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Main conclusionPlant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants.Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant–microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.

Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350plant species. A few peanut cultivars were found to possess stable and durable bacterial wiltresistance (BWR). Genomics-assisted breeding can accelerate the process of developing resistant cultivars by using diagnostic markers. Here, we deployed sequencing-based trait mappingapproach, QTL-seq, to discover genomic regions, candidate genes and diagnostic markers for BWR in a recombination inbred line population (195 progenies) of peanut. The QTL-seq analysis identified one candidate genomic region on chromosome B02 significantly associated with BWR.Mapping of newly developed single nucleotide polymorphism (SNP) markers narrowed down theregion to 2.07 Mb and confirmed its major effects and stable expressions across three environments. This candidate genomic region had 49 non synonymous SNPs affecting 19 putative candidate genes including seven putative resistance genes (R-genes). Two diagnostic markers were successfully validated in diverse breeding lines and cultivars and could be deployed in genomics-assisted breeding of varieties with enhanced BWR.

Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson’s correlation demonstrated that the abundance of Arthrobacter and Lysobacter , which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

Plant‐pathogenic Ralstonia strains cause bacterial wilt disease by colonizing xylem vessels of many crops, including tomato. Host resistance is the best control for bacterial wilt, but resistance mechanisms of the widely used Hawaii 7996 tomato breeding line (H7996) are unknown. Using growth in ex vivo xylem sap as a proxy for host xylem, we found that Ralstonia strain GMI1000 grows in sap from both healthy plants and Ralstonia‐infected susceptible plants. However, sap from Ralstonia‐infected H7996 plants inhibited Ralstonia growth, suggesting that in response to Ralstonia infection, resistant plants increase inhibitors in their xylem sap. Consistent with this, reciprocal grafting and defence gene expression experiments indicated that H7996 wilt resistance acts in both above‐ and belowground plant parts. Concerningly, H7996 resistance is broken by Ralstonia strain UW551 of the pandemic lineage that threatens highland tropical agriculture. Unlike other Ralstonia, UW551 grew well in sap from Ralstonia‐infected H7996 plants. Moreover, other Ralstonia strains could grow in sap from H7996 plants previously infected by UW551. Thus, UW551 overcomes H7996 resistance in part by detoxifying inhibitors in xylem sap. Testing a panel of xylem sap compounds identified by metabolomics revealed that no single chemical differentially inhibits Ralstonia strains that cannot infect H7996. However, sap from Ralstonia‐infected H7996 contained more phenolic compounds, which are known to be involved in plant antimicrobial defence. Culturing UW551 in this sap reduced total phenolic levels, indicating that the resistance‐breaking Ralstonia strain degrades these chemical defences. Together, these results suggest that H7996 tomato wilt resistance depends in part on inducible phenolic compounds in xylem sap. Ralstonia infection induces antimicrobial phenolics in xylem sap of the wilt‐resistant tomato breeding line Hawaii 7996; these are detoxified by Ralstonia strains that can break wilt resistance.

As a kind of soil-borne epidemic disease, bacterial wilt (BW) is one of the most serious diseases in tomatoes in southern China, which may significantly reduce food quality and the total amount of yield. Hyperspectral remote sensing can detect crop diseases in the early stages and offers potential for BW detection in tomatoes. Tomatoes in southern China are commonly cultivated in greenhouses or bird nets, limiting the application of remote sensing based on natural sunlight. To resolve these issues, we collected the spectrum of tomatoes firstly using the HS-VN1000B Portable Intelligent Spectrometer, which is equipped with a simulated solar light source. We then proposed a tomato BW detection model based on some optimal spectral features. Specifically, these optimal features, including vegetation indexes and principal components (PCs), were extracted by the sequential forward selection (SFS), the simulated annealing (SA), and the genetic algorithm (GA) and were finally fed into the support vector machine (SVM) classifier to detect diseased tomatoes. The results showed that the infected and healthy tomatoes exhibit different spectral characteristics for both leave and stem spectra, especially for near-infrared bands. In addition, the BW detecting model built by the combination of GA and SVM (GA-SVM) achieved the best performance with overall accuracies (OA) of 90.7% for leaves and 92.6% for stems. Compared with the results based on leaves, spectral features of stems provided better accuracy, indicating that the symptom of early infection of BW is more significant in tomato stems than in leaves. Further, the reliability of the GA-SVM tomato stem model was verified in our 2022 experiment with an OA of 88.6% and an F1 score of 0.80. Our study provides an effective means to detect BW disease of tomatoes in the early stages, which could help farmers manage their tomato production and effectively prevent pesticide abuse.

Background Fungal communities around plant roots play crucial roles in maintaining plant health. Nonetheless, the responses of fungal communities to bacterial wilt disease remain poorly understood. Here, the structure and function of fungal communities across four consecutive compartments (bulk soil, rhizosphere, rhizoplane and root endosphere) were investigated under the influence of bacterial wilt disease. Results The results showed that bacterial wilt disease caused different assembly patterns of fungal communities in the bulk soil, rhizosphere, rhizoplane and endosphere. Under the influence of bacterial wilt disease, a decreased fungal diversity was observed in the rhizoplane and endosphere, and completely different kinds of fungal genera were enriched in the four compartments. The complexity and stability of fungal networks were less affected, but the number of key fungal members in networks were significantly reduced in diseased samples. Functional predictions based on FUNGuild suggested that with the pathogen infection, saprotrophic fungi were increased in the bulk soil, but pathotrophic fungi (potential plant and animal pathogens) were increased in the rhizosphere, rhizoplane and endosphere. Conclusion This work provides a deep insight into the effects of bacterial wilt disease on fungal communities along the soil-root continuum, and is helpful to identify plant-associated beneficial fungi to resist plant disease. Clinical trial number Not applicable.

Plant growth-promoting rhizobacteria (PGPR) is a microbial population found in the rhizosphere of plants that can stimulate plant development and restrict the growth of plant diseases directly or indirectly. In this study, 90 rhizospheric soil samples from five agro climatic zones of chilli (Capsicum annuum L.) were collected and rhizobacteria were isolated, screened and characterized at morphological, biochemical and molecular levels. In total, 38% of rhizobacteria exhibited the antagonistic capacity to suppress Ralstonia solanacearum growth and showed PGPR activities such as indole acetic acid production by 67.64% from total screened rhizobacteria isolates, phosphorus solubilization by 79.41%, ammonia by 67.75%, HCN by 58.82% and siderophore by 55.88%. We performed a principal component analysis depicting correlation and significance among plant growth-promoting activities, growth parameters of chilli and rhizobacterial strains. Plant inoculation studies indicated a significant increase in growth parameters and PDS1 strain showed maximum 71.11% biocontrol efficiency against wilt disease. The best five rhizobacterial isolates demonstrating both plant growth-promotion traits and biocontrol potential were characterized and identified as PDS1—Pseudomonas fluorescens (MN368159), BDS1—Bacillus subtilis (MN395039), UK4—Bacillus cereus (MT491099), UK2—Bacillus amyloliquefaciens (MT491100) and KA9—Bacillus subtilis (MT491101). These rhizobacteria have the potential natural elicitors to be used as biopesticides and biofertilizers to improve crop health while warding off soil-borne pathogens. The chilli cv. Pusa Jwala treated with Bacillus subtilis KA9 and Pseudomonas fluorescens PDS1 showed enhancement in the defensive enzymes PO, PPO, SOD and PAL activities in chilli leaf and root tissues, which collectively contributed to induced resistance in chilli plants against Ralstonia solanacearum. The induction of these defense enzymes was found higher in leave tissues (PO—4.87-fold, PP0—9.30-fold, SOD—9.49-fold and PAL—1.04-fold, respectively) in comparison to roots tissue at 48 h after pathogen inoculation. The findings support the view that plant growth-promoting rhizobacteria boost defense-related enzymes and limit pathogen growth in chilli plants, respectively, hence managing the chilli bacterial wilt.

Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.

Rebuilding soil healthy microbiota is very important for preventing bacterial wilt. A 3-year-long field trial was conducted in China as follows: T1 (conventional fertilization), T2 (T1 + liming), T3 (T1 + bioorganic fertilizer), and T4 (T2 + bioorganic fertilizer). Fluorescence quantitative PCR and high-throughput sequencing were employed to study the dynamics of Ralstonia solanacearum population, microbial community, and network organizations between bacteria and quality-related variables. After 3 years of bioremediation, the control efficacy of tobacco bacterial wilt reached 61.30% and the occurrence delayed by approximately 40 days in T4, which had the highest tobacco yield and output value. The pathogen population of T4 remained below 106 copies/g soil during the entire growth period. Role-shifts prevailed among the network members. Microbes were unipathically associated with variables in T1 but multiplex in T4. In conclusion, soil bioremediation rebuilds a healthy soil microbiota and forms a more interactive and relevant micro-system, thus effectively controlling tobacco bacterial wilt.Key points• This is the first time to effectively bio-control tobacco bacterial wilt in practical production in China, as well as to high-efficiently use the organic waste, thus promoting the organic cycling of the environment.• Soil bioremediation can effectively control soil-borne disease by rebuilding soil healthy microbiota and reducing abundance of pathogenic bacteria, thereby to prevent the soil borne disease occurrence.• After the soil remediated, microbes associated with soil and tobacco characteristics changed from unipathical to multiplex, and the keystone species play different roles compared with the original soil, thus signifying the complexity of multi-species interactions and achieving a closely relevant micro-system, which was ecologically meaningful to the environment.

Aim: The secretion of allelochemicals from plant roots plays a key role in soil sickness and soil-borne disease. The goal of this study was to investigate the role of allelopathic chemicals in Ralstonia solanacearum-in-fected tobacco roots. Methods: The organic acids investigated in the present study are major components of tobacco root exudates. Through a swarming assay, we assessed the chemotaxis and colonization of R. solanacearum in response to organic acids. Results: Fumaric acid was detected, and the results showed that this acid could serve as a semiochemical for attracting R. solanacearum and inducing the formation of biofilms of this species. The results also revealed that cinnamic and myristic acids play significant roles on swarming motility and chemotaxis. In addition, cinnamic, myristic and fumaric acids could enhance the expression of chemotaxis and motility-related genes in R. solanacearum cultured in minimal medium. Furthermore, these three acids promote R. solanacearum colonization and accelerate disease progression in tobacco. Conclusion: Cinnamic, myristic and fumaric acids could serve as semiochemical attractants to induce the colonization and infection of R. solanacearum. The results of the present study enhance our understanding of the ecological effects of plant root exudates in plantmicrobe interactions and help to reveal the relationship between tobacco bacterial wilt and the autotoxins and allelochemicals that accumulate from root exudates.