. We found that seed density peaked at intermediate soil depths. We also detected genotypic differences among cohorts as well as between cohorts and extant plants. Genetic diversity did not decline with depth, indicating that the observed pattern of differentiation is not due to attrition. Patterns of differentiation within and among extant marshes also suggest that local populations persist as aggregates of small clones, likely reflecting repeated seedling recruitment and low immigration from admixed regional gene pools. These findings indicate that persistent and stratified soil-stored seed banks merit further consideration as resources for reconstructing decadal-to-century long records that can lend insight into the tempo and nature of ecological and evolutionary processes that shape populations over time.
Savanna plant and soil carbon data from different burn seasons and histories across Mole National Park, Ghana
<p>Aboveground plant pool and belowground (soil plus root) carbon data for a space-for-time substitution survey of different burn seasons and histories across Mole National Park, Ghana. Carbon data was collected to determine the impact of unintentional late growing season wildfires on carbon storage in a protected area dominated by early growing season prescribed burning land management. The methodology and findings from the study are detailed in the below publication:</p> <p>Awuah J, Smith SW, Speed JDM, Graae BJ. 2022. Can seasonal fire management reduce the risk of carbon loss from wildfires in a protected Guinea savanna? Ecosphere, e4283. https://doi. 88 org/10.1002/ecs2.4283 </p> <p>This data repository contains the following data (and descriptive metadata): </p> <p>(1) Study_site_coordinates: locations for 28 sites surveyed in 2016 as part of an ecosystem carbon stock assessment</p> <p>(2) Aboveground_carbon: aboveground tree, shrub, herbaceous vegetation, deadwood and litter carbon stocks estimated from either destructive biomass sampling or allometric equations. Aboveground carbon data are presented per site. </p> <p>(3) LOI_to_carbon_conversion: a subset of soil samples were analysed for both loss on ignition (LOI) and automated dry combustion using an elemental analyser, the latter more accurate for carbon determination and used to correct LOI values. </p> <p>(4) Belowground_carbon: combined soil and root carbon collected collected to a maximum depth of 17 cm, and split into four soil layers (0-2 cm, 2-7 cm, 7-12 cm and 12-17 cm). </p> <p>MCD14DL MODIS Active Fire Detections data used to defined different burn seasons and histories for sites has not been uploaded and is freely available from online sources detailed in the journal article. </p>
Data for: Soil microbiota explain differences in herbivore resistance between native and invasive populations of a perennial herb
<p><span>Soil microbiota can either slow down or facilitate plant invasions through their effects on plant performance. Associations with soil microbiota can also modify other plant traits such as herbivore resistance, which can indirectly affect the outcome of plant introductions. </span></p> <p><span>We studied the effects of soil microbiota on the perennial herbaceous legume <em>Lupinus polyphyllus</em> that hosts nitrogen-fixing mutualistic bacteria. We compared the plant performance, herbivore resistance, and volatile organic compounds (VOCs) of plants from native (North American) and invasive (Finnish) populations of the species that were inoculated with intact or autoclaved soil from an invasive population. </span></p> <p><span>We found that plants of both origins greatly benefited from the intact soil inoculum with respect to all performance measures considered, suggesting that beneficial nitrogen-fixing rhizobia in the soil play a major role in shaping plant phenotypes. For three traits, effects of the intact soil inoculum were stronger in plants of native origin than in plants of invasive origin (number of leaves, herbivore resistance, and total biomass). With the intact soil inoculum, plants of invasive origin were more resistant to snails than plants of native origin. Strikingly, differences in resistance to snails between plants of different origins disappeared entirely when soil microbes were reduced. Soil inoculum treatment altered the composition of the leaf VOC bouquet similarly regardless of plant origin. </span></p> <p><span>Synthesis: These results demonstrate the ability of <em>L. polyphyllus</em> to associate with and benefit from putatively novel soil microbiota including rhizobia, which has likely contributed to its invasion success. Furthermore, it appears that the invasive populations have adapted to be less reliant on their symbionts, which further facilitates species spread. To our knowledge, this is the first study to demonstrate that differences in herbivore resistance between native and invasive plant populations of the same species can depend entirely on soil microbiota.</span></p>
Data for meta-analysis of the soil greenhouse gas emissions
<p><span>Exploring the </span><span>responses of greenhouse gases (GHGs) emissions to land use conversion or reversion is significant for taking effective land use measures to alleviate global warming.</span> <span>A global meta-analysis was conducted to analyze the responses of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) emissions to land use conversion or reversion, and determine their temporal evolution, driving factors and potential mechanisms. Our results showed that CH4 and N2O responded positively to land use conversion while CO2 responded negatively to the changes from natural herb and secondary forest to plantation. By comparison, CH4 responded negatively to land use reversion and N2O also showed negative response to the reversion from agricultural land to forest. The conversion of land use weakened the function of natural forest and grassland as CH4 sink and the artificial nitrogen (N) addition for plantation increased N source for N2O release from soil, while the reversion of land use could alleviate them to some degree. Besides, soil carbon would impact CO2 emission for a long time after land use conversion, and secondary forest reached the methane uptake level similar to that of primary forest after over 40 years. N2O responses had negative relationships with time interval under the conversions from forest to plantation, secondary forest and pasture. In addition, meta-regression indicated that CH4 had correlations with several environmental variables, and carbon-nitrogen ratio had contrary relationships with N2O emission responses to land use conversion and reversion.</span> <span>And the importance of driving factors displayed that CO2, CH4 and </span><span>N2O</span><span> response to land use conversion and reversion were easily affected by NH4+ and soil moisture, </span><span>mean annual temperature</span><span> and NO3-, total nitrogen and </span><span>mean annual temperature</span><span>, respectively.</span> <span>This study would provide enlightenment for scientific land management and reducing of GHG emissions.</span></p>
Archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil
<p>This is the archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil; submitted to the Journal Science of the Total Environment.</p>
Data for "Mineral soils are an important intermediate storage pool of black carbon in boreal forests"
<p>This data is used in the publication "Mineral soils are an important intermediate storage pool of black carbon in boreal forests".</p> <p>The column plot_id uniquely represents each sample plot in the study and matches the columns of the same name in the complementary dataset "<a href="https://doi.org/10.5281/zenodo.5078669">Dataset for 'Climatic Variation Drives Loss and Restructuring of Carbon and Nitrogen in Boreal Forest Wildfire'</a>". Odd numbers are burnt plots, while the burnt plot_id plus 1 is its paired control.</p> <p>Columns are labeled with the name of sampled soil layer and entries are their associated BC:W values. BC:W is unitless (formed by dividing grams black carbon by grams sample weight). Empty spots mean there was no material at the plot to collect.</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.