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Dao Y, Yu J, Yang M, Han J, Fan C, Pang X. DNA metabarcoding analysis of fungal community on surface of four root herbs. CHINESE HERBAL MEDICINES 2024; 16:143-150. [PMID: 38375056 PMCID: PMC10874771 DOI: 10.1016/j.chmed.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/06/2022] [Accepted: 01/25/2023] [Indexed: 02/21/2024] Open
Abstract
Objective Angelicae Sinensis Radix (ASR, Danggui in Chinese), Cistanches Herba (CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma (PG, Renshen in Chinese), and Panacis Quinquefolii Radix (PQ, Xiyangshen in Chinese), widely used as medicine and dietary supplement around the world, are susceptible to fungal and mycotoxin contamination. In this study, we aim to analyze their fungal community by DNA metabarcoding. Methods A total of 12 root samples were collected from three main production areas in China. The samples were divided into four groups based on herb species, including ASR, CH, PG, and PQ groups. The fungal community on the surface of four root groups was investigated through DNA metabarcoding via targeting the internal transcribed spacer 2 region (ITS2). Results All the 12 samples were detected with fungal contamination. Rhizopus (13.04%-74.03%), Aspergillus (1.76%-23.92%), and Fusarium (0.26%-15.27%) were the predominant genera. Ten important fungi were identified at the species level, including two potential toxigenic fungi (Penicillium citrinum and P. oxalicum) and eight human pathogenic fungi (Alternaria infectoria, Candida sake, Hyphopichia burtonii, Malassezia globosa, M. restricta, Rhizopus arrhizus, Rhodotorula mucilaginosa, and Ochroconis tshawytschae). Fungal community in ASR and CH groups was significantly different from other groups, while fungal community in PG and PQ groups was relatively similar. Conclusion DNA metabarcoding revealed the fungal community in four important root herbs. This study provided an important reference for preventing root herbs against fungal and mycotoxin contamination.
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Affiliation(s)
- Yujie Dao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jingsheng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Meihua Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chune Fan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiaohui Pang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Heck DW, Hay F, Pethybridge SJ. Enabling Population Biology Studies of Stemphylium vesicarium from Onion with Microsatellites. PLANT DISEASE 2023; 107:3886-3895. [PMID: 37330630 DOI: 10.1094/pdis-04-23-0706-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is dominant within the foliar disease complex affecting onion production in New York (NY). The disease causes premature defoliation and significant reductions in bulb weight and quality. Foliar diseases of onion are usually managed by an intensive fungicide program, but SLB management is complicated by resistance to multiple single-site modes of action. The design of integrated disease management strategies is limited by incomplete knowledge surrounding the dominant sources of S. vesicarium inoculum. To facilitate genomic-based studies of S. vesicarium populations, nine microsatellite markers were developed. The markers were multiplexed into two PCR assays containing four and five fluorescently labeled microsatellite markers. Initial testing of the S. vesicarium isolates found the markers were highly polymorphic and reproducible with an average of 8.2 alleles per locus. The markers were used to characterize 54 S. vesicarium isolates from major NY onion production regions in 2016 (n = 27) and 2018 (n = 27). Fifty-two multilocus genotypes (MLGs) were identified between these populations. Genotypic and allelic diversities were high in both the 2016 and 2018 populations. A greater degree of genetic variation was observed within populations than between years. No distinct pattern of MLGs according to population was identified and some MLGs were closely related between 2016 and 2018. The lack of evidence for linkage among loci also was strongly suggestive of clonal populations with only minor differences between the two populations. These microsatellite markers will be a foundational resource for the testing of hypotheses surrounding the population biology of S. vesicarium and therefore informing disease management.
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Affiliation(s)
- Daniel W Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Frank Hay
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
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Hay F, Heck DW, Klein A, Sharma S, Hoepting C, Pethybridge SJ. Spatiotemporal Dynamics of Stemphylium Leaf Blight and Potential Inoculum Sources in New York Onion Fields. PLANT DISEASE 2022; 106:1381-1391. [PMID: 34798786 DOI: 10.1094/pdis-07-21-1587-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is the dominant foliar disease affecting large-scale onion production in New York. The disease is managed by fungicides, but control failures are prevalent and are attributed to fungicide resistance. Little is known of the relative role of inoculum sources in initiation and spread of SLB epidemics. Plate testing of 28 commercially available organic onion seedlots from 2016 and 2017 did not detect S. vesicarium. This finding suggests that although S. vesicarium has been reported as seed-transmitted, this is unlikely to be a significant inoculum source in commercially available organic seed lots and even less so in fungicide-treated seed used to establish conventional fields. The spatial and spatiotemporal dynamics of SLB epidemics in six onion fields were evaluated along linear transects in 2017 and 2018. Average SLB incidence increased from 0 to 100% throughout the cropping seasons with an average final lesion length of 28.3 cm. Disease progress was typical of a polycyclic epidemic and the logistic model provided the best fit to 83.3% of the datasets. Spatial patterns were better described by the beta-binomial than binomial distribution in half of the datasets (50%) and random patterns were more frequently observed by the index of dispersion (59%). Geostatistical analyses also found a low frequency of datasets with aggregation (60%). Spatiotemporal analysis of epidemics detected that the aggregation was influenced by disease incidence. However, diseased units were not frequently associated with the previous time period according to the spatiotemporal association function of spatial analyses by distance indices. Variable spatial patterns suggested mixed inoculum sources dependent upon location, and likely an external inoculum source at the sampling scale used in this study. A small-plot replicated trial was also conducted in each of 2 years to quantify the effect of S. vesicarium-infested onion residue on SLB epidemics in a field isolated from other onion fields. SLB incidence was significantly reduced in plots without residue compared with those in which residue remained on the soil surface. Burial of infested residue also significantly reduced epidemic progress in 1 year. The effect of infested onion residue on SLB epidemics in the subsequent onion crop suggests rotation or residue management may have a substantial effect on epidemics. However, the presence of an inoculum source external to fields in onion production regions, as indicated by a lack of spatial aggregation, may reduce the efficacy of in-field management techniques.
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Affiliation(s)
- Frank Hay
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Daniel W Heck
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Audrey Klein
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Sandeep Sharma
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Christy Hoepting
- Cornell Vegetable Program, Cornell Cooperative Extension, Albion, NY 14424
| | - Sarah J Pethybridge
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456
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Hay F, Stricker S, Gossen BD, McDonald MR, Heck D, Hoepting C, Sharma S, Pethybridge S. Stemphylium Leaf Blight: A Re-Emerging Threat to Onion Production in Eastern North America. PLANT DISEASE 2021; 105:3780-3794. [PMID: 34546780 DOI: 10.1094/pdis-05-21-0903-fe] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Stemphylium leaf blight (SLB), caused by Stemphylium vesicarium, is a foliar disease of onion worldwide, and has recently become an important disease in the northeastern United States and Ontario, Canada. The symptoms begin as small, tan to brown lesions on the leaves that can progress to defoliate plants. Crop loss occurs through reduced photosynthetic area, resulting in smaller, lower-quality bulbs. Leaf necrosis caused by SLB also can compromise bulb storage, as green leaves are required for the uptake of sprout inhibitors applied prior to harvest. The pathogen can overwinter on infested onion residue and infected volunteer plants. Asymptomatic weedy hosts near onion fields may also be a source of inoculum. Production of ascospores of the teleomorph (Pleospora allii) peaks in early spring in northeastern North America, often before the crop is planted, and declines rapidly as daily mean air temperatures rise. Conidia are usually present throughout the growing season. Application of fungicides is a standard practice for management of the complex of fungi that can cause foliar diseases of onion in this region. Recent assessments have shown that populations of S. vesicarium in New York and Ontario are resistant to at least three single-site mode-of-action fungicides. Three disease prediction systems have been developed and evaluated that may enable growers to reduce the frequency and/or number of fungicide applications, but the loss of efficacious fungicides due to resistance development within S. vesicarium populations threatens sustainability. The lack of commercially acceptable onion cultivars with sufficient resistance to reduce the number of fungicides for SLB also limits the ability to manage SLB effectively. Integrated disease management strategies for SLB are essential to maintain profitable, sustainable onion production across eastern North America.
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Affiliation(s)
- Frank Hay
- Cornell AgriTech, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Sara Stricker
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Bruce D Gossen
- Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel Heck
- Cornell AgriTech, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Christy Hoepting
- Cornell Cooperative Extension, Cornell Vegetable Program, Albion, NY 14411, U.S.A
| | - Sandeep Sharma
- Cornell AgriTech, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Sarah Pethybridge
- Cornell AgriTech, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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Roylawar P, Khandagale K, Randive P, Shinde B, Murumkar C, Ade A, Singh M, Gawande S, Morelli M. Piriformospora indica Primes Onion Response against Stemphylium Leaf Blight Disease. Pathogens 2021; 10:1085. [PMID: 34578118 PMCID: PMC8472787 DOI: 10.3390/pathogens10091085] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 12/11/2022] Open
Abstract
The root-endophytic fungus Piriformospora indica (=Serendipita indica) has been revealed for its growth-promoting effects and its capacity to induce resistance in a broad spectrum of host plants. However, the bioefficacy of this fungus had not yet been tested against any pathogen affecting onion (Allium cepa). In this study, the biocontrol potency of P. indica against onion leaf blight, an impacting disease caused by the necrotrophic fungal pathogen Stemphylium vesicarium, was evaluated. First, it was proved that colonisation of onion roots by P. indica was beneficial for plant growth, as it increased leaf development and root biomass. Most relevantly, P. indica was also effective in reducing Stemphylium leaf blight (SLB) severity, as assessed under greenhouse conditions and confirmed in field trials in two consecutive years. These investigations could also provide some insight into the biochemical and molecular changes that treatment with P. indica induces in the main pathways associated with host defence response. It was possible to highlight the protective effect of P. indica colonisation against peroxidative damage, and its role in signalling oxidative stress, by assessing changes in malondialdehyde and H2O2 content. It was also showed that treatment with P. indica contributes to modulate the enzymatic activity of superoxide dismutase, catalase, phenylalanine ammonia-lyase and peroxidase, in the course of infection. qPCR-based expression analysis of defence-related genes AcLOX1, AcLOX2, AcPAL1, AcGST, AcCHI, AcWRKY1, and AcWRKY70 provided further indications on P. indica ability to induce onion systemic response. Based on the evidence gathered, this study aims to propose P. indica application as a sustainable tool for improving SLB control, which might not only enhance onion growth performance but also activate defence signalling mechanisms more effectively, involving different pathways.
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Affiliation(s)
- Praveen Roylawar
- ICAR-Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune 410505, India; (P.R.); (P.R.); (M.S.)
- Tuljaram Chaturchand College of Arts, Science and Commerce, Baramati, Pune 413102, India;
- Department of Botany, Sangamner Nagarpalika Arts, D. J. Malpani Commerce, B. N. Sarda Science College, Sangamner, Ahamadnagar 422605, India
| | - Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (K.K.); (A.A.)
| | - Pragati Randive
- ICAR-Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune 410505, India; (P.R.); (P.R.); (M.S.)
| | - Bharat Shinde
- Vidya Pratishthan’s Arts, Science & Commerce College, Baramati, Pune 413133, India;
| | | | - Avinash Ade
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India; (K.K.); (A.A.)
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune 410505, India; (P.R.); (P.R.); (M.S.)
| | - Suresh Gawande
- ICAR-Directorate of Onion and Garlic Research (DOGR), Rajgurunagar, Pune 410505, India; (P.R.); (P.R.); (M.S.)
| | - Massimiliano Morelli
- CNR-IPSP Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70124 Bari, Italy;
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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