Root rot of pea: characterization and biocontrol of the soil-borne disease complex including Aphanomyces euteiches

Pea root rot is an increasing constraint in most of intensive pea cropping areas across the globe. The pathogenic complex responsible for the disease is composed of soil-borne fungal and oomycete pathogens such as Fusarium solani, F.oxysporum, F. avenaceum, F. culmorum, Rhizoctonia solani, Thielaviopsis basicola, Ascochyta pinodella, Pythium spp., Aphanomyces euteiches and probably others not yet identified. The diversity of their ecological and pathogenic properties can explain the worldwide dispersion of the disease and the absence of chemical, agricultural or genetic control tools. My research program aims at characterizing the parasitic consortium occurring in the North of France and at…

Mechanisms involved in spatial and temporal mobility of disease patches caused by Rhizoctonia solani in sugar beet field : Induction of antagonists within disease patch

National audience; Rhizoctonia solani AG 2-2 causes damping-off and root rot on sugar beet in patches that are highly mobile both on spatial and temporal scales. They never occur in the same place where they were in the previous season. The aim of the present study was to uncover the mechanisms underlying the dynamics of disease patches. It was observed that soil inoculum potential was higher within diseased patch than in healthy area. However, the dormant pathogen in healthy area was stimulated by addition of buckwheat meal more than that in diseased patch. In addition soil from diseased area was more suppressive towards the disease. We did not observe significant differences in bacterial …

Nomenclature of potato blemishes needs rationalisation

International audience

The control of soil borne vascular diseases: Limits of genetic resistance of cultivars and rootstocks for controlling Fusarium oxysporum f. sp. melonis (melon) and Verticillium sp. (eggplant)

After using resistant cultivars or resistant rootstocks for many years to control soil-borne pathogenic fungi causing wilt disease, growers observe more and more frequently wilt like symptoms in their melon and eggplant cultures. Ctifl, in close collaboration with INRA, regional extension services, and seed companies, set up a study designed to investigate the causative pathological agents. The results show the prevalence of Fusarium oxysporum f. sp. melonis race 1-2 yellowing on melon and of Verticillium dahlia on eggplant. Both pathogens are often found together with other pathogenic soil fungi, which act as aggravating factors. The isolates of F. oxysporum f. sp. melonis collected from i…

Field trials design to assess sugar beet varieties resistance to Rhizoctonia solani : results from the R2B project

Avis de l'Anses relatif à une demande d'évaluation de 4 substances naturelles à usage biostimulant : le saule, la prêle des champs, l’huile essentielle de menthe des champs et la léonardite.

Les substances naturelles à usage biostimulant (SNUB) sont définies dans le cadre de la réglementation applicable au niveau national. Conformément au point 4° de l'article L. 255-5 du code rural et de la pêche maritime, les SNUB sont dispensées d'une autorisation de mise sur le marché. Toutefois, elles sont soumises à une procédure d’autorisation et d’évaluation, dont les modalités sont fixées par voieréglementaire et codifiées à l'article D. 255-30-11 du code rural et de la pêche maritime.Ainsi, une SNUB est autorisée, le cas échéant avec des prescriptions particulières d’utilisation, par son inscription sur une liste annexée à l'arrêté du 27 avril 20162 et publiée par arrêté du ministre c…

Suppressiveness of 18 composts against 7 pathosystems : variability in pathogen response

International audience; Compost is often reported as a substrate that is able to suppress soilborne plant pathogens, but suppression varies according to the type of compost and pathosystem. Reports often deal with a single pathogen while in reality crops are attacked by multiple plant pathogens. The goal of the present study was to evaluate the disease suppression ability of a wide range of composts for a range of plant pathogens. This study was conducted by a consortium of researchers from several European countries. Composts originated from different countries and source materials including green and yard waste, straw, bark, biowaste and municipal sewage. Suppressiveness of compost-amende…

Ecological role of mycotoxin and consequences of the presence of mycotoxins in crop residues on the survival and pathogenic activity of Fusarium graminearum

Recovery of mutants impaired in pathogenicity after transposition of Impala in Fusarium oxysporum f.sp. melonis

The ability of transposon impala to inactivate genes involved in pathogenicity was tested in Fusarium oxysporum f. sp. melonis. Somatic excision of an impala copy inserted in the nitrate reductase-encoding niaD gene was positively selected through a phenotypic assay based on the restoration of nitrate reductase activity. Independent excision events were analyzed molecularly and shown to carry reinsertedimpala in more than 70% of the cases. Mapping of reinserted impala elements on large NotI-restriction fragments showed that impala transposes randomly. By screening 746 revertants on plants, a high proportion (3.5%) of mutants impaired in their pathogenic potential was recovered. According t…

Complexity of the tripartite interaction in the rhizosphere: case of soil-borne pathogenic fungi with the holoparasitic plant Phelipanche ramosa and its host plant

Fusariose du cyclamen : travaux sur la lutte biologique. Phytoma-La défense des végétaux

SPEIPM; Fusariose du cyclamen : travaux sur la lutte biologique. Phytoma-La défense des végétaux

Investing induced resistance and competition as a biocontrol strategy of Fusarium oxysporum f.sp. cubense using non-pathogenic Fusarium oxysporum

Isolation and characterization of nonpathogenic Fusarium oxysporum isolates from the rhizosphere of healthy banana plants

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; One of the most serious diseases of banana is fusarium wilt, caused by Fusarium oxysporum f.sp. cubense (Foc). The objectives of this study were to isolate and identify nonpathogenic F. oxysporum strains from soils suppressive to banana wilt, and to determine the diversity of these isolates. More than 100 Fusarium strains were isolated from the rhizosphere of banana plants and identified to species level. Pathogenicity testing was carried out to confirm that these isolates were nonp…

La protection agroécologique appliquée

National audience; Le sol est un milieu complexe. Son étude et l’acquisition de références solides sur ses interactions avec les cultures s’inscrit dans la durée. En pratique, il est d’ores et déjà possible d’appliquer certains principes agroécologiques à la protection contre les bioagresseurs pendant la phase d’implantation, en les adaptant à chaque situation et aux objectifs visés.

Micro-organismes et interactions biotiques

International audience

Expression de quelques PR protéines dans des cultures cellulaires et des plantes de tomate inoculées avec une souche pathogène ou une souche protectrice de Fusarium oxysporum

Identification of potential mycoherbicides using a metabarcoding approach

National audience

Characterization of Fusarium oxysporum populations by growth parameter evaluation in microtiter plates

Trophic competition for the C source is the main mechanism involved in the interaction between pathogenic and non-pathogenic populations of Fusarium oxysporum. Therefore, a phenotypical characterization based on the growth characteristics of these populations will provide classical genotypical characterizations with additionnal information of ecological significance.

The soil as a reservoir for antagonists to plant diseases

The soil is often considered the milieu providing support for plant roots, water and nutrients for plant growth. But it is also considered a hostile environment harbouring plant pathogenic nematodes, bacteria and fungi. The most common attitude is to try to eliminate the plant pathogenic organisms by biocidal treatments such as methyl bromide fumigation, which are dangerous for man and the environment. Beside this pathogen eradication strategy, another approach to control soil-borne plant diseases consists in studying the plant-pathogen interactions at the cellular and molecular level to create new resistant cultivars or to develop new plant protection products based on elicitation of plant…

Evaluation of Nonpathogenic Fusarium oxysporum and Pseudomonas fluorescens for Panama Disease Control

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Nonpathogenic Fusarium oxysporum endophytes from healthy banana roots were evaluated for their ability to reduce Fusarium wilt of banana (Panama disease). Isolates were identified morphologically and by using species-specific primers. Pathogenicity was confirmed by inoculating banana plantlets in the greenhouse. Nonpathogenic F. oxysporum isolates were grouped into 14 haplotype groups by polymerase chain reaction restriction fragment length polymorphism analysis of the intergenic sp…

Identification of the pathogens responsible for the surface deteriorations on the potato tubers

Biocontrol of weeds toxic to human and animal health

imson weed (Datura stramonium L.) is an invasive weed plant that produces alkaloids that are particularly toxic to humans (crop contamination) and animals (fodder). The objective of my research project is to find a biocontrol solution based on the use of fungi (even oomycetes) and/or plant extracts to control this plant in agricultural plots. At first, I focus on the research of mycoherbicides. The presence of pathogens or phytotoxic metabolites for jimson weed in a panel of non-infested soils to highly infested soils is tested by applying aqueous extracts or filtrates (0.2µm) of these soil extracts to datura seeds placed on germination paper under controlled temperature and humidity condit…

Nouveaux concepts de gestion des bioagresseurs du sol par approche conservatoire de leur biodiversité

Fusariose du cyclamen : vers un outil de détection précoce

SPEIPM; Fusariose du cyclamen : vers un outil de détection précoce

Biocontrol of the parasitic plant species Phelipanche ramosa, using rapeseed rhizosphere fungi or phytotoxic metabolites

International audience

Maîtrise de communautés microbiennes pour lutter contre les maladies d'origine tellurique

Détection et identification de Fusarium spp. dans le réseau hydrique d’un centre hospitalier universitaire

Typing of anastomosis groups of Rhizoctonia solani by restriction analysis of ribosomal DNA.

A method based on restriction analysis of polymerase chain reaction (PCR)-amplified ribosomal DNA was developed for the rapid characterization of large populations of Rhizoctonia solani at the anastomosis group (AG) level. The restriction maps of the internal transcribed spacers (ITS) sequences were compared for 219 isolates of R. solani belonging to AG-1 to AG-12 and AG-BI, representing diverse geographic and host range origins. Four discriminant restriction enzymes (MseI, AvaII, HincII, and MunI) resolved 40 restriction fragment length polymorphism (RFLP) types among the 219 ITS sequences of R. solani. Each RFLP type could be assigned to a single AG except for two RFLP types, which were c…

Diversity and interactions among strains of Fusarium oxysporum : application to biological control.

International audience

Functionnal aspects of biodiversity in relation to plant health

 Texte intégral; The most visible impact of human activities on biodiversity concerns species which are part of our cultural heritage but a huge part of the diversity is still hidden, mainly in the ocean, in extreme environments and of course in the soil. Although some estimations can be proposed, they are all considered as under-evaluations of the putative number of taxa that could be present on (in?) the planet Earth. Despite it is not yet known, this biodiversity contributes to different services through the functioning of ecosystems, and thus influences the sustainability of these ecosystems. This was the case for instance when the unsuspected major roles of the archeabacteria in the bi…

Modeling in Microbial Ecology

SPE IPM; International audience; The bases and the principles of modeling in microbial community ecology and biogeochemistry are presented and discussed. Several examples are given. Among them, the fermentation process is largely developed, thus demonstrating how the model allows determining the microbial population growth rate, the death rate, and the maintenance rate. More generally, these models have been used to increase the development of bioenergetic formulations which are presently used in biogeochemical models (Monod, Droop, DEB models). Different types of interactions (competition, predation, and virus–bacteria) are also developed. For each topic, a complete view of the models used…

Hydro-contamination fongique par Fusarium spp. en milieu hospitalier pendant une période de construction

Détermination des causes de l'apparition des altérations superficielles du tubercule de pomme de terre

Determinisms of plant and microbiome interactions : a multidisciplinary approach involving high-throughput phenotyping

International audience

Cause and duration of mustard incorporation effects on soil-borne plant pathogenic fungi

International audience; Two fungal plant pathogens, Rhizoctonia solani AG 2-2 and Fusarium oxysporum f.sp. lini, were studied in relation to general responses of soil fungi and bacteria following incorporation of Brassica juncea. Our aim was to understand to what extent the changes in the biological and physicochemical characteristics of the soil could explain the effects on the studied pathogens and diseases, and to determine the temporal nature of the responses. Short-term effects of mustard incorporation (up to 4 months) were investigated in a microcosm experiment, and compared with a treatment where composted plant material was incorporated. In a field experiment, the responses were fol…

Épidémiologie de populations de Fusarium oxysporum et F. dimerum en milieu hospitaliers à Dijon et Nancy

Fusarium oxysporum et F. dimerum sont des champignons d'origine tellurique présents dans de nombreux écosystèmes terrestres mais ils ont été récemment détectés dans les systèmes de distribution d'eau de bâtiments hospitaliers1. Une enquête épidémiologique incluant divers bâtiments hospitaliers sur différents sites, des complexes non-hospitaliers et des maisons individuelles a été menée pendant deux ans dans deux villes françaises, Dijon et Nancy. Les champignons ont été détectés seulement dans les canalisations de bâtiments hospitaliers et n'ont pas été détectés dans celles des autres immeubles ni dans l'eau du réseau urbain. Cette distribution surprenante s'explique par une combinaison de …

Are soils suppressive to fungal diseases the sources of biocontrol agents ?

Soils suppressive to soil-borne diseases are defined by a low disease incidence in spite of the presence of a virulent pathogen and a susceptible plant. In many cases, the inhibition of the disease development relies on the activity of the resident soil microbiome. Suppressiveness can be transmitted to conducive soil by mixing a small amount of suppressive soil into the conducive one. To identify microbial taxons linked to the suppressive phenotype of soils, culture independent-based methods have been employed to analyze and compare microbial diversities in two different soils suppressive (respectively conducive) to either Fusarium wilt of flax or Rhizoctonia diseases of sugar beet. Metagen…

The potential of nonpathogenic Fusarium oxysporum and other biological control organisms for suppressing fusarium wilt of banana

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; The aim of this study was to evaluate the ability of nonpathogenic F. oxysporum and Trichoderma isolates from suppressive soils in South Africa to suppress fusarium wilt of banana in the glasshouse. Several biological control agents and commercial biological control products were included in the study. The isolates were first screened in vitro on potato dextrose agar. In glasshouse evaluations, the fungal and bacterial isolates were established on banana roots before they were repla…

Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum

Contents   Summary  529 I. Biological control of plant diseases: state of the art  530 II. Main modes of action of biological control agents  530 III. The protective strains of F. oxysporum: an unexplored model  532 IV. Future directions for the study of the protective capacity of strains of F. oxysporum  539 V. How to make biological control successful in the field?  540   References  541 Summary Plant diseases induced by soil-borne plant pathogens are among the most difficult to control. In the absence of effective chemical control methods, there is renewed interest in biological control based on application of populations of antagonistic micro-organisms. In addition to Pseudomonas spp. a…

Soil suppressiveness to plant diseases

Prod 2018-286 SPE BIOmE IPM INRA; International audience

Defense Responses of Fusarium oxysporum to 2,4-Diacetylphloroglucinol, a Broad-Spectrum Antibiotic Produced by Pseudomonas fluorescens

A collection of 76 plant-pathogenic and 41 saprophytic Fusarium oxysporum strains was screened for sensitivity to 2,4-diacetylphloroglucinol (2,4-DAPG), a broad-spectrum antibiotic produced by multiple strains of antagonistic Pseudomonas fluorescens. Approximately 17% of the F. oxysporum strains were relatively tolerant to high 2,4-DAPG concentrations. Tolerance to 2,4-DAPG did not correlate with the geographic origin of the strains, formae speciales, intergenic spacer (IGS) group, or fusaric acid production levels. Biochemical analysis showed that 18 of 20 tolerant F. oxysporum strains were capable of metabolizing 2,4-DAPG. For two tolerant strains, analysis by mass spectrometry indicated…

Adaptation inattendue de populations de Fusarium oxysporum et F. Dimerum au milieu aquatique urbain des conduites d'eau de bâtiments hospitaliers à Dijon et Nancyξ

National audience; Fusarium oxysporum et F. dimerum sont des champignons d'origine tellurique présents dans de nombreux écosystèmes terrestres mais ils ont été récemment détectés dans les systèmes de distribution d'eau de bâtiments hospitaliers. Une enquête épidémiologique incluant divers bâtiments hospitaliers sur différents sites, des complexes non-hospitaliers et des maisons individuelles a été menée pendant 2 ans dans deux villes françaises Dijon et Nancy. Les champignons ont été détectés seulement dans les canalisations de bâtiments hospitaliers et n'ont pas été détectés dans celles des autres immeubles ni dans l'eau du réseau urbain. Cette distribution surprenante s'explique par une c…

Inoculations Microbiennes et Lutte Biologique

RésiLens: A research project aiming at identifying bruchid and root rot resistance sources in lentil (Lens culinaris)

National audience; Introducing legumes in modern cropping systems increases crop diversity and reduces the use of external inputs. It thus contributes to achieving sustainable food and feed production. Lentil (Lens culinaris Medik.) is an environmentally friendly, nutritious, protein-rich legume food crop. It is grown in a wide range of climatic conditions and fixes atmospheric nitrogen through bacterial symbiosis. In France, lentil cultivated areas are continuously increasing but are still largely inferior to the areas cultivated with cereals or other legumes such as pea and faba bean. One of the most serious problems for lentil cultivation is due to the insect pests known as seed beetles …

Risque phytosanitaire (ARP) portant sur Fusarium oxysporum f. sp. cubense (agent pathogène responsable de la maladie de Panama) pour les départements d'Outre-mer

Risque phytosanitaire (ARP) portant sur [i]Fusarium oxysporum[/i] f. sp.[u] cubense[/u] (agent pathogène responsable de la maladie de Panama) pour les départements d'Outre-mer

Étude du développement saprophyte de [i]F. graminearum[/i] champignon pathogène du blé et producteur de mycotoxines

SPE affiche, résumé; Troisième plante cultivée au monde derrière le maïs et le riz, première en ce qui concerne les échanges commerciaux, le blé est l’un des aliments prépondérants en production animale et les produits issus de sa transformation sont à la base de l’alimentation humaine. La fusariose est l’une des principales pathologies fongiques touchant les cultures de blé : elle provoque notamment un dessèchement des épis touchés. Un « pool » de champignons appartenant aux genres Fusarium et Microdochium est responsable de cette maladie. Celle-ci est connue depuis longtemps puisque F. graminearum, l’agent principal de la pathologie, a été décrit en 1839 (Schwabe, Flora Anhaltina 2). Outr…

Ecologie des champignons phytopathogènes du sol. Intérêt pour les cultures. Nouveaux concepts de gestion des bioagresseurs du sol par approche conservatoire de leur biodiversité

communication orale invitée; absent

Méthodes indirectes : prophylaxie et méthodes culturales. Lutte contre les maladies telluriques en grandes cultures et protection des cultures légumières

SPE

Ecological fitness of the biocontrol agent Fusarium oxysporum Fo47 in soil and its impact on the soil microbial communities

Some nonpathogenic strains of Fusarium oxysporum can control Fusarium diseases responsible for severe damages in many crops. Success of biological control provided by protective strains requires their establishment in the soil. The strain Fo47 has proved its efficacy under experimental conditions, but its ecological fitness has not been carefully studied. In a series of microcosm studies, the ability of a benomyl-resistant mutant Fo47b10 to establish in two different soils was demonstrated. One year after its introduction at two concentrations in the disinfected soils, the biocontrol agent (BCA) established at similar high population densities, whereas in the nondisinfected soils it survive…

Genetic diversity of Rhizoctonia solani associated with potato tubers in France.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The soilborne fungus Rhizoctonia solani is a pathogen of many plants and causes severe damage in crops around the world. Strains of R. solani from the anastomosis group (AG) 3 attack potatoes, leading to great yield losses and to the downgrading of production. The study of the genetic diversity of the strains of R. solani in France allows the structure of the populations to be determined and adapted control strategies against this pathogen to be established. …

Involvement of various anastomosis groups of Rhizoctonia solani in the superficial blemishes on potato tubers

Collection de Microorganismes d’Intérêt Agro-Environnemental (MIAE)

Étude du développement saprophyte de Fusarium graminearum, champignon pathogène du blé et producteur de mycotoxines

National audience; Troisième plante cultivée au monde derrière le maïs et le riz, première en ce qui concerne les échanges commerciaux, le blé est l’un des aliments prépondérants en production animale et les produits issus de sa transformation sont à la base de l’alimentation humaine. La fusariose est l’une des principales pathologies fongiques touchant les cultures de blé : elle provoque notamment un dessèchement des épis touchés. Un « pool » de champignons appartenant aux genres Fusarium et Microdochium est responsable de cette maladie. Celle-ci est connue depuis longtemps puisque F. graminearum, l’agent principal de la pathologie, a été décrit en 1839 (Schwabe, Flora Anhaltina 2). Outre …

Effect of the host-plant and the soil-type on the diversity of soilborne populations of fluorescent pseudomonds and of Fusarium oxysporum

International audience

Ecological role of mycotoxins in wheat crop residues and consequences on the multitrophic interactions in the soil and further development of Fusarium graminearum

Format du poster : 21 X 29,7; absent

Utilisation et comparaison de méthodes de caractérisation moléculaire appliquées au genre Fusarium dans le cadre de la gestion de la collection de Microorganismes d’Intérêt Agro-Environnemental (MIAE)

Affiche; Les champignons microscopiques du genre Fusarium (phylum des Ascomycètes) sontresponsables de nombreuses maladies sur plantes (blé, tomate, palmier …) engendrant de fortespertes de rendement. Ils sont par ailleurs responsables de la production de mycotoxines quipeuvent avoir un impact non négligeable en santé animale et humaine.

Time dependent response of Rhizoctonia solani to mustard incorporation

SPE;EA communication orale, résumé; International audience

Identification des agents pathogènes du sol associés aux altérations superficielles du tubercule de pomme de terre

Biocontrol of Phelipanche ramosa, a parasitic weed of rapeseed in France, using soil-borne fungi

National audience; Phelipanche ramosa is a major holoparasitic weed, which became a major agronomic problemfor rapeseed crops in France. Weed control in rapeseed does not have a direct impact on thisparasitic weed whose half of the reproductive cycle occurs on the root system of its host. Since1990, broomrape expanded its distribution area starting from the Poitou-Charentes region.Necrosis symptoms on broomrapes from this region should be indicators of potentialpathogenic fungi. Furthermore, these pathogenic fungi should be able to infest differentbroomrape stages. The aim of my thesis is to contribute to the evaluation of an integrated controlsolution for this parasitic weed and focus on t…

Biocontrol of the parasitic plant species Phelipanche ramosa, using rapeseed rhizosphere fungi or phytotoxic metabolites they produce.

Phelipanche ramosa (L.) Pomel, branched broomrape, is a major root-holoparasitic damaging weed with a large host range besides a strong adaptation to rapeseed. Broomrape seed germination is necessarily triggered by host root exudates. This ensures that they germinate close to a host root where they attach and establish a vascular connection to take up water and nutrients. No efficient broomrape management technique has been validated yet. Biocontrol could be an alternative but there is currently no biological control agent on the market. Indeed tripartite interactions between the host plant, the parasitic plant and a pathogenic agent of the latter are complex and poorly understood. The obje…

Biocontrol against the root parasitic plant species Phelipanche ramosa, branched broomrape of tobacco

The branched orobanche, Phelipanche ramosa L., is an obligate parasitic weed that has become, in France, a major agronomic problem in tobacco crops; yield and quality losses can be total and cause growers to reduce the producing area due to lack of available healthy plots or to abandon the crop. Because chemical management is not effective, biocontrol is certainly the alternative to propose but there is currently no biological control agent on the market to meet the expectations of producers and control this parasitic plant. Only a few microorganisms or molecules, are presented as potential and promising candidates in conclusion of scientific articles but the finalization is absent. A colle…

Interest of cultural practices to manage soilborne diseases

Identification des agents pathogènes du sol associés responsables des altérations superficielles du tubercule de pomme de terre

Pathogenic variability and genetic characterization of Rhizoctonia solani AG-2-2 causing crown and root rot on sugar beet in France

Légumineuses et qualité sanitaire des sols

communication orale invitée; absent

Genetic diversity of Fusarium oxysporum and related species pathogenic on tomato in Algeria and other Mediterranean countries

In order to characterize the pathogen(s) responsible for the outbreak of fusarium diseases in Algeria, 48 Fusarium spp. isolates were collected from diseased tomato in Algeria and compared with 58 isolates of Fusarium oxysporum originating from seven other Mediterranean countries and 24 reference strains. Partial sequences of the translation elongation factor EF-1α gene enabled identification of 27 isolates as F. oxysporum, 18 as F. commune and three as F. redolens among the Algerian isolates. Pathogenicity tests confirmed that all isolates were pathogenic on tomato, with disease incidence greater at 28°C than at 24°C. All isolates were characterized using intergenic spacer (IGS) DNA typing…

CA-SYS: A long term experimental platform on agroecology at various scales

National audience; The French National Institute for Agricultural Research (INRA) has established an ambitious, multiscale, agricultural experimental infrastructure (the CA-SYS platform) as a collaboration between the Research Unit, Agroécologie (Dijon, eastern France), and the Experimental Research Unit, Domaine d’Epoisses (20 km next to Dijon). CA-SYS covers an area of 120 ha, and is divided into 47 fields, each of which has drainage and can be irrigated, and will be initiated in autumn 2018. The aims of CA-SYS are to: i) design and evaluate new agroecological systems; ii) study the transition from current farming systems towards these new agroecological systems, with goals that include a…

Microorganisms and Biotic Interactions

SPE IPM; Most ecosystems are populated by a large number of diversified microorganisms, which interact with one another and form complex interaction networks. In addition, some of these microorganisms may colonize the surface or internal parts of plants and animals, thereby providing an additional level of interaction complexity. These microbial relations range from intraspecific to interspecific interactions, and from simple short-term interactions to intricate long-term ones. They have played a key role in the formation of plant and animal kingdoms, often resulting in coevolution; they control the size, activity level, and diversity patterns of microbial communities. Therefore, they modul…

Root rot of pea : characterization and biocontrol of the soil-borne disease complex including Aphanomyces euteiches

Pea root rot is an increasing constraint in most of intensive pea cropping areas across the globe. The pathogenic complex responsible for the disease is composed of soil-borne fungal and oomycete pathogens such as Fusarium solani, F.oxysporum, F. avenaceum, F. culmorum, Rhizoctonia solani, Thielaviopsis basicola, Ascochyta pinodella, Pythium spp., Aphanomyces euteiches and probably others not yet identified. The diversity of their ecological and pathogenic properties can explain the worldwide dispersion of the disease and the absence of chemical, agricultural or genetic control tools. My research program aims at characterizing the parasitic consortium occurring in the North of France and at…

Impact de pratiques culturales sur les caractéristiques du sol

National audience; Plusieurs caractéristiques d'un sol ont été évaluées dans une parcelle expérimentale du Ctifl, suite à l'apport d'amendements organiques ou une biodésinfection (culture de radis fourrager, broyage et enfouissement, roulage, bâchage avec film plastique puis semis de carottes). Les résultats de la première année montrent que la biodésinfection a un impact marqué sur les communautés de microbes et de nématodes des sols, et que cette pratique réduit significativement la sensibilité des sols à la fonte de semis due à R. solani.

Investigation of side-effects of repeated applications of coppersulfate on microbial activities and biodiversity in order to define bioindicator groups of soil contamination by copper

International audience

Characterization of field isolates of Trichoderma antagonistic towards Rhizoctonia solani

Rhizoctonia solani AG 2-2 is a phytopathogenic fungus causing damping off and root rot in sugar beet. The disease occurs in the form of patches. In monoculture, these patches are highly mobile and never occur at the same place where they were observed the previous year. The soil from within patches was found more suppressive towards the disease than soil from healthy area. Comparison of the microbial genetic structures between the different soil samples suggested that Trichoderma spp. were involved in the increased suppressiveness. Trichoderma spp. are well known for their antagonistic activities. The aim of the present study was to characterize sixteen Trichoderma isolates isolated from wi…

Production and characterization of pathogenicy-deficient mutants of Fusarium oxysporum f. sp. melonis

Adaptation of Fusarium oxysporum and Fusarium dimerum to the specific aquatic environment provided by the water systems of hospitals.

SPE IPM MERS EA; International audience; Members of the Fusarium group were recently detected in water distribution systems of several hospitals in the world. An epidemiological investigation was conducted over 2 years in hospital buildings in Dijon and Nancy (France) and in non-hospital buildings in Dijon. The fungi were detected only within the water distribution systems of the hospital buildings and also, but at very low concentrations, in the urban water network of Nancy. All fungi were identified as Fusarium oxysporum species complex (FOSC) and Fusarium dimerum species complex (FDSC) by sequencing part of the translation elongation factor 1- alpha (TEF-1a) gene. Very low diversity was …

Fusarium species recovered from the water distribution system of a French university hospital

Abstract Dijon Hospital is a French tertiary care institution undergoing major renovation, and different microbiological controls revealed the presence of Fusarium spp. in the water distribution system. Because some Fusarium spp. can cause life-threatening opportunistic infections in immunocompromised patients, an 8-month survey was conducted in two hospital sites in order to evaluate the prevalence of the fungi in the water system. In 2 units of one hospital site, 100% of the samples of tap-water were positive, with high concentrations of Fusarium spp. (up to 10 5  cfu/L). In the second hospital site, 94% of samples were positive, but generally with lower concentrations. The analysis of tr…

Impact d'amendements organiques sur la structure des communautés microbienne des sols : Choix des méthodes, validation et résultats

Molecular tools to monitor a biocontrol agent and to assess its environmental impacts

The use of non pathogenic strains of Fusarium oxysporum has been proposed to control Fusarium diseases responsible for severe damages in many crops of economical importance. In order to monitor the biocontrol strain Fo47 after application in greenhouse and field, we have developed a specific molecular tool based on a sequence characterized amplified region (SCAR). Primers targeting a 210-bp fragment were designed to set up a real time PCR assay allowing the identification of the biocontrol strain and its quantification in environmental samples. The assay enabled specific detection of the strain in soils without cross detection of autochthonous populations of F. oxysporum. After its introduc…

Diversité des populations pathogènes de Fusarium oxysporum associés à la tomate en Algérie et sur le pourtour Méditerranéen

Fusarium oxysporum f. sp. cyclaminis: Identification of specific molecular markers for improved disease prevention

Fusarium oxysporum is a well-known soil-borne and ubiquitous fungus. The species includes a high diversity of saprophytic and pathogenic populations. The phytopathogenic ones are subdivided into formae speciales according to their host specificity. The forma specialis cyclaminis (FoCy) is causing Fusarium wilt only on cyclamen. It causes damages during the entire production line and can raise more than 50 % losses. FoCy is considered as the more destructive pathogen on cyclamen. To achieve a better understanding of the disease and a more efficient and eco-friendly way of control, we aim at finding a specific molecular marker allowing for early detection and quantification of the pathogen an…

Caractérisation de populations microbiennes tolérantes au chlordécone à partir de sols contaminés des Antilles

Le chlordécone (CLD), un insecticide organochloré utilisé en Martinique et en Guadeloupe pendant 20 ans afin de lutter contre le charançon du bananier, contamine des sols agricoles des Antilles posant un problème environnemental qui est devenu un problème majeur de santé publique. Il n’existe que très peu d’évidence rapportant la biodégradation de cet insecticide, classé depuis 2009 comme polluant organique persistant (POP) par la convention de Stockholm. L’objectif de ce travail est de rechercher des éléments indiquant la biotransformation du CLD dans les sols contaminés des Antilles. Des cultures par enrichissement ont été établies à partir d’échantillons de sols contaminés pour isoler de…

Functionnal aspects of biodiversity towards biocontrol in agricultural soils

Fusarium oxysporum f. sp. melonis chez le melon, enseignements issus du projet VASCUlég

Fusarium wilt of melon, caused by Fusariumoxysporum f.sp. melonis (F.o.melonis),is still a major problem for growers. Aresearch programme was therefore developpedincluding 23 partners (VASCUlég).Analysing the situation revealed that thebioagressors are adapting, particularlyF.o.melonis race 1.2 whether it be on its ownor associated with other pathogens. Molecularcharacterisation of the F.o.melonisstrains shows strong genetic diversity.However, new sources of resistance to therace 1.2 of F.o.melonis were identified. Thisresult must be used in combination with acertain number of other complementarytechniques tested within the framework ofthe project, such as the cropping system,biofumigation,…

La santé des plantes passe par la santé des sols

Diversité génétique au sein de la forme spéciale cyclaminis de Fusarium oxysporum et recherche d’un marqueur spécifique

Le cyclamen est la 3e plante fleurie la plus vendue en France. Une des maladies dommageables de cette culture est la fusariose, causée par Fusarium oxysporum f. sp. cyclaminis (FoCy). Cette forme spéciale, inféodée au cyclamen n’est pas différenciable des autres formes spéciales et souches saprophytes. En se développant dans le xylème, FoCy entraîne la mort de la plante. Quand les symptômes externes apparaissent, la plante est condamnée. La lutte chimique est inefficace, la lutte variétale est inexistante, et les mesures prophylactiques sont difficilement applicables. Pour détecter le pathogène précocement et améliorer la lutte, nous nous sommes intéressés à sa diversité génétique. Pour cel…

Use of sewage sludge compost and Trichoderma asperellum isolates to supress Fusarium wilt of tomato

It has been reported that plant growth media amended with composted bark suppress Fusarium wilts whereas media amended with composted municipal sludge aggravate this disease. However, in this study, a compost prepared from vegetable and animal market wastes, sewage sludge and yard wastes showed a high ability to suppress Fusarium wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici race 1. The ability of this compost to suppress Fusarium wilt of tomato was compared with that of a peat mix (peat:vermiculite, 1:1 v/v) and a naturally suppressive soil from Chateaurenard, France. The compost and the soil from Chateaurenard were highly suppressive, whereas the peat mix was highly condu…

Inundative biocontrol has its limits and … solutions

Evaluation of fungicides and sterilants for potential application in the management of Fusarium wilt of banana

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Fusarium wilt is considered one of the most important diseases of bananas. The disease can only be managed by using resistant cultivars and by preventing its introduction into new fields. The objectives of this study were to evaluate newly available fungicides, in vitro and in vivo, for their efficacy against the responsible pathogen Fusarium oxysporum f.sp. cubense, and to evaluate surface sterilants that could be used for sterilization purposes. Of the fung…

Soilborne fungi with herbicidal action to control the weed seedbank

Moyens communs: ensemble des ressources biologiques (ERB)

communication orale invitée; absent

Mycelial development of Fusarium oxysporum in the vicinity of tomato roots

The patterns of mycelial development (length and branching) of five strains of Fusarium oxysporum were measured in the vicinity of tomato and wheat roots. Two strains were of f. sp. lycopersici, two of f. sp. radicis-lycopersici and the fifth was a non-pathogenic strain currently used as a biocontrol agent. Hyphal extension and branching were measured microscopically using a CCD camera and an image analyser. Furthermore, the role of soluble root exudates, insoluble root materials, glucose supply, and nitrogen supply (casamino acids) on mycelial development was investigated. Each strain had its own pattern of development in the absence of a root. Fungal development of all five strains was st…

DEXi Fusariose de l’ail : Prototype d’outil d’évaluation multicritère en vue de la maitrise du risque de développement de la fusariose de l’ail (Fusarium proliferatum)

Micro-organismes et interactions biotiques. Chapitre 11

Partie 3: Les habitats microbiens: diversité, adaptation et interactions; National audience

Changes in soil suppressiveness to fusarium wilt and side effects resulting from the introduction of a non-pathogenic strain of Fusarium oxysporum into soils

International audience

Use of protective strains of Fusarium oxysporum to control fusarium wilts

Concepts and methods to assess phytosanitary quality of soils

Chapitre 9.4 : Plant-microbe interactions and soil quality; International audience

Isolement de champignons d’un andosol de Guadeloupe contaminé à la chlordécone : caractérisation de leurs tolérances

Verticillium chez l'aubergine à travers le projet Vasculeg. Bioagresseurs présents et caractérisation (1ère partie)

Vascular wilt diseases of vegetable crops remain a major problem for eggplant growers in particular. After having used genetic resistance to Verticillium for several years, they are again confronted with the same problems. The VASCUleg project has led to a precise evaluation of the current situation on farms. Apart from the fungus that causes vascular disease, other pathogens are also present creating a whole range of bioagressors in different zones of production. The characterisation of isolated strains is quite complicated due to the complexity of Verticllium: new classification of Verticillium species, difficult identification of races and low aggressiveness of strains. V. dahliae is onl…

Modes of action for biological control of Fusarium wilt of banana using non-pathogenic Fusarium oxysporum

Ecologie microbienne du sol- Intérêt pour les cultures

communication orale invitée; absent

Orobanche rameuse du tabac (Phelipanche ramosa L.) : Identifier de nouvelles solutions conventionnelles et de biocontrôle

The branching broomrape, Phelipanche ramosa L. is an obligate parasitic plant, which in a few years became a major agronomic problem for tobacco crops in France. Two approaches, aiming at controlling broomrape were tested within the framework of the ELIOT project grouping Arvalis, the CT2F cooperative and the INRA center of Dijon. The first relates to sulfonylurea herbicides, including rimsulfuron and sulfosulfuron and a systemic herbicide of the cyclohexanediones family, clethodim. The results, although instructive, do not reflect an effective control of broomrape. The second approach deals with the search for soil-borne fungi that are pathogenic to broomrape. A large number of fungal stra…

Méthodes alternatives de lutte contre les maladies des plantes

Production of a mixed inoculum of Fusarium oxysporum Fo47 and Pseudomonas fluorescens C7 to control Fusarium diseases

International audience

NatAdGES : a project dedicated to the mitigation of greenhouse gas emissions (N2O) by soils

International audience

Wanted : pathogenesis-related marker molecules for Fusarium oxysporum

Summary Although Fusarium oxysporum pathogens cause severe wilts in about 80 botanical species, the mechanisms of pathogenicity and symptom induction are poorly understood. Knowledge about the genetic and biochemical pathways involved in the pathogenesis of F. oxysporum would be invaluable in getting targets for both fungicide development and search for biocontrol agents. In this respect, we described the main approaches that have been developed to identify some mechanisms underlying the pathogenesis of F. oxysporum . During the last decades, the potential functions triggering of F. oysporum pathogenicity have mainly been investigated by comparing soilborne pathogenic strains with nonpathog…

Sol, biodiversité et pratiques culturales

A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals.

ABSTRACT Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This S…

Characterization of field isolates of Trichoderma antagonistic against Rhizoctonia solani.

The aim of the present study was to characterize sixteen isolates of Trichoderma originating from a field of sugar beet where disease patches caused by Rhizoctonia solani were observed. Use of both molecular and morphological characteristics gave consistent identification of the isolates. Production of water-soluble and volatile inhibitors, mycoparasitism and induced systemic resistance in plant host were investigated using in vitro and in vivo tests in both sterilized and natural soils. This functional approach revealed the intra-specific diversity as well as biocontrol potential of the different isolates. Different antagonistic mechanisms were evident for different strains. The most antag…

Ensemble de Ressources Biologiques dédiées à l'Agroécologie (INRA, Dijon). Mieux connaître, conserver et utiliser les ressources du sol.

National audience; Les spécificités de la problématique biodiversité dans le domaine agricole sont directement liées à l'ensemble des ressources génétiques, qu'elles soient microbiennes, végétales ou animales, et nécessitent la prise en compte de ces multiples composantes, leur fonctionnalité et leurs interactions pour en assurer la conservation et la valorisation. Gérer ces ressources biologiques consiste à les préserver in situ, mais aussi, à les inventorier, les caractériser et les évaluer, les conserver ex situ éventuellement, les régénérer et les diffuser ainsi que les connaissances afférentes. En collaboration avec le CRB Ferdinand Cabanne (http://www.crbferdinandcabanne.fr/) du CHU d…

Build up of patches caused by Rhizoctonia solani

Rhizoctonia solani is a complex species that is composed of different anastomosis groups (AG). Although these different AGs show differences in their host ranges, generally R. solani is a phytopathogenic species with a wide spectrum of hosts. It has the ability to grow as a saprotroph, which further complicates its behaviour as a parasite. The losses caused by R. solani are very important and need a sustainable management strategy. The patchy appearance of the disease caused by this pathogen is well-known. The patches show within and between season dynamics. The factors which affect the spread of the disease can be grouped into three main categories: host plant, pathogen and environment. Ho…

SCAR-based real time PCR to identify a biocontrol strain (T1) of Trichoderma atroviride and study its population dynamics in soils.

Strains of Trichoderma spp. are known for their antagonistic properties against plant pathogens, some are already on the market, others are under development. In order to launch a strain on the market its perfect identification at the species and strain levels is needed. The aim of this study is to (i) design a SCAR marker for specific identification of strain T1 of Trichoderma atroviride and (ii) monitor population dynamics of this strain in soil by real time PCR. A primer pair targeting a 141-bp fragment enabled specific detection of this strain without cross detection of autochthonous populations of Trichoderma in several field soils. In two soils, population dynamics assessed by real ti…

Can Rhizoctonia solani disease be naturally controlled in a sugar beet field ?

International audience

Recherche de bioindicateurs d'impact du recyclage de produits résiduaires organiques en sols cultivés : lien avec la disponibilité de micropolluants organiques et métalliques

Impact of deoxynivalenol on soil microflora and fauna

F. graminearum is an important pathogen that causes head blight of cereal crops as wheat and maize. It also produces the mycotoxins (as Deoxynivalenol=DON) which are toxic to the human and animals. During the off season the pathogen survives in the soil, on weeds and in crop residues. A 24 weeks study was conducted in controlled conditions (microcosms of natural soil, 17 °C, 80% WHC) to test whether the presence of DON in the wheat crop residues gives competitive advantage to F. graminearum over the other soil microflora and fauna to survive and develop a primary inoculum during the decomposition process. This study was carried out in the presence of the whole soil biota (i.e. fungi, bacter…

WG Multitrophic interactions in soil

INRASPEIPM; WG Multitrophic interactions in soil. Future IPM 3.0

Évaluation de bioindicateurs d'impact du recyclage de produits résiduaires organiques en sols cultivés: lien avec les modifications des caractéristiques physico-chimiques du sol

Communication orale, résumé étendu; absent

Déterminisme du pouvoir protecteur d’une souche de Fusarium oxysporum : recherches de gènes impliqués lors de l’interaction avec la tomate

New developments towards high throughput phenotyping studies devoted to innovative plant breeding tools

Vers une protection agroécologique des cultures en phase d’implantation

Prod 2020-1b SPE IPM INRA; National audience; Principales bioagressions des semences et des plantules Déterminants des dynamiques populationnelles des bioagresseurs des semences et des plantules Bases pour une protection agroécologique des cultures en phase d’implantation

Soil health through soil disease suppression: Which strategy from descriptors to indicators?

International audience; Soil is a component of primary importance in crop production, even if it is often neglected, or only regarded as a physical support for the growth of plants. However, with the increasing societal concerns for the sustainability of agriculture, soil must be considered as a living system. Its quality results from the multiple interactions among physicochemical and biological components, notably the microbial communities, primordial for soil function. Crops are threatened by soil-borne diseases. These are often difficult to control, because of the “hidden” status of the pathogens and also because of the absence, noxiousness or lack of efficacy of chemical treatments. In…

Use of marked strains of pathogenic (FOL8) and protective (FO47) Fusarium oxysporum to visualize their interactions with the tomato root in soil

Several modes of action have been proposed to explain the biocontrol capacity of the Fusarium oxysporum protective strain Fo47, especially competition with the pathogen for root colonization. Confocal microscopy has been used to visualize the interactions between the ransformed strains and the tomato root in soil. A disinfested soil was infested by Fo47 GFP, Fol8 DsRed2, or both fungi together at several concentrations before transplanting tomato seedlings. The general pattern of soil and root colonization was similar for the two fungi, but the saprophytic development of Fo47 was faster than that of the pathogenic strain. Conidia, at the surface of soil particles, germinated as early as 18 …

Phenotype characterization of Fo47 mutants affected in their biocontrol activity

National audience

Contamination des circuits d’alimentation en eau par Fusarium

La decouverte de micromycetes du genre Fusarium dans le reseau hydrique du CHU de Dijon nous a conduit a mettre en place un protocole hospitalier de recherche clinique (PHRC) dont l’objectif a ete de decrire en prospectif, dans le temps et dans l’espace, la contamination par Fusarium dans l’eau de 2 CHU francais (Dijon et Nancy), a des periodes d’activites de restructuration et de construction. Cette etude a ainsi permis de mettre en evidence la presence chronique de Fusarium spp. dans les circuits de distribution de l’eau de certains bâtiments hospitaliers. Nous avons en effet observe que ces micromycetes etaient « installes » dans le reseau, que leur densite de population variait au cours…

Identification et caractérisation de candidats d'origine naturelle à action herbicide pour contrôler les adventices

Les produits phytopharmaceutiques (ou pesticides) utilisés aujourd'hui en agriculture sont pointés du doigt pour leurs impacts potentiels sur l’environnement et les écosystèmes et pour les risques qu’ils sont susceptibles d’engendrer pour la santé animale et humaine (Inserm, 2013). Les objectifs majeurs de la thèse sont d’isoler et identifier des microorganismes pathogènes des adventices, et d’acquérir des connaissances sur les mécanismes de l'interaction plante adventicemicroorganismes dans le cadre du développement de bioherbicides pour contrôler les adventices. Outre une analyse bibliographique sur l'état des connaissances relatif aux interactions adventicesmicroorganismes, le travail de…

Ecologie des champignons phytopathogènes du sol