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45 results for “Root exudation”
Root Exudation Simulation Experiment in a Red Oak Stand at Harvard Forest 2011
Root exudation is thought to increase the activity of microbes and the exoenzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The nitrogen (N) content of microbial biomass and exoenzymes may introduce a stoichiometric constraint on the ability of microbes to effectively utilize the root exudates, particularly if the exudates are rich in C but low in N. We combined a theoretical model of microbial activity with an exudation experiment to test the hypothesis that the ability of soil microbes to utilize root exudates for the synthesis of additional biomass and exoenzymes is constrained by N availability. The field experiment simulated exudation by automatically pumping solutions of chemicals often found in root exudates (“exudate mimics”) containing C alone or C in combination with N (C:N ratio of 10) through microlysimeter “root simulators” into intact forest soils in two 50-day experiments. The delivery of C-only exudate mimics increased microbial respiration but had no effect on microbial biomass or exoenzyme activities. By contrast, experimental delivery of exudate mimics containing both C and N significantly increased microbial respiration, microbial biomass, and the activity of exoenzymes that decompose low molecular weight components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exoenzymes that degrade high molecular weight SOM (e.g., polyphenols, lignin). The modeling results were consistent with the experiments; simulated delivery of C-only exudates induced microbial N-limitation, which constrained the synthesis of microbial biomass and exoenzymes. Exuding N as well as C alleviated this stoichiometric constraint in the model, allowing for increased exoenzyme production, the priming of decomposition, and a net release of N from SOM (i.e., mineralization). The quantity of N released from SOM in the model simulations was
Data on respiration, substrate incorporation, and soil compound concentration in response to simulated root exudation
<p>In this study we used reverse microdialysis to release a mixture of <sup>13</sup>C-labeled substrates into intact meadow and forest soil cores (6-hour long) to simulate root exudation. We utilized three different artificial root exudates: sugars (glucose, fructose), organic acids (acetate, succinate), and a combination of sugars and organic acids (glucose, fructose, acetate, succinate); alongside a water-only control for comparison.</p> <p>We collected compounds from soil solutions and measured respiration. Due to <sup>13</sup>C-labeled substrate we could differentiate between substrate-derived respiration and SOM-derived respiration. Additionally, we extracted lipid fatty acids from soil and measured their <sup>13</sup>C incorporation.<br><br></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>
Collection of exudates from wild type mycorrhizal and non mycorrhizal roots
<p>The aim of the experiment was to define a protocol for root exudates collection from tomato plants (<em>Solanum lycoipersicum </em>cv. M82) colonized or not with <em>Funneliformis mosseae</em>, a very common mycorrhizal fungus in nature. Mycorrhizal plants were grown on sandy soil under well-watered conditions under low nitrogen and phosphorus level alongside their not-inoculated control, non mycorrhizal, plants. Exudates were collected by washing the medium with 1 volume of sterile distilled water. Collections have been performed on mature mycorrhizas (50 days from inoculum) collecting root exudates every 4 days for 4 times. After the last collection, plants were sampled and some plant traits measured. Root exudate samples will be analysed by UNITO-DISAFA in terms of total organic carbon, organic acids, amino acids, enzymes (phosphatase and phytase) and SL content.</p>
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>
Mycorrhizal fungi alter root exudation to cultivate a beneficial microbiome for plant growth
<p>Arbuscular mycorrhizal (AM) fungi traditionally form symbioses with most plant species. Although AM fungi have critical effects on microbial communities, the pathways showing how AM fungi shape rhizosphere bacterial communities and their functions are rarely explored. Through three systematic experiments, AM fungi-bacteria interactions were first investigated in the rhizosphere of <em>Lotus</em> <em>japonicus</em>, then the interactions were confirmed by a second experiment with wild-type and a mycorrhiza-defective mutant <em>ljcbx</em> of <em>L</em>. <em>japonicus</em>. The mechanisms were presented by adding core bacteria and AM fungi to the plant rhizosphere with the third experiment. We found that AM fungi-bacteria interactions enhanced host plant growth and identified a core bacterial group that uniquely enhanced host plant growth. Adding core bacteria and AM fungi promoted host growth and nutrient acquisition compared to adding AM fungi or core bacteria independently. Allelopathic substances secreted by AM fungal colonizing host roots to recruit the rhizosphere bacteria were detected by the multi-omics joint analysis, showing that arachidonic acid was the main allelopathic substance that affected AM fungi–bacteria interactions. Our findings provide direct evidence that mycorrhizal infection simulated root exudation, such as arachidonic acid, recruited a beneficial microbiome to the host rhizosphere, increasing plant growth and soil nutrient turnover.</p>
Plant growth strategy determines the magnitude and direction of drought-induced changes in root exudates in subtropical forests
<p><span>Root exudates are an important pathway for plant-microbial interactions and are highly sensitive to climate change.</span> <span>However, how extreme drought affects root exudates and the main components, as well as species-specific differences in response magnitude and direction, are poorly understood. In this study, root exudation rates of total carbon (C) and its components (e.g., sugar, organic acid, and amino acid) were measured under the control and extreme drought treatments (i.e., 70% throughfall reduction) by <em>in situ</em> collection of four tree species with different growth rates in a subtropical forest. We also quantified soil properties, root morphological traits, and mycorrhizal infection rates to examine the driving factors underlying variations in root exudation. Our results showed that extreme drought significantly decreased root exudation rates of total C, sugar, and amino acid by 17.8%, 30.8%, and 35.0%, respectively, but increased root exudation rate of organic acid by 38.6%, which were largely associated with drought-induced changes in tree growth rates, root morphological traits, and mycorrhizal infection rates. Specifically, trees with relatively high growth rates were more responsive to drought for root exudation rates compared to those with relatively low growth rates, which were closely related to root morphological traits and mycorrhizal infection rates. These findings highlight the importance of plant growth strategy in mediating drought-induced changes in root exudation rates. The co-ordinations among root exudation rates, root morphological traits, and mycorrhizal symbioses in response to drought could be incorporated into land surface models to improve the prediction of climate change impacts on rhizosphere C dynamics in forest ecosystems. </span></p>
Data from: Rhizodeposition through root senescence and root exudation of atmospheric C and N by legumes is controlled by traits indicative of resource acquisition and root development
<p><span>Legume crop production has many benefits for agricultural systems. Through the rhizodeposition process, they release a significant amount of C and N into the soil, increasing soil organic C and reducing the use of N fertilizer. Rhizodeposition is known as a dynamic process influenced by many factors. </span></p> <p><span>The aim of this study was to study the contribution of root exudation and root senescence to the rhizodeposition of atmospheric C and N during vegetative and reproductive growth in annual and perennial legumes and to understand how this is linked to the fixation capacities of C and N and root functional traits.</span></p> <p><span>An original approach that combined <sup>13</sup>CO<sub>2</sub> labeling and the <sup>15</sup>N dilution method was developed to measure the rhizodeposition of atmospheric C and N throughout plant growth by two annual grain legumes (pea and faba bean) and two perennial forage legumes (white and crimson clovers).</span></p> <p><span>C rhizodeposition was found to increase proportionally with N rhizodeposition during reproductive development and the differences observed between species were related to the C and N fixation abilities. The use of root traits such as specific root length, root tissue density, and root dry matter content suggests a strong contribution of root exudation to C rhizodeposition at vegetative growth and a strong contribution of root senescence to both C and N rhizodeposition during reproductive growth.</span></p> <p><span><em><strong>Synthesis:</strong></em> Both C and N rhizodeposition appeared to be controlled by traits indicative of resource acquisition and root development. </span></p>
Species phylogeny, ecology and root traits as predictors of root exudate composition
<p>In this study, a total of 65 neophytes (alien species introduced after 1500 A.D.), belonging to 51 genera and 25 families, occurring in the Czech Republic, were used. The species set represented plant families only from eudicots with Asteraceae, Brassicaceae Amaranthaceae, Polygonaceae and Fabaceae as the major families having 4 or more species. We measured different root morphological and biochemical traits (including exudate profiles) of these plant species grown in a controlled system. </p>
Data from: Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks
<p><span>Plants can suppress the growth of other plants by modifying soil properties. These negative plant-soil feedbacks are often species-specific, suggesting that some plants possess resistance strategies. However, the underlying mechanisms remain largely unknown. </span><span>Here, we investigated if and how benzoxazinoids, a class of dominant secondary metabolites that are exuded into the soil by maize and other cereals, influence plant-soil feedbacks. </span><span>We find that three out of five tested crop species suppress maize (<em>Zea mays</em>) performance via negative plant-soil feedbacks relative to the mean across species. This effect is partially alleviated by the capacity of maize plants to produce benzoxazinoids. Soil complementation with purified benzoxazinoids is sufficient to restore the protective effect for benzoxazinoid-deficient mutants. Sterilization and re-inoculation experiments suggest that benzoxazinoid-mediated protection acts via changes in soil biota. Substantial variation of the protective effect between experiments and soil types illustrates that its magnitude is context-dependent. In summary, our study demonstrates that plant secondary metabolites can confer resistance to negative plant-soil feedbacks. These findings expand the functional repertoire of plant secondary metabolites and reveal a mechanism by which plants can resist negative soil feedbacks. The uncovered phenomenon may represent a promising avenue to stabilize plant performance in crop rotations in the future.</span></p>
Plant growth strategy determines the magnitude and direction of drought-induced changes in root exudates in subtropical forests
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Fungal, bacterial & plant biomass data: Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere
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Data from: Root-exuded benzoxazinoids can alleviate negative plant-soil feedbacks
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Mycorrhizal fungi alter root exudation to cultivate a beneficial microbiome for plant growth
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Data from: Rhizodeposition through root senescence and root exudation of atmospheric C and N by legumes is controlled by traits indicative of resource acquisition and root development
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Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula
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Data from: The Automated Root Exudate System (ARES): a method to apply solutes at regular intervals to soils in the field
1) Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field. 2) The ARES is a gravity-fed drip irrigation system comprising a reservoir bottle connected via a timer to a micro-hose irrigation grid covering c. 1 m2; 24 drip-tips are inserted into the soil to 4-cm depth to apply solutions into the rooting zone. We installed two ARES subplots within existing litter removal and control plots in a temperate deciduous woodland. We applied either an artificial root exudate solution (RE) or a procedural control solution (CP) to each subplot for 1 min d-1 during two growing seasons. To investigate the influence of root exudation on soil carbon dynamics, we measured soil respiration monthly and soil microbial biomass at the end of each growing season. 3) The ARES applied the solutions at a rate of c. 2 L m-2 wk-1 without significantly increasing soil water content. The application of RE solution had a clear effect on soil carbon dynamics but the response varied by litter treatment. Across two growing seasons, soil respiration was 25% higher in RE compared to CP subplots in the litter removal treatment, but not in the control plots. By contrast, we observed a significant increase in microbial biomass carbon (33%) and nitrogen (26%) in RE subplots in the control litter treatment. 4) The ARES is an effective, low-cost method to apply experimental solutions directly into the rooting zone in the field. The installation of the systems entails minimal disturbance to the soil and little maintenance is required. Although we used ARES to apply root exudate solution, the method can be used to apply many other treatments involving solute inputs at regular intervals in a wide range of ecosystems.
Nitrogen fixation and crop productivity enhancements codriven by intercrop root exudates and key rhizosphere bacteria
<p>1. Crop diversity management is widely used to increase agricultural productivity and sustainability. Recent studies have demonstrated that maize root exudates can drive interspecific facilitation to enhance N<sub>2</sub> fixation of bean in intercropping systems. However, the mechanisms of N<sub>2</sub> fixation enhancement stimulated by root exudates in the intercropping systems remain unclear.</p> <p>2. Four experiments were designed to provide a progressively deeper understanding of how root exudates stimulate microbial-mediated N<sub>2</sub> fixation. First, the effects of faba bean/maize intercropping on yields and soil microbial communities were determined in a field experiment. Second, root-derived interspecific facilitation was evaluated using a root partitioning approach. Third, the key microbial taxa in the faba bean rhizosphere were traced using<sup> 13</sup>C-labeled maize root exudates. Fourth, the codriven mechanism of maize root exudates and microorganisms in the faba bean rhizosphere were explored.</p> <p>3. Faba bean/maize intercropping with maize residue return increased the yields of faba bean (26%), maize (27%), and broccoli (9.1%) compared to that under monocropping. Nodulin-like 4 (NODL4), chalcone-flavanone isomerase (CFI), and early nodulin-like (ENODL2) gene expression in faba bean roots intercropped with maize increased by 1.5-2.3-fold compared to that observed under monoculture. More than half of the N<sub>2</sub> fixation of faba bean increase under intercropping was due to interactions with microorganisms. Nine key bacterial genera in the faba bean rhizosphere were identified by <sup>13</sup>C-DNA based stable isotope probing analysis. Among them <i>Agromyces</i>, <i>Arthrobacter</i>, <i>Bacillus</i>, <i>Lysobacter</i>, and <i>Paenibacillus</i> directly fix N<sub>2</sub>, while <i>Gemmatimonas</i>, <i>Heliobacillus</i>, <i>Natronocella</i>, and <i>Sorangium</i> increase the N<sub>2</sub> fixation capacity of Azotobacter by providing additional carbon sources. These key bacteria triggered by maize root exudates played an important role in the rhizosphere facilitation of intercropping.</p> <p>4. <i>Synthesis and applications</i>. We demonstrated a novel root-root facilitation of N<sub>2</sub> fixation and increased crop yields codriven by root exudates and rhizosphere bacteria under faba bean/maize intercropping, and nine key bacteria associated with this process were identified by <sup>13</sup>C-DNA based stable isotope probing. We recommend the adoption and optimization of intercropping systems with residue return to reduce the shortcomings of continuous cropping and to increase the sustainability of crop <a>production</a>.</p>
Data from: Density and root exudates mediate Arabidopsis response to copper
<p>Premise of the study: Plants grown at high densities show increased tolerance to heavy metals for reasons that are not clear. A potential explanation is the release of citrate by plant roots, which binds metals and prevents uptake. Thus, pooled exudates at high plant densities could increase tolerance. We tested this exclusion facilitation hypothesis using mutants of <em>Arabidopsis thaliana </em>defective in citrate exudation.</p> <p>Methods: Wild type <em>Arabidopsis</em> and two allelic mutants for the <em>Ferric Reductase Defective 3</em> (<em>FRD3</em>) gene were grown at four densities and watered with copper sulfate at four concentrations. Plants were harvested before bolting and dried. Shoot biomass was measured, and shoot material and soil were digested in nitric acid. Copper contents were determined by atomic absorption.</p> <p>Key results: In the highest copper treatment, density-dependent reduction in toxicity was observed in the wild type but not in <em>FRD3</em> mutants. For both mutants, copper concentrations per gram biomass were up to seven times higher thanwild type plants, depending on density and copper treatment. In all genotypes, total copper accumulation was greater at higher plant densities. Plant size variation increased with density and copper treatment because of heterogeneous distribution of copper throughout the soil.</p> <p>Conclusions: These results support the hypothesis that citrate exudation is responsible for density-dependent reductions in toxicity of metals. Density-dependent copper uptake and growth in contaminated soils underscores the importance of density in ecotoxicological testing. In soils with a heterogenous distribution of contaminants, competition for non-toxic soil regions may drive size hierarchies and determine competitive outcomes. </p>
FIGURE. Stem, roots, and buds of C. spongifolia. A. Cross section of stem in B, showing clear, gummy exudate. B. Mature stem with decumbent part at left, erect part at right, roots and rootlets, brown leaf scars, and single adaxial buds (arrows). C. Young stem, with single, adaxial bud revealed. Scale bars = 2 cm (Bach Ma NP, 2018, 2021). Photos: NVD and PJM. in Colocasia spongifolia sp. nov. (Araceae) in southern China and central Vietnam
FIGURE. Stem, roots, and buds of C. spongifolia. A. Cross section of stem in B, showing clear, gummy exudate. B. Mature stem with decumbent part at left, erect part at right, roots and rootlets, brown leaf scars, and single adaxial buds (arrows). C. Young stem, with single, adaxial bud revealed. Scale bars = 2 cm (Bach Ma NP, 2018, 2021). Photos: NVD and PJM.
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