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309 results for “Plant roots”
Root Systems of Individual Plants Worldwide 2022
The above- and below-ground sizes and shapes of plants strongly influence plant competition, community structure, and plant-environment interactions, but the plant size and shape across climate regimes remain incompletely understood. In this study I seek to understand how plant geometries respond to varying climates via trade-offs in shoot height and width, and root depth and spread. I more than doubled the Root Systems of Individual Plants (RSIP) database to contain 5,647 observations, to our knowledge the largest database describing the maximum rooting depth, lateral spread, and shoot size of terrestrial plants in the world. Shoot size and root system size strongly covary. Across climatic gradients woody plants show deeper-narrower root systems in arid climates and taller shoots in humid climates. Phylogeny greatly influences shoot size. Rooting depth is primarily influenced by climate seasonality and lateral root spread is strongly influenced by shoot size. Using our newly expanded global database I found that shoot size covaries strongly with rooting system size; however, these relationships are not static across the climate space, as the geometries of plants shift considerably.
Above ground plant, belowground stem and root biomass in Arctic Long-term Ecological Research's 2006 moist acidic tussock tundra experimental sites, 2012, Toolik Lake, Alaska.
Above ground plant, belowground stem and root biomass was measured in moist acidic tussock tundra experimental sites established in 2006 by the Arctic Long-term Ecological Research site (ARC-LTER. Control plots and plots amended with three different levels of nitrogen(N) and phosphorus(P), F10 (10 g/m2 N and 5 g/m2 P); F5 (5 g/m2 N and 2.5 g/m2 P); F2 (2 g/m2 N and 1 g/m2 P), were sampled.
Root fungi isolated from common Louisiana marsh plants 2017-18.
Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here we collected data to investigate environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three-four dominant plant species from each of three sites of varying salinity. We provide data on abundance and taxonomy of the isolated fungal taxa as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD).
Plant and root biomass, nitrogen, carbon, and phosphorus concentrations in a mesic acidic tussock tundra experimental site established in 1981(MAT81) and harvested in 2015, Arctic LTER, Toolik Lake, Alaska.
Plant and root biomass, nitrogen, carbon, and phosphorus were measured in 2015 in the Arctic LTER tussock tundra experimental site (MAT81). This site was established in 1981 and has been harvested in previous years (see Shaver and Chapin Ecological Monographs, 61(1), 1991, pp.1-31, https://doi.org/10.2307/1942997). Data tables include the biomass for each harvested quadrat and block summaries for percent carbon, nitrogen, and phosphorus for control and fertilized plots from the original 4-block design. New control plots, established in 2015, are in a separate data table and include biomass, percent carbon, nitrogen, and phosphorus for each quadrat.
Plant root simulator nutrient availability data in the black sand extended growing season experiment, 2018 - 2020.
As a result of climate change, the Rocky Mountain Front Range is experiencing warmer summers and earlier snowmelt. Due to the importance of snow for regulating soil temperature, growing season length, and available moisture in alpine ecosystems, even small shifts in the snow-free period could have large impacts. The focus of the Black Sand Extended Growing Season Length Experiment is to examine how terrain-related differences in climate exposure influence the way alpine habitats respond to climate change via earlier snowmelt. To simulate how climate exposure may affect plant communities, NWT LTER researchers established 5 experimental sites, each containing a pair 10 x 40m rectangular plots. These sites include north and south facing aspects, subalpine and alpine tundra meadows and a range of hydrological conditions (e.g. dry meadows, moist meadows, wet meadows). We accelerated snowmelt in one plot at each site by adding chemically inert black sand, while keeping the second plot as an unmanipulated control; black sand was added to control plots after snow had naturally melted. We used open top warming chambers (OTCs) to increase summer temperature in three subplots within each of the 10 x 40 m plots. This dataset includes plant nutrient availability as measured using plant root simulator probes.
Rapid root to leaf uptake of inorganic and amino acid nitrogen in three dryland plant species.
Our aim was to quantify inorganic and organic nitrogen (N) uptake and compare short-term nutrient acquisition patterns among three dryland plant species: Bouteloua eriopoda, Achnatherum hymenoides, and Gutierrezia sarothrae collected from a mixed grassland community in the Northern Chihuahuan Desert to better understand how asynchronous resource availability may influence biotic interactions and nutrient retention in these ecosystems. We collected living plants from two locations within the Sevilleta National Wildlife Refuge and transplanted them into pots maintained in the greenhouse with supplemental light and water for two months. We then conducted a greenhouse experiment using these species to compare nutrient uptake of 15N-labeled ammonium (NH4+), nitrate (NO3-), and glutamate (an amino acid) over 12 to 48 hours. Our study examined three main questions: (1) How rapidly do these dryland plants take up available soil N?, (2) Does leaf uptake differ among inorganic and amino acid N forms?, and (3) Do plant species differ in the speed or form of short-term N uptake?. In the greenhouse, we applied one of three isotopic 15N tracers directly to plant roots and quantified N uptake and recovery in leaves after 12, 24, and 48 hours. We found that plants took up inorganic and amino acid N to leaves as rapidly as 12 h following application, and N uptake more than doubled between 24 and 48 h. Inorganic N uptake was 3-4x higher than organic N uptake in all three species, and plants took up ammonium and nitrate at 2-3x faster rates than glutamate. On average, B. eriopoda had higher inorganic N recovery and uptake speeds, while G. sarothrae had the highest organic N uptake over time. A. hymenoides root to leaf uptake was ~50% lower than the other two species after 48 h. Plants showed similar patterns of short-term foliar uptake and recovery indicating a lack of niche partitioning by N form among the three dryland species measured. Our results suggest that soil inorganic N, par
Scanned images of monocultures and mixtures of six grassland plant species roots, and of simulated fine roots
<p>Soil core samples were taken from a multi-species grassland experiment with field plots of monocultures and mixtures of six grassland plant species: <em>Lolium perenne</em> L. (PRG),<em> Phleum pratense</em> L. (TIM), <em>Trifolium pratense</em> L. (RC), <em>Trifolium repens</em> L. (WC), <em>Cichorium intybus </em>L. (CHIC), and <em>Plantago lanceolata </em>L.. The multi-species plots had a two species mixture with <em>Trifolium repens </em>L. and<em> Lolium perenne</em> L. (PRGWC), and a 6 species mixture with all species mentioned above. The cores were separated into soil depths of 0-10 cm, 10-15 cm and 15-20 cm and the roots separated from the soil.</p> <p>A ground-truth image set was created to simulate fine roots using fishing line. The fishing line used was a clear copolymer monofilament (Greys<sup>TM</sup> Greylon Tippet Material 3 lb), measured using a scanning electron microscope (Hitachi SU8200) to be 0.14 mm in diameter. The fishing line was used in its clear colour or coloured black using a permanent marker to simulate unstained and stained fine roots respectively. The fishing line was cut into lengths of 30 cm or 5 cm. </p> <p>Roots and fishing line were scanned using an Epson Perfection V800 flatbed scanner at 600 dpi. </p> <p>The Roots ZIP file contains a folder for the scanned root images and the Line zip file contains a folder with the scanned fishing line. The excel spreadsheet describes the naming convention for the images.</p> <p>Further details about the root sampling and image acquisition can be found in the publication that analyses these images: <a href="https://doi.org/10.1002/ppj2.20034">https://doi.org/10.1002/ppj2.20034</a></p>
Root symbionts alter the volatile profile of herbivore-infested tomato plants and aid the attraction of a predator
<p>Beneficial root microbes are among the most frequently used biocontrol agents in cropping systems, since they have been shown to promote plant growth and crop yield. Moreover, they are able to enhance protection against pathogens and insect herbivores by activating plant resistance mechanisms. Plant defense responses against herbivorous insects include the induction of metabolic pathways involved in the synthesis of defense-related metabolites. These metabolites include volatile organic compounds (VOCs), which attract natural enemies of the herbivores as a form of indirect resistance. Considering that beneficial root microbes may affect direct herbivore resistance, we hypothesized that also indirect resistance may be affected. We tested this hypothesis in a study system composed of tomato, the arbuscular mycorrhizal fungus <em>Rhizophagus irregularis</em>, the growth-promoting fungus <em>Trichoderma harzianum</em>, the generalist chewing herbivore <em>Spodoptera exigua </em>and the omnivorous predator<em> Macrolophus pygmaeus</em>. Using a Y-tube olfactometer we found that <em>M. pygmaeus</em> preferred plants with <em>S. exigua </em>herbivory, but microbe-inoculated plants more than non-inoculated ones. We used a targeted GC-MS approach to assess the impact of beneficial microbes on the emission of volatiles twenty-four hours after herbivory to explain the choice of <em>M. pygmaeus</em>. We observed that the volatile composition of the herbivore-infested plants differed from that of the non-infested plants, which was driven by the higher emission of green leaf volatile compounds, methyl salicylate, and several monoterpenes and sesquiterpenes. Inoculation with microbes had only a marginal effect on the emission of some terpenoids in our experiment. Gene expression analysis showed that the marker genes involved in the jasmonic and salicylic acid pathways were differentially expressed in the microbe-inoculated plants after herbivory. Our results pinpoint the role of root symbionts in determining plant-microbe-insect interactions up to the third trophic level, and elucidates their potential to be used in plant protection.</p>
Supplementary material 3 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
Supplementary material 3 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
Reproducibility package for Using root economics traits to predict biotic plant soil-feedbacks
<p>Using root economics space to predict biotic plant soil-feedbacks presents a novel framework linking below ground ecological theory to plant soil feedback effects. We show how to calculate root functional distance and location of two plant species in root economics space and how these measures can help to predict the strength and direction of the plant soil feedback between them. </p> <p>Contains data and scripts to reproduce analysis and figures for the manuscript (https://github.com/ggpmrutten/linkingRES-PSF)</p>
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>
Effects of permafrost thaw on nitrogen availability and plant-soil interactions in a boreal Alaskan lowland: III - Root Abundance 2013
This dataset examines shifts in rooting along a lowland boreal permafrost thaw chronosequence. Data was collected in 2013 at the APEX Beta and forested study plots, located adjacent to the BNZ experimental forest.
Post-fire succession in 1994 Hajdukovich Creek Burn: measurements of root biomass, shoot biomass, total plant C content, total plant N content for aspen and spruce
This dataset contains measurements of root biomass, shoot biomass, total plant C, and total plant N of 10 aspen and 10 spruce saplings harvested in one severely burned and one lightly burned site in the 1994 Hajdukovich Creek burn.
Root biomass data: Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Root biomass carbon and nitrogen: Old-Field Chronosequence: Plant Productivity
The goal of this research is to study the change in plant growth and species distribution during succession. Annual plant growth above ground is annually sampled in more than 20 fields from 4 permanently marked 3m x 4m plots in each field. These fields were previously cultivated, but then abandoned from agriculture at various times in the past. The fields were left undisturbed for plants to develop from seeds within the soil or brought into the fields by wind or animals. The fields included in this study are 4, 5, 10, 24, 26, 28, 35, 39, 41, 45, 53, 70, 72, 77 and the Lawrence strip that was abandoned in 1988. This experiment was started in 1987 by lead investigators David Tilman and Johannes Knops. In 2001 new sampling was started in positions similar to the E054 plots in these E014 fields: 21, 27, 32, 40, 44, 47, 76. Past work at CDR and elsewhere has demonstrated an overriding influence of fire frequency in maintaining prairie openings and oak savanna at the prairie-forest border. Fire regimes harm some types of species while favoring others and drive light and nutrient dynamics, which in turn drive community functional attributes and diversity levels. Ultimately, fire frequency interacts with climate, N deposition, land use, and biotic invasion to determine the outcomes of tree-grass interactions and the dynamics of vegetation at ecotones such as the prairie-forest border in Minnesota. In 2006 each field was divided in half, and one half randomly chosen for periodic prescribed burning (a fire every other year). We anticipate that the burned half will continue succession to prairie grassland while the unburned half will become white pine stands if seed sources are nearby, or will otherwise undergo extremely slow succession to oaks.
Root images of rice plant
<p>These root images of rice plant were used for<em> </em>analysising root morphological indexs like length, diameter, surface area and volume by the image anaiysis software like <em>WinRhizo</em>. These grayscale images of roots were obtained using an EPSON1680 scanner.</p>
Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
<p><span>Supplementary Data 4 from the manuscript "Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants". </span></p> <p><span>A concatenated alignment of all samples and all loci. This file was used for branch length estimation and not directly for phylogeny reconstruction (though an extraction of each subtree taxonomic samples subset from this alignment would be the alignment used to produce the scaffolded subtrees that were described in the paper). Sequences are labeled by well and can be mapped back to taxon for sub-setting and further use using Supplementary Data 1. </span></p>
Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks
<p class="RealLife">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 dispersion 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 spatial structure moderated changes in AM fungal composition produced differential feedbacks on plant growth. Our results identify symbiont spatial structure within plant roots as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with cascading effects on plant communities.</p>
Deciphering the interactions between plant species and their main fungal root pathogens in mixed grassland communities
<p>1. Plant diversity can reduce the risk of plant disease, but positive, and neutral effects have also been reported. These contrasting relationships suggest that plant community composition, rather than diversity per se, affects disease risk. Here, we investigated how diversity and composition of plant communities drive root-associated pathogen accumulation belowground.</p> <p>2. In a temperate grassland biodiversity experiment, containing 16 plant species (forbs and grasses), we determined the abundance of root-associated fungal pathogens in individual plant species growing in monocultures and in 4-species mixtures through Illumina MiSeq amplicon sequencing.</p> <p>3. In the plant monocultures, we identified three major fungal pathogens that differed in host range: <em>Paraphoma chrysanthemicola</em>, associated with roots of forb species of the Asteraceae family, <em>Slopeiomyces cylindrosporus</em>, associated with grass species, and <em>Rhizoctonia solani</em>, associated with multiple forb and grass species. In mixtures, there was no significant reduction in relative abundance of these pathogens in their host species as compared to monocultures. However, in mixtures, there was a significant increase in relative abundance of each pathogen in several non-host and host plant species. Across mixtures, plant community composition affected pathogen relative abundance in individual plant species. This effect was driven by the presence of a particular neighbouring plant species (depending on the pathogen), rather than functional group composition (i.e. grass/forb ratio) or averaged pathogen pressure (based on monocultures) of all neighbours. Specifically, the presence of neighbour host species <em>Achillea millefolium</em> significantly increased <em>P. chrysanthemicola</em>, but decreased <em>R. solani</em> relative abundance in several host and non-host plant species in mixtures.</p> <p>4. Synthesis: Our results indicate that interactions between different plant species – both host and non-hosts – and fungal pathogens underlie effects of plant diversity on root pathogen abundance. Non-host species may act as pathogen reservoirs in diverse plant communities, as they harboured certain pathogens in mixtures, but not in monocultures. Additionally, particular host species can strongly affect pathogen abundance in other (host and non-host) plant species in plant mixtures, suggesting clear effects of species identity in the diversity-disease relationship. Belowground disease risk thus depends on plant community composition rather than diversity per se, via specific interactions between plant species and their root-associated pathogens.</p>
Supplementary material 1 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
Supplementary material 1 from: Bongard C, Butler K, Fulthorpe R (2013) Investigation of fungal root colonizers of the invasive plant Vincetoxicum rossicum and co-occurring local native plants in a field and woodland area in Southern Ontario. Nature Conservation 4: 55-76. https://doi.org/10.3897/natureconservation.4.3578
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