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Gao W, Han Y, Chen L, Tan X, Liu J, Xie J, Li B, Zhao H, Yu S, Tu H, Feng B, Yang F. Fusion data from FT-IR and MALDI-TOF MS result in more accurate classification of specific microbiota. Analyst 2023; 148:5650-5657. [PMID: 37800908 DOI: 10.1039/d3an01108a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Microbes are usually present as a specific microbiota, and their classification remains a challenge. MALDI-TOF MS is particularly successful in library-based microbial identification at the species level as it analyzes the molecular weight of peptides and ribosomal proteins. FT-IR allows more accurate classification of bacteria at the subspecies level due to the high sensitivity, specificity and repeatability of FT-IR signals from bacteria, which is not achievable with MALDI-TOF MS. Previous studies have shown that more accurate identification results can be obtained by the fusion of FT-IR and MALDI-TOF MS spectral data. Here, we constructed 20 groups of model microbiota samples and used FT-IR, MALDI-TOF MS, and their fusion data to classify them. Hierarchical clustering analysis (HCA) showed that the classification accuracy of FT-IR, MALDI-TOF MS, and the fusion data was 85%, 90%, and 100%, respectively. These results indicate that both FT-IR and MALDI-TOF MS can effectively classify specific microbiota, and the fusion of their spectral data could improve the classification accuracy. The FT-IR and MALDI-TOF MS data fusion strategy may be a promising technology for specific microbiota classification.
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Affiliation(s)
- Wenjing Gao
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Ying Han
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | | | - Xue Tan
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Jieyou Liu
- Zhuhai DL Biotech Co., Ltd, Zhuhai, Guangdong 519041, China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bin Li
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Huilin Zhao
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Huabin Tu
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Bin Feng
- Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
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Valente MT, Orzali L, Manetti G, Magnanimi F, Matere A, Bergamaschi V, Grottoli A, Bechini S, Riccioni L, Aragona M. Rapid molecular assay for the evaluation of clove essential oil antifungal activity against wheat common bunt. FRONTIERS IN PLANT SCIENCE 2023; 14:1130793. [PMID: 37342131 PMCID: PMC10277744 DOI: 10.3389/fpls.2023.1130793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023]
Abstract
Common bunt of durum wheat (DW), Triticum turgidum L. ssp. durum (Desf.) Husn., is caused by the two closely related fungal species belonging to Tilletia genus (Tilletiales, Exobasidiomycetes, Ustilaginomycotina): Tilletia laevis Kühn (syn. T. foetida (Wallr.) Liro.) and T. caries (DC) Tul. (syn. T. tritici (Bjerk.) G. Winter). This is one of the most devastating diseases in wheat growing areas worldwide, causing considerable yield loss and reduction of wheat grains and flour quality. For these reasons, a fast, specific, sensitive, and cost-effective method for an early diagnosis of common bunt in wheat seedlings is urgent. Several molecular and serological methods were developed for diagnosis of common bunt in wheat seedlings but at late phenological stages (inflorescence) or based on conventional PCR amplification, with low sensitivity. In this study, a TaqMan Real Time PCR-based assay was developed for rapid diagnosis and quantification of T. laevis in young wheat seedlings, before tillering stage. This method, along with phenotypic analysis, was used to study conditions favoring pathogen infection and to evaluate the effectiveness of clove oil-based seed dressing in controlling the disease. The overall results showed that: i) the Real Time PCR assay was able to quantify T. laevis in young wheat seedlings after seed dressing by clove oil in different formulations, greatly reducing times of analysis. It showed high sensitivity, detecting up to 10 fg of pathogen DNA, specificity and robustness, allowing to directly analyze crude plant extracts and representing a useful tool to speed up the tests of genetic breeding for disease resistance; ii) temperature was a critical point for disease development when using wheat seeds contaminated by T. laevis spores; iii) at least one of the clove oil-based formulations tested was able to efficiently control wheat common bunt, suggesting that clove oil dressing could represent a promising tool for managing the disease, especially in sustainable farming.
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Affiliation(s)
- Maria Teresa Valente
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Laura Orzali
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Giuliano Manetti
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Francesco Magnanimi
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Antonio Matere
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Valentino Bergamaschi
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Alessandro Grottoli
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Sara Bechini
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Luca Riccioni
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
| | - Maria Aragona
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), Rome, Italy
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Martín I, Gálvez L, Guasch L, Palmero D. Fungal Pathogens and Seed Storage in the Dry State. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223167. [PMID: 36432896 PMCID: PMC9697778 DOI: 10.3390/plants11223167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 05/27/2023]
Abstract
Seeds can harbor a wide range of microorganisms, especially fungi, which can cause different sanitary problems. Seed quality and seed longevity may be drastically reduced by fungi that invade seeds before or after harvest. Seed movement can be a pathway for the spread of diseases into new areas. Some seed-associated fungi can also produce mycotoxins that may cause serious negative effects on humans, animals and the seeds themselves. Seed storage is the most efficient and widely used method for conserving plant genetic resources. The seed storage conditions used in gene banks, low temperature and low seed moisture content, increase seed longevity and are usually favorable for the survival of seed-borne mycoflora. Early detection and identification of seed fungi are essential activities to conserve high-quality seeds and to prevent pathogen dissemination. This article provides an overview of the characteristics and detection methods of seed-borne fungi, with a special focus on their potential effects on gene bank seed conservation. The review includes the following aspects: types of seed-borne fungi, paths of infection and transmission, seed health methods, fungi longevity, risk of pathogen dissemination, the effect of fungi on seed longevity and procedures to reduce the harmful effects of fungi in gene banks.
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Affiliation(s)
- Isaura Martín
- Plant Genetic Resource Centre (CRF), National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28805 Alcalá de Henares, Spain
| | - Laura Gálvez
- Department of Agricultural Production, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 4, 28040 Madrid, Spain
| | - Luis Guasch
- Plant Genetic Resource Centre (CRF), National Institute for Agricultural and Food Research and Technology (INIA-CSIC), 28805 Alcalá de Henares, Spain
| | - Daniel Palmero
- Department of Agricultural Production, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 4, 28040 Madrid, Spain
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Sedaghatjoo S, Mishra B, Forster MK, Becker Y, Keilwagen J, Killermann B, Thines M, Karlovsky P, Maier W. Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis. IMA Fungus 2022; 13:11. [PMID: 35672841 PMCID: PMC9172201 DOI: 10.1186/s43008-022-00098-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractTilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.
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He T, Xu T, Muhae-Ud-Din G, Guo Q, Liu T, Chen W, Gao L. ITRAQ-Based Proteomic Analysis of Wheat ( Triticum aestivum) Spikes in Response to Tilletia controversa Kühn and Tilletia foetida Kühn Infection, Causal Organisms of Dwarf Bunt and Common Bunt of Wheat. BIOLOGY 2022; 11:865. [PMID: 35741386 PMCID: PMC9220156 DOI: 10.3390/biology11060865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/24/2022] [Accepted: 05/29/2022] [Indexed: 12/15/2022]
Abstract
Dwarf bunt and common bunt diseases of wheat are caused by Tilletia controversa Kühn and Tilletia foetida Kühn, respectively, and losses caused by these diseases can reach 70-80% in favourable conditions. T. controversa and T. foetida are fungal pathogens belonging to the Exobasidiomycetes within the basidiomycetous smut fungi (Ustilaginomycotina). In order to illuminate the proteomics differences of wheat spikes after the infection of T. controversa and T. foetida, the isobaric tags for relative and absolute quantification (iTRAQ) technique was used for better clarification. A total of 4553 proteins were differentially detected after T. controversa infection; 4100 were upregulated, and 453 were downregulated. After T. foetida infection, 804 differentially expressed proteins were detected; 447 were upregulated and 357 were downregulated. In-depth data analysis revealed that 44, 50 and 82 proteins after T. controversa and 9, 6 and 16 proteins after T. foetida were differentially expressed, which are antioxidant, plant-pathogen interaction and glutathione proteins, respectively, and 9 proteins showed results consistent with PRM. The top 20 KEGG enrichment pathways were identified after pathogen infection. On the basis of gene ontology, the upregulated proteins were linked with metabolic process, catalytic activity, transferase activity, photosynthetic membrane, extracellular region and oxidoreductase activity. The results expanded our understanding of the proteome in wheat spikes in response to T. controversa and T. foetida infection and provide a basis for further investigation for improving the defense mechanism of the wheat crops.
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Affiliation(s)
- Ting He
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining 810016, China;
| | - Tongshuo Xu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
| | - Ghulam Muhae-Ud-Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
| | - Qingyun Guo
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai University, Xining 810016, China;
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.H.); (T.X.); (G.M.-U.-D.); (T.L.); (W.C.)
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