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1. Two decades of epidemiological surveillance of the pine wood nematode in France reveal its absence despite suitable conditions for its establishment

Author

Nicolas Mariette, Hoël Hotte, Anne-Marie Chappé, Marie Grosdidier, Géraldine Anthoine, Corinne Sarniguet, Odile Colnard, Emmanuel Kersaudy, Marie-Thérèse Paris, Emmanuel Koen, and Laurent Folcher

Subjects
Bursaphelenchus xylophilus, Priority quarantine pest, National monitoring programme, Monochamus spp., Forest, Forestry, SD1-669.5
Abstract

Abstract Key message This study takes stock of the first 20 years (2000–2019) of monitoring the pine wood nematode (PWN) in metropolitan France. While PWN was never found in the wild during this period, it was reported in some wood-based commodities entering or circulating on French territory. This stresses the importance of remaining extremely vigilant, as the conditions found in France, especially weather conditions, could be particularly suitable for the pest’s establishment. Context The pine wood nematode (PWN) Bursaphelenchus xylophilus, responsible for pine wilt disease (PWD), is one of the most important forest tree pests worldwide. It is thus the focus of many monitoring programmes. In the European Union, for example, it is categorised as a priority quarantine pest, so each member state is obliged to monitor the PWN on its territory. Aims The first objective of this paper was to describe PWN monitoring in metropolitan France, namely how it is organised and whether it has led to the nematode’s detection. Secondly, we wished to investigate what the levels of PWD expression for host pines infected by B. xylophilus would be in France. Thirdly, we wanted to find out whether other Bursaphelenchus species had been found on French territory during these two decades of PWN monitoring. Methods We analysed data from samples collected in the framework of the monitoring programme between 2000 and 2019 to track the PWN in its host pines, its insect vector (Monochamus spp.) and in wood-based commodities imported into or circulating in metropolitan France. We also generated risk maps of PWD expression based on an evapo-transpiration model using climate data for the period 2000–2019. Results This monitoring, which was regularly reinforced from 2000 to 2019, consisted of sampling and analysing around 18,000 wood samples and 66,000 insects over this period. Although the PWN was not detected in pine stands or within its insect vector, some wood-based commodities were found to be contaminated. Risk maps of PWD expression show that in the most recent years (2015–2019), the weather conditions in a large fraction of metropolitan France were suited to PWD expression, mostly with a delay (i.e., latency) between infection and observable wilt symptoms. PWN monitoring has also revealed the presence of other Bursaphelenchus species, most of which were discovered for the first time in metropolitan France and are described herein. Conclusion While metropolitan France is still free of the PWN, this study emphasises the need to remain cautious as the French territory appears particularly suitable for this pest’s establishment. Furthermore, our research has led us to propose some ideas on how to improve PWN monitoring.

Published
2023
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2. The hidden diversity of the potato cyst nematode Globodera pallida in the south of Peru

Author

Romain Thevenoux, Laurent Folcher, Magali Esquibet, Didier Fouville, Josselin Montarry, and Eric Grenier

Subjects
genetic differentiation, genetic diversity, microsatellites, speciation, Evolution, QH359-425
Abstract

Abstract Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.

Published
2020
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3. Diversity of plant parasitic nematodes characterized from fields of the French national monitoring programme for the Columbia root-knot nematode

Author

Nathan Garcia, Eric Grenier, Alain Buisson, and Laurent Folcher

Subjects
Medicine, Science
Abstract

Plant parasitic nematodes are highly abundant in all agrosystems and some species can have a major impact on crop yields. To avoid the use of chemical agents and to find alternative methods to manage these pests, research studies have mainly focused on plant resistance genes and biocontrol methods involving host plants or natural enemies. A specific alternative method may consist in supporting non-damaging indigenous species that could compete with damaging introduced species to decrease and keep their abundance at low level. For this purpose, knowledge about the biodiversity, structure and functioning of these indigenous communities is needed in order to carry out better risk assessments and to develop possible future management strategies. Here, we investigated 35 root crop fields in eight regions over two consecutive years. The aims were to describe plant parasitic nematode diversity and to assess the potential effects of cultivation practices and environmental variables on communities. Community biodiversity included 10 taxa of plant parasitic nematodes. Despite no significant abundance variations between the two sampling years, structures of communities varied among the different regions. Metadata collected for the past six years, characterizing the cultural practices and soils properties, made it possible to evaluate the impact of these variables both on the whole community and on each taxon separately. Our results suggest that, at a large scale, many variables drive the structuration of the communities. Soil variables, but also rainfall, explain the population density variations among the geographical areas. The effect of the variables differed among the taxa, but fields with few herbicide applications and being pH neutral with low heavy metal and nitrogen concentrations had the highest plant parasitic nematode densities. We discuss how these variables can affect nematode communities either directly or indirectly. These types of studies can help to better understand the variables driving the nematode communities structuration in order to support the abundance of indigenous non-damaging communities that could compete with the invasive species.

Published
2022

4. Changes in parasitoid communities over time and space: a historical case study of the maize pest Ostrinia nubilalis.

Author

Laurent Folcher, Denis Bourguet, Denis Thiéry, Laurent Pélozuelo, Michel Phalip, Alain Weissenberger, Nathalie Eychenne, Catherine Regnault-Roger, and Marc Delos

Subjects
Medicine, Science
Abstract

Understanding the ways in which human environmental modifications affect biodiversity is a key challenge in conservation planning, pest control and evolutionary ecology. Parasitoid communities, particularly those associated with agricultural pests, may be susceptible to such modifications. We document here changes in the larval parasitoid communities of Ostrinia nubilalis--the main pest of maize--and its sibling species O. scapulalis, based on two historical datasets, one collected from 1921-1928 and the other from 2001-2005. Each of these datasets encompasses several years and large geographical areas and was based on several thousands/millions of host larvae. The 80-year interval between the two datasets was marked by a decrease in O. nubilalis parasitism to about two thirds its initial level, mostly due to a decrease in the rate of parasitism by hymenopterans. However, a well balanced loss and gain of species ensured that species richness remained stable. Conversely, O. scapulalis displayed stable rates of parasitism over this period, with a decline in the species richness of its parasitoid community. Rates of parasitism and species richness in regions colonized by O. nubilalis during the 1950s were one half to one third those in regions displaying long-term colonisation by this pest. During the recent human activity-driven expansion of its range, O. nubilalis has neither captured native parasitoids nor triggered parasite spill back or spill over.

Published
2011
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5. A synthesis of biological invasion hypotheses associated with the introduction–naturalisation–invasion continuum

Author

Ella Z. Daly, Olivier Chabrerie, Francois Massol, Benoit Facon, Manon C.M. Hess, Aurélie Tasiemski, Frédéric Grandjean, Matthieu Chauvat, Frédérique Viard, Estelle Forey, Laurent Folcher, Elise Buisson, Thomas Boivin, Sylvie Baltora‐Rosset, Romain Ulmer, Patricia Gibert, Gabrielle Thiébaut, Jelena H. Pantel, Tina Heger, David M. Richardson, David Renault, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, CHU Lille, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Etude et Compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Technische Universität München = Technical University of Munich (TUM), Stellenbosch University, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), The authors were supported by InEE-CNRS via a funded network dedicated to Biological Invasions (Groupement de Recherche Invasions Biologiques, InvaBio, 2014–2022, CNRS 3647). The research was funded by the ASICS project (ANR-20-EBI5-0004, BiodivERsA, BiodivClim call 2019–2020), and the French Polar Institute Paul-Emile Victor (Project 136 ‘SubAntEco', French Polar Institute). DMR acknowledges support from Mobility 2020 project no. CZ.02.2.69/0.0/0.0/18_053/0017850 (Ministry of Education, Youth and Sports of the Czech Republic) and long-term research development project RVO 67985939 (Czech Academy of Sciences). TH received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project number HE 5893/8-1., ANR-20-EBI5-0004,ASICS,ASsessing and mitigating the effects of climate change and biological Invasions on the spatial redistribution of biodiversity in Cold environmentS(2020), RIOU, Christine, ASsessing and mitigating the effects of climate change and biological Invasions on the spatial redistribution of biodiversity in Cold environmentS - - ASICS2020 - ANR-20-EBI5-0004 - BiodivERsA - VALID, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and University of Duisburg-Essen

Subjects
[SDE] Environmental Sciences, niche, invasion ecology, invasiveness, alien populations, [SDE]Environmental Sciences, hypothesis, dispersal, geographic expansion, Biologie, phenotypic plasticity, Ecology, Evolution, Behavior and Systematics, invasibility
Abstract

International audience; With the advent of the Anthropocene, biological invasions have reached an unprecedented level, and the number of species introductions is still increasing in an ever-changing world. Despite major advances in invasion science, significant debate and lack of clarity remain surrounding the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions. Empirical studies show divergent impacts of alien populations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of alien populations, which hinders the creation of a unified theory of biological invasions. Compounding these issues is the plethora of hypotheses that aim to explain invasion success, which can be unclear and contradictory. We propose a synthesis that categorizes hypotheses along a timeline of invasion. We sorted invasion hypotheses along the invasion timeline, and considered population, community and ecosystem levels. This temporal sorting of invasion concepts shows that each is relevant at a specific stage of the invasion. Although concepts and empirical findings on alien species may appear contradictory, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

Published
2023
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6. Can quarantine plant-parasitic nematodes within wastes be managed by useful tools in a circular economy approach?

Author

Hoël Hotte, Marie-Sophie Neveux, Fabrice Ollivier, Nicolas Mariette, Laurent Folcher, Anne-Claire Le Roux, Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and This work was supported by the CASDAR program of the French Ministry of Agriculture ‘NEMATOOLS’, coordinated by FN3PT (A-C. Le Roux) in partnership with ANSES and INRAE.

Subjects
Waste stabilization ponds, Environmental Engineering, Nematoda, Swine, MESH: Waste Management, MESH: Recycling, Incineration, Management, Monitoring, Policy and Law, MESH: Nematoda, Heat treatment, Waste Management, MESH: Incineration, Animals, Humans, Chlorination, Globodera, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Recycling, MESH: Animals, MESH: Chlorine, Waste Management and Disposal, MESH: Swine, MESH: Humans, Composting, Methanation, General Medicine, MESH: Refuse Disposal, Refuse Disposal, MESH: Cattle, Quarantine, Cattle, Chlorine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MESH: Quarantine
Abstract

International audience; Seen as an integral part of sustainable development, circular economy represents a model of production and consumption notably based on the limitation of both resource wastage and environmental impact. Laboratories and commercial companies working on plant pathogens, in particular quarantine species, must effectively disinfect their waste to avoid disseminating these organisms. The methods used for waste disinfection can however incur high energy costs or pose environmental and human health hazards. Here, we tested the effectiveness of five disinfection methods - chlorination, heat treatment, composting, mesophilic methanation and waste stabilization ponds - on plant-parasitic nematodes belonging to the genera Globodera and Meloidogyne. For the widely used chlorination and heat treatment methods, we showed that they can be very effective in inactivating nematodes at relatively low chlorine doses and temperatures (60 °C-3 min and 50 °C-30 min), respectively. For the three other disinfection methods tested, initially designed for waste recycling, we obtained different levels of efficiency. Composting and mesophilic methanation (based on cattle or pig slurry) both led to the complete elimination of nematodes, even for short treatment durations. However, waste stabilization ponds showed contrasting results, ranging from virtually no effect to high levels of inactivation of nematodes. Our study demonstrates that it is possible to use more environmentally friendly disinfection methods to control plant-parasitic nematodes. In particular, this finding paves the way towards the treatment of infected plant materials using composting or methanation, providing that disinfection is still reached under other (real-life) treatment conditions, especially with other kinds of waste. Both composting and methanation recycle and thus valorize infected waste; they are viable alternatives to landfilling or incineration, thereby demonstrating the usefulness of a circular economy approach.

Published
2022
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7. The hidden diversity of the potato cyst nematode Globodera pallida in the south of Peru

Author

Magali Esquibet, Laurent Folcher, Romain Thevenoux, Josselin Montarry, Didier Fouville, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut National de la Recherche Agronomique, Conseil Régional de Bretagne, Anses, European Food Safety Authority (EFSA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nématologie, and Laboratoire de la Santé des Végétaux

Subjects
0106 biological sciences, 0301 basic medicine, Species complex, microsatellite, Nematodes, [SDV]Life Sciences [q-bio], Population, lcsh:Evolution, Potato cyst nematode, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Genetics, lcsh:QH359-425, Globodera pallida, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Genetic diversity, biology, Original Articles, genetic diversity, 15. Life on land, biology.organism_classification, Phylogeography, 030104 developmental biology, speciation, Evolutionary biology, Genetic structure, Microsatellite, Original Article, genetic differentiation, General Agricultural and Biological Sciences
Abstract

Our knowledge of the diversity of potato cyst nematodes in their native areas still remains patchy and should be improved. A previous study based on 42 Peruvian Globodera pallida populations revealed a clear south to north phylogeographic pattern, with five well‐supported clades and maximum diversity observed in the south of Peru. In order to investigate this phylogeographic pattern more closely, we genotyped a larger collection of Peruvian populations using both cathepsin L gene sequence data and a new set of 13 microsatellite loci. Using different genetic analyses (STRUCTURE, DAPC), we consistently obtained the same results that led to similar conclusions: the presence of a larger genetic diversity than previously known suggesting the presence of cryptic species in the south of Peru. These investigations also allowed us to clarify the geographic borders of the previously described G. pallida genetic clades and to update our knowledge of the genetic structure of this species in its native area, with the presence of additional clades. A distance‐based redundancy analysis (dbRDA) was also carried to understand whether there was a correlation between the population genetic differentiation and environmental conditions. This analysis showed that genetic distances observed between G. pallida populations are explained firstly by geographic distances, but also by climatic and soil conditions. This work could lead to a revision of the taxonomy that may have strong implications for risk assessment and management, especially on a quarantine species.

Published
2020
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8. Image based species identification of Globodera quarantine nematodes using computer vision and deep learning

Author

A. Buisson, Laurent Folcher, Romain Thevenoux, Heloïse Villessèche, Nicolas Parisey, Eric Grenier, Van Linh Le, Marie Beurton-Aimar, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Nématologie (LSV Rennes), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Modélisation Mathématique pour l'Oncologie (MONC), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Institut Bergonié [Bordeaux], UNICANCER-UNICANCER-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), ANSES, Conseil Régional Bretagne, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Institut Bergonié [Bordeaux], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Nématologie, Laboratoire de la Santé des Végétaux, and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)

Subjects
0106 biological sciences, Species complex, Globodera rostochiensis, Computer science, [SDV]Life Sciences [q-bio], Potato cyst nematode, Horticulture, 01 natural sciences, Convolutional neural network, Automation, Nematode taxonomy, Discriminative model, Machine learning, Globodera pallida, biology, business.industry, Landmarks, Deep learning, Forestry, Pattern recognition, 04 agricultural and veterinary sciences, biology.organism_classification, Computer Science Applications, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Identification (biology), Artificial intelligence, business, Morphometrics, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; Identification of plant parasitic nematode species is usually achieved following morphobiometric analysis, which requires a certain level of expertise and remains time consuming. Moreover, molecular and morphological discrimination of a number of emergent or cryptic species is sometimes difficult. Finding a way to achieve morphological characterisation quickly and accurately would greatly advance nematology science. Here, we developed a complete method in order to identify the two quarantine nematode species Globodera pallida and Globodera rostochiensis. First, we chose discriminative metrics on the stylet of nematodes that are able to be used by algorithms in order to build an automated process. Second, we used a custom computer vision algorithm (CCVA) and a convolutional neural network (CNN) to measure our metrics of interest. Third, we compared the CCVA and CNN predictions and their discriminative power to distinguish closely related species. Results show accurate identification of G. pallida and G. rostochiensis with the two methods, despite small-scale divergence (one to five µm depending on the metric used). However, the error rate is higher for Globodera mexicana, suggesting that the algorithms are too specific. Nonetheless, these methods represent a promising novel approach to automated morphological identification of nematodes and Globodera species in particular.

Published
2021
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9. Biological Invasion Theories: Merging Perspectives from Population, Community and Ecosystem Scales

Author

Laurent Folcher, Sylvie Baltora-Rosset, Patricia Gibert, Matthieu Chauvat, Laurent Amsellem, Aurélie Tasiemski, Olivier Chabrerie, David Renault, Jelena H. Pantel, Elise Buisson, Manon C.M. Hess, Estelle Forey, Frédérique Viard, Thomas Boivin, Benoit Facon, Frédéric Grandjean, Gabrielle Thiébaut, Julie Braschi, Romain Ulmer, Laurence Affre, David M. Richardson, Romain Thevenoux, François Massol, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut de recherche pour la conservation des zones humides méditerranéennes, NGE-GUINTOLI, Department of Computer Science, Mathematics, and Environmental Science, The American University of Paris, Naturalia-Environnement, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Stellenbosch University, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), GdR CNRS 3647 Invasions Biologiques, Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN), Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Naturalia-Environnement, Ingénierie en écologie, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Leydet, Michelle, Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV)

Subjects
0106 biological sciences, [SDE] Environmental Sciences, invasiveness, Population, Introduced species, 010603 evolutionary biology, 01 natural sciences, Novel ecosystem, phenotypic plasticity, 03 medical and health sciences, Empirical research, evolution, hybrid ecosystem, Ecosystem, education, dispersal, non-native populations, 030304 developmental biology, Abiotic component, historical ecosystem, 0303 health sciences, education.field_of_study, Ecology, Timeline, 15. Life on land, geographic expansion, Geography, [SDE]Environmental Sciences, Biological dispersal, novel ecosystem, ecology, invasibility
Abstract

International audience; Biological invasions have reached an unprecedented level and the number of introduced species is still increasing worldwide. Despite major advances in invasion science, the determinants of success of introduced species, the magnitude and dimensions of their impact, and the mechanisms sustaining successful invasions are still debated. Empirical studies show divergent impacts of nonnativepopulations on ecosystems and contrasting effects of biotic and abiotic factors on the dynamics of non-native populations; this is hindering the emergence of a unified theory of biological invasions. We propose a synthesis that merges perspectives from population, community, and ecosystem levels. Along a timeline of ecosystem transformation driven by nonnative species, from historical to human-modified ecosystems, we order invasion concepts and theories to clarify their chaining and relevance during each step of the invasion process. This temporal sorting of invasion concepts shows that each concept is relevant at a specific stage of theinvasion. Concepts and empirical findings on non-native species may appear contradictory. However, we suggest that, when mapped onto an invasion timeline, they may be combined in a complementary way. An overall scheme is proposed to summarise the theoretical dynamics of ecosystems subjected to invasions. For any given case study, this framework provides a guide through the maze of theories and should help choose the appropriate concepts according to the stage of invasion.

Published
2019
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10. Impact of native plant-parasitic nematode communities on the establishment of Meloidogyne chitwoodi

Author

N. Garcia, Fabrice Ollivier, Laurent Folcher, A. Buisson, C. Sarniguet, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Brittany Regional Council, French Agency for Food, Environmental and Occupational Health & Safety, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, competition phenomenon, Plant Science, Horticulture, 01 natural sciences, nématode parasite, quarantine species, 03 medical and health sciences, pomme de terre, Botany, Genetics, biology, meloidogyne chitwoodi, parasite de quarantaine, Native plant, biology.organism_classification, plant-parasitic nematode communities, 030104 developmental biology, Nematode, Meloidogyne chitwoodi, potato, Agronomy and Crop Science, original experimental design, compétition interspécifique, 010606 plant biology & botany
Abstract

Among plant-parasitic nematodes (PPNs), the species Meloidogyne chitwoodi constitutes an important agricultural issue and is listed as a quarantine species in the EU. This study investigated whether PPN communities can affect the establishment and expansion of M. chitwoodi during a simulated introduction. An original experimental design was developed on potato in the glasshouse involving four PPN communities derived from a single natural one that was initially grown on different host plants. Meloidogyne chitwoodi was inoculated at two different densities (50 or 1000 second-stage juveniles (J2) per pot). After 4 months, M. chitwoodi was more abundant in the community showing a low overall abundance of PPNs, decreased in the other PPN communities and failed to establish in five pots out of 80. Results showed that establishment - even starting from a very low inoculum - can occur in all communities even if indigenous PPNs in the community affect the expansion through interspecific competition. The reverse interaction was also observed as PPN taxa were generally less abundant in the 1000 M. chitwoodi J2 inoculation treatments. The proportion of M. chitwoodi males produced was higher in the community showing low overall PPN abundance, suggesting a strong sensitivity of M. chitwoodi to intraspecific competition. The presented results suggest that a low abundance of indigenous PPNs presents a higher risk of expansion of M. chitwoodi even if the introduced inoculum is low.

Published
2018
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11. Withdrawal of maize protection by herbicides and insecticides increases mycotoxins contamination near maximum thresholds

Author

Xavier Reboud, Nathalie Eychenne, Marc Delos, Laurent Folcher, Reboud, Xavier, Vigiweed project [ANR-OGM 003], and Eric Lichtfouse

Subjects
0106 biological sciences, Fusarium, Integrated pest management, Agroecology, Biotic interaction, Risk assessment, Pest control, Ostrinia nubilalis, Environmental Engineering, [SDV]Life Sciences [q-bio], 01 natural sciences, Crop, chemistry.chemical_compound, Mycotoxin, 2. Zero hunger, biology, business.industry, Crop yield, fungi, food and beverages, 15. Life on land, Pesticide, biology.organism_classification, 010602 entomology, chemistry, Agronomy, 13. Climate action, Agriculture, business, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; AbstractEnvironmental and economic issues affect decision-making for whether or not to control small infestations of pests and pathogens in crops. Even where no crop yield loss is expected, other risks may be evident, such as the slow accumulation of pathogen inocula. The prevalence of toxins, arising from biotic interactions with fungal diseases, can alter crop quality rather than quantity. Thus, farmer decisions for whether to tolerate pest infestation must take into account several direct and immediate and/or delayed potential risks. Published scientific evidence on the co-occurrence of risk factors resulting from the presence of different pests and pathogens are largely absent, and this has stifled the adoption of integrated pest management. Here, we tested how the withdrawal of herbicide and insecticide protection in maize, alone and in combination, might induce higher prevalence of up to 23 mycotoxins in the crop at harvest. The experiment was conducted over 4 years in 29 fields in the south west of France. The test involved a comparison of paired samples collected from treated and untreated plots. All nine major mycotoxins that were observed in more than 4 % of the samples showed highly variable concentrations both between fields and years. The overall trend following the cessation of pesticide protection, however, is for higher levels of mycotoxins and up to a six-fold increased in nivalenol mean concentration (to 202.3 μg kg−1 of maize seeds) compared to its treated control. Overall mycotoxin concentrations approached 55–67 % of their maximum acceptable rate, a situation of reduced security margin that could lead to economic penalties and market restrictions. We found that the removal of herbicides had a greater impact than that of insecticides on the prevalence of mycotoxins, which differs from the expectation stated in the literature. This finding is further reinforced by the observation that certain species of weeds harbor several species of Fusarium. This means that weeds not only play a role as crop competitors but also as reservoirs of inoculum in the field. Our findings illustrate the importance of sanitary evaluation when the implementation of new cropping systems will alter the distribution and occurrence of pests and pathogens.

Published
2016
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12. Mise en évidence et première caractérisation d'une espèce cryptique au sein du complexe Globodera pallida

Author

Thevenoux, Romain, Laboratoire de santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agrocampus Ouest, Éric Grenier, Laurent Folcher, STAR, ABES, Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Automatic morphometry, Diversité génétique, Nématode à kyste, Morphométrie automatisée, Cyst nematodes, Integrative taxonomy, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Genetic diversity, Taxonomie intégrative
Abstract

Cyst Nematodes of the genus Globodera are among the most studied plant parasitic nematodes because of their economic impact on crop production. Originated from high plains of the Andes, this genus would have been imported in Europe during the late XIXth century. The existence of a cryptic species complex within G. pallida – one of the most damaging species in the genus – is questioned. The taxonomic revision of this species could have major consequences on both risk assessment and management. During this work, an integrative taxonomic approach was implemented and has involved three disciplinary fields: genetics, morphometry and biology. Genetic diversity investigation revealed two groups differing from G. pallida. This study also raises the question of the processes implied in this divergence, apparently distinct for these two groupsMorphological differentiation was also demonstrated with an automatic image analysis tool. This tool was specifically developed for this work and is an innovative approach in studying the morphometry of this genus. This differentiation is based on the combined integration of three metrics adapted to automatic morphometry. Differential study of each entity ‘s host-range showed differences between studied groups. This differentiation is observed thanks to the investigation of the quantitative aspect of the nematode multiplication. Overall, these results bring the necessary evidence to claim the existence of a new species. This discovery questions the need for adapting surveillance and management methods against nematodes of the genus Globodera., Les nématodes à kyste du genre Globodera sont parmi les phytoparasites les plus étudiés de par l’impact économique qu’ils peuvent engendrer sur les productions agricoles. Originaire des hauts plateaux de la cordillère des Andes ce genre aurait été importé en Europe à la fin du XIX siècle. L’existence d’un complexe d’espèce cryptique chez G. pallida, nématode phytoparasites d’importance au sein du genre, est questionnée. La révision taxonomique de cette espèce peut avoir des conséquences fortes en termes d’épidémiologie, d’évaluation et de gestion des risques. Durant ce travail une approche de taxonomie intégrative impliquant trois champs disciplinaires, génétique, morphométrique et biologique, a été développée sur un panel de populations sud-américaines pour délimiter de nouvelles frontières au sein de cette espèce. L’exploration de la diversité génétique a permis de révéler l’exitence de deux groupes fortement distants de G. pallidaCette étude questionne aussi les processus impliqués dans cette divergence qui semblent distincts pour ces deux groupes. L’existence d’une différenciation morphologique a été observée grâce à un outil d’analyse d’image automatisé créé spécifiquement pour ce travail. Le développement de l’outil constitue une approche novatrice pour l’étude de la morphométrie dans ce genre et plus généralement chez les nématodes. Cette différenciation s’appuie sur l’intégration combinée de trois métriques adaptées à la morphométrie automatisée. Enfin, l’étude de la capacité de ces entités à se développer aux dépens de certaines plantes a elle aussi rapporté des

Published
2020

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