Research activities of the Plant Health Laboratory
The research activities of the Plant Health Laboratory focus on:
- the characterisation of quarantine and emerging pests in all fields: bacteriology, entomology, mycology, nematology and virology. This characterisation uses approaches based on diagnosis, taxonomy and population characterisation;
- the epidemiology of diseases and the dynamics of invasions;
- the mechanisms responsible for the spread of pests such as weeds, insect pests and insect vectors of pathogens;
- the ecology of weeds and invasive plants;
- the detection and characterisation of non-listed genetically modified organisms (GMOs).
In parallel, the LSV maintains its analytical capacities at a high level by participating in research and development programmes. To achieve this, the research questions addressed in responses to calls for tenders for national (CASDAR, ANR) and international (Horizon Europe, PRIMA, Euphresco) collaborative projects primarily involve pests, and focus on:
- the biological characterisation and phylogeny of emerging pests or those considered to pose a risk;
- the study by molecular typing or sequencing of the genetic diversity, structure and adaptive potential of their populations;
- possible vector organisms and their geographical distribution.
In addition, the LSV is involved in studying the spread of pests, for example by improving sampling techniques, characterising biological cycles and identifying factors determining the success of introduction and establishment.
The LSV seeks to systematically promote the results obtained, during the most renowned national and international symposia in its fields of expertise and in A and A+ journals having the most significant impact. Training through research, especially doctoral research, makes a major contribution to the LSV's research activities.
Research projects
Mycology unit
Development of tools for the characterisation and detection of fungi posing emerging risks to pome fruit crops: Alternaria spp. and Venturia spp.
Funding: Special Fund for Agricultural and Rural Development (CASDAR)
Partners: ANSES's Lyon Laboratory, Interprofessional Technical Centre for Fruit and Vegetables (CTIFL), Research Institute on Horticulture and Seeds in Angers, FREDON Auvergne Rhône-Alpes, secondary school for general education and agricultural technology in Valence.
This project aims to optimise the control of pests of pome fruit trees by acquiring knowledge on two major genera of pathogenic fungi: Venturia spp. and Alternaria spp. In particular, this will involve developing detection tools; reviewing the distribution of these pathogens in France; identifying, within the two major species complexes, the pathogenicity genes involved in the diseases they cause; characterising their resistance to the main plant protection products used in orchards; developing a protocol for trapping spores in field conditions; and identifying the geographic origin of the Alternaria strains found in France.
Euphresco projects
Euphresco is a network of organisations funding research projects and coordinating national research in the area of plant protection. The overall goals are to support international coordination and collaboration in the area of plant protection research and to become a strong, long-term network of funders that fully incorporates existing and new members.
Mycology unit
Reduce risk assessment uncertainty: suitability of Mediterranean citrus production areas for Phyllosticta citricarpa
Funding: European Food Safety Authority (EFSA)
Partners: IVIA (Spain), NIB (Slovenia), ISA (Tunisia)
This project’s objective is to reduce uncertainties associated with the risk of introduction of the fungus P. citricarpa, the causal agent of citrus black spot (CBS) disease, in Mediterranean citrus production areas. It will improve knowledge on the epidemiology of the disease and climate suitability for its establishment in the Mediterranean Basin.
Mycology unit
Smart and Innovative monitoring of airborne fungal invaders by molecular methods
Funding: LabEx ARBRE
Partners: INRAE, University of Lorraine
The SIAMOIS project aims to capitalise on the National Aerobiological Surveillance Network (RNSA), used for the microscopic monitoring of human allergen particles, to study and monitor certain fungal species. It intends to use this network as a molecular monitoring tool for certain quarantine and regulated fungal species, for the epidemiological evaluation of forest pathogenic fungi and the study of airborne fungal communities.
BVO unit
Measuring and mapping plant virus diversity on an ecosystem scale
Funding: French National Research Agency
Partners: INRAE, CIRAD La Réunion, Tour du Valat Research Institute, Mascarin National Botanical Conservatory, CNRS, Arizona State University (United States), University of Cape Town and University of the Western Cape (South Africa)
This international project is being coordinated by CIRAD in Montpellier for a period of four years.
It aims to better understand exchanges of viruses between natural or managed ecosystems and cultivated species. This study will improve knowledge on these interactions between environments that are responsible for numerous emerging viruses, by mapping the genetic traces of viral adaptations and evolutionary fingerprints and by characterising substitutions and recombinations within viral genomes. To achieve this, the teams will work simultaneously on several natural and cultivated ecosystems and their interfaces.
Mycology unit
Smart and Innovative monitoring of airborne fungal invaders by molecular methods
Funding: LabEx ARBRE
Partners: INRAE, University of Lorraine
The SIAMOIS project aims to capitalise on the National Aerobiological Surveillance Network (RNSA), used for the microscopic monitoring of human allergen particles, to study and monitor certain fungal species. It intends to use this network as a molecular monitoring tool for certain quarantine and regulated fungal species, for the epidemiological evaluation of forest pathogenic fungi and the study of airborne fungal communities.
Quarantine unit
Research and Development Project for a citrus fruit sector with high added value in AlUla
Funding: French Agency for AlUla Development (AFALULA)
Partners: CIRAD, INRAE, Mas Bachès, Agro Prospective Marrakech
The international High Value Citrus for AlUla project aims to develop a sustainable, high-added-value citrus fruit sector in the AlUla region of Saudi Arabia, which would like to diversify its economic activities and capitalise on the genetic resources of its citrus fruit. This project is coordinated by CIRAD. ANSES is in charge of health evaluations relating to citrus fruit quality for the research and development component.
BVO unit
European Virus Archive – GLOBAL
Funding: European Union as part of the INFRAIA call – Horizon 2020
This project has 38 partners from around the world, including the LSV. Led by the University of Marseille, it aims to provide the scientific and industrial community with access to collections of strains of human, animal and plant viruses. These strains will help anticipate new emerging agents and will also constitute reference material required for experimentation, research, and the validation of detection methods in laboratories worldwide.
Nematology unit
Collectively managing varietal resistance to populations of potato cyst nematodes
Funding: Special Fund for Agricultural and Rural Development (CASDAR)
Partners: DGAL, INRAE, French Federation of Seed Potato Producers, Arvalis-Plant Institute, French Association of Potato Breeders (ACVNPT), Noirmoutier Cooperative
This project was initiated in response to the discovery, in Northern Europe, of populations of virulent nematodes in potato varieties considered as resistant. It has five objectives: the epidemiological surveillance and characterisation of the nematode populations present in France; the characterisation of the virulence level of Globodera populations that may be present; the analysis of the individual and collective strategies of professionals in the potato sector and the identification of new sustainable methods for the management of resistance; the development of molecular markers associated with resistance factors for G. pallida and G. rostochiensis from various sources of resistance; and the phenotypic characterisation of multi-resistant plant material in laboratories and in conditions of natural infestation.
BVO unit
Pantoea stewartii and new diagnostic tools
Funding: Euphresco
The aim of this project is to propose, at European level, a protocol for the detection and identification of the bacterium Pantoea stewartii subsp. stewartii on maize plants and seeds. It is promoting and integrating technological breakthroughs capable of distinguishing between the subspecies stewartii and indologenes. It complements a previous Euphresco project that led to the amendment of the diagnostic protocol of the European and Mediterranean Plant Protection Organization (EPPO) for this bacterium.
ERB unit
Funding: European Food Safety Authority (EFSA)
Partners: EFSA, Joint Research Centre of the European Commission
The objective of the Horizon Scanning project is the forward-looking analysis of the media and scientific literature with the aim of identifying new and emerging pests in the European Union. It has also led to the design of a system for classifying new and emerging pests, to identify those requiring a risk analysis by EFSA or changes to border control measures.
Mycology unit
Reliable detection of pathogens in soil
Funding: Euphresco
Partners: Naktuinbouw (Netherlands), AGES (Austria), CREA (Italy), PPIS (Israel), FMFA (Germany), CFIA and UG (Canada), MARE (Cyprus), UKZUZ (Czech Republic), IPPNAAS (Ukraine), MAFF (Slovenia)
The objective of this project is to develop a method for extracting DNA from soil that could be used with larger volumes than those conventionally proposed for commercial extraction kits. DNA extraction from larger amounts of soil will enable more representative samples to be analysed for the detection of major pathogenic micro-organisms in plants.
BVO unit
Epidemiology and diagnosis of potato phytoplasmas and 'Candidatus Liberibacter solanacearum' and their contribution to risk management in potato and other crops
Funding: Euphresco
This project, following on from the previous Euphresco PhyLib and PhyLib II projects, will contribute to improving knowledge on the bacteria responsible for vegetative disorders in potatoes: bacteria in phloem (sap-transporting tissue), bacteria of the phytoplasma group, and the bacterial species Candidatus Liberibacter solanacearum.
Mycology unit
Sampling and analysis of asymptomatic citrus fruits and leaf litter to detect the infection of Phyllosticta citricarpa
Funding: Euphresco
Partners: CREA (Italy), BBI (Greece), ISA (Tunisia), European and Mediterranean Plant Protection Organization
This project aims to improve detection techniques for the Phyllosticta citricarpa quarantine fungus, the causal agent of citrus black spot (CBS), especially for asymptomatic treated fruit that is nonetheless infected. The project also aims to evaluate sampling strategies to be used for the detection of this parasite on asymptomatic fruit.
Quarantine unit
Protecting mirabelle and damson plum crops from plum pox
Funding: FranceAgriMer
Partners: INRAE, FREDON, Experimental Orchard of Alsace (VEREXAL), Regional Association for Fruit Experimentation of Eastern France (AREFE), Grand-Est Regional Directorate for Food, Agriculture and Forestry
The objective of the SharkSecure project is to protect mirabelle and damson plum crops from plum pox by providing producers and risk managers with new knowledge and detection protocols. Coordinated by INRAE Montpellier, this project has seven national partners, including ANSES. ANSES's research work focuses on the early detection of the disease.
Mycology unit
Improving methods for the identification of Phytophthora ramorum outbreaks in France
Funding: Directorate General for Food (DGAL)/French Forest Health Department (DSF)
Partners: INRAE, University of Lorraine
This project aims to develop methods for identifying forest and nursery outbreaks of Phytophthora ramorum in Brittany, in order to help the DGAL manage the risks posed by these outbreaks in natural environments.
UCR unit
Funding: European H2020 programme
Partners: Agrinnova, Federal Department of Economic Affairs, Education and Research (EAER) – Agroscope, Loewe Biochemica GmbH, Bioreba AG, EPPO, Fera Science Ltd, National Institute of Biology, ClearDetections B.V, Netherlands Food and Consumer Product Safety Authority, Gembloux Agro-Bio Tech - University of Liège, International Plant Analysis and Diagnostics, Sediag SAS, Stichting Wageningen Research, PIORIN, Council for Agricultural Research and Economics
The goal of Valitest was to improve diagnostic tools for plant pests such as bacteria, viruses, nematodes and fungi. This detection is essential for taking measures against these harmful organisms as early as possible, both to limit the damage to plants and to avoid their dispersion in the environment. Central to the project was the validation of pest detection kits. The performance of 83 tests, designed to detect 11 pests, was assessed. The project also examined the statistical studies needed to validate these diagnostic tools, the quality and harmonisation of the reference materials used to assess the tests and the assessment of the laboratories' ability to use the diagnostic tests, and sought to identify the expectations of test users, producers and the services for which the diagnostic results are intended.
Nematology unit
Global warming and distribution of root-knot nematode species of the tropical group
Funding: Euphresco
Partners: AIS (Slovenia), INIAV (Portugal), CFE and CIEPQPF (Portugal), NPPO (Netherlands), Institute Tamiš (Serbia)
Tropical nematodes of the group Meloidogyne spp. are considered an emerging problem for plant health in Europe. This project aims to anticipate the potential damage these species can cause to crops of economic importance, in particular in a context of climate change. The goals are to map the distribution of tropical species in Slovenia, France, Portugal and Serbia, evaluate the survival ability of M. incognita and M. arenaria in the climatic conditions of continental Europe, validate biochemical and molecular methods for the diagnosis of these tropical nematodes, and generate, for each tropical species found in Europe, maps showing the risk of spread.
Diagnosis and epidemiology of tropical plants
Funding: ANSES, CIRAD, University of Reunion Island
The scientific and research partnership agreement defines the collaboration between:
- ANSES's Plant Health Laboratory, Tropical Pests and Pathogens unit (RAPT)
- and the CIRAD/University of Reunion Island joint research unit (UMR) on Plant Communities and Biological Invaders in Tropical Environments (PVBMT)
This collaboration has the following three objectives:
• Improve knowledge of emerging pathogen populations;
• Develop innovative diagnostic methods and tools for plant health;
• Contribute to international monitoring of plant health in geographical areas related to the French overseas regions and territories.
It targets organisms responsible for diseases in plant sectors of major economic importance for these overseas territories and/or of strategic importance for continental Europe (bacterial diseases associated with citrus or the Ralstonia solanacearum species complex, bacterial and viral diseases affecting banana, sugar cane, tropical roots and tubers, etc.).
The agreement also takes the "climate change" component into account in the research themes and projects.
Rapid and Efficient Detection and Identification of severe strains of citrus tristeza virus (CTV)
Funding: Euphresco
This project aims to simplify the diagnosis of Closterovirus tristezae (CTV) isolates by developing rapid and effective molecular tests for the detection and identification of specific CTV strains.
To achieve this objective, the project includes the following activities:
- A full review of the diagnostic tools and tests currently used or under development for the detection of CTV;
- Compilation of a wide range of reference material (CTV-infected asymptomatic and symptomatic citrus plants) in order to encompass the various CTV isolates;
- In silico analysis of viral cDNA sequences and design of primers or probes for molecular detection and identification of specific CTV strains;
- Organisation of an inter-laboratory test to validate the protocols identified or developed.
Ralstonia pseudosolanacearum and Ralstonia syzygii: emerging threats in and outside Europe. Study on the epidemiology and the development and validation of detection and identification protocols
Funding: Euphresco
The aim of this project is to set up a platform for exchanging knowledge between bacteriologists working on R. pseudosolanacearum and R. syzygii in the fields of diagnostics, research and epidemiology. This platform could enable multinational collaboration, for example to launch research projects, share collections and develop harmonised detection and identification protocols. In particular, this development and harmonisation is scheduled to be carried out through an inter-laboratory validation test.
Epidemiological surveillance and biocontrol in the South-West Indian Ocean – Phase 2
Funding: EU-Interreg VI Indian Ocean
EpiBioOI-II aims to implement and strengthen capacity at regional and national levels for environmental protection and the promotion of sustainable agriculture in the South-West Indian Ocean. Close attention is being paid to the management of invasive macro-organisms and emerging plant diseases in the region.
In particular, the RAPT unit is contributing to Action 4 "Surveillance and diagnosis of viruses, bacteria and fungi that are pathogenic to banana crops in the Comoros and Mauritius".
This project initially aims to assess the state of health of banana plantations in the Comoros and Mauritius with regard to the main viral, bacterial and fungal diseases of banana plants (prevalence, geographical distribution) and to study the diversity of the pathogens that cause them. The data collected will then be used to recommend more effective control strategies for these plant pathogens, thus contributing to food security in the target countries.
An integrated set of novel approaches to counter the emergence and proliferation of invasive and virulent soil borne nematodes
Funding: Horizon Europe (European Commission)
Partners: ANSES/INRAE NemAlliance cluster and 16 other European or international consortium partners
Soil-borne nematodes pose a risk to global food production. Causing estimated annual losses of 110 billion euros worldwide, root-knot nematodes and potato cyst nematodes (including five quarantine species) rank first and second in the Top 10 of high-impact plant-parasitic nematodes. Recent reports document the emergence of new problems linked to these nematodes in tomato and potato crops in Europe and beyond. These nematode problems are due to global warming and genetic selection. For decades, non-specific environmentally harmful plant protection products have been used in management. Growing awareness of their negative impact has led to the gradual elimination of most nematicides. There is therefore an urgent need for new, sustainable control strategies. NEM-EMERGE aims to provide a range of sustainable, science-based solutions for agriculture. It has adopted the principles of integrated pest control (i.e. optimised crop rotation programmes, tailored host-plant resistance and optimal use of soil’s inherent antagonistic potential). The development of monitoring and risk assessment tools is encouraged to support plant health authorities in their decision-making. NEM-EMERGE is thus part of the transition towards sustainable agriculture, in line with the EU's Farm to Fork strategy, contributing to the ambitious targets set by the Green Deal.
Study of intra/interspecific variability and assessment of the risk of an emerging tropical nematode becoming established on crops of major importance in France
Funding: ANSES/CIRAD (IRD for part of its operation)
Partners: ANSES, CIRAD, IRD and INRAE (NemAlliance cluster)
In a context where plant protection product-based solutions are banned, the management of quarantine or emerging plant-parasitic nematodes requires an in-depth risk assessment and the search for alternative solutions. In particular, these solutions can draw on the study, in the face of invasion, of the resistance of native plant-parasitic nematode communities that do not damage crops. In this context, one species emerging in Europe, Meloidogyne graminicola, is regarded as invasive. Including M. graminicola in the work reflects the effects of climate change and other global changes, with a view to anticipating the rise of emerging nematodes in our latitudes. Characterising the least resistant native communities should help determine the types of agrosystems most at risk. The aim of studying the genetic and morphobiometric diversity and aggressiveness of M. graminicola populations originating from Italy and South-East Asia is to produce evolving questions and molecular markers capable of providing information on the various pathotypes identified.
Analysis of orientation in plant-parasitic nematodes using innovative tools combining microfluidics and digital trajectometry
Funding: INRAE (SPE call for projects)
Partners: ANSES/INRAE NemAlliance cluster
The aim of the NemaTrack project is to develop innovative experimental devices for precisely characterising and quantifying the attraction to chemical stimuli in plant-parasitic nematodes of the Globodera and Meloidogyne genera. This project draws on approaches involving mathematics, IT and, more specifically, digital vision and scientific computing. This scientific strategy enables important life traits to be studied in detail in these organisms, particularly the search for hosts and sexual partners.
Funding: ANSES (internal call for projects)
Partners: joint project involving six ANSES laboratories
Assessment of the shotgun metagenomic approach for studying microbiomes and detecting genes of interest
The ASTEROIDE project is in line with the Agency's "animal health", "plant health", "food safety" and "antimicrobial resistance" cross-functional themes. Its aim is to assess the relevance of the shotgun metagenomics tool for exploring two scientific questions:
- what level of taxonomic resolution can be achieved using shotgun metagenomics to study microbial communities or the circulation of viral strains in matrices of interest to the teams involved?
- Can this approach detect genes of interest and if so, under what conditions?
Infection by plant-parasitic soil organisms in microgravity (CNES call for research projects)
Funding: CNES (CNES call for projects)
Partners: ANSES/INRAE NemAlliance cluster
The IMOTEP research project has put forward the hypothesis that the organisms studied by the Nematology unit have exceptional resistance capacities that have not yet been identified. Although nematodes are known to be extremophilic, no species of plant-parasitic nematode have so far been studied in the conditions found in space. The project objectives are therefore to:
- test survival skills in the vacuum of space;
- assess the infectivity and reproductive capacity of plant-parasitic nematode species in a microgravity environment on host plant crops intended as food for space missions.
ANR AgriBiodiv (2022-2025): link to the project on the ANR page
Fellow (2024-2027): link to the FRB website