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Zhang L, Ma D, Yu Y, Luo W, Jiang S, Feng S, Chen Z. Advances in biomacromolecule-functionalized magnetic particles for phytopathogen detection. Talanta 2024; 281:126876. [PMID: 39277940 DOI: 10.1016/j.talanta.2024.126876] [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: 04/05/2024] [Revised: 08/20/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Due to the increasing crop losses caused by common and newly emerging phytopathogens, there is a pressing need for the development of rapid and reliable methods for phytopathogen detection and analysis. Leveraging advancements in biochemical engineering technologies and nanomaterial sciences, researchers have put considerable efforts on utilizing biofunctionalized magnetic micro- and nanoparticles (MPs) to develop rapid and reliable systems for phytopathogen detection. MPs facilitate the rapid, high-throughput analysis and in-field applications, while the biomacromolecules, which play key roles in the biorecognitions, interactions and signal amplification, determine the specificity, sensitivity, reliability, and portability of pathogen detection systems. The integration of MPs and biomacromolecules provides dimensionality- and composition-dependent properties, representing a novel approach to develop phytopathogen detection systems. In this review, we summarize and discuss the general properties, synthesis and characterization of MPs, and focus on biomacromolecule-functionalized MPs as well as their representative applications for phytopathogen detection and analysis reported over the past decade. Extensively studied bioreceptors, such as antibodies, phages and phage proteins, nucleic acids, and glycans that are involved in the recognitions and interactions, are covered and discussed. Additionally, the integration of MPs-based detection system with portable microfluidic devices to facilitate their in-field applications is also discussed. Overall, this review focuses on biomacromolecule-functionalized MPs and their applications for phytopathogen detection, aiming to highlight their potential in developing advanced biosensing systems for effective plant protection.
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Affiliation(s)
- Libo Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China.
| | - Dumei Ma
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Youbo Yu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Wiewei Luo
- The Ninth Medical Center of Chinese PLA General Hospital, Chaoyang District, Beijing, 100101, China
| | - Shilong Jiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Sheng Feng
- Department of Pathology and Laboratory Medicine, Boston University, Boston, MA, 02118, USA
| | - Zhuo Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, 550025, China.
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2
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Alieva R, Sokolova S, Zhemchuzhina N, Pankin D, Povolotckaia A, Novikov V, Kuznetsov S, Gulyaev A, Moskovskiy M, Zavyalova E. A Surface-Enhanced Raman Spectroscopy-Based Aptasensor for the Detection of Deoxynivalenol and T-2 Mycotoxins. Int J Mol Sci 2024; 25:9534. [PMID: 39273480 PMCID: PMC11394982 DOI: 10.3390/ijms25179534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
The quality of food is one of the emergent points worldwide. Many microorganisms produce toxins that are harmful for human and animal health. In particular, mycotoxins from Fusarium fungi are strictly controlled in cereals. Simple and robust biosensors are necessary for 'in field' control of the crops and processed products. Nucleic acid-based sensors (aptasensors) offer a new era of point-of-care devices with excellent stability and limits of detection for a variety of analytes. Here we report the development of a surface-enhanced Raman spectroscopy (SERS)-based aptasensor for the detection of T-2 and deoxynivalenol in wheat grains. The aptasensor was able to detect as low as 0.17% of pathogen fungi in the wheat grains. The portable devices, inexpensive SERS substrate, and short analysis time encourage further implementation of the aptasensors outside of highly equipped laboratories.
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Affiliation(s)
- Rugiya Alieva
- Chemistry Department of Lomonosov Moscow State University, Moscow 119991, Russia
| | - Svetlana Sokolova
- Chemistry Department of Lomonosov Moscow State University, Moscow 119991, Russia
| | - Natalia Zhemchuzhina
- All-Russian Research Institute of Phytopathology, Bolshiye Vyazemy 143050, Russia
| | - Dmitrii Pankin
- Center for Optical and Laser Materials Research, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Anastasia Povolotckaia
- Center for Optical and Laser Materials Research, St. Petersburg State University, St. Petersburg 199034, Russia
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
| | - Vasiliy Novikov
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Kuznetsov
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Anatoly Gulyaev
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
| | - Maksim Moskovskiy
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
| | - Elena Zavyalova
- Chemistry Department of Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Scientific Agroengineering Center VIM, Moscow 109428, Russia
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3
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Novi VT, Aboubakr HA, Moore MJ, Zarouri A, Juzwik J, Abbas A. A rapid LAMP assay for the diagnosis of oak wilt with the naked eye. PLANT METHODS 2024; 20:119. [PMID: 39103934 DOI: 10.1186/s13007-024-01254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Oak wilt disease, caused by Bretziella fagacearum is a significant threat to oak (Quercus spp.) tree health in the United States and Eastern Canada. The disease may cause dramatic damage to natural and urban ecosystems without management. Early and accurate diagnosis followed by timely treatment increases the level of disease control success. RESULTS A rapid assay based on loop mediated isothermal amplification (LAMP) was first developed with fluorescence detection of B. fagacearum after 30-minute reaction time. Six different primers were designed to specifically bind and amplify the pathogen's DNA. To simplify the use of this assay in the field, gold nanoparticles (AuNPs) were designed to bind to the DNA amplicon obtained from the LAMP reaction. Upon inducing precipitation, the AuNP-amplicons settle as a red pellet visible to the naked eye, indicative of pathogen presence. Both infected and healthy red oak samples were tested using this visualization method. The assay was found to have high diagnostic sensitivity and specificity for the B. fagacearum isolate studied. Moreover, the developed assay was able to detect the pathogen in crude DNA extracts of diseased oak wood samples, which further reduced the time required to process samples. CONCLUSIONS In summary, the LAMP assay coupled with oligonucleotide-conjugated gold nanoparticle visualization is a promising method for accurate and rapid molecular-based diagnosis of B. fagacearum in field settings. The new method can be adapted to other forest and plant diseases by simply designing new primers.
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Affiliation(s)
- Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Hamada A Aboubakr
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Melanie J Moore
- USDA Forest Service, Northern Research Station, 55108, St. Paul, MN, U.S.A
| | - Akli Zarouri
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Jennifer Juzwik
- USDA Forest Service, Northern Research Station, 55108, St. Paul, MN, U.S.A
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A..
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Manzoor S, Nabi SU, Rather TR, Gani G, Mir ZA, Wani AW, Ali S, Tyagi A, Manzar N. Advancing crop disease resistance through genome editing: a promising approach for enhancing agricultural production. Front Genome Ed 2024; 6:1399051. [PMID: 38988891 PMCID: PMC11234172 DOI: 10.3389/fgeed.2024.1399051] [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: 03/11/2024] [Accepted: 04/22/2024] [Indexed: 07/12/2024] Open
Abstract
Modern agriculture has encountered several challenges in achieving constant yield stability especially due to disease outbreaks and lack of long-term disease-resistant crop cultivars. In the past, disease outbreaks in economically important crops had a major impact on food security and the economy. On the other hand climate-driven emergence of new pathovars or changes in their host specificity further poses a serious threat to sustainable agriculture. At present, chemical-based control strategies are frequently used to control microbial pathogens and pests, but they have detrimental impact on the environment and also resulted in the development of resistant phyto-pathogens. As a replacement, cultivating engineered disease-resistant crops can help to minimize the negative impact of regular pesticides on agriculture and the environment. Although traditional breeding and genetic engineering have been instrumental in crop disease improvement but they have certain limitations such as labour intensity, time consumption, and low efficiency. In this regard, genome editing has emerged as one of the potential tools for improving disease resistance in crops by targeting multiple traits with more accuracy and efficiency. For instance, genome editing techniques, such as CRISPR/Cas9, CRISPR/Cas13, base editing, TALENs, ZFNs, and meganucleases, have proved successful in improving disease resistance in crops through targeted mutagenesis, gene knockouts, knockdowns, modifications, and activation of target genes. CRISPR/Cas9 is unique among these techniques because of its remarkable efficacy, low risk of off-target repercussions, and ease of use. Some primary targets for developing CRISPR-mediated disease-resistant crops are host-susceptibility genes (the S gene method), resistance genes (R genes) and pathogen genetic material that prevents their development, broad-spectrum disease resistance. The use of genome editing methods has the potential to notably ameliorate crop disease resistance and transform agricultural practices in the future. This review highlights the impact of phyto-pathogens on agricultural productivity. Next, we discussed the tools for improving disease resistance while focusing on genome editing. We provided an update on the accomplishments of genome editing, and its potential to improve crop disease resistance against bacterial, fungal and viral pathogens in different crop systems. Finally, we highlighted the future challenges of genome editing in different crop systems for enhancing disease resistance.
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Affiliation(s)
- Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, Srinagar, India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, India
| | | | - Gousia Gani
- Division of Basic Science and Humanities, FOA-SKUAST-K, Wadura, Srinagar, India
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB, Canada
| | - Ab Waheed Wani
- Department of Horticulture, LPU, Jalander, Punjab, India
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganism, Mau, Uttar Pradesh, India
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5
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Julius L, Saeed MM, Kuijpers T, Sandu S, Henihan G, Dreo T, Schoen CD, Mishra R, Dunne NJ, Carthy E, Ducrée J, Kinahan DJ. Low-High-Low Rotationally Pulse-Actuated Serial Dissolvable Film Valves Applied to Solid Phase Extraction and LAMP Isothermal Amplification for Plant Pathogen Detection on a Lab-on-a-Disc. ACS OMEGA 2024; 9:3262-3275. [PMID: 38284094 PMCID: PMC10809376 DOI: 10.1021/acsomega.3c05117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
The ability of the centrifugal Lab-on-a-Disc (LoaD) platform to closely mimic the "on bench" liquid handling steps (laboratory unit operations (LUOs)) such as metering, mixing, and aliquoting supports on-disc automation of bioassay without the need for extensive biological optimization. Thus, well-established bioassays, normally conducted manually using pipettes or using liquid handling robots, can be relatively easily automated in self-contained microfluidic chips suitable for use in point-of-care or point-of-use settings. The LoaD's ease of automation is largely dependent on valves that can control liquid movement on the rotating disc. The optimum valving strategy for a true low-cost and portable device is rotationally actuated valves, which are actuated by changes in the disc spin-speed. However, due to tolerances in disc manufacturing and variations in reagent properties, most of these valving technologies have inherent variation in their actuation spin-speed. Most valves are actuated through stepped increases in disc spin-speed until the motor reaches its maximum speed (rarely more than 6000 rpm). These manufacturing tolerances combined with this "analogue" mechanism of valve actuation limits the number of LUOs that can be placed on-disc. In this work, we present a novel valving mechanism called low-high-low serial dissolvable film (DF) valves. In these valves, a DF membrane is placed in a dead-end pneumatic chamber. Below an actuation spin-speed, the trapped air prevents liquid wetting and dissolving the membrane. Above this spin-speed, the liquid will enter and wet the DF and open the valve. However, as DFs take ∼40 s to dissolve, the membrane can be wetted, and the disc spin-speed reduced before the film opens. Thus, by placing valves in a series, we can govern on which "digital pulse" in spin-speeding a reagent is released; a reservoir with one serial valve will open on the first pulse, a reservoir with two serial valves on the second, and so on. This "digital" flow control mechanism allows the automation of complex assays with high reliability. In this work, we first describe the operation of the valves, outline the theoretical basis for their operation, and support this analysis with an experiment. Next, we demonstrate how these valves can be used to automate the solid-phase extraction of DNA on on-disc LAMP amplification for applications in plant pathogen detection. The disc was successfully used to extract and detect, from a sample lysed off-disc, DNA indicating the presence of thermally inactivated Clavibacter michiganensis ssp. michiganensis (Cmm), a bacterial pathogen on tomato leaf samples.
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Affiliation(s)
- Lourdes
AN Julius
- Fraunhofer
Project Centre at Dublin City University, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
- School
of Physical Sciences, Dublin City University, Dublin D09 V209, Ireland
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
| | - Muhammad Mubashar Saeed
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
- SFI Centre
for Research Training in Machine Learning (ML-Laboratories), Dublin City University, Dublin D09 V209, Ireland
| | - Tim Kuijpers
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
| | - Sergei Sandu
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
| | - Grace Henihan
- Fraunhofer
Project Centre at Dublin City University, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
- School
of Physical Sciences, Dublin City University, Dublin D09 V209, Ireland
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
| | - Tanja Dreo
- National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Cor D Schoen
- Wageningen
University and Research, 6708 PB Wageningen, The Netherlands
| | - Rohit Mishra
- Fraunhofer
Project Centre at Dublin City University, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
- School
of Physical Sciences, Dublin City University, Dublin D09 V209, Ireland
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
| | - Nicholas J Dunne
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
| | - Eadaoin Carthy
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
| | - Jens Ducrée
- School
of Physical Sciences, Dublin City University, Dublin D09 V209, Ireland
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
| | - David J Kinahan
- National
Centre for Sensor Research (NCSR), Dublin
City University, Dublin D09 V209, Ireland
- Biodesign
Europe, Dublin City University, Dublin D09 V209, Ireland
- School
of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin D09 V209, Dublin, Ireland
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Kapytina A, Kolchenko M, Kerimbek N, Pozharskiy AS, Nizamdinova G, Taskuzhina A, Adilbayeva K, Khusnitdinova M, Amidullayeva M, Moisseyev R, Kachiyeva Z, Gritsenko D. Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan. Viruses 2024; 16:96. [PMID: 38257796 PMCID: PMC10819362 DOI: 10.3390/v16010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.
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Affiliation(s)
- Anastasiya Kapytina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Mariya Kolchenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Nazym Kerimbek
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alexandr S. Pozharskiy
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Gulnaz Nizamdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Aisha Taskuzhina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kamila Adilbayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Marina Khusnitdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Malika Amidullayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Ruslan Moisseyev
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Zulfiya Kachiyeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Research Institute of Applied and Fundamental Medicine, Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Dilyara Gritsenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
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7
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Tanny T, Sallam M, Soda N, Nguyen NT, Alam M, Shiddiky MJA. CRISPR/Cas-Based Diagnostics in Agricultural Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11765-11788. [PMID: 37506507 DOI: 10.1021/acs.jafc.3c00913] [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: 07/30/2023]
Abstract
Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.
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Affiliation(s)
- Tanzena Tanny
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Mayers Road, Nambour, QLD 4560, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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8
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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9
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Mishra R, Julius LA, Condon J, Pavelskopfa P, Early PL, Dorrian M, Mrvova K, Henihan G, Mangwanya F, Dreo T, Ducrée J, Macdonald NP, Schoen C, Kinahan DJ. Plant pathogen detection on a lab-on-a-disc using solid-phase extraction and isothermal nucleic acid amplification enabled by digital pulse-actuated dissolvable film valves. Anal Chim Acta 2023; 1258:341070. [PMID: 37087288 DOI: 10.1016/j.aca.2023.341070] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023]
Abstract
By virtue of its ruggedness, portability, rapid processing times, and ease-of-use, academic and commercial interest in centrifugal microfluidic systems has soared over the last decade. A key advantage of the LoaD platform is the ability to automate laboratory unit operations (LUOs) (mixing, metering, washing etc.) to support direct translation of 'on-bench' assays to 'on-chip'. Additionally, the LoaD requires just a low-cost spindle motor rather than specialized and expensive microfluidic pumps. Furthermore, when flow control (valves) is implemented through purely rotational changes in this same spindle motor (rather than using additional support instrumentation), the LoaD offers the potential to be a truly portable, low-cost and accessible platform. Current rotationally controlled valves are typically opened by sequentially increasing the disc spin-rate to a specific opening frequency. However, due lack of manufacturing fidelity these specific opening frequencies are better described as spin frequency 'bands'. With low-cost motors typically having a maximum spin-rate of 6000 rpm (100 Hz), using this 'analogue' approach places a limitation on the number of valves, which can be serially actuated thus limiting the number of LUOs that can be automated. In this work, a novel flow control scheme is presented where the sequence of valve actuation is determined by architecture of the disc while its timing is governed by freely programmable 'digital' pulses in its spin profile. This paradigm shift to 'digital' flow control enables automation of multi-step assays with high reliability, with full temporal control, and with the number of LUOs theoretically only limited by available space on the disc. We first describe the operational principle of these valves followed by a demonstration of the capability of these valves to automate complex assays by screening tomato leaf samples against plant pathogens. Reagents and lysed sample are loaded on-disc and then, in a fully autonomous fashion using only spindle-motor control, the complete assay is automated. Amplification and fluorescent acquisition take place on a custom spin-stand enabling the generation of real-time LAMP amplification curves using custom software. To prevent environmental contamination, the entire discs are sealed from atmosphere following loading with internal venting channels permitting easy movement of liquids about the disc. The disc was successfully used to detect the presence of thermally inactivated Clavibacter michiganensis. Michiganensis (CMM) bacterial pathogen on tomato leaf samples.
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Affiliation(s)
- Rohit Mishra
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland; School of Physical Sciences, Dublin City University, Dublin, Ireland; National Centre for Sensor Research (NCSR), Dublin City University, Dublin, Ireland; Biodesign Europe, Dublin City University, Dublin, Ireland.
| | - Lourdes An Julius
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Jack Condon
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Patricija Pavelskopfa
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Philip L Early
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland; School of Physical Sciences, Dublin City University, Dublin, Ireland; School of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin, Dublin, Ireland
| | - Matthew Dorrian
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Katarina Mrvova
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Grace Henihan
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Faith Mangwanya
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Tanya Dreo
- National Institute of Biology, Ljubljana, Slovenia
| | - Jens Ducrée
- School of Physical Sciences, Dublin City University, Dublin, Ireland
| | - Niall P Macdonald
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland
| | - Cor Schoen
- Wageningen University Research, Wageningen, the Netherlands
| | - David J Kinahan
- Fraunhofer Project Centre at Dublin City University, Dublin City University, Glasnevin, Dublin, Ireland; National Centre for Sensor Research (NCSR), Dublin City University, Dublin, Ireland; Biodesign Europe, Dublin City University, Dublin, Ireland; School of Mechanical and Manufacturing Engineering, Dublin City University, Glasnevin, Dublin, Ireland.
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10
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Delmiglio C, Waite DW, Lilly ST, Yan J, Elliott CE, Pattemore J, Guy PL, Thompson JR. New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand. Viruses 2023; 15:v15020418. [PMID: 36851632 PMCID: PMC9964515 DOI: 10.3390/v15020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
To protect New Zealand's unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies.
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Affiliation(s)
- Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
| | - David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Sonia T. Lilly
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia
| | - Paul L. Guy
- Department of Botany, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Jeremy R. Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence: (C.D.); (J.R.T.)
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11
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Ivanov AV, Safenkova IV, Drenova NV, Zherdev AV, Dzantiev BB. Comparison of Biosensing Methods Based on Different Isothermal Amplification Strategies: A Case Study with Erwinia amylovora. BIOSENSORS 2022; 12:1174. [PMID: 36551141 PMCID: PMC9776058 DOI: 10.3390/bios12121174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Isothermal amplifications allow for the highly sensitive detection of nucleic acids, bypassing the use of instrumental thermal cycling. This work aimed to carry out an experimental comparison of the four most promising techniques: recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) coupled with lateral flow test or coupled with additional amplification based on CRISPR/Cas12a resulting from the fluorescence of the Cas12a-cleaved probe. To compare the four amplification techniques, we chose the bacterial phytopathogen Erwinia amylovora (causative agent of fire blight), which has a quarantine significance in many countries and possesses a serious threat to agriculture. Three genes were chosen as the targets and primers were selected for each one (two for RPA and six for LAMP). They were functionalized by labels (biotin, fluorescein) at the 5' ends for amplicons recognition by LFT. As a result, we developed LAMP-LFT, LAMP-CRISPR/Cas, RPA-LFT, and RPA-CRISPR/Cas for E. amylovora detection. The detection limit was 104 CFU/mL for LAMP-LFT, 103 CFU/mL for LAMP-CRISPR/Cas, and 102 CFU/mL for RPA-LFT and RPA-CRISPR/Cas. The results of four developed test systems were verified by qPCR on a panel of real samples. The developed assays based on RPA, LAMP, CRISPR/Cas12a, and LFT are rapid (30-55 min), user-friendly, and highly sensitive for E. amylovora detection. All proposed detection methods can be applied to fire blight diagnosis and effective management of this disease.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Natalia V. Drenova
- All-Russian Plant Quarantine Centre, Pogranichnaya Street 32, Bykovo, 140150 Ramenskoe, Moscow Region, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
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12
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Sarcina L, Macchia E, Loconsole G, D'Attoma G, Bollella P, Catacchio M, Leonetti F, Di Franco C, Elicio V, Scamarcio G, Palazzo G, Boscia D, Saldarelli P, Torsi L. Fast and Reliable Electronic Assay of a Xylella fastidiosa Single Bacterium in Infected Plants Sap. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203900. [PMID: 36031404 PMCID: PMC9596825 DOI: 10.1002/advs.202203900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Pathogens ultra-sensitive detection is vital for early diagnosis and provision of restraining actions and/or treatments. Among plant pathogens, Xylella fastidiosa is among the most threatening as it can infect hundreds of plant species worldwide with consequences on agriculture and the environment. An electrolyte-gated transistor is here demonstrated to detect X. fastidiosa at a limit-of-quantification (LOQ) of 2 ± 1 bacteria in 0.1 mL (20 colony-forming-unit per mL). The assay is carried out with a millimeter-wide gate functionalized with Xylella-capturing antibodies directly in saps recovered from naturally infected plants. The proposed platform is benchmarked against the quantitave polymerase chain reaction (qPCR) gold standard, whose LOQ turns out to be at least one order of magnitude higher. Furthermore, the assay selectivity is proven against the Paraburkholderia phytofirmans bacterium (negative-control experiment). The proposed label-free, fast (30 min), and precise (false-negatives, false-positives below 1%) electronic assay, lays the ground for an ultra-high performing immunometric point-of-care platform potentially enabling large-scale screening of asymptomatic plants.
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Affiliation(s)
- Lucia Sarcina
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | - Eleonora Macchia
- Dipartimento di Farmacia – Scienze del FarmacoUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | | | - Giusy D'Attoma
- Institute for Sustainable Plant Protection CNRBari70125Italy
| | - Paolo Bollella
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | - Michele Catacchio
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | - Francesco Leonetti
- Dipartimento di Farmacia – Scienze del FarmacoUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | - Cinzia Di Franco
- Istituto di Fotonica e Nanotecnologie CNRc/o Dipartimento Interateneo di FisicaUniversità degli Studi di Bari Aldo MoroBari70125Italy
| | - Vito Elicio
- Agritest SrlTecnopolisCasamassimaBA70010Italy
| | - Gaetano Scamarcio
- Istituto di Fotonica e Nanotecnologie CNRc/o Dipartimento Interateneo di FisicaUniversità degli Studi di Bari Aldo MoroBari70125Italy
- Dipartimento Interateneo di FisicaUniversità degli Studi di Bari Aldo MoroBari70125Italy
| | - Gerardo Palazzo
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
| | - Donato Boscia
- Institute for Sustainable Plant Protection CNRBari70125Italy
| | | | - Luisa Torsi
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro”Bari70125Italy
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13
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Early identification of fungal leaf blight disease (Alternaria alternate) on Platycladus orientalis plants by using gas chromatography-ion mobility spectrometry. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Abdelsalam NR, Hasan ME, Javed T, Rabie SMA, El-Wakeel HEDMF, Zaitoun AF, Abdelsalam AZ, Aly HM, Ghareeb RY, Hemeida AA, Shah AN. Endorsement and phylogenetic analysis of some Fabaceae plants based on DNA barcoding. Mol Biol Rep 2022; 49:5645-5657. [PMID: 35655052 PMCID: PMC9262781 DOI: 10.1007/s11033-022-07574-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/26/2022] [Indexed: 12/23/2022]
Abstract
Background DNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene) of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the “MatK” chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa. Methods and Results MatK gene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade. Conclusion Moreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore, MatK gene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.
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Affiliation(s)
- Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt.
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Samar M A Rabie
- Agricultural Botany Department, Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Houssam El-Din M F El-Wakeel
- Agricultural Botany Department, Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Amera F Zaitoun
- Agricultural Botany Department, Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Aly Z Abdelsalam
- Genetics Department, Faculty of Agriculture, Ain-Shams University, Ain Shams, Egypt
| | - Hesham M Aly
- Department of Forestry and Wood Technology, Horticulture Institute, Agriculture Research Center, Antoniadis Botanical Garden, Alexandria, 21554, Egypt
| | - Rehab Y Ghareeb
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Borg El-Arab, Alexandria, 21934, Egypt
| | - Alaa A Hemeida
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Punjab, Pakistan
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15
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Nganga EM, Kyallo M, Orwa P, Rotich F, Gichuhi E, Kimani JM, Mwongera D, Waweru B, Sikuku P, Musyimi DM, Mutiga SK, Ziyomo C, Murori R, Wasilwa L, Correll JC, Talbot NJ. Foliar Diseases and the Associated Fungi in Rice Cultivated in Kenya. PLANTS 2022; 11:plants11091264. [PMID: 35567265 PMCID: PMC9105481 DOI: 10.3390/plants11091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.
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Affiliation(s)
- Everlyne M. Nganga
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Martina Kyallo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Philemon Orwa
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Felix Rotich
- Department of Water and Agricultural Resource Management, School of Agriculture, University of Embu, Embu P.O. Box 6-60100, Kenya; (P.O.); (F.R.)
| | - Emily Gichuhi
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - John M. Kimani
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - David Mwongera
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - Bernice Waweru
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Phoebe Sikuku
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - David M. Musyimi
- Department of Botany, School of Physical and Biological Sciences, Maseno University, Kisumu P.O. Box 3275-40100, Kenya; (E.M.N.); (P.S.); (D.M.M.)
| | - Samuel K. Mutiga
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
- Correspondence:
| | - Cathrine Ziyomo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya; (M.K.); (B.W.); (C.Z.)
| | - Rosemary Murori
- Department of Entomology and Plant Pathology, Division of Agriculture, The University of Arkansas System, Fayetteville, AR 72701, USA;
| | - Lusike Wasilwa
- Kenya Agricultural and Livestock Research Organization, Kaptagat Road, Loresho, Nairobi P.O. Box 57811-00200, Kenya; (E.G.); (J.M.K.); (D.M.); (L.W.)
| | - James C. Correll
- Eastern and Southern Region Office, International Rice Research Institute, ILRI Complex, Old Naivasha Road, Nairobi P.O. Box 30709-00100, Kenya;
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich NR4 7UH, UK;
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Muramoto J, Parr DM, Perez J, Wong DG. Integrated Soil Health Management for Plant Health and One Health: Lessons From Histories of Soil-borne Disease Management in California Strawberries and Arthropod Pest Management. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.839648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many soil health assessment methods are being developed. However, they often lack assessment of soil-borne diseases. To better address management strategies for soil-borne disease and overall soil and plant health, the concept of Integrated Soil Health Management (ISHM) is explored. Applying the concept of Integrated Pest Management and an agroecological transdisciplinary approach, ISHM offers a framework under which a structure for developing and implementing biointensive soil health management strategies for a particular agroecosystem is defined. As a case study, a history of soil-borne disease management in California strawberries is reviewed and contrasted with a history of arthropod pest management to illustrate challenges associated with soil-borne disease management and the future directions of soil health research and soil-borne disease management. ISHM system consists of comprehensive soil health diagnostics, farmers' location-specific knowledge and adaptability, a suite of soil health management practices, and decision support tools. As we better understand plant-soil-microorganism interactions, including the mechanisms of soil suppressiveness, a range of diagnostic methodologies and indicators and their action thresholds may be developed. These knowledge-intensive and location-specific management systems require transdisciplinary approaches and social learning to be co-developed with stakeholders. The ISHM framework supports research into the broader implications of soil health such as the “One health” concept, which connects soil health to the health of plants, animals, humans, and ecosystems and research on microbiome and nutrient cycling that may better explain these interdependencies.
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Gomez-Gutierrez SV, Goodwin SB. Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2022; 13:857673. [PMID: 35371152 PMCID: PMC8965322 DOI: 10.3389/fpls.2022.857673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 05/31/2023]
Abstract
Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.
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Climent E, Rurack K. Streifenschnelltest mit ppt‐Empfindlichkeit durch Kombination von Elektrochemilumineszenz‐Detektion mit Aptamer‐gesteuerter Indikatorfreisetzung aus mesoporösen Nanopartikeln. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Estela Climent
- Fachbereich Chemische und Optische Sensorik Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str. 11 12489 Berlin Deutschland
| | - Knut Rurack
- Fachbereich Chemische und Optische Sensorik Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str. 11 12489 Berlin Deutschland
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Climent E, Rurack K. Combining Electrochemiluminescence Detection with Aptamer-Gated Indicator Releasing Mesoporous Nanoparticles Enables ppt Sensitivity for Strip-Based Rapid Tests. Angew Chem Int Ed Engl 2021; 60:26287-26297. [PMID: 34595818 PMCID: PMC9298832 DOI: 10.1002/anie.202110744] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/02/2021] [Indexed: 12/11/2022]
Abstract
The combination of electrogenerated chemiluminescence (ECL) and aptamer-gated indicator delivering (gAID) magnetic mesoporous silica nanoparticles embedded into glass fibre paper functionalised with poly(ethyleneglycol) and N-(3-triethoxysilylpropyl)diethanolamine allowed the development of a rapid test that detects penicillin directly in diluted milk down to 50±9 ppt in <5 min. Covalent attachment of the aptamer "cap" to the silica scaffold enabled pore closure through non-covalent electrostatic interactions with surface amino groups, while binding of penicillin led to a folding-up of the aptamer thus releasing the ECL reporter Ru(bpy)32+ previously loaded into the material and letting it be detected after lateral flow by a smartphone camera upon electrochemical excitation with a screen printed electrode inserted into a 3D-printed holder. The approach is simple, generic and presents advantages with respect to sensitivity, measurement uncertainty and robustness compared with conventional fluorescence or electrochemical detection, especially for point-of-need analyses of challenging matrices and analytes at ultra-trace levels.
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Affiliation(s)
- Estela Climent
- Chemical and Optical Sensing DivisionBundesanstalt für Materialforschung und -prüfung (BAM)Richard-Willstätter-Str. 1112489BerlinGermany
| | - Knut Rurack
- Chemical and Optical Sensing DivisionBundesanstalt für Materialforschung und -prüfung (BAM)Richard-Willstätter-Str. 1112489BerlinGermany
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Mansotra R, Vakhlu J. Comprehensive account of present techniques for in-field plant disease diagnosis. Arch Microbiol 2021; 203:5309-5320. [PMID: 34410444 DOI: 10.1007/s00203-021-02529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/19/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
The early detection of plant pathogens is an appropriate preventive strategy for the management of crop yield and quality. For this reason, effective diagnostic techniques and tools, which are simple, specific, rapid and economic, are needed to be developed. Although several such technologies have been developed still most of them suffer one or the other limitation. Major limitations of the widely used diagnostic methods are requirement of trained staff and laboratory setup. Development of point-of-care diagnostic devices (handy portable devices) that require no specialized staff and can directly be used in fields is need of the hour. The aim of this review is to compile the information on current promising techniques that are in use for plant-pathogen diagnosis. Additionally, it focuses on the latest in-field pathogen diagnostic techniques with associated advantages and limitations.
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Affiliation(s)
- Ritika Mansotra
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - Jyoti Vakhlu
- Metagenomic Laboratory, School of Biotechnology, University of Jammu, Jammu, India.
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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