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Sabri M, El Handi K, Valentini F, De Stradis A, Cara O, Calvano CD, Bianco M, Trani A, Elbeaino T. Nisin-based therapy: a realistic and eco-friendly biocontrol strategy to contrast Xylella fastidiosa subsp. pauca infections in planta. Front Microbiol 2024; 15:1406672. [PMID: 38812684 PMCID: PMC11133578 DOI: 10.3389/fmicb.2024.1406672] [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: 03/25/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
The lack of sustainable strategies for combating Xylella fastidiosa (Xf) highlights the pressing need for novel practical antibacterial tools. In this study, Lactococcus lactis subsp. lactis strain ATCC 11454 (L. lactis), known for its production of nisin A, was in vitro tested against Xf subsp. pauca. Preliminary investigations showed that nisin A was involved in a strong antagonistic activity exhibited by L. lactis against Xf. Thus, the efficacy of nisin A was comprehensively assessed through a combination of in vitro and in planta experiments. In vitro investigations employing viable-quantitative PCR, spot assay, turbidity reduction assay, fluorescence microscopy, and transmission electron microscopy demonstrated nisin's robust bactericidal effect on Xf at a minimal lethal concentration of 0.6 mg/mL. Moreover, results from fluorescence and transmission electron microscopies indicated that nisin directly and rapidly interacts with the membranes of Xf cells, leading to the destruction of bacterial cells in few minutes. In in planta tests, nisin also demonstrated the ability to tackle Xf infections within Nicotiana benthamiana plants that remained asymptomatic 74 days post inoculation. Furthermore, RPLC-ESI-MS/MS analyses showed that nisin translocated to all parts of the plants and remains intact for up to 9 days. For the first time, this study underscores the nisin-based strategy as a realistic and eco-friendly approach to be further investigated against Xf infections in the field.
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Affiliation(s)
- Miloud Sabri
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
| | - Kaoutar El Handi
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
| | - Franco Valentini
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
| | - Angelo De Stradis
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), University of Bari, Bari, Italy
| | - Orges Cara
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
- Department of Soil, Plant and Food Science, University of Bari, Bari, Italy
| | | | | | - Antonio Trani
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
| | - Toufic Elbeaino
- International Centre for Advanced Mediterranean Agronomic Studies (CIHEAM of Bari), Bari, Italy
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Naples, Italy
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Krugner R, Rogers EE, Burbank LP, Wallis CM, Ledbetter CA. Insights Regarding Resistance of 'Nemaguard' Rootstock to the Bacterium Xylella fastidiosa. PLANT DISEASE 2022; 106:2074-2081. [PMID: 35253489 DOI: 10.1094/pdis-01-22-0136-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: 06/14/2023]
Abstract
'Nemaguard' is a commonly used rootstock for almond and stone fruits due to resistance to nematodes and enhanced scion vigor. Nemaguard also happens to be resistant to strains of Xylella fastidiosa that cause almond leaf scorch disease. Previous research showed that prior to June-budding, this rootstock can prevent infection of almond nursery stock by X. fastidiosa. Further, the rootstock also promotes recovery from infection in susceptible almond scions. Objectives of this study were to 1) compare movement and bacterial populations of X. fastidiosa in almond and Nemaguard, 2) determine whether the metabolic profile of infected versus noninfected plants of each species correspond with differences in pathogen distribution, and 3) evaluate the impact of feeding on Nemaguard on transmission efficiency and pathogen populations in insects. Results showed limited or no movement of X. fastidiosa beyond the point of mechanical inoculation in Nemaguard, whereas X. fastidiosa was detected in susceptible almond and isolated from plant samples distal to the point of inoculation. Large differences in the concentration of phenolic compounds between Nemaguard and almond were also found, although this was not impacted by infection status. After acquiring X. fastidiosa from infected plants, vector access periods of up to 14 days on Nemaguard neither reduced pathogen populations in vectors nor reduced transmission efficiency of X. fastidiosa to susceptible plants when compared with similar vector-access periods on susceptible grapevines. Results suggest Nemaguard, in spite of having high phenolic concentrations in its xylem, does not directly impact X. fastidiosa survival and that future research should focus on identification of potential physical traits that prevent bacterial attachment, multiplication, or movement within the plant.
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Affiliation(s)
- Rodrigo Krugner
- USDA-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Elizabeth E Rogers
- USDA-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MD 21702-5023
| | - Lindsey P Burbank
- USDA-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Christopher M Wallis
- USDA-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Craig A Ledbetter
- USDA-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
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Velasco-Amo MP, Arias-Giraldo LF, Olivares-García C, Denancé N, Jacques MA, Landa BB. Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain. PLANTS (BASEL, SWITZERLAND) 2022; 11:1562. [PMID: 35736713 PMCID: PMC9228473 DOI: 10.3390/plants11121562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022]
Abstract
Xylella fastidiosa (Xf) is a phytopathogenic bacterium with a repertoire of self-replicating genetic elements, including plasmids, pathogenicity islands, and prophages. These elements provide potential avenues for horizontal gene transfer both within and between species and have the ability to confer new virulence traits, including the ability to colonize new host plants. However, they can also serve as a 'footprint' to type plasmid-bearing strains. Genome sequencing of several strains of Xf subsp. fastidiosa sequence type (ST) 1 from Mallorca Island, Spain, revealed the presence of a 38 kb plasmid (pXFAS_5235). In this study, we developed a PCR-based typing approach using primers targeting the traC gene to determine the presence of pXFAS_5235 plasmid or other plasmids carrying this gene in a world-wide collection of 65 strains X. fastidiosa from different subspecies and STs or in 226 plant samples naturally infected by the bacterium obtained from the different outbreaks of Xf in Spain. The traC gene was amplified only in the plant samples obtained from Mallorca Island infected by Xf subsp. fastidiosa ST1 and from all Spanish strains belonging to this ST. Maximum-likelihood phylogenetic tree of traC revealed a close relatedness among Spanish and Californian strains carrying similar plasmids. Our results confirm previous studies, which suggested that a single introduction event of Xf subsp. fastidiosa ST1 occurred in the Balearic Islands. Further studies on the presence and role of plasmids in Xf strains belonging to the same or different subspecies and STs can provide important information in studies of epidemiology, ecology, and evolution of this plant pathogen.
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Affiliation(s)
- María Pilar Velasco-Amo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14004 Córdoba, Spain; (L.F.A.-G.); (C.O.-G.)
| | - Luis F. Arias-Giraldo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14004 Córdoba, Spain; (L.F.A.-G.); (C.O.-G.)
| | - Concepción Olivares-García
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14004 Córdoba, Spain; (L.F.A.-G.); (C.O.-G.)
| | - Nicolás Denancé
- Groupe d’Étude et de controle des Variétes Et des Semences GEVES, CEDEX, F-49071 Beaucouzé, France;
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France;
| | - Marie-Agnès Jacques
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France;
| | - Blanca B. Landa
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), 14004 Córdoba, Spain; (L.F.A.-G.); (C.O.-G.)
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Baroja U, Garin I, Vallejo N, Caro A, Ibáñez C, Basso A, Goiti U. Molecular assays to reliably detect and quantify predation on a forest pest in bats faeces. Sci Rep 2022; 12:2243. [PMID: 35145165 PMCID: PMC8831491 DOI: 10.1038/s41598-022-06195-7] [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: 08/07/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Targeted molecular methods such as conventional PCR (cPCR) and quantitative PCR (qPCR), combined with species-specific primers and probes, are widely applied for pest species detection. Besides, the potential of qPCR to quantify DNA in samples makes it an invaluable molecular tool to infer the predation levels on specific prey by analysing predators’ stools. Nevertheless, studies on the diet of bats failed to find any empirical relationship, and it remains to be evaluated. Thus, we developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, the pine processionary, Thaumetopoea pityocampa, in bats’ faeces. Further, we empirically compared a range of different known DNA concentrations (input) of the target species mixed with mocks and bat faecal samples against DNA abundances yielded by qPCR (output) for a quantitative assessment. Overall, cPCR showed a lower detection rate than qPCR, but augmenting the replicate effort from one to three replicates led to a greater increase in the detection rate of the cPCR (from 57 to 80%) than the qPCR (from 90 to 99%). The quantitative experiment results showed a highly significant correlation between the input and output DNA concentrations (t = 10.84, p < 0.001) with a mean slope value of 1.05, indicating the accuracy of our qPCR assay to estimate DNA abundance of T. pityocampa in bat faeces. The framework of this study can be taken as a model to design similar assays applicable to other species of interest, such as agricultural pests or insects of public health concern.
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Affiliation(s)
- Unai Baroja
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain.
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Amaia Caro
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Basque Country, Spain
| | - Carlos Ibáñez
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio 26, 41092, Seville, Spain
| | - Andrea Basso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, Padova, Italy
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
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Xylella fastidiosa in Olive: A Review of Control Attempts and Current Management. Microorganisms 2021; 9:microorganisms9081771. [PMID: 34442850 PMCID: PMC8397937 DOI: 10.3390/microorganisms9081771] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2013, Xylella fastidiosa Wells et al. has been reported to infect several hosts and to be present in different areas of Europe. The main damage has been inflicted on the olive orchards of southern Apulia (Italy), where a severe disease associated with X. fastidiosa subspecies pauca strain De Donno has led to the death of millions of trees. This dramatic and continuously evolving situation has led to European and national (Italian and Spanish) measures being implemented to reduce the spread of the pathogen and the associated olive quick decline syndrome (OQDS). Research has been also carried out to find solutions to better and directly fight the bacterium and its main insect vector, Philaenus spumarius L. In the course of this frantic effort, several treatments based on chemical or biological substances have been tested, in addition to plant breeding techniques and integrated pest management approaches. This review aims to summarize the attempts made so far and describe the prospects for better management of this serious threat, which poses alarming questions for the future of olive cultivation in the Mediterranean basin and beyond.
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Widmer TL, Costa JM. Impact of the United States Department of Agriculture, Agricultural Research Service on Plant Pathology: 2015-2020. PHYTOPATHOLOGY 2021; 111:1265-1276. [PMID: 33507089 DOI: 10.1094/phyto-09-20-0393-ia] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
There is an increasing need to supply the world with more food as the population continues to grow. Research on mitigating the effects of plant diseases to improve crop yield and quality can help provide more food without increasing the land area devoted to farming. National Program 303 (NP 303) within the U.S. Department of Agriculture, Agricultural Research Service is dedicated to research across multiple fields in plant pathology. This review article highlights the research impact within NP 303 between 2015 and 2020, including case studies on wheat and citrus diseases and the National Plant Disease Recovery System, which provide specific examples of this impact.
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Affiliation(s)
- Timothy L Widmer
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - José M Costa
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
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Hodgetts J, Glover R, Cole J, Hall J, Boonham N. Genomics informed design of a suite of real-time PCR assays for the specific detection of each Xylella fastidiosa subspecies. J Appl Microbiol 2021; 131:855-872. [PMID: 33098196 DOI: 10.1111/jam.14903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/27/2020] [Accepted: 10/15/2020] [Indexed: 11/27/2022]
Abstract
AIMS Existing methods for the identification of the subspecies of Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and the associated plant health response to outbreaks and interceptions. METHODS AND RESULTS Diagnostic markers were identified using a comparative genomics approach to allow fine differentiation of the very closely related subspecies. Five qPCR assays were designed to allow specific detection of X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, X. fastidiosa subsp. pauca, X. fastidiosa subsp. morus and X. fastidiosa subsp. sandyi. All assays were validated according to the European and Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2). CONCLUSIONS All of the assays were shown to be specific to the target subspecies and all the assays could be used to detect femtogram quantities of X. fastidiosa DNA. SIGNIFICANCE AND IMPACT OF THE STUDY At present, diagnosing the subspecies of X. fastidiosa requires multiple conventional PCR assays (although only available for three of the five subspecies) or multi-locus sequence typing which takes several days. By comparison, the new assays provide a substantial reduction in the turnaround time for direct identification to the subspecies level in as little as 75 min.
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Affiliation(s)
- J Hodgetts
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - R Glover
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - J Cole
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - J Hall
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - N Boonham
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK.,Institute for Agri-Food Research and Innovation, University of Newcastle, Newcastle upon Tyne, UK
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Moralejo E, Gomila M, Montesinos M, Borràs D, Pascual A, Nieto A, Adrover F, Gost PA, Seguí G, Busquets A, Jurado-Rivera JA, Quetglas B, García JDD, Beidas O, Juan A, Velasco-Amo MP, Landa BB, Olmo D. Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe. Commun Biol 2020; 3:560. [PMID: 33037293 PMCID: PMC7547738 DOI: 10.1038/s42003-020-01284-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
The recent introductions of the bacterium Xylella fastidiosa (Xf) into Europe are linked to the international plant trade. However, both how and when these entries occurred remains poorly understood. Here, we show how almond scorch leaf disease, which affects ~79% of almond trees in Majorca (Spain) and was previously attributed to fungal pathogens, was in fact triggered by the introduction of Xf around 1993 and subsequently spread to grapevines (Pierceʼs disease). We reconstructed the progression of almond leaf scorch disease by using broad phylogenetic evidence supported by epidemiological data. Bayesian phylogenetic inference predicted that both Xf subspecies found in Majorca, fastidiosa ST1 (95% highest posterior density, HPD: 1990–1997) and multiplex ST81 (95% HPD: 1991–1998), shared their most recent common ancestors with Californian Xf populations associated with almonds and grapevines. Consistent with this chronology, Xf-DNA infections were identified in tree rings dating to 1998. Our findings uncover a previously unknown scenario in Europe and reveal how Pierce’s disease reached the continent. Eduardo Moralejo et al. report a phylogenetic reconstruction tracing the origin and progression of a European outbreak of the almond scorch disease pathogen Xylella fastidiosa (Xf). Their data suggest Xf was introduced into Europe via grafting from infected Californian buds and was subsequently spread by the meadow spittlebug to multiple plant hosts.
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Affiliation(s)
- Eduardo Moralejo
- Tragsa, Empresa de Transformación Agraria, Delegación de Baleares, 07005, Palma de Majorca, Spain.
| | - Margarita Gomila
- Microbiology (Biology Department), University of the Balearic Islands, 07122, Palma de Majorca, Spain
| | - Marina Montesinos
- Tragsa, Empresa de Transformación Agraria, Delegación de Baleares, 07005, Palma de Majorca, Spain
| | - David Borràs
- Serveis de Millora Agrària i Pesquera, Govern de les illes Balears, 07009, Palma de Majorca, Spain
| | - Aura Pascual
- Tragsa, Empresa de Transformación Agraria, Delegación de Baleares, 07005, Palma de Majorca, Spain
| | - Alicia Nieto
- Serveis de Millora Agrària i Pesquera, Govern de les illes Balears, 07009, Palma de Majorca, Spain
| | - Francesc Adrover
- Serveis de Millora Agrària i Pesquera, Govern de les illes Balears, 07009, Palma de Majorca, Spain
| | - Pere A Gost
- Servei d'Agricultura, Conselleria d'Agricultura, Pesca i Alimentació; Govern de les illes Balears, 07006, Palma de Majorca, Spain
| | - Guillem Seguí
- Microbiology (Biology Department), University of the Balearic Islands, 07122, Palma de Majorca, Spain
| | - Antonio Busquets
- Microbiology (Biology Department), University of the Balearic Islands, 07122, Palma de Majorca, Spain
| | - José A Jurado-Rivera
- Laboratory of Genetics (Biology Department), University of the Balearic Islands, 07122, Palma de Majorca, Spain
| | - Bàrbara Quetglas
- Servei d'Agricultura, Conselleria d'Agricultura, Pesca i Alimentació; Govern de les illes Balears, 07006, Palma de Majorca, Spain
| | - Juan de Dios García
- Servei d'Agricultura, Conselleria d'Agricultura, Pesca i Alimentació; Govern de les illes Balears, 07006, Palma de Majorca, Spain
| | - Omar Beidas
- Servei d'Agricultura, Conselleria d'Agricultura, Pesca i Alimentació; Govern de les illes Balears, 07006, Palma de Majorca, Spain
| | - Andreu Juan
- Servei d'Agricultura, Conselleria d'Agricultura, Pesca i Alimentació; Govern de les illes Balears, 07006, Palma de Majorca, Spain
| | - María P Velasco-Amo
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004, Córdoba, Spain
| | - Blanca B Landa
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004, Córdoba, Spain
| | - Diego Olmo
- Serveis de Millora Agrària i Pesquera, Govern de les illes Balears, 07009, Palma de Majorca, Spain
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Elbeaino T, Incerti O, Dakroub H, Valentini F, Huang Q. Development of an FTP-LAMP assay based on TaqMan real-time PCR and LAMP for the specific detection of Xylella fastidiosa De Donno and mulberry strains in both plants and insect vectors. J Microbiol Methods 2020; 175:105992. [PMID: 32589892 DOI: 10.1016/j.mimet.2020.105992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 10/24/2022]
Abstract
We developed two real-time detection assays, TaqMan real-time PCR and LAMP, using primers and probe designed based on a sequence annotated to code for a Haemagglutinin-related protein (Hg) of Xylella fastidiosa (Xf), a gene uniquely present in the Italian olive (De Donno of olive) and American mulberry strains, for specific detection of the target Xf strains. These assays were validated with DNA samples extracted from Xf-infected plant samples and from two species of insect vectors (Philaenus spumarius, Ps; and Neophilaenus campestris, Nc). Both techniques were proven to be highly sensitive (100 fg of Xf-genomic DNA) and specific to the Italian De Donno and American mulberry strains of Xf. When our LAMP was utilized in a duplex manner by combining with previously published universal primers and probe for detection of all Xf-subspecies and strains, the duplex LAMP showed high versatility in the simultaneous detection and differentiation of the Italian De Donno and American mulberry stains form other subspecies/strains. Furthermore, the Hg gene-specific LAMP primers and TaqMan probe were exploited to develop a new approach; henceforth referred to as the Fluorescence of TaqMan Probe upon Dequenching - Loop mediated Isothermal Amplification (FTP-LAMP). In the FTP-LAMP, the Xf-Hg specific fluorophore-quenched probe was added to a standard LAMP reaction and fluoresces only when bound to its target, allowing for a sequence-specific detection of the Xf-Italian De Donno and American mulberry strains in a LAMP context. Our FTP-LAMP assay showed to be highly sensitive detecting down to 100 fg genomic DNA of Xf, when tested on Xf-genomic DNA extracted from infected plants, DAS-ELISA-crude saps and insect vectors. Furthermore, the assay showed high specificity (98.7% vs 89% for LAMP) when applied on DNA templates from insect vectors. With the addition of an extra target sequence-specific probe acting as a direct Xf-specific dye, the FTP-LAMP has gained more specificity and reduced one of the main problems of the LAMP assay (false positives) when used for detecting of Xf in insect vectors. To the best of our knowledge, this study reports the development of the first LAMP assay and the first novel FTP-LAMP method for specific detection of the Italian De Donno and the American mulberry strains of Xf. Together with the Xf universal LAMP primers in a duplex approach, the FTP-LAMP could represent a useful tool not only for the specific detection of the olive-associated strain in Italy, but also to differentiate the De Donno strain from other strains of Xf already reported in Italy and Europe (Germany, France, Spain and Portugal).
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Affiliation(s)
- Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, BA, Italy.
| | - Ornella Incerti
- Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, BA, Italy
| | - Hiba Dakroub
- Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, BA, Italy
| | - Franco Valentini
- Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, BA, Italy
| | - Qi Huang
- Floral and Nursery Plants Research Unit, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe. SUSTAINABILITY 2020. [DOI: 10.3390/su12114508] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.
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11
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Dussault‐Benoit C, Arsenault‐Labrecque G, Sonah H, Belzile F, Bélanger RR. Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes. MOLECULAR PLANT PATHOLOGY 2020; 21:318-329. [PMID: 31908142 PMCID: PMC7036360 DOI: 10.1111/mpp.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
The soybean-Phytophthora sojae interaction operates on a gene-for-gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour-intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.
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Affiliation(s)
| | | | - Humira Sonah
- Department of PhytologyUniversité LavalQuébecQCCanada
- National Agri‐Food Biotechnology Institute (NABI)MohaliIndia
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Burbank LP, Sisterson MS, O'Leary ML. Infection of Blueberry Cultivar 'Emerald' with a California Pierce's Disease Strain of Xylella fastidiosa and Acquisition by Glassy-Winged Sharpshooter. PLANT DISEASE 2020; 104:154-160. [PMID: 31697223 DOI: 10.1094/pdis-05-19-1126-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: 06/10/2023]
Abstract
Bacterial leaf scorch disease caused by Xylella fastidiosa occurs in southern highbush blueberry varieties in the southeastern United States. Susceptibility to X. fastidiosa varies by blueberry cultivar, and these interactions are often strain-specific. Xylella fastidiosa subsp. fastidiosa is the causal agent of Pierce's disease in grapevines, and it has been problematic in the San Joaquin Valley of California since the introduction of the glassy-winged sharpshooter (Homalodisca vitripennis). The glassy-winged sharpshooter is known to feed on blueberry, a crop that is expanding in the San Joaquin Valley. Currently, little is known about the potential for the spread of X. fastidiosa between grape and blueberry in this region. The ability of a Pierce's disease strain of X. fastidiosa from the San Joaquin Valley to cause disease in southern highbush blueberry and the potential for the glassy-winged sharpshooter to transmit X. fastidiosa between blueberry and grapevine were investigated. Experimental inoculations showed that the X. fastidiosa subsp. fastidiosa strain Bakersfield-1 can cause disease in blueberry cv. Emerald, and that the glassy-winged sharpshooter can acquire X. fastidiosa from artificially inoculated blueberry plants under laboratory conditions. Understanding the possibility for X. fastidiosa strains from the San Joaquin Valley to infect multiple crops grown in proximity is important for area-wide pest and disease management.
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Affiliation(s)
- Lindsey P Burbank
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Mark S Sisterson
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Michael L O'Leary
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
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Dupas E, Briand M, Jacques MA, Cesbron S. Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues. FRONTIERS IN PLANT SCIENCE 2019; 10:1732. [PMID: 31956326 PMCID: PMC6951419 DOI: 10.3389/fpls.2019.01732] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Xylella fastidiosa (Xf) is an insect-borne bacterium confined to the xylem vessels of plants. This plant pathogen has a broad host range estimated to 560 plant species. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspecies fastidiosa, multiplex, and pauca. Initially limited to the Americas, Xf has been detected in Europe since 2013. As management of X. fastidiosa outbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Thus, we developed various tetraplex and triplex quantitative PCR (qPCR) assays for X. fastidiosa detection and subspecies identification in planta in a single reaction. We designed primers and probes using SkIf, a bioinformatics tool based on k-mers, to detect specific signatures of the species and subspecies from a data set of 58 genome sequences representative of X. fastidiosa diversity. We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies of X. fastidiosa, and on samples from various environmental and inoculated host plants. Sensitivity of simplex assays was equal or slightly better than the reference protocol on purified DNA. Tetraplex qPCR assays had the same sensitivity than the reference protocol and allowed X. fastidiosa detection in all spiked matrices up to 103 cells.ml-1. Moreover, mix infections of two to three subspecies could be detected in the same sample with tetraplex assays. In environmental plant samples, the tetraplex qPCR assays allowed subspecies identification when the current method based on multilocus sequence typing failed. The qPCR assays described here are robust and modular tools that are efficient for differentiating X. fastidiosa subspecies directly in plant samples.
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Affiliation(s)
- Enora Dupas
- IRHS, Agrocampus-Ouest, INRA, University of Angers, SFR 4207 QuaSaV, Beaucouzé, France
- French Agency for Food, Environmental and Occupational Health & Safety, Plant Health Laboratory, Angers, France
| | - Martial Briand
- IRHS, Agrocampus-Ouest, INRA, University of Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, Agrocampus-Ouest, INRA, University of Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Sophie Cesbron
- IRHS, Agrocampus-Ouest, INRA, University of Angers, SFR 4207 QuaSaV, Beaucouzé, France
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Conti M, Cinget B, Vivancos J, Oudemans P, Bélanger RR. A Molecular Assay Allows the Simultaneous Detection of 12 Fungi Causing Fruit Rot in Cranberry. PLANT DISEASE 2019; 103:2843-2850. [PMID: 31469361 DOI: 10.1094/pdis-03-19-0531-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cranberry fruit rot (CFR) is arguably one of the most limiting factors of cranberry (Vaccinium macrocarpon) production throughout its growing areas. The disease is caused by a group of closely related fungi that require identification using long and cumbersome steps of isolation and microscopic observations of structural features. The objective of this study was to develop a molecular assay to simultaneously detect and discriminate 12 of the most important fungal species reported to be pathogenic on cranberry fruit to facilitate the diagnosis of CFR. As the first approach, internal transcribed spacers and large subunit regions of all fungi were sequenced and confirmed with sequences available in the NCBI database. These data were used to develop primers able to differentiate seven of the 12 species. The five remaining species, including three in the Phacidiaceae family and two in the Glomerellaceae family, were differentiated on the basis of a more discriminant marker, the translation elongation factor 1-α. Two PCR reactions were optimized to clearly delineate the 12 species. The multiplex test was first validated using pure fungal cultures; it was subsequently validated using fruit collected in cranberry beds in eastern Canada. In the latter case, the test was rigorous enough to clearly discriminate the fungal pathogens from contaminants. Within the tested samples, Physalospora vaccinii and Coleophoma empetri were most commonly found. This molecular test offers scientists, diagnosticians, and growers a powerful tool that can rapidly and precisely identify fungi causing CFR so they can implement appropriate control methods.
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Affiliation(s)
- Matteo Conti
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Benjamin Cinget
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
| | - Julien Vivancos
- Laboratoire d'expertise et de Diagnostic en Phytoprotection, Quebec City, Québec, Canada
| | - Peter Oudemans
- Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, The State University of New Jersey, Chatsworth, NJ, U.S.A
| | - Richard R Bélanger
- Centre de Recherche en Innovation des Végétaux, Université Laval, Quebec City, Québec, Canada
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