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[hal-05069786] Apport des recherches sur le microbiote aux futures stratégies de biocontrôle - Résultats du projet VITAE
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ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05069786v2
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[hal-05559195] Challenges in microbial interaction inference from time series
Standard procedure: When inferring ecological interactions from time series, the procedure is to use the Lotka-Volterra model, and a specific algorithm "gradient matching" (GM). Issue: Even though it is highly efficient numerically, precise understanding of the inference is lacking. Furthermore, the precision of series reconstruction is not always correlated to the precision of interaction inference, which raises the issue of practical identifiability. Contribution: By using an intermediate model, we are able to study better the parameter estimation. We find that GM presents some limitations, and study ways to circumvent them. Application: We present two different experimental setups and data, that are representative of microbial population series.
ano.nymous@ccsd.cnrs.fr.invalid (Felix Roy) 19 Mar 2026
https://inria.hal.science/hal-05559195v1
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[hal-03858395] The functional microbiome of grapevine throughout plant evolutionary history and lifetime
European grapevine is a complex holobiont composed of two plant genomes, that of the scion (Vitis vinifera L.) and the rootstock (Vitis spp.), and a multitude of microbial genomes that collectively form the microbiome. The grapevine microbiome has been extensively described over the last decade, primarily using metabarcoding approaches. Unfortunately, metabarcoding data alone provide little information on microbial functions and outcomes of plant-microbe interactions. Here we review knowledge about the microorganisms that have a demonstrated influence, positive or negative, on the performance of the grapevine holobiont. Our review encompasses bacteria, filamentous fungi, yeasts, oomycetes and viruses. It covers aboveground and belowground microorganisms, including arbuscular mycorrhizal and ectomycorrhizal fungi. We focus on taxa and functions that protect the plant against pathogens and pests, promote growth, increase tolerance to abiotic stresses and highlight those involved in disease and decline. As the outcomes of plant-microbe interactions are labile, we examine the dynamics and functions of grapevine-microbiome interactions over both the plant lifetime and the plant evolutionary history, beginning with plant domestication. Based on the knowledge and gaps we identify, we suggest field sampling designs, culture-based experiments, molecular tools and theoretical analysis methods, including shotgun metagenomics and network models, that could be used in future research to uncover and leverage the full functional potential of the grapevine microbiome.
ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 29 Nov 2022
https://hal.inrae.fr/hal-03858395v1
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[hal-05297196] Deciphering microbial interactions protecting grapevine against downy mildew: Integrating field studies and synthetic community approaches
Grapevine hosts numerous microorganisms that impact its health and growth. Among the key pathogens are Plasmopara viticola (downy mildew) and Erysiphe necator (powdery mildew). When these pathogens colonize grapevine leaves, they encounter the resident microbiome, which can act as a barrier to their growth through various ecological interactions. Additional interactions may occur in the soil and litter but these have been largely overlooked. A current challenge is to identify microbiome members that naturally regulate mildews and find management practices that support these natural antagonists. To address this, we analyzed leaf and soil microbiomes in vineyard plots with long-term epidemiological records. We compared microbial community compositions between plots with contrasting disease susceptibilities and between symptomatic and asymptomatic tissues. Using differential abundance analyses, Random Forest algorithms, and network learning methods, we identified potential antagonists or facilitators. Microbial taxa of interest for downy mildew were found in the topsoil, which serves as both a microbial reservoir and the overwintering site for pathogen oospores, and in the phyllosphere, where pathogen zoospores enter leaves. The leaf endosphere contained very few taxa of interest. The diversity of microbial communities was not consistently related to disease susceptibility, suggesting that susceptibility is more related to the abundance of specific microbial taxa. Several taxa were integrated into Synthetic Microbial Communities (SynComs) and tested against downy mildew in vitro and in the field, aiming to develop microbial biocontrol of grapevine diseases and move towards pesticide-free viticulture.
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297196v1
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[hal-04842411] Developing a culturomic approach to build a collection of grapevine foliar microorganisms with potential biocontrol activity against downy mildew
A culturomic approach involves the use of a range of different culture conditions coupled with a high-throughput method of identification to be able to isolate and identify microorganisms in a sample. A number of studies have shown that using plant-based culture media rather than conventional media that contain chemically synthesized or animal-based extracts can successfully increase the cultivability of plant-associated microbiota. This study aimed to use a culturomic approach to build a collection of grapevine foliar microorganisms, which can subsequently be used to build Synthetic microbial Communities (SynComs) for biocontrol of downy mildew (caused by Plasmopara viticola). For the collection, leaves were sampled from parcels that showed high and low susceptibility to downy mildew. Alongside four conventional culture media, we developed a grapevine leaf based culture medium to cultivate epiphytic and endophytic bacteria, yeast and filamentous fungi. We proceeded to identify the isolates by MALDI-TOF MS and Sanger sequencing. Overall, we isolated 1091 microorganisms including 544 bacteria, 217 yeast and 330 filamentous fungi. We were able to identify 86% of the isolates with 93 total genera identified across the five culture media used. Using the grapevine leaf based culture medium enabled the cultivation of 4 genera of bacteria, 1 yeast genus and 13 genera of filamentous that were not seen on the other media.
ano.nymous@ccsd.cnrs.fr.invalid (Aarti Jaswa) 17 Dec 2024
https://hal.science/hal-04842411v1
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[hal-04180612] Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection
Vineyards harbor a myriad of microorganisms that interact with each other and with the grapevines. Some microorganisms are plant pathogens, such as the oomycete Plasmopara viticola that causes grapevine downy mildew. Others, such as plant growth promoting bacteria and disease biocontrol agents, have a positive influence on vine health. The present study aims to (1) investigate whether vine-based culture media increase the cultivability of the grapevine microbiota, in comparison to standard culture media and (2) identify and isolate bacterial taxa naturally present in grapevine leaves and significantly more abundant in plots showing low susceptibility to downy mildew.
ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 27 Feb 2025
https://hal.science/hal-04180612v2
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[hal-05297768] Identifier des consortiums microbiens qui interfèrent avec les agents pathogènes de la vigne
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ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 19 Mar 2026
https://hal.science/hal-05297768v1
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[hal-03741209] Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture
Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as inf luencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.
ano.nymous@ccsd.cnrs.fr.invalid (Romain Darriaut) 01 Aug 2022
https://hal.inrae.fr/hal-03741209v1
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[hal-05298248] Gérer le microbiote de la vigne pour réduire l’utilisation des pesticides - Synthèse des résultats du WP1 du projet VITAE et perspectives
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ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 06 Oct 2025
https://hal.science/hal-05298248v1
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[hal-05298256] Towards microbiota-based disease management of downy mildew
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ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 06 Oct 2025
https://hal.science/hal-05298256v1
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[hal-05300289] Mining belowground and aboveground microbiome data to identify microbial biomarkers of grapevine health and yield
Vineyards host a wide diversity of microorganisms that interact both with plants and among themselves. Some are pathogens, such as the oomycete Plasmopara viticola, which causes grapevine downy mildew (DM). Others contribute positively to vine health by protecting against pathogens, enhancing resistance to abiotic stress, and improving nutrient uptake. In recent years, beneficial plant-microbe and microbe-microbe interactions, as well as the conservation of microbial diversity, have attracted increasing attention as potential alternatives to fungicide and fertilizer use in viticulture, and as a means to improve vineyard resilience to multiple stresses, including those related to climate change. In this study, we aimed to (i) identify microbial candidates for the biocontrol of DM and (ii) identify microbial biomarkers associated with high and stable yields over time. We analyzed the microbiota in (i) leaves and topsoil from seven pairs of vineyard plots with contrasting susceptibility to DM, based on long-term epidemiological records from the Bordeaux region, and (ii) roots and soil from ten pairs of vineyard plots with contrasting yields, based on long-term yield data from the Champagne region. Using differential abundance analyses, the Random Forest algorithm, and Threshold Indicator Taxa Analysis (TITAN), we identified fungal and bacterial taxa that were significantly more abundant in plots with low DM susceptibility and in those with high and stable yields. Our results revealed that several basidiomycete yeast species were significantly more abundant in the grapevine phyllosphere of plots with low DM susceptibility, while taxa affiliated with arbuscular mycorrhizal fungi were significantly enriched in plots with high and stable yields. These findings highlight specific microbial taxa, living both above- and belowground, that act as biomarkers of grapevine health and yield. However, causal relationships between specific microbial taxa and vine performance remain to be demonstrated. To this end, I will present results from in vitro confrontation assays between basidiomycete yeast consortia and P. viticola, illustrating how mining microbiome data can guide the identification of microbial taxa beneficial to grapevine.
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 07 Oct 2025
https://hal.science/hal-05300289v1
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[hal-05593559] Developing a culturomic approach to build a collection of grapevine foliar microorganisms with potential applications in disease biocontrol
Isolation and conservation of plant-associated microorganisms in pure cultures is important to be able to understand their influence on plant health. However, capturing the whole range of microbial taxa detected by culture-independent approaches remains labour-intensive and challenging since a large proportion fail to grow under laboratory conditions. Culturomic approaches that involve using a variety of culture conditions coupled with high-throughput identification methods are a recommended strategy to effectively capture plant-associated microbial diversity. A number of studies have demonstrated that using plant-based culture media rather than conventional laboratory media is an efficient strategy for increasing the cultivability of plant-associated microorganisms. This study aimed to develop a culturomic approach to build a collection of grapevine foliar microorganisms with potential applications for the biocontrol of foliar diseases. We developed and tested a custom grapevine leaf-based culture medium (GLA) to better mimic the leaf habitat and consequently try to increase the cultivability of foliar microorganisms. Of the 90 genera that were isolated, 17 were isolated exclusively on GLA including 4 bacteria, 1 yeast, and 12 filamentous fungi. Overall, using the GLA allowed for the isolation of a number of taxa that are of interest for their biocontrol potential against plant pathogens. Interestingly, it was also effective for isolating and speeding up the growth of slow-growing filamentous fungi associated with grapevine trunk diseases. Using a combination of laboratory media and the custom GLA resulted in a collection that was representative of 12.5 % of bacterial genera and 17.6 % of fungal genera detected on grapevine leaves. This collection will serve as a repository of pure cultures for conducting experiments. Candidates will be screened and tested both individually and in consortia for potential applications in microbial biocontrol against grapevine diseases, particularly Plasmopara viticola (grapevine downy mildew), with the ultimate goal of developing effective biocontrol products and moving towards more sustainable viticulture.
ano.nymous@ccsd.cnrs.fr.invalid (Aarti D Jaswa) 16 Apr 2026
https://hal.science/hal-05593559v1
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[hal-05566929] Une méthode accessible pour évaluer la pollinisation animale des cultures, déployable de la parcelle à la France entière
La pollinisation animale, centrale pour la majorité des espèces cultivées, est susceptible de devenir limitante du fait du déclin des pollinisateurs. Les outils existants pour mesurer la contribution des pollinisateurs au rendement des cultures sont difficilement transposables à de grandes surfaces, comme celle d'une exploitation agricole ou d'un territoire. Nous proposons un nouvel indicateur de la pollinisation animale. Cet indicateur est simple à produire car il ne nécessite que des données de dépendance des cultures aux pollinisateurs et de rendement des cultures sur un ensemble de parcelles. Nous montrons que, modulo quelques points de vigilance dans l'interprétation, cet indicateur permet de comparer des sites entre eux, d'identifier des zones de déficit de pollinisation animale, et de mettre en évidence les effets des pratiques agricoles et du paysage sur cette pollinisation.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Porcher) 25 Mar 2026
https://hal.inrae.fr/hal-05566929v1
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[hal-05285133] Co-conception de scénarios de complémentarités culture-élevage pour la réduction des pesticides à l'échelle d'un territoire
Les interactions entre culture et élevage sont une piste de réduction des pesticides à l'échelle des territoires. Notre étude a porté sur la co-conception de scénarios intégrant ces interactions sur la Plaine Ouest de Montpellier. Dans le cadre d'une démarche participative mobilisant l'outil Co-Click'Eau, trois scénarios ont permis d'explorer des stratégies de réduction des pesticides différentes : diversification agricole pour l'alimentation locale, préservation de la biodiversité et maximisation des interactions cultureélevage. La démarche a permis de mobiliser une grande diversité d'acteurs autour de l'enjeu de la réduction des pesticides. Les résultats montrent en quoi l'élevage peut contribuer à limiter l'usage des pesticides tout en répondant à d'autres enjeux portés par les acteurs du territoire. Cette approche a permis de mettre en évidence des convergences possibles entre stratégies et souligne la nécessité d'une coordination accrue des acteurs.
ano.nymous@ccsd.cnrs.fr.invalid (Myrto Parmantier) 26 Sep 2025
https://hal.inrae.fr/hal-05285133v1
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[hal-05071357] Pulses in branded agri-food products: the African and global situation
Using text mining methods, we explored the diversity of pulses used in around 350,000 agri-food products launched on the market over the last decade and referenced in the GNPD-Mintel database. The position of soya in comparison with other legumes identified as pulses and promoted by the United Nations were compared worldwide. The positioning of the different species in the list of ingredients and in the products' description have made it possible to assess their relative importance in the branded food offered to consumers. The supremacy of soya was observed worldwide. Such result is confirmed in African countries even though fewer number of products were referenced there. This original method opens up new perspectives for monitoring the use of crops in the food market and its evolution over time and space.
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 16 May 2025
https://hal.inrae.fr/hal-05071357v1
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[hal-05031215] Effet de l'écimage des adventices sur leurs nuisibilités
L'écimage est une technique curative qui consiste à couper les parties aériennes hautes des adventices après floraison et avant grenaison, limitant ainsi le retour au stock semencier de graines viables et limiter la gêne ou les impuretés à la récolte. L'efficacité de l'écimage, son effet sur la compétition entre culture et adventice ainsi que son incidence sur le stock des semences sont peu documentés. Pourtant ces informations sont essentielles, notamment dans la gestion des adventices. Cette technique est supposée efficace si elle empêche une majorité de graines adventices d'alimenter le stock semencier, mais son succès dépend de la date et de la hauteur de l'écimage. En 2022, des essais sur 9 parcelles de blé ont comptabilisé 80 770 graines de vulpins, dont 12 242 ont été testées pour leur viabilité. En moyenne, 40 % des graines sont écimées, ce taux augmentant de 35 % à 55 % entre le 20/05 et le 15/06. Un écimage parfait pourrait atteindre 60 %, voire 70 %. La viabilité des graines écimées est de 11,2 % en moyenne, augmentant avec la date d'écimage, mais non influencée par la hauteur de l'épi. Un écimage agressif affectant le feuillage impacte peu le rendement du blé.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Cordeau) 11 Apr 2025
https://hal.inrae.fr/hal-05031215v1
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[hal-05031046] Motifs de semis, traits et proportions d'espèces pour la gestion agroécologique des adventices dans les associations légumineuse-céréale
L'objectif de cette étude était d'évaluer par simulation avec le modèle FLORSYS, paramétré et évalué préalablement, les effets, en l'absence de stress azoté ou hydrique, d'associations bispécifiques légumineuse-céréale sur la dynamique des adventices et la production des cultures. Sept proportions d'espèces, neuf motifs spatiaux de semis et quatre mélanges (triticale-féverole, blé-féverole, blé-pois, orge-pois) ont été comparés aux cultures pures. Les simulations montrent que (1) les associations orgepois et triticale-féverole contrôlent le mieux les adventices, (2) le motif alternant un rang de céréale et un rang de légumineuse, d'une part, et les proportions d'espèces avec deux tiers de céréales, d'autre part, maximisent les rendements et minimisent les pertes dues aux adventices, (3) la biomasse adventice en association est supérieure ou égale à celle en céréale pure mais toujours inférieure à celle en légumineuse pure et, (4) l'association bénéficie surtout aux légumineuses grâce à la compétition exercée sur les adventices par la céréale associée.
ano.nymous@ccsd.cnrs.fr.invalid (Pierre Lebreton) 11 Apr 2025
https://hal.inrae.fr/hal-05031046v1
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[hal-05029433] Identification d'idéotypes variétaux pour la gestion des adventices : Exemple du pois associé au blé
Associer le pois (Pisum sativum L.) au blé (Triticum aestivum L.) peut réduire l'infestation et les dommages causés par les adventices. Nous avons mené des expériences virtuelles avec le modèle FLORSYS afin d'identifier, en fonction du dispositif d'association et de la flore adventice, (1) les paramètres clé du pois (traits) qui déterminent le rendement et le contrôle des adventices dans les associations pois blé, (2) les combinaisons optimales des valeurs des paramètres du pois et du blé, ainsi que les techniques culturales de l'association, pour maximiser ces objectifs. Les simulations ont inclus des variétés existantes (5 pois et 3 blé) et virtuelles (5 et 10). Les associations ont réduit la perte de rendement du pois due aux adventices (de 30 % pour la variété la moins tolérante aux adventices) et l'infestation du champ (14 %). Un rendement élevé en pois dans les associations infestées d'adventices nécessite une variété de pois à haut potentiel de rendement, une variété de blé suppressive des adventices, et des techniques culturales préventives des adventices. Les résultats ont été synthétisés dans des tableaux de conseils.
ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Colbach) 10 Apr 2025
https://hal.inrae.fr/hal-05029433v1
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[hal-05028941] Rôle des couverts d'interculture et de leurs modes de destruction dans la régulation des adventices
L'étude visait à (i) identifier les pratiques de gestion des couverts pour réduire les adventices dans les cultures suivantes et (ii) quantifier les effets intentionnels ou non de méthodes de destruction des couverts/adventices/repousses. Les couverts d'interculture ont significativement réduit les adventices en interculture de 68 % à 94 % selon leur composition, mais ces effets sont moins visibles dans les cultures. La fertilisation des couverts augmente la biomasse des couverts sans avantage compétitif sur les adventices. L'irrigation des couverts au semis a été inefficace ou contreproductive, augmentant la biomasse adventice en interculture sans effet dans les cultures suivantes. Le travail du sol, le désherbage électrique et le bioherbicide se sont avérées efficaces pour détruire le couvert en place, mais le travail du sol stimule de nouvelles germinations. Le désherbage électrique, ne permet pas, comme les rouleaux, de faire un effet mulch avec le couvert et favorise aussi des levées d'adventices. Les rouleaux ont des efficacités de destruction faibles quand le couvert est peu développé ou trop ligneux. Les résultats sont donc très inféodés au couvert semé et aux conditions météorologiques.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Cordeau) 10 Apr 2025
https://hal.inrae.fr/hal-05028941v1
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[hal-04810661] Recommend and guarantee: testing an insurable treatment protocol for reducing pesticide use in vineyards
Recommend and guarantee: Testing an insurable treatment protocol for reducing pesticide use in vineyards<p>There is considerable uncertainty surrounding the status of sanitary threats to crop production in real time.</p><p>The ratio between the direct costs of pesticide treatments and the costs associated with yield losses would suggest that risk minimization strategies include treatments that are unnecessary, while this is not known when they are selected, and that therefore cause harm to health and the environment. How can we determine the real proportion of such unnecessary treatments and support the direct economic risk of eliminating them? This article focuses on French wine production, known for its high per-unit-area use of fungicides, to describe the testing of an insurable treatment protocol. This protocol has enabled a 30-55% reduction in the use of fungicides between 2019 and 2022 and is combined with an incentive system for the payment of compensation in the event of losses, complementing the current system for covering climatic risks.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Marc Raynal) 29 Nov 2024
https://hal.inrae.fr/hal-04810661v1
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[hal-04799292] Development and validation of a method for assessing the sustainability of farms: IDEA4, its tools and uses
The ACTION project validated the use of the IDEA4 method (Farm Sustainability Indicators 4 th version) with three major outcomes: i) its versatility for use in a variety of contexts (education, research, agricultural advice, support, public action) and in a majority of farming systems (crops, livestock, orchards, viticulture, and market gardening); ii) its functionality, underpinned by three freely accessible tools (Excel calculator, IDEATools and the WEB-IDEA platform); and iii) the establishment of a broad collaborative community of around 300 IDEA4 users (advisers, teachers, researchers and farmers) who have conducted more than 800 farm diagnoses using IDEA4. In the field of education, this method's dual sustainability approach (consisting of three dimensions and five properties of sustainability) enhances its pedagogical performance. In the area of research, IDEA4 contributes to the expansion of knowledge on the sustainability of transitions. The forthcoming WEB-IDEA 2.0 platform will pave the way for national open data sets on the sustainability of French agriculture.
ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Zahm) 22 Nov 2024
https://hal.inrae.fr/hal-04799292v1
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[hal-04728156] Préconiser et garantir : essai d'un protocole de traitement assurable pour la réduction des pesticides en viticulture
Une importante incertitude entoure l'état des menaces sanitaires en temps réel sur les productions végétales. Selon le rapport entre les coûts directs des traitements phytosanitaires et ceux associés aux pertes de rendement, une stratégie de minimisation des risques peut inclure des traitements inutiles, mais non connus comme tels au moment de la décision, entraînant des nuisances sanitaires et environnementales. Comment déterminer la part réelle de ces traitements inutiles, et soutenir la prise de risque économique directe de leur suppression ? Cet article consacré à la production viticole française, connue pour sa forte utilisation de fongicides, décrit l'expérimentation d'un protocole de traitement assurable sur quatre années, ayant permis une baisse des fongicides de 30 à 55 % entre 2019 et 2022, associé à un système incitatif de versement d'indemnités en cas de pertes, complétant le système actuel de couverture des risques climatiques.
ano.nymous@ccsd.cnrs.fr.invalid (Marc Raynal) 09 Oct 2024
https://hal.inrae.fr/hal-04728156v1
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[hal-04590908] Développement et validation d'une méthode d'évaluation de la durabilité des exploitations agricoles. IDEA4, ses outils et ses usages
Le projet ACTION a validé l’usage de la méthode IDEA4 (Indicateurs de Durabilité d’une Exploitation Agricole version 4) avec trois résultats majeurs : 1) sa capacité à être utilisée pour différents usages (enseignement, recherche conseil, accompagnement, action publique) et pour la majorité des systèmes (grandes cultures, élevages, arboriculture, viticulture et maraîchage), 2) son opérationnalité avec ses trois outils libres d’accès (calculateur Excel, IDEATools et plateforme WEB-IDEA), 3) la création d’une large communauté collaborative d’environ 300 utilisateurs d’IDEA4 (conseillers, enseignants, chercheurs et agriculteurs) ayant réalisé un peu plus de 800 diagnostics d’exploitation. Dans l’enseignement, sa double lecture de la durabilité (3 dimensions et 5 propriétés de la durabilité) renouvelle sa capacité pédagogique. En recherche, IDEA4 élargit les connaissances sur la durabilité des transitions. La future plateforme WEB- IDEA 2.0 ouvre la voie de l’open data national des données de la durabilité de la Ferme France.
ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Zahm) 28 May 2024
https://hal.inrae.fr/hal-04590908v1
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[hal-04583640] Des freins de la spécialisation aux opportunités de la diversification pour un territoire sans pesticides
Le bassin de Saffré est une zone agricole de 5 800 ha qui alimente un captage d’eau potable. Ses acteurs se sont engagés vers le non-usage de pesticides à horizon 2040. Une démarche de recherche y est menée pour contribuer à cet objectif. Elle a mis en lumière des atouts, une part importante de prairies et d’exploitations déjà en AB, mais aussi des menaces. En particulier, les surfaces en herbe déclinent au profit de cultures plus consommatrices de pesticides et la baisse conjoncturelle de la demande pour les produits bio freine les conversions. Pour s’affranchir des limites de filières longues spécialisées, certaines exploitations innovent en diversifiant leurs débouchés par la vente directe, ou en diversifiant leurs productions en valorisant les complémentarités cultures-élevage. Ces innovations seront valorisées pour un territoire sans pesticides en 2040.
ano.nymous@ccsd.cnrs.fr.invalid (Remy Ballot) 22 May 2024
https://hal.inrae.fr/hal-04583640v1
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[hal-04583002] Une arboriculture sans produits phytosanitaires de synthèse dans le Pilat, verrouillages et perspectives de transformation
Une production dynamique de pommes qualitatives s’est développée au sein du Parc Naturel Régional du Pilat grâce aux conditions pédoclimatiques favorables et à l'ingéniosité des producteurs locaux, mais également à l'utilisation de produits phytosanitaires de synthèse. Nous avons conduit un diagnostic sociotechnique en enquêtant une diversité d’acteurs de la filière afin d’identifier les processus de verrouillage pouvant expliquer la difficulté des systèmes arboricoles de se passer de produits phytosanitaires de synthèse. Nous avons caractérisé un système sociotechnique organisé autour d’une coopérative agricole commercialisant des pommes à la grande distribution et au marché de gros, ainsi que des dynamiques de niche. Ces éléments, et leurs interconnections, nous permettent d’identifier de possibles trajectoires de transitions sociotechniques vers une arboriculture sans produits phytosanitaires de synthèse.
ano.nymous@ccsd.cnrs.fr.invalid (Anna Hirson-Sagalyn) 22 May 2024
https://hal.inrae.fr/hal-04583002v1
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[hal-05598288] Comparing Methods for Measuring Predation: Toward a Quantitative–Informative Indicator of Natural Pest Control
The transition to insecticide-free pest management requires field-based measurements of natural regulation capturing trophic networks driving pest suppression. Conventional proxies (pest abundance, predator abundance, and richness) fail to quantify actual predation or species contributions. A quantitative-informative indicator must couple trophic interactions, spanning specialist to generalist predators, with specific predation rates (daily prey consumed per predator). We evaluated major predation quantification methods in relation to their potential to inform such an indicator. These included four direct approaches (predator observation, sentinel prey, exclusion devices, predation signs), two indirect approaches (prey remains and molecular traces in predator guts), and three inferential approaches (trait-based analyses, population dynamics modelling, and inference from molecular prey detection). Seven criteria guided the comparison: type of predation measurement, taxonomic resolution for prey and predators, capacity to reveal trophic links, applicability across predator diversity, generality of results, and practical feasibility. We also compared the few approaches for converting molecular detection data into quantitative estimates of predation. Our synthesis highlights inference from molecular prey detection as the most promising and versatile method, as it simultaneously reveals trophic interactions and yields data that can be translated into predation rates. In contrast, common methods such as exclusion devices provide broad estimates of pest suppression but obscure trophic complexity, limiting ecological insight and constraining targeted management in favor of the most effective predator species. Integrating molecular detection with modeling inference emerges as a robust way to estimate predation rates on multiple pests across entire predator communities. This combination offers a powerful framework for developing a biological control indicator, though practical implementation will require improved molecular assays and more effective sampling strategies in the field.
ano.nymous@ccsd.cnrs.fr.invalid (Yann Tricault) 21 Apr 2026
https://hal.science/hal-05598288v1
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[hal-05587477] The capacity to suppress wheat crown rot disease occurs naturally in contrasted farm soils
Crown rot caused by Fusarium graminearum is a major wheat disease, but only a few soils are known to suppress this disease. Here, 49 French soils were screened in greenhouse plant tests to determine their capacity to limit wheat crown rot upon seed inoculation with F. graminearum. As many as 14 of the soils (29%) showed disease suppressiveness, whereas 15 soils were disease-conducive and 20 soils of intermediate status. The suppressive soils originated from different regions, but overall higher disease symptoms were found with North-West soils. The suppressive soils represented various soil types, i.e. Cambisols, Fluvisols, Leptosols and Luvisols. Chemical properties did not differ markedly in suppressive vs conducive soils, but organic carbon content was lower in suppressive soils than in conducive soils. Overall, soil suppressiveness to F. graminearum-mediated crown rot disease was rather widespread in French regions and present across contrasted farm soils.
ano.nymous@ccsd.cnrs.fr.invalid (Alix Catry) 24 Apr 2026
https://hal.science/hal-05587477v1
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[hal-04673412] Combining methods and knowledges for monitoring environmental policies on a territorial scale: spatial disaggregation of pesticides sales through land use data, reglementary information and expert knowledges
1.Introduction Understanding the pesticides uses across a region is crucial for evaluating environmental policy effectiveness, guide environmental monitoring and implement targeted actions (Martin et al., 2023). However, when detailed on-the-ground data on phytosanitary practices and pollutant measurements are scarce or unavailable, the use of appropriate indicators with suitable spatial and temporal resolutions becomes imperative. We present a method for allocating the annual sales of plant protection products on a territorial scale according to agricultural land use. This method provides a spatial and temporal estimate of the application of plant protection products, and is primarily intended for use by local authorities needing to carry out temporal and spatial diagnoses. The method draws upon a nationwide approach proposed by Martin et al. (2023) and Lungarska et al. (2024) in France, with the aim of enhancing and implementing it on a local scale. 2.Materials and methods The method in based on the disaggregation of sales declaration information at the postal code level (BNV-d), based on the detailed land use information at the agricultural parcel scale (more than 350 different crops) provided by the Land Parcel Identification System (LPIS), and the registered uses of products (i.e., the target crops and the registered doses) from the authorisation marketing database (E-phy). This disaggregation encompasses the consideration of infrastructures in non-agricultural zones that could potentially be treated with these products, agricultural practices such as organic farming, and the evolution of legislation concerning the application of pesticides. As some pesticides have several registered uses per crop (i.e., different targets), a reference dose per pesticide and per crop is calculated with the median of all the uses. Users can interact with the method to refine the information on phytosanitary practices within the investigated area. This enables the mobilisation of local expertise, which allows for the adjustment of the target crops and the reference doses applied per plant protection product. The objective is to more accurately reflect the actual phytosanitary practices in the studied area. Subsequently, the refined disaggregated information is reaggregated into a comprehensive territorial-scale resolution. This resolution provides the user with relevant information, as the quantity of active ingredient, to monitor pesticides over time and land use category (e.g., by crop, by non-agricultural land uses). Furthermore, data disaggregated at the plot level within the territory can be used to trace pressures that vary from one point to another for a given substance. The data employed by this method are freely accessible, with records available from 2015 onwards, typically with a maximum lag of two years. 3.Results and Discussion The method was implemented in a number of different territories across France, each characterised by varying land uses, geomorphological features, and phytosanitary challenges. The implementation process engaged a range of local stakeholders, including government agencies and local organisations, underlining the collaborative nature of the method. The method is currently undergoing further developments, with a specific focus on refining the spatial units associated with the administrative postal code of pesticide sales (i.e., the parcels to which products sold in a postal area are effectively applied). Additionally, the inclusion of real data on pesticide applications obtained from farmers' notebooks is being considered. This will lead to a significant improvement in the results produced by the method.
ano.nymous@ccsd.cnrs.fr.invalid (Marco Carozzi) 20 Aug 2024
https://hal.science/hal-04673412v1
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[hal-04214377] Spatialiser des ventes de produits phytosanitaires en prenant en compte les spécificités locales des pratiques
Ce travail de modélisation vise à établir un diagnostic temporel et spatial des ventes des produits phytosanitaires en combinant bases de données statistiques et expertise territoriale. Le modèle combine l’information spatialisée des ventes au niveau du code postal (BNV-d) avec celle de l’occupation du sol au niveau de la parcelle agricole fournie par le registre parcellaire graphique (RPG) et par le RPG complété, incluant également les infrastructures du territoire potentiellement traitées par ces produits. L’expertise locale est mobilisée pour affiner des informations standard sur les usages des produits, comme les doses d’application et les cultures cibles, ou encore la réalité des applications sur certaines parcelles issue de registres phytosanitaires. La disponibilité actuelle des données est à une ou deux années d’écart et notre modélisation repose sur l’hypothèse que les produits sont utilisés au cours de l’année de leur achat (sans stock) . Le modèle estime les quantités de produits et de substances appliquées sur une unité spatiale d’intérêt (parcelle, territoire) ou sur des usages spécifiques (cultures). Le modèle est restreint au périmètre du territoire, prend en compte les méthodes de production (agriculture conventionnelle ou biologique), et il est sensible aux contextes locaux grâce à l’expertise des animateurs sur le terrain.
ano.nymous@ccsd.cnrs.fr.invalid (Matthieu Descout) 22 Sep 2023
https://hal.inrae.fr/hal-04214377v1
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[hal-05230402] PHYTOS-EXPLORER: supporting data-driven decisionmaking to reduce pesticide use at the territorial scale Session: Farming Practice Diversity in Agroecological Transitions: From Typologies to Analytical Tools
Monitoring pesticide use at the territorial scale is imperative for evaluating environmental policies, guiding local action plans, and mitigating risks to ecosystems, human health, and biodiversity. However, the scarcity of fine-scale data on pesticide applications poses a significant challenge in this regard. The Phytos-Explorer tool has been developed for the purpose of spatially disaggregating pesticide sales data and combining it with high-resolution land use information, approved product uses, and local expertise. The tool utilises a range of data sources, including national pesticide sales records (BNVD), agricultural parcel data (LPIS), and geographical land cover datasets, to allocate pesticide use estimates to particular crops and landscapes. This process is then validated through the application of expert knowledge and case studies. The application of the model across four contrasting territories demonstrated its ability to capture inter-annual trends, substitution dynamics, and crop-specific usage patterns. The validation process against ground-truth data demonstrated the efficacy of fungicides, herbicides, and growth regulators, with the performance of insecticides being comparatively lower. The findings of the study demonstrate the importance of incorporating local expertise in order to enhance the accuracy of the results. Whilst the present limitations encompass reporting delays and uncertainties associated with on-farm stockpiling, Phytos-Explorer evinces considerable potential to facilitate evidence-based decision-making for farmers, land managers and policymakers by enabling targeted interventions and tracking progress towards pesticide reduction.
ano.nymous@ccsd.cnrs.fr.invalid (Marco Carozzi) 29 Aug 2025
https://hal.inrae.fr/hal-05230402v1
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[hal-05325705] Modelling pest control and vector-borne disease spread to explore landscape and agricultural management strategies: the SimBAL agent-based model
1. As the urgency to transition to sustainable agricultural systems grows, tools are required to support stakeholders, including farmers and advisors, in designing agricultural landscapes that strengthen ecosystem services. Landscape management is key to support natural pest control, allowing to reduce pesticide use. But the contextspecific nature of trophic interactions induces that, in practice, it is hardly feasible to test different changes in landscapes that are conducive to pest control and that guarantee it sufficiently to dispense with pesticide use. An alternative is to explore in silico the large-scale deployment of management options to help stakeholders, including policy makers, make choices and gain confidence in landscape management and selecting priorities. 2. We developed a spatially explicit modelling tool which has a general scope, and which is currently developed for the case of aphid dynamics in agricultural landscapes according to spatio-temporal host plant availability and natural enemy predation. The epidemiological consequences on the transmission of beet yellowing virus are considered. The availability of host plants for the aphid depends on farming practices (crop diversity, sowing and spraying dates, implementation of semi-natural features). The aim here is to limit this availability at population level and, in particular, to break the space-time continuities leading to massive colonisation of sugar beet. This logic is reversed for predation by natural enemies, with the aim of fostering resources and shelter continuity to promote their abundance and aphid control potential within the landscape. 3. An analysis of the model behavior, a sensitivity analysis and a calibration of the model were carried out. Sim-BAL outputs are consistent with current knowledge on aphid and infection dynamics. The model is able to represent inter-annual variability in sugar beet infection rates in the fields, and to discriminate landscapes that are suppressive towards aphids. 4. SimBAL was developed with the aim of exploring and comparing landscape scenarios to foster natural pest control, rather than being a precise predictive tool. The model can be used to test landscape scenarios based on the expressed priorities of stakeholders, and therefore favors transparency in decision-making. It is a solid tool for collective action in the management of territorial issues.
ano.nymous@ccsd.cnrs.fr.invalid (Gaëlle van Frank) 13 Feb 2026
https://hal.science/hal-05325705v2
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[hal-05548674] Pesticide reduction in the French wine industry and its effect on production risk
Pesticide reduction in the French wine industry and its effect on production risk.
ano.nymous@ccsd.cnrs.fr.invalid (K Hervé Dakpo) 12 Mar 2026
https://hal.inrae.fr/hal-05548674v1
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[hal-05333556] Operationalizing collective action for crop diversity in-situ management: insights from a decentralized collective design approach
The modernization of agriculture in Northern countries has led to a loss of crop diversity, as well as a loss of knowledge, know-how and rights of farmers regarding on-farm seed breeding. In France, the Réseau Semences Paysannes (RSP) brings together collectives of actors (farmers, bakers, citizens, gardeners) mobilized in a quest to reclaim these aspects. Within the framework of the decentralized participatory breeding program conducted in collaboration with INRAE, farmers have co-constructed knowledge in terms of dynamic management of heterogeneous wheat populations. Yet, as the RSP network grows, these actors face new types of challenges regarding collective action. To address them, we proposed to consider peasant seeds as « common unknowns » rather than « common goods » and we adapted and applied an innovative design approach drawing upon the KCP (Knowledge-Concept-Proposals) method. This approach consisted in implementing, from 2019 to 2021, five decentralized design workshops with local seed breeding collectives. The replication of design workshops in different contexts provided a framework for interaction among RSP members, allowed the sharing of both scientific and experiential knowledge. Noteworthily, it fostered the generation of many proposals for enhancing collective action, and led to the development of operational proposals with a view to implement them in the future. This methodology-oriented paper mainly describes the decentralized design approach implemented, its outputs and outcomes, as well as its interests and limits in the context of crop diversity management. It also analyses how the workshop outputs enriches previous works in the field; in particular how such a participatory design approach leads to produce original operational solutions to respond to challenges identified in the literature.
ano.nymous@ccsd.cnrs.fr.invalid (Elsa T Berthet) 28 Oct 2025
https://hal.science/hal-05333556v1
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[hal-04350134] Des ateliers pour concevoir collectivement des expérimentations sur les associations céréales - légumineuses à la ferme. Poster présenté à la rencontre « À la recherche des blés »
Projet de recherche visant à accompagner l’émergence d’une agriculture sans pesticides, en déployant la biodiversité cultivée (populations, mélanges de variétés et d’espèces) au niveau intra-parcelle.
ano.nymous@ccsd.cnrs.fr.invalid (Elsa T. Berthet) 18 Dec 2023
https://hal.science/hal-04350134v1
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[hal-04672656] Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence
In an era marked by rapid global changes, the reinforcement and modernization of plant health surveillance systems have become imperative. Sixty-five scientists present here a research agenda for an enhanced and modernized plant health surveillance to anticipate and mitigate disease and pest emergence. Our approach integrates a wide range of scientific fields (from life, social, physical and engineering sciences) and identifies the key knowledge gaps, focusing on anticipation, risk assessment, early detection, and multi-actor collaboration. The research directions we propose are organized around four complementary thematic axes. The first axis is the anticipation of pest emergence, encompassing innovative forecasting, adaptive potential, and the effects of climatic and cropping system changes. The second axis addresses the use of versatile broad-spectrum surveillance tools, including molecular or imaging diagnostics supported by artificial intelligence, and monitoring generic matrices such as air and water. The third axis focuses on surveillance of known pests from new perspectives, i.e., using novel approaches to detect known species but also anticipating and detecting, within a species, the populations or genotypes that pose a higher risk. The fourth axis advocates the management of plant health as a commons through the establishment of multi-actor and cooperative surveillance systems for long-term data-driven alert systems and information dissemination. We stress the importance of integrating data and information from multiple sources through open science databases and metadata, alongside developing methods for interpolating and extrapolating incomplete data. Finally, we advocate an Integrated Health Surveillance approach in the One Health context, favoring tailored and versatile solutions to plant health problems and recognizing the interconnected risks to the health of plants, humans, animals and the environment, including food insecurity, pesticide residues, environmental pollution and alterations of ecosystem services.
ano.nymous@ccsd.cnrs.fr.invalid (S. Soubeyrand) 26 Aug 2024
https://hal.inrae.fr/hal-04672656v1
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[hal-05526495] Colonization and spatiotemporal distribution of bruchid pests in lentil and faba bean fields
BACKGROUND: Lentils (Lens culinaris Medikus, 1787) and faba beans (Vicia faba Linnaeus, 1753) are important crops in France facing threats from Bruchus spp. We analyzed 59 lentil and 45 faba bean fields across four French regions over three growing seasons (2019-2020 to 2021-2022). We investigated the diversity, colonization patterns and spatiotemporal distribution of bruchids at different crop phenological stages and distances from field edges. RESULTS: Bruchus rufimanus Boheman, 1833 and Bruchus signaticornis Gyllenhal, 1833 were the only species emerging from faba beans (97.8%) and lentils (99.5%), respectively. B. rufimanus colonization was concentrated during pod development, maintaining a balanced male-female ratio throughout. B. signaticornis exhibited a colonization period of ≈1 month, with a gradual increase in female proportion over time. The spatial distribution of bruchids and damage were relatively uniform within fields, indicating strong dispersal capabilities. A significant positive correlation, with a high degree of dispersion, was identified between female abundance and bruchid-damaged grains. CONCLUSION: We confirmed that B. rufimanus and B. signaticornis were the only species damaging faba beans and lentils in France, respectively. The homogeneous spatial distribution suggests a strong dispersal ability of bruchids. The high degree of dispersion in the relationship between female abundance and bruchid-damaged grains highlights the importance of regulatory factors influencing larval and egg survival. These results, together with the presence of B. signaticornis in faba beans, emphasize the need for species-specific, phenology-based and spatially informed integrated pest management strategies, to mitigate the impact of bruchids and reduce reliance on chemical in their control.
ano.nymous@ccsd.cnrs.fr.invalid (Anastasia Chery-Lagrange) 25 Feb 2026
https://hal.inrae.fr/hal-05526495v1
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[hal-05117262] Crop diversity reduces pesticide use more efficiently with refined diversification strategies
Pesticides assured food security for decades, but have left humanity with degraded soils, polluted water, and biodiversity losses. Enhanced crop diversity contributes to the regulation of insect pests, weeds, and diseases, and is therefore assumed to allow pesticide reduction. At the cropping system scale, pesticide use is affected more by crop species than by the number of crops, because crops have contrasting sensitivities to pests and contrasting pesticide requirements. Here, we disentangled the effects of diversity from the effects of crop species, for 1285 cropping systems in French commercial arable farms, using 28 indicators of functional diversity. A composite diversity metric, combining indicators with the greatest explanatory power, accounted for 8% of the pesticide use variance, much less than the variance due to crop species. The results suggest that reducing agricultural reliance on pesticides through diversification is feasible when different components of diversity—namely, crop species and diversity features—are combined.
ano.nymous@ccsd.cnrs.fr.invalid (Yaoyun Zhang) 17 Jun 2025
https://hal.inrae.fr/hal-05117262v1
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[hal-05232413] How contracting in the value chain can reduce farmer's exposure to risks and enhance crop diversification ? A case study approach in the crop sector in France
Marketing contracts are widely used to organise the exchanges in minor crop value chains facing uncertainty. In this study, we investigate how this vertical coordination tool can incentivize farmers to adopt grain-legumes in their crop rotations by transferring part the production and market risks to downstream firms. The risk transfer mechanism is analysed using a methodology based on surveys of chain of agents involved in a given value chain. We examine 5 case studies based on the type of legume and the organisation of the value chain. The results show that the payment system, the design of the contracts and the material and immaterial resources reinforced by the relationship between farmers and downstream firms, especially technical knowledge resources, contribute to reduce farmer’s exposure to risks and favour the development of the legume value chain, which is key for the agro-ecological transition.
ano.nymous@ccsd.cnrs.fr.invalid (Auguste Bréavoine) 01 Sep 2025
https://hal.inrae.fr/hal-05232413v1
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[hal-05247368] Increasing crop diversity reduces pesticides across diverse production situations
Pesticides have caused significant losses of biodiversity and pose a threat to human health. Crop diversification is proposed as a major solution to achieve the needed pesticide reduction in agriculture, by moderating the pressure of weeds, insect pests, and fungal diseases. According to the pest triangle framework, the impact of a pest outbreak depends on the interactions between crop, pest, and the environment. Diversifying crop sequences in a cropping system could impact the interactions between the three factors and recalibrate the need for pesticides to control pests and avoid yield losses. A previous study found that pesticide use, measured by the Treatment Frequency Index at the cropping system level, is affected both by crop species and crop diversity (assessed in this study through the number of crops), with crop species having a greater impact. However, to our knowledge, no study has quantified the role of the farming environment in the effect of crop diversity on regulating pest pressure, and limiting the need for pesticides. In this study, we used the classification and regression trees method to identify six clusters of production situations with contrasting levels of pesticide use, taking into account the nature of crop species grown. Our results show that production situations, the crop species, and crop diversity, jointly shaped pesticide reliance at the cropping system level. Specifically, production situations explained 5.6% of the variance in total pesticide use. Crop diversification by adding one extra crop reduced total Treatment Frequency Index by 0.10, after filtering out the influences of production situation, and this effect was significant across all pesticide groups, namely herbicides, fungicides, and insecticides. Our findings provide evidence that increasing crop diversity consistently reduces pesticide reliance across diverse production conditions. These insights highlight the potential of crop diversification as an effective and scalable strategy for sustainable pest management.
ano.nymous@ccsd.cnrs.fr.invalid (Yaoyun Zhang) 09 Sep 2025
https://hal.science/hal-05247368v1
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[hal-05265454] GWASpipe: a Nexflow pipeline for GWAS analyses incorporating quality control
Genome-wide association studies (GWAS) are powerful tools to link genetic variants with phenotypic traits. However, running GWAS involves several complex steps, including VCF preprocessing, quality control, population structure and relatedness correction, and selecting the right statistical models. We developed GWASpipe, an easy-to-use and automated pipeline to make GWAS more accessible, especially for non-expert users. GWASpipe is built with Nextflow[1] and follows nf-core standards. All tools are packaged in Singularity containers, ensuring reproducibility and easy deployment on any computing system. The pipeline includes :Data quality control, Filtering of low-quality variants and individuals, Population structure analysis, Kinship calculation, Association testing using two R packages (MM4LMM[2] et GAPIT[3] )
ano.nymous@ccsd.cnrs.fr.invalid (Sophia Marguerit) 17 Sep 2025
https://hal.inrae.fr/hal-05265454v1
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[hal-05564088] Combining wheat with multi-species prairie strips reduces the development of Septoria tritici blotch
Crop diversification, notably through intercropping, is known for regulating disease development in agroecosystems. However, intercropping usually involves two or three species, limiting its potential to enhance ecosystem multifunctionality. This study investigates the impact of “agroprairies”, a cropping system design consisting of alternating narrow strips of wheat and multispecies prairies (∼12 species), on the development of Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), a major foliar disease in wheat. Two complementary field experiments were conducted. The first one monitored the incidence and severity of STB under natural epidemic conditions across combinations of four wheat cultivars and four prairie mixtures with contrasted functional traits. The second experiment used above-canopy inoculation on a subset of treatments to assess disease dynamics under high disease pressure, independent of physical barrier effects. Rhizosphere microbiomes were analyzed before inoculation to evaluate enrichment in taxa associated with plant defense and disease suppression. Under natural conditions, STB incidence and severity were reduced by 52% and 41% in two agroprairie types compared to monocrop. Prairie biomass and specific leaf area (SLA) were identified as key factors associated with this reduction. When the disease was inoculated above the canopy, this reduction effect disappeared, highlighting the dominant role of physical barriers in disease regulation. However, one agroprairie treatment still reduced disease progression by 18%, suggesting the involvement of additional regulatory mechanisms. Microbiome analysis revealed shifts in bacterial beta diversity and an enrichment of potentially beneficial taxa in the wheat rhizosphere, although no direct link with disease regulation was established.
ano.nymous@ccsd.cnrs.fr.invalid (Lisa Besson) 31 Mar 2026
https://isara.hal.science/hal-05564088v1
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[hal-05567992] The red palm weevil chemical ecology in the OMICS and post-genomic eras
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Jacquin-Joly) 26 Mar 2026
https://hal.inrae.fr/hal-05567992v1
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[hal-05567453] Plam weevil odorant receptors: Omics, functional characterization, and evolution
The Red Palm Weevil, Rhynchophorus ferrugineus (Olivier), is the most destructive and invasive insect pest of palm trees worldwide. The weevils synchronizes mass gathering on palm trees for feeding and mating, regulated by a male-produced pheromone. As an environmental-friendly control solution, this pheromone is used in blend with plant volatile compounds as synergists to trap weevils for population monitoring and mass trapping. However, the molecular bases of the red palm weevil olfactory mechnisms are still poorly understood. To fullfil this gap, we generated omics data using Illumina and PacBio, and manually curated chemosensory genes, especially chemosensory receptors. In insects, chemosensory receptors include three main families, the odorant receptors (ORs) involved in volatile detection at a distance or close range, the gustatory receptors (GRs) involved in detection at contact, and the ionotropic receptors (IRs) involved in olfaction and taste. Manual curation allowed us to annotate an impressive number of IRs, the highest number of IRs described in Coleoptera so far. We identified less GRs than reported earlier, and extended the previously described repertoire of ORs. We evidenced tandem duplication of key ORs, whose function could be addressed by heterologous expression in Drosophila neurons coupled to single-sensillum recording and extensive screenings of volatile organic compounds. The observed response spectra led us to proposing a scenario for OR functional specialization. Our collection of curated chemosensory genes constitutes a valuable resource for such functional characterization, and our functional data pinpoint interesting volatiles to be included in olfactory-based control strategies of this weevil.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Jacquin-Joly) 25 Mar 2026
https://hal.inrae.fr/hal-05567453v1
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[hal-05567471] Red palm weevil omics bring insights into its chemical ecology and the evolution of Coleoptera pheromone receptors
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Montagné) 25 Mar 2026
https://hal.inrae.fr/hal-05567471v1
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[hal-05567958] The red palm weevil Rhynchophorus ferrugineus in the OMICS and post-genomic eras
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Stéphanie Robin) 26 Mar 2026
https://hal.inrae.fr/hal-05567958v1
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[hal-05296080] Integrating sheep into vineyards: diversity of farmers' agronomic logics and trajectories
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Elsa Robelot) 03 Oct 2025
https://hal.inrae.fr/hal-05296080v1
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[hal-04732691] Analysis of practice change in vineyard farms according to their engagement in the agroecological transition
Viticulture is facing numerous challenges such as the reduction of pesticide use, and agroecology is increasingly being presented as a solution. However, there is a lack of knowledge about how winegrowers design innovations to foster the principles of agroecology. This study aims to analyze the innovations implemented by a range of farmers who are more or less committed to the agroecological transition. Special attention is given to the systemic approach and the scale of reflection when developing these innovations. To assess the level of agroecology on each farm, a grid structured by 7 main principles divided into 20 indicators was developed. Agronomic logics were formulated to analyze the systemic reasoning behind these innovations. The analysis of the grid showed a wide diversity in the progress of the agroecological transition among the surveyed farms. The agroecology principles that most explained the differences between farms with low and high agroecological global scores were synergy, efficiency, and social and solidarity-based economy. A comparison of the agronomic logics of two farms showed that the farm with the highest agroecology score employed systemic reasoning and mobilized several resources when changing its practices, in contrast to the farm with a low agroecology score. A method will be developed to conduct this analysis on all the farms surveyed.
ano.nymous@ccsd.cnrs.fr.invalid (Elsa Robelot) 11 Oct 2024
https://hal.science/hal-04732691v1
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[hal-03910768] Water limitation affects weed competitive ability for light. A demonstration using a model‐based approach combined with an automated watering platform
Climate change is driving the need to investigate responses to water limitation of morphological traits involved in competition for light, the main resource for which crops and weeds compete in conventional temperature and tropical cropping systems, to better understand field crop-weed dynamics. Our objective was to develop an innovative approach to quantify weed species responses to water limitation, using three species. This approach combined (1) key morphological traits involved in competition for light (taken from a mechanistic crop-weed model) as criteria to analyse responses to water limitation and (2) a pot/greenhouse platform allowing automated precision-watering and daily quantification of soil water availability in each pot. For all species and growth stages, increased plant height per unit of aboveground biomass and production of smaller/thicker leaves were the most noteable responses. Plants with a strong increase in plant height per unit of aboveground biomass in response to water limitation maintained high levels of specific leaf area, even at low soil water availability. Increases in biomass allocation to roots (vs. aboveground parts) and leaves (vs. stems and reproductive organs) were also observed, but not for all species and growth stages. Overall, these effects of water limitation on morphological traits indicate strong interactions between competition for light and water.
ano.nymous@ccsd.cnrs.fr.invalid (Delphine Moreau) 14 Jun 2023
https://hal.inrae.fr/hal-03910768v1
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[hal-04015586] Guide méthodologique pour le diagnostic des freins et leviers sociotechniques aux processus d’innovation dans des systèmes agri-alimentaires
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Marion Casagrande) 02 May 2023
https://hal.inrae.fr/hal-04015586v2
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[anses-05512285] Evaluation of a Plant Disease Surveillance System Using the Animal-Health OASIS Method: Application to Sharka in France
Disease surveillance is a keystone of human, animal, and plant health. It contributes to the prevention and management of epidemics. Over the past two decades, several methodological frameworks have been developed for the evaluation of human and animal health surveillance systems, but such approaches are still lacking in plant health. Here, we aimed at providing one of the first evaluations of a plant pest surveillance system. We applied the semi-quantitative OASIS method, already successfully used for the evaluation of centralized surveillance in animal health, to the French surveillance system of sharka, a viral disease of Prunus trees. A four-member evaluation team conducted semi-directed interviews with 29 professionals covering the different institutions and functions involved in this surveillance system. The evaluation showed that the main strength of the current system is its organization into well-performing regional units that enable adjusting the national surveillance strategy for the application of locally relevant control measures. The main opportunities for improvement were related to system coordination and science-based exploitation of the surveillance data for long-term disease control. We have provided a proof of concept that there is no other obstacle than vocabulary issues to the transposition of the OASIS method to plant diseases, which opens up the possibility to assess other surveillance systems and thus enables to improve their efficiency.
ano.nymous@ccsd.cnrs.fr.invalid (Norman Daurelle) 16 Feb 2026
https://anses.hal.science/anses-05512285v1
