A Powerful LAMP Weapon against the Threat of the Quarantine Plant Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens

Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum

Curtobacterium flaccumfaciens (Microbacteriaceae), a plant-pathogenic coryneform species includes five pathovars with valid names and a number of proposed - but unvalidated - new members. In this study, phenotypic features and DNA similarity indexes were investigated among all C. flaccumfaciens members. Results showed that the C. flaccumfaciens pv. poinsettiae strains causing bacterial canker of Euphorbia pulcherrima in the USA as well as the orange-/red-pigmented strains of C. flaccumfaciens pv. flaccumfaciens pathogenic on dry beans in Iran are too distinct from each other and from the type strain of the species to be considered members of C. flaccumfaciens. Hence, the latter two groups were elevated at the species level as C. poinsettiae sp. nov. (ATCC 9682T = CFBP 2403T = ICMP 2566T = LMG 3715T = NCPPB 854T as type strain), and C. aurantiacum sp. nov. (50RT = CFBP 8819T = ICMP 22071T as type strain). Within the emended species C. flaccumfaciens comb. nov., yellow-pigmented strains causing bacterial wilt of dry beans and those causing bacterial canker of Euphorbia pulcherrima in Europe were retained as C. flaccumfaciens pv. flaccumfaciens and C. flaccumfaciens pv. poinsettiae, respectively; while taxonomic position of the sugar beet pathogen C. flaccumfaciens pv. beticola ATCC BAA144PT was confirmed. The newly described onion pathogen C. allii was also reclassified as C. flaccumfaciens pv. allii with the pathotype strain LMG 32517PT. Furthermore, C. flaccumfaciens pv. basellae causing bacterial leaf spot of malabar spinach (Basella rubra) was transferred to C. citreum pv. basellae with ATCC BAA143PT as pathotype.

Current trends in management of bacterial pathogens infecting plants

Plants are continuously challenged by different pathogenic microbes that reduce the quality and quantity of produce and therefore pose a serious threat to food security. Among them bacterial pathogens are known to cause disease outbreaks with devastating economic losses in temperate, tropical and subtropical regions throughout the world. Bacteria are structurally simple prokaryotic microorganisms and are diverse from a metabolic standpoint. Bacterial infection process mainly involves successful attachment or penetration by using extracellular enzymes, type secretion systems, toxins, growth regulators and by exploiting different molecules that modulate plant defence resulting in successful colonization. Theses bacterial pathogens are extremely difficult to control as they develop resistance to antibiotics. Therefore, attempts are made to search for innovative methods of disease management by the targeting bacterial virulence and manipulating the genes in host plants by exploiting genome editing methods. Here, we review the recent developments in bacterial disease management including the bioactive antimicrobial compounds, bacteriophage therapy, quorum-quenching mediated control, nanoparticles and CRISPR/Cas based genome editing techniques for bacterial disease management. Future research should focus on implementation of smart delivery systems and consumer acceptance of these innovative methods for sustainable disease management.

Point-of-Care DNA Amplification for Disease Diagnosis and Management

Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.

Detection and Control of Pantoea agglomerans Causing Plum Bacterial Shot-Hole Disease by Loop-Mediated Isothermal Amplification Technique

Plum bacterial shot-hole caused by Pantoea agglomerans (P. agglomerans) is one of the primary bacterial diseases in plum tree planting areas, resulting in abnormal growth of plum trees and severe economic losses. Early diagnosis of P. agglomerans is crucial to effectively control plant diseases. In this study, loop-mediated isothermal amplification (LAMP) analysis for genome-specific gene sequences was developed for the specific detection of P. agglomerans. We designed the LAMP primers based on the gyrB gene of P. agglomerans. The best reaction system was 0.2 μmol·L-1 for outer primer F3/B3 and 1.6 μmol·L-1 for inner primer FIP/BIP. The LAMP reaction was optimal at 65°C for 60 min based on the color change and gel electrophoresis. This technology distinguished P. agglomerans from other control bacteria. The detection limit of the LAMP technology was 5 fg·μl-1 genomic DNA of P. agglomerans, which is 1,000 times that of the traditional PCR detection method. The LAMP technology could effectively detect the DNA of P. agglomerans from the infected leaves without symptoms after indoor inoculation. Furthermore, the LAMP technology was applied successfully to detect field samples, and the field control effect of 0.3% tetramycin after LAMP detection reached 82.51%, which was 7.90% higher than that of conventional control. The proposed LAMP detection technology in this study offers the advantages of ease of operation, visibility of results, rapidity, accuracy, and high sensitivity, making it suitable for the early diagnosis of plum bacteria shot-hole disease.

Innovative Detection of the Quarantine Plant Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens, Causal Agent of Bacterial Wilt of Leguminous Plants

Specific, sensitive, and rapid detection of quarantine and regulated plant pathogens is pivotal for the control of the diseases they cause. Here, we describe the PCR-based methods which have been developed for Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), quarantine plant pathogenic bacterium for EU and causal agent of bacterial wilt of Leguminous plants. These methods include an end-point and a real-time PCR test, and a LAMP assay. Their threshold analytical limits range from 100 to 10 fg of DNA template per reaction and are currently used worldwide for routine testing for Cff from laboratory to field scale.

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.