Fusarium basal rot (FBR) poses a serious threat to onion (Allium cepa L.) production worldwide. In South Korea, FBR is primarily associated with Fusarium oxysporum, F. commune, and F. proliferatum. To investigate the relationship between effector gene profiles and virulence, we screened 34 isolates collected from FBR-affected fields for 14 Secreted in Xylem (SIX) genes and three additional effector candidates (CRX1, CRX2, and C5). F. oxysporum isolates carrying the effector suite SIX3, SIX5, SIX7, SIX9, SIX10, SIX12, SIX14, together with CRX1, CRX2 and C5, exhibited significantly higher aggressiveness on onion seedlings and bulbs than effector-negative strains. Among F. commune isolates lacking SIX genes, those carrying both CRX1 and CRX2 tended to show greater pathogenicity than CRX-negative strains. Nevertheless, SIX-negative strains still caused substantial seedling loss and bulb-rot, indicating the involvement of SIX-independent virulence factors. All F. proliferatum isolates were comparably pathogenic to SIX-negative F. oxysporum and F. commune strains, and uniformly carried SIX2-1 and CRX2, with a subset also harboring the SIX2-2 homologue. Across all isolates, SIX9 was the most frequently detected SIX gene and was markedly enriched in strains exhibiting strong pathogenicity. We developed and validated a SIX9-targeted quantitative PCR (qPCR) assay that specifically detects SIX9-positive Fusarium isolates (mainly F. oxysporum and F. commune), with detection limits of 1 pg of DNA or 10⁴ conidia/g soil. These findings enhance our understanding of effector repertoires contributing to Fusarium pathogenicity on onion and provide a molecular tool to support FBR diagnosis.

Wildfire, caused by Pseudomonas amygdali pv. tabaci (Pat), is a severe bacterial disease of soybean [Glycine max (L.) Merr.]. Enhancing resistance to wildfire is an important breeding goal, yet genetic studies remain limited. This study aimed to identify quantitative trait loci (QTL) associated with partial resistance to Pat using a Daepung × Taekwang recombinant inbred line (RIL) population. Sixty RILs were evaluated for resistance to the Pat isolate 'W14-M1'. Two QTL associated with resistance to Pat were identified on chromosomes 4 and 5, explaining 14.1% and 19.1% of the phenotypic variance, respectively. Daepung contributed the resistance alleles at both loci. The identified genomic regions overlapped with previously reported resistance QTL for bacterial, fungal, and nematode Pathogens. These findings indicate that Daepung is a valuable source of resistance to Pat, and the detected QTL may facilitate the development of molecular markers for pyramiding multiple disease resistance traits in soybean breeding program.

Bacterial identification and classification are commonly performed based on the sequence of the 16S rRNA and several gold-standard marker genes, such as gyrB and recA. However, certain bacterial genera, including Xanthomonas and Pseudomonas, present challenges in clear classification at the species or subspecies level using these single-marker genes. Here, we explored the potential of the rfbA gene as a novel marker for bacterial classification. The rfbA gene, involved in lipopolysaccharide synthesis, is a conserved gene present in most gram-negative bacteria and is sufficiently short (approximately 850 bp). In this study, we identified that rfbA has undergone host-specific adaptive evolution, distinguishing it from conserved housekeeping genes. Therefore, we targeted Xanthomonas and Pseudomonas species to demonstrate the utility of rfbA in resolving taxonomic challenges at the pathovar level. These differences were strongly associated with the hosts of the respective strains, suggesting a potential evolutionary link between rfbA variation and host specificity.

Plant diseases remain a major threat to global food production, causing significant yield losses and economic impact worldwide. Early and precise disease detection is crucial for effective crop management, yet conventional diagnostic approaches are often slow, labor-intensive, and rely on specialized expertise that may not be widely accessible. Recent advances in artificial intelligence (AI), particularly deep learning-based image analysis, offer scalable and automated solutions for plant disease recognition. This review critically examines forty-one peer-reviewed studies published between 2008 and 2025, selected following PRISMA guidelines from major scientific databases. We summarize key methodological developments, including convolutional neural networks, vision transformers, transfer and few-shot learning, and multimodal sensing approaches, highlighting their reported performance and limitations. Although many models achieve high accuracy in controlled datasets, their effectiveness often decreases under real-field conditions due to environmental variability, limited training data, and practical deployment constraints. We discuss existing challenges and propose future research directions, emphasizing improved robustness in field environments, development of lightweight and explainable models suitable for edge deployment, and integration with precision agriculture systems. This review aims to guide the design of reliable, practical, and scalable AI-driven plant disease detection strategies.

Radiation-based disinfection is a validated approach for controlling microbes and plant pathogens in agriculture and the food chain. Botrytis cinerea, a major necrotrophic pathogen of many crops, is a pertinent target for such non-chemical treatments. Here, we compared the effectiveness of gamma and X-ray irradiation with an emphasis on dose rate as a process variable, and assessed survival/regrowth on potato dextrose agar and loss of pathogenicity on strawberry fruit. At a fixed total dose of 6 kGy, gamma irradiation showed a clear dose-rate dependence: 0.5 kGy h⁻¹ permitted regrowth within 28 days, 1.0 kGy h⁻¹ resulted in lagged regrowth beginning after day 14, whereas 2.0 kGy h⁻¹ yielded no regrowth during the observation period. X-ray treatment at 6 kGy (≈2.5 kGy h⁻¹) likewise resulted in no colony expansion for a period of up to 28 days. Culture negativity was concordant with loss of pathogenicity on strawberries, supporting culture negativity as a practical disinfection endpoint. Collectively, these results indicate that, under our conditions, the critical disinfection dose (D_crit) for B. cinerea is ≤6 kGy when delivered at ≥2.0 kGy h⁻¹ (gamma) or at approximately 2.5 kGy h⁻¹ (X-ray), and that dose rate materially modulates survival/repair dynamics at a given total dose. This study defines process windows for effective application of irradiation and supports the practical deployment of radiation disinfection for quarantine and postharvest management of B. cinerea.

Recently, we reported that Brevibacillus brevis HK544, which produces edeine B1 (EB1), exhibits promising antimicrobial activity against plant pathogens. To elucidate its antibacterial mechanisms against Erwinia amylovora, the causal agent of fire blight, we conducted label-free shotgun proteomic analysis of E. amylovora TS3128 treated with B. brevis culture filtrate (CF) or purified EB1. Comparative analysis showed significant (over twofold) changes in 45 of 624 and 81 of 846 quantified proteins following CF and EB1 treatments, respectively. Functional categorization revealed altered abundances of proteins associated with energy production, ribosome biogenesis, and cell wall/membrane/ envelope biogenesis in both treatments. Notably, 42 and 75 translation-related proteins were differentially expressed in CF- and EB1-treated samples, respectively, consistent with the proposed translation-inhibitory activity of EB1. These findings provide insights into the cellular targets and antibacterial mode of action of B. brevis HK544 and EB1, supporting their potential as biocontrol agents against fire blight.

Soil-borne fungal and oomycete pathogens endanger global crop production, highlighting the need for sustainable alternatives to chemical fungicides. In this study, an antagonistic actinomycete isolated from agricultural soil was identified as Streptomyces hachijoensis JCK-6068 through 16S rRNA sequencing and phylogenetic analysis. S. hachijoensis JCK-6068 exhibited broad-spectrum antifungal and antioomycete activity in dual-culture and minimum inhibitory concentration assays. Biochemical characterization revealed the production of multiple hydrolytic enzymes, including cellulase, chitinase, protease, and gelatinase, along with the phytohormone indole-3-acetic acid. Volatile organic compounds produced by JCK-6068 strongly inhibited pathogen growth in vitro, and gas chromatography- mass spectrometry identified 2-methyl-2-bornene as the predominant component. In vivo assays demonstrated that curative application of the 10-fold diluted fermentation broth provided effective control of creeping bentgrass dollar spot (74.31%), pepper Phytophthora blight (68.88%), cucumber Fusarium wilt (61.11%), and cucumber damping-off (88.89%). Preventive treatment with 1000-fold dilution of fermentation broth is as effective as chemical fungicides in controlling cucumber damping-off and Fusarium wilt. Furthermore, treatment of PR1::GUS transgenic Arabidopsis thaliana seedlings with JCK-6068-derived materials induced strong PR1 expression, indicating elicitor activity consistent with salicylic acid-responsive defenses signaling. To facilitate practical application, a wettable powder formulation derived from the n-butanol extract of JCK-6068 was evaluated under greenhouse conditions, achieving 91.67% control of cucumber Fusarium wilt at a 500-fold dilution and 77.78% control of cucumber damping-off at a 250-fold dilution, comparable to commercial chemical fungicides. Collectively, these findings highlight the multifaceted biocontrol potential of S. hachijoensis JCK-6068 as a sustainable biocontrol agent for soil-borne fungal disease.

The Ralstonia solanacearum species complex (RSSC) is a major soil-borne pathogen of solanaceous crops. During a field experiment originally designed to monitor rhizosphere and episphere microbiomes in two pepper cultivars, a naturally emerging and asymptomatic Ralstonia dominance event was detected in the rhizosphere without visible wilt symptoms. This unexpected occurrence provided an opportunity to characterize asymptomatic RSSC dynamics and their microbial interactions under field conditions. Full-length 16S rRNA amplicon sequencing showed that one ASV (Sq_1) was nearly absent from the episphere but increased sharply in the rhizosphere from week 3 onward, dominating 20–80% of samples during weeks 7–10. Phylogenetic comparison with 93 historical Korean RSSC isolates placed Sq_1 within a 16S-defined lineage corresponding to pepper-associated R. pseudosolanacearum biovars 3 and 4. Sq_1 abundance accounted for a large portion of β-diversity turnover in the rhizosphere. After within-plot correlations were meta-analyzed, selected taxa were evaluated using a Bayesian pairwise compositional Lotka–Volterra (pcLV) model, which identified three taxa (Sq_272, TRA3-20; Sq_178, Bradyrhizobium; and Sq_124, Bryobacter) that consistently exerted inhibitory effects on Sq_1 per-interval growth. Supported by the longitudinal design and the high accuracy of PacBio full-length 16S sequencing, these findings highlight potential microbial suppressors of RSSC and demonstrate the utility of pcLV modeling for resolving directional interactions at the ASV level.

Burkholderia glumae, the causal agent of bacterial panicle blight in rice, is a major threat to global rice production. Although the NtrB–NtrC two-component system is a well-established regulator of nitrogen assimilation in many bacteria, its role in B. glumae has remained undefined. In this study, we constructed a ntrC deletion mutant of B. glumae BGR1 to investigate the contribution of NtrC to nitrogen metabolism and virulence. Under nitrogen-limited conditions in minimal medium supplemented with a single nitrogen source, the mutant exhibited markedly impaired growth, particularly when ammonium or glutamine served as the sole nitrogen source. Loss of ntrC also resulted in significant reductions in swimming motility, biofilm formation, and toxoflavin production, while extracellular protease activity was unaffected. In pathogenicity assays, the mutant caused substantially milder symptoms in both rice seedlings and flowering panicles, despite showing no difference in bacterial population levels in planta compared with the wild-type. These findings demonstrate that NtrC is essential for efficient nitrogen utilization and for full virulence expression in rice. This study provides evidence that the NtrB–NtrC system links nitrogen metabolism with virulence expression in B. glumae.