Find research datasets worth reusing

openCustomDec 2003View details →

Root biomass on Northern Hog Island at the Virginia Coast Reserve 1991-1992

The data include live fine root biomass, dead fine root biomass, and detrital material. biomass was sampled at 10, 20,30 and 40 cm depths. All data are in g/m-squared separated by depth. Fine roots were less than or equal to 2 mm diameter. Roots were extracted from dune and swale plant communities across a barrier island chronosequence.

openCustomJan 1996View details →

Fine root production on Hog Island chronosequence at the Virginia Coast Reserve . 1991

The data include live fine roots (less than or equal to 2 mm diameter). Root growth was sampled at 10, 20, 30 and 40 cm depth. All data are in g/meter square/year. Fine roots were extracted along a chronosequence of barrier island and dune communities.

openCustomSep 1998View details →

Minirhizotron Root Data for Hog Island, VA 1992-1998

Minirhizotron data from fertilization experiment. On 36-year old dune ridge on Hog Island from 1992 to 1998. These tubes were sampled twice a year with the fall data from 1992 included. In most cases 26 frames were sampled randomly within specific depth intervals and digitized for each tube. Plot 1 was discontinued after 10/93 and Plot 2 was discontinued after 4/93. In this data set if there were no roots in a frame then no ROOT ID appears and length and width are 0. fertilization treatment = In 1992, three applications of 15 gN / m2 (March, June, October). After 1992, 15 gN / m2 applied once per year (mid-summer) through 1998.

openCustomDec 2000View details →

Fine Root Biomass on North Hog Chronosequence, Virginia Coast Reserve, 1991-1992

A sequential coring method was used to determine live fine-root biomass (LFRB) along a barrier island dune and swale chronosequence on Hog Island, VA, between February 1991 and February 1992.

opencc-by-4.0Dec 2019View details →

Tandem Tag Assay Optimized for Semi-automated in vivo Autophagic Activity Measurement in Arabidopsis thaliana roots

This is demo data set for AuTToFlux, the semi-automated assay for in vivo autophagic activity measurement in Arabidopsis thaliana roots. The protocol and software required for the assay are available here: <a href="https://github.com/jonasoh/AuTToFlux">https://github.com/jonasoh/AuTToFlux</a>

opencc-by-4.0May 2020View details →

Data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation

Collection of data files used in the paper titled: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation. Additional dataset which covers the noise study CT scans and digital volume correlation noise studies can be found in DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3361832</a> Data contains the following: <ul> <li>X-ray CT data for the interrupted direct shear tests of a soil sample containing a Willow plant. The first file is the specimen scanned unloaded, followed by seven incremental shear load steps to 20 mm shear displacement. Files are 8-bit unsigned and 1800x1800x1600px. Voxel resolution is 0.04642 mm. <ol> <li>20180430_HUTCH_1839_DJB_willow_C_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_A_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_B_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_C_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_D_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_E_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_F_8-bit_1800x1800x1600.raw</li> <li>20180430_HUTCH_1839_DJB_willow_C_Load_G_8-bit_1800x1800x1600.raw</li> </ol> </li> <li>Direct shear vs. displacement data is presented in an Excel spreadsheet: <ul> <li>All_load_data_with_reducing_area.xlsx</li> </ul> </li> <li>Normal and shear strain DVC data which has been averaged and plotted against specimen depth is presented in an Excel spreadsheet: <ul> <li>Average_slice_vs_depth_data_all_samples_all_loads3.xlsx</li> </ul> </li> <li>CT scan metadata giving information to the scan settings, voxel resolution, etc. is contained in a .zip file which consists of .xtekct and .XML files generated from the Nikon CT scanner. <ul> <li>CT_Scan_Metadata.zip</li> </ul> </li> <li>Drawings and Solidworks CAD files of the direct shear test rig are contained within the .zip file. There are a number of parts to the assembly. The file SSSB1003-5.SLDASM contains the complete assembly of the direct shear rig and will help identify the part names. The folder CAD_Drawings contains pdf documents of the part drawings. <ul> <li>Direct_Shear_Drawings_Solidworks_Files.zip</li> </ul> </li> <li>Tabulated DVC data taken at 32x32x32px subset size is contained inside a .zip file. These consist of tab separated .dat files from unloaded (data_1.dat) through incremental load steps Load A, Load B... Load G, (data_2.dat, data_3.dat... data_8.dat). The structure of the .dat file contains columns of data with each column number corresponding to the following: (1) x, (2) y (3) z, (4) vx, (5) vy,  (6) vz, (7) exx, (8) eyy, (9) ezz, (10) exy, (11) exz, (12) eyz, (13) volumetric strain, (14) is valid. Columns 1-3 are subset positions in mm, 4-6 are displacements in mm, 7-9 are normal strains, 10-12 are shear strains, 13 is volumetric strain and 14 is a binary value indicating if the subset is valid. <ul> <li>DVC_Load_Data_Willow_C.zip</li> </ul> </li> <li>Tabulated DVC data applied to the load step CT data at 32, 48, 64, 96, 128 pixels is presented in the .zip files containing .dat tab separated files. The structure of the .dat files is described in the previous bullet point. These files were used to construct the noise study applied to incrementally loaded CT data by sampling regions away from the shear zone where the strain signals are close to zero. <ul> <li>DVC_Noise_Study_Data_Load_Steps_Willow_C.zip</li> </ul> </li> <li>Processed noise study data which compares the effects of DVC subset size is presented in the .xlsx file. This file contains both the controlled noise experiment data (stationary, magnification and rigid body motion) and noise study data applied to incrementally loaded data using sampled regions away from the shear zone where the strain signals are close to zero. <ul> <li>Willow_C_Processed_Noise_study2.xlsx</li> </ul> </li> <li>Tabulated data which compares the local x displacement vs depth profile from DVC and direct measurement of root position is contained in the following Excel spreadsheet file: <ul> <li>X_Displacement_Root_and_DVC_Comparison_Willow C.xlsx</li> </ul> </li> </ul>

opencc-zeroMay 2020View details →

Data from: The effect of root-associated microbes on plant growth and chemical defence traits across two contrasted elevations,

1. Ecotypic differences in plant growth and anti-herbivore defence phenotypes are determined by the complex interactions between the abiotic and the biotic environment. 2. Root-associated microbes (RAMs) are pervasive in nature, vary over climatic gradients, and have been shown to influence the expression of multiple plant functional traits related to biomass accumulation and biotic interactions. We addressed how variation in climatic conditions between lowland and sub-alpine habitats in the Alps and RAMs can independently or interactively affect plant growth and anti-herbivore defence trait expression. 3. To address the contribution of climate and RAMs on growth and chemical defences of high- and low-elevation Plantago major ecotypes, we performed a full-factorial reciprocal transplant field experiment at two elevations. We coupled it with plant functional trait measurements and metabolomics analyses. 4. We found that local growing climatic conditions mostly influenced how the ecotypes grew, but we also found that the high- and low-elevation ecotypes improved biomass accumulation if in the presence of their own-elevation RAMs. Second, we found that while chemical defence expression was affected by climate, they were also more highly expressed when plants were inoculated with low elevation RAMs. 5. Synthesis – Our research demonstrated that RAMs from contrasted elevations impact how plants grow or synthesize toxic secondary metabolites. At low elevation, where biotic interactions are stronger, RAMs enhance plant biomass accumulation and the production of toxic secondary metabolites.

opencc-zeroJun 2020View details →

Independent evolutionary changes in fine-root traits among main clades during the diversification of seed plants

Rationale: Changes in fine-root morphology are typically associated with transitions from the ancestral arbuscular mycorrhizal (AM) to the alternative ectomycorrhizal (ECM) or non-mycorrhizal (NM) associations. However, the modifications in root morphology may also coincide with new modifications in leaf hydraulics and growth habit during angiosperm diversification. These hypotheses have not been evaluated concurrently, which limits our understanding of the causes of fine-root evolution. Methods: To explore the evolution of fine-root systems, we assembled a 600+ species database to reconstruct historical changes in seed plants over time. We utilize ancestral reconstruction approaches together with phylogenetically informed comparative analyses to test whether changes in fine-root traits were most strongly associated with mycorrhizal affiliation, leaf hydraulics or growth form. Key Results: Our findings show significant shifts in root diameter, specific root length and root tissue density as angiosperms diversified, largely independent from leaf changes or mycorrhizal affiliation. Growth form was the only factor associated with fine-root traits in statistical models including mycorrhizal association and leaf venation, suggesting substantial modifications in fine-root morphology during transitions from woody to non-woody habits. Conclusion: Divergences in fine-root systems were crucial in the evolution of seed plant lineages, with important implications for ecological processes in terrestrial ecosystems.

opencc-zeroJul 2020View details →

Data for: Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways

Premise of Study Plant endophytic bacterial strains can influence plant traits such as leaf area and root length. Yet, the influence of more complex bacterial communities in regulating overall plant phenotype is less explored. Here, we conducted two complementary experiments to test if we can predict plant phenotype response to changes in microbial community composition. Methods In the first study, we inoculated a single genotype of Populus deltoideswith individual root endophytic bacteria and measured plant phenotype. Next, single inoculation data were used to predict phenotypic traits in mixed three-member community inoculations, which we tested in the second experiment. Key Results When in isolation, each bacterial endophyte significantly but weakly altered plant phenotype relative to non-inoculated plants. In mixture, bacterial strain BurkholderiaBT03, constituted at least 98% of community relative abundance. Yet, plant resource allocation and tissue nutrient concentrationswere disproportionately influenced by Pseudomonas sp.GM17, GM30, and GM41. We found a 10% increase in leaf mass fraction and a 11% decrease in root mass fraction when replacingPseudomonas GM17 with GM41 in communities containing both Pseudomonas GM30 and BurkholderiaBT03. Conclusions Our results indicate that interactions among endophytic bacteria may drive plant phenotype over the contribution of each strain individually. Additionally, we have shown that low-abundant strains contribute to plant phenotype challenging the assumption that the dominant strains will drive plant function.

opencc-zeroJul 2020View details →

Data from: Local soil legacy effects in a multi-species grassland community are underlain by root foraging and soil nutrient availability

1. Plant soil legacies consisting of species-specific microbial communities are hypothesized to play a critical, structuring role in plant species co-existence processes. Plant species are thought to perform worse on soil conditioned by the same species compared to soil of other species, which serves as a self-limitation mechanism and averts mono-dominance of strong competitors. Here we test in a multi-species community setting, whether root colonisation and resource utilisation of soil patches with distinct soil legacies, are consistent with this hypothesis. 2. We grew eight grassland species together in an outdoor mesocosm setup in unconditioned soil and created soil patches in these communities conditioned by one of four plant species, or a soil mixture of all four. During two subsequent growing seasons, we tested the effect of these conditioned soil patches on belowground root colonisation into the patches of each surrounding plant species using a novel sequencing based approach. In addition, we tested the effect of soil conditioning on local root functioning by injecting tracers into the soil patches and measuring the recovery in aboveground biomass. 3. Against expectations, plant species did not place less roots in own soil patches compared to foreign soil patches, nor did species take up less tracer from own compared to foreign soil patches. Using structural equation modelling, we found that tracer uptake of the plant species was to a varying degree explained by root densities in the various soil patches and by differing soil nutrient availability of the soil patches. We conclude that soil legacy effects are inextricably connected to soil nutrient availability, which needs to be taken into account in plant-soil feedback research to understand the processes that shape plant communities. 4. Synthesis. We found that soil legacy effects in complex, multi-species semi-field conditions did not match expectations based on theory and experiments in controlled conditions. Among the many complicating factors that may modify or even overrule soil legacy effects in semi-field settings, we identified soil nutrient availability as a critical force that may, together with soil biota, shape plant species co-existence processes.

opencc-zeroAug 2020View details →

Root trait responses to drought are more heterogeneous than leaf trait responses

Drought can strongly modify plant diversity and ecosystem processes. As droughts are expected to intensify in the future, it is important to better understand plant responses to this global driver. Root traits are an overlooked but powerful predictor of plant responses to drought because they are in direct contact with the soil environment and are responsible for taking up nutrients and water. Here, we determine which root traits are sensitive to drought and the magnitude of that response. We also tested whether root trait relationships with shoot biomass are affected by drought and to what extent all these responses depend on plant species identity. To do so, we conducted a glasshouse experiment with 24 plant species grown in pots (10 replicates per species), which included grasses, forbs and legumes. All replicates were well watered during the first month and then half of them were kept under drought (30 % water holding capacity (WHC)), with the other half serving as control (70 % WHC). After two months of treatment, leaf and root traits were measured. Leaf traits had a strong and more uniform response to drought compared to root traits. Root trait responses were variable and differed among plant species. Overall, grasses and several forbs had increased root diameter with drought while forbs had decreased specific root surface area (SRSA) and specific root length (SRL). Increase of root diameter and reduction of root elongation or sacrificing fine roots are different strategies that may promote nutrient and water acquisition, depending on plant species identity. Our results identify changes in root morphological traits as mechanisms to likely tolerate drought and highlight that, although such drought responses are species-specific, they are phylogenetically clustered.

opencc-zeroAug 2020View details →

Soil fungi and fine root biomass mediate drought-induced reductions in soil respiration

Climate change has increased the frequency and intensity of droughts, with potential impacts on carbon (C) release from soil (i.e., soil respiration, Rs). Although numerous studies have investigated drought-induced changes in Rs, how roots and the soil microbial community regulate responses of Rs to drought remains unclear. We conducted a 4-year field experiment (2014 - 2017) with three treatments (i.e., 70% rainfall reduction, control and ambient) in a subtropical forest to examine effects of drought on Rs and its components [i.e., autotrophic (Ra) and heterotrophic respiration (Rh)] and explore the mechanisms underlying these effects. Drought significantly decreased Rs by 17% averaged over the 4 years, but it had no significant effect in the first experimental year. The decrease in Rs was mediated by soil fungi and fine root biomass. Fine root biomass was correlated negatively with Ra and Rs under drought, but positively in the control treatment. Furthermore, drought treatments increased physiological stress in the bacterial community. Microclimate, root biomass, and microbial biomass jointly explained 79% and 65% of the variance in Rs for the control and drought treatments, respectively. Structural equation model (SEM) analysis indicated that microclimate affected Rs via its impact on fine root biomass and (under drought conditions) on fungal biomass. Our results highlight the complex interactions between microclimate, roots and soil microbes in regulating Rs under drought in subtropical forest ecosystems. Incorporating these interactions into land surface models may improve predictions of climate change impacts on forest ecosystems.

opencc-zeroAug 2020View details →

Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a>

opencc-by-4.0Apr 2020View details →

data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)

Data sets and trees for the Rasplus et al. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1 *.phy = Data sets (phylip format) [see Table 2 of the paper for more details]. - mergeR1R2.phy : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads) - mergeR1R2_GCinfmean.phy : loci with GC content inferior or equal to mean GC content - mergeR1R2_GCsupmean.phy : loci with GC content strictly superior to mean GC content - mergeR1R2_LS3.phy : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade") - mergeR1R2_PCA.phy : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach   Fig*.nwk : Trees (newick format) that were obtained for the different data sets. Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees).    Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees. This file can be opened in Mesquite to get reconstruction of ancestral character states

opencc-zeroOct 2020View details →

Carbohydrate depletion in roots impedes phosphorus nutrition of forest trees

The aim of the study was to determine the effect of belowground plant-derived carbohydrates on P uptake, P concentrations and enzymes activities related to P mobilization in roots, ectomycorrhizas and soil and on the abundances of P-related genes in soil bacteria. We report data from a girdling experiment in two temperate beech forest with contrasting soil phosphorus concentrations. We used soil cores and the fractions of the organic layer and mineral topsoil separately one and eight weeks after the girdling treatment. We collected bulk soil, rhizosphere and root. We provide data on soil for pH, water extractable organic carbon mineral elements in soil, and soil enzyme activities. Enzyme activities are shown for the bulk soil and the rhizosphere We provide data for microbial P, microbial biomass, gene abundances of P-related genes for soil bacteria, and phospholipid fatty acids. We provide data on root biomass, carbohydrates, total P, soluble, other root mineral nutrients, and phopphatase and enzyme activities. The data set further contain 33P labelling data for P uptake into roots.

opencc-zeroOct 2020View details →

Allometry rather than abiotic drivers explains biomass allocation among leaves, stems and roots of Artemisia across a large environmental gradient in China

1. Biomass allocation patterns reflect the adaptive strategies of plants growing in different environments, which is a central issue in comparative plant ecology and evolution. However, the factors underpinning specific allocation patterns across organs and the existence of general rules governing allocation remain contentious. Optimal partitioning theory (OPT) states that plants can respond to resource availability by allocating relatively more biomass to the organ that captures the most limiting resources to optimize growth. In contrast, allometric partitioning theory (APT) postulates that biomass allocation among organs is a power function of plant size independently of environmental variation. As phylogenetic and growth form constraints (e.g. formation of inert heartwood in tree clades) may also affect biomass allocation, comparison among and within closely related taxa of rather similar growth form may enable a more direct testing of which of these two theories prevails. 2. To test whether OPT or APT was prevalent at wide geographic scale, we investigated biomass allocation patterns among leaves, stems and roots of 1022 plants of 63 Artemisia species (Asteraceae) collected along broad climate (annual mean temperature range -4.9 to 18.0 °C, annual mean precipitation range 193 to 1668 mm) and soil gradients (soil carbon content range 1.6 to 15.4 kg C m-2) in central and eastern China. 3. There were strong allometric relationships among leaf mass (ML), stem mass (MS) and root mass (MR) at both inter- and intraspecific level. Moreover, the interspecific and intraspecific patterns were not different from general patterns for pooled plants, i.e. ML/MR and ML/MS, but not MS/MR, generally decreased with plant size. However, the three organ mass ratios were not responsive to broad climatic or soil gradients after the effect of plant size was removed. 4. Synthesis. Our results generally support APT instead of OPT, suggesting that Artemisia plants have evolved an allometric strategy rather than relying on adjustment of allocation among organs to adapt to the broadly varying environments at the regional scale. For follow-up research, we hypothesize that the strong allometric constraints on biomass allocation should depend on strong physiological adaptive responses of the different organs of Artemisia to environmental gradients.

opencc-zeroOct 2020View details →

Spatial mapping of root systems reveals diverse strategies of soil exploration and resource contest in grassland plants

1. When foraging and competing for belowground resources, plants have to coordinate the behaviour of thousands of root tips in a manner similar to that of eusocial animal colonies. While well described in animals, we know little about the spatial behaviour of plants, particularly at the level of individual roots. 2. Here, we employed statistical methods previously used to describe animal ranging behaviour to examine root system overlap and the efficiency of root positioning in eight grassland species grown in monocultures and mixtures along a gradient of neighbour densities. 3. Species varied widely in their ability to distribute roots efficiently, with the majority of species showing significant root aggregation at very fine spatial scales. Extensive root system overlap was observed in species mixtures, indicating a lack of territoriality at the level of whole root systems. However, with increasing density of competitors, several species withdrew roots from the periphery of foraging ranges and increased intraplant root aggregation in the remaining area, which may indicate consolidation of foraging areas under competitive pressure. 4. Several species exhibited responses consistent with resource contest in species mixtures where encounters with competitors' roots triggered increased root aggregation at the expense of foraging efficiency. Such responses only occurred in mixtures of species with comparable competitive abilities but were absent in asymmetric species combinations. 5. Synthesis. Combining fine-scale measurement of plant root distributions with spatial statistics yields new insights into plant behavioural strategies with significant potential to impact resource foraging efficiency and productivity.

opencc-by-4.0Nov 2020View details →

Training dataset and final models used in "Digging roots is easier with AI"

See the paper ''Digging roots is easier with AI' for an explanation of how the models and datasets were created. The images are extracted from the larger datasets available from 10.5281/zenodo.4300067 using the RootPainter software.

opencc-by-4.0Nov 2020View details →

Dataset and manual counts used in "Digging roots is easier with AI"

Please see the paper "Digging roots is easier with AI" how the images were captured and the manual counting was performed for the three destructive sampling procedures.