We presented an integrative hyperspectral approach for the rapid and non-invasive detection of rice blast (Magnaportheoryzae) that moves beyond traditional index-based methods. Leaf and canopy-level reflectance data (350 nm-2500 nm) were smoothed using Savitzky-Golay polynomials, standardised with Standard Normal Variate (SNV) and Multiplicative Scatter Correction (MSC) and then differentiated to highlight subtle infection signals. Dimensionality reduction methods including Principal Component Analysis (PCA), t-Distributed Stochastic Neighbour Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP) revealed clear separations between healthy and diseased spectra, while cosine similarity and the Spectral Angle Mapper (SAM) measured illumination-invariant spectral differences. A Random Forest impurity analysis identified the ten most informative wavelengths, enabling the evaluation of over one million band combinations. From this, we developed the Rice Blast Index (RBI = (R1068-R1560) / (R1068 + R1560)), which outperformed Normalized Difference Vegetation Index (NDVI) and Photochemical Reflectance Index (PRI), achieving an F1-score of 0.95 and Cohen's kappa of 0.93 across independent growing seasons. New structural diagnostics, including lagged correlation, spectral autocorrelation and feature persistence, were introduced to quantify redundancy and identify stable biochemical absorption zones, notably a 38 nm region around 680 nm and a 1470 nm region linked with chlorophyll-protein features. Outlier spectra were removed with an Isolation Forest algorithm, improving robustness by 4.7 %. The average processing time was 18 ms per spectrum, enabling real-time scouting. Together, these elements deliver a unified, end-to-end framework that combines advanced pre-processing, dimensionality reduction, anomaly rejection, machine-learning-based band selection and new structural metrics. This framework improves early rice blast surveillance and offers a transferable template for hyperspectral phenotyping of diverse crop stresses, effectively bridging fine-scale sensitivity with field-scale applicability in precision agriculture.

Bacterial wilt caused by Ralstonia pseudosolanacearum remains one of the most destructive diseases threatening brinjal production worldwide, as effective management options are limited, resistance in cultivated varieties is often unstable, and chemical control measures are largely ineffective and environmentally unsustainable. In this study, we profiled the rhizobacterial microbiomes of wilt-susceptible Solanum melongena and wilt-resistant S. torvum cultivated in contrasting soils from Cameroon and India representing non-endemic and endemic regions of bacterial wilt. A combined culture-dependent methodology together with 16 S rRNA amplicon sequencing was used to elucidate the structure and functional attributes of the microbial communities. Soil origin was the principal factor influencing microbiome composition (PERMANOVA R2 = 0.34, p = 0.001), followed by host genotype (R2 = 0.21) and root niche (R2 = 0.14). The wilt-resistant S. torvum consistently supported higher bacterial diversity and was enriched with core taxa, including Bacillus and Methanocella. Fourteen rhizobacterial isolates, mainly Bacillus spp., showed strong antagonistic activity against R. pseudosolanacearum. Metabolomic analyses using LC-QTOF-MS/MS and GC-MS indicated the production of lipopeptides and polyketides by Bacillus spp., while Pseudomonas plecoglossicida produced phenazine derivatives and indole-3-acetic acid. In greenhouse experiments, Bacillus cereus, B. velezensis, and Priestia megaterium significantly improved seed germination and seedling vigor at inoculum densities of 106-108 CFU mL-1. Together, these results show that brinjal-associated rhizobacteria, particularly Bacillus spp. and P. plecoglossicida, contribute to bacterial wilt suppression and offer potential for sustainable disease management.

We used culture-dependent methods to isolate endophytic fungi from various tissues of maize (Zea mays L.), including leaves, cobs and roots. The study assessed the diversity of endophytic fungal communities in maize cultivated under long-term conservation agriculture practices in northern India, specifically conservative tillage (CT) and reduced tillage (RT). Endophytes were identified using ITS-rDNA sequencing to determine their distribution patterns within asymptomatic maize tissues. Leaf tissues harboured endophytic genera such as Alternaria, Aspergillus, Cladosporium, Fusarium, Penicillium and Sarocladium. Premature cobs contained Alternaria, Aspergillus, Cladosporium, Fusarium, Kalmusia, Mucor, Penicillium and Sarocladium. Root tissue of maize also contained important genera like Aspergillus, Cladosporium, Curvularia, Fusarium, Penicillium and Purpureocillium. Across both tillage systems, leaf tissues consistently yielded Alternaria, Aspergillus, Cladosporium, Fusarium and Penicillium. Root tissues under both tillage systems frequently harboured Aspergillus and Penicillium. Kalmusia, Mucor, Penicillium and Sarocladium were observed exclusively under the RT system. The findings reveal distinct distribution patterns shaping the maize mycobiome under varying agronomic conditions.

The main aim of this study was to develop an eco-friendly edible coating based on fenugreek gum (FG) functionalized with finger millet phenolic (FMP) extract and to evaluate its effect on the postharvest quality of Kinnow mandarins. Coating formulations comprising FG, GP1 (10

Bacterial wilt, caused by Ralstonia solanacearum, is a serious disease affecting a wide range of crops globally. Race 4 strains, which primarily infect Zingiberaceae crops such as cardamom (Elettaria cardamomum) and ginger (Zingiber officinale), remain poorly characterised at the genomic level, limiting understanding of their host adaptation, pathogenicity, and ecological behaviour. In this study, the complete genome of R. solanacearum strain CaRs-Mep, a Race 4, biovar 3, phylotype I isolated from wilted small cardamom in Kerala, India, was sequenced, assembled, and annotated, providing the first detailed genomic insight into a Zingiberaceae-infecting strain. The genome spans similar to 5. 5.6 Mb across 13 scaffolds, with a GC content of 67. 09%, and encodes 5, 227 genes, including 101 virulence- associated genes and 40 antibiotic resistance genes. Functional analysis identified 132 metabolic pathways, including terpenoid and betalain biosynthesis, degradation of volatile compounds such as limonene and pinene, and secondary metabolite production, suggesting adaptation to volatile-rich Zingiberaceae tissues. The CaRs-Mep strain carries a complete set of secretion systems (Type II, III, IV, and VI), plant cell wall-degrading enzymes, siderophore biosynthesis genes, and multidrug efflux pumps, indicating a strong and versatile infection strategy. CAZyme analysis showed enrichment of glycoside hydrolases and glycosyltransferases, supporting tissue colonisation and host interaction. Phylogenomic analysis placed CaRs-Mep in phylotype I, forming a distinct clade among Zingiberaceae- infecting Race 4 strains, indicating host specialisation. Comparative pan-genome analysis of other representative RSSC strains revealed a large accessory genome, reflecting genomic plasticity and niche-specific adaptation. The findings show that CaRs-Mep combines virulence factors, metabolic versatility, and stress tolerance to efficiently infect hosts in the Zingiberaceae. Notable features include pathways for volatile compound degradation, expanded secretion systems, a diverse CAZyme repertoire, and multiple efflux-mediated resistance genes. This first genome-scale study of a Zingiberaceae-infecting Race 4 strain provides essential information on its evolution, host specificity, and mechanisms of pathogenicity. The genome also provides a foundation for further studies on disease management, diagnostics, and the development of strategies to control bacterial wilt in cardamom, ginger, and related crops.

Anthracnose caused by Colletotrichum gloeosporioides is a major postharvest disease of banana, resulting in 30–40

The use of yeasts as biocontrol agents to prevent post-harvest fruit diseases offers a promising alternative to synthetic fungicides. Volatile organic compounds (VOCs) of microbial origin represent an effective strategy for managing post-harvest decay. This study systematically evaluates the role of VOCs produced by the antagonistic yeast Hanseniaspora uvarum LE‑1 against Alternaria alternata, Colletotrichum musae, and Penicillium italicum, causing post-harvest diseases in apples, bananas, and oranges, respectively. In preliminary dual‑plate assays, H. uvarum LE‑1 achieved approximately 50

Cassava ( Manihot esculenta Crantz) stem and root rot caused by Fusarium falciforme is a major constraint to production. This study characterised rhizoplane bacteriome shifts across agroecosystems with contrasting disease incidence and identified microbial indicators and potential biocontrol agents using 16S rRNA gene amplicon sequencing, culture-dependent isolation, and functional assays. Microbial richness was highest in diseased wetlands (Chao1: 601.60 ± 10.37), followed by healthy wetlands (581.20 ± 14.39) and uplands (547.97 ± 5.74), while evenness remained comparable among ecosystems. Pseudomonadota dominated all sites (~ 64%). Bacteroidota, Planctomycetota, and Actinomycetota were enriched in healthy wetlands but declined in diseased sites, whereas Verrucomicrobiota increased in diseased roots (7.35%). Pseudomonas dominated uplands (29.7%), while Aeromonas, Salmonella, and Devosia were associated with disease. The conserved core microbiome comprised Aquicella, Enterobacter, Klebsiella, Sodalis , and Salmonella. Network analysis identified Geminigeraceae as a keystone taxon and revealed predominantly cooperative interactions between bacteria and fungi. Among 195 isolates, Bacillus subtilis ULB_36 and Bacillus stercoris ULB_12 exhibited strong inhibition of F. falciforme (83.33% and 78.52%), significantly reduced disease severity, and enhanced plant growth, comparable to fungicide treatments. These findings demonstrate that cassava stem and root rot are associated with disruption of the rhizoplane bacteriome and the loss of beneficial taxa. Agroecosystem-specific microbial signatures and core bacteriome members provide insights into cassava–microbe interactions, while native Bacillus strains offer promising niche-adapted biocontrol solutions for sustainable management of cassava stem and root rot.

The growing global population, expected to reach 9.7 billion, is driving an increased demand for food production. While chemical crop protection is commonly used, concerns over its environmental impact and safety have shifted focus toward developing safer and more sustainable alternatives. Biological control of Maydis leaf blight (MLB) in maize, through naturally occurring endophytic bacteria from the phyllosphere, presents an eco-friendly option. The phyllosphere, home to diverse microbial communities collectively known as the phyllomicrobiome, holds significant potential for biocontrol strategies. The maize phyllomicrobiome was analyzed using both microbial metabarcoding and conventional microbiological techniques. Diversity analysis was conducted for both total and culturable microbiomes. Endophytic bacterial isolates were assessed for their functional potential, followed by field validation. The expression of maize candidate genes was analyzed using qPCR. Through 16S rRNA gene sequencing, ten distinct bacterial species were identified from the maize phyllosphere: Alcaligenes (2), Brevundimonas (2), Pseudomonas (3), Microbacterium (1), Proteus (1), and Stenotrophomonas (1). Over 50

Bacterial blight, caused by Xanthomonas axonopodis pv. punicae, remains a significant constraint to pomegranate cultivation, necessitating sustainable alternatives to chemical and antibiotic-based control. In this study, 24 epiphytic bacterial strains isolated from the pomegranate phylloplane were evaluated for their biocontrol potential through integrated metabolomic, volatilomic, in vitro, and greenhouse analyses. LC-MS/MS profiling revealed the presence of bioactive metabolites such as Bacillomycin D, Fengycin, and Iturin A in Bacillus spp.; Macrolactin (6.3 μg/mL), Macrolactin W (4.1 μg/mL), and sucrose palmitate (2.8 μg/mL) in Erwinia; and Cyclo (l-Pro-l-Tyr), Tryptophol, Dapdiamide A and B, and Pantocin A and B in Pantoea. GC-MS analysis identified (E)-3-Butylidene-4,5-dihydroisobenzofuran-1(3H)-one as a dominant volatile compound across multiple isolates. Among the strains, Pantoea dispersa Pg-Slp6 emerged as the most promising, exhibiting the highest phosphate solubilization (84.5 μg/mL), indole-3-acetic acid production (28.6 μg/mL), siderophore activity (CAS index 0.86), and significant pathogen suppression (72.3 % inhibition in vitro; 61.5 % disease reduction in greenhouse trials). Metabolite-mediated bioassays confirmed complete inhibition of X. axonopodis pv. punicae by secondary metabolites from Bacillus amyloliquefaciens P2-1 and P. dispersa Pg-Slp6. Whole-genome sequencing of P. dispersa Pg-Slp6 revealed gene clusters associated with secondary metabolite biosynthesis, xenobiotic degradation, and plant growth-promoting traits, affirming its multifunctional capabilities. Phylogenetic analysis based on 100 conserved protein-coding genes placed P. dispersa Pg-Slp6 in a distinct clade, underscoring its unique genomic identity. These findings establish P. dispersa Pg-Slp6 as a robust candidate for developing phylloplane-adapted microbial formulations aimed at the eco-friendly and effective management of bacterial blight in pomegranate.

Rice blast, caused by Magnaporthe oryzae, remains a major constraint to global rice production, typically presenting as necrotic lesions on infected leaves. To investigate the bacterial communities associated with these lesions, we employed a novel “Microbiome Imprinting-Metabarcoding” approach, which generated comprehensive microbial datasets (203.34 Mb) from two blast-infected rice cultivars, aromatic Pusa Basmati 1 (PB1) and non-aromatic VL Dhan 85. Metabarcoding analysis revealed the consistent presence of several dominant bacterial genera, including Pantoea, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pseudomonas, and Chryseobacterium, across both cultivars. Notably, bacterial diversity was reduced in blast lesions compared to healthy phylloplane tissues. Lesion samples comprised 28 genera (Shannon Diversity Index: 1.66; Chao1 richness: 326.86), whereas healthy leaves harbored 48 genera (Shannon Diversity Index: 1.98; Chao1 richness: 361.82). Linear discriminant effect size (LEfSe) analysis identified specific genera such as Bifidobacterium, Desemzia, Acidovorax, and Mucilaginibacter that were uniquely associated with the dysbiotic microbial communities in infected tissues. Core microbiome analysis further revealed ten genera shared between both cultivars, with Pantoea and Allorhizobium emerging as the most abundant. These findings offer new insights into the composition and dynamics of lesion-associated bacterial communities in rice blast and highlight potential microbial targets for the development of improved disease management strategies. Graphical abstract on Dysbiosis of the Rice Leaf Phyllomicrobiome Induced by Magnaporthe oryzae Infection: Evidence from Metabarcoding and Microbiome Imprinting

Bacterial blight of pomegranate caused by Xanthomonas axonopodis pv. punicae poses significant challenges to sustainable cultivation, necessitating eco-friendly management strategies, and this study explores the role of the phylloplane microbiome in disease suppression through metabarcoding, traditional microbiology, and antibacterial screening of microbial candidates. Here, we mapped the phylloplane microbiome of pomegranate cultivar 'Bhagwa' during bacterial blight development using metabarcoding sequencing (2,443,834 reads), traditional microbiological methods (nutrient-rich and minimal media), and scanning electron microscopy. We observed shifts in microbial diversity, with Xanthomonas typically released through stomata as the blight progressed from water-soaked early lesion to advanced necrotic lesion. The Shannon diversity index peaked at 2.6 in early necrotic stages but dropped to 2.1 in advanced blight. Proteobacteria and Firmicutes were the dominant phyla, with significant compositional changes between disease stages. Bacillus species were prevalent throughout, peaking in both early and severe lesions. Pantoea and Curtobacterium increased during severe blight, while Exiguobacterium thrived on the abaxial surface. A core microbiome, including Pantoea, Enterobacter, and Pseudomonas, remained consistent across stages. Antibacterial screening of 116 bacterial candidates, dominated by Pantoea (32), Bacillus (18), and Pseudomonas (11), revealed multipronged activities against X. axonopodis pv. punicae. Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-Slp-6 suppressed the pathogen through secreted metabolites, while Pantoea dispersa Pg-Slp-6, Pseudomonas oryzihabitans Pg-Slp-82, and Pantoea dispersa Pg-slp-117 exhibited volatile-mediated suppression. Among these, Bacillus amyloliquefaciens P2-1 and Pantoea dispersa Pg-slp-6 showed 55% and 42% blight suppression, respectively, highlighting their potential as biocontrol agents.

Sesame phyllody disease poses a serious threat to sesame cultivation, often leading to complete crop failure due to the absence of resistant varieties and lack of effective chemical treatments. To explore sustainable alternatives, this study investigated the foliar microbiome by comparing microbial communities in healthy and phyllody-infected sesame plants from severely affected fields. Through combined culture-based techniques and DNA sequencing, we identified 3108 bacterial OTUs spanning several key genera, including Pantoea, Pseudomonas, Allorhizobium, and Xanthomonas. Phytoplasma, the known causal agent, was detected exclusively in symptomatic plants. Co-occurrence network analysis revealed distinct microbial associations: healthy plants showed balanced interactions with Pantoea, Pseudomonas, and Sphingomonas as central hubs, whereas infected plants exhibited a denser, more complex network, indicating phytoplasma-driven shifts in microbial structure. From culturable isolates, 72 bacterial strains were recovered, with Pantoea being predominant in both plant types. Functional predictions highlighted microbial association with nutrient metabolism and biosynthesis of alpha-linolenic acid, a naturally abundant compound in sesame. This first study of the sesame foliar microbiome provides valuable insights into plant-microbiome-phytoplasma interactions and lays a foundation for developing microbiome-based, eco-friendly strategies to manage sesame phyllody disease in the future.

A fluorescence imaging and real-time quantitative PCR (qPCR) approach was established to enable both qualitative and quantitative assessment of Magnaporthe oryzae colonization on rice leaf surfaces. Stable GFP-expressing transformants were generated using Agrobacterium tumefaciens-mediated transformation within 10–12 days and confirmed by PCR with gene-specific primers. Expression of the gfp-gene was validated in planta using epifluorescence and confocal laser scanning microscopy. These transformants facilitated visualization of fungal colonization patterns on rice leaves over time. For quantitative estimation, a qPCR assay targeting the gfp-transgene was standardized, achieving a detection sensitivity of 0.3 femtograms of DNA. Absolute quantification showed an increase in pathogen biomass from 1.1 × 102 to 2.8 × 104 within 48 h post-inoculation on both rice and wheat leaves. This integrated strategy, combining gfp-based imaging with qPCR, offers a reliable tool for tracking Magnaporthe oryzae colonization on the phylloplane and holds potential for application in host resistance screening and pathogenesis research.

Phylloplane-associated bacteria contribute significantly to sustainable plant disease management by modulating host defense mechanisms and directly antagonizing pathogens. In this study, Pseudomonas oryzihabitans Pg-Slp82, a dominant phylloplane isolate from pomegranate, was evaluated for its potential as a biocontrol agent against Xanthomonas axonopodis pv. punicae, the causal agent of bacterial blight. Whole-genome sequencing revealed a 5.0 Mb genome comprising 7,193 coding sequences, including 1,029 hypothetical proteins, 15 tRNAs, 15 rRNAs, and 60 repetitive elements, indicating a genomically diverse strain with potential biocontrol traits. Transcriptomic analysis of P. oryzihabitans Pg-Slp82-treated pomegranate leaves generated 403 million reads (GC content 49–50

Powdery mildew (PM) caused by Erysiphe necator (Schw.) Burrill is one of the most important constraints in enhancing grapevine productivity. The study focused on identifying stable and highly resistant grapevine genotypes against PM across multiple environments, while assessing conditions favouring optimal trait expression. Forty-two genotypes were evaluated over three consecutive seasons (2021-2023) using disease severity index (DSI), morphological and biochemical analysis. Resistant genotypes, such as Vitis parviflora, Pusa Navrang and V. jacquemontii exhibited lower stomatal density, increased leaf thickness and enhanced antioxidant activities. Significant G x S interactions were employed using additive main effects and multiplicative interaction and genotype (AMMI) and genotype-environment interaction (GGE) biplot analysis based on disease severity index data. The estimation of stability indices, i.e. WAASB is used for selecting highly resistant genotypes. The multi-trait stability index (MTSI) method in evaluating 18 traits highlighted V. parviflora, Chardonnay, 110 Richter, Pusa Navrang and Male hybrid as the most promising genotypes. These genotypes exhibited lower DSI and no notable changes in photosynthetic pigments in diseased leaves. High heritability of PAL, PPO and total phenols underscores their potential as key targets for selection. Similarly, high heritability of the DSI (81-93 %) confirms a strong genetic basis, with V. parviflora, 110 Richter, Pusa Navrang and Male Hybrid emerging as the most stable resistant genotypes. These genotypes were identified as stable performers under natural PM pressure and could serve as candidates for breeding programs, enabling the development of resistant grape cultivars and thus reducing the need for fungicide use in disease-prone regions.

Maize (Zea mays L.) is an important cereal crop, significantly contributing to the global economy and advancing plant genetic research. One of the most serious diseases, maydis leaf blight (MLB), incited by Bipolaris maydis, reduces the yield and quality of maize. The present study was carried out during rainy (kharif) season (June–Oct) of 2022 and 2023 at ICAR-Indian Agriculture Research Institute, New Delhi to identify promising phyllosphere endophytic bacteria against Bipolaris maydis as an appropriate alternative to the traditional commercial fungicides, which also aligns with the goal of promoting sustainable and eco-friendly agriculture. Three different concentrations of phyllosphere endophytic bacteria, viz. Stentrophomonas maltophilia, Brevundimonas olei and Pseudomonas aeruginosa were investigated for MLB disease reduction and activation of maize biochemical defence system against Bipolaris maydis after seed priming. The recorded in planta percent disease index (PDI) data were analysed using a randomized block design (RBD) while all replications for biochemical assay were arranged in a completely randomized design (CRD) and subjected to the analysis of variance (ANOVA). Disease scoring in both seasons recorded the lowest PDI at the highest concentration of Stentrophomonas maltophila, followed by Brevundimonas olei and Pseudomonas aeruginosa. Biochemical activities of phenylalanine ammonia-lyase (PAL), PR protein β-1,3- glucanase, and non-enzymatic antioxidant including total polyphenol with total sugar content were recorded for both inoculated and uninoculated set of treatments. In addition, seeds primed with the highest concentration 1.0 at OD600 of Stentrophomonas maltophilia and Brevundimonas olei recorded elevated sugar levels, enzymatic as well as non- enzymatic activities after Bipolaris maydis inoculation. This study demonstrated that the changes in biochemical activities correspond with the developmental stages of the pathogen Bipolaris maydis which inhibited its growth. The biochemical defence activities varied differentially during disease progression on the host plant.

Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems—Coringa and Pichavaram—using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70

Powdery mildew caused by Erysiphe necator poses a major challenge for grapevine cultivation. This study investigates how stomatal and structural traits influence resistance to this pathogen across diverse Vitis genotypes. Microscopic analysis revealed significant variations in stomatal characteristics. The sunken stomata were observed in V. parviflora, V. jacquemontii, V. rupestris x V. berlandieri (110 Richter) and V. rupestris (St. George) with lower stomatal density. Genotypes with raised stomata had larger stomatal complex areas. Following inoculation with E. necator (accession No. 52218), the Vitis genotypes showed a distinct resistance response. Susceptible V. vinifera genotypes had high pathogen penetration rates, with 71% of infection attempts forming haustoria. In contrast, V. parviflora, V. jacquemontii, and hybrids such as V. rupestris x V. berlandieri and V. riparia x V. cinerea exhibited programmed cell death (PCD)-mediated resistance, arresting up to 55 per cent of penetration attempts limiting hyphal growth. Cryo-SEM images further indicated sparse fungal growth on the resistant genotypes. The genotype V. parviflora possessed dense trichomes and long wax stripes along the epidermal cells covering leaf veins on the adaxial leaf surface, thus causing a physical barrier against the pathogen. Comparative analyses showed that callose deposition and epicuticular wax significantly contributed to early-stage pathogen defence, while reactive oxygen species and rapid PCD activation triggered hypersensitive responses, enhancing wax deposition and active PCD responses are critical for Vitis sp. resistance to powdery mildew, offering valuable insights for breeding programmes.

Pseudomonas putida BP25 is a black pepper endophytic bacterium exhibiting promising antifungal activity against several economically important plant pathogens especially Phytophthora capsici, Magnaporthe oryzae, and Colletotrichum gloeosporioides. In the present study, we report the complete genome sequence of P. putida BP25, comprising a single circular chromosome of 5.79 Mb (Scaffold N50: 5777593 bp; Contig N50:114500 bp) with 5389 predicted genes and a G + C content of 62.92