The search for new sustainable approaches to crop disease management is fueled by growing ecological and health problems related to the overuse of chemical pesticides and the emergence of compound resistance. Biopesticides, defined as biological control agents derived from living organisms or their metabolites (microorganisms, plants, or natural compounds), offer a potential solution. These biological products can act through safe and targeted modes of action. The taxonomic and functional diversity of biopesticides is first examined in detail in this review, followed by an in-depth study of their molecular mechanisms for pathogen control. To better understand how biopesticides can be improved for enhanced efficacy in the field, we explore recent advances in omics technologies, genetic enhancement, and formulation strategies. The review examines how biopesticides can be integrated into real-world agroecosystems, with a focus on their use in organic farming, integrated disease management, and their interactions with other biological inputs. To improve application uniformity and support the systematic and large-scale integration of biopesticides into agricultural production systems, this review identifies the main existing constraints, regulatory gaps, and future research priorities.
{"title":"Biopesticides for a sustainable agriculture: Prospects and challenges in disease management","authors":"Rachid Lahlali , Mohamed Kouighat , Mohammed Khadiri , Abdellatif Boutagayout , Göksel Özer , Salah-Eddine Laasli , Abdelaaziz Farhaoui","doi":"10.1016/j.pmpp.2025.103096","DOIUrl":"10.1016/j.pmpp.2025.103096","url":null,"abstract":"<div><div>The search for new sustainable approaches to crop disease management is fueled by growing ecological and health problems related to the overuse of chemical pesticides and the emergence of compound resistance. Biopesticides, defined as biological control agents derived from living organisms or their metabolites (microorganisms, plants, or natural compounds), offer a potential solution. These biological products can act through safe and targeted modes of action. The taxonomic and functional diversity of biopesticides is first examined in detail in this review, followed by an in-depth study of their molecular mechanisms for pathogen control. To better understand how biopesticides can be improved for enhanced efficacy in the field, we explore recent advances in omics technologies, genetic enhancement, and formulation strategies. The review examines how biopesticides can be integrated into real-world agroecosystems, with a focus on their use in organic farming, integrated disease management, and their interactions with other biological inputs. To improve application uniformity and support the systematic and large-scale integration of biopesticides into agricultural production systems, this review identifies the main existing constraints, regulatory gaps, and future research priorities.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103096"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145883430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-24DOI: 10.1016/j.pmpp.2025.103095
Shazma Gulzar , Yaxing Xu , Chunxia Huang , Xiaoquan Li , Weiyou Zou , Yue Meng , Rahat Sharif , Zuxiang Su , Chunxiang Xu
Fusarium oxysporum f. sp. cubense, the causal agent of Fusarium wilt, poses a significant threat to banana production. The plant microbiota plays a vital role in disease resistance. However, the relationship between the susceptible and resistant mutant associated microbiota is limited. We investigated taxonomic and functional differences in bacterial and fungal communities between a banana Fusarium wilt (Foc 1) susceptible cultivar ‘Guangfen 1’ (GF, ABB genome) and its resistant mutant (GFR). We used high-throughput Illumina sequencing of 16S rRNA genes and ITS_V1 regions, by sampling the rhizosphere soil, pseudostem and roots. Bacterial and fungal communities were more diverse in rhizosphere soil than plant organs. The rhizosphere of GFR exhibited lower bacterial and fungal alpha diversity (Shannon index) than GF. The dominant bacteria identified in rhizosphere of GFR included members of Acidobacteriota, Proteobacteria, Actinobacteriota and Chloroflexi. The dominant fungi in GFR were Mortierellomycota and Basidiomycota, while GF was enriched in Ascomycota. LEfSe identified 15 distinct bacterial biomarker taxa in rhizosphere of GF and 28 in GFR. For fungi, Agaricales was the only biomarker taxon found in the rhizosphere of GFR. KEGG pathways further revealed that xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and amino acid metabolism were prominent in GFR. In a dual culture assay, strains 1–61 and 4–28 showed significant antagonistic activity against Foc 1 and 4, respectively. Together, these findings demonstrate that Fusarium wilt resistance in banana is associated with differences in microbial communities and functions that may contribute to enhanced disease suppression.
{"title":"Taxonomical and functional microbial community profiling in Fusarium wilt-resistant and susceptible banana plants","authors":"Shazma Gulzar , Yaxing Xu , Chunxia Huang , Xiaoquan Li , Weiyou Zou , Yue Meng , Rahat Sharif , Zuxiang Su , Chunxiang Xu","doi":"10.1016/j.pmpp.2025.103095","DOIUrl":"10.1016/j.pmpp.2025.103095","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em> f. sp. <em>cubense</em>, the causal agent of Fusarium wilt, poses a significant threat to banana production. The plant microbiota plays a vital role in disease resistance. However, the relationship between the susceptible and resistant mutant associated microbiota is limited. We investigated taxonomic and functional differences in bacterial and fungal communities between a banana Fusarium wilt (<em>Foc</em> 1) susceptible cultivar ‘Guangfen 1’ (GF, ABB genome) and its resistant mutant (GFR). We used high-throughput Illumina sequencing of 16S rRNA genes and ITS_V1 regions, by sampling the rhizosphere soil, pseudostem and roots. Bacterial and fungal communities were more diverse in rhizosphere soil than plant organs. The rhizosphere of GFR exhibited lower bacterial and fungal alpha diversity (Shannon index) than GF. The dominant bacteria identified in rhizosphere of GFR included members of Acidobacteriota, Proteobacteria, Actinobacteriota and Chloroflexi. The dominant fungi in GFR were <em>Mortierellomycota</em> and <em>Basidiomycota</em>, while GF was enriched in <em>Ascomycota</em>. LEfSe identified 15 distinct bacterial biomarker taxa in rhizosphere of GF and 28 in GFR. For fungi, Agaricales was the only biomarker taxon found in the rhizosphere of GFR. KEGG pathways further revealed that xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and amino acid metabolism were prominent in GFR. In a dual culture assay, strains 1–61 and 4–28 showed significant antagonistic activity against <em>Foc</em> 1 and 4, respectively. Together, these findings demonstrate that Fusarium wilt resistance in banana is associated with differences in microbial communities and functions that may contribute to enhanced disease suppression.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103095"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-24DOI: 10.1016/j.pmpp.2025.103098
Furkan Ulaş , Rachid Lahlali , Salah-Eddine Laasli , Muhammad Aasim , Abdelfattah Dababat , Muhammad Sameeullah , Mustafa İmren
Abiotic and biotic stress factors pose a significant threat to plant productivity and global food security. This review uses bibliometric analysis and literature synthesis to comprehensively examine the role of artificial intelligence (AI) and machine learning (ML) techniques in plant stress management. A total of 5369 publications retrieved from the Web of Science database between 2010 and 2024 were analysed using VOSviewer to evaluate publication trends, countries, institutions, and keywords. China, the US, and India were identified as the leading countries, with deep learning, convolutional neural networks, and image-based diagnostic methods emerging as key areas. The second phase revealed that DL architectures such as YOLO, EfficientNet, and Transformer, as well as methods like remote sensing and hyperspectral imaging, can accurately detect abiotic (drought, salinity, water, and heavy metals) and biotic (fungal, bacterial, and viral) stress. Machine learning (ML) algorithms such as support vector machine (SVM), random forest (RF), and artificial neural network (ANN) have also been found to be effective in stress prediction. However, challenges such as data imbalance, model interpretability, and high computational requirements persist. To address these issues, open-access datasets, low-cost and transparent models, multimodal sensing systems, and ethical AI approaches are recommended. This review contributes to the field by highlighting strategic and technical gaps in the development of scalable and sustainable AI-supported plant stress management systems.
非生物和生物胁迫因素对植物生产力和全球粮食安全构成重大威胁。本文采用文献计量学分析和文献综合的方法，全面考察了人工智能（AI）和机器学习（ML）技术在植物逆境管理中的作用。利用VOSviewer对2010年至2024年间从Web of Science数据库中检索到的5369篇出版物进行分析，评估出版趋势、国家、机构和关键词。中国、美国和印度被确定为领先国家，深度学习、卷积神经网络和基于图像的诊断方法成为关键领域。第二阶段表明，像YOLO、EfficientNet和Transformer这样的DL架构，以及像遥感和高光谱成像这样的方法，可以准确地检测非生物（干旱、盐度、水和重金属）和生物（真菌、细菌和病毒）的压力。机器学习（ML）算法，如支持向量机（SVM）、随机森林（RF）和人工神经网络（ANN）也被发现在应力预测中是有效的。然而，诸如数据不平衡、模型可解释性和高计算需求等挑战仍然存在。为了解决这些问题，建议采用开放获取数据集、低成本和透明模型、多模态传感系统和合乎道德的人工智能方法。这篇综述通过强调可扩展和可持续的人工智能支持的植物胁迫管理系统开发中的战略和技术差距，为该领域做出了贡献。
{"title":"Artificial intelligence applications in abiotic and biotic plant stress management: A comprehensive bibliometric and literature review","authors":"Furkan Ulaş , Rachid Lahlali , Salah-Eddine Laasli , Muhammad Aasim , Abdelfattah Dababat , Muhammad Sameeullah , Mustafa İmren","doi":"10.1016/j.pmpp.2025.103098","DOIUrl":"10.1016/j.pmpp.2025.103098","url":null,"abstract":"<div><div>Abiotic and biotic stress factors pose a significant threat to plant productivity and global food security. This review uses bibliometric analysis and literature synthesis to comprehensively examine the role of artificial intelligence (AI) and machine learning (ML) techniques in plant stress management. A total of 5369 publications retrieved from the Web of Science database between 2010 and 2024 were analysed using VOSviewer to evaluate publication trends, countries, institutions, and keywords. China, the US, and India were identified as the leading countries, with deep learning, convolutional neural networks, and image-based diagnostic methods emerging as key areas. The second phase revealed that DL architectures such as YOLO, EfficientNet, and Transformer, as well as methods like remote sensing and hyperspectral imaging, can accurately detect abiotic (drought, salinity, water, and heavy metals) and biotic (fungal, bacterial, and viral) stress. Machine learning (ML) algorithms such as support vector machine (SVM), random forest (RF), and artificial neural network (ANN) have also been found to be effective in stress prediction. However, challenges such as data imbalance, model interpretability, and high computational requirements persist. To address these issues, open-access datasets, low-cost and transparent models, multimodal sensing systems, and ethical AI approaches are recommended. This review contributes to the field by highlighting strategic and technical gaps in the development of scalable and sustainable AI-supported plant stress management systems.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103098"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-24DOI: 10.1016/j.pmpp.2025.103099
Yuerong Zhang , Kewei Hua , Benni Ma , Chen Yang, Panpan Zhu, Bingqian Hu, Humana Azhar, Qingru Geng, Fengqin Song, Jun Tian, Kunlong Yang
Aspergillus flavus is a predominant fungal contaminant, producing aflatoxin B1 (AFB1), one of the most potent mycotoxins posing serious risks to global food safety. In this study, we evaluated the antifungal efficacy of Bacillus velezensis ATC-AL and its active antifungal substances (AAS) against A. flavus and other mycotoxin-producing fungi. The AAS treatment displayed broad-spectrum antifungal activity, completely suppressing AFB1 synthesis at a minimum inhibitory concentration of 8 μL/mL. It also significantly reduced deoxynivalenol (DON) accumulation by Fusarium graminearum, indicating multi-target antitoxin potential. Mechanistic analyses revealed that AAS disrupts fungal membrane integrity and induces oxidative stress, as evidenced by elevated reactive oxygen species (ROS) levels, lipid peroxidation, and structural damage to the cell membrane and cell wall in A. flavus. Metabolomic profiling further revealed perturbations in the TCA cycle, glutathione metabolism, and nucleic acid biosynthesis, consistent with mitochondrial dysfunction and impaired energy metabolism. Correspondingly, AAS treatment caused a collapse in mitochondrial membrane potential and decreased ATP levels, suggesting apoptosis-like cell death. In grain kernel assays, AAS significantly inhibited fungal colonization and eliminated mycotoxin production, effectively protecting grains from infection by A. flavus and F. graminearum. Collectively, these findings demonstrate that B.velezensis ATC-AL functions as a promising biocontrol agent acting through multiple antifungal and anti-mycotoxin pathways, offering a sustainable strategy for mitigating fungal contamination and mycotoxin risk in grain storage systems.
{"title":"Bacillus velezensis ATC-AL suppresses mycotoxin-producing fungi by disrupting membrane integrity and inducing mitochondrial dysfunction","authors":"Yuerong Zhang , Kewei Hua , Benni Ma , Chen Yang, Panpan Zhu, Bingqian Hu, Humana Azhar, Qingru Geng, Fengqin Song, Jun Tian, Kunlong Yang","doi":"10.1016/j.pmpp.2025.103099","DOIUrl":"10.1016/j.pmpp.2025.103099","url":null,"abstract":"<div><div><em>Aspergillus flavus</em> is a predominant fungal contaminant, producing aflatoxin B1 (AFB<sub>1</sub>), one of the most potent mycotoxins posing serious risks to global food safety. In this study, we evaluated the antifungal efficacy of <em>Bacillus velezensis</em> ATC-AL and its active antifungal substances (AAS) against <em>A. flavus</em> and other mycotoxin-producing fungi. The AAS treatment displayed broad-spectrum antifungal activity, completely suppressing AFB<sub>1</sub> synthesis at a minimum inhibitory concentration of 8 μL/mL. It also significantly reduced deoxynivalenol (DON) accumulation by <em>Fusarium graminearum</em>, indicating multi-target antitoxin potential. Mechanistic analyses revealed that AAS disrupts fungal membrane integrity and induces oxidative stress, as evidenced by elevated reactive oxygen species (ROS) levels, lipid peroxidation, and structural damage to the cell membrane and cell wall in <em>A. flavus</em>. Metabolomic profiling further revealed perturbations in the TCA cycle, glutathione metabolism, and nucleic acid biosynthesis, consistent with mitochondrial dysfunction and impaired energy metabolism. Correspondingly, AAS treatment caused a collapse in mitochondrial membrane potential and decreased ATP levels, suggesting apoptosis-like cell death. In grain kernel assays, AAS significantly inhibited fungal colonization and eliminated mycotoxin production, effectively protecting grains from infection by <em>A. flavus</em> and <em>F. graminearum</em>. Collectively, these findings demonstrate that <em>B.velezensis</em> ATC-AL functions as a promising biocontrol agent acting through multiple antifungal and anti-mycotoxin pathways, offering a sustainable strategy for mitigating fungal contamination and mycotoxin risk in grain storage systems.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103099"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cotton (Gossypium sp.) is world's leading natural fiber crop and contribute to textile and oil industries, generating an estimated worldwide annual economic impact of USD 600 billion. Global cotton production is projected to rise from 126.5 million bales (2022-23) to approximately 141 million bales (2031-32) at annual growth rate of 1.6 %. Despite its economic importance, yield is affected by climate change, pest outbreaks and soil degradation. Traditional breeding and transgenic approaches have improved cotton yield and insect tolerance but remain slow and limited by the species complex allotetraploid genome, extensive gene redundancy, low transformation efficiency. Genome editing tools, especially CRISPR-Cas9 offer targeted modification in yield and stress response related genes. This can help to increase improvement in yield, drought, salinity stress and pest resistance while minimizing off target effects and regulatory concerns associated with conventional genetically modified (GM) crops. This review discuss the recent advancements of CRISPR-Cas9 mediated genome editing in cotton, showing how specific gene editing (GhPDS, GhCLA1, GhAOC2, Gh14-3-3d) have revealed functional links between stress response pathways and plant defense signaling. It also include mechanistic insights into salicylic acid (SA) - jasmonic acid (JA) - ethylene (ET) cross talk, ROS regulation and secondary metabolite biosynthesis, and outline emerging strategies to overcome transformation and off-target limitations. Future research should integrate multi-omics, prime editing and pathogen-effector interaction studies to increase the molecular breeding of resilient cotton cultivars.
{"title":"Molecular insights into cotton defense and stress regulation: CRISPR-Cas9 mediated editing of key genes in biotic and abiotic stress pathways","authors":"Suraj Prakash , Radha , Shubham Punia , Manoj Kumar , Baohong Zhang , Sangram Dhumal , Marisennayya Senapathy , Sunil Kumar , Sunil Puri","doi":"10.1016/j.pmpp.2025.103097","DOIUrl":"10.1016/j.pmpp.2025.103097","url":null,"abstract":"<div><div>Cotton (<em>Gossypium sp.</em>) is world's leading natural fiber crop and contribute to textile and oil industries, generating an estimated worldwide annual economic impact of USD 600 billion. Global cotton production is projected to rise from 126.5 million bales (2022-23) to approximately 141 million bales (2031-32) at annual growth rate of 1.6 %. Despite its economic importance, yield is affected by climate change, pest outbreaks and soil degradation. Traditional breeding and transgenic approaches have improved cotton yield and insect tolerance but remain slow and limited by the species complex allotetraploid genome, extensive gene redundancy, low transformation efficiency. Genome editing tools, especially CRISPR-Cas9 offer targeted modification in yield and stress response related genes. This can help to increase improvement in yield, drought, salinity stress and pest resistance while minimizing off target effects and regulatory concerns associated with conventional genetically modified (GM) crops. This review discuss the recent advancements of CRISPR-Cas9 mediated genome editing in cotton, showing how specific gene editing (<em>GhPDS</em>, <em>GhCLA1</em>, <em>GhAOC2</em>, <em>Gh14-3-3d</em>) have revealed functional links between stress response pathways and plant defense signaling. It also include mechanistic insights into salicylic acid (SA) - jasmonic acid (JA) - ethylene (ET) cross talk, ROS regulation and secondary metabolite biosynthesis, and outline emerging strategies to overcome transformation and off-target limitations. Future research should integrate multi-omics, prime editing and pathogen-effector interaction studies to increase the molecular breeding of resilient cotton cultivars.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103097"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145924610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-24DOI: 10.1016/j.pmpp.2025.103094
Padma Priya D , Sharanabasav Huded , I.K. Kalappanavar , J. Harish , Shripad Kulkarni , Eshwar , P.S. Tippannavar
Groundnut (Arachis hypogaea L.) is a major oilseed crop cultivated worldwide; however, its seeds are highly susceptible to fungal infections, leading to deterioration in both quality and commercial value. The present study evaluated the fungal diversity associated with groundnut seeds collected from farmers’ fields and local Agricultural Produce Market Committee (APMC) markets in four northern districts of Karnataka, India, namely Bagalkot, Dharwad, Gadag, and Haveri. Across all samples, seven fungal genera were identified: Aspergillus niger, A. flavus, Fusarium oxysporum, Macrophomina phaseolina, Penicillium citrinum, Rhizopus stolonifer, and Ceratobasidium spp. The highest fungal diversity was recorded in Gadag (n = 7), followed by Haveri (n = 6). Macrophomina phaseolina and R. stolonifer were predominant in Bagalkot, Haveri, and Gadag districts. Among sterilized market samples, Dharwad recorded the highest cumulative percent mycoflora seed infection (60.83 %), whereas in unsterilized market and farmer samples, Haveri exhibited the highest total fungal contamination (TFC) of 73.42 % and 66.91 %, respectively. M. phaseolina was the most frequently isolated species from sterilized market (68.09 %) and farmer samples (70.99 %). In unsterilized farmer samples, R. stolonifer (52.08 %) was predominant, while in unsterilized market samples, M. phaseolina was highly dominant (94.25 %). Molecular characterization of the predominant pathogens was carried out using multiple DNA barcoding regions, including ITS and RPB2 genes for ascomycetous pathogens (M. phaseolina, A. niger, R. stolonifer, A. flavus, F. oxysporum, and P. citrinum), while ITS and β-tubulin genes were used for the basidiomycetous pathogen (Ceratobasidium sp.). Subsequent phylogenetic analysis revealed close genetic relationships with isolates from similar agro-climatic regions, indicating minimal genetic variability among strains. The results emphasize the need for improved hygiene and storage practices by farmers and APMC markets to minimize fungal incidence and safeguard groundnut seed health.
{"title":"Comparative analysis of prevalence and morpho-molecular diversity of major seed-borne fungal contamination in groundnut seeds from field and market sources in northern Karnataka, India","authors":"Padma Priya D , Sharanabasav Huded , I.K. Kalappanavar , J. Harish , Shripad Kulkarni , Eshwar , P.S. Tippannavar","doi":"10.1016/j.pmpp.2025.103094","DOIUrl":"10.1016/j.pmpp.2025.103094","url":null,"abstract":"<div><div>Groundnut (<em>Arachis hypogaea</em> L.) is a major oilseed crop cultivated worldwide; however, its seeds are highly susceptible to fungal infections, leading to deterioration in both quality and commercial value. The present study evaluated the fungal diversity associated with groundnut seeds collected from farmers’ fields and local Agricultural Produce Market Committee (APMC) markets in four northern districts of Karnataka, India, namely Bagalkot, Dharwad, Gadag, and Haveri. Across all samples, seven fungal genera were identified: <em>Aspergillus niger</em>, <em>A. flavus</em>, <em>Fusarium oxysporum</em>, <em>Macrophomina phaseolina</em>, <em>Penicillium citrinum</em>, <em>Rhizopus stolonifer</em>, and <em>Ceratobasidium</em> spp. The highest fungal diversity was recorded in Gadag (n = 7), followed by Haveri (n = 6). <em>Macrophomina phaseolina</em> and <em>R. stolonifer</em> were predominant in Bagalkot, Haveri, and Gadag districts. Among sterilized market samples, Dharwad recorded the highest cumulative percent mycoflora seed infection (60.83 %), whereas in unsterilized market and farmer samples, Haveri exhibited the highest total fungal contamination (TFC) of 73.42 % and 66.91 %, respectively. <em>M. phaseolina</em> was the most frequently isolated species from sterilized market (68.09 %) and farmer samples (70.99 %). In unsterilized farmer samples, <em>R. stolonifer</em> (52.08 %) was predominant, while in unsterilized market samples, <em>M. phaseolina</em> was highly dominant (94.25 %). Molecular characterization of the predominant pathogens was carried out using multiple DNA barcoding regions, including ITS and <em>RPB2</em> genes for ascomycetous pathogens (<em>M. phaseolina, A. niger, R. stolonifer, A. flavus, F. oxysporum,</em> and <em>P. citrinum</em>), while ITS and <em>β-tubulin</em> genes were used for the basidiomycetous pathogen (<em>Ceratobasidium</em> sp.). Subsequent phylogenetic analysis revealed close genetic relationships with isolates from similar agro-climatic regions, indicating minimal genetic variability among strains. The results emphasize the need for improved hygiene and storage practices by farmers and APMC markets to minimize fungal incidence and safeguard groundnut seed health.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103094"},"PeriodicalIF":3.3,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Climate change has resulted in the emergence of several plant pathogens, which have caused a huge yield loss to crops globally. Among them, a soil-borne necrotrophic fungus Macrophomina phaseolina (Tassi) Goid is an economically important pathogen because of its wide host range and geographic distribution. The pathogen causes dry root rot of chickpeas, a serious disease threatening chickpea production in Ethiopia. Isolates of M. phaseolina were obtained from symptomatic chickpea roots from ten districts across three zones in Central Ethiopia. The isolates were examined for variability in their morpho-genetic and pathogenic characteristics. A significant variation in colony growth and sclerotia traits was observed among the isolates. At 72 h after incubation, 21 isolates were rated as fast-growing, six as medium-growing, and two isolates as slow-growing. The isolates had a colony growth rate ranging from 9.4 to 17.1 mm day−1. The isolates had four colony pigmentations: pale-grey, grey, black, and greenish-grey. Four isolates were classified as having small-sized sclerotia, whereas five were medium, and 20 isolates were large-sized. The sclerotia of the isolates exhibited four morpho-types: round, oblong, ovoid, and irregular. Principal component analysis (PCA) revealed that morphological characters accounted for the greatest variation among the isolates. The pathogenicity of the isolates varied from strongly to highly virulent on chickpeas. Using morphological and pathogenicity traits, principal coordinate analysis clustered the isolates into four groups, whereas hierarchical cluster analysis into ten groups. The isolates revealed 99.7–100 % ITS and LSU rDNA sequence identity to several reference isolates deposited in GenBank. This study documented basic information for designing management strategies for this emerging pathogen in Ethiopia.
{"title":"Morpho-genetic and pathogenic characterization of Macrophomina phaseolina (Tassi) Goid isolates causing dry root rot of chickpea (Cicer arietinum L.) in Ethiopia","authors":"Solomon Tamiru , Berhanu Bekele , Thangavel Selvaraj , Thelma Caine , Negussie Efa Gurmessa , Alan Buddie","doi":"10.1016/j.pmpp.2025.103090","DOIUrl":"10.1016/j.pmpp.2025.103090","url":null,"abstract":"<div><div>Climate change has resulted in the emergence of several plant pathogens, which have caused a huge yield loss to crops globally. Among them, a soil-borne necrotrophic fungus <em>Macrophomina phaseolina</em> (Tassi) Goid is an economically important pathogen because of its wide host range and geographic distribution. The pathogen causes dry root rot of chickpeas, a serious disease threatening chickpea production in Ethiopia. Isolates of <em>M. phaseolina</em> were obtained from symptomatic chickpea roots from ten districts across three zones in Central Ethiopia. The isolates were examined for variability in their morpho-genetic and pathogenic characteristics. A significant variation in colony growth and sclerotia traits was observed among the isolates. At 72 h after incubation, 21 isolates were rated as fast-growing, six as medium-growing, and two isolates as slow-growing. The isolates had a colony growth rate ranging from 9.4 to 17.1 mm day<sup>−1</sup>. The isolates had four colony pigmentations: pale-grey, grey, black, and greenish-grey. Four isolates were classified as having small-sized sclerotia, whereas five were medium, and 20 isolates were large-sized. The sclerotia of the isolates exhibited four morpho-types: round, oblong, ovoid, and irregular. Principal component analysis (PCA) revealed that morphological characters accounted for the greatest variation among the isolates. The pathogenicity of the isolates varied from strongly to highly virulent on chickpeas. Using morphological and pathogenicity traits, principal coordinate analysis clustered the isolates into four groups, whereas hierarchical cluster analysis into ten groups. The isolates revealed 99.7–100 % ITS and LSU rDNA sequence identity to several reference isolates deposited in GenBank. This study documented basic information for designing management strategies for this emerging pathogen in Ethiopia.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103090"},"PeriodicalIF":3.3,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fusarium oxysporum is a well-known soil-borne pathogen that causes severe vascular wilting in many important crops worldwide. F. oxysporum f. sp. lycopersici (Fol) specifically affects tomatoes, leading to significant economic losses. Therefore, it is crucial to understand the molecular mechanisms underlying the pathogenesis of this pathogen. Tomato and Fol have been found to be engaged in an evolutionary arms race. Three physiological races, (1, 2 and 3) of Fol are identified based on their specific pathogenicity to different tomato cultivars. Fol employs several strategies to perceive its host and cause infection, like evading PTI by secreting proteases and also with the help of point mutations in the AVR gene. Fol's pathogenesis mechanism also involves activation of several transcription factors, secretion of toxic metabolites (e.g., fusaric acid), cell wall-degrading enzymes (e.g., polygalacturonase), and small RNAs like Fol-milR1 that impair the host immune response. In counter, the tomato plants have evolved effective defense mechanisms against the Fol attack. While no PAMP/PRR pair has been identified in tomato-Fol interactions till date, effector-triggered immunity is mediated by the recognition of the AVR effector proteins by the resistance proteins of the I locus. Moreover, as part of their defense mechanism, tomato plants secrete defense molecules like α-tomatine and chitinases to counter Fol attack, along with phytohormones like salicylic acid, which regulates susceptibility and also regulates defense genes during Fol attack by certain endogenous miRNA that targets R genes at the level of transcript and provides innate immunity.
尖孢镰刀菌（Fusarium oxysporum）是一种众所周知的土传病原体，在世界上许多重要作物中引起严重的维管萎蔫。F. oxysporum F. sp. lycopersici （Fol）特别影响番茄，导致重大的经济损失。因此，了解这种病原体发病机制的分子机制是至关重要的。人们发现番茄和番茄正在进行一场进化军备竞赛。根据对不同番茄品种的致病性，鉴定了Fol生理小种（1、2、3）。foll采用了几种策略来感知宿主并引起感染，比如通过分泌蛋白酶和借助AVR基因的点突变来逃避PTI。foll的发病机制还涉及多种转录因子的激活、有毒代谢物（如fusaric酸）、细胞壁降解酶（如聚半乳糖醛酸酶）的分泌以及损害宿主免疫应答的foll - milr1等小rna。相反，番茄植物已经进化出有效的防御机制来抵御福尔的攻击。虽然到目前为止还没有发现PAMP/PRR对在番茄- fol相互作用中被发现，但效应触发免疫是由I位点的抗性蛋白对AVR效应蛋白的识别介导的。此外，作为番茄防御机制的一部分，番茄植株分泌α-番茄素、几丁质酶等防御分子，以及水杨酸等植物激素，通过内源性miRNA在转录水平上靶向R基因，在foll攻击时调节易感性，也调节防御基因，提供先天免疫。
{"title":"Genomic insights into tomato-Fusarium relationship: Plant-pathogen interactions and virulence mechanisms","authors":"Yashoda Nandan Tripathi , Richa Raghuwanshi , Ram Sanmukh Upadhyay","doi":"10.1016/j.pmpp.2025.103093","DOIUrl":"10.1016/j.pmpp.2025.103093","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em> is a well-known soil-borne pathogen that causes severe vascular wilting in many important crops worldwide. <em>F. oxysporum</em> f. sp. <em>lycopersici</em> (Fol) specifically affects tomatoes, leading to significant economic losses. Therefore, it is crucial to understand the molecular mechanisms underlying the pathogenesis of this pathogen. Tomato and Fol have been found to be engaged in an evolutionary arms race. Three physiological races, (1, 2 and 3) of Fol are identified based on their specific pathogenicity to different tomato cultivars. Fol employs several strategies to perceive its host and cause infection, like evading PTI by secreting proteases and also with the help of point mutations in the AVR gene. Fol's pathogenesis mechanism also involves activation of several transcription factors, secretion of toxic metabolites (e.g., fusaric acid), cell wall-degrading enzymes (e.g., polygalacturonase), and small RNAs like Fol-milR1 that impair the host immune response. In counter, the tomato plants have evolved effective defense mechanisms against the Fol attack. While no PAMP/PRR pair has been identified in tomato-Fol interactions till date, effector-triggered immunity is mediated by the recognition of the AVR effector proteins by the resistance proteins of the I locus. Moreover, as part of their defense mechanism, tomato plants secrete defense molecules like α-tomatine and chitinases to counter Fol attack, along with phytohormones like salicylic acid, which regulates susceptibility and also regulates defense genes during Fol attack by certain endogenous miRNA that targets <em>R</em> genes at the level of transcript and provides innate immunity.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103093"},"PeriodicalIF":3.3,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.pmpp.2025.103092
Reza Khakvar , Girish Pulinkala , Maya Baghdy Sar , Jan Komorowski
Cryptic infections in crops—especially fresh-consumed vegetables—pose a significant threat to food safety, as low-abundance pathogens often escape conventional diagnostics. Whole-genome shotgun metagenomic sequencing (WGS) offers high-resolution detection but generates complex datasets that challenge standard bioinformatics pipelines. This study evaluates a rule-based machine learning (RBML) approach using k-mer profiles from tomato WGS metagenomic datasets. Forty-two tomato samples with varying symptoms were collected and sequenced. Infection status was determined using three independent computational tools (MetaPhlAn, Kraken2/Bracken, and CLC Genomics) and validated by PCR assays targeting known pathogens; 29 of 31 bioinformatically-positive samples were PCR-confirmed, while all 11 non-infected samples were PCR-negative. K-mer profiles (k = 10 bp) were generated using KMC3, filtered to exclude sequences with ≤15 % relative abundance variation between infected and non-infected samples, and processed through Monte Carlo Feature Selection (MCFS) and Boruta algorithms. The union of top-ranked features yielded 30 biologically validated k-mers. Biological validation included BLASTn mapping of selected k-mers to reference pathogen and endophyte. Five biologically interpretable IF-THEN rules were derived using R.ROSETTA, C5.0 and Random Forest that achieved an overall accuracy of 89 %, a precision of 0.80, and an F1-score of 0.68 under leave-one-out cross-validation. These rules capture microbial abundance shifts rather than absolute pathogen presence, offering interpretable diagnostics for precision agriculture. While limited by sample size, this proof-of-concept demonstrates RBML's potential to detect subtle infection signatures from WGS data with biological transparency and future work should validate its robustness across larger and more diverse datasets.
{"title":"A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data","authors":"Reza Khakvar , Girish Pulinkala , Maya Baghdy Sar , Jan Komorowski","doi":"10.1016/j.pmpp.2025.103092","DOIUrl":"10.1016/j.pmpp.2025.103092","url":null,"abstract":"<div><div>Cryptic infections in crops—especially fresh-consumed vegetables—pose a significant threat to food safety, as low-abundance pathogens often escape conventional diagnostics. Whole-genome shotgun metagenomic sequencing (WGS) offers high-resolution detection but generates complex datasets that challenge standard bioinformatics pipelines. This study evaluates a rule-based machine learning (RBML) approach using k-mer profiles from tomato WGS metagenomic datasets. Forty-two tomato samples with varying symptoms were collected and sequenced. Infection status was determined using three independent computational tools (MetaPhlAn, Kraken2/Bracken, and CLC Genomics) and validated by PCR assays targeting known pathogens; 29 of 31 bioinformatically-positive samples were PCR-confirmed, while all 11 non-infected samples were PCR-negative. K-mer profiles (k = 10 bp) were generated using KMC3, filtered to exclude sequences with ≤15 % relative abundance variation between infected and non-infected samples, and processed through Monte Carlo Feature Selection (MCFS) and Boruta algorithms. The union of top-ranked features yielded 30 biologically validated k-mers. Biological validation included BLASTn mapping of selected k-mers to reference pathogen and endophyte. Five biologically interpretable IF-THEN rules were derived using R.ROSETTA, C5.0 and Random Forest that achieved an overall accuracy of 89 %, a precision of 0.80, and an F1-score of 0.68 under leave-one-out cross-validation. These rules capture microbial abundance shifts rather than absolute pathogen presence, offering interpretable diagnostics for precision agriculture. While limited by sample size, this proof-of-concept demonstrates RBML's potential to detect subtle infection signatures from WGS data with biological transparency and future work should validate its robustness across larger and more diverse datasets.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103092"},"PeriodicalIF":3.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145796875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.pmpp.2025.103091
Sameer Konda, Vaikuntavasan Paranidharan
“Huanglongbing”(HLB), or citrus greening, is one of the most destructive citrus diseases globally, with particularly severe effects on mandarin. The disease is associated with the phloem-limited bacterium ‘Candidatus Liberibacter asiaticus’, which reduces fruit yield, juice quality, and tree longevity, causing major economic losses in mandarin-producing regions of Asia. Transmission occurs predominantly by Asian citrus psyllid (Diaphorina citri), while grafting also provides an efficient pathway for orchard-level spread. Experimental transmission through dodder and occasional seed detection have been reported, though their epidemiological relevance is limited or uncertain. Once established, ‘Ca. L. asiaticus’ disrupts phloem transport, leading to characteristic symptoms including blotchy leaf mottle, lopsided fruit with aborted seeds, canopy thinning and progressive decline. Yield reductions of 40–60 % have been documented in mandarins in India, Nepal, and Southeast Asia, underscoring their high susceptibility compared with sweet orange and grapefruit. This review synthesizes current evidence on the epidemiology, symptom expression and transmission biology of HLB with a dedicated focus on mandarins, and outlines integrated management strategies such as the use of certified nursery stock, suppression of psyllid vectors, removal of infected trees, and orchard sanitation that are essential to sustaining mandarin cultivation in HLB-endemic regions.
{"title":"Characterization and transmission of “huanglongbing” (‘Candidatus Liberibacter asiaticus’) with emphasis on mandarin orange (Citrus reticulata)","authors":"Sameer Konda, Vaikuntavasan Paranidharan","doi":"10.1016/j.pmpp.2025.103091","DOIUrl":"10.1016/j.pmpp.2025.103091","url":null,"abstract":"<div><div>“Huanglongbing”(HLB), or citrus greening, is one of the most destructive citrus diseases globally, with particularly severe effects on mandarin. The disease is associated with the phloem-limited bacterium ‘<em>Candidatus</em> Liberibacter asiaticus’, which reduces fruit yield, juice quality, and tree longevity, causing major economic losses in mandarin-producing regions of Asia. Transmission occurs predominantly by Asian citrus psyllid (<em>Diaphorina citri</em>), while grafting also provides an efficient pathway for orchard-level spread. Experimental transmission through dodder and occasional seed detection have been reported, though their epidemiological relevance is limited or uncertain. Once established, ‘<em>Ca</em>. <em>L. asiaticus</em>’ disrupts phloem transport, leading to characteristic symptoms including blotchy leaf mottle, lopsided fruit with aborted seeds, canopy thinning and progressive decline. Yield reductions of 40–60 % have been documented in mandarins in India, Nepal, and Southeast Asia, underscoring their high susceptibility compared with sweet orange and grapefruit. This review synthesizes current evidence on the epidemiology, symptom expression and transmission biology of HLB with a dedicated focus on mandarins, and outlines integrated management strategies such as the use of certified nursery stock, suppression of psyllid vectors, removal of infected trees, and orchard sanitation that are essential to sustaining mandarin cultivation in HLB-endemic regions.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103091"},"PeriodicalIF":3.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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