Foliar Spraying of Chlorpyrifos Triggers Plant Production of Linolenic Acid Recruiting Rhizosphere Bacterial Sphingomonas sp

Understanding the ternary interaction of crop plants, fungal pathogens, and rhizobacteria in response to global warming

Climate change is altering the equilibrium of the Earth's biosphere, imposing unpredictable survival dynamics on terrestrial organisms. This includes the intricate interactions between fungal pathogens and crop plants, which are pivotal for global food security. Rising temperatures are expected to exacerbate the prevalence of crop-pathogenic fungi worldwide, yet research on how crops respond to this imminent threat remains limited. Here, we identified predominant potential pathogens and antagonistic bacteria in vegetable fields in Shandong Province, China, revealing the near-ubiquitous presence of Fusarium oxysporum and Bacillus species in sampled soils of cucumber, tomato, chili, and ginger. Through simulated warming experiments within a temperature range of 20-40 °C and an experimental period of 3 days, we investigated the ternary interaction among vegetables and isolated F. oxysporum strain 05, and Bacillus sp. strain 31. Elevated temperatures enhanced F. oxysporum biomass and virulence, yet also stimulated vegetables to allocate more nutrients via root exudates. This enriched rhizospheric antagonistic Bacillus populations, it also boosted the expression of antifungal lipopeptide biosynthetic genes (bamb and ItuA) and auxin production in Bacillus sp. strain 31. This enrichment promoted plant growth and maintained a relatively stable level of pathogenic fungi. Our study unveiled a nuanced and complex interplay among crop plants, fungal pathogens, and rhizobacteria, that could inform future agricultural practices, and advance our understanding of crop survival strategies to bolster crop resilience and safeguard global food security under ongoing climate change.

Early inoculation and bacterial community assembly in plants: A review

The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.

Nanoplastic and phthalate induced stress responses in rhizosphere soil: Microbial communities and metabolic networks

The widespread use of plastic products in agriculture has introduced micro-nano plastics (MNPs) and dibutyl phthalate (DBP) into soil ecosystems, disrupting microbial communities and altering metabolite profiles. However, their effects on the rhizosphere soil characteristics of medicinal plants like dandelion remain understudied. This study systematically examined the impact of PS NPs and DBP on rhizosphere microbial communities and metabolites by integrating high-throughput sequencing with liquid chromatography-mass spectrometry. Results demonstrated that individual and combined exposures to PS NPs and DBP decreased soil pH, organic matter content, and enzyme activities while reshaping the diversity, structure, and composition of rhizosphere bacteria and fungi. Notably, bacterial network stability and complexity increased under combined exposure, while fungal networks became more simplified, with a 33.72 % decrease in positive correlations. We identified potential PS NPs and DBP-degrading bacteria and biomarkers, including Nocardioides, Pseudarthrobacter, and Arenimonas. We revealed that co-exposure elevated differential soil metabolites associated with tyrosine metabolism and steroid biosynthesis. The significant positive associations between rhizosphere microorganisms and metabolites highlighted that metabolite accumulation was a key microbial response mechanism to stress. However, within the complex soil environment, the compensatory actions of microorganisms and metabolites were insufficient to mitigate the detrimental effects of PS NPs and DBP, resulting in continued inhibition of dandelion growth by 38.66 %. Consequently, these findings highlight that soil fungi and metabolism play key roles in responding to stress and influencing crop growth, providing novel insights into the impact of nanoparticle and plasticizer exposure on medicinal plant cultivation.

Rhizosphere microbes facilitate the break of chlamydospore dormancy and root colonization of rice false smut fungi

Dormant chlamydospore germination of fungal pathogens directly affects disease occurrence and severity. The rice false smut (RFS) fungus Ustilaginoidea virens produces abundant chlamydospores, but their germination process and roles in plant infection remain unclear. Here, we found that soil-borne chlamydospores are a major source of U. virens inoculum and impact RFS development. Rhizosphere microbiome analysis of high-susceptibility (HS) and low-susceptibility (LS) rice varieties revealed that HS varieties recruited bacteria from the Sphingomonadaceae family, thereby facilitating the breakdown of chlamydospore dormancy through secreted exopolysaccharides. Hyphae formed by germinating chlamydospores grew on the root surfaces, invaded the root cortex, and grew intercellularly, potentially spreading further to aboveground plant parts. Furthermore, field experiments confirmed that treating the root with 30% prothioconazole and 20% zinc thiazole effectively reduced RFS incidence. Overall, these findings enhance our understanding of chlamydospore germination in natural environments and inform strategies for disease control.

Chitosan-oligosaccharide alleviates chlorpyrifos-induced biochemical and developmental toxicity and reduces its accumulation in wheat (Triticum aestivum L.)

Chlorpyrifos (CHP) contamination affects agricultural land and poses significant risks to plants and humans. Chitosan-oligosaccharide (COS) enhances plant resilience under stress and boosts the activity of enzymes metabolizing exogenous substances. This study aimed to explore the potential and mechanism of COS in mitigating CHP phytotoxicity and reducing CHP accumulation through both pot and field experiments. The results indicated that CHP exposure caused oxidative stress and decreased photosynthesis by 18.5 % in wheat. COS up-regulated the expression of antioxidant enzyme genes in CHP-stressed plants, resulting in a 12.1 %-29.4 % increase in antioxidant enzyme activity, which resulted in an 11.3 %-12.8 % reduction in reactive oxygen species (ROS) and an 11.5 %-14.7 % reduction in malondialdehyde (MDA) content in leaves and roots, respectively. Additionally, COS increased chlorophyll content by 6.6 % by regulating genes related to chlorophyll metabolism, enhancing photosynthesis by 13.6 %. COS also reduced CHP uptake and accelerated its metabolism by upregulating CYP450, GST, and lignin biosynthesis-related genes. Wheat treated with COS exhibited a 26.7 %-28.7 % reduction in grains' CHP content, resulting in a lower health risk index (HRI). These findings provide novel insights into the potential of COS in alleviating CHP phytotoxicity and reducing its accumulation.

Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management

The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.

Effects of different concentrations of chlormequat chloride on bacterial community composition and diversity in peanut soil

The application of pesticides may have significant impacts on soil environment and communities. In order to understand the deep relationship between the application of chlormequat chloride (CC) and the bacterial community in peanut soil, high-resolution characterization was performed using peanut soil samples (12 points; 0-20 cm rhizosphere soil) from untreated and sprayed with different concentrations of CC. Experimental data showed that with the increase of concentration, operational taxonomic units (OTUs) richness showed a decreasing tendency. The OTUs richness at low concentration (D, 50% CC diluted 5000 times, 45 g ai/ha), medium concentration (M, 50% CC diluted 300 times, 75 g ai/ha), and high concentration (G, 50% CC diluted 1000 times, 225 g ai/ha) were 5583, 5430, and 3910, respectively. Low concentrations increased the composition and relative abundance of soil bacterial communities. In contrast, high concentrations significantly reduced bacterial diversity. As the concentration of CC increases, the abundance of Proteobacteria decreases, while the abundance of Firmicutes and Bacteroidetes increases. The number of Acidobacterium and Bacteroidetes increased in groups D and M, while it decreased in group G. D, M and G groups showed a decrease in the abundance of Pseudomonas, polaromonas, and Azovibrio compared to CK, while the abundance of Flavobacterium increased. In addition, the abundance of Rahnella1 decreased in groups D and M, while the abundance increased in group G. The main metabolic pathways included the metabolisms of nucleotides, terpenoids, polyketides, other amino acids, cofactors, vitamins, lipids, glycan biosynthesis, energy, carbohydrates, xenobiotics, amino acids, and other secondary metabolites.

Chemotaxis of rhizosphere Pseudomonas sp. induced by foliar spraying of lanthanum reduces cadmium uptake by pakchoi

Foliar application of rare earth micronutrient of lanthanum (La) exhibits great potential in reducing cadmium (Cd) uptake in crops, the underlying mechanisms controlling the interaction between Cd toxicity-relieved crops and soil microbiota are poorly understood. In this study, LaCl3 with the concentrations of 10 and 30 μM was sprayed on pakchoi (Brassica chinensis L.) planting on Cd contaminated solution and soil to determine the changes of root metabolites and rhizosphere bacterial communities. Compared to the control, Cd concentration in pakchoi leaves was significantly decreased by 30.9 % and 22.6 % with the high group under both hydroponic and pot culture by applying 30 μM LaCl3. Herein, the concrete evidence is provided that pakchoi plants in response to foliar-spraying La under soil or solution Cd toxicity can promote the root secretion of amino acids, resulting in a strong enrichment of nitrogen-related microorganisms. To probe this linkage, a Pseudomonas representative specie was isolated that had the ability of consuming alanine, the most oversecreted root exudate due to La application. Further results demonstrated that this strain had the capacities for alleviating Cd toxicity and enhancing crop growth by immobilizing Cd and secreting plant-beneficial metabolites. This study reveals a plant-extrudate-microbiome feedback loop for responding to La-relieved Cd toxicity in crops by the chemotaxis of rhizosphere Pseudomonas toward alanine secreted by pakchoi.

The effects of different halogenated-pyrethroid pesticides on soil microbial community

The application of pesticides increases crop yields but affects the structure and function of the soil microbial community. Halogens are common functional modification groups in chemical compounds, and innovative pesticides have been developed on the basis of these groups. However, the effects of different halogen substituents on soil microorganisms remain unclear. This study investigated the effects of three pyrethroid pesticides (deltamethrin, cypermethrin, and cyfluthrin) on the soil microbiota. Our results revealed that all these pesticides significantly reduced the stability of the bacterial communities and decreased bacterial diversity at high concentrations. Compared with deltamethrin (Br-) and cypermethrin (Cl-), low concentrations (0.5 mg/kg) of cyfluthrin (F-) increased soil bacterial diversity by 23.14 % and increased the potential for nitrogen fixation by 2.00 % and nitrification by 3.39 %, thus making it a relatively eco-friendly option. Our findings provide new insights into the potential ecological effects of halogenated pyrethroid pesticides on soil ecosystems.

Metabolic crosstalk between roots and rhizosphere drives alfalfa decline under continuous cropping

Considerable biological decline of continuously cropped alfalfa may be tightly linked to rhizosphere metabolism. However, plant-soil feedbacks and age-related metabolic changes in alfalfa stands remain unexplored. The aim of this study was to identify the linkages of rhizosphere and root metabolites, particularly autotoxins and prebiotics, to alfalfa decline under continuous cropping. We performed liquid chromatography-mass spectrometry for non-targeted metabolomic profiling of rhizosphere soils and alfalfa roots in 2- and 6-year-old stands. Differentially abundant metabolites that responded to stand age and associated metabolic pathways were identified. Compared with bulk soils, rhizosphere soils were enriched with more triterpenoid saponins (e.g., medicagenic acid glycosides), which showed inhibitory effects on seed germination and seedling growth. These autotoxic metabolites were accumulated in the old stand age, and their relative abundances were negatively correlated with plant growth, yield, and quality traits, as well as soil total nitrogen and alkali-hydrolyzable nitrogen concentrations. In contrast, prebiotic metabolites, represented by glycerolipids (e.g., glycerophosphocholine) and fatty acyls (e.g., colnelenic acid), were depleted in rhizosphere soils in the old stand. The relative abundances of glycerolipids and fatty acyls were positively correlated with plant traits and soil available phosphorus and alkali-hydrolyzable nitrogen concentrations. Age-induced changes in the rhizosphere metabolome mirrored the reprogramming patterns of root metabolome. The pathways of terpenoid backbone biosynthesis and plant hormone signal transduction, as well as metabolism of galactose, glycerophospholipid, and ɑ-linolenic acid in alfalfa roots were affected by stand age. The upregulation of terpenoid backbone biosynthesis in alfalfa roots of old plants, which stimulated triterpenoid saponin biosynthesis and exudation. Rhizosphere accumulation of autotoxins was accompanied by depletion of prebiotics, leading to soil degradation and exacerbating alfalfa decline. This research aids in the development of prebiotics to prevent and manage continuous cropping obstacles in alfalfa.

Trifolium repens L. recruits root-associated Microbacterium species to adapt to heavy metal stress in an abandoned Pb-Zn mining area

Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction between heavy metal-stressed plants and the microbiota are poorly understood. In this study, we screened and isolated representative amplicon sequence variants (strain M4) from rhizosphere soil samples of Trifolium repens L. growing in areas with high concentrations of heavy metals. To investigate the microecological mechanisms by which T. repens adapts to heavy metal stress in abandoned mining areas, we conducted potting experiments, bacterial growth promotion experiments, biofilm formation experiments, and chemotaxis experiments. The results showed that high concentrations of heavy metals significantly altered the rhizosphere bacterial community structure of T. repens and significantly enriched Microbacterium sp. Strain M4 was demonstrated to significantly increased the biomass and root length of T. repens under heavy metal stress. Additionally, L-proline and stigmasterol could promote bacterial growth and biofilm formation and induce chemotaxis for strain M4, suggesting that they are key rhizosphere secretions of T. repens for Microbacterium sp. recruitment. Our results suggested that T. repens adapted the heavy metal stress by reshaping rhizosphere secretions to modify the rhizosphere microbiota.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5-13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.

Sediment contamination alters the submersed macrophyte Vallisneria natans and root-associated microbiome profiles during phytoremediation

The submerged plant Vallisneria natans plays an important role in the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. In this study, V. natans and sediments were collected from different V. natans natural vegetation zones, and sediment mesocosms were set up for phytoremediation tests. In addition, commercial-grade V. natans were obtained from the Fish-Bird-Flower market for comparison with phytoremediation. Phytoremediation using V. natans from natural growth significantly increased the degradation of PAHs in Dashui Harbor (0.0148±0.0015 d-1) and Taihu Lake bay sediments (0.0082±0.0010 d-1) but not in commercial-grade V. natans. Transplanted V. natans from natural growth had a significant (p=0.002) effect on PAH degradation, especially in highly PAH-contaminated sedimentary environments. The distinct bacterial communities were strongly affected by sediment type and V. natans type, which contributed to different phytoremediation patterns. Less complex but more stable microbial co-occurrence networks play key roles in improving PAH phytoremediation potential. In addition, V. natans from natural growth in highly PAH-contaminated sediment could adapt to PAH stress by exuding tryptophan metabolites to assemble health-promoting microbiomes. This study provides novel evidence that initial microbial and physicochemical characteristics of sediment and submerged plant types should be considered in the use of bioremediation management strategies for organic pollutant-contaminated sediments.

Combined Transcriptomics and Metabolomics Analysis Reveals Profenofos-Induced Invisible Injury in Pakchoi (Brassica rapa L.) through Inhibition of Carotenoid Accumulation

Profenofos insecticide poses risks to nontarget organisms including mammals and hydrobionts, and its effects on crops are not known. This study examined the invisible toxicity of profenofos on pakchoi (Brassica rapa L.), using transcriptome and metabolome analyses. Profenofos inhibited the photosynthetic efficiency and light energy absorption by leaves and severely damaged the chloroplasts, causing the accumulation of reactive oxygen species (ROS). Metabolomic analysis confirmed that profenofos promoted the conversion of β-carotene into abscisic acid (ABA), as evidenced by the upregulation of the carotenoid biosynthesis pathway genes: zeaxanthin epoxidase (ZEP), 9-cis-epoxycarotenoid dioxygenase (NCED3), and xanthoxin dehydrogenase (XanDH). The inhibitory effects on carotenoid accumulation, photosynthesis, and increased ABA and ROS contents of the leaves led to invisible injury and stunted growth of the pakchoi plants. The findings of this study revealed the toxicological risk of profenofos to nontarget crops and provide guidance for the safe use of insecticides.

Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly

Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.

Maize Root Exudates Promote Bacillus sp. Za Detoxification of Diphenyl Ether Herbicides by Enhancing Colonization and Biofilm Formation

Diphenyl ether herbicides are extensively utilized in agricultural systems, but their residues threaten the health of sensitive rotation crops. Functional microbial strains can degrade diphenyl ether herbicides in the rhizosphere of crops, facilitating the restoration of a healthy agricultural environment. However, the interplay between microorganisms and plants in diphenyl ether herbicides degradation remains unclear. Thus, the herbicide-degrading strain Bacillus sp. Za and the sensitive crop, maize, were employed to uncover the interaction mechanism. The degradation of diphenyl ether herbicides by strain Bacillus sp. Za was promoted by root exudates. The strain induced root exudate re-secretion in diphenyl ether herbicide-polluted maize. We further showed that root exudates enhanced the rhizosphere colonization and the biofilm biomass of strain Za, augmenting its capacity to degrade diphenyl ether herbicide. Root exudates regulated gene fliZ, which is pivotal in biofilm formation. Wild-type strain Za significantly reduced herbicide toxicity to maize compared to the ZaΔfliZ mutant. Moreover, root exudates promoted strain Za growth and chemotaxis, which was related to biofilm formation. This mutualistic relationship between the microorganisms and the plants demonstrates the significance of plant-microbe interactions in shaping diphenyl ether herbicide degradation in rhizosphere soils. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

A risk entropy approach for linking pesticides and soil bacterial communities

Pesticides play a vital role in ensuring modern agricultural production, but also adversely affecting soil health. Microorganisms are the cornerstone of soil ecology, however, to date, there are few unified standards to measure the risk of soil pesticide residues to soil microbial community. To compensate for this gap, we collected soil samples from 55 orchards and monitored and risk-assessed 165 pesticides to microbial community in the soil. Results showed that a total of 137 pesticides were detected in all samples. Pesticide residues significantly influenced the microbial diversity and community structure in orchard soils, particularly fungicides and herbicides. The risk entropy of each pesticide was calculated in all samples and it was found that 60% of the samples had a "pesticide risk" (Risk quotient > 0.01), where the relative abundance significantly increased in 43 genera and significantly decreased in 111 genera (p < 0.05). Through multiple screens, we finally identified Bacillus and Sphingomonas as the most abundant sensitive genera under pesticide perturbation. The results showed that despite the complexity of the effects of pesticide residues on soils health, we could reveal them by identifying changes in soil bacterial, especially by the differences of microbial biomarkers abundance. The present study could provide new insights into the research strategy for pesticide pollution on soil microbial communities. ENVIRONMENTAL IMPLICATION: The risk of pesticide residues in soil needs to be quantified and standardized. We believe that microorganisms can be used as a marker to indicate soil pesticide residue risk. For this end, we investigated the residues of 165 pesticides in 55 orchard soil samples, calculated pesticide risk entropy and their effects on the soil microbial community. Through multiple analyzing and screening, we ultimately identified that, out of the 154 detected biomarkers, Bacillus and Sphingomonas were the most abundant sensitive genera under pesticide perturbation, which have the potential to be used as key biomarkers of soil microbiomes induced by pesticide perturbation.

The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment

Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.