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28 results for “root sampling”
Flume Erosion Testing Data of Root-Permeated and Organic Matter Amended Soil Samples Using Three Streambank Boundary Conditions.
The data published here is expected to accompany one publicly available dissertation (Chapter 6 of dissertation) and one separate journal publication. Once published and available online, the metadata will be updated with the relevant article information. The journal article/dissertation will have additional information regarding the published datasets and the methods used to collect the data. All data collected from these studies, and the accompanying Acoustic Doppler Profiler MATLAB files, are presented here. Journal Article title: Artificial Roots and Soil Microorganisms Increase Soil Resistance to Fluvial Erosion
Environmental Data for Soil, Leaf, and Root samples Boston Street Trees and Massachusetts Rural and Urban Forests in Summer 2021
This dataset provides detailed environmental and tree-level data and metadata for over 850 samples collected from 91 trees across an urban-to-rural gradient in Massachusetts. The dataset captures key variables characterizing urban environmental gradients, including soil moisture, pH, temperature, and nitrogen availability. Tree-level attributes include species identification, diameter at breast height (DBH), and growth rate based on previous tree census data. Geographic coordinates and site-specific context (urban forest, rural forest, street tree, forest edge, forest interior) are included to enable spatial analyses. The microbial sequence data associated with this environmental metadata can be found in the NCBI SRA under BioProject accession number PRJNA1297772.
Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana
<p>Plants exude a plethora of compounds, both above- and below ground, to communicate with their environment. Although much is known about this communication above ground, we are only beginning to fathom the identity, level of variation, and role of below-ground chemical signals in a plant’s life. There have been many challenges associated with establishing a standardized methodology for studying root-exuded compounds, thus their role in plant-environment communication is still not well described.</p> <p>Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant <em>Arabidopsis thaliana</em>. We highlight key challenges associated with sampling strategies and develop a framework for analyzing narrow and broad-scale patterns in root exudate composition of a large sample set of natural <em>A. thaliana</em> accessions.</p> <p>Our method consists of <em>in vitro</em> cultivation of individual seedlings inside a plastic mesh followed by a short hydroponic sampling period in micro quantities of ultrapure water. The mesh eases handling individual plants of varying sizes, thus making this setup advantageous for large-scale characterization of root exudates of individual plants in axenic conditions, and can be easily extended for prolonged temporal exudate collection experiments. Furthermore, a short sampling duration minimizes the experiment duration from days to mere hours, and is validated by yielding sufficient signal even with the small volume of sampling solution. An untargeted metabolic profiling analytical approach using ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-QTOF-MS), followed by compound identification using open access software MZMine3 and SIRIUS 5, was used to capture a broad picture of the root exudate composition of <em>A. thaliana</em> accessions. This methodology can be broadly applied for investigating the role of root exudates as signals involved in plant belowground interactions. We report the first findings from the analysis here with results from Columbia genotype.</p> <p>We include here</p> <p> </p> <p>In <strong>Raw datafiles</strong>: The raw datasets obtained from MZmine 3 analysis, which contains aligned features of Columbia genotypes (Sheet1) as well as control samples (Sheet2). The dataset consists of <em>feature (row)ID, average (mass-to-charge ratios) m/z</em> and <em>retention times (RT)</em> across samples for individual features. It also includes sample-specific information including <em>feature status, name, m/z, RT, feature peak height,</em> and <em>area</em>. We also include a filtered datasheet excluding the features obtained in control as well as samples (Sheet3). Sheet 4 contains the phenotypic data on the number of leaves and rosette size of the 28 replicates at the time of sampling, along with the total peak area for each sample from MZmine data.</p> <p>In <strong>Supplementary tables</strong>: The 354 metabolites obtained after filtering out control features are listed with their <em>mass-to-charge ratios</em>, <em>retention times, and the mean, variance and coefficient of variation of the peak areas </em>(Supplementary Table 1). Supplementary Table 2 details the features identified by SIRIUS 5 with their <em>mass-to-charge ratios, retention times, chemical formula, chemical annotations,</em> and corresponding <em>probabilities scored by SIRIUS</em></p> <p>In <strong>Extended data analysis:</strong> Contains supporting data analysis for reproducibility and validity of our method for root exudate collection and analysis in <em>Arabidopsis thaliana.</em> These extended data analyses enhance the understanding of the relationship between plant phenotypic traits, peak area, and variation in compound abundance</p>
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton. in Spesovicornea Pacltovae Gen. Nov. Et Sp. Nov., A New Elateroid Sporomorph From The Bohemian Cenomanian (Czech Republic)
Text-fig. 3. Borehole section in the Blansko Graben with lithology, distribution of palynomorphs, macroflora and macrofauna (modified after Čech, unpublished report). 1 – Spesovicornea pacltovae, 2 – Platanus sp., 3 – Myrtophyllum angustum (VEL.) KNOBOCH, 4 – Gleichenia sp.), 5 – percentage of land-derived palynomorphs, 6 – percentages of marine palynomorphs, 7 – glauconite, 8 – pyrite nodules, 9 – macrofauna, 10 – productive palynological samples, 11 – carbonized roots, 12 – conglomerate, 13 – sandstone, 14 – claystone, 15 – coal, 16 – granite and granodiorite of the Brno pluton.
Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species - Sampling Raw Data
<p>Sampling Raw Data for the manuscript "<strong>Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species </strong>" </p> <p>R Code for producing the sunburst plots from the data obtained by classyFire</p> <p> </p>
Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities
<p>Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging.</p> <p><span><span><span><span><span><span><span><span><span><span><span>Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species meta-reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multi-species root samples are mapped to this meta-reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>The msGBS signal of 111 mock-mixture root samples, with up to 8 plant species per sample, was used to calculate the within-species abundance. Optional subsequent calibration yielded the across-species abundance. The within- and across-species abundances highly correlated (R<sup>2 </sup>range 0.72-0.94 and 0.85-0.98, respectively) to the biomass-based species abundance. Compared to a qPCR based method which was previously used to analyze the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><a>msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions.</a></span></span></span></span></span></span></span></span></span></span></span></p> <p>This dataset belongs to the article "<span><span><span><span><span><span><span><span><span><span><span><b>msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities</b>". </span></span></span></span></span></span></span></span></span></span></span>msGBS is a technique that uses Genotyping By Sequencing on mixed plant species root samples which, after a filtering step to increase the taxonomic resolution and calibration, is able to estimate plant species abundances. </p> <p>The article uses data of two different experiment:</p> <ol> <li>the Jena field survay (13 plant species) and</li> <li>the Dutch field survay (120 plant species).</li> </ol>
Gene catalogs and KEGG annotation related to root metagenomic samples
<p><span>Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of </span><span>crop </span><span>root microbiome</span><span>s</span><span>. Combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (</span><span>68.9 % </span><span>from isolates) </span><span>and 1,817 novel species,</span><span> expanding crop root bacterial diversity by </span><span>290.6%</span><span>. The crop root viral genome collection (CRVC) contains 9,736 nonredundant viral genomes, with 1,572 previously unreported genus-level clusters in crop roots. From these data, we identified conserved bacterial </span><span>functions</span><span> enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria–virus </span><span>connections</span><span> in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture. </span></p> <p> </p> <p>The gene sets of 14 datasets are available under this accession.</p>
Data from: Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting
Open the record for dataset details and reuse information.
Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities
Open the record for dataset details and reuse information.
Supplementary material 2 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
: Data type: species data
Figure 6 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 6 Colonial morphotypes of Posidoniomycesatricolor in vitro (type isolate BRK-21). a Compact morphotype with substrate mycelium b, d compact colonies with a cerebriform pattern c colony of P.atricolor on PCA e rhizoidal and compact (arrow) daughter colonies on PCA washed with sterile tap water f detail of the colonies encircled in e; g, h terminal capitate swellings on the surface of compact colonies i–k conspicuous swellings on aerial mycelium. Scale bars: 500 μm (a, d), 1000 μm (b, c), 5 mm (e), 200 μm (f), 100 μm (g), 20 μm (h).
Figure 5 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 5 In vivo root colonisation pattern and in vitro cultural aspects of Posidoniomycesatricolor. a In vivo colonisation on the root surface (arrows) and in the hypodermis (asterisks) of P.oceanicabDSE colonisation on the root surface c germinating microsclerotia stained with trypan blue (arrows) d compact colony developed from microsclerotia (arrow) e surface-sterilised root segments yielding P.atricolor compact colonies (black arrows), sometimes with substrate mycelium (white arrows) f compact colonial morphotype g mycelial colonial morphotype h mycelial morphotype developing from microsclerotia (arrows) in transversal section. Scale bars: 20 μm (a, b), 50 μm (c), 100 μm (d), 200 μm (f, h), 500 μm (g).
Figure 2 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 2 Map of the Mediterranean Sea with location of our 32 sampling sites. For further details see Table 1.
Figure 4 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 4 Phylogram and map showing a distribution pattern of Posidoniomycesatricolor. a Phylogram generated from maximum likelihood analysis based on ITS sequence data for Posidoniomycesatricolor and representatives of the Aigialaceaeb map of the Mediterranean Sea with our 32 sampling sites. Sites in blue, orange, violet and green colour indicate locations of P.atricolor strains with corresponding mutations in ITS2 sequences.
Figure 3 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 3 Phylogram generated from maximum likelihood analysis based on combined nucLSU, nucSSU and RPB2 sequence data for Posidoniomycesatricolor and the Aigialaceae. Species names given in bold are type species. The ex-type of the taxonomic novelty is in bold and blue. An asterisk (*) indicates branches with ML BS = 100% and PP values = 1.0. Branch support of nodes ≥ 70 % ML BS and ≥ 0.90 PP is indicated above or below branches.
Figure 1 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
Figure 1 The dominant Mediterranean seagrass Posidoniaoceanica. a Overall appearance, note dense branched root system of the seagrass (encircled) bPosidoniaoceanica growing on an approx. 1.5 m thick layer of matte c typical habitat of the dominant Mediterranean seagrass, note the layer of shed seagrass leaves on the seabed.
Supplementary material 1 from: Vohník M, Borovec O, Kolaříková Z, Sudová R, Réblová M (2019) Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica. MycoKeys 55: 59-86. https://doi.org/10.3897/mycokeys.55.35682
: Data type: species data
Gene expression profiles from multimodal patch-seq neuron samples of the pig dorsal root ganglion
GEO Series GSE263466. Sus scrofa. 226 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing of GmPHD6 over-expression and RNAi transgenic hairy roots and the control samples of K599
GEO Series GSE85077. Glycine max. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq study on root samples from Olea europaea cultivars
GEO Series GSE152236. Olea europaea. 72 samples. Type: Expression profiling by high throughput sequencing.
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