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182 results for “exudates”
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>
Analysis of bacteria, inflammation, and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing - Dataset
<p>Dataset for "<strong>Analysis of bacteria, inflammation, and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing</strong>". Data were generated from samples collected to a biobank from suction blister wounds at various timepoints during a clinical trial (<a href="https://clinicaltrials.gov/study/NCT05378997?term=NCT05378997&rank=1"><strong>NCT05378997</strong></a>). Data include concentration of bacteria in swab and dressing fluid samples, neutrophil proteins (HNE, MPO, and HBP), cytokines (IFN-gamma, interleukin IL-1beta, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, TNF-alpha) and total protein measured in dressing fluid samples, and bacterial species identified by MALDI-TOF in swab and dressing fluid samples.</p>
Figure 1 in About the nutrition of Cleroclytus semirufus Kraatz, 1884 (Coleoptera, Cerambycidae) with the exudate of the Fire blight of fruit crops
Figure 1.Cleroclytus semirufus: A - habitus, dorsal view; B - nutrition on the flowers of Spiraea; C, D - feeding on exudate of the bacterium Erwinia amylovora on an apple tree.
SBC LTER: REEF: Exudation of dissolved organic carbon by the giant kelp Macrocystis pyrifera
We estimated rates of DOC exudation by Macrocystis pyrifera using short-term (2-4 hours) in situ incubations of entire blades and portions of stipes in the kelp forest at Mohawk Reef near Santa Barbara, California, USA (34o 23.660’ N, 119o 43.800’ W). Incubations of blades were conducted within 2 m of the sea surface at midday on eight dates between October 2007 and August 2011 to investigate the effects of blade growth stage, nutrient status (as indicated by C:N ratio determined using an Exeter Analytical CE-440 CHN/O/S elemental analyzer), epiphyte load, sea surface irradiance, and sea surface temperature on rates of DOC release from intact blades.
Dataset on the Chemistry of Australian Plant Exudates from Historical Collection
<p>FT-IR.zip: FT-IR dataset<br> GC-MS.zip: GC-MS dataset<br> ICP-MS.zip: ICP-MS dataset<br> Py-GC-MS.zip: Py-GC-MS dataset<br> XRS C K-edge.zip: X-ray Raman spectroscopy dataset at the carbon K edge<br> XRS O K-edge.zip: X-ray Raman spectroscopy dataset at the carbon O edge</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>
Complement Inhibition With Eculizumab for the Treatment of Non-Exudative Macular Degeneration (AMD)
ClinicalTrials.gov study NCT00935883. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Evaluation of AGN-150998 in Exudative Age-related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT01397409. IPD Sharing: Not stated. Countries: 8. Publications: 1.
ProspectiveTrial of Proton Beam Combined With Anti-VEGF Therapy for Exudative Age-related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT01213082. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sirolimus in Conjunction With Eylea vs Eylea Alone for Exudative AMD
ClinicalTrials.gov study NCT02732899. IPD Sharing: NO. Countries: 1. Publications: 1.
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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