Physiological and Molecular Plant Pathology最新文献_第3页

Taxonomical and functional microbial community profiling in Fusarium wilt-resistant and susceptible banana plants 香蕉抗枯萎病和敏感枯萎病植物的分类和功能微生物群落分析

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-24 DOI: 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.

香蕉枯萎病的病原菌尖孢镰刀菌（Fusarium oxysporum f. sp. cubense）对香蕉生产构成了严重威胁。植物微生物群在抗病性中起着至关重要的作用。然而，易感和耐药突变相关菌群之间的关系是有限的。研究了香蕉枯萎病（Fusarium wilt, Foc 1）易感品种“广粉1号”（GF， ABB基因组）与其抗性突变体（GFR）在细菌和真菌群落分类和功能上的差异。通过对根际土壤、假茎和根的取样，采用高通量Illumina测序技术对16S rRNA基因和ITS_V1区域进行测序。根际土壤中细菌和真菌群落的多样性高于植物器官。GFR根际细菌和真菌α多样性（Shannon指数）低于GF根际。GFR根际的优势菌群包括酸杆菌门、变形菌门、放线菌门和绿菌门。GFR中的优势真菌为Mortierellomycota和担子菌cota，而GF富集于子囊菌cota。LEfSe在GF根际和GFR根际分别鉴定出15个和28个不同的细菌生物标志物分类群。真菌方面，Agaricales是唯一在GFR根际发现的生物标志物分类群。KEGG途径进一步表明，外源生物降解和代谢、其他次生代谢产物的生物合成以及氨基酸代谢在GFR中发挥着重要作用。在双培养实验中，菌株1 - 61和菌株4 - 28分别对Foc 1和Foc 4表现出显著的拮抗活性。总之，这些发现表明香蕉的枯萎病抗性与微生物群落和功能的差异有关，这可能有助于增强疾病抑制。

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引用次数: 0

Artificial intelligence applications in abiotic and biotic plant stress management: A comprehensive bibliometric and literature review 人工智能在非生物和生物植物胁迫管理中的应用：综合文献计量学和文献综述

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-24 DOI: 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。

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引用次数: 0

Bacillus velezensis ATC-AL suppresses mycotoxin-producing fungi by disrupting membrane integrity and inducing mitochondrial dysfunction velezensis ATC-AL通过破坏膜完整性和诱导线粒体功能障碍来抑制产生霉菌毒素的真菌

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-24 DOI: 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.

黄曲霉是一种主要的真菌污染物，产生黄曲霉毒素B1 (AFB1)，这是对全球食品安全构成严重风险的最有效的真菌毒素之一。在本研究中，我们评估了velezensis ATC-AL及其活性抗真菌物质（AAS）对A. flavus和其他产生真菌毒素的真菌的抑菌效果。AAS处理表现出广谱抗真菌活性，最低抑菌浓度为8 μL/mL，可完全抑制AFB1的合成。它还能显著减少镰刀菌对脱氧雪腐镰刀菌醇（DON）的积累，显示出多靶点抗毒素潜力。机制分析表明，AAS破坏真菌膜完整性并诱导氧化应激，其表现为活性氧（ROS）水平升高、脂质过氧化以及对黄曲霉细胞膜和细胞壁的结构损伤。代谢组学分析进一步揭示了TCA循环、谷胱甘肽代谢和核酸生物合成的扰动，与线粒体功能障碍和能量代谢受损一致。相应地，AAS处理引起线粒体膜电位塌陷和ATP水平降低，提示细胞凋亡样死亡。在籽粒试验中，原子吸收光谱法能显著抑制真菌定植，消除霉菌毒素的产生，有效地保护籽粒免受黄曲霉和禾粒霉的侵染。总之，这些研究结果表明，bvelezensis ATC-AL作为一种有前景的生物防治剂，通过多种抗真菌和抗霉菌毒素途径发挥作用，为减轻粮食储存系统中的真菌污染和霉菌毒素风险提供了一种可持续的策略。

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引用次数: 0

Molecular insights into cotton defense and stress regulation: CRISPR-Cas9 mediated editing of key genes in biotic and abiotic stress pathways 棉花防御和胁迫调控的分子洞察：CRISPR-Cas9介导的生物和非生物胁迫途径中关键基因的编辑

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-24 DOI: 10.1016/j.pmpp.2025.103097

Suraj Prakash , Radha , Shubham Punia , Manoj Kumar , Baohong Zhang , Sangram Dhumal , Marisennayya Senapathy , Sunil Kumar , Sunil Puri

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.

棉花（Gossypium sp.）是世界上主要的天然纤维作物，为纺织和石油工业做出了贡献，估计每年在全球产生6000亿美元的经济影响。全球棉花产量预计将从1.265亿包（2022-23年）增加到约1.41亿包（2031-32年），年增长率为1.6%。尽管其经济意义重大，但产量受到气候变化、虫害爆发和土壤退化的影响。传统的育种和转基因方法虽然提高了棉花产量和抗虫性，但受物种复杂的异源四倍体基因组、广泛的基因冗余和低转化效率的限制，其速度较慢。基因组编辑工具，特别是CRISPR-Cas9，提供了对产量和应激反应相关基因的靶向修饰。这有助于提高产量、干旱、盐胁迫和抗虫害能力，同时最大限度地减少与传统转基因作物有关的脱靶效应和监管问题。这篇综述讨论了CRISPR-Cas9介导的棉花基因组编辑的最新进展，展示了特异性基因编辑（GhPDS, GhCLA1, GhAOC2, Gh14-3-3d）如何揭示胁迫反应途径和植物防御信号之间的功能联系。它还包括对水杨酸(SA) -茉莉酸(JA) -乙烯（ET）串音，ROS调节和次生代谢物生物合成的机制见解，并概述了克服转化和脱靶限制的新兴策略。未来的研究应结合多组学、引物编辑和病原-效应物互作研究，加强抗逆性棉花品种的分子育种。

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引用次数: 0

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 印度卡纳塔克邦北部花生种子中主要真菌污染的流行率和形态分子多样性的比较分析

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-24 DOI: 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.

花生（arachhis hypogaea L.）是世界范围内种植的主要油料作物；然而，它的种子极易受到真菌感染，导致质量和商业价值下降。本研究评估了从印度卡纳塔克邦北部4个地区（即Bagalkot、Dharwad、Gadag和Haveri）农民田地和当地农产品市场委员会（APMC）市场收集的花生种子相关的真菌多样性。在所有样品中鉴定出7个真菌属：黑曲霉、黄曲霉、尖孢镰刀菌、phaseolmacrophomina、柑橘青霉、匍匐茎根霉和Ceratobasidium spp，其中Gadag （n = 7）的真菌多样性最高，Haveri （n = 6）次之。Bagalkot区、Haveri区和Gadag区以菜绿大蠹和匍匐茎蠹为主。在消毒后的市场样品中，达瓦德的累积菌群感染率最高（60.83%），而在未消毒的市场和农民样品中，Haveri的总真菌污染（TFC）最高，分别为73.42%和66.91%。菜绿支原体是消毒后的市场（68.09%）和农民（70.99%）中分离最多的菌种。在未消毒的农民样品中，稻蠹蛾（52.08%）占优势，而在未消毒的市场样品中，菜籽白蠹蛾占高度优势（94.25%）。利用多个DNA条形码区对优势病原菌进行分子鉴定，包括子囊菌病原菌（phaseolina、A. niger、R. stolonifer、A. flavus、F. oxysporum和P. citriinum）的ITS和RPB2基因，而担子菌病原菌（Ceratobasidium sp.）的ITS和β-微管蛋白基因。随后的系统发育分析显示，与来自相似农业气候区域的分离株有密切的遗传关系，表明菌株之间的遗传变异最小。研究结果强调，农民和APMC市场需要改善卫生和储存实践，以尽量减少真菌的发病率，保障花生种子的健康。

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引用次数: 0

Morpho-genetic and pathogenic characterization of Macrophomina phaseolina (Tassi) Goid isolates causing dry root rot of chickpea (Cicer arietinum L.) in Ethiopia 埃塞俄比亚鹰嘴豆干根腐病病原菌的形态发生及致病特性研究

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-20 DOI: 10.1016/j.pmpp.2025.103090

Solomon Tamiru , Berhanu Bekele , Thangavel Selvaraj , Thelma Caine , Negussie Efa Gurmessa , Alan Buddie

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.

气候变化导致了几种植物病原体的出现，给全球农作物造成了巨大的产量损失。其中，一种土壤传播的坏死性真菌phaseolina (Tassi) Goid因其广泛的寄主范围和地理分布而成为一种重要的经济病原体。该病菌引起鹰嘴豆干腐病，严重威胁埃塞俄比亚鹰嘴豆生产。从埃塞俄比亚中部3个地区的10个县的有症状鹰嘴豆根中分离出菜绿分枝杆菌。对分离株进行了形态遗传和致病特性的变异检测。菌落生长和菌核性状在不同菌株间有显著差异。培养72 h后，21株为快速生长菌株，6株为中等生长菌株，2株为缓慢生长菌株。菌株的菌落生长速率为9.4 ~ 17.1 mm day−1。分离株有四种菌落色素：浅灰色、灰色、黑色和绿灰色。4株菌核为小型菌核，5株为中型菌核，20株为大型菌核。菌核呈圆形、长圆形、卵形和不规则4种形态。主成分分析（PCA）表明，各菌株的形态性状差异最大。分离株对鹰嘴豆的致病性从强毒到高毒不等。利用形态和致病性特征，主坐标分析将分离物聚为4个类群，层次聚类分析将分离物聚为10个类群。分离株ITS和LSU rDNA序列与GenBank中多个参考分离株的同源性为99.7 ~ 100%。本研究记录了埃塞俄比亚这一新兴病原体设计管理策略的基本信息。

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引用次数: 0

Genomic insights into tomato-Fusarium relationship: Plant-pathogen interactions and virulence mechanisms 番茄-镰刀菌关系的基因组分析：植物-病原体相互作用和毒力机制

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-19 DOI: 10.1016/j.pmpp.2025.103093

Yashoda Nandan Tripathi , Richa Raghuwanshi , Ram Sanmukh Upadhyay

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。

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引用次数: 0

A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data 一个透明的基于规则的框架，使用k-mer谱来检测番茄全基因组宏基因组数据中的隐性感染

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-18 DOI: 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.

农作物的隐性感染——尤其是新鲜食用的蔬菜——对食品安全构成了重大威胁，因为低丰度的病原体往往无法通过常规诊断。全基因组霰弹枪宏基因组测序（WGS）提供高分辨率检测，但产生复杂的数据集，挑战标准的生物信息学管道。本研究使用来自番茄WGS宏基因组数据集的k-mer谱评估了基于规则的机器学习（RBML）方法。收集了42个不同症状的番茄样本并进行了测序。使用三个独立的计算工具（mepllan， Kraken2/Bracken和CLC Genomics）确定感染状态，并通过针对已知病原体的PCR检测进行验证；31个生物信息学阳性样本中有29个经pcr确认，而11个未感染样本均为pcr阴性。使用KMC3生成k -mer谱（k = 10 bp），过滤以排除感染和未感染样本之间相对丰度差异≤15%的序列，并通过蒙特卡罗特征选择（MCFS）和Boruta算法进行处理。排名靠前的特征的结合产生了30个生物学验证的k-mers。生物学验证包括选定k-mers的BLASTn定位，以参考病原体和内生菌。使用R.ROSETTA、C5.0和Random Forest导出了5个生物学上可解释的IF-THEN规则，总体准确度为89%，精密度为0.80，在留一交叉验证下的f1评分为0.68。这些规则捕捉的是微生物丰度的变化，而不是病原体的绝对存在，为精准农业提供了可解释的诊断。虽然受样本量的限制，但这一概念验证表明，RBML具有从WGS数据中检测细微感染特征的潜力，并且具有生物透明度，未来的工作应该在更大、更多样化的数据集上验证其稳健性。

{"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}

引用次数: 0

Characterization and transmission of “huanglongbing” (‘Candidatus Liberibacter asiaticus’) with emphasis on mandarin orange (Citrus reticulata) 黄龙冰（' Candidatus Liberibacter asiaticus '）的鉴定与传播——以柑桔（Citrus reticulata）为重点

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-18 DOI: 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.

“黄龙病”（HLB）是全球最具破坏性的柑橘病害之一，对柑橘的影响尤其严重。该疾病与韧皮部限制细菌“亚洲自由Candidatus Liberibacter asiaticus”有关，该细菌会降低水果产量、果汁质量和树木寿命，给亚洲柑橘产区造成重大经济损失。传播主要发生在亚洲柑橘木虱（Diaphorina citri），而嫁接也为果园水平传播提供了有效途径。已报告通过菟丝子和偶尔的种子检测进行实验性传播，但其流行病学相关性有限或不确定。一旦建立，Ca。L. asiaticus破坏韧皮部运输，导致特征性症状，包括斑叶斑驳，果实不对称，种子流产，冠层变薄和逐渐衰退。据记载，印度、尼泊尔和东南亚的柑橘产量下降了40 - 60%，这表明与甜橙和葡萄柚相比，柑橘的易感性更高。这篇综述综合了目前关于HLB的流行病学、症状表达和传播生物学的证据，并概述了综合管理策略，如使用经认证的苗木、抑制木虱媒介、去除受感染的树木和果园卫生，这些都是维持HLB流行地区柑橘种植所必需的。

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引用次数: 0

Bioactivity and mechanisms of Ewingella americana for the control of Alternaria leaf spot on peanut 美洲艾温氏菌防治花生赤斑病的生物活性及机理研究

IF 3.3 3区农林科学 Q2 PLANT SCIENCES

Physiological and Molecular Plant Pathology

Pub Date : 2025-12-16 DOI: 10.1016/j.pmpp.2025.103088

Xuan Wang , Yi-Zhou Chen , Xiao-Di Qiu , Lei Chen , Yong-Mei Teng , Cheng Ding , Yan-Ting Huang , Su-Yan Wang , Si-Yuan Liu , Bin Ding , Pedro Laborda , Su-Qin Zhu

Bacterial biocontrol agents are emerging as a suitable alternative for the management of fungal diseases, avoiding the use of toxic fungicides. Commercial biocontrol currently relies heavily on the well-known genera Bacillus and Pseudomonas; however, there is a critical need to discover and characterize novel bacterial agents with unique ecological niches and modes of action. Although Ewingella americana is a bacterial mycoparasite that causes black rot in various edible mushrooms, such as Agaricus bisporus and Pleurotus ostreatus, its potential use for the management of fungal diseases remains completely unexplored. In this study, Alternaria alternata was identified via morphological analysis and ITS, EF1-α, and GADPH sequencing as the causal agent of leaf spot in peanut plants in Nantong, China. Interestingly, a new E. americana strain, NJC80, was found coexisting with A. alternata in symptomatic peanut leaves. NJC80 inhibited A. alternata mycelial growth and spore germination, and exhibited a variety of antifungal mechanisms, including production of antifungal metabolites, competition for nutrients, and mycoparasitism. In plant growth chamber, preventive application of 1 × 10⁸ cells/mL NJC80 reduced Alternaria leaf spot disease index in peanut leaves by 76.3 %, showing higher efficacy than the commercial fungicide tebuconazole, 56.9 % inhibitory efficacy. Preventive application of 1 × 10⁸ cells/mL NJC80 reduced Alternaria leaf spot disease index in a peanut field by 85.9 %. This is the first report on the use of E. americana for biocontrol purposes, revealing its potential as a novel bacterial biocontrol agent for fungal disease management.

细菌生物防治剂正在成为管理真菌疾病的合适选择，避免使用有毒的杀菌剂。商业生物防治目前严重依赖于众所周知的芽孢杆菌和假单胞菌属；然而，迫切需要发现和表征具有独特生态位和作用模式的新型细菌制剂。尽管美洲Ewingella是一种细菌性支寄生虫，可在各种食用菌（如双孢蘑菇和平菇）中引起黑腐病，但其在真菌疾病管理方面的潜在用途仍未被完全探索。本研究通过形态分析和ITS、EF1-α和GADPH测序，鉴定了南通花生叶片斑斑病的致病因子为互花alternnaria alternata。有趣的是，在有症状的花生叶片中发现了一种新的美洲大肠杆菌菌株NJC80与交替大肠杆菌共存。NJC80抑制了异交霉菌丝生长和孢子萌发，并表现出多种抗真菌机制，包括抗真菌代谢物的产生、营养物质的竞争和真菌寄生。在植物生长室内，预防施用1 × 108个细胞/mL NJC80可使花生叶片稻瘟病指数降低76.3%，效果优于市售杀菌剂苯唑唑，抑制效果为56.9%。预防施用1 × 108个细胞/mL NJC80可使花生地稻瘟病指数降低85.9%。这是第一份关于美洲E. americana用于生物防治目的的报告，揭示了其作为一种新型细菌生物防治剂用于真菌疾病管理的潜力。

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引用次数: 0