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Grunwald DJ, Stroschein SM, Grinstead S, Mollov D, Rioux RA, Rakotondrafara AM. Targeting the Highly Conserved 3' Untranslated Region of Iris Severe Mosaic Virus for Sensitive Monitoring of the Disease Prevalence in Iris Production. PLANT DISEASE 2023; 107:3763-3772. [PMID: 37386702 DOI: 10.1094/pdis-04-23-0631-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: 07/01/2023]
Abstract
Iris severe mosaic virus (ISMV, Potyviridae) can threaten the sustainability of iris production and the marketability of the plants. Effective intervention and control strategies require rapid and early detection of viral infections. The wide range of viral symptoms, from asymptomatic to severe chlorosis of the leaves, renders diagnosis solely based on visual indicators ineffective. A nested PCR-based diagnostic assay was developed for the reliable detection of ISMV in iris leaves and in rhizomes. Considering the genetic variability of ISMV, two primer pairs were designed to detect the highly conserved 3' untranslated region (UTR) of the viral genomic RNA. The specificity of the primer pairs was confirmed against four other potyviruses. The sensitivity of detection was enhanced by one order of magnitude using diluted cDNA and a nested approach. Nested PCR facilitated detecting ISMV on field-grown samples beyond the capabilities of a currently available immunological test and in iris rhizome, which would facilitate ensuring clean stock is planted. This approach dramatically improves the detection threshold of ISMV on potentially low virus titer samples. The study provides a practical, accurate, and sensitive tool for the early detection of a deleterious virus that infects a popular ornamental and landscape plant.
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Affiliation(s)
- Derrick J Grunwald
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
| | | | - Sam Grinstead
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD 20705
| | - Dimitre Mollov
- Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Renée A Rioux
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
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Lawaju BR, Yan G, Whitworth J. Development of a Droplet Digital PCR Assay for Detection and Quantification of Stubby Root Nematode, Paratrichodorus allius, in Soil. PLANT DISEASE 2023; 107:3344-3353. [PMID: 37115564 DOI: 10.1094/pdis-03-23-0439-sr] [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
The stubby root nematode Paratrichodorus allius is an important plant-parasitic nematode species within the Trichodoridae family. It can directly harm the plants by feeding on the roots or indirectly by transmitting Tobacco rattle virus. These nematodes are mostly diagnosed either by traditional microscopic methods or a polymerase chain reaction (PCR)-based method. Droplet digital PCR (ddPCR) is a novel PCR technique which is sensitive and precise in quantifying DNA templates of the test samples. In this study, we developed a ddPCR assay to detect and quantify P. allius in soil. The specificity and sensitivity of the assay was first determined using P. allius nematode DNA or DNA from sterilized soil artificially inoculated with P. allius, and the assay was used to quantify P. allius populations in field soils. The assay did not detect nematodes other than P. allius, thus showing high specificity. It was able to detect P. allius equivalent to a 0.01 and 0.02 portion of a single nematode in soil DNA and nematode DNA extracts, respectively. Highly linear relationships between DNA copy numbers from ddPCR and serial dilutions of known concentrations were observed with DNA from P. allius nematodes (R2 = 0.9842) and from artificially infested soil (R2 = 0.9464). The P. allius populations from field soils determined by ddPCR were highly correlated with traditional microscopic counts (R2 = 0.7963). To our knowledge, this is the first report of applying ddPCR to detect and quantify stubby root nematode in soil. The results of this study support the potentiality of a ddPCR assay as a new research tool in diagnostics of plant-parasitic nematodes.
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Affiliation(s)
- Bisho Ram Lawaju
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Guiping Yan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Jonathan Whitworth
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210
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3
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Manzoor S, Nabi SU, Baranwal VK, Verma MK, Parveen S, Rather TR, Raja WH, Shafi M. Overview on century progress in research on mosaic disease of apple (Malus domestica Borkh) incited by apple mosaic virus/apple necrotic mosaic virus. Virology 2023; 587:109846. [PMID: 37586234 DOI: 10.1016/j.virol.2023.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Apple mosaic is widely distributed disease throughout the apple growing regions leading to the major adverse effects both qualitatively and quantitatively. Earlier the apple mosaic virus-ApMV was regarded as the only causal agent of the disease, but recently a novel virus apple necrotic mosaic virus-ApNMV have been reported as the causal pathogen from various apple growing countries. Accurate diagnosis of disease and detection of ApMV and ApNMV are of utmost importance, because without this ability we can neither understand nor control this disease. Both the viruses are mostly controlled through quarantine, isolation, sanitation and certification programs depending on sensitive and specific detection methods available. Here we review the 100-year progress in research on apple mosaic disease, which includes history, yield losses, causal agents, their genome organization, replication, traditional to recent detection methods, transmission, distribution and host range of associated viruses and management of the disease.
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Affiliation(s)
- Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201, India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India.
| | | | - Mahendra K Verma
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Shugufta Parveen
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Tariq Rasool Rather
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025, India
| | - Wasim H Raja
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Mansoor Shafi
- Department of Plant Resources and Environment, Jeju National University, Jeju-si, 63243, Republic of Korea
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4
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Zhao Y, Shao J, Jin Z, Zheng W, Yao J, Ma W. Plasmon-enhanced electroreduction activity of Au-AgPd Janus nanoparticles for ochratoxin a detection. Food Chem 2023; 412:135526. [PMID: 36731235 DOI: 10.1016/j.foodchem.2023.135526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
Ochratoxin A (OTA) was a dangerous biological toxin, and would easily contaminate food and induced food safety problems. The development of electrochemical aptasensors by designing strong and anti-interfere electroactive labels could improve the sensitivity and accuracy of OTA detection. In this contribution, novel electroactive Au-AgPd Janus NPs were firstly synthesized and exhibited electroreduction signal at -0.4 V, owing to the reduction process of Pd2+. The electroreduction signal was amplified 1.5 times under local surface plasmon resonance (LSPR) excitation, which could improve the sensitivity of OTA detection. Plasmon-enhanced electroreduction principle of Au-AgPd Janus NPs was verified, which endowed electrochemical aptasensor with high accuracy and anti-interference ability for OTA detection. Au-AgPd Janus NPs served as electrochemical beacon achieved sensitive and accurate OTA detection with the limit of detection (LOD) of 0.98 pM. This work opens up new directions for the construction of electroactive heterostructures for the sensitive and accurate biotoxins electroanalytical applications.
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Affiliation(s)
- Yuan Zhao
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Center for Photoresponsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Juanjuan Shao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, Hebei 061100, China
| | - Zhao Jin
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Center for Photoresponsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wangwang Zheng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Center for Photoresponsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jie Yao
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Center for Photoresponsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Ma
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Batra AR, Cottam D, Lepesteur M, Dexter C, Zuccala K, Martino C, Khudur L, Daniel V, Ball AS, Soni SK. Development of A Rapid, Low-Cost Portable Detection Assay for Enterococci in Wastewater and Environmental Waters. Microorganisms 2023; 11:microorganisms11020381. [PMID: 36838346 PMCID: PMC9960780 DOI: 10.3390/microorganisms11020381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Waterborne diseases are known as a leading cause of illness and death in both developing and developed countries. Several pathogens can be present in contaminated water, particularly waters containing faecal material; however, routine monitoring of all pathogens is not currently possible. Enterococcus faecalis, which is present in the microflora of human and animals has been used as a faecal indicator in water due to its abundance in surface water and soil. Accurate and fast detection methods are critical for the effective monitoring of E. faecalis in the environment. Although conventional and current molecular detection techniques provide sufficient sensitivity, specificity and throughput, their use is hampered by the long waiting period (1-6 days) to obtain results, the need for expensive laboratory equipment, skilled personnel, and cold-chain storage. Therefore, this study aimed to develop a detection system for E. faecalis that would be simple, rapid, and low-cost, using an isothermal DNA amplification assay called recombinase polymerase amplification (RPA), integrated with a lateral flow assay (LFA). The assay was found to be 100% selective for E. faecalis and capable of detecting rates as low as 2.8 × 103 cells per 100 mL from water and wastewater, and 2.8 × 104 cells per 100 mL from saline water. The assay was completed in approximately 30 min using one constant temperature (38 °C). In addition, this study demonstrated the quantitation of E. faecalis using a lateral flow strip reader for the first time, enhancing the potential use of RPA assay for the enumeration of E. faecalis in wastewater and heavily contaminated environmental waters, surface water, and wastewater. However, the sensitivity of the RPA-LFA assay for the detection of E. faecalis in tap water, saline water and in wastewater was 10-1000 times lower than that of the Enterolert-E test, depending on the water quality. Nevertheless, with further improvements, this low-cost RPA-LFA may be suitable to be used at the point-of-need (PON) if conjugated with a rapid field-deployable DNA extraction method.
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Affiliation(s)
- Alka Rani Batra
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
- Correspondence: ; Tel.: +61-399256594
| | - Darren Cottam
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Muriel Lepesteur
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Carina Dexter
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Kelly Zuccala
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Caroline Martino
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, VIC 3085, Australia
| | - Leadin Khudur
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
| | - Vivek Daniel
- School of Science, RMIT University, Melbourne, VIC 3083, Australia
| | - Andrew S. Ball
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
| | - Sarvesh Kumar Soni
- ARC Training Centre for the Transformation of Australia’s Biosolids Resource, School of Science, RMIT University, Bundoora West, VIC 3083, Australia
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Shao H, Zhang P, Peng D, Huang W, Kong LA, Li C, Liu E, Peng H. Current advances in the identification of plant nematode diseases: From lab assays to in-field diagnostics. FRONTIERS IN PLANT SCIENCE 2023; 14:1106784. [PMID: 36760630 PMCID: PMC9902721 DOI: 10.3389/fpls.2023.1106784] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Plant parasitic nematodes (PPNs) cause an important class of diseases that occur in almost all types of crops, seriously affecting yield and quality and causing great economic losses. Accurate and rapid diagnosis of nematodes is the basis for their control. PPNs often have interspecific overlays and large intraspecific variations in morphology, therefore identification is difficult based on morphological characters alone. Instead, molecular approaches have been developed to complement morphology-based approaches and/or avoid these issues with various degrees of achievement. A large number of PPNs species have been successfully detected by biochemical and molecular techniques. Newly developed isothermal amplification technologies and remote sensing methods have been recently introduced to diagnose PPNs directly in the field. These methods have been useful because they are fast, accurate, and cost-effective, but the use of integrative diagnosis, which combines remote sensing and molecular methods, is more appropriate in the field. In this paper, we review the latest research advances and the status of diagnostic approaches and techniques for PPNs, with the goal of improving PPNs identification and detection.
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Affiliation(s)
- Hudie Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Pan Zhang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling-an Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanren Li
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Enliang Liu
- Grain Crops Institute, XinJiang Academy of Agricultural Sciences, Urumqi, China
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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7
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Ahmed FK, Alghuthaymi MA, Abd-Elsalam KA, Ravichandran M, Kalia A. Nano-Based Robotic Technologies for Plant Disease Diagnosis. NANOROBOTICS AND NANODIAGNOSTICS IN INTEGRATIVE BIOLOGY AND BIOMEDICINE 2023:327-359. [DOI: 10.1007/978-3-031-16084-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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8
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Point-of-Care Lateral Flow Detection of Viable Escherichia coli O157:H7 Using an Improved Propidium Monoazide-Recombinase Polymerase Amplification Method. Foods 2022; 11:3207. [PMCID: PMC9602316 DOI: 10.3390/foods11203207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The detection of both viable and viable but non-culturable (VBNC) Escherichia coli O157:H7 is a crucial part of food safety. Traditional culture-dependent methods are lengthy, expensive, laborious, and unable to detect VBNC. Hence, there is a need to develop a rapid, simple, and cost-effective detection method to differentiate between viable/dead E. coli O157:H7 and detect VBNC cells. In this work, recombinase polymerase amplification (RPA) was developed for the detection of viable E. coli O157:H7 through integration with propidium monoazide (PMAxx). Initially, two primer sets, targeting two different genes (rfbE and stx) were selected, and DNA amplification by RPA combined with PMAxx treatment and the lateral flow assay (LFA) was carried out. Subsequently, the rfbE gene target was found to be more effective in inhibiting the amplification from dead cells and detecting only viable E. coli O157:H7. The assay’s detection limit was found to be 102 CFU/mL for VBNC E. coli O157:H7 when applied to spiked commercial beverages including milk, apple juice, and drinking water. pH values from 3 to 11 showed no significant effect on the efficacy of the assay. The PMAxx-RPA-LFA was completed at 39 °C within 40 min. This study introduces a rapid, robust, reliable, and reproducible method for detecting viable bacterial counts. In conclusion, the optimised assay has the potential to be used by the food and beverage industry in quality assurance related to E. coli O157:H7.
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Development of a Novel Primer–TaqMan Probe Set for Diagnosis and Quantification of Meloidogyne enterolobii in Soil Using qPCR and Droplet Digital PCR Assays. Int J Mol Sci 2022; 23:ijms231911185. [PMID: 36232487 PMCID: PMC9569833 DOI: 10.3390/ijms231911185] [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: 08/19/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Early detection of pathogens before the planting season is valuable to forecast disease occurrence. Therefore, rapid and reliable diagnostic approaches are urgently needed, especially for one of the most aggressive root knot nematodes, Meloidogyne enterolobii. In this study, we developed a novel primer–TaqMan probe set aimed at M. enterolobii. The primer–probe set was successfully applied in the identification and quantification of M. enterolobii via qPCR technology. It was also suitable for improved PCR technology, known as ddPCR analyses, and this work presents the first application of this technology for plant parasitic nematodes. Compared with qPCR, ddPCR exhibited better performance with regard to analytical sensitivity, which can provide a more accurate detection of M. enterolobii concealed in field soil. In addition, we generated standard curves to calculate the number of eggs in soil using the qPCR and ddPCR platforms. Hopefully, the results herein will be helpful for forecasting disease severity of M. enterolobii infection and adopting effective management strategies.
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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] [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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11
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Formisano L, Miras-Moreno B, Ciriello M, Zhang L, De Pascale S, Lucini L, Rouphael Y. Between Light and Shading: Morphological, Biochemical, and Metabolomics Insights Into the Influence of Blue Photoselective Shading on Vegetable Seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:890830. [PMID: 35693176 PMCID: PMC9174935 DOI: 10.3389/fpls.2022.890830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
High nursery densities reduce the seedling quality due to the competition for light. High light intensity, shading, and blue light depletion activate morphophysiological and metabolomic responses in plants, resulting in size modification to gain an advantage over neighboring plants. Our research aimed to unravel the effects of light intensity and quality on nursery seedlings at the morphological and biochemical levels. To this aim, the effect of black shading and blue photoselective shading nets were investigated in terms of morphometric, ionomic, and untargeted metabolomics signatures in Cucurbita pepo L., Citrullus lanatus L., Solanum lycopersicum L., and Solanum melongena L. seedlings. Plant height, diameter, sturdiness index, leaf area, specific leaf area, shoot/root ratio, and mineral content (by ion chromatography-IC) were evaluated. In C. pepo L and C. lanatus L., the blue net reduced the shoot/root and chlorophyll a/b ratios and increased stem diameter and total chlorophyll content. The black net increased plant height, stem diameter, and sturdiness index in Solanum lycopersicum L. and Solanum melongena L. At the same time, unshading conditions reduced leaf area, specific leaf area, shoot/root ratio, and total chlorophyll content. The blue net improved the sturdiness index and quality of C. pepo L. and C. lanatus L. Such impact on morphological parameters induced by the different shading conditions was corroborated by a significant modulation at the metabolomics level. Untargeted metabolomic phytochemical signatures of the selected plants, and the subsequent multivariate analysis coupled to pathway analysis, allowed highlighting a broad and diverse biochemical modulation. Metabolomics revealed that both primary and secondary metabolism were largely affected by the different shading conditions, regardless of the species considered. A common pattern arose to point at the activation of plant energy metabolism and lipid biosynthesis, together with a generalized down accumulation of several secondary metabolites, particularly phenylpropanoids. Our findings indicate an intriguing scientific interest in the effects of selective shading and its application to other species and different phenological stages.
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Affiliation(s)
- Luigi Formisano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Begoña Miras-Moreno
- Department for Sustainable Food Process, DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Michele Ciriello
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Leilei Zhang
- Department for Sustainable Food Process, DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Stefania De Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Jiao J, Yang M, Zhang T, Zhang Y, Yang M, Li M, Liu C, Song S, Bai T, Song C, Wang M, Pang H, Feng J, Zheng X. A sensitive visual method for onsite detection of quarantine pathogenic bacteria from horticultural crops using an LbCas12a variant system. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128038. [PMID: 34953258 DOI: 10.1016/j.jhazmat.2021.128038] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Pre-planting testing of seeds and plantlets for the existence of quarantine pathogens is an important phytosanitary measure. The CRISPR-mediated molecular diagnostic methodologies are being developed for pathogens detection, but many challenges remain. Here, we profiled an engineered Crispr/LbCas12a variant (LbCas12a-5M) that has more robust trans-cleavage activity and a wider PAM sequences (TNTN) preference than wild type. We developed a procedure for screening specific sequences of bacterial plant pathogens, and the designed species-specific crRNA displayed no cross-reactions with other bacterial species. Combined with a simple extraction of bacterial DNA, an LbCas12a-5M-based visual detection technique was established and optimized for detecting quarantine pathogens Erwinia amylovora and Acidovorax citrulli with detection limits up to 40 CFU/reaction and a sensitivity consistent with qPCR assay. This protocol was faster and simpler than qPCR, requiring 40 min or less from sample preparation. We further validated the potential application of the method by showing that it can be used for rapid and accurate diagnosis of A. citrulli on seeds of watermelon, with 100% agreement with the results of qPCR assay. The developed method simplifies the detection of pathogens and provides cost-effective countermeasures to quarantine interventions.
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Affiliation(s)
- Jian Jiao
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou 450002, China
| | - Mengjie Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Tengfei Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Yingli Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Mengli Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Ming Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shangwei Song
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Tuanhui Bai
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Chunhui Song
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Miaomiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongguang Pang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China.
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13
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Murolo S, Moumni M, Mancini V, Allagui MB, Landi L, Romanazzi G. Detection and Quantification of Stagonosporopsis cucurbitacearum in Seeds of Cucurbita maxima Using Droplet Digital Polymerase Chain Reaction. Front Microbiol 2022; 12:764447. [PMID: 35087483 PMCID: PMC8788924 DOI: 10.3389/fmicb.2021.764447] [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: 08/25/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022] Open
Abstract
Stagonosporopsis cucurbitacearum is an important seedborne pathogen of squash (Cucurbita maxima). The aim of our work was to develop a rapid and sensitive diagnostic tool for detection and quantification of S. cucurbitacearum in squash seed samples, to be compared with blotter analysis, that is the current official seed test. In blotter analysis, 29 of 31 seed samples were identified as infected, with contamination from 1.5 to 65.4%. A new set of primers (DB1F/R) was validated in silico and in conventional, quantitative real-time PCR (qPCR) and droplet digital (dd) PCR. The limit of detection of S. cucurbitacearum DNA for conventional PCR was ∼1.82 × 10–2 ng, with 17 of 19 seed samples positive. The limit of detection for ddPCR was 3.6 × 10–3 ng, which corresponded to 0.2 copies/μl. Detection carried out with artificial samples revealed no interference in the absolute quantification when the seed samples were diluted to 20 ng. All seed samples that showed S. cucurbitacearum contamination in the blotter analysis were highly correlated with the absolute quantification of S. cucurbitacearum DNA (copies/μl) in ddPCR (R2 = 0.986; p ≤ 0.01). Our ddPCR protocol provided rapid detection and absolute quantification of S. cucurbitacearum, offering a useful support to the standard procedure.
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Affiliation(s)
- Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Marwa Moumni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.,Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, Ariana, Tunisia
| | - Valeria Mancini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Mohamed Bechir Allagui
- Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, Ariana, Tunisia
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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14
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Pandey AK, Basandrai AK, Basandrai D, Boddepalli VN, Rathore A, Adapala G, Nair RM. Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection. PLANT DISEASE 2021; 105:2001-2010. [PMID: 33599514 DOI: 10.1094/pdis-12-20-2722-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: 06/12/2023]
Abstract
Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Abhay K Pandey
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad-502324, TS, India
- Tea Research Association, North Bengal Regional R & D Center, Nagrakata-735225, West Bengal, India
| | - Ashwani K Basandrai
- Department of Plant Pathology, College of Agriculture, CSK Himachal Pradesh Agricultural University, Palampur-176062, Himachal Pradesh, India
| | - Daisy Basandrai
- Department of Genetics and Plant Breeding, College of Agriculture, CSK Himachal Pradesh Agricultural University, Palampur-176062, Himachal Pradesh, India
| | | | - Abhishek Rathore
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad-502324, TS, India
| | - Gopikrishna Adapala
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad-502324, TS, India
| | - Ramakrishnan M Nair
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad-502324, TS, India
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15
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Rani A, Ravindran VB, Surapaneni A, Mantri N, Ball AS. Review: Trends in point-of-care diagnosis for Escherichia coli O157:H7 in food and water. Int J Food Microbiol 2021; 349:109233. [PMID: 34022616 DOI: 10.1016/j.ijfoodmicro.2021.109233] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022]
Abstract
Escherichia coli O157:H7, a Shiga-producing E. coli is a major pathogenic E. coli strain which since the early 1980s has become a crucial food and water-borne pathogen. Several management strategies can be applied to control the spread of infection; however early diagnosis represents the optimum preventive strategy to minimize the infection. Therefore, it is crucial to detect this pathogen in a fast and efficient manner in order to reduce the morbidity and mortality. Currently used gold standard tests rely on culture and pre-enrichment of E. coli O157:H7 from the contaminated source; they are time consuming and laborious. Molecular methods such as polymerase chain reaction are sensitive; however, they require expensive instrumentation. Therefore, there is a requirement for Accurate, Sensitive, Specific, User friendly, Rapid, Equipment free and Deliverable (ASSURED) detection methods for use in the laboratory and in the field. Emerging technologies such as isothermal amplification methods, biosensors, surface enhanced Raman Spectroscopy, paper-based diagnostics and smartphone-based digital methods are recognized as new approaches in the field of E. coli O157:H7 diagnostics and are discussed in this review. Mobile PCR and CRISPR-Cas diagnostic platforms have been identified as new tools in E. coli O157:H7 POC diagnostics with the potential for implementation by industry. This review describes advances and progress in the field of E. coli O157:H7 diagnosis in the context of food and water industry. The focus is on emerging high throughput point-of-care (POC) E. coli O157:H7 diagnostics and the requirement for the transformation to service routine diagnostics in the food and water industry.
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Affiliation(s)
- Alka Rani
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, School of Science, RMIT University, Bundoora West, Victoria 3083, Australia.
| | - Vivek B Ravindran
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, School of Science, RMIT University, Bundoora West, Victoria 3083, Australia
| | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, School of Science, RMIT University, Bundoora West, Victoria 3083, Australia; South East Water, Frankston, Victoria 3199, Australia
| | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne, Victoria 3083, Australia
| | - Andrew S Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, School of Science, RMIT University, Bundoora West, Victoria 3083, Australia
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16
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Li P, Li M, Zhang F, Wu M, Jiang X, Ye B, Zhao Z, Yue D, Fan Q, Chen H. High-efficient nucleic acid separation from animal tissue samples via surface modified magnetic nanoparticles. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Precision Agriculture Digital Technologies for Sustainable Fungal Disease Management of Ornamental Plants. SUSTAINABILITY 2021. [DOI: 10.3390/su13073707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ornamental plant production constitutes an important sector of the horticultural industry worldwide and fungal infections, that dramatically affect the aesthetic quality of plants, can cause serious economic and crop losses. The need to reduce the use of pesticides for controlling fungal outbreaks requires the development of new sustainable strategies for pathogen control. In particular, early and accurate large-scale detection of occurring symptoms is critical to face the ambitious challenge of an effective, energy-saving, and precise disease management. Here, the new trends in digital-based detection and available tools to treat fungal infections are presented in comparison with conventional practices. Recent advances in molecular biology tools, spectroscopic and imaging technologies and fungal risk models based on microclimate trends are examined. The revised spectroscopic and imaging technologies were tested through a case study on rose plants showing important fungal diseases (i.e., spot spectroscopy, hyperspectral, multispectral, and thermal imaging, fluorescence sensors). The final aim was the examination of conventional practices and current e-tools to gain the early detection of plant diseases, the identification of timing and spacing for their proper management, reduction in crop losses through environmentally friendly and sustainable production systems. Moreover, future perspectives for enhancing the integration of all these approaches are discussed.
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18
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Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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19
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Ali Q, Ahmar S, Sohail MA, Kamran M, Ali M, Saleem MH, Rizwan M, Ahmed AM, Mora-Poblete F, do Amaral Júnior AT, Mubeen M, Ali S. Research advances and applications of biosensing technology for the diagnosis of pathogens in sustainable agriculture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:9002-9019. [PMID: 33464530 DOI: 10.1007/s11356-021-12419-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/06/2021] [Indexed: 05/06/2023]
Abstract
Plant diseases significantly impact the global economy, and plant pathogenic microorganisms such as nematodes, viruses, bacteria, fungi, and viroids may be the etiology for most infectious diseases. In agriculture, the development of disease-free plants is an important strategy for the determination of the survival and productivity of plants in the field. This article reviews biosensor methods of disease detection that have been used effectively in other fields, and these methods could possibly transform the production methods of the agricultural industry. The precise identification of plant pathogens assists in the assessment of effective management steps for minimization of production loss. The new plant pathogen detection methods include evaluation of signs of disease, detection of cultured organisms, or direct examination of contaminated tissues through molecular and serological techniques. Laboratory-based approaches are costly and time-consuming and require specialized skills. The conclusions of this review also indicate that there is an urgent need for the establishment of a reliable, fast, accurate, responsive, and cost-effective testing method for the detection of field plants at early stages of growth. We also summarized new emerging biosensor technologies, including isothermal amplification, detection of nanomaterials, paper-based techniques, robotics, and lab-on-a-chip analytical devices. However, these constitute novelty in the research and development of approaches for the early diagnosis of pathogens in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, People's Republic of China
| | - Sunny Ahmar
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Muhammad Aamir Sohail
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Muhammad Kamran
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
| | - Mohsin Ali
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Muhammad Hamzah Saleem
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Agha Mushtaque Ahmed
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University Tandojam, Hyderabad, Sindh, 70060, Pakistan
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, 3460000, Talca, Chile.
| | - Antônio Teixeira do Amaral Júnior
- Laboratório de Melhoramento Genético Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil
| | - Mustansar Mubeen
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, 38000, Pakistan.
- Department of Biological Sciences and Technology, China Medical University, Taichung, 40402, Taiwan.
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20
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Rani A, Ravindran VB, Surapaneni A, Shahsavari E, Haleyur N, Mantri N, Ball AS. Evaluation and comparison of recombinase polymerase amplification coupled with lateral-flow bioassay for Escherichia coli O157:H7 detection using diifeerent genes. Sci Rep 2021; 11:1881. [PMID: 33479307 PMCID: PMC7820579 DOI: 10.1038/s41598-021-81312-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serotype O157:H7 is a food and waterborne zoonotic pathogen causing gastroenteritis in humans. Rapid and simple detection in water and food is imperative to control its spread. However, traditional microbial detection approaches are time-consuming, expensive and complex to operate at the point-of-care without professional training. We present a rapid, simple, sensitive, specific and portable method for detection of E. coli O157:H7 in drinking water, apple juice and milk. We evaluated the effect of gene selection in detecting E. coli O157:H7 using recombinase polymerase amplification coupled with a lateral flow assay using rfbE, fliC and stx gene targets. As low as 100 ag and 1 fg DNA, 4-5 CFU/mL and 101 CFU/mL of E. coli O157:H7 was detected using the stx and rfbE gene targets respectively with 100% specificity, whilst the detection limit was 10 fg DNA and 102 CFU/mL for the fliC gene target, with 72.8% specificity. The RPA-LFA can be completed within 8 min at temperatures between 37 and 42 °C with reduced handling and simple equipment requirements. The test threshold amplification of the target was achieved in 5-30 min of incubation. In conclusion, RPA-LFA represents a potential rapid and effective alternative to conventional methods for the monitoring of E. coli O157:H7 in food and water.
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Affiliation(s)
- Alka Rani
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia.
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Aravind Surapaneni
- South East Water, Frankston, VIC, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
| | | | | | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
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21
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Jain A, Sarsaiya S, Chen J, Wu Q, Lu Y, Shi J. Changes in global Orchidaceae disease geographical research trends: recent incidences, distributions, treatment, and challenges. Bioengineered 2020; 12:13-29. [PMID: 33283604 PMCID: PMC8806279 DOI: 10.1080/21655979.2020.1853447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Many of the Orchidaceae species are threatened due to environmental changes and over exploitation for full fill global demands. The main objective of this article was critically analyzed the recent global distribution of Orchidaceae diversity, its disease patterns, microbial disease identification, detection, along with prevention and challenges. Critical analysis findings revealed that Orchidaceae growth and developments were affected indirectly or directly as a result of complex microbial ecological interactions. Studies have identified many species associated with orchids, some are pathogenic and cause symptoms such as soft rot, brown rot, brown spot, black rot, wilt, foliar, root rot, anthracnose, leaf spot. The review was provided the comprehensive data to evaluate the identification and detection of microbial disease, which is the most important challenge for sustainable cultivation of Orchidaceae diversity. Furthermore, this article is the foremost of disease triggering microbes, orchid relations, and assimilates various consequences that both promoted the considerate and facts of such disease multipart, and will permit the development of best operative disease management practices.
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Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China.,Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi, Guizhou, China.,Laboratory, CES Analytical and Research Services India Private Limited (Formerly Known as Creative Enviro Services) , Bhopal, Madhya Pradesh, India
| | - Jishuang Chen
- Bioresource Institute for Healthy Utilization, Zunyi Medical University , Zunyi, Guizhou, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Yuanfu Lu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University , Zunyi, Guizhou, China
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22
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Cheng Y, Tang X, Gao C, Li Z, Chen J, Guo L, Wang T, Xu J. Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops. Pathogens 2020; 9:pathogens9030223. [PMID: 32197350 PMCID: PMC7157645 DOI: 10.3390/pathogens9030223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
Bast fibers and products derived from them are undergoing a resurgence in demand in the global market. However, fungal diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of bast fiber crops in many parts of the world. Thus, there is a high demand for effective control and prevention strategies against fungal pathogens. Having rapid, specific, sensitive, and cost-effective tests that can be used for early and accurate diagnosis of disease agents is an essential step of such strategies. The objective of this study was to review the current status of research on molecular diagnosis of fungal pathogens on bast fiber crops. Our search of PubMed identified nearly 20 genera of fungal pathogens on bast fiber crops, among which the five most common genera were Colletotrichum, Pythium, Verticillium, Fusarium, and Golovinomyces. The gene regions that have been used for molecular identifications of these fungi include internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), ß-tubulin, calmodulin (CAL), histone subunit 3 (H3), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), etc. We summarize the molecular assays that have been used to identify these fungi and discuss potential areas of future development for fast, specific, and accurate diagnosis of fungal pathogens on bast fiber crops.
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Affiliation(s)
- Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Xiaoyu Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
- Department of Biology, McMaster University, Hamilton, L8S 4K1, Canada
- Correspondence:
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23
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Baldi P, La Porta N. Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry. FRONTIERS IN PLANT SCIENCE 2020; 11:570862. [PMID: 33193502 PMCID: PMC7655913 DOI: 10.3389/fpls.2020.570862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 05/14/2023]
Abstract
Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.
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Affiliation(s)
- Paolo Baldi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Paolo Baldi,
| | - Nicola La Porta
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), San Michele a/Adige, Trento, Italy
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