Rice bakanae disease, caused by Fusarium species, has recently emerged as an important threat to non-Basmati rice production in Eastern and North-Eastern India. Due to the limited availability of efficient fungicides and the rise of fungicidal resistance, sustainable alternatives are urgently needed. In the present study, we aimed to identify and characterize effective Plant Growth-Promoting Rhizobacteria (PGPR) from the rhizosphere of medicinal plants to manage bakanae disease and enhance rice productivity. A total of 158 rhizobacterial strains were isolated and screened for in vitro antagonism against four Fusarium species (F. fujikuroi, F. verticillioides, F. proliferatum, and F. sacchari). Ten promising isolates were identified and evaluated for extracellular enzyme production and plant growth-promoting (PGP) traits. The strains were tested through seed bio-priming in two rice cultivars, Pooja (Highly Susceptible) and Chandan (Moderately resistant), under glasshouse conditions. Molecular characterization via 16S rRNA sequencing identified the elite strains as Bacillus, Priestia and Paenibacillus species. Among these, Priestia megaterium (CRM-37) exhibited the highest mycelial inhibition (up to 89.00
Fusarium oxysporum is one of the most important soil-borne pathogens affecting garlic production worldwide because of its wide host range and significant economic impact. This study aimed to characterize the population structure of garlic-associated Fusarium oxysporum isolates collected from major garlic-producing regions of Türkiye using pathogenicity, vegetative compatibility, β-tubulin-based phylogenetic analysis, and haplotype diversity. Thirty isolates obtained from garlic basal plates were evaluated morphologically and molecularly. Phylogenetic analysis based on the β-tubulin gene confirmed that all isolates belonged to the Fusarium oxysporum species complex (FOSC). Vegetative compatibility analysis classified the isolates into two vegetative compatibility groups (VCGs), with each isolate assigned to a single VCG. Cross-pathogenicity assays on garlic, onion, and leek revealed considerable variation in virulence among isolates, indicating differences in host adaptation within the population. Haplotype analysis identified four haplotypes with a haplotype diversity (Hd) of 0.4064, indicating moderate genetic diversity. The predominance of a single haplotype together with the occurrence of multiple haplotypes within the two VCGs suggests that vegetative compatibility and β-tubulin haplotypes represent complementary aspects of population structure rather than directly corresponding classifications. Overall, the results demonstrate that garlic-associated FOSC populations in Türkiye exhibit limited genetic differentiation despite considerable phenotypic variation in pathogenicity. This study provides new insights into the population biology of garlic-associated FOSC and establishes a basis for future epidemiological, phylogenetic, and disease management studies.
In the state of Pernambuco, Brazil, coffee has been grown in highland areas, whose climatic conditions differ from other typically producing regions. Despite the large number of small coffee producers and the production potential, there is no information on coffee leaf rust (CLR) epidemic and its management in this region. Thus, this study established the CLR progress curve in highland areas of Brazilian Northeast, and to evaluated some strategies to control the disease, including the use of fungicides and coffee resistant genotypes. In this study, the CLR epidemic showed a temporal progress that differed from the typical production regions in Brazil, starting between April and May, and achieving the maximum intensity between August and September. This progress coincided with the rainy period in the region. The effectiveness of the fungicides to control the disease was variable, and the most effective control was obtained with the application of flutriafol via soil in April, at the beginning of the rainy season. Some coffee genotypes (Tupi IAC 1669-20, Obatã IAC 1669-20, and Katipó) showed resistance to CLR, and should be preferentially cultivated in the highland areas. Our results provide valuable information on CLR in highland areas in Brazilian Northeast. This information will help coffee growers to establish disease management strategies, aiming at an effective control and, consequently, an increased yield in the region.
As an important ornamental tree species, Bauhinia blakeana is susceptible to leaf spot disease caused by Colletotrichum endophyticum. This study aimed to screen for biocontrol strains with high antagonistic activity against this pathogen. Through isolation and identification, Bacillus atrophaeus strain SF9 was found to exhibit significant inhibitory effects on C. endophyticum. To enhance its biocontrol efficacy, fermentation conditions were systematically optimized. Under the optimized parameters 2
Cryptostegia grandiflora (rubber vine) is an invasive weed in tropical and subtropical regions worldwide and is listed as a Weed of National Significance in Australia. The rust Maravalia cryptostegiae, deliberately introduced to Australia as a biocontrol agent, contributes to long-term suppression, but does not provide complete control, making herbicide intervention necessary in many land-use contexts. For integrated weed management (IWM) to be effective, chemical and biological controls must complement rather than conflict, yet herbicide-rust compatibility has rarely been quantified. We developed a 14-day laboratory workflow to assess compatibility by combining in vitro spore germination and detached-leaf infection assays with image-based analysis. Treatments included metsulfuron-methyl (MM), a recommended foliar herbicide for rubber vine, and a novel herbistatic analogue (COT-MM). Both the herbicide and the herbistatic analogue reduced spore germination and leaf infection relative to the blank, but neither differed from the surfactant, indicating strong adjuvant-mediated inhibition. No detectable difference between MM and COT-MM was demonstrated. This rapid workflow detected early antagonism between foliar herbicide formulations and M. cryptostegiae and identified the adjuvant as a major contributor. Integrating such assays into herbicide discovery and management planning will help ensure that chemical and biological tactics reinforce one another, supporting more sustainable IWM of invasive weeds.
Plant disease resistance is increasingly recognized as an emergent property of the plant holobiont, shaped not only by host genotype and pathogen virulence but also by the composition and function of associated microbial communities. The plant holobiont provides a framework for understanding how microbiome assembly across compartments, including the rhizosphere, phyllosphere, endosphere, and seeds, influences plant health and disease outcomes. Current evidence shows that disease-modulating microbiomes are structured by ecological filters such as host genotype, root exudation, environmental conditions, and transmission processes. These microbial communities contribute to disease suppression through direct pathogen inhibition, microbiome-modulated immunity and induced systemic resistance, recruitment of protective microbiota, and community-level suppression in disease-suppressive soils. Translational opportunities arising from this framework include microbiome-informed disease management, synthetic communities, microbiome engineering, endophyte deployment, microbiome transplantation, and microbiome-assisted breeding. Despite this promise, practical application remains constrained by context dependence, incomplete mechanistic resolution, and limited field validation. The holobiont perspective offers a more ecologically realistic framework for developing durable and sustainable crop protection strategies. Progress in this area will depend on integrating ecological theory, multi-omics approaches, and field-based validation to translate plant holobiont research into robust disease management applications.
Endofungal and endohyphal bacteria live inside fungal vegetative or reproductive structures, whereas mycelium-associated bacteria may include bacteria attached to or residing within fungal mycelia. These bacteria can protect fungal hosts from mycophagous organisms and influence fungal interactions with plants. In this study, mycelium-associated bacteria (MAB) were recovered from the mycelium of Pythium aphanidermatum, which causes damping-off disease in several vegetable crops, including cucumber, tomato, and cabbage. Four bacterial strains, designated as PyEB1, PyEB2, PyEB3, and PyEB4, were isolated from Py. aphanidermatum mycelium. Based on 16S ribosomal RNA gene sequences, these MAB isolates were assigned to Pseudomonas, with closest GenBank matches to P. yamanorum (PyEB1), P. brenneri (PyEB2), and P. gessardii (PyEB3 and PyEB4). The cell-free culture supernatant of Pseudomonas sp. PyEB1 induced wilting in tomato seedlings under in vitro conditions, while soil inoculation with the bacterium caused visible chlorosis and stunting. Gas chromatography-mass spectrometry analysis tentatively identified Advastab 405, by library matching, as the predominant component in the hexane extract of the culture supernatant of Pseudomonas sp. PyEB1. Live cultures of PyEB1 reduced recoverable metalaxyl in liquid medium by up to 79.7
Citrus quick decline (CQD) is an emerging disorder threatening citrus orchards in southern Iran. The disease causes rapid wilting, leaf desiccation, and death of trees within weeks, leading to significant yield losses. Despite extensive surveys, no known pathogen had been consistently associated with this syndrome. Using next-generation sequencing (NGS), a novel betacytorhabdovirus, tentatively named citrus quick decline-associated virus (CQDaV), was identified in citrus trees showing decline symptoms in Kerman Province. The viral genome displayed the canonical betacytorhabdovirus genome organization (3′-N-P-P3-M-G-L-5′). Phylogenetic analysis based on the complete L protein sequence placed the virus within the genus Betacytorhabdovirus, with Glycyrrhiza betacytorhabdovirus 1 as its closest recognized relative. The presence of CQDaV was confirmed by reverse transcription quantitative PCR in some symptomatic trees but was absent in healthy controls. This study reports the molecular characterization of a novel betacytorhabdovirus infecting citrus, which was found to be associated with symptomatic trees showing rapid decline in southern Iran.
Among the various pathogens that cause sugar beet root rot, Rhizoctonia solani is one of the most destructive species globally. This pathogen causes damping-off and root rot during field growth and storage, leading to crop yield losses; therefore, the development of environmentally friendly prevention and control strategies targeting this organism is urgently needed. This study aimed to evaluate, through laboratory and greenhouse experiments, the biological control potential of Bacillus subtilis against the sugar beet root rot pathogen R. solani, and to investigate their plant growth-promoting properties. Pathogenicity tests revealed that all tested fungal isolates were capable of infecting sugar beet plants and causing root rot symptoms. Among them, isolate KA 3 showed the highest percentage of damping-off and root rot severity. Therefore, the most aggressive isolate was selected for subsequent antagonistic and greenhouse experiments. This study employed the dual culture method for in vitro screening. The 15 Bacillus strains isolated from the sugar beet rhizosphere exhibited varying levels of antagonistic activity. Among them, B. subtilis strain K 2 had the strongest activity, with a mycelia inhibition rate of 62.51
Elsinoe perseae, the causal agent of avocado scab disease, is a high-priority biosecurity threat to the Australian avocado industry. Symptom-based diagnosis is unreliable, and morphological identification is hindered by the slow growth of Elsinoe species on artificial media and the absence of a sexual reproductive stage in the field and in axenic culture. Consequently, a rapid and reliable molecular diagnostic tool capable of detecting the pathogen directly from infected fruit or leaf tissue is essential. In this study, we developed a quantitative PCR (qPCR) assay targeting two genomic regions: the internal transcribed spacer 1 (ITS1) region of the rDNA and the RNA polymerase II subunit B (rpb2) gene. The assay can be applied in either singleplex or duplex formats. Both the ITS- and rpb2-targeted assays consistently detected E. perseae DNA from pure cultures. However, detection in infected avocado leaf and fruit tissues was primarily driven by the ITS assay, whereas the rpb2 assay exhibited reduced sensitivity, likely reflecting differences in copy number between multicopy rDNA regions and the single-copy rpb2 gene. No cross-reactivity was observed against other Elsinoe species or common fungal pathogens of avocado. High analytical sensitivity was achieved, with reliable detection of both targets at concentrations of 10³ copies/µL of synthetic gBlocks dsDNA and 0.1 ng/µL of genomic DNA, using a conservative threshold of Ct ≤ 30. Assay performance was unaffected by minor variations in qPCR reagents and instrument platforms. This assay provides a rapid, sensitive, and highly specific diagnostic tool for biosecurity applications, supporting accurate detection, surveillance, and early response to potential incursions of E. perseae.
Black rot disease, caused by the seed-borne bacterial pathogen Xanthomonas campestris pv. campestris (Xcc), reduces cabbage yield, featuring V-shaped chlorotic lesions along leaf margins. In December 2024, typical black rot symptoms were observed on cabbage plants in Churamonkathi Union, Jessore District, Bangladesh. Bacteria isolated from symptomatic leaf tissues on King’s medium B base agar were consistent with Xcc based on morphological and biochemical characteristics. Pathogenicity was confirmed by Koch’s postulates, with characteristic symptoms reproduced on healthy cabbage plants 7–14 days after inoculation (DAI). These pathogenic isolates were consolidated as Xcc by Xcc-specific primers (Xcc_53F/R). Subsequently, race determination using race-specific primers revealed that all pathogenic isolates belonged to race 1, as the primer pair Xcc_R2_89.2 F/R produced a 1523 bp amplicon. Partial 16S rRNA gene sequencing of one representative isolate and phylogenetic analysis confirmed its identity as Xcc. This study provides the morpho-molecular confirmation and race detection of Xcc race 1 causing black rot on cabbage in Bangladesh, where the pathogen was previously reported only from mustard seeds without detailed characterization. The findings will facilitate the development of effective disease management strategies for sustainable cabbage production in the country.
Peach powdery mildew caused by Podosphaera pannosa (Wallr.: Fr.) de Bary (syn. Sphaerotheca pannosa) is a major fungal disease in peach orchards of Iran. During the 2023–2024 growing seasons, a commercial orchard planted with the local cultivar ‘Zafarani’, with a history of severe powdery mildew infection, located in the Zayandeh Rood region, was selected to evaluate the integrated effects of green pruning and fungicide applications on disease management. Two fungicide mixtures were tested: pydiflumetofen + difenoconazole (Miravis Duo® SC, 20
Almond trunk diseases can cause a significant decline in orchard productivity and profitability through limb and tree death. Several pathogens have been implicated in the trunk disease complex in Australia, with Diplodia seriata reported as most prominent. These pathogens can infect through wounds, such as those created during pruning or other mechanical processes. Fungicide and biological products are registered for managing these diseases in California, but there is only one wound dressing product registered for trunk diseases in Australia. In three in vitro experiments, 21 treatments, including fungicides and biological controls, were evaluated for the inhibition of mycelial growth of five trunk disease pathogens: Colletotrichum acutatum, Collophora rubra, Diplodia seriata, Eutypa lata and Pleurostoma richardsiae. Most treatments reduced mycelial growth of most pathogens by 50–100
The leaf spot poses a growing threat to sorghum health. The screening isolate GL-2 was identified as Alternaria burnsii. Among the tested fungicides, fludioxonil exhibited the highest potency, with a median effective concentration (EC50) of 0.16 mg L− 1. Two combinations showed synergistic effects: pyraclostrobin: flusilazole at a ratio of 0.60:1 (synergy ratio, SR = 1.75) and fludioxonil: procymidone at 0.28:1 (SR = 1.58). The latter combination demonstrated the most effective disease suppression, achieving 83.61
We report the first identification and complete genome sequence of a watermelon silver mottle virus (WSMoV) isolate, designated WSMoV-MC, infecting bitter gourd (Momordica charantia L.) from Fujian Province, China. The tripartite genome, comprising large (L, 8,914 nt), medium (M, 4,872 nt), and small (S, 3,555 nt) RNA segments, encodes five typical tospoviral proteins. Sequence analysis revealed that WSMoV-MC shares the highest nucleotide identity (> 99
Hylocereus spp, commonly known as the pitaya, pitahaya or dragon fruit, has substantial nutritional and medicinal significance. From 2025 to 2026, pitaya plants in the orchard of Western Ghats (Coimbatore) exhibited symptoms of stem canker. Initially minor, circular, chlorotic, pitted spots that gradually developed into reddish-brown flecks were observed. Based on morphological characteristics and molecular sequence of the internal transcribed spacer (ITS) region, the pathogen was identified as Neoscytalidium dimidiatum. BLASTn analyses revealed 99–100
