Root signals that mediate mutualistic interactions in the rhizosphere

Early developmental shifts in root exudation profiles of five Zea mays L. genotypes

Root exudates impact soil-plant-microbe interactions and play important roles in ecosystem functioning and plant growth. During early plant development the root rhizosphere may change drastically. For maize (Zea mays L.), one of the world's most important crop species, little is known about root exudation patterns during early plant development. We determined abundance and composition of root exudation among maize genotypes from five inbred lines across three early plant development stages (Emergence, V1-2, and V3-4). We characterized the exudates for non-purgeable organic carbon and performed non-targeted metabolomics with high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). Across all genotypes, plant development stage had a significant influence on both abundance and composition of exudates. Exudation rates (mg C per cm2 root area d-1) were highest in the emergence stage and logarithmically decreased with plant development. In the emergence stage, the roots released predominantly sugars (most indicative: glucose and fructose) and the metabolite richness was generally higher than in later stages. Secondary compounds (e.g. phenolics, benzoxazinoids, or mucilage) increased significantly in later development stages. Differences in the composition of exudates between genotypes may be related to their respective development strategies, with genotypes accumulating more biomass releasing relatively more compounds related to root establishment (growth and rhizosphere development, e.g. mucilage, fatty and organic acids) and slower developing genotypes relatively more metabolites related to maintenance and defense (e.g. phenolics). Our results shed light onto the early dynamics of maize root exudation and rhizosphere establishment, over a phenotypical spectrum of genotypes.

Navigating nitrogen sustainability with microbiome-associated phenotypes

Crop microbiomes promote plant health through various mechanisms, including nutrient provisioning. However, agriculture neglected the importance of these microbiome-associated phenotypes (MAPs) in conventional management approaches originating from the Green Revolution. Green Revolution innovations, such as nitrogen fertilizers and high-yielding germplasm, supported an increase in global crop yields. Yet these advances also led to many environmental issues, including disruptions in microbially mediated nitrogen transformations that have reduced reliance on microbiomes for sustainable nitrogen acquisition. Overcoming the challenges introduced by the Green Revolution requires a shift toward ecologically informed agronomic strategies that incorporate MAPs into breeding and management decisions. Agriculture in the Anthropocene needs to mindfully manage crop microbiomes to decouple agrochemical inputs from profitable yields, minimizing the environmental repercussions of modern agriculture.

Root RADAR: how 'rhizocrine' signals allow roots to detect and respond to their soil environment and stresses

Agricultural intensification coupled with changing climate are causing soils to become increasingly vulnerable to stresses such as drought, soil erosion, and compaction. The mechanisms by which roots detect and respond to soil stresses remain poorly understood. Recent breakthroughs show that roots release volatile and soluble hormone signals into the surrounding soil, then monitor their levels to sense soil stresses. Our review discusses how hormones can act 'outside the plant' as 'rhizocrine' signals that function to improve plant resilience to different soil stresses. We also propose a novel signalling paradigm which we term 'root RADAR' where 'rhizocrine' levels change in soil in response to environmental stresses, feeding back to roots and triggering adaptive responses.

Ralstonia solanacearum infection induces tobacco root to secrete chemoattractants to recruit antagonistic bacteria and defensive compounds to inhibit pathogen

BACKGROUND

Plant root exudates play crucial roles in maintaining the structure and function of the whole belowground ecosystem and regulating the interactions between roots and soil microorganisms. Ralstonia solanacearum causes bacterial wilt disease in many plants, while root exudate-mediated inhibition of pathogen infection is poorly understood. Here, we characterize the chemical divergence between root exudates of healthy and diseased tobacco plants and the effects of that variability on the rhizosphere microbial community and the occurrence of bacterial wilt.

RESULTS

Compared with the healthy plants, root exudates in diseased plants showed distinct exudation patterns and metabolite profiles including increased amounts of flavonoids, phenylpropanoids, terpenoids and defense-related hormones, as well as distinct bacterial community composition, as illustrated by an increased abundance of Ralstonia and decreased abundances of Bacillus and Streptomyces in diseased plants rhizosphere. Pathogen infection stimulated roots to secrete more defensive compounds to inhibit pathogen growth. Change of root exudates modulated rhizosphere microbial community. Specific root exudates could benefit plants by attracting antagonistic Bacillus amyloliquefaciens and inhibiting pathogens. Bacillus amyloliquefaciens could utilize specific root exudates as carbon sources. Benzyl cinnamatel promoted the biofilm formation and colonization of B. amyloliquefaciens on roots.

CONCLUSION

To defend against pathogen invasion, tobacco plants recruited antagonistic and plant growth-promoting rhizobacteria to the rhizosphere by modifying root exudate profiles. Specific signal molecules are recommended to recruit beneficial microorganisms for controlling bacterial wilt. The results provide insights concerning the metabolic divergence of root exudates integral to understanding root-microorganism interaction. © 2024 Society of Chemical Industry.

Root separation modulates AMF diversity and composition in tomato-potato onion intercropping systems

Plant-plant interactions shape arbuscular mycorrhizal fungi (AMF) communities in rhizosphere soil, with tomato/potato-onion intercropping emerging as a promising agro-ecological strategy to optimize resource utilization. However, the role of root separation methods in modulating AMF diversity within intercropping systems remains unclear. Specifically, whether the AMF community in the rhizosphere of tomato and potato-onion intercropping differs from monoculture and how root separation methods modulate these effects. This study evaluates the effects of various root separation methods (no separation, 0.45 μm nylon membrane, 38 μm nylon membrane, and solid separation) on AMF diversity and composition in tomato/potato-onion intercropping and monoculture systems. High-throughput Illumina MiSeq sequencing was used to assess AMF diversity indices (Ace, Chao1, Shannon, and Simpson), and Principal Coordinate Analysis evaluated community structure. Results showed that the non-separation mode achieved the highest Ace and Chao1 indices, indicating greater richness, while intercropping lowered Shannon and Simpson indices. Intercropping significantly reduced Glomerales but increased Paraglomerales, under the non-separation mode. Similarly, it decreased Glomus while increasing Paraglomus in the rhizosphere of both crops. Principal Coordinate Analysis revealed that root separation distinctly altered AMF community structure, reflecting specific barrier effects on AMF interactions. Intercropping increased AMF abundance in the tomato rhizosphere but reduced it in potato-onion as shown by 18S rRNA gene abundance. These findings emphasize that minimizing root separation in intercropping enhances AMF diversity and functionality, providing valuable insights for sustainable agricultural management. Understanding the role of root interactions in shaping AMF communities can help optimizing intercropping strategies to improve soil health and nutrient dynamics.

Evolutionary Trajectories of Shoots vs. Roots: Plant Volatile Metabolomes Are Richer but Less Structurally Diverse Belowground in the Tropical Tree Genus Protium

The breadth and depth of plant leaf metabolomes have been implicated in key interactions with plant enemies aboveground. In particular, divergence in plant species chemical composition-amongst neighbors, relatives, or both-is often suggested as a means of escape from insect herbivore enemies. Plants also experience strong pressure from enemies such as belowground pathogens; however, little work has been carried out to examine the evolutionary trajectories of species' specialized chemistries in both roots and leaves. Here, we examine the GCMS detectable phytochemistry (for simplicity, hereafter referred to as specialized volatile metabolites) of the tropical tree genus Protium, testing the hypothesis that phenotypic divergence will be weaker belowground compared to aboveground due to more limited dispersal by enemies. We found that, after controlling for differences in chemical richness, roots expressed less structurally diverse compounds than leaves, despite having higher numbers of specialized volatile metabolites, and that species' phylogenetic distance was only positively correlated with compound structural distance in roots, not leaves. Taken together, our results suggest that root specialized volatile metabolites exhibit significantly less phenotypic divergence than leaf specialized metabolites and may be under relaxed selection pressure from enemies belowground.

Transcriptomic response of wetland microbes to root influence

Wetlands are hotspots for carbon and nutrient cycling. The important role of plant-microbe interactions in driving wetland biogeochemistry is widely acknowledged, prompting research into their molecular biological basis for a deeper understanding of these processes. We analyzed transcriptomic responses of soil microbes to root exudates in coastal wetland soils using 13CO2 pulse labeling. Metatranscriptomics revealed 388 upregulated and 11 downregulated genes in response to root exudates. The Wood-Ljungdahl pathway and dissimilatory sulfate reduction/oxidation were the most active microbial pathways independent of root influence, whereas pathways with the strongest upregulation in response to root influence were related to infection, stress response, and motility. We demonstrate shifts within the active community toward higher relative abundances of Betaproteobacteria, Campylobacterota, Kiritimatiellota, Lentisphaerota, and Verrucomicrobiota in response to exudates. Overall, this study improves our mechanistic understanding of wetland plant-soil microbe interactions by revealing the phylogenetic and transcriptional response of soil microorganisms to root influence and exudate input.

Plant microbiome technology for sustainable agriculture

Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.

Structurally diverse specialized metabolites of maize and their extensive biological functions

Maize originated in southern Mexico and various hybrid varieties have been bred during domestication. All maize tissues are rich in specialized plant metabolites (SPMs), which allow the plants to resist the stresses of herbivores and pathogens or environmental factors. To date, a total of 95 terpenoids, 91 phenolics, 31 alkaloids, and 6 other types of compounds have been identified from maize. Certain volatile sesquiterpenes released by maize plants attract the natural enemies of maize herbivores and provide an indirect defensive function. Kauralexins and dolabralexins are the most abundant diterpenoids in maize and are known to regulate and stabilize the maize rhizosphere microbial community. Benzoxazinoids and benzoxazolinones are the main alkaloids in maize and are found in maize plants at the highest concentrations at the seedling stage. These two kinds of alkaloids directly resist herbivory and pathogenic infection. Phenolics enhance the cross-links between maize cell walls. Meanwhile, SPMs also regulate plant-plant relationships. In conclusion, SPMs in maize show a large diversity of chemical structures and broad-spectrum biological activities. We use these to provide ideas and information to enable the improvement of maize resistances through breeding and to promote the rapid development of the maize industry.

Euglena mutabilis exists in a FAB consortium with microbes that enhance cadmium tolerance

BACKGROUND

Synthetic algal-fungal and algal-bacterial cultures have been investigated as a means to enhance the technological applications of the algae. This inclusion of other microbes has enhanced growth and improved stress tolerance of the algal culture. The goal of the current study was to investigate natural microbial consortia to gain an understanding of the occurrence and benefits of these associations in nature. The photosynthetic protist Euglena mutabilis is often found in association with other microbes in acidic environments with high heavy metal (HM) concentrations. This may suggest that microbial interactions are essential for the protist's ability to tolerate these extreme environments. Our study assessed the Cd tolerance of a natural fungal-algal-bacterial (FAB) association whereby the algae is E. mutabilis.

RESULTS

This study provides the first assessment of antibiotic and antimycotic agents on an E. mutabilis culture. The results indicate that antibiotic and antimycotic applications significantly decreased the viability of E. mutabilis cells when they were also exposed to Cd. Similar antibiotic treatments of E. gracilis cultures had variable or non-significant impacts on Cd tolerance. E. gracilis also recovered better after pre-treatment with antibiotics and Cd than did E. mutabilis. The recoveries were assessed by heterotrophic growth without antibiotics or Cd. In contrast, both Euglena species displayed increased chlorophyll production upon Cd exposure. PacBio full-length amplicon sequencing and targeted Sanger sequencing identified the microbial species present in the E. mutabilis culture to be the fungus Talaromyces sp. and the bacterium Acidiphilium acidophilum.

CONCLUSION

This study uncovers a possible fungal, algal, and bacterial relationship, what we refer to as a FAB consortium. The members of this consortium interact to enhance the response to Cd exposure. This results in a E. mutabilis culture that has a higher tolerance to Cd than the axenic E. gracilis. The description of this interaction provides a basis for explore the benefits of natural interactions. This will provide knowledge and direction for use when creating or maintaining FAB interactions for biotechnological purposes, including bioremediation.

How the root bacterial community of Ficus tikoua responds to nematode infection: enrichments of nitrogen-fixing and nematode-antagonistic bacteria in the parasitized organs

Plant-parasitic nematodes (PPNs) are among the most damaging pathogens to host plants. Plants can modulate their associated bacteria to cope with nematode infections. The tritrophic plant-nematode-microbe interactions are highly taxa-dependent, resulting in the effectiveness of nematode agents being variable among different host plants. Ficus tikoua is a versatile plant with high application potential for fruits or medicines. In recent years, a few farmers have attempted to cultivate this species in Sichuan, China, where parasitic nematodes are present. We used 16S rRNA genes to explore the effects of nematode parasitism on root-associated bacteria in this species. Our results revealed that nematode infection had effects on both endophytic bacterial communities and rhizosphere communities in F. tikoua roots, but on different levels. The species richness increased in the rhizosphere bacterial communities of infected individuals, but the community composition remained similar as compared with that of healthy individuals. Nematode infection induces a deterministic assembly process in the endophytic bacterial communities of parasitized organs. Significant taxonomic and functional changes were observed in the endophytic communities of root knots. These changes were characterized by the enrichment of nitrogen-fixing bacteria, including Bradyrhizobium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and nematode-antagonistic bacteria, such as Pseudonocardia, Pseudomonas, Steroidobacter, Rhizobacter, and Ferrovibrio. Our results would help the understanding of the tritrophic plant-nematode-bacterium interactions in host plants other than dominant crops and vegetables and would provide essential information for successful nematode management when F. tikoua were cultivated on large scales.

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.

Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis

Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.

The Complex Interplay between Arbuscular Mycorrhizal Fungi and Strigolactone: Mechanisms, Sinergies, Applications and Future Directions

Plants, the cornerstone of life on Earth, are constantly struggling with a number of challenges arising from both biotic and abiotic stressors. To overcome these adverse factors, plants have evolved complex defense mechanisms involving both a number of cell signaling pathways and a complex network of interactions with microorganisms. Among these interactions, the relationship between symbiotic arbuscular mycorrhizal fungi (AMF) and strigolactones (SLs) stands as an important interplay that has a significant impact on increased resistance to environmental stresses and improved nutrient uptake and the subsequent enhanced plant growth. AMF establishes mutualistic partnerships with plants by colonizing root systems, and offers a range of benefits, such as increased nutrient absorption, improved water uptake and increased resistance to both biotic and abiotic stresses. SLs play a fundamental role in shaping root architecture, promoting the growth of lateral roots and regulating plant defense responses. AMF can promote the production and release of SLs by plants, which in turn promote symbiotic interactions due to their role as signaling molecules with the ability to attract beneficial microbes. The complete knowledge of this synergy has the potential to develop applications to optimize agricultural practices, improve nutrient use efficiency and ultimately increase crop yields. This review explores the roles played by AMF and SLs in plant development and stress tolerance, highlighting their individual contributions and the synergistic nature of their interaction.

Metabolomic and transcriptomic analyses of rice plant interaction with invasive weed Leptochloa chinensis

Introduction

Leptochloa chinensis is an annual weed in paddy fields, which can engage in competition with rice, leading to a severe yield reduction. However, theunderlying mechanism governing this interaction remain unknown.

Methods

In this study, we investigated the mutual inhibition between rice and the weed undermono-culture and co-culture conditions. We found that the root exudates of both species played essential roles in mediating the mutual inhibition. Further metabolomic analysis identified a significant number of differential metabolites. These metabolites were predominantly enriched in the phenylpropanoid and flavonoid biosynthesis pathways in weed and rice. Transcriptomic analysis revealed that the differentially expressed genes responding to the interaction were also enriched in these pathways.

Results

Phenylpropanoid and flavonoid biosynthesis pathways are associated with allelopathy, indicating their pivotal role in the response of rice-weed mutual inhibition.

Discussion

Our findings shed light on the conserved molecular responses of rice and L. chinensis during theirinteraction, provide evidence to dissect the mechanisms underlying the allelopathic interaction and offer potential strategies for weed management in rice paddies.

Small volatile lipophilic molecules induced belowground by aphid attack elicit a defensive response in neighbouring un-infested plants

In pioneering studies on plant-aphid interactions, we have observed that Vicia faba plants infested by aphids can transmit signals via the rhizosphere that induce aboveground defence in intact, neighbouring plants. The aphid parasitoid Aphidius ervi is significantly attracted towards intact broad bean plants grown in a hydroponic solution previously harbouring Acyrtosiphon pisum-infested plants. To identify the rhizosphere signal(s) possibly mediating this belowground plant-plant communication, root exudates were collected using Solid-Phase Extraction (SPE) from 10-day old A. pisum-infested and un-infested Vicia faba plants hydroponically grown. To verify the ability of these root exudates to trigger defence mechanisms against the aphids we added them to V. fabae plants grown in hydroponic solution, and tested these plants in the wind-tunnel bioassay to assess their attractiveness towards the aphids' parasitoids A. ervi. We identified three small volatile lipophilic molecules as plant defence elicitors: 1-octen-3-ol, sulcatone and sulcatol, in SPE extracts of A. pisum-infested broad bean plants. In wind tunnel assays, we recorded a significant increase in the attractiveness towards A. ervi of V. faba plants grown in hydroponic solution treated with these compounds, compared to plants grown in hydroponic treated with ethanol (control). Both 1-octen-3-ol and sulcatol have asymmetrically substituted carbon atoms at positions 3 and 2, respectively. Hence, we tested both their enantiomers alone or in mixture. We highlighted a synergistic effect on the level of attractiveness towards the parasitoid when testing the three compounds together in respect to the response recorded against them singly tested. These behavioural responses were supported by the characterization of headspace volatiles released by tested plants. These results shed new light on the mechanisms underlying plant-plant communication belowground and prompt the use of bio-derived semiochemicals for a sustainable protection of agricultural crops.

Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains

Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

Population Response of Rhizosphere Microbiota of Garden Pea Genotypes to Inoculation with Arbuscular Mycorrhizal Fungi

This study of a legume's rhizosphere in tripartite symbiosis focused on the relationships between the symbionts and less on the overall rhizosphere microbiome. We used an experimental model with different garden pea genotypes inoculated with AM fungi (Rhizophagus irregularis and with a mix of AM species) to study their influence on the population levels of main trophic groups of soil microorganisms as well as their structure and functional relationships in the rhizosphere microbial community. The experiments were carried out at two phenological cycles of the plants. Analyzes were performed according to classical methods: microbial population density defined as CUF/g a.d.s. and root colonization rate with AMF (%). We found a proven dominant effect of AMF on the densities of micromycetes and actinomycetes in the direction of reduction, suggesting antagonism, and on ammonifying, phosphate-solubilizing and free-living diazotrophic Azotobacter bacteria in the direction of stimulation, an indicator of mutualistic relationships. We determined that the genotype was decisive for the formation of populations of bacteria immobilizing mineral NH4+-N and bacteria Rhizobium. We reported significant two-way relationships between trophic groups related associated with soil nitrogen and phosphorus ions availability. The preserved proportions between trophic groups in the microbial communities were indicative of structural and functional stability.

Distinct chemical resistance-inducing stimuli result in common transcriptional, metabolic, and nematode community signatures in rice root and rhizosphere

Induced resistance (IR), a phenotypic state induced by an exogenous stimulus and characterized by enhanced resistance to future (a)biotic challenge, is an important component of plant immunity. Numerous IR-inducing stimuli have been described in various plant species, but relatively little is known about 'core' systemic responses shared by these distinct IR stimuli and the effects of IR on plant-associated microbiota. In this study, rice (Oryza sativa) leaves were treated with four distinct IR stimuli (β-aminobutyric acid, acibenzolar-S-methyl, dehydroascorbic acid, and piperonylic acid) capable of inducing systemic IR against the root-knot nematode Meloidogyne graminicola and evaluated their effect on the root transcriptome and exudome, and root-associated nematode communities. Our results reveal shared transcriptional responses-notably induction of jasmonic acid and phenylpropanoid metabolism-and shared alterations to the exudome that include increased amino acid, benzoate, and fatty acid exudation. In rice plants grown in soil from a rice field, IR stimuli significantly affected the composition of rhizosphere nematode communities 3 d after treatment, but by 14 d after treatment these changes had largely reverted. Notably, IR stimuli did not reduce nematode diversity, which suggests that IR might offer a sustainable option for managing plant-parasitic nematodes.

Root exudate sesquiterpenoids from the invasive weed Ambrosia trifida regulate rhizospheric Proteobacteria

The adaption of Ambrosia trifida to the environment to which it has been introduced is crucial to its successful invasion. Microbial diversity analyses suggested that the abundance of Proteobacteria was relatively high in rhizospheric soil surrounding A. trifida roots. Three of these bacterial taxa were isolated and identified as Acinetobacter sp. LHD-1, Pseudomonas sp. LHD-12, and Enterobacter sp. LHD-19. Furthermore, three sesquiterpenoids were authenticated as the main metabolites in the root exudates of A. trifida, and include one new germacrane sesquiterpenoid (1E,4E)-germacrdiene-6β,15-diol (2) and two known sesquiterpenoids, (E)-4β,5α-epoxy-7αH-germacr-1(10)-ene-2β,6β-diol (1) and (2R)-δ-cadin-4-ene-2,10-diol (3). Their chemical structures were elucidated using NMR spectroscopy and single crystal X-ray diffraction analyses. In UPLC-MS/MS analyses, compounds 1-3 showed values of 10.29 ± 2.21, 0.02 ± 0.01, and 0.78 ± 0.52 μg/g FW, respectively, in A. trifida rhizospheric soil. Interestingly, those compounds were able to inhibit the growth of Acinetobacter sp. LHD-1 and promote the growth of Enterobacter sp. LHD-19 where concentrations were close to those secreted into rhizospheric soil. Furthermore, the rhizospheric bacteria Acinetobacter sp. LHD-1 and Enterobacter sp. LHD-19 were able to regulate the growth of A. trifida seedlings in potted planting verification experiments. Interestingly, root exudate sesquiterpenoids could also improve the concentration of IAA in Enterobacter sp. LHD-19, indicating that this bacterium may promote plant growth through regulating the IAA pathway. These results provided new evidence for the rapid adaptation of plants to new environments, allowing their invasive behavior.

Microbe Related Chemical Signalling and Its Application in Agriculture

The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

The wheat secreted root proteome: Implications for phosphorus mobilisation and biotic interactions

Root secreted acid phosphatases and organic anions are widely perceived as major players of plant phosphorus (P) mobilisation from the rhizosphere under P limiting growth conditions. Previous research indicated that other mechanisms play a role, especially in species with fine roots, such as wheat. In this study we characterised the plant-derived extracellular proteome of wheat roots by profiling root tip mucilage, soluble root secreted and root tip proteomes. Extracellular acid phosphatases and enzymes of the central carbon metabolism were targeted using selected reaction monitoring. More than 140 proteins with extracellular localisation prediction were identified in mucilage. P starvation induced proteins predicted to be localised to the apoplast which are related to cell wall modification and defence in both, root tip and soluble root-secreted proteomes. Glycolytic enzymes were strongly increased in abundance by P limitation in root tips, as were PEPC and plastidial MDH. Soluble acid phosphatases were not identified in extracellular protein samples. Our results indicate that root tip mucilage contains proteins with the functional potential to actively shape their immediate environment by modification of plant structural components and biotic interactions. Wheat acid phosphatases appear to play a minor role in P mobilisation beyond the immediate root surface. SIGNIFICANCE: Phosphorus (P) is a plant growth limiting nutrient in many agricultural situations and the development of phosphorus efficient crops is of paramount importance for future agricultural management practices. As P is relatively immobile in soils, processes occurring at the root-soil interface, the rhizosphere, are suspected to play a key role in plant-induced P mobilisation. According to the current view, the secretion of extracellular acid phosphatases and organic anions enhances P mobilisation within several millimetres beyond the root surface, either directly or indirectly through the selection and appropriate soil microbes. However, the mechanisms of P mobilisation in species with fine roots, such as wheat, and the role of other secreted root proteins are poorly understood. Here, we carried out the profiling of wheat root tip mucilage, soluble root secreted and root tip proteomes. We analysed proteome changes in response to P starvation. We found that proteins with a predicted localisation to the apoplast made up a major proportion of stress-responsive proteins. Acid phosphatases were not identified within extracellular protein samples, which were enriched in proteins with predicted extracellular localisation. The absence of extracellular APases was further validated by multiple reaction monitoring. Our data indicates that wheat acid phosphatases play a minor role in P mobilisation beyond the immediate root surface and provides a resource for breeding strategies and further investigations of the functional roles of root tip-released proteins in the rhizosphere under P limitation.

Herbivory shapes the rhizosphere bacterial microbiota in potato plants

Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by several different herbivores, but the effects of multiple herbivore types on the plant microbiome remain to be determined. Here, we first tested whether feeding by different herbivores (aphids, nematodes and slugs) produces a shift in the rhizosphere bacterial microbiota associated with potato plants. Then, we expanded this question asking whether the identity of the herbivore produces different effects on the rhizosphere microbial community. While we found shifts in microbial diversity and structure due to herbivory, we observed that the herbivore identity does not influence the diversity or community structure of bacteria thriving in the rhizosphere. However, a deeper analysis revealed that the herbivores differentially affected the structure of the network of microbial co-occurrences. Our results have the potential to increase our ability to predict how plant microbiomes assemble and aid our understanding of the role of plant microbiome in plant responses to biotic stress.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions

An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.

Root exudate signals in plant-plant interactions

Plant-to-plant signalling is a key mediator of interactions among plant species. Plants can perceive and respond to chemical cues emitted from their neighbours, altering survival and performance, impacting plant coexistence and community assembly. An increasing number of studies indicate root exudates as key players in plant-to-plant signalling. Root exudates mediate root detection and behaviour, kin recognition, flowering and production, driving inter- and intra-specific facilitation in cropping systems and mixed-species plantations. Altered interactions may be attributed to the signalling components within root exudates. Root ethylene, strigolactones, jasmonic acid, (-)-loliolide and allantoin are signalling chemicals that convey information on local conditions in plant-plant interactions. These root-secreted signalling chemicals appear ubiquitous in plants and trigger a series of belowground responses inter- and intra-specifically, involving molecular events in biosynthesis, secretion and action. The secretion of root signals, mainly mediated by ATP-binding cassette transporters, is critical. Root-secreted signalling chemicals and their molecular mechanisms are rapidly revealing a multitude of fascinating plant-plant interactions. However, many root signals, particularly species-specific signals and their underlying mechanisms, remain to be uncovered due to methodological limitations and root-soil interactions. A thorough understanding of root-secreted chemical signals and their mechanisms will offer many ecological implications and potential applications for sustainable agriculture.

Reduced Root Secretion of Valine in Rosa-Microbe Interaction Contributes to the Decreased Colonization of Pathogenic Agrobacterium tumefaciens

Root exudates play a critical role in root-microbe interactions. Agrobacterium tumefaciens causes crown gall disease in multiple plant species, but rose root exudate-mediated inhibition of Agrobacterium in the rhizosphere is poorly understood. In this study, the influence of preinoculation with beneficial bacteria or pathogens on root exudates and subsequent colonization by A. tumefaciens was investigated in a split-root system. We found that preinoculation of rose plants in a split-root system with Bacillus velezensis CLA178 or A. tumefaciens C58 inhibited subsequent colonization by C58. Root secretion of valine had positive effects on the chemotaxis, biofilm formation, colonization of C58, and crown gall disease severity, but valine secretion decreased significantly when Rosa multiflora plants were preinoculated with CLA178 or C58. These results indicated that rose plants reduced root secretion of valine in response to microbial colonization, thereby reducing the colonization of Agrobacterium colonization and disease severity. This study provides new insights into the root exudate-mediated interactions of rose plants, B. velezensis, and A. tumefaciens and proposes a potential way to control crown gall disease.

Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems

Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.

Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices.

IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere

The microbiota associated to xerophyte is a "black box" that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.

Mapping Reaction-Diffusion Networks at the Plant Wound Site With Pathogens

The rich collection of microbes colonizing the plant root making up the rhizosphere function as a multigenomic organ for nutrient distribution. The extent to which its dynamic mutualistic cellular order depends on morphogenic signaling, while likely, remains unknown. We have shown that reaction-diffusion chemical networks constructed with model plant and bacterial metabolites can mimic processes ranging from oxidative burst kinetics to traveling waves and extracellular stationary state reaction-diffusion networks for spatiotemporal ordering of the rhizosphere. Plant parasites and pathogens can be limited by host attachment require dynamic informational networks and continue to provide insight into what controls the rhizosphere. Here we take advantage of Agrobacterium tumefaciens, a plant pathogen with a gated receptor that requires simultaneous perception of two plant metabolites. Genetic manipulations have created receptors allowing each metabolite concentration to be correlated with pathogen behavior. The development of the florescent strains used here provide initial maps of the reaction-diffusion dynamics existing in the rhizosphere, revealing significant differences in the signaling landscape of host and non-host plants before and after wounding, specifically highlighting networks that may inform rhizosphere organization.

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production

Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

Ridge Tillage Improves Soil Properties, Sustains Diazotrophic Communities, and Enhances Extensively Cooperative Interactions Among Diazotrophs in a Clay Loam Soil

Reduced tillage practices [such as ridge tillage (RT)] have been potential solutions to the weed pressures of long-term no tillage (NT) and the soil-intensive disturbances caused by conventional tillage [such as moldboard plow (MP) tillage]. Although soil diazotrophs are significantly important in global nitrogen (N) cycling and contribute to the pool of plant-available N in agroecosystems, little is currently known about the responses of diazotrophic communities to different long-term tillage practices. In the current study, we investigated the differences among the effects of NT, RT, and MP on soil properties, diazotrophic communities, and co-occurrence network patterns in bulk and rhizosphere soils under soybean grown in clay loam soil of Northeast China. The results showed that RT and MP led to higher contents of total C, N, and available K compared to NT in both bulk and rhizosphere soils, and RT resulted in higher soybean yield than NT and MP. Compared to NT and RT, MP decreased the relative abundances of free-living diazotrophs, while it promoted the growth of copiotrophic diazotrophs. Little differences of diazotrophic community diversity, composition, and community structure were detected between RT and NT, but MP obviously decreased diazotrophic diversity and changed the diazotrophic communities in contrast to NT and RT in bulk soils. Soil nitrogenous nutrients had negative correlations with diazotrophic diversity and significantly influenced the diazotrophic community structure. Across all diazotrophs' networks, the major diazotrophic interactions transformed into a cooperatively dominated network under RT, with more intense and efficient interactions among species than NT and MP. Overall, our study suggested that RT, with minor soil disturbances, could stabilize diazotrophic diversity and communities as NT and possessed highly positive interactions among diazotrophic species relative to NT and MP.

Plant Secondary Compounds in Soil and Their Role in Belowground Species Interactions

Knowledge of the effect of plant secondary compounds (PSCs) on belowground interactions in the more diffuse community of species living outside the rhizosphere is sparse compared with what we know about how PSCs affect aboveground interactions. We illustrate here that PSCs from foliar tissue, root exudates, and leaf litter effectively influence such belowground plant-plant, plant-microorganism, and plant-soil invertebrate interactions. Climatic factors can induce PSC production and select for different plant chemical types. Therefore, climate change can alter both quantitative and qualitative PSC production, and how these compounds move in the soil. This can change the soil chemical environment, with cascading effects on both the ecology and evolution of belowground species interactions and, ultimately, soil functioning.

Tritrophic interactions follow phylogenetic escalation and climatic adaptation

One major goal in plant evolutionary ecology is to address how and why tritrophic interactions mediated by phytochemical plant defences vary across species, space, and time. In this study, we tested three classical hypotheses about plant defences: (i) the resource-availability hypothesis, (ii) the altitudinal/elevational gradient hypothesis and (iii) the defence escalation hypothesis. For this purpose, predatory soil nematodes were challenged to hunt for root herbivores based on volatile cues from damaged or intact roots of 18 Alpine Festuca grass species adapted to distinct climatic niches spanning 2000 meters of elevation. We found that adaptation into harsh, nutrient-limited alpine environments coincided with the production of specific blends of volatiles, highly attractive for nematodes. We also found that recently-diverged taxa exposed to herbivores released higher amounts of volatiles than ancestrally-diverged species. Therefore, our model provides evidence that belowground indirect plant defences associated with tritrophic interactions have evolved under two classical hypotheses in plant ecology. While phylogenetic drivers of volatile emissions point to the defence-escalation hypothesis, plant local adaptation of indirect defences is in line with the resource availability hypothesis.

Abed RM, Ning Chai Y, N. Al-Rawahi A, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A. Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance

Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.

Plant defense resistance in natural enemies of a specialist insect herbivore

Certain adapted insect herbivores utilize plant toxins for self-defense against their own enemies. These adaptations structure ecosystems and limit our capacity to use biological control agents to manage specialized agricultural pests. We show that entomopathogenic nematodes that are exposed to the western corn rootworm, an important agricultural pest that sequesters defense metabolites from maize, can evolve resistance to these defenses. Resisting the plant defense metabolites likely allows the nematodes to infect and kill the western corn rootworm more efficiently. These findings illustrate how predators can counter the plant-based resistance strategies of specialized insect herbivores. Breeding or engineering biological control agents that resist plant defense metabolites may improve their capacity to kill important agricultural pests such as the western corn rootworm.

Plants defend themselves against herbivores through the production of toxic and deterrent metabolites. Adapted herbivores can tolerate and sometimes sequester these metabolites, allowing them to feed on defended plants and become toxic to their own enemies. Can herbivore natural enemies overcome sequestered plant defense metabolites to prey on adapted herbivores? To address this question, we studied how entomopathogenic nematodes cope with benzoxazinoid defense metabolites that are produced by grasses and sequestered by a specialist maize herbivore, the western corn rootworm. We find that nematodes from US maize fields in regions in which the western corn rootworm was present over the last 50 y are behaviorally and metabolically resistant to sequestered benzoxazinoids and more infective toward the western corn rootworm than nematodes from other parts of the world. Exposure of a benzoxazinoid-susceptible nematode strain to the western corn rootworm for 5 generations results in higher behavioral and metabolic resistance and benzoxazinoid-dependent infectivity toward the western corn rootworm. Thus, herbivores that are exposed to a plant defense sequestering herbivore can evolve both behavioral and metabolic resistance to plant defense metabolites, and these traits are associated with higher infectivity toward a defense sequestering herbivore. We conclude that plant defense metabolites that are transferred through adapted herbivores may result in the evolution of resistance in herbivore natural enemies. Our study also identifies plant defense resistance as a potential target for the improvement of biological control agents.

Bacterial Diversity and Community Structure in Typical Plant Rhizosphere

Bacteria play a vital role in the quality of soil, health, and the production of plants. This has led to several studies in understanding the diversity and structure in the plant rhizosphere. Over the years, there have been overwhelming advances in molecular biology which have led to the development of omics techniques which utilize RNA, DNA, or proteins as biomolecules; these have been gainfully used in plant–microbe interactions. The bacterial community found in the rhizosphere is known for its colonization around the roots due to availability of nutrients, and composition, and it affects the plant growth directly or indirectly. Metabolic fingerprinting enables a snapshot of the metabolic composition at a given time. We review metabolites with ample information on their benefit to plants and which are found in rhizobacteria such as Pseudomonas spp. and Bacillus spp. Exploring plant-growth-promoting rhizobacteria using omics techniques can be a true success story for agricultural sustainability.

Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms

Since the discovery of penicillin in 1928 and throughout the 'age of antibiotics' from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. © 2019 Society of Chemical Industry.

Allelochemicals and Signaling Chemicals in Plants

Plants abound with active ingredients. Among these natural constituents, allelochemicals and signaling chemicals that are released into the environments play important roles in regulating the interactions between plants and other organisms. Allelochemicals participate in the defense of plants against microbial attack, herbivore predation, and/or competition with other plants, most notably in allelopathy, which affects the establishment of competing plants. Allelochemicals could be leads for new pesticide discovery efforts. Signaling chemicals are involved in plant neighbor detection or pest identification, and they induce the production and release of plant defensive metabolites. Through the signaling chemicals, plants can either detect or identify competitors, herbivores, or pathogens, and respond by increasing defensive metabolites levels, providing an advantage for their own growth. The plant-organism interactions that are mediated by allelochemicals and signaling chemicals take place both aboveground and belowground. In the case of aboveground interactions, mediated air-borne chemicals are well established. Belowground interactions, particularly in the context of soil-borne chemicals driving signaling interactions, are largely unknown, due to the complexity of plant-soil interactions. The lack of effective and reliable methods of identification and clarification their mode of actions is one of the greatest challenges with soil-borne allelochemicals and signaling chemicals. Recent developments in methodological strategies aim at the quality, quantity, and spatiotemporal dynamics of soil-borne chemicals. This review outlines recent research regarding plant-derived allelochemicals and signaling chemicals, as well as their roles in agricultural pest management. The effort represents a mechanistically exhaustive view of plant-organism interactions that are mediated by allelochemicals and signaling chemicals and provides more realistic insights into potential implications and applications in sustainable agriculture.

Phosphorus forms affect the hyphosphere bacterial community involved in soil organic phosphorus turnover

Interactions between bacteria and arbuscular mycorrhizal (AM) fungi play a significant role in mediating organic phosphorus (P) transformations and turnover in soil. The bacterial community in soil is largely responsible for mobilization of the soil organic P pool, and the released P is taken up by extraradical AM hyphae, which mediate its use for plant growth. However, the functional microbiome involved in organic P mineralization in the hyphosphere remains poorly understood. The aim of this study was to determine how AM hyphae-associated bacterial communities related to P turnover in the hyphosphere of leek (Allium porrum) respond to different forms of soil P. Using a compartmented microcosm, leek was grown with the AM fungus Funneliformis mosseae, and the extraradical mycelium of F. mosseae was allowed to grow into a separate hyphal compartment containing either no added P, or P as KH₂PO₄ or phytin. High-throughput sequencing showed that the alkaline phosphatase (ALP)-harboring bacterial community associated with the AM hyphae was dominated by Sinorhizobium, Bradyrhizobium, Pseudomonas, and Ralstonia and was significantly changed in response to different P treatments, with Pseudomonas showing higher relative abundance in organic P treatments than in control and inorganic P treatments. Pseudomonas was also the major genus harboring the β-propeller phytase (BPP) gene in the hyphosphere, but the BPP-harboring community structure was not affected by the presence of different P forms. These results demonstrate the profound differences in ALP- and BPP-harboring bacterial communities in the hyphosphere at bacterial genus level, providing new insights to link bacteria and biogeochemical P cycling driven in association with mycorrhizal hyphae.

The symbiotic bacteria Alcaligenes faecalis of the entomopathogenic nematodes Oscheius spp. exhibit potential biocontrol of plant- and entomopathogenic fungi

Soil-dwelling entomopathogenic nematodes (EPNs) kill arthropod hosts by injecting their symbiotic bacteria into the host hemolymph and feed on the bacteria and the tissue of the dying host for several generations cycles until the arthropod cadaver is completely depleted. The EPN-bacteria-arthropod cadaver complex represents a rich energy source for the surrounding opportunistic soil fungal biota and other competitors. We hypothesized that EPNs need to protect their food source until depletion and that the EPN symbiotic bacteria produce volatile and non-volatile exudations that deter different soil fungal groups in the soil. We isolated the symbiotic bacteria species (Alcaligenes faecalis) from the EPN Oscheius spp. and ran infectivity bioassays against entomopathogenic fungi (EPF) as well as against plant pathogenic fungi (PPF). We found that both volatile and non-volatile symbiotic bacterial exudations had negative effects on both EPF and PPF. Such deterrent function on functionally different fungal strains suggests a common mode of action of A. faecalis bacterial exudates, which has the potential to influence the structure of soil microbial communities, and could be integrated into pest management programs for increasing crop protection against fungal pathogens.

Contribution of different predator guilds to tritrophic interactions along ecological clines

The strengths of interactions between plants, herbivores, and predators are predicted to relax with elevation. Despite the fundamental role predators play in tritrophic interactions, high-resolution experimental evidence describing predation across habitat gradients is still scarce in the literature and varies by predator. With this opinion paper, we look at how tritrophic strength of systems including different vertebrate and invertebrate predator guilds changes with elevation. Specifically, we focus on how birds, ants, parasitoids, and nematodes exert top-down pressure as predators and propose ways, in which each group could be better understood through elevational gradient studies. We hope to enrich future perspectives for disentangling the different biotic and abiotic factors underlying predator-mediated trophic interactions in a diversity of habitats.

Protecting maize from rootworm damage with the combined application of arbuscular mycorrhizal fungi, Pseudomonas bacteria and entomopathogenic nematodes

Diabrotica virgifera virgifera LeConte, the western corn rootworm (WCR), is the most destructive pest of maize in North America, and has recently spread across central Europe. Its subterranean larval stages are hard to reach with pesticides and it has evolved resistance to conventional management practices. The application of beneficial soil organisms is being considered as a sustainable and environmental friendly alternative. In a previous study, the combined application in wheat fields of arbuscular mycorrhizal fungi, entomopathogenic Pseudomonas bacteria, and entomopathogenic nematodes was found to promote growth and protection against a natural pest infestation, without negative cross effects. Because of the insect-killing capacity of the bacteria and nematodes, we hypothesized that the application of these organisms would have similar or even greater beneficial effects in WCR-infested maize fields. During three consecutive years (2015–2017), we conducted trials in Missouri (USA) in which we applied the three organisms, alone or in combinations, in plots that were artificially infested with WCR and in non-infested control plots. For two of the three trials, we found that in plots treated with entomopathogenic nematodes and/or entomopathogenic Pseudomonas bacteria, roots were less damaged than the roots of plants in control plots. During one year, WCR survival was significantly lower in plots treated with Pseudomonas than in control plots, and the surviving larvae that were recovered from these plots were lighter. The bacterial and nematodes treatments also enhanced yield, assessed as total grain weight, in one of the trials. The effects of the treatments varied considerable among the three years, but they were always positive for the plants.

Plant health: feedback effect of root exudates-rhizobiome interactions

The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.

Inoculation of Rhizoglomus irregulare or Trichoderma atroviride differentially modulates metabolite profiling of wheat root exudates

Root exudation patterns are linked to, among other things, plant growth, plant-microbe interaction and the priming effect. In this work, two complementary metabolomic approaches (both liquid and gas chromatography coupled to mass spectrometry) were applied to investigate the modulation of root exudation imposed by two beneficial fungi (substrate treatment of Trichoderma atroviride AT10, substrate application of Rhizoglomus irregulare BEG72 and seed treatment with T. atroviride AT10) on wheat (Triticum aestivum L.). The inoculation with R. irregulare elicited significant increases (by 18%, 39% and 20%) in the shoot, root dry biomass and root-to-shoot ratio compared to untreated plants, whereas inoculation with T. atroviride, as a substrate drench or as a seed coating, exhibited intermediate values for these parameters. The metabolomic approach demonstrated a broad chemical diversity, with more than 2900 compounds annotated in the root exudates. Overall, the Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) supervised modelling highlighted a distinctive modulation of the metabolic profile in the root exudates as a function of both fungal inoculation and means of application. Most of the differences could be ascribed to lipids (sterols and membrane lipids), phenolic compounds and terpenoids, siderophores and chelating acids, derivatives of amino acids and phytohormones, and as such, the interaction between the wheat roots and beneficial fungi resulted in a complex response in terms of root exudates, likely involving a cascade of processes. Nonetheless, the changes imposed by plant-microbe interactions can contribute to the support of the biostimulant effects of both T. atroviride and R. irregulare.

Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere

In plants, the root is a typical sink organ that relies exclusively on the import of sugar from the aerial parts. Sucrose is delivered by the phloem to the most distant root tips and, en route to the tip, is used by the different root tissues for metabolism and storage. Besides, a certain portion of this carbon is exuded in the rhizosphere, supplied to beneficial microorganisms and diverted by parasitic microbes. The transport of sugars toward these numerous sinks either occurs symplastically through cell connections (plasmodesmata) or is apoplastically mediated through membrane transporters (MST, mononsaccharide tranporters, SUT/SUC, H+/sucrose transporters and SWEET, Sugar will eventually be exported transporters) that control monosaccharide and sucrose fluxes. Here, we review recent progresses on carbon partitioning within and outside roots, discussing membrane transporters involved in plant responses to biotic and abiotic factors.