Green mold, caused by Penicillium digitatum, remains one of the most destructive postharvest citrus diseases. In this study, indigenous endophytic strain, Bacillus subtilis L1–21 was applied to citrus fruits and associated culturable epiphytic and endophytic microorganism were subsequently isolated and screened for antagonistic activity against P. digitatum. A total of 21 bacterial and 7 fungal isolates were recovered, among which 6 bacterial strains showed in vitro antagonism. Three highly effective isolates (strains 2, 14, and 16) were selected and combined with endophyte L1–21 to construct three Bacillus-based synergistic consortia (SynCom-1, 2, 3). In dual-culture assays, single strains inhibited P. digitatum by 53–66%, whereas SynCom treatments achieved up to 90% inhibition. In vivo assays further showed that SynCom-3 provided > 95% disease suppression compared with untreated controls. Defense-related activities (peroxidase; POD, chitinase, lipase, phenylalanine ammonia-lyase; PAL and protease) and fruit acids (organic acids and sugars) were quantified, indicating that endophyte treatments were associated with treatment-dependent modulation of host physiological and defense responses during pathogen challenge. In addition, microbiome profiling showed that endophyte L1–21 application caused shifts in citrus-associated beneficial microbiome composition and differential enrichment of multiple bacterial taxa (Bacillus, Levilactobacillus, Leuconostoc) and suppressed opportunistic genera such as Kozakia and Shimwellia. Overall, these results support the development of indigenous Bacillus-based SynCom as a promising biocontrol candidate against citrus green mold and provide an ecological context for endophyte L1–21-associated microbiome changes.

To develop sustainable alternatives to chemical fungicides for postharvest disease, we evaluated the efficacy and mechanism of Bacillus subtilis L1–21 against green mold on citrus, revealing its dual action as a potent antagonist and a regulator of the fruit microbiome. In in vivo tests, the B. subtilis L1–21 significantly reduced green mold caused by Penicillium digitatum. The control group reached the disease indices of 50 and 82 after 3 and 7 days, respectively. In contrast, fruits treated with endophyte L1–21 (concentrations from 1 ×10⁶ to 1 ×10⁹ CFU/mL) showed notably lower disease indices (p < 0.05). On day 3, the lowest disease index was 1.9 at 1 × 10⁷ CFU/mL. The maximum 7-day control effect was observed at 1 × 10⁸ CFU/mL, with 26.6 disease index, resulting in over 67.4% biocontrol efficacy. These results suggest that the citrus endophyte L1–21 is an effective postharvest biocontrol agent, with 1 × 10⁸ CFU/mL the most promising concentration for practical use. Additionally, B. subtilis L1–21 significantly affected citrus-associated microbial communities both inside and on the surface of the fruits. Endophytic diversity indices showed slight, non-significant decreases (p> 0.05), whereas epiphytic communities showed significant increases in richness, evenness, and phylogenetic diversity (p < 0.05), consistent with microbial dynamics observed in harvested fruits. Principal coordinate and radial analyses revealed clear clustering differences between treatment and control groups, indicating shifts in microbial composition. Functional predictions indicated changes in amino acid, carbohydrate, and lipid metabolism, as well as energy production, implying that the metabolic capacity of citrus microbiomes was distinct in the present of endophyte L1–21. Taxonomic analysis showed Bacillinae predominance among endophytes and Proteobacteria among epiphytes. Network analyses indicated enhanced microbial interactions following the application of L1–21. Overall, these findings confirm that B. subtilis L1–21 not only effectively manages the postharvest green mold pathogen, but also have marked differences in microbial diversity, structure, and function, supporting its potential as an eco-friendly postharvest biocontrol agent for citrus fruits.

Citrus Huanglongbing (HLB), caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease worldwide, with no efficient cure currently available. CLas pathogen exhibits seasonal variations in China and adversely affects the native citrus endophytic microbiome. Recent research on the citrus endophytic microbiome has identified the promising biocontrol strategies for mitigating HLB, particularly through the manipulation of plant–microbe–pathogen interactions. Here, we provide empirical evidence from a decade (2015–2025) of research focusing on indigenous citrus endophyte, notably Bacillus subtilis L1-21, which demonstrates remarkable efficacy in reducing CLas in the diseased citrus fields with biocontrol effect exceeding 95

The synergistic occurrence of citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) and root rot severely threatens the global citrus industry. In this study, field surveys were conducted across nine major citrus-producing regions in seven provinces of China. Highly pathogenic strains, Phytophthora nicotianae CR62 and Fusarium solani CR15, were selected as targets for screening Trichoderma strains for mycoparasitic activity. Compatibility and metabolic cross-feeding with the HLB-controlling strain Bacillus subtilis L1-21 enabled the construction of a cross-kingdom SynCom. Pot experiments evaluated plant growth promotion and root rot control, while high-throughput sequencing (16S rRNA/ITS) elucidated the regulatory mechanisms of rhizosphere microbiomes. The results showed that HLB and root rot co-occurred widely in the field, with oomycetes (Phytophthora spp. and Pythium spp.) accounting for 65.22% of root rot pathogens. P. nicotianae and F. solani exhibited the highest pathogenicity, whereas no significant correlation was detected between the root rot disease index and CLas titer. Targeted screening showed that T. asperellum NY-1 exerted more than 60% inhibition against root rot pathogens and exhibited high compatibility with B. subtilis L1-21. Moreover, the cell-free filtrate of NY-1 significantly reshaped the global metabolic profile of L1-21, primarily by modulating amino acid and energy metabolism, as well as ABC transporter pathways, thereby comprehensively altering its cellular metabolic activities. Importantly, the SynCom NL significantly promoted plant growth and increased rhizosphere urease and sucrase activities after 90 days of treatment. SynCom NL enriched beneficial microbes (Bacillus, Sphingomonas, Trichoderma, Humicola), suppressed pathogens (Fusarium, Penicillium, Neocosmospora), and activated root defense enzymes (SOD, CAT, PAL, PPO), boosting root protection and achieving 92.86 ± 8.25% root rot control. Overall, the Trichoderma-Bacillus cross-kingdom SynCom targeting the HLB-root rot disease complex provides a technical foundation for integrated biocontrol and sustainable citrus production.

The systematic study particularly those affected by the cross-kingdom pathogen Klebsiella pneumoniae, remains exclusive in a special domain. We unravel the dynamics of the cross-kingdom interactions involving mice and maize plants. Here, we constructed rpoS mutants from three different strains of K. pneumoniae [WKpE4 (from environment), WKpC4 (from maize plant) and WKp138 (clinical)], examining maize and murine response to disease after pathogen inoculation. The integrated approach utilized phenotypic and visual assay of both organisms and histopathological assays with the Murine Grimace Scale (MGS) to gain unprecedented insights into mice subjective pain experiences. We distinguished the mutant from the wild-type response to environmental and virulence factors, demonstrating ΔKpE4 is more sensitive to acid, UV, while ΔKpC4 is more sensitive to temperature, oxidative, osmotic and starvation stress. Mutant strains, particularly ΔKpC4 enhanced growth rates in plants comparable to parental wild strains. ΔKpC4 is less virulent in mice, causing less pain with higher bacterial recovery in various organs. ΔKp138 showed more sensitive towards stress assays whereas less disease occurrence in both plants and mice compared to WKp138 strains. These cross-kingdom findings facilitated the crucial role of rpoS in weakening defense against diseases in organisms. In addition, it bridges existing knowledge gaps in understanding rpoS responses across different organisms, their host-pathogen interactions, adaptive responses to stresses, and food borne illness in animals providing new avenues for therapeutic interventions and management approaches in pathosystem.

Bacterial wilt poses a great threat to tobacco production, and therefore finding efficient biocontrol resources is crucial for disease control. Bacterial colonization in the host plant is considered one of the key factors associated with the biocontrol efficiency against pathogens. However, limited information is available regarding optimal colonization density and formulation strategies for broad-spectrum biocontrol against multiple pathogens. Here, a promising biocontrol strain was selected from several antagonistic candidates, and its broad-spectrum antibacterial activity was confirmed through plate confrontation and pot experiments. The selected antagonistic bacteria were also transformed with a green fluorescent plasmid via natural transformation. After verifying its characteristics, the strain colonization and control efficacy were assessed. Potential Bacillus velezensis TS08 showed the highest antagonistic activity against the tobacco bacterial wilt pathogen, with the value D/d of the outer and inner diameters of the inhibition zone against the pathogen SBQR of bacterial wilt (D is the outer diameter of the inhibition zone, d is the inner diameter of the inhibition zone) reached 2.03, and exhibited broad-spectrum antagonism against the ginger blast pathogen (Ralstonia solanacearum) and leaf blight pathogen (Xanthomonas oryzae). Furthermore, B. velezensis TS08-mediated control effect of more than 75% was recorded against R. solanacearum in pot experiments. In addition, the biocontrol strain demonstrated excellent biofilm formation, motility, and soil colonization, resulting in a remarkable control effect of more than 97% even after 15 days. In addition, optimal control was achieved at a soil initial concentration of 1.16 × 107 CFU/g for TS08, even tobacco plants were recovered after pathogen invasion. The study concluded that B. velezensis TS08 could be a potential biocontrol agent that effectively prevents and control not only the tobacco bacterial wilt and bacterial leaf blight pathogens, but also stabilizes the host environment through soil colonization.

BACKGROUND:Root rot disease has seriously restricted the development of the apple industry Worldwide. After being infected by pathogens, the microbial communities of rhizosphere soil and leaves may change. We found that apple and persimmon intercropping can reduce the occurrence of apple root rot achieving a relative control efficacy of 80.3% following persimmon intercropping. RESULTS:Here, we investigate the effect of intercropping with persimmon tree on rhizosphere microbiome and leaf endophytes. For this, we tested the rhizosphere soil and leaves of healthy and infected apple trees during intercropping. The soil and leaves of healthy and infected root rot apple trees, persimmon trees, and intercropping were collected (during sampling time, apple trees were 5 years old, and persimmon trees were 3 years old). The high-throughput sequencing was performed on the Illumina Miseq platform to analyze the leaf endophytic bacterial and soil microbial communities. We further revealed that infection by root rot pathogens severely impacts the synergistic effects between endophytes and the composition of rhizosphere microbial communities. The intercropping between apple and persimmon trees can modulate apple leaf endophytes and rhizosphere microbial communities. Importantly, the relative abundance of Pantoea and Serratia increased significantly in the leaves of apple trees affected by root rot. We argue that bacteria such as Pantoea and Serratia are conducive to the occurrence of root rot. Notably, Bacillus and Trichoderma were significantly reduced in the rhizosphere of apples with root rot trees; however, persimmon trees and apple trees can maintain the relative abundance of beneficial species or improve the abundance compared with healthy apple trees. CONCLUSIONS:The overall study concludes that intercropping apples and persimmons maintains the beneficial microbial balance and plant growth and helps to prevent dysbiosis caused by pathogens. Based on this shift in microbiome balance, a management strategy for apple root rot is discussed.

The endophytic microbiomes are key determinants of plant health, contributing to disease resistance, growth promotion, and tolerance to abiotic stresses, such as temperature fluctuations. The optimization of endophytes efficacy and their microbiota role in suppressing tomato-spotted wilt virus (TSWV) diseases under different temperatures remains unexplored. We hypothesized that TSWV-infected plants treated with endophytes recruit beneficial microbiota to suppress the disease progression and adapt to environmental stress by regulating distinct molecular pathways. In this study, Bacillus amyloliquefaciens strains (DJB5, YN48, Mg6) and a consortium (DYM) are evaluated for temperature-dependent biocontrol efficacy. At 25 degrees C, biocontrol efficacy peaked, with endophytes reducing disease severity by 4-16 % and TSWV accumulation by 14.9-36.3 %, markedly outperforming cooler (10 degrees C) and warmer (40 degrees C) conditions Endophyte-treated plants enriched Firmicutes-and Bacillus-dominated microbiota, effectively suppressing TSWV infection, whereas untreated plants showed higher relative abundance of Proteobacteria, Actinobacteriota, and stress-associated genera, including Paracoccus and Sphingomonas. Functional pathways analysis revealed that endophyte treatment enhanced photosynthesis, hormone signaling, energy metabolism, and nitrogen and phosphorus levels assimilation. At low temperature (10 degrees C), photosynthesis and metabolic pathways are upregulated, facilitating adaptation to cold stress, while balance regulation at 25 degrees C, supported optimal plant health. In contrast, at 40 degrees C, gene expression stability suggested limited adaptation to heat stress. This study reveals temperature's role in shaping the efficacy of endophytes as biocontrol agents and their interaction with plant microbiota. The finding provides foundational insights into optimizing endophyte-based strategies for sustainable disease management under diverse environmental conditions. Further exploration of microbial resilience and functional stability is essential to enhancing biocontrol strategies in climate-stressed agricultural systems.

BACKGROUNDTomato-spotted wilt virus (TSWV) from the Tospovirus genus affects over 1000 plant species, including key crops, and traditional control methods often prove inadequate. This study investigates the effectiveness of Bacillus amyloliquefaciens and Bacillus subtilis in reducing TSWV infection, enhancing plant growth, and strengthening defense in Nicotiana benthamiana. The aim is to assess Bacillus as a sustainable biocontrol alternative, offering an eco-friendly solution for managing TSWV disease in agriculture.RESULTSHere, we report the efficacy of five Bacillus isolates (out of 15 tested) - B. amyloliquefaciens (DJB5, YN48, YN28, Mg6) and B. subtilis L1-21 - significantly reducing TSWV copies per gram in N. benthamiana leaves, using a half-leaf assay. In glasshouse trials, isolates DJB5, YN48, and Mg6 decreased TSWV copies per gram by 75.7%, 83.6%, and 88.2%, with biocontrol efficacy rates of 91.2%, 94.1%, and 95.7% respectively. All the isolates consistently mitigated the symptoms of TSWV, reduced the disease severity, and area under the disease progress curve (AUDPC) at 21 days post-inoculation. Additionally, these isolates enhanced plant growth parameters, including shoot and root length, leaf number, area, and biomass. The application of endophytes in the infected plants activated antioxidant defense enzymes by elevating the activities of polyphenol oxidase (PPO), peroxidase (POD), superoxide dismutase (SOD), and chitinase. However, defense-related enzymes, such as malondialdehyde (MDA), catalase (CAT), phenylalanine ammonia-lyase (PAL), total phenol, and beta-1,3-glucanase decreased as TSWV infection reduced in the leaves.CONCLUSIONOur findings indicate that B. amyloliquefaciens isolates, DJB5, YN48, and Mg6, effectively manage TSWV by activating plant defense, reducing virus load, reducing TSWV symptoms, and promoting plant growth. (c) 2024 Society of Chemical Industry.

Metabolites of plant and microbial origin have a great influence on plant-microbe interactions. Members from Bacillus subtilis are known to produce a plethora of metabolites that shape plant responses towards biotic and abiotic stresses. Similarly, endophyte B. subtilis L1-21 efficiently controls the Huanglongbing (HLB) causing pathogen: Candidatus Liberibacter asiaticus (CLas). However, the molecular mechanisms are highly elusive. Herein, our study highlights the critical role of endophyte L1-21 inplanta-produced surfactin in its colonization in citrus plants and regulation of plant-microbe interactions by comparing three gene knockout mutants triangle srfAA- L1-21, triangle sfp-L1-21, and triangle pel-L1-21. All three mutants exhibited reduced pathogen control and colonization efficiency compared to wild-type (WT) L1-21, but knockout mutant deficient of surfactin triangle srfAA-L1-21 was significantly impaired in the abovementioned functions as compared to triangle sfp-L1-21 and triangle pel-L1-21. Further, triangle srfAA-L1-21 could not activate various metabolic pathways in citrus as WT-L1-21. Integrated metabolomictranscriptomic analysis reveals that important secondary metabolites such as flavonoids, volatile organic compounds, and lignins were highly accumulated in citrus plants treated with WT-L1-21 as compared to triangle srfAA- L1-21, highlighting the role of surfactin as an elicitor of the defense system in citrus-HLB pathosystem. Interestingly, auxin-related metabolites and transcripts were also downregulated in triangle srfAA-L1-21 compared to WT- L1-21 showing that surfactin might also influence plant-microbe interactions through metabolic reprogramming. Further, higher enrichment of Bacilli with WT-L1-21 might corresponds to surfactin-mediated regulation of community-related behavior in Bacilli. To the best of our knowledge, this is the first study reporting the role of surfactin from Bacillus endophyte in metabolic reprogramming in citrus-HLB pathosystem and mounting defense response against C Las pathogen.

Potato common scab, caused by Streptomyces species, is a widespread soil-borne disease that poses a significant threat to potato cultivation globally. In this study, a Bacillus velezensis D7-8 strain was isolated from a potato. This endophytic bacterium exhibited broad-spectrum antifungal activity, and pot trials demonstrated that the D7-8 strain effectively controlled potato common scab with an efficacy of 42.07%. The complete genome sequence of the D7-8 strain was sequenced and subsequently identified as B. velezensis through multiple bioinformatic methods, primarily through structural variation analysis of whole-genome sequences. The machine learning method predicted that the expression profiles of colinear genes among closely related Bacillus species were highly consistent. Metabolite analysis of crude extracts using ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UPLC-Q-Exactive HRMS) revealed that D7-8 produces bioactive compounds, including surfactin and fengycin, both known for their antimicrobial properties. This study elucidates the antagonistic effect of B. velezensis D7-8 against Streptomyces acidiscabies and provides a valuable reference for future research on accurate microbial identification.

Background: Maize is easily contaminated by Aspergillus flavus, and the aflatoxin produced by A. flavus has been classified as a Group 1 carcinogen, for which there are currently no effective control measures. Biological control is regarded as an environmentally friendly and safe approach. Strains ZH179, ZH409, and ZH99 are three bacteria isolated from our laboratory that exhibit antagonistic effects against A. flavus. We conducted experiments to investigate their biocontrol efficacy. Results: The experimental results demonstrated that these three strains effectively inhibited A. flavus on plates and stored maize seeds. Identification revealed that ZH179 is Bacillus velezensis, while ZH409 and ZH99 are B. amyloliquefaciens. We also identified lipopeptide synthetase-related genes, including srfAA, srfAD, fenA, fenB, ituA, ituB, ituD, bmyA, bmyB, and bmyC, in these three strains. Furthermore, LC-MS analysis confirmed that these strains could produce lipopeptide compounds such as surfactin, fengycin, iturin, and bacillomycin. Using the Oxford cup method, we found that the lipopeptide compounds produced by these strains can inhibit the growth of A. flavus. Conclusion: These findings suggest that strains ZH179, ZH409, and ZH99 have good control effects on A. flavus during the storage of maize, primarily due to the lipopeptide compounds. This study provides a theoretical basis for using these three strains in the biological control of A. flavus.

Although bacterial leaf blight (BLB) poses a threat to rice yields in Bangladesh, locally validated resistance profiles are limited. This study addresses this gap by identifying key resistance genes and evaluating their distribution in widely cultivated rice varieties in the Mymensingh region of Bangladesh. This study aimed to identify bacterial leaf blight resistance genes (Xa4, Xa5, Xa7, Xa13, and Xa21) present in rice varieties cultivated in Mymensingh, a prominent rice-producing region in Bangladesh. We genotyped symptomatic leaves (n = 187) from 10 varieties at 14 locations in Mymensingh using diagnostic markers for Xa4, Xa5, Xa7, xXa13, and Xa21; selected amplicons were Sanger-sequenced and analyzed (NJ trees, 1,000 bootstraps). The results revealed distinct resistance gene profiles: BRRI Dhan-49 presented the recessive gene Xa13; BRRI Dhan-51 possessed multiple resistance genes ( Xa2, Xa7, and Xa5); and BRRI Dhan-34 contained the Xa4, Xa5, and Xa7 genes. Compared with single-gene varieties, varieties characterized by different resistance genes demonstrated superior protection against bacterial blight, outperforming. Phylogenetic analyses revealed that the Bangladeshi varieties exhibit a close genetic relationship, reflecting a localized breeding history and adaptation, which distinguishes them from other international rice varieties. Multi-gene varieties (BRRI Dhan-51, Dhan-34) offer stronger field protection than single-gene materials, supporting gene pyramiding and germplasm diversification for durable BLB resistance in Bangladesh.

The predominant disease afflicting citrus fruits is postharvest green mold, which is caused by the fungus Penicillium digitatum (Pd). On a global scale, this disease incurs substantial economic losses, particularly in arid and subtropical regions. The absence of advanced storage facilities in underdeveloped and developing nations exacerbates these losses, with damage rates in these regions reaching nearly 30% in developed countries. Currently, synthetic fungicides such as imazalil, thiabendazole, and benomyl are employed to mitigate green mold on citrus fruits. However, applying these fungicides poses environmental hazards, contributes to carcinogenic risks for users, and has increased pathogen resistance. Furthermore, the production of mycotoxins by Pd and the mycotoxin patulin by Penicillium expansum presents significant public health concerns. Consequently, using fungicides is increasingly viewed as inappropriate, prompting researchers to explore alternative strategies that ensure both environmental and consumer safety while establishing sustainable control measures. This includes biological control methods, such as epiphytic and endophytic antagonists, and genome editing techniques, which can manage pathogenic microbes without adverse environmental or human health effects. Ongoing research aims to elucidate the interactions between plants and pathogens, including infection and disease resistance mechanisms. Additionally, it is imperative to investigate the roles of beneficial bacteria and other microbial agents, particularly Bacillus strains and antagonistic bacteria such as Kloeckera apiculata and Bacillus subtilis, in inhibiting green mold. Recent advancements in genome sequencing and improvements in genetic transformation systems have facilitated a deeper understanding of Pd pathogenicity, citrus resistance mechanisms, and interactions between citrus antagonists and Pd. This review synthesizes recent findings on Pd pathogenicity, plant resistance, molecular interactions between pathogens and host plants, and the efficacy of microbial biocontrol agents, as well as the potential impacts of antagonists on Pd infection.

Microbiomes are sustained through infinite yet mutually interacting microbial communities, with bacteria and fungi serving as the major constituents. In recent times, microbial interventions have become popular for microbiome manipulation to achieve sustainable goals. Whether and how the introduced biocontrol agent drives fungal microbial assemblages (mycobiome) and the role of interkingdom signaling in shaping the microbiome structure and function remain poorly understood. Here, we implemented wild-type (WT) Bacillus subtilis L1-21 and its quorum quenching (QQ) mutants (L1-21Δytnp, and L1-21Δyxel) individually and as consortia to explore the enrichment patterns of key mycobiome members in Huanglongbing (HLB) infected citrus compartments including leaf endosphere, root endosphere, and rhizosphere soil. The application of WT and its QQ mutants produced differential mycobiome enrichment across citrus compartments. Our findings reveal that application of WT B. subtilis enriched beneficial fungi such as Trichoderma (15.82 %) in leaf endosphere. In contrast, pathogenic fungi Fusarium (47.5 %) and Gibberella (0.47 %) involved in citrus root decline were adundant in the L1-21Δytnp treated root endosphere while Nigrospora (11 %) was predominant in L1-21Δyxel treated leaf endosphere, affirming the role of bacterial quorum sensing (QS) molecules in shaping the fungal community composition. In general, based on the fungal functional prediction, fungal pathogens were highly abundant in mutant-treated plants, particularly in leaf endosphere (L1-21Δytnp: 25 %; L1-21Δyxel: 36.35 %) compared to WT (20.93%). Additionally, some fungal members exhibited strong compartment specificity and both mutants induced distinct mycobiome shifts in rhizosphere soil, leaf, and root endopshere. In conclusion, B. subtilis QQ modifies bacterial QS networks facilitating beneficial fungi to establish, while loss of QQ leads to enrichment of pathogenic fungal groups. Our study provides a direct link of perception and regulation of mycobiome through bacterial-based QS and QQ system, and its association with disease outcomes.

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Bacillus subtilis XF-1 is a well-investigated biocontrol agent against the biotrophic Plasmodiophora brassicae Woron., the causal agent of clubroot disease of cruciferous crops. The present study demonstrates that XF-1 could efficiently control clubroot disease via leaf spraying and provides an understanding of the biocontrol mechanisms. High-performance thin-layer chromatography (HTPLC) analysis indicated the presence of fengycin-type cyclopeptides in the supernatant. A ppsB deletion mutant of XF-1 resulted in no fengycin production, significantly reduced the lysis rate of testing spores in vitro and the primary infection rate of root hair in vivo, and decreased the protection value against clubroot disease under the greenhouse conditions. Confocal laser scanning microscopy proved that fengycin was not required for leaf internalization and root colonization. Moreover, the expression level of the ppsB gene in XF-1 was regulated by its cell density in root during interaction with P. brassicae. In addition, the ΔppsB mutant of XF-1 could not efficiently control disease because it led to a lower activation level of the jasmonic acid and salicylic acid signaling pathways in roots, which are necessary for the plant defense reaction upon pathogen invasion. Altogether, the present study provides a new understanding of specific cues in the interaction between B. subtilis and P. brassicae as well as insights into the application of B. subtilis in agriculture.

Plant health is closely related to microbial communities present in specific host increasingly challenged by pathogen attack. Soil-borne diseases cause an imbalance of the already colonized plant rhizosphere microbial community, resulting in restricting agricultural production. In this study, tobacco black shank (TBS), caused by Phytophthora nicotianae was used as a disease model to explore the impact of rhizosphere microorganisms on tobacco health and assessed the use of introduced microbes to mitigate the spread of disease in an environment-friendly way. Here, field investigation confirmed that the higher pathogen load in the field was directly proportional to the higher disease index. We isolated 223 strains of bacteria from the tobacco rhizosphere soil in Yuxi City, Yunnan, China and confirmed eight candidate strains with potential antagonism against P. nicotianae. The strains were further identified as Bacillus based on morphology, physiological and biochemical characteristics, and molecular analysis. Under field conditions, sterilized and non-sterilized rhizospheric soil showed significant differences in terms of pathogen growth. Our results indicated potential bacteria in the tobacco rhizosphere have a protective effect against TBS. Notably, eight potential Bacillus strains and simple synthetic microbial consortium as the antagonistic group could reduce the number of the pathogen in soil effectively and resist the TBS in the greenhouse. P. nicotianae and rhizosphere antagonists co-affect tobacco health, and proved that potential microbes could effectively reduce a load of P. nicotianae and control plant diseases in an ecological friendly way for plant health and protection.

Banana crop ranks among the most crucial fruit and food crops in tropical and subtropical areas. Despite advancements in production technology, diseases such as cordana leaf spot, caused by Neocordana musae, remain a significant challenge, reducing productivity and quality. Traditional chemical controls are becoming less effective due to the development of resistance in target pathogens, which pose significant environmental and health concerns. Consequently, there is growing attention toward the development of biocontrol strategies. Here, we identified a new bacterial strain, Bacillus stercoris 92p, from the rhizosphere soil of banana. We evaluated its ability to suppress the growth of N. musae and other fungal pathogens that cause leaf spot disease in bananas. The inhibitory effect of B. stercoris 92p were checked using dual culture assays, microscopic observations, and pot experiments. Furthermore, the biocontrol mechanisms were investigated using whole-genome sequencing and biochemical analyses. The results showed that B. stercoris 92p exhibited significant antifungal activity against N. musae and other fungal pathogens, with inhibition rates exceeding 70%. Microscopic examination revealed significant morphological alterations in the hyphae and conidia of the tested pathogens. In pot experiments, B. stercoris 92p effectively reduced the severity of cordana leaf spot, achieving a biocontrol efficacy of 61.55%. Genomic analysis and biochemical tests indicated that B. stercoris 92p produces various antifungal compounds, including lipopeptides (fengycins and surfactins), hydrolytic enzymes (proteases and amylases), and phosphate-solubilizing metabolites. In conclusion, the study highlights that B. stercoris could potentially be used as a potential biological control agent against cordana leaf spot.

The murine model is invaluable for studying intricate interactions among gut microbes; hosts; and diseases. However; the impact of genetic variations in the murine microbiome; especially in disease contexts such as Klebsiella pneumoniae (Kp) infection; still needs to be explored. Kp; an opportunistic global pathogen; is becoming increasingly prevalent in regions like Asia; especially China. This study explored the role of the gut microbiota during Kp infection using mouse model; including wild-type and rpoS mutants of Kp138; KpC4; and KpE4 from human; maize; and ditch water; respectively. Under stress conditions; RpoS reconfigures global gene expression in bacteria; shifting the cells from active growth to survival mode. Our study examined notable differences in microbiome composition; finding that Lactobacillus and Klebsiella (particularly in WKp138) were the most abundant genera in mice guts at the genus level in all wild-type treated mice. In contrast; Firmicutes were predominant in the healthy control mice. Furthermore; Clostridium was the dominant genus in all mutants; mainly in ∆KpC4; and was absent in wild-type treated mice. Differential abundance analysis identified that these candidate taxa potentially influence disease progression and pathogen virulence. Functional prediction analysis showed that most bacterial groups were functionally involved in biosynthesis; precursor metabolites; degradation; energy generation; and metabolic cluster formation. These findings challenge the conventional understanding and highlight the need for nuanced interpretations in murine studies. Additionally; this study sheds light on microbiome–immune interactions in K. pneumoniae infection and proposes new potential therapeutic strategies.