Composition Of Root Exudates Research Articles

Regulation of root-associated microbiomes and root exudates by different tobacco species

BackgroundThe root-associated microbiomes are crucial in promoting plant growth and development through symbiotic interactions with their hosts. Plants may shape their microbiomes by secreting specific root exudates. However, the potential mechanisms how plant species determine root exudates and drive microbiome assembly have been little studied. In this study, three wild tobaccos and one cultivated tobacco were used to investigate the commonalities and differences of both root-associated microbiomes and root exudates.ResultsAmplicon sequencing results suggested that tobacco species significantly affected microbial communities in both the rhizosphere and root endosphere, with the strongest impact on the fungal community in the root endosphere. The microbial networks of wild tobacco species were more stable than that of the cultivated tobacco, and fungal members played a more important role in the networks of wild tobacco species, while bacterial members did so in the cultivated tobacco. The rhizosphere bacteria of wild tobacco species showed a higher functional diversity than that of the cultivated tobacco, while the bacteria in the root endosphere presented a contrary pattern. Metabolomics analysis showed significant differences in the composition and abundance of root exudates among the four tobacco species, and the greatest difference was found between the three wild species and the cultivated one. Correlation analysis showed the strongest correlation between metabolites and rhizosphere bacteria, in which O-benzoic acid (2-methoxybenzoic acid) had the most positive correlations with rhizosphere bacteria, while β-ureidoisobutenoic acid had the most negative correlations with rhizosphere bacteria. The rhizosphere bacteria Streptomyces, Hydrophilus and Roseobacter had the strongest positive correlations with metabolites, and the rhizosphere bacterium Nitrobacter had the most negative correlations with metabolites.ConclusionThis study revealed the differences of microbial communities and root exudates in the rhizosphere and root endosphere of four tobacco species, which can further improve our understanding of plant–microbiome interactions during crop domestication.Graphical

Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils

BackgroundCover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.ResultsHere, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.ConclusionsWe highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.BPG5Z_iDvqR4KrAs2TcSTiVideo

Saltbush seedlings (Atriplex spp.) shed border-like cells from closed-type root apical meristems

Australian saltbush (Atriplex spp.) survive in exceptionally saline environments and are often used for pasture in semi-arid areas. To investigate the impact of salinity on saltbush root morphology and root exudates, three Australian native saltbush species (Atriplex nummularia, Atriplex amnicola, and Atriplex vesicaria) were grown in vitro in optimised sterile, semi-hydroponic systems in media supplemented with different concentrations of salt (NaCl). Histological stains and chromatographic techniques were used to characterise the root apical meristem (RAM) type and root exudate composition of the saltbush seedlings. We report that saltbush species have closed-type RAMs, which release border-like cells (BLCs). Monosaccharide content, including glucose and fructose, in the root mucilage of saltbush was found to be uniquely low, suggesting that saltbush may minimise carbon release in polysaccharides of root exudates. Root mucilage also contained notable levels of salt, plus increasing levels of unidentified compounds at peak salinity. Un-esterified homogalacturonan, xyloglucan, and arabinogalactan proteins between and on the surface of BLCs may aid intercellular adhesion. At the highest salinity levels, root cap morphology was altered but root:shoot ratio remained consistent. While questions remain about the identity of some components in saltbush root mucilage other than the key monosaccharides, this new information about root cap morphology and cell surface polysaccharides provides avenues for future research.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes

BackgroundTrees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.ResultsOur study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism.ConclusionsThis study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities.2SWtA3_gUD-Xt4Z7N25436Video

Comprehensive characterization of the rhizosphere metabolome: A novel method for non-targeted analysis of Lotus japonicus root exudates

Plant root exudates play a pivotal role in shaping soil dynamics and the microbial community in the rhizosphere. The chemical composition of root exudates includes primary and secondary metabolites, including amino acids, organic acids, flavonoids, and small peptides. Comprehensive characterization of root exudates will allow for a better understanding of rhizosphere processes and interactions, but analysis of root exudates is hindered by complicated collection setups, time-consuming sample preparation, and a lack of definitive annotations within metabolomics. We present a method optimized for non-targeted analysis of primary and secondary metabolites in root exudate samples using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry. The method was tested on root exudates from Lotus japonicus, collected using distinct and well-established sampling methods: a hydroponic-soil-hybrid approach, as well as a modification of a soil-leaching method, thus exemplifying the versatility of the analysis method. The method allows for non-targeted screening of plant metabolites, and provides low detection limits (0.002–0.05 μg/mL) and high recoveries (78 ± 30%), though a matrix effect was observed for certain plant metabolites. Detection of a large number of features was achieved (670–2785) of which the majority could be putatively annotated at the compound class level. Of these, 14 features were putatively annotated to a specific structure with high confidence, three of which were confirmed with analytical reference standards. The method can be used for investigation of the overall change in root exudation, as well as for investigating significant changes in metabolites in response to intraenous and extraneous parameters.

Genetic and ecological inheritance of plant growth-promoting rhizobacteria

Abstract Background The utilization of beneficial (Rhizo) bacteria, as an alternative to traditional fertilizers, has emerged as an eco-friendly strategy for ameliorating sustainable agricultural production. This approach aims to reduce the use of agrochemicals and minimize environmental pollution. Scope This review provides an updated insight into the ecological impact of plant growth-promoting rhizobacteria (PGPR), focusing on the resident microbiome and its potential transferability to the next generation of plants. Conclusion In this context, PGPR are assumed to alter the rhizosphere microbiome by outcompeting the existing taxa through nutrient deprivation, acidification of the environment, metabolites production, and consequently, increasing the copiotrophic taxa. Such modifications can maximize the beneficial interactions of plant-PGPR by increasing the bioavailability of nutrients and handling diverse signaling pathways. The effects of interactions within the PGPR-root system can adjust the composition of root exudates and influence the release of bioactive molecules by the root, especially under stress conditions, which can act as signals to reactivate and recruit the beneficial microbes in the rhizosphere and endosphere in favor of the plants. Such changes in microbiome structure can occur gradually over time, even if the survival rate of PGPR in soil and their re-colonization efficiency inside plant tissue are limited. The aforementioned modifications in the rhizosphere and plant microbiome have the potential to increase the survival chances of the progeny plants growing under the same stress conditions. Establishing a comprehensive and robust knowledge framework that addresses all of these issues is critical for significantly advancing the field of microbe-plant interactions and for developing reliable applications of PGPR.

Root exudation and rhizosphere microbial assembly are influenced by novel plant trait diversity in carrot genotypes

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites more strongly associated with fungal than bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

Bioinoculation with Pseudomonas aeruginosa P4 enhances the peanut root nodulation and nutrient status while enriching the plant-beneficial bacteria in rhizosphere

Fluorescent Pseudomonas species are well-known as effective plant growth promoting rhizobacteria (PGPR), yet are relatively less explored for their multitrophic benefits. This study demonstrates the impact of P. aeruginosa P4 (P4) on peanut growth, nutrient status of plant and soil as well as the rhizobacterial community. Enhanced root length (53%), root weight (74%) and shoot weight (48%) in P4-treated plants, with increased potash and phosphorus levels of rhizospheric soil, correlated with indole-3-acetic acid and organic acid producing abilities of P4. Remarkably, increased nodule (87%) and pod (47%) numbers in P4-treated plants could be attributed to ∼16.3 % higher accumulation of iron, which in turn could be due to siderophore producing ability of P4. Amplified Ribosomal DNA Restriction Analysis (ARDRA)-based analysis at the approximate onset of nodulation and subsequent 16S rDNA-based metagenomic analysis estimated a significant distinction in the rhizomicrobial community diversity and abundance across control and P4-treated rhizospheres, plausibly due to P4-induced alterations in root exudate composition. Enrichment of plant-beneficial genera like Planctomyces, Mesorhizobium, Ensifer, Azospirillum, Bacillus, Nitrospira and Candidatus Nitrososphaera in P4-treated rhizosphere, could be driven by both altered root exudation and enhanced mineral nutrient availability in soil. In contrast, reduced abundance of Pseudomonas genus in P4-treated peanut rhizosphere could be attributed to direct or indirect competition between the inoculant and the resident Pseudomonas species. Collectively, a non-nitrogen-fixer P4 benefited nitrogen fixation in peanut, apparently indirectly by improving the iron nutrition and mobilization of plant-beneficial rhizobacterial species; an aspect that could be useful in determining PGPR efficacy and strategizing PGPR-mediated rhizosphere engineering.

Root Exudates Metabolic Profiling Confirms Distinct Defense Mechanisms Between Cultivars and Treatments with Beneficial Microorganisms and Phosphonate Salts Against Verticillium Wilt in Olive Trees.

Root exudates play a key role in the life cycle of Verticillium dahliae, the causal agent of Verticillium wilt diseases, because they induce microsclerotia germination to initiate plant infection through the roots. In olive plants, the genotype and the application of biological control agents (BCAs) or phosphonate salts influence the ability of root exudates to decrease V. dahliae viability. Understanding the chemical composition of root exudates could provide new insights into the mechanisms of olive plant defense against V. dahliae. Therefore, the main goal of this study was to analyze the metabolomic profiles of root exudates collected from the olive cultivars Arbequina, Frantoio, and Picual subjected to treatment with BCAs (Aureobasidium pullulans AP08, Bacillus amyloliquefaciens PAB-024) or phosphonate salts (copper phosphite, potassium phosphite). These treatments were selected due to their effectiveness as inducers of resistance against Verticillium wilt in olive plants. Our metabolomic analysis revealed that the olive cultivars exhibited differences in root exudates, which could be related to the different degrees of susceptibility to V. dahliae. The composition of root exudates also changed with the application of BCAs or phosphonate fertilizer, highlighting the complex and dynamic nature of the interactions between olive cultivars and treatments preventing V. dahliae infections. Thus, the identification of genotype-specific metabolic changes and specific metabolites induced by these treatments emphasizes the potential of resistance inducers for enhancing plant defense and promoting the growth of beneficial microorganisms.

FUNCTIONING OF MICROORGANISMS IN THE RHIZOSPHERE OF PLANTS

The functioning of living organisms in nature is possible only due to active interaction with microbiota. It is typical for phytobionts, the microbial cenosis of which is even more diverse. Plants contribute to the spread of microorganisms in the rhizosphere by releasing root exudates. The chemical composition of these exudates varies in different plant species and depends on the significant number of factors that affect their growth and development. The components of the plant root exudates stimulate expansion in the rhizosphere of microorganisms, useful for the plant growth. This microbiota improves the mineral life of plants considerably, stimulating their growth with biologically active compounds, increasing the availability of a number of microelements for them, protecting the growth of plants from phytopathogens and phytophages. It provides significant stimulation for the growth and development of phytobionts. It has been shown that microbial groups in the rhizosphere can induce some changes in the composition of plant root exudates.

Spatial and temporal detection of root exudates with a paper-based microfluidic device

Root exudates control critical processes in the rhizosphere, retaining water, selecting for beneficial microorganisms or solubilising nutrients prior to uptake by the plant. Analysing root exudation patterns however is challenging because existing methods are often destructive and unable to resolve spatial and temporal variations in the production of root exudates. Here, we present a paper-based microfluidic device with integrated colorimetric sensors for the continuous extraction and analysis of root exudates along plant roots. The microfluidic device used standard filter paper wax printer to create channels for water to carry the exudates towards the sensors. TiO2 nanotubes/alginate hydrogel-based sensors were used to analyse the glucose content of the root exudates of living plants. The study shows that the paper microfluidic substrate successfully extracts the released glucose from the root, and transfers it to the hydrogel-based sensor to be colorimetrically detected from independent sections of the root at different times, up to 7 days. This method was tested on two different wheat varieties Triticum aestivum (rgt Tocayo and Filon varieties), where significant differences in exudation patterns were recorded. This research demonstrates the feasibility of low-cost technological solution for high precision screening and diagnostic of the biochemical composition of root exudates.

The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion.

Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.

Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed

Roots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant–plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other’s root systems.

Metabolic response of peanut (Arachis hypogaea L.) to Sclerotium rolfsii Sacc. in root exudates system

ABSTRACT In the current study the metabolic response of peanut root exudates to Sclerotium rolfsii Sacc. infection was analyzed in plant-pathogen interaction systems. The analytical methodology employed in this study entailed the utilization of ultra-high-performance liquid chromatography coupled with tandem quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) in relation to metabolomics. The experimental findings have demonstrated that pathogen infection induces significant variations in both the composition and abundance of peanut root exudates. A total of 322 metabolites were identified in peanut root exudates, among which 19 metabolites showed significant differences under pathogen infection. The results of the orthogonal partial least squares score discriminant analysis (OPLS) and hierarchical cluster analysis (HCA) plots clearly demonstrated that the metabolic profiling effectively distinguished between peanut plants inoculated with S. rolfsii Sacc. and the healthy control plants that were not inoculated. Pathogen infection is associated with five metabolic pathways, the most correlated being arginine and proline metabolism and ABC transporters.

Comparative analysis on root exudate and rhizosphere soil bacterial assembly between tomatoes and peppers infected by Ralstonia

BackgroundThe rhizosphere environment regulated by root secretory activity and rhizosphere microbial interactions plays an essential role in resisting soil-borne diseases, while the host species is an important factor that affects the composition of root exudates and rhizosphere microbiomes. However, few studies have been done on the characteristics of root exudates and bacterial communities in terms of composition, diversity, and functional potential when host plants of different species are subjected to the same disease.ResultsIn this study, we examined the rhizosphere soil bacteria and root exudates of both healthy and diseased tomatoes and peppers employing metabolomics and amplicon techniques. Our findings indicated that variations existed in both root exudates and the bacterial community among different host species and health states. The diversities of both rhizosphere metabolites and bacterial communities were significantly reduced in different diseased plants. Although pepper and tomato resisted the invasion of Ralstonia by recruiting different potentially beneficial bacteria, their rhizosphere bacterial communities had the same functional potential. In comparison to diseased rhizosphere soil, healthy rhizosphere soil had many more functional pathways associated with disease suppression and plant growth.ConclusionsThis study highlighted the crucial role of host plants in shaping the rhizosphere environment and revealed the variation characteristics of root exudates and rhizosphere bacteria of different host plants induced by the same disease.Graphical

Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.

Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.

Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome

Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.

The dynamic interplay of root exudates and rhizosphere microbiome

The rhizosphere microbiome plays a vital role in plant growth, health, and nutrient acquisition. One of the key factors that shape the composition and function of the rhizosphere microbiome is root exudates, the complex mixture of organic compounds released by plant roots. Root exudates serve as a source of energy and nutrients for the rhizosphere microbiome, as well as a means of communication between plants and microbes. The dynamic interplay between root exudates and rhizosphere microbiome is a complex and highly regulated process that involves multiple feedback loops and interactions. Recent studies have revealed that the composition and quantity of root exudates are modulated by a range of biotic and abiotic factors, including plant genotype, soil type, nutrient availability, and microbial community structure. In turn, the rhizosphere microbiome can influence the production and composition of root exudates, through processes such as nutrient cycling, plant hormone synthesis, and modulation of plant defense responses. Understanding the dynamics of root exudates and rhizosphere microbiomes is crucial for developing effective strategies for microbiome engineering, plant-microbe symbiosis, and sustainable agriculture. This review provides an overview of the current state of knowledge on the dynamic interplay between root exudates and rhizosphere microbiomes, highlighting the key factors and mechanisms that govern this complex relationship.

Biochar-based Bacillus subtilis inoculant for enhancing plants disease prevention: microbiota response and root exudates regulation

Plants regulate root exudates to form the composition of rhizosphere microbial community and resist disease stress. Many studies advocate intervention with biochar (BC) and exogenous microbe to enhance this process and improve plant defenses. However, the mechanism by which BC mediates exogenous microorganisms to enhance root exudate-soil microbial defensive feedback remains unclear. Here, a BC-based Bacillus subtilis SL-44 inoculant (BC@SL) was prepared to investigate the defensive feedback mechanism for plants, which enhanced plant growth and defense more than BC or SL-44 alone. BC@SL not only strengthened the direct inhibition of Rhizoctonia solani Rs by solving the problem of reduced viability of a single SL-44 inoculant but also indirectly alleviated the Rs stress by strengthening plant defensive feedback, which was specifically manifested by the following: (1) increasing the root resistance enzyme activities (superoxide dismutase up to 3.5 FC); (2) increasing the abundance of beneficial microbe in soil (0.38–16.31% Bacillus); and (3) remodeling the composition of root exudates (palmitic acid 3.95–6.96%, stearic acid 3.56–5.93%, 2,4 tert-butylphenol 1.23–2.62%, increasing citric acid 0.94–1.81%, and benzoic acid 0.97–2.13%). The mechanism reveals that BC@SL can enhance the positive regulatory effect between root exudates and microorganisms by optimizing their composition. Overall, BC@SL is a stable and efficient new solid exogenous soil auxiliary, and this study lays the foundation for the generalization and application of green pesticides.Graphical

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Background Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions. Methods Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions. Results Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software. Conclusions The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.