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Ali Q, Zheng H, Rao MJ, Ali M, Hussain A, Saleem MH, Nehela Y, Sohail MA, Ahmed AM, Kubar KA, Ali S, Usman K, Manghwar H, Zhou L. Advances, limitations, and prospects of biosensing technology for detecting phytopathogenic bacteria. Chemosphere 2022; 296:133773. [PMID: 35114264 DOI: 10.1016/j.chemosphere.2022.133773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 05/22/2023]
Abstract
Phytopathogenic bacteria cause severe economic losses in agricultural production worldwide. The spread rates, severity, and emerging plant bacterial diseases have become serious threat to the sustainability of food sources and the fruit industry. Detection and diagnosis of plant diseases are imperative in order to manage plant diseases in field conditions, greenhouses, and food storage conditions as well as to maximize agricultural productivity and sustainability. To date, various techniques including, serological, observation-based, and molecular methods have been employed for plant disease detection. These methods are sensitive and specific for genetic identification of bacteria. However, these methods are specific for genetic identification of bacteria. Currently, the innovative biosensor-based disease detection technique is an attractive and promising alternative. A biosensor system involves biological recognition and transducer active receptors based on sensors used in plant-bacteria diagnosis. This system has been broadly used for the rapid diagnosis of plant bacterial pathogens. In the present review, we have discussed the conventional methods of bacterial-disease detection, however, the present review mainly focuses on the applications of different biosensor-based techniques along with point-of-care (POC), robotics, and cell phone-based systems. In addition, we have also discussed the challenges and limitations of these techniques.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, 210095, China.
| | - Hongxia Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Muhammad Junaid Rao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, PR China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yasser Nehela
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Rd, Lake Alfred, FL, 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Agha Mushtaque Ahmed
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University Tando Jam, Sindh, Pakistan
| | - Kashif Ali Kubar
- Faculty of Agriculture, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, 90150, Balochistan, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Allama Iqbal Road, 38000, Faisalabad, Pakistan
| | - Kamal Usman
- Agricultural Research Station, Office of VP for Research & Graduate Studies, Qatar University, 2713, Doha, Qatar
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China.
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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Tripathi A, Rai A, Dubey SC, Akhtar J, Kumar P. DNA barcode, multiplex PCR and qPCR assay for diagnosis of pathogens infecting pulse crops to facilitate safe exchange and healthy conservation of germplasm. Arch Microbiol 2021; 203:2575-2589. [PMID: 33683395 DOI: 10.1007/s00203-021-02259-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/06/2021] [Accepted: 02/20/2021] [Indexed: 10/22/2022]
Abstract
The DNA barcodes were developed from ITS region for the identification of fungal plant pathogens namely, Alternaria alternata and A. tenuissima both causing leaf spots, Ascochyta rabiei causing Ascochyta blight, Fusarium oxysporum f. sp. ciceris causing wilt, Macrophomina phaseolina causing dry root rot, Rhizoctonia solani causing web blight and wet root rot, Sclerotium (Athelia) rolfsii causing collar rot, Sclerotinia sclerotiorum causing stem rot and Cercospora canescens and Pseudocercospora cruenta both causing leaf spots in pulse crops. Barcode compliance for A. alternata (DBTPQ001-18), A. tenuissima (DBTPQ002-18), A. rabiei (DBTPQ003-18), F. oxysporum f. sp. ciceris (DBTPQ004-18), M. phaseolina (DBTPQ005-18), R. solani (DBTPQ006-18), S. rolfsii (DBTPQ007-18), S. sclerotiorum (DBTPQ008-18), C. canescens (DBTPQ009-18) and P. cruenta (DBTPQ029-20) have been generated based on the Barcode of Life Data System (BOLD) system. In addition to ITS, other genomic regions were also explored and on the basis of sequence variation they were ranked as TEF-α > SSU > LSU > β-tubulin. These genes could be considered for secondary barcode and phylogenetic relatedness. ITS-based markers for the detection of A. alternata (BAA2aF and BAA2aR) and R. solani (BRS17cF and BRS17cR) were developed which provided 400 bp and 220 bp amplicons, respectively. While, for F. oxysporum f. sp. ciceris, COX1-based marker (FOCox1F and FOCox3R) was developed which amplified 150 bp. The markers proved highly specific and sensitive with detection limit of 0.0001 ng of template DNA using qPCR and simultaneously detected these three pathogens. The DNA barcodes and diagnostics developed are suitable for quick and reliable detection of these pathogens during quarantine processing and field diagnostics.
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Affiliation(s)
- Aradhika Tripathi
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Anjali Rai
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Sunil Chandra Dubey
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
| | - Jameel Akhtar
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Pardeep Kumar
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
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Kesanakurti P, Belton M, Saeed H, Rast H, Boyes I, Rott M. Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control. J Virol Methods 2016; 236:35-40. [PMID: 27387642 DOI: 10.1016/j.jviromet.2016.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 05/30/2016] [Accepted: 07/03/2016] [Indexed: 11/21/2022]
Abstract
The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).
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Hyun IH, Chang SY, Lee MY, Kim MK, Choi W. Seed-borne Brachycladium penicillatum Intercepted under Plant Quarantine Inspection in Korea. Mycobiology 2012; 40:205-207. [PMID: 23115515 PMCID: PMC3483399 DOI: 10.5941/myco.2012.40.3.205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 08/24/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
A fungus detected from the importing seeds of Papaver rhoeas under plant quarantine inspection in Korea was identified as Brachycladium penicillatum Corda. It differed in morphological characteristics from a similar species, B. papaveris, which was known to form no macroconidiophores and no microsclerotia. Since the first interception in 2006, this fungus has frequently been found from importing seeds of Papaver spp. It was detected from 31 out of 282 seed consignments imported from 2006 to 2011. To prevent its introduction to Korea, the seed consignments infested by B. penicillatum were destroyed or reshipped.
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Affiliation(s)
- Ik-Hwa Hyun
- Risk Management Division, Animal, Plant and Fisheries Quarantine and Inspection Agency, Anyang 430-822, Korea
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Hyun IH, Heo NY, Chang SY, Heo JY, Mel'nik V. Identification of three fungi newly intercepted from importing plants in Korea. Mycobiology 2005; 33:243-244. [PMID: 24049509 PMCID: PMC3774895 DOI: 10.4489/myco.2005.33.4.243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Indexed: 06/02/2023]
Abstract
Three fungi newly intercepted from importing plants were identified in 2004. They were Ascochyta chrysanthemi on Lactuca sativa from China, A. spinaciicola on Spinacia oleracea from Denmark, and Leptosphaerulina australis on Brassica oleracea var. capitata from China. The characters of these fungi were described and illustrated.
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Affiliation(s)
- Ik-Hwa Hyun
- Central Post-Entry Quarantine Station, National Plant Quarantine Service, Suwon 443-400, Korea
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