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2,078 results for “soil data”
All data and code from Honeyman, et al. 2022: Statistical learning and uncommon soil microbiota explain biogeochemical responses after wildfire
<p>The zipped folder contains all data and code necessary to reproduce analyses from the manuscript. Note that raw sequencing reads are available at NCBI SRA under BioProject PRJNA767436.</p>
Data from: Plant diversity improves resistance of plant biomass and soil microbial communities to drought
<p>1. Biodiversity is known to affect ecosystem resistance and have implications for the maintenance of ecosystem functions and services under climate change. Compared to numbers of studies focusing on aboveground vegetation, the response of belowground communities to abiotic stresses along plant diversity gradients is often ignored and is considered an important knowledge gap in ecosystem ecology. Here we conducted an integrative research to evaluate the resistance of plant biomass, and soil microbial communities and associated functional profiles to drought under varying plant diversity.</p> <p>2. We carried out a three-year manipulation experiment by factorially controlling plant diversity gradient (1, 2, 4, and 8 species richness) and soil moisture treatment (drought and non-drought), and investigated the responses of plant biomass, soil bacterial and fungal diversity and community composition, soil glomalin, and five key soil enzymes.</p> <p>3. We found that plant diversity significantly improved the resistance of soil fungal communities and microbial functional profiles characterized by soil glomalin and five key enzymes, which was partly driven by the availability and accessibility of soil resources (e.g., soil moisture and organic matter) mediated by plant diversity. Further, our results indicated that the enhanced resistance of fungal communities was consistent with ecological insurance theory that diverse fungal communities at high plant diversity had a higher probability of containing taxa that adapt to drought.</p> <p>4. <em>Synthesis</em>. Our study provides novel empirical insights into the mechanism underlying the regulatory effect of plant diversity on resistance of aboveground vegetation and belowground biota to drought, with implications for understanding ecosystem response to climate change and improving biodiversity conservation practices.</p>
Data from: Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island
<p>Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype-level DNA sequence data for soil mesofauna assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local-scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonisation and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.</p>
Spectra induce polarization data of bacteria in soil
<p><span>Real-time monitoring of microbial activity in porous media is still facing critical challenges because conventional analytical procedures are intrusive. Induced polarization (IP) has shown promises as a non-intrusive monitoring approach of such process. However, there is still a </span><span>lack of quantitative analysis of soil column experiments to show how IP-based parameters can be related to the density of bacteria. </span><span>The </span><span>evolution of </span><span>bacteria density and induced polarization is here performed in a soil-packed column experiment using </span><span>Pseudomonas Aeruginosa O1 (PAO1).</span></p> <p><span><span>A quantitative relationship between the quadrature conductivity and the bacteria density is</span> <span>established and then used </span><span>to assess bacteria growth and decay</span><span> and </span><span>infer the Monod kinetic parameters. The </span><span>Monod kinetic parameters inferred from the column experiments mimicking field conditions are different from those obtained from a batch experiment.</span></span></p>
GPM_API - Global Hourly Soil Moisture from GPM IMERG Data - 2015
<p><strong># GPM_API 2015</strong></p> <p>GPM_API data root: <a href="https://zenodo.org/record/6489998">https://zenodo.org/record/6489998</a></p> <p><strong># Related article:</strong></p> <p>Ramsauer, T., & Marzahn, P. (2023). Global Soil Moisture Estimation based on GPM IMERG Data using a Site Specific Adjusted Antecedent Precipitation Index. <em>International Journal of Remote Sensing</em>, 44(2), 542-566.</p> <p>Article: <a href="https://doi.org/10.1080/01431161.2022.2162351">https://doi.org/10.1080/01431161.2022.2162351</a></p> <p>Free PDF: <a href="https://www.tandfonline.com/eprint/6VHQ7JCCJXSPAMG3PVIG/full?target=10.1080/01431161.2022.2162351">www.tandfonline.com/eprint/6VHQ7JCCJXSPAMG3PVIG/full?target=10.1080/01431161.2022.2162351</a></p>
Data to accompany: Seedling responses to soil moisture amount versus pulse frequency in a dominant semi-arid shrub
<p>The timing, frequency and quantity of rainfall is rapidly changing in dryland regions, leading to profound alterations to dryland plant communities. Understanding dryland plant responses to future rainfall scenarios is crucial for implementing proactive management strategies, particularly in light of intensive changes to land cover concurrent with climate change. One such change is woody plant encroachment, an increasing abundance of woody plant species in areas formerly dominated by grasslands or savannas. The continued encroachment of <em>P.</em> <em>velutina</em> will depend, in part, on seedling capacity to establish and thrive under future climate conditions. Seedling performance is primarily impacted by soil moisture conditions that are governed by precipitation amount (quantity) and frequency. We hypothesized that H1) seedling performance would be enhanced by both greater soil moisture and greater pulse frequency, such that seedlings with similar mean soil moisture would perform best under high moisture pulse frequency. Alternatively, H2) mean soil moisture would have greater influence than pulse frequency, such that at a given pulse frequency would have little influence on seedling performance. The hypotheses were tested by growing 256 <em>P. velutina </em>seedlings under two distinct soil moisture treatments, each of which was maintained by two different pulse frequency treatments. Contrary to H1, mean soil moisture had far greater impact than pulse frequency on seedling growth, photosynthetic gas exchange, leaf chemistry and biomass allocation. These results indicate that <em>P. velutina</em> seedling establishment may be more responsive to rainfall amount than rainfall frequency.</p>
Data from: Do microorganism stoichiometric alterations affect carbon sequestration in paddy soil subjected to phosphorus input?
Ecological stoichiometry provides a powerful tool for integrating microbial biomass stoichiometry with ecosystem processes, opening far-reaching possibilities for linking microbial dynamics to soil carbon (C) metabolism in response to agricultural nutrient management. Despite its importance to crop yield, the role of phosphorus (P) with respect to ecological stoichiometry and soil C sequestration in paddy fields remains poorly understood, which limits our ability to predict nutrient-related soil C cycling. Here, we collected soil samples from a paddy field experiment after 7 years of superphosphate application along a gradient of 0, 30, 60, 90 (P-0 through P-90, respectively) kg P ha-1 y-1 in order to evaluate the role of exogenous P on soil C sequestration through regulating microbial stoichiometry. P fertilization increased soil total organic C and labile organic C by 1-14% and 4-96%, respectively, while rice yield is a function of the activities of soil β-1, 4-glucosidase (BG), acid phosphatase (AP) and the level of available soil P through a stepwise linear regression model. P input induced C limitation as reflected by decreases in the ratios of C:P in soil and microbial biomass. An ecoenzymatic ratio indicating microbial investment in C versus P acquisition, i.e., ln(BG):ln(AP), changed the ecological function of microbial C acquisition and was stoichiometrically related to P input. This mechanism drove a shift in soil resource availability by increasing bacterial community richness and diversity, and stimulated soil C sequestration in the paddy field by enhancing C degradation-related bacteria for the breakdown of plant-derived carbon sources. Therefore, the decline in the C:P stoichiometric ratio of soil microorganism biomass under P input was beneficial for soil C sequestration, which offered a "win-win" relationship for the maximum balance point between C sequestration and P availability for rice production in the face of climate change.
Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.
Data from: Soil CO2 and O2 concentrations illuminate the relative importance of weathering and respiration to seasonal soil gas fluctuations
[No abstract entered]
Data for "Reactive nitrogen input and low rainfall mitigate soil respiration responses to warming"
<p>This dataset is used to make tables and figures for the paper entitled "Reactive nitrogen input and low rainfall mitigate soil respiration responses to warming" submitted to Ecology Letters in July 2022. It contains field monitoring data on soil respiration and ecosystem productivity and a meta-analysis database.</p>
Data from: Plant-litter-soil feedbacks in common grass species are slightly negative and only marginally modified by litter exposed to insect herbivory
<p>Purpose Insect herbivory affects plant growth, nutrient and secondary metabolite concentrations and litter quality. Changes to litter quality due to insect herbivory can alter decomposition, with knock on effects for plant growth mediated through the plantlitter- soil feedback pathway. </p> <p>Methods Using a multi-phase glasshouse experiment, we tested how changes in shoot and root litter quality of fast- and slow-growing grass caused by insect herbivores affect the performance of response plants in the soil in which the litter decomposed. </p> <p>Results We found that insect herbivory resulted in marginal changes to litter quality and did not affect growth when plants were grown with fast- versus slow-growing litter. Overall, presence of litter resulted in reduced root and shoot growth and this effect was significantly more negative in shoots versus roots. However, this effect was minimal, with a loss of c. 1.4% and 3.1% dry weight biomass in roots versus shoots, respectively. Further, shoot litter exposed to insect herbivory interacted with response plant identity to affect root growth.</p> <p>Conclusions Our results suggest that whether litter originates from plant tissues exposed to insect herbivory or not and its interaction with fast- versus slow-growing grasses is of little importance, but species-specific responses to herbivory-conditioned litter can occur. Taken collectively, the overall role of the plant-litter-soil feedbackpathway, as well as its interaction with insect herbivory, is unlikely to affect broader ecosystem processes in this system.</p>
Raw data: Soil microbes drive aboveground plant–pathogen–insect interactions
<p class="MsoNormal"><span>Plants interact with a large diversity of microbes and insects, both below and above ground. While studies have shown that belowground microbes affect the performance of plants and aboveground organisms, we lack insights into how belowground microbial communities may shape interactions between aboveground pathogens and insects. We investigated how soil microbiomes and aboveground organisms affect plant growth and development, and whether differences in soil microbiomes influence interactions between aboveground organisms. We conducted a growth-chamber experiment with oak seedlings (<em>Quercus robur</em>) growing in three soils with similar abiotic soil properties but with distinct natural soil microbiomes.</span> Seedlings were subjected to single or dual attack by powdery mildew (<em>Erysiphe alphitoides</em>) and aphids (<em>Tuberculatus annulatus</em>), either in the presence or absence of prior attack by a free-feeding caterpillar (<em>Phalera bucephala</em>). <span>Soil microbiomes were associated with differences in seedling height, and seedlings with multiple aboveground organisms had more but smaller leaves than healthy seedlings. The soil microbiome affected the severity of powdery mildew infection, and mediated the impact of co-occurring aboveground organisms on aphid population size. Our study highlights that plant performance is affected by natural soil microbiomes as well as aboveground organisms, and that natural soil microbiomes can affect interactions between pathogens and insects. These findings are important to understand species interactions in natural systems, as well as for practical applications, such as manipulation of soil microbiomes to manage agricultural pests and diseases.</span></p>
Soil respiratation data for the Yellow River Delta coastal wetlands
<p>Continuous soil respiration data which is composed of heterotrophic respiration and autotrophic respiration</p>
Data from : Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China
<p><b>Aim: </b>There have been numerous studies of forest-soil microbial biogeography, but an integrated view of edaphic factors, plant, climatic factors, and geographic distance in determining the variation of bacterial community and assembly processes remains unclear at large spatial scales. Here, we analyzed the factors affecting the biogeographic pattern and assembly processes of soil bacterial communities under 58 tree species in five natural mountain forests.</p> <p><b>Location: </b>Eastern China.</p> <p><b>Major taxa studied: </b>Bacterial communities.</p> <p><b>Methods: </b>Hierarchical partitioning analysis and distance decay models were performed to evaluate the relative contributions of plant phylogeny, environmental, and spatial variables to the composition of bacterial communities. We applied the Nearest Taxon Index (NTI), β-Nearest Taxon Index (βNTI), and the modified Raup-Crick metric to reveal the mechanisms of bacterial assembly processes.</p> <p><b>Results: </b>We found that plant phylogeny accounted for a significant, but minor, fraction (0.7%) of the variation in composition of bacterial communities. In contrast, soil pH was the primary determinant of bacterial diversity and community composition, independently explaining 68.6% and 69.9% of the variation, respectively. Based on the NTI analysis, bacterial community assembly was more phylogenetically clustered with increasing soil pH. Variable selection was the predominant process explaining bacterial community assembly when differences in soil pH were ≥ 0.83, whereas homogenizing dispersal dominated when differences in soil pH were < 0.83. However, there was no significant relationship between plant phylogenetic distance and βNTI.</p> <p><b>Main conclusions: </b>Our findings provide strong evidence that soil pH predominantly determines bacterial distribution and mediates the relative impact of stochasticity and determinism in soil bacterial community assembly. This suggests that climate-change associated forest soil acidification could have a dramatic impact on soil bacterial diversity, composition, and function.</p>
Data supporting "Soil stratum tides"
<p>This archive contains data that support the conclusions of the manuscript "Soil stratum tides". Detailed information is provided in the .xlsx file.</p> <p> </p> <table> <tbody> <tr> <td> <p><strong>Sheet No.</strong></p> </td> <td> <p><strong>Data type</strong></p> </td> <td> <p><strong>Unit</strong></p> </td> <td> <p><strong>Borehole</strong></p> </td> <td> <p><strong>Figure in manuscript</strong></p> </td> </tr> <tr> <td> <p>1</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-1</p> </td> <td> <p>2</p> </td> </tr> <tr> <td> <p>2</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-2</p> </td> <td> <p>2</p> </td> </tr> <tr> <td> <p>3</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-3</p> </td> <td> <p>2</p> </td> </tr> <tr> <td> <p>4</p> </td> <td> <p>Groundwater level</p> </td> <td> <p>m</p> </td> <td> <p>BO-1</p> </td> <td> <p>2</p> </td> </tr> <tr> <td> <p>5</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-1</p> </td> <td> <p>3</p> </td> </tr> <tr> <td> <p>6</p> </td> <td> <p>Groundwater level tidal fluctuation</p> </td> <td> <p>m</p> </td> <td> <p>BO-1</p> </td> <td> <p>3</p> </td> </tr> <tr> <td> <p>7</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-1</p> </td> <td> <p>4</p> </td> </tr> <tr> <td> <p>8</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-2</p> </td> <td> <p>4</p> </td> </tr> <tr> <td> <p>9</p> </td> <td> <p>Soil tidal strain</p> </td> <td> <p>µε</p> </td> <td> <p>BO-3</p> </td> <td> <p>4</p> </td> </tr> <tr> <td> <p>10</p> </td> <td> <p>Temperature</p> </td> <td> <p>°C</p> </td> <td> <p>BO-1</p> </td> <td> <p>S4</p> </td> </tr> <tr> <td> <p>11</p> </td> <td> <p>Strain for interrogator stability testing</p> </td> <td> <p>µε</p> </td> <td> <p>N/A</p> </td> <td> <p>S5</p> </td> </tr> <tr> <td> <p>11</p> </td> <td> <p>Temperature for interrogator stability testing</p> </td> <td> <p>°C</p> </td> <td> <p>N/A</p> </td> <td> <p>S5</p> </td> </tr> <tr> <td> <p>12</p> </td> <td> <p>River water level</p> </td> <td> <p>m</p> </td> <td> <p>N/A</p> </td> <td> <p>S6</p> </td> </tr> </tbody> </table>
Data set: Native forest conversion alters soil macroinvertabrate diversity and soil quality in tropical mountain landscapes of northern Ecuador
<p>Data set an related material of the article entitled: Native forest conversion alters soil macroinvertabrate diversity and soil quality in tropical mountain landscapes of northern Ecuador</p>
Data for: A general framework for modelling thermal and hydric constraints on eggs developing in soil
<p>Data files to reproduce all the figures and appendices of "A general framework for modelling thermal and hydric constraints on eggs developing in soil".</p>
Sequence data of 190 tea plantations soil microorganisms
<p>The file contains 190 clean fastq data for soil samples from 19 different types of tea plantations in two districts of Pu'er city, which designed for the study of soil bacterial communities .The tea plantations all belong to Pu'er city, Yunnan province from China.</p>
Data of: Quantitative imaging of the 3-D distribution of cation adsorption sites in undisturbed soil
<p>Here you can find the data underlying our article 'Quantitative imaging of the 3-D distribution of cation<br> adsorption sites in undisturbed soil' in the journal SOIL. In case there are any questions please contact the corresponding author directly. </p>
Neutron tomography data collected with MCP detector (soil specimen)
<p>Neutron tomography data collected with MCP detector in July 2016 at the ISIS Neutron Spallation Source, UK as part of the scientific commissioning of the neutron imaging beamline, IMAT.</p> <p>Different projection angles were acquired over an angular range of 180° (first 41 projections with angular step of 3° and the last 14 projections with angular step of 4°).</p> <p> </p>
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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.
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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.