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Singh S, Narine LL, Willoughby JR, Eckhardt LG. Remote sensing-based detection of brown spot needle blight: a comprehensive review, and future directions. PeerJ 2025; 13:e19407. [PMID: 40416626 PMCID: PMC12103847 DOI: 10.7717/peerj.19407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 04/10/2025] [Indexed: 05/27/2025] Open
Abstract
Pine forests are increasingly threatened by needle diseases, including Brown Spot Needle Blight (BSNB), caused by Lecanosticta acicola. BSNB leads to needle loss, reduced growth, significant tree mortality, and disruptions in global timber production. Due to its severity, L. acicola is designated as a quarantine pathogen in several countries, requiring effective early detection and control of its spread. Remote sensing (RS) technologies provide scalable and efficient solutions for broad-scale disease surveillance. This study systematically reviews RS-based methods for detecting BSNB symptoms, assessing current research trends and potential applications. A comprehensive bibliometric analysis using the Web of Science database indicated that direct RS applications for BSNB remain scarce. However, studies on other needle diseases demonstrated the effectiveness of multisource RS techniques for symptom detection, spatial mapping, and severity assessment. Advancements in machine learning (ML) and deep learning (DL) have further improved RS capabilities for automated disease classification and predictive modeling in forest health monitoring. Climate-driven factors, such as temperature and precipitation, regulate the distribution and severity of emerging pathogens. Geospatial analyses and species distribution modeling (SDM) have been successfully applied to predict BSNB pathogen's range expansion under changing climatic conditions. Integrating these models with RS-based monitoring enhances early detection and risk assessment. However, despite these advancements, direct RS applications for BSNB detection remain limited. This review identifies key knowledge gaps and highlights the need for further research to optimize RS-based methodologies, refine predictive models, and develop early warning systems for improved forest management.
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Affiliation(s)
- Swati Singh
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, AL, USA
| | - Lana L. Narine
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, AL, USA
| | - Janna R. Willoughby
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, AL, USA
| | - Lori G. Eckhardt
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, AL, USA
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Guinet C, Buronfosse M, Tanguay P, Frey P, Ioos R. Development of a New Tool to Detect Melampsora medusae f. sp. tremuloidae Causing Rust Disease on Populus tremuloides. PLANT DISEASE 2025; 109:792-799. [PMID: 39453668 DOI: 10.1094/pdis-07-24-1477-sc] [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: 10/26/2024]
Abstract
Melampsora medusae f. sp. tremuloidae is a quarantine organism for the European Union. In North America, this fungus causes rust disease on Populus tremuloides. In Europe, Populus tremula, an aspen closely related to P. tremuloides, is widespread and plays an important ecological role. Introduction of M. medusae f. sp. tremuloidae into Europe could be a major risk if this forma specialis could evolve and become virulent on P. tremula. To date, no PCR-based assay exists to specifically detect M. medusae f. sp. tremuloidae. In this study, a sensitive and specific real-time PCR assay has been developed based on the 28S rDNA. The assay proved to be reliable using many real-time PCR kits and platforms. It can be used to monitor the introduction and the spread of M. medusae f. sp. tremuloidae in the context of phytosanitary regulations.
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Affiliation(s)
- Cécile Guinet
- ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE 1480, Malzéville, France
| | - Marius Buronfosse
- ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE 1480, Malzéville, France
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Canada
| | - Pascal Frey
- Université de Lorraine, INRAE, IAM F-54000, Nancy, France
| | - Renaud Ioos
- ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE 1480, Malzéville, France
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Tubby K, Forster J, Mullett M, Needham R, Smith O, Snowden J, McCartan S. Can the Seed Trade Provide a Potential Pathway for the Global Distribution of Foliar Pathogens? An Investigation into the Use of Heat Treatments to Reduce Risk of Dothistroma septosporum Transmission via Seed Stock. J Fungi (Basel) 2023; 9:1190. [PMID: 38132790 PMCID: PMC10744699 DOI: 10.3390/jof9121190] [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: 11/08/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
The international plant trade results in the accidental movement of invasive pests and pathogens, and has contributed significantly to recent range expansion of pathogens including Dothistroma septosporum. Seeds are usually thought to present a lower biosecurity risk than plants, but the importation of Pinus contorta seeds from North America to Britain in the mid-1900s, and similarities between British and Canadian D. septosporum populations suggests seeds could be a pathway. Dothistroma septosporum has not been isolated from seeds, but inadequately cleaned seed material could contain infected needle fragments. This case study investigated whether cone kilning, and wet and dry heat treatments could reduce D. septosporum transmission without damaging seed viability. Pinus needles infected with D. septosporum were incubated alongside cones undergoing three commercial seed extraction processes. Additional needles were exposed to temperatures ranging from 10 to 67 °C dry heat for up to 48 h, or incubated in water heated to between 20 and 60 °C for up to one hour. Pinus sylvestris seeds were exposed to 60 and 65 dry heat °C for 48 h, and further seed samples incubated in water heated to between 20 and 60 °C for up to one hour. Dothistroma septosporum survived the three kilning processes and while seeds were not damaged by dry heat exceeding 63.5 °C, at this temperature no D. septosporum survived. Wet heat treatments resulted in less than 10% pathogen survival following incubation at 40 °C, while at this temperature the seeds suffered no significant impacts, even when submerged for one hour. Thus, commercial seed kilning could allow D. septosporum transmission, but elevated wet and dry heat treatments could be applied to seed stock to minimise pathogen risk without significantly damaging seed viability.
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Affiliation(s)
- Katherine Tubby
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
| | - Jack Forster
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
| | - Martin Mullett
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Phytophthora Research Centre, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Robert Needham
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
| | - Olivia Smith
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
| | - James Snowden
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
| | - Shelagh McCartan
- Forest Research, Forestry Commission, Alice Holt Lodge, Farnham GU10 4LH, UK (M.M.); (O.S.); (J.S.); (S.M.)
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Mesanza N, Barnes I, van der Nest A, Raposo R, Berbegal M, Iturritxa E. Genetic Diversity of Lecanosticta acicola in Pinus Ecosystems in Northern Spain. J Fungi (Basel) 2023; 9:651. [PMID: 37367587 DOI: 10.3390/jof9060651] [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: 05/01/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
Lecanosticta acicola is one of the most damaging species affecting Pinus radiata plantations in Spain. Favourable climatic conditions and unknown endogenous factors of the pathogen and host led to a situation of high incidence and severity of the disease in these ecosystems. With the main aim of understanding the factors intrinsic to this pathogenic species, a study of the population structure in new established plantations with respect to older plantations was implemented. The genetic diversity, population structure and the ability of the pathogen to spread was determined in Northern Spain (Basque Country), where two thirds of the total Pinus radiata plantations of Spain are located. From a total of 153 Lecanosticta acicola isolates analysed, two lineages were present; the southern lineage, which was prevalent, and the northern lineage, which was scarce. A total of 22 multilocus genotypes were detected with a balanced composition of both mating types and evidence for sexual reproduction. In addition to the changing environmental conditions enhancing disease expression, the complexity and diversity of the pathogen will make it difficult to control and to maintain the wood productive system fundamentally based on this forest species.
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Affiliation(s)
- Nebai Mesanza
- Neiker-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, Granja Modelo s/n, Antigua Carretera Nacional 1, Km. 355, 01192 Arkaute, Spain
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0083, South Africa
| | - Ariska van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0083, South Africa
| | - Rosa Raposo
- ICIFOR, INIA-CSIC, Carretera La Coruña Km 7.5, 28040 Madrid, Spain
| | - Mónica Berbegal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera S/N, 46022 Valencia, Spain
| | - Eugenia Iturritxa
- Neiker-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, Granja Modelo s/n, Antigua Carretera Nacional 1, Km. 355, 01192 Arkaute, Spain
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Tubby K, Adamčikova K, Adamson K, Akiba M, Barnes I, Boroń P, Bragança H, Bulgakov T, Burgdorf N, Capretti P, Cech T, Cleary M, Davydenko K, Drenkhan R, Elvira-Recuenco M, Enderle R, Gardner J, Georgieva M, Ghelardini L, Husson C, Iturritxa E, Markovskaja S, Mesanza N, Ogris N, Oskay F, Piškur B, Queloz V, Raitelaitytė K, Raposo R, Soukainen M, Strasser L, Vahalík P, Vester M, Mullett M. The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola. FOREST ECOLOGY AND MANAGEMENT 2023; 536:120847. [PMID: 37193248 PMCID: PMC10165473 DOI: 10.1016/j.foreco.2023.120847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 05/18/2023]
Abstract
European forests are threatened by increasing numbers of invasive pests and pathogens. Over the past century, Lecanosticta acicola, a foliar pathogen predominantly of Pinus spp., has expanded its range globally, and is increasing in impact. Lecanosticta acicola causes brown spot needle blight, resulting in premature defoliation, reduced growth, and mortality in some hosts. Originating from southern regions of North American, it devastated forests in the USA's southern states in the early twentieth century, and in 1942 was discovered in Spain. Derived from Euphresco project 'Brownspotrisk,' this study aimed to establish the current distribution of Lecanosticta species, and assess the risks of L. acicola to European forests. Pathogen reports from the literature, and new/ unpublished survey data were combined into an open-access geo-database (http://www.portalofforestpathology.com), and used to visualise the pathogen's range, infer its climatic tolerance, and update its host range. Lecanosticta species have now been recorded in 44 countries, mostly in the northern hemisphere. The type species, L. acicola, has increased its range in recent years, and is present in 24 out of the 26 European countries where data were available. Other species of Lecanosticta are largely restricted to Mexico and Central America, and recently Colombia. The geo-database records demonstrate that L. acicola tolerates a wide range of climates across the northern hemisphere, and indicate its potential to colonise Pinus spp. forests across large swathes of the Europe. Preliminary analyses suggest L. acicola could affect 62% of global Pinus species area by the end of this century, under climate change predictions. Although its host range appears slightly narrower than the similar Dothistroma species, Lecanosticta species were recorded on 70 host taxa, mostly Pinus spp., but including, Cedrus and Picea spp. Twenty-three, including species of critical ecological, environmental and economic significance in Europe, are highly susceptible to L. acicola, suffering heavy defoliation and sometimes mortality. Variation in apparent susceptibility between reports could reflect variation between regions in the hosts' genetic make-up, but could also reflect the significant variation in L. acicola populations and lineages found across Europe. This study served to highlight significant gaps in our understanding of the pathogen's behaviour. Lecanosticta acicola has recently been downgraded from an A1 quarantine pest to a regulated non quarantine pathogen, and is now widely distributed across Europe. With a need to consider disease management, this study also explored global BSNB strategies, and used Case Studies to summarise the tactics employed to date in Europe.
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Affiliation(s)
- K. Tubby
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, United Kingdom
| | - K. Adamčikova
- Department of Plant Pathology and Mycology, Institute of Forest Ecology, Slovak Academy of Sciences, Akademická 2, 94901 Nitra, Slovak Republic
| | - K. Adamson
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - M. Akiba
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - I. Barnes
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - P. Boroń
- Department Forest Ecosystems Protection, University of Agriculture in Kraków, 31-425 Kraków, Poland
| | - H. Bragança
- Instituto Nacional de Investigação Agrária e Veterinária I. P. and GREEN-IT Bioresources for Sustainability, ITQB NOVA, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - T. Bulgakov
- Department of Plant Protection, Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Yana Fabritsiusa Street 2/28, Sochi 354002, Krasnodar Region, Russia
| | - N. Burgdorf
- Bavarian State Institute of Forestry, Hans-Carl-von-Carlowitz-Platz 1, 85354 Freising, Germany
| | - P. Capretti
- University of Florence, DAGRI Department of Agricultural, Food, Environmental and Forest Sciences and Technologies, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - T. Cech
- Austrian Research Centre for Forests BFW, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - M. Cleary
- Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre, Sundsvägen 3, 230 503 Alnarp, Sweden
| | - K. Davydenko
- Ukrainian Research Institute of Forestry & Forest Melioration, Kharkiv, Ukraine
- Swedish University of Agricultural Science, Uppsala, Sweden
| | - R. Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - M. Elvira-Recuenco
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Investigación Forestal (INIA-CIFOR), 28040 Madrid, Spain
| | - R. Enderle
- Institute for Plant Protection in Horticulture and Urban Green, Julius Kuehn Institute, Braunschweig, Germany
| | - J. Gardner
- Scion, Private Bag 3020, Rotorua 3046, New Zealand
| | - M. Georgieva
- Forest Research Institute, Bulgarian Academy of Sciences, 132 “St. Kliment Ohridski” Blvd., 1756 Sofia, Bulgaria
| | - L. Ghelardini
- University of Florence, DAGRI Department of Agricultural, Food, Environmental and Forest Sciences and Technologies, Piazzale delle Cascine 18, 50144 Firenze, Italy
| | - C. Husson
- Département de la santé des forêts, DGAL, SDQSPV, Ministère de l’Agriculture et de l’Alimentation, Paris, France
| | - E. Iturritxa
- Neiker BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 01192 Arkaute, Spain
| | - S. Markovskaja
- Institute of Botany, Nature Research Centre, Žaliųjų Ežerų St. 47, Lt-08406 Vilnius, Lithuania
| | - N. Mesanza
- Neiker BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 01192 Arkaute, Spain
| | - N. Ogris
- Slovenian Forestry Institute, Večna pot 2, SI-1000 Ljubljana, Slovenia
| | - F. Oskay
- Faculty of Forestry, Çankırı Karatekin University, 18200 Çankırı, Turkey
| | - B. Piškur
- Slovenian Forestry Institute, Večna pot 2, SI-1000 Ljubljana, Slovenia
| | - V. Queloz
- Centre of Forest Research, National Institute for Agricultural and Food Research and Technology (INIA), C. Coruna, 28040 Madrid, Spain
| | - K. Raitelaitytė
- Institute of Botany, Nature Research Centre, Žaliųjų Ežerų St. 47, Lt-08406 Vilnius, Lithuania
| | - R. Raposo
- Forest Science Institute (ICIFOR), Instituto Nacional de Investigación Agraria (INIA, CSIC), Ctra. Coruña km 7.5, 28040 Madrid, Spain
| | - M. Soukainen
- Laboratory and Research Division, Plant Analytics Unit, Finnish Food Authority, Mustialankatu 3, 00790 Helsinki, Finland
| | - L. Strasser
- Bavarian State Institute of Forestry, Hans-Carl-von-Carlowitz-Platz 1, 85354 Freising, Germany
| | - P. Vahalík
- Department of Forest Management and Applied Geoinformatics, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 1, 613 00, Czech Republic
| | - M. Vester
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - M. Mullett
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ellie L Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Yanan Guo
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | | | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hannah M McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Christiaan R Schol
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
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7
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Siddique AB, Menke L, Dinedurga M, Albrectsen BR. Molecular studies of rust on European aspen suggest an autochthonous relationship shaped by genotype. FRONTIERS IN PLANT SCIENCE 2023; 14:1111001. [PMID: 36890907 PMCID: PMC9986475 DOI: 10.3389/fpls.2023.1111001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.
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8
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van der Nest A, Wingfield MJ, Sadiković D, Mullett MS, Marçais B, Queloz V, Adamčíková K, Davydenko K, Barnes I. Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe. Front Genet 2023; 14:1103331. [PMID: 36873952 PMCID: PMC9978111 DOI: 10.3389/fgene.2023.1103331] [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: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 02/18/2023] Open
Abstract
Dothistroma needle blight (DNB) is an important disease of Pinus species that can be caused by one of two distinct but closely related pathogens; Dothistroma septosporum and Dothistroma pini. Dothistroma septosporum has a wide geographic distribution and is relatively well-known. In contrast, D. pini is known only from the United States and Europe, and there is a distinct lack of knowledge regarding its population structure and genetic diversity. The recent development of 16 microsatellite markers for D. pini provided an opportunity to investigate the diversity, structure, and mode of reproduction for populations collected over a period of 12 years, on eight different hosts in Europe. In total, 345 isolates from Belgium, the Czech Republic, France, Hungary, Romania, Western Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, and Ukraine were screened using microsatellite and species-specific mating type markers. A total of 109 unique multilocus haplotypes were identified and structure analyses suggested that the populations are influenced by location rather than host species. Populations from France and Spain displayed the highest levels of genetic diversity followed by the population in Ukraine. Both mating types were detected in most countries, with the exception of Hungary, Russia and Slovenia. Evidence for sexual recombination was supported only in the population from Spain. The observed population structure and several shared haplotypes between non-bordering countries provides good evidence that the movement of D. pini in Europe has been strongly influenced by human activity in Europe.
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Affiliation(s)
- Ariska van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Dušan Sadiković
- Slovenian Forestry Institute, Ljubljana, Slovenia.,Southern Swedish Forest Research Centre, Swedish University of Agricultural Science, Alnarp, Sweden
| | - Martin S Mullett
- Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Benoit Marçais
- Université de Lorraine, INRAE-Grand-Est, UMR1136 Interactions Arbres, Microorganismes, Nancy, France
| | - Valentin Queloz
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Katarina Adamčíková
- Institute of Forest Ecology Slovak Academy of Sciences, Department of Plant Pathology and Mycology, Nitra, Slovakia
| | - Kateryna Davydenko
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, Uppsala, Sweden.,Ukrainian Forest Research Institute, Forestry and Forest Melioration, Kharkiv, Ukraine, Slovakia
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Laas M, Adamson K, Barnes I, Janoušek J, Mullett MS, Adamčíková K, Akiba M, Beenken L, Braganca H, Bulgakov TS, Capretti P, Cech T, Cleary M, Enderle R, Ghelardini L, Jankovský L, Markovskaja S, Matsiakh I, Meyer JB, Oskay F, Piškur B, Raitelaitytė K, Sadiković D, Drenkhan R. Diversity, migration routes, and worldwide population genetic structure of Lecanosticta acicola, the causal agent of brown spot needle blight. MOLECULAR PLANT PATHOLOGY 2022; 23:1620-1639. [PMID: 35957598 PMCID: PMC9562577 DOI: 10.1111/mpp.13257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 05/29/2023]
Abstract
Lecanosticta acicola is a pine needle pathogen causing brown spot needle blight that results in premature needle shedding with considerable damage described in North America, Europe, and Asia. Microsatellite and mating type markers were used to study the population genetics, migration history, and reproduction mode of the pathogen, based on a collection of 650 isolates from 27 countries and 26 hosts across the range of L. acicola. The presence of L. acicola in Georgia was confirmed in this study. Migration analyses indicate there have been several introduction events from North America into Europe. However, some of the source populations still appear to remain unknown. The populations in Croatia and western Asia appear to originate from genetically similar populations in North America. Intercontinental movement of the pathogen was reflected in an identical haplotype occurring on two continents, in North America (Canada) and Europe (Germany). Several shared haplotypes between European populations further suggests more local pathogen movement between countries. Moreover, migration analyses indicate that the populations in northern Europe originate from more established populations in central Europe. Overall, the highest genetic diversity was observed in south-eastern USA. In Europe, the highest diversity was observed in France, where the presence of both known pathogen lineages was recorded. Less than half of the observed populations contained mating types in equal proportions. Although there is evidence of some sexual reproduction taking place, the pathogen spreads predominantly asexually and through anthropogenic activity.
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Affiliation(s)
- Marili Laas
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Kalev Adamson
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Josef Janoušek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Martin S. Mullett
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Katarína Adamčíková
- Department of Plant Pathology and MycologyInstitute of Forest Ecology, Slovak Academy of SciencesNitraSlovak Republic
| | - Mitsuteru Akiba
- Kyushu Research Center, Forestry and Forest Products Research InstituteKumamotoJapan
| | - Ludwig Beenken
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Helena Braganca
- Instituto Nacional de Investigação Agrária e Veterinária IP.OeirasPortugal
- GREEN‐IT Bioresources for Sustainability, ITQB NOVAOeirasPortugal
| | - Timur S. Bulgakov
- Department of Plant ProtectionFederal Research Centre the Subtropical Scientific Centre of the Russian Academy of SciencesKrasnodarRussia
| | - Paolo Capretti
- Department of Agricultural, Food, Environmental and Forest Sciences and TechnologiesUniversity of FlorenceFlorenceItaly
| | - Thomas Cech
- Austrian Research Centre for ForestsDepartment of Forest ProtectionViennaAustria
| | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
| | - Rasmus Enderle
- Institute for Plant Protection in Horticulture and ForestsJulius Kuehn InstituteBraunschweigGermany
| | - Luisa Ghelardini
- Department of Agricultural, Food, Environmental and Forest Sciences and TechnologiesUniversity of FlorenceFlorenceItaly
| | - Libor Jankovský
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | | | - Iryna Matsiakh
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
- Institute of Forestry and Park GardeningUkrainian National Forestry UniversityLvivUkraine
- National Forestry Agency of GeorgiaTbilisiGeorgia
| | - Joana B. Meyer
- Forest Protection and Forest Health SectionFederal Office for the Environment FOENBernSwitzerland
| | - Funda Oskay
- Faculty of ForestryÇankırı Karatekin UniversityÇankırıTurkey
| | | | | | - Dušan Sadiković
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
- Slovenian Forestry InstituteLjubljanaSlovenia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
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Radoslava J, Katarína A. Development and changes in pathogens population causing Dothistroma needle blight in Pinus nigra plantation in Strážovské vrchy Mts. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Oskay F, Lehtijärvi A, Lehtijärvi HTD. Detection and Identification of the Causal Agents of Dothistroma Needle Blight. Methods Mol Biol 2022; 2536:155-166. [PMID: 35819604 DOI: 10.1007/978-1-0716-2517-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dothistroma needle blight (DNB) is one of the most damaging foliage diseases of pine in plantations and natural forests worldwide and is caused by two closely related fungi: Dothistroma septosporum and D. pini, which are virtually impossible to differentiate from each other based on morphology. Although diagnosis of DNB based on symptoms is relatively reliable in the later stages of the disease when fruit bodies (conidiomata) are formed, for diagnosis in the early stages, as well as identification of the causal agent at species level, molecular methods are required. In addition, reliable and sensitive diagnostics before sporulation is a prerequisite for early detection to minimize accidental introductions of disease through movement of infected plant materials, especially seedlings. While amplification and sequencing of the ITS region of the rDNA alone is not reliable to differentiate the two species, conventional PCR (cPCR) using species-specific primers or mating type-specific primers and quantitative PCR (qPCR) are widely used and accepted molecular methods to identify and differentiate the DNB pathogens, either from cultures or directly from needles.
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Affiliation(s)
- Funda Oskay
- Faculty of Forestry, Çankırı Karatekin University, Çankırı, Turkey.
| | - Asko Lehtijärvi
- Isparta University of Applied Sciences, Sütçüler Prof. Dr. Hasan Gürbüz Vocational School, Isparta, Turkey
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Comparative assessment of spray nozzles efficacy in the control of fusarium head blight in the barley crops using developed quantitative PCR assay. EUREKA: LIFE SCIENCES 2021. [DOI: 10.21303/2504-5695.2021.001873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusarium species infect cereal spikes during anthesis and cause Fusarium head blight (FHB), a destructive disease of cereal crops with worldwide economic relevance. The necessity for these phytopathogenic fungi effective control becomes increasingly important for the production of both cultivated plants and those plants seeds. Fungicide application is a key methodology for controlling the disease development and mycotoxin contamination in cereals. Polymerase chain reaction (PCR) is currently the most commonly admitted DNA-based technology for specific, rapid and precise Fusarium detection. We have developed and patented the method for detection and quantitative determination of phytopathogenic fungi F. avenaceum and F. graminearum in plant seeds using Real-Time PCR with a pair of primers, designed to amplify sequences of the internal transcribed spacer at the ribosomal RNA gene cluster of those phytopathogenic fungi. This study was aimed to perform a comparative assessment of the efficacy of different spray nozzles for antifungal treatment to control F. avenaceum and F. graminearum infection of barley grains using a developed qPCR diagnostic system. A single application of a fungicide (active ingredient's content: 250 g/l propiconazole, 80 g/l cyproconazole) at BBCH 65 (middle of flowering) was carried out. For this purpose, four spray nozzles with different technical characteristics were used: Flat Fan 030, Amistar 030, Defy 3D 030 and Vegetable 060 (Pentair, USA). DNA-based fungi detection and identification was performed using conventional PCR and developed qPCR. The level of mycotoxins in barley grain was determined using enzyme-linked immunosorbent assay (ELISA). Grain count in the ear of barley and thousand seed weight (TSW) were also examined.
A single application of the fungicide inhibited the development of FHB and is accompanied by the slight increase of TSW values in treated plants. It was found, that the most effective fungicide was against F. avenaceum and F. graminearum. The inhibitory effect depended on sprayer type. According to qPCR results, the best performance was achieved when using Amistar 030 and Flat Fan (FF) 030 sprayers. The average concentration of deoxynivalenol (DON) content in all barley grain samples were up to 4 times higher than the permissible level. Overall, because of the high contamination levels, found in tested samples, it is possible to state that a single application of the fungicide at the flowering phase was not able to effectively reduce DON contamination in barley samples.
The developed test-system for qPCR provides new important information in the study of the effectiveness of fungicides and development of strategies to control FHB in cereals, not achievable with conventional PCR.
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Molecular-Based Reappraisal of a Historical Record of Dothistroma Needle Blight in the Centre of the Mediterranean Region. FORESTS 2021. [DOI: 10.3390/f12080983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this work, we rechecked, using species-specific Loop mediated isothermal AMPlification (LAMP) diagnostic assays followed by sequencing of fungal isolates at the beta-2-tubulin (tub2) gene region, a historical and never confirmed report of Dothistroma needle blight (DNB) in the introduced Monterey pine (Pinus radiata D. Don) in the mountains in the extreme tip of southern Italy. The report dates back to the mid-1970s, and predates the molecular-based taxonomic revision of the genus Dothistroma that defined the species accepted today. In the fall of 2019, symptomatic needles of Monterey pine and Corsican pine (Pinus nigra subsp. laricio (Poir.) Palib. ex Maire) were sampled in the area of the first finding. The applied diagnostic methods revealed the presence of Dothistroma septosporum (Dorogin) M. Morelet on both pine species. In this way, we: (i) confirmed the presence of the disease; (ii) clarified the taxonomic identity of the causal agent now occurring at that site; (iii) validated the species-specific LAMP diagnostic protocol we recently developed for Dothistroma for use on a portable field instrument, and (iv) showed that the pathogen now also attacks the native P. nigra subsp. laricio, a species particularly susceptible to the disease, indigenous to the mountains of Calabria, which is one of the very few areas where the species’ genetic resources are conserved. Comparative genetic analysis of the rare populations of D. septosporum found in the central Mediterranean region and in the native range of P. nigra subsp. laricio could help to clarify the history of the spread of the pathogen in southern Europe and better evaluate the risk it poses to the conservation of native pine species.
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Rapid Detection of Pine Pathogens Lecanosticta acicola, Dothistroma pini and D. septosporum on Needles by Probe-Based LAMP Assays. FORESTS 2021. [DOI: 10.3390/f12040479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Needle blights are serious needle fungal diseases affecting pines both in natural and productive forests. Among needle blight agents, the ascomycetes Lecanosticta acicola, Dothistroma pini and D. septosporum are of particular concern. These pathogens need specific, fast and accurate diagnostics since they are regulated species in many countries and may require differential management measures. Due to the similarities in fungal morphology and the symptoms they elicit, these species are hard to distinguish using morphological characteristics. The symptoms can also be confused with those caused by insects or abiotic agents. DNA-based detection is therefore recommended. However, the specific PCR assays that have been produced to date for the differential diagnosis of these pathogens can be applied only in a well-furnished laboratory and the procedure takes a relatively long execution time. Surveillance and forest protection would benefit from a faster diagnostic method, such as a loop-mediated isothermal amplification (LAMP) assay, which requires less sophisticated equipment and can also be deployed directly on-site using portable devices. LAMP assays for the rapid and early detection of L. acicola, D. pini and D. septosporum were developed in this work. Species-specific LAMP primers and fluorescent assimilating probes were designed for each assay, targeting the beta tubulin (β-tub2) gene for the two Dothistroma species and the elongation factor (EF-1α) region for L. acicola. Each reaction detected its respective pathogen rapidly and with high specificity and sensitivity in DNA extracts from both pure fungal cultures and directly from infected pine needles. These qualities and the compatibility with inexpensive portable instrumentation position these LAMP assays as an effective method for routine phytosanitary control of plant material in real time, and they could profitably assist the management of L. acicola, D. pini and D. septosporum.
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Development of a Rapid Loop-Mediated Isothermal Amplification Assay for the Detection of Dothistroma septosporum. FORESTS 2021. [DOI: 10.3390/f12030362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A Loop-Mediated Isothermal Amplification (LAMP) assay was developed for the detection of the pine pathogen Dothistroma septosporum (G. Dorog.) M. Morelet. The specificity of the LAMP assay was tested using a selection of pine needle fungi, including Dothistroma pini Hulbary, and Lecanosticta acicola (Thüm.) Syd.; only D. septosporum DNA was amplified by the test. In terms of sensitivity, the assay was able to detect as little as 1 pg of total D. septosporum DNA. This assay enables DNA extracted from diseased host needles to be rapidly tested for the presence of D. septosporum using relatively simple to operate equipment away from a fully equipped molecular biology laboratory.
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Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O. Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants. BMC Microbiol 2020; 20:296. [PMID: 33004016 PMCID: PMC7528614 DOI: 10.1186/s12866-020-01972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.
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Affiliation(s)
| | | | - Aude Chabirand
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Aurélie Moreau
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | - Amal Moumène
- Université de La Réunion, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Paola Campos
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | | | - Myriam Gaudeul
- Herbier national (P), Muséum National d'Histoire Naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound) Agricultural Services, Réduit, Mauritius
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Luchi N, Ioos R, Santini A. Fast and reliable molecular methods to detect fungal pathogens in woody plants. Appl Microbiol Biotechnol 2020; 104:2453-2468. [PMID: 32006049 PMCID: PMC7044139 DOI: 10.1007/s00253-020-10395-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 01/19/2020] [Indexed: 12/11/2022]
Abstract
Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.
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Affiliation(s)
- Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy.
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Unit of Mycology, Domaine de Pixérécourt, 54220, Malzéville, France
| | - Alberto Santini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano, 10, I-50019, Sesto Fiorentino (Firenze), Italy
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Loit K, Adamson K, Bahram M, Puusepp R, Anslan S, Kiiker R, Drenkhan R, Tedersoo L. Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Appl Environ Microbiol 2019; 85:e01368-19. [PMID: 31444199 PMCID: PMC6803294 DOI: 10.1128/aem.01368-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/18/2019] [Indexed: 02/06/2023] Open
Abstract
Culture-based molecular identification methods have revolutionized detection of pathogens, yet these methods are slow and may yield inconclusive results from environmental materials. The second-generation sequencing tools have much-improved precision and sensitivity of detection, but these analyses are costly and may take several days to months. Of the third-generation sequencing techniques, the portable MinION device (Oxford Nanopore Technologies) has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performances of two third-generation sequencing instruments, MinION and Sequel (Pacific Biosciences), in identification and diagnostics of fungal and oomycete pathogens from conifer (Pinaceae) needles and potato (Solanum tuberosum) leaves and tubers. We demonstrate that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose due to a high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches. Using the metagenomics approach with shortened DNA extraction and incubation times, we performed the entire MinION workflow, from sample preparation through DNA extraction, sequencing, bioinformatics, and interpretation, in 2.5 h. We advocate the use of MinION for rapid diagnostics of pathogens and potentially other organisms, but care needs to be taken to control or account for multiple potential technical biases.IMPORTANCE Microbial pathogens cause enormous losses to agriculture and forestry, but current combined culturing- and molecular identification-based detection methods are too slow for rapid identification and application of countermeasures. Here, we develop new and rapid protocols for Oxford Nanopore MinION-based third-generation diagnostics of plant pathogens that greatly improve the speed of diagnostics. However, due to high error rate and technical biases in MinION, the Pacific BioSciences Sequel platform is more useful for in-depth amplicon-based biodiversity monitoring (metabarcoding) from complex environmental samples.
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Affiliation(s)
- Kaire Loit
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Riinu Kiiker
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Natural History Museum, University of Tartu, Tartu, Estonia
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van der Nest A, Wingfield MJ, Janoušek J, Barnes I. Lecanosticta acicola: A growing threat to expanding global pine forests and plantations. MOLECULAR PLANT PATHOLOGY 2019; 20:1327-1364. [PMID: 31309681 PMCID: PMC6792179 DOI: 10.1111/mpp.12853] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lecanosticta acicola causes brown spot needle blight (BSNB) of Pinus species. The pathogen occurs mostly in the Northern Hemisphere but has also been reported in Central America and Colombia. BSNB can lead to stunted growth and tree mortality, and has resulted in severe damage to pine plantations in the past. There have been increasingly frequent new reports of this pathogen in Europe and in North America during the course of the past 10 years. This is despite the fact that quarantine practices and eradication protocols are in place to prevent its spread. TAXONOMY Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Dothideomycetes; Subclass Dothideomycetidae; Order Capniodales; Family Mycosphaerellaceae; Genus Lecanosticta. HOST RANGE AND DISTRIBUTION Lecanosticta spp. occur on various Pinus species and are found in North America, Central America, South America (Colombia), Europe as well as Asia. DISEASE SYMPTOMS Small yellow irregular spots appear on the infected pine needles that become brown over time. They can be surrounded by a yellow halo. These characteristic brown spots develop to form narrow brown bands that result in needle death from the tips down to the point of infection. Needles are prematurely shed, leaving bare branches with tufts of new needles at the branch tips. Infection is usually most severe in the lower parts of the trees and progresses upwards into the canopies. USEFUL WEBSITES The EPPO global database providing information on L. acicola (https://gd.eppo.int/taxon/SCIRAC) Reference genome of L. acicola available on GenBank (https://www.ncbi.nlm.nih.gov/genome/?term=Lecanosticta+acicola) JGI Gold Genome database information sheet of L. acicola sequenced genome (https://gold.jgi.doe.gov/organism?xml:id=Go0047147).
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Affiliation(s)
- Ariska van der Nest
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Josef Janoušek
- Phytophthora Research CenterMendel University in BrnoBrnoCzech Republic
| | - Irene Barnes
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
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Laas M, Adamson K, Drenkhan R. A look into the genetic diversity of Lecanosticta acicola in northern Europe. Fungal Biol 2019; 123:773-782. [PMID: 31542194 DOI: 10.1016/j.funbio.2019.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/28/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
For northern Europe Lecanosticta acicola is an emerging pine needle pathogen. This study gives a first look into the population genetics of the pathogen in Estonia, the first population documented in that region. The main aim of this study was to investigate the genetic diversity and population structure of the pathogen in this new region for the fungus. For this purpose, 104 isolates from 2010 to 2017 were analysed with 11 microsatellite and mating type markers. The stand where the pathogen's jump from an exotic host to the native Scots pine was recorded was also involved in this analysis. The analysis revealed low genetic diversity and a high number of clones that indicated L. acicola is an invasive species in northern Europe. Results suggest that several separate introductions have taken place and anthropogenic activity has apparently affected the spread of the pathogen. Clonal reproduction is dominating and although sexual reproduction is possible, it probably takes place infrequently.
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Affiliation(s)
- Marili Laas
- Estonian University of Life Sciences, Institute of Forestry and Rural Engineering, Fr. R. Kreutzwaldi 5, 51006, Tartu, Estonia.
| | - Kalev Adamson
- Estonian University of Life Sciences, Institute of Forestry and Rural Engineering, Fr. R. Kreutzwaldi 5, 51006, Tartu, Estonia
| | - Rein Drenkhan
- Estonian University of Life Sciences, Institute of Forestry and Rural Engineering, Fr. R. Kreutzwaldi 5, 51006, Tartu, Estonia
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Ahmed Y, Hubert J, Fourrier-Jeandel C, Dewdney MM, Aguayo J, Ioos R. A Set of Conventional and Multiplex Real-Time PCR Assays for Direct Detection of Elsinoë fawcettii, E. australis, and Pseudocercospora angolensis in Citrus Fruits. PLANT DISEASE 2019; 103:345-356. [PMID: 30566843 DOI: 10.1094/pdis-05-18-0798-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Elsinoë fawcettii, E. australis, and Pseudocercospora angolensis are causal agents of citrus scab and spot diseases. The three pathogens are listed as quarantine pests in many countries and are subject to phytosanitary measures to prevent their entry. Diagnosis of these diseases based on visual symptoms is problematic, as they could be confused with other citrus diseases. Isolation of E. fawcettii, E. australis, and P. angolensis from infected tissues is challenging because they grow slowly on culture media. This study developed rapid and specific detection tools for the in planta detection of these pathogens, using either conventional PCR or one-tube multiplex real-time PCR. Primers and hybridization probes were designed to target the single-copy protein-coding gene MS204 for E. fawcettii and E. australis and the translation elongation factor (Tef-1α) gene for P. angolensis. The specificity of the assays was evaluated by testing against DNA extracted from a large number of isolates (102) collected from different citrus-growing areas in the world and from other hosts. The newly described species E. citricola was not included in the specificity test due to its unavailability from the CBS collection. The detection limits of conventional PCR for the three pathogens were 100, 100, and 10 pg μl-1 gDNA per reaction for E. fawcettii, E. australis, and P. angolensis, respectively. The quadruplex qPCR was fully validated assessing the following performance criteria: sensitivity, specificity, repeatability, reproducibility, and robustness. The quadruplex real-time PCR proved to be highly sensitive, detecting as low as 243, 241, and 242 plasmidic copies (pc) μl-1 of E. fawcettii, E. australis, and P. angolensis, respectively. Sensitivity and specificity of this quadruplex assay were further confirmed using 176 naturally infected citrus samples collected from Ethiopia, Cameroon, the United States, and Australia. The quadruplex assay developed in this study is robust, cost-effective, and capable of high-throughput detection of the three targets directly from citrus samples. This new detection tool will substantially reduce the turnaround time for reliable species identification and allow rapid response and appropriate action.
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Affiliation(s)
- Yosra Ahmed
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France; and Agricultural Research Center, Plant Pathology Research Institute, Giza- Egypt
| | - Jacqueline Hubert
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Céline Fourrier-Jeandel
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Megan M Dewdney
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Jaime Aguayo
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
| | - Renaud Ioos
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) Laboratoire de la Santé des Végétaux, Unité de Mycologie, Domaine de Pixérécourt, 54220 Malzéville, France
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Esvaran VG, Mohanasundaram A, Mahadeva S, Gupta T, Ponnuvel KM. Development and comparison of real-time and conventional PCR tools targeting β-tubulin gene for detection of Nosema infection in silkworms. J Parasit Dis 2018; 43:31-38. [PMID: 30956443 DOI: 10.1007/s12639-018-1053-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/07/2018] [Indexed: 11/29/2022] Open
Abstract
Microsporidiosis (Pebrine) caused by the microsporidian parasite is one of the important devastating disease which affect the silk production leading to an unprofitable harvest. Till date ribosomal RNA (rRNA) gene was used as a target for detection of microsporidian species. In this study, we describe conventional and SYBR green based real-time PCR techniques alternatively targeting β-tubulin gene for quantitative detection of microsporidia infecting both the mulberry and non-mulberry silkworms. The modified DNA extraction method followed in our study was found to be easy, economical and could be used for both conventional and real time PCR as template. The real time qPCR revealed the expression of β-tubulin gene in different infected tissues of the silkworm Bombyx mori. The sensitivity of the SYBR green based real time PCR was found to be 100 times more than the conventional PCR and PCR was found more sensitive than the microscopic examination. The developed method did not produce any false positive results with the other silkworm pathogens and healthy silkworm. The data suggest that both the developed PCR methods targeting β-tubulin gene could be used effectively in quarantine process at seed centres for early detection of microsporidian infection in silkworms.
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Affiliation(s)
- Vijaya Gowri Esvaran
- Genomics Division, Seribiotech Research Laboratory, Carmelaram - Post, Kodathi, Bangalore, 560035 India
| | - Aarthi Mohanasundaram
- Genomics Division, Seribiotech Research Laboratory, Carmelaram - Post, Kodathi, Bangalore, 560035 India
| | - Shruthi Mahadeva
- Genomics Division, Seribiotech Research Laboratory, Carmelaram - Post, Kodathi, Bangalore, 560035 India
| | - Tania Gupta
- Genomics Division, Seribiotech Research Laboratory, Carmelaram - Post, Kodathi, Bangalore, 560035 India
| | - Kangayam M Ponnuvel
- Genomics Division, Seribiotech Research Laboratory, Carmelaram - Post, Kodathi, Bangalore, 560035 India
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Adamson K, Mullett MS, Solheim H, Barnes I, Müller MM, Hantula J, Vuorinen M, Kačergius A, Markovskaja S, Musolin DL, Davydenko K, Keča N, Ligi K, Priedite RD, Millberg H, Drenkhan R. Looking for relationships between the populations of Dothistroma septosporum in northern Europe and Asia. Fungal Genet Biol 2017; 110:15-25. [PMID: 29223582 DOI: 10.1016/j.fgb.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/06/2017] [Accepted: 12/05/2017] [Indexed: 01/29/2023]
Abstract
Dothistroma septosporum, a notorious pine needle pathogen with an unknown historical geographic origin and poorly known distribution pathways, is nowadays found almost in all areas inhabited by pines (Pinus spp.). The main aim of this study was to determine the relationship between North European and East Asian populations. In total, 238 Eurasian D. septosporum isolates from 11 countries, including 211 isolates from northern Europe, 16 isolates from Russian Far East and 11 isolates from Bhutan were analysed using 11 species-specific microsatellite and mating type markers. The most diverse populations were found in northern Europe, including the Baltic countries, Finland and European Russia. Notably, D. septosporum has not caused heavy damage to P. sylvestris in northern Europe, which may suggest a long co-existence of the host and the pathogen. No indication was obtained that the Russian Far East or Bhutan could be the indigenous area of D. septosporum, as the genetic diversity of the fungus there was low and evidence suggests gene flow from northern Europe to Russian Far East. On the western coast of Norway, a unique genetic pattern was observed, which differed from haplotypes dominating other Fennoscandian populations. As an agent of dothistroma needle blight, only D. septosporum was documented in northern Europe and Asia, while D. pini was found in Ukraine and Serbia.
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Affiliation(s)
- Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia.
| | | | | | - Irene Barnes
- Department of Genetics, FABI, University of Pretoria, Pretoria, South Africa
| | | | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Martti Vuorinen
- Natural Resources Institute Finland (Luke), Suonenjoki, Finland
| | - Audrius Kačergius
- Vokė Branch of Lithuanian Research Centre for Agriculture and Forestry, Vilnius, Lithuania
| | | | - Dmitry L Musolin
- Saint Petersburg State Forest Technical University, Saint Petersburg, Russia
| | - Kateryna Davydenko
- Department of Biotechnology and Environment, Kharkiv Zooveterinary Academy, Kharkiv, Ukraine; Department Forest Mycology and Plant Pathology, Swedish Universiy of Agriculture Science, Uppsala, Sweden
| | - Nenad Keča
- Faculty of Forestry-University of Belgrade, Belgrade, Serbia
| | - Karli Ligi
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | | | - Hanna Millberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
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Janoušek J, Wingfield MJ, Monsivais JGM, Jankovský L, Stauffer C, Konečný A, Barnes I. Genetic Analyses Suggest Separate Introductions of the Pine Pathogen Lecanosticta acicola Into Europe. PHYTOPATHOLOGY 2016; 106:1413-1425. [PMID: 26714104 DOI: 10.1094/phyto-10-15-0271-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lecanosticta acicola is a heterothallic ascomycete that causes brown spot needle blight on native and nonnative Pinus spp. in many regions of the world. In this study we investigated the origin of European L. acicola populations and estimated the level of random mating of the pathogen in affected areas. Part of the elongation factor 1-α gene was sequenced, 11 microsatellite regions were screened, and the mating type idiomorphs were determined for 201 isolates of L. acicola collected from three continents and 17 host species. The isolates from Mexico and Guatemala were unique, highly diverse and could represent cryptic species of Lecanosticta. The isolates from East Asia formed a uniform and discrete group. Two distinct populations were identified in both North America and Europe. Approximate Bayesian computation analyses strongly suggest independent introductions of two populations from North America into Europe. Microsatellite data and mating type distributions indicated random recombination in the populations of North America and Europe. Its intercontinental introduction can most likely be explained as a consequence of the movement of infected plant material. In contrast, the spread of L. acicola within Europe appears to be primarily due to conidial dispersion and probably also ascospore dissemination.
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Affiliation(s)
- Josef Janoušek
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Michael J Wingfield
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - José G Marmolejo Monsivais
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Libor Jankovský
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Christian Stauffer
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Adam Konečný
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Irene Barnes
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
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Robène I, Perret M, Jouen E, Escalon A, Maillot MV, Chabirand A, Moreau A, Laurent A, Chiroleu F, Pruvost O. Development and validation of a real-time quantitative PCR assay to detect Xanthomonas axonopodis pv. allii from onion seed. J Microbiol Methods 2015; 114:78-86. [DOI: 10.1016/j.mimet.2015.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/30/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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Barnes I, Wingfield MJ, Carbone I, Kirisits T, Wingfield BD. Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity. Ecol Evol 2014; 4:3642-61. [PMID: 25478155 PMCID: PMC4224538 DOI: 10.1002/ece3.1200] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 11/09/2022] Open
Abstract
Dothistroma septosporum is a haploid fungal pathogen that causes a serious needle blight disease of pines, particularly as an invasive alien species on Pinus radiata in the Southern Hemisphere. During the course of the last two decades, the pathogen has also incited unexpected epidemics on native and non-native pine hosts in the Northern Hemisphere. Although the biology and ecology of the pathogen has been well documented, there is a distinct lack of knowledge regarding its movement or genetic diversity in many of the countries where it is found. In this study we determined the global population diversity and structure of 458 isolates of D. septosporum from 14 countries on six continents using microsatellite markers. Populations of the pathogen in the Northern Hemisphere, where pines are native, displayed high genetic diversities and included both mating types. Most of the populations from Europe showed evidence for random mating, little population differentiation and gene flow between countries. Populations in North America (USA) and Asia (Bhutan) were genetically distinct but migration between these continents and Europe was evident. In the Southern Hemisphere, the population structure and diversity of D. septosporum reflected the anthropogenic history of the introduction and establishment of plantation forestry, particularly with Pinus radiata. Three introductory lineages in the Southern Hemisphere were observed. Countries in Africa, that have had the longest history of pine introductions, displayed the greatest diversity in the pathogen population, indicating multiple introductions. More recent introductions have occurred separately in South America and Australasia where the pathogen population is currently reproducing clonally due to the presence of only one mating type.
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Affiliation(s)
- Irene Barnes
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
| | - Michael J Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
| | - Ignazio Carbone
- Department of Plant Pathology, Center for Integrated Fungal Research, North Carolina State University Raleigh, North Carolina, 27695
| | - Thomas Kirisits
- Department of Forest and Soil Sciences (DFS), Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), University of Natural Resources and Life Sciences, Vienna (BOKU) Vienna, Austria
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
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Hu J, Johnson EG, Wang NY, Davoglio T, Dewdney MM. qPCR Quantification of Pathogenic Guignardia citricarpa and Nonpathogenic G. mangiferae in Citrus. PLANT DISEASE 2014; 98:112-120. [PMID: 30708603 DOI: 10.1094/pdis-04-13-0465-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus black spot, a major citrus disease caused by Guignardia citricarpa, was recently introduced in Florida. The nonpathogenic fungal endophyte G. mangiferae is commonly found in the same citrus tissues as G. citricarpa. Quantitative polymerase chain reaction (qPCR) assays based on internal transcribed spacer (ITS)-1 genes were developed to detect, quantify, and distinguish between these morphologically similar organisms in environmental samples. The primer/probe sets GCITS and GMITS were more than 95% efficient in single-set reactions in complex environmental DNA samples. Detection of 10 fg of G. citricarpa and G. mangiferae DNA was possible. Pycnidiospore disruption resulted in detection of single pycnidiospores with 78 (59 to 102; 95% confidence interval [CI]) and 112 (92 to 136; 95% CI) ITS copies for G. citricarpa and G. mangiferae, respectively. Detection was from partially decomposed leaves where fruiting bodies cannot be morphologically distinguished. Temperature and wetting period have significant effects on Guignardia spp. pseudothecia production in leaf litter. Based on relative biomass or the proportion of nuclei detected, G. citricarpa and G. mangiferae respond more strongly to wetting period than temperature. This qPCR assay will provide additional epidemiological data on black spot in tissues where G. citricarpa and G. mangiferae are not easily distinguished.
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Affiliation(s)
- Jiahuai Hu
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850
| | - Evan G Johnson
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850
| | - Nan-Yi Wang
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850
| | - Tiago Davoglio
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850
| | - Megan M Dewdney
- Citrus Research and Education Center, University of Florida, Lake Alfred 33850
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Boutigny AL, Guinet C, Vialle A, Hamelin RC, Andrieux A, Frey P, Husson C, Ioos R. Optimization of a real-time PCR assay for the detection of the quarantine pathogen Melampsora medusae f. sp. deltoidae. Fungal Biol 2013; 117:389-98. [PMID: 23809649 DOI: 10.1016/j.funbio.2013.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/23/2013] [Accepted: 04/02/2013] [Indexed: 11/26/2022]
Abstract
Melampsora medusae (Mm), one of the causal agents of poplar rust, is classified as an A2 quarantine pest for European Plant Protection Organization (EPPO) and its presence in Europe is strictly controlled. Two formae speciales have been described within Mm, Melampsora medusae f. sp. deltoidae (Mmd), and Melampsora medusae f. sp. tremuloidae (Mmt) on the basis of their pathogenicity on Populus species from the section Aigeiros (e.g. Populus deltoides) or Populus (e.g. Populus tremuloides), respectively. In this study, a real-time polymerase chain reaction (PCR) assay was developed allowing the detection of Mmd, the forma specialis that is economically harmful. A set of primers and hydrolysis probe were designed based on sequence polymorphisms in the large ribosomal RNA subunit (28S). The real-time PCR assay was optimized and performance criteria of the detection method, i.e. sensitivity, specificity, repeatability, reproducibility, and robustness, were assessed. The real-time PCR method was highly specific and sensitive and allowed the detection of one single urediniospore of Mmd in a mixture of 2 mg of urediniospores of other Melampsora species. This test offers improved specificity over currently existing conventional PCR tests and can be used for specific surveys in European nurseries and phytosanitary controls, in order to avoid introduction and spread of this pathogen in Europe.
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Affiliation(s)
- Anne-Laure Boutigny
- ANSES Laboratoire de la Santé des Végétaux, Unité de Mycologie, IFR110 EFABA, Domaine de Pixérécourt, BP 90059, 54220 Malzéville, France.
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Scientific Opinion on the risk to plant health posed by Dothistroma septosporum (Dorog.) M. Morelet (Mycosphaerella pini E. Rostrup, syn. Scirrhia pini) and Dothistroma pini Hulbary to the EU territory with the identification and evaluation of risk reduct. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Ioos R, Fourrier C, Wilson V, Webb K, Schereffer JL, de Labrouhe DT. An optimized duplex real-time PCR tool for sensitive detection of the quarantine oomycete Plasmopara halstedii in sunflower seeds. PHYTOPATHOLOGY 2012; 102:908-917. [PMID: 22671026 DOI: 10.1094/phyto-04-12-0068-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plasmopara halstedii, the causal agent of downy mildew of sunflower, is an oomycete listed as a quarantine pathogen. This obligate parasite resides in a quiescent state in seeds of sunflower and can be spread from seed production areas to areas of crop production by international seed trade. To prevent the spread or the introduction of potentially new genotypes or fungicide-tolerant strains, an efficient method to detect P. halstedii in sunflower seed is required. This work reports the optimization of a real-time detection tool that targets the pathogen within sunflower seeds, and provides statistically validated data for that tool. The tool proved to be specific and inclusive, based on computer simulation and in vitro assessments, and could detect as few as 45 copies of target DNA. A fully optimized DNA extraction protocol was also developed starting from a sample of 1,000 sunflower seeds, and enabled the detection of <1 infected seed/1,000 seeds. To ensure reliability of the results, a set of controls was used systematically during the assays, including a plant-specific probe used in a duplex quantitative polymerase chain reaction that enabled the assessment of the quality of each DNA extract.
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Affiliation(s)
- Renaud Ioos
- Laboratoire de la Santé des Végétaux, Unité de Mycologie, Malzéville, France.
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Wijayawardene NN, Udayanga D, Mckenzie EH, Wang Y, Hyde KD. The Future of Coelomycete Studies. CRYPTOGAMIE MYCOL 2012. [DOI: 10.7872/crym.v33.iss3.2012.381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fabre B, Ioos R, Piou D, Marçais B. Is the emergence of Dothistroma needle blight of pine in France caused by the cryptic species Dothistroma pini? PHYTOPATHOLOGY 2012; 102:47-54. [PMID: 22165983 DOI: 10.1094/phyto-02-11-0036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Dothistroma needle blight (DNB) emerged in France in the past 15 years. This disease is induced by two closely related species: Dothistroma septosporum and D. pini. Although both species are currently present in France, only D. septosporum was reported in the past. We investigated whether a recent arrival of D. pini in France could be a cause of the DNB emergence. We analyzed herbarium specimens of pine needles with DNB symptoms using polymerase chain reaction techniques to study the past frequency of D. pini in France. We also determined the present distribution within the country of D. septosporum and D. pini and compared it with the spatial pattern of DNB reported in the Département de la Santé des Forêts (DSF; French forest health monitoring agency) database. Although D. pini was detected on herbarium specimens from 1907 and 1965, it was not frequent in France in the past. Today, it is frequent, although not present throughout the country, being absent from the north and the east. There is no relationship between the D. pini distribution in France and the spatial pattern of DNB reported in the DSF database. Thus, the emergence of DNB in France cannot be explained by a recent arrival of D. pini.
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Affiliation(s)
- B Fabre
- INRA Nancy, INRA/UHP, Champenoux, France
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Langrell SRH. Nested polymerase chain reaction-based detection of Dothistroma septosporum, red band needle blight of pine, a tool in support of phytosanitary regimes. Mol Ecol Resour 2011; 11:749-52. [PMID: 21676203 DOI: 10.1111/j.1755-0998.2011.02996.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Red band needle blight is one of the most important foliar diseases of Pinus species and is of increasing international forest health and biosecurity concern. To provide a rapid identification technique for this pathogen in support of official control measures, a nested polymerase chain reaction-based diagnostic assay that employs species-specific primer sets has been developed. The assay is able to detect the presence of the pathogen direct from pine needles, irrespective of host species, to within 10 fg of target DNA, the equivalent of approximately 2-3 ascospores or hyphael cells.
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Affiliation(s)
- Stephen R H Langrell
- Laboratoire de Pathologie Forestière, Unité de Recherches en Santé Végétale, Centre de Recherches de Bordeaux, Institute National de la Recherche Agronomique, BP81, 33883 Villenave d'Ornon Cedex, France.
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Genetics of dothistromin biosynthesis of Dothistroma septosporum: an update. Toxins (Basel) 2010; 2:2680-98. [PMID: 22069571 PMCID: PMC3153176 DOI: 10.3390/toxins2112680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 10/30/2010] [Accepted: 11/02/2010] [Indexed: 02/02/2023] Open
Abstract
Dothistroma needle blight is one of the most devastating fungal pine diseases worldwide. The disease is characterized by accumulation in pine needles of a red toxin, dothistromin, that is chemically related to aflatoxin (AF) and sterigmatocystin (ST). This review updates current knowledge of the genetics of dothistromin biosynthesis by the Dothistroma septosporum pathogen and highlights differences in gene organization and regulation that have been discovered between the dothistromin and AF/ST systems. Some previously reported genes are promoted or demoted as ‘dothistromin genes’ based on recent research. A new dothistromin gene, norB, is reported, and evidence of dothistromin gene homologs in other Dothideomycete fungi is presented. A hypothesis for the biological role of dothistromin is outlined. Finally, the impact that the availability of the D. septosporum genome sequence will have on dothistromin research is discussed.
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