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[hal-05839312] Minimum distance classification for nonlinear dynamical systems
We address the problem of classifying trajectories or sequences generated by nonlinear dynamical systems, where each class corresponds to a distinct dynamical system. We propose Dynafit, a kernelbased method that learns a distance metric between training data and the underlying dynamics. New observations are assigned to the class whose dynamics best fit the observations according to the learned metric. The learning algorithm approximates the Koopman operator, which globally linearizes the dynamics in a (potentially infinite-dimensional) feature space associated with a kernel function. The distance metric is computed in the feature space independently of its dimensionality by exploiting the kernel trick commonly used in machine learning. The kernel function can be tailored to incorporate prior knowledge of the dynamics when available. We consider a classical test example, the logistic map as a discrete dynamical system, and derive analytically the kernel function from the polynomial Koopman basis that exactly linearizes the dynamics. Dynafit is applicable to a wide range of classification tasks involving nonlinear dynamical systems and sensors. We illustrate its effectiveness through three examples: chaos detection in the logistic map, recognition of handwritten dynamical patterns, and classification of visual dynamic textures.
ano.nymous@ccsd.cnrs.fr.invalid (Dominique Martinez) 26 Oct 2026
https://hal.science/hal-05839312v1
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[hal-05652738] Spatio-temporal field, landscape and meteorological datasets describing bruchid beetle populations, grain damage and parasitism in faba bean and lentil fields in France
This dataset provides a multi-scale and multi-year characterization of population, grain damage and larval parasitism of bruchid beetle populations (Coleoptera: Chrysomelidae: Bruchinae) populations, i.e. Bruchus rufimanus Boheman, 1833 and Bruchus signaticornis Gyllenhal, 1833. This dataset covers 45 faba bean (Vicia faba Linnaeus, 1753) and 60 lentil (Lens culinaris Medikus, 1787) fields across four major production regions in France. Data were collected over three consecutive growing seasons (2019-2020 to 2021-2022) across three phenological crop stages (vegetative, flowering, and young pods) and at five distances from field edge to capture spatio-temporal dynamics. Datasets include bruchid counts, grain damage as well as parasitism rates by micro-hymenoptera (mainly Triaspis cf.<p>thoracica Curtis, 1860). Field observations are integrated with environmental variables, including GISbased landscape metrics (land use, semi-natural habitats, and hedgerow length) calculated at 500, 1000, and 2000 m buffer radii from field observation plots. Additionally, daily meteorological data from the SAFRAN platform (https://agroclim.inrae.fr/siclima/) at a resolution of 8-km grid and then aggregated per crop stage, covering temperature thresholds, precipitation, and wind speed.Agricultural management information, such as crop sowing dates, varieties, tillage and pest management, is also provided for each of the 105 fields. This integrated dataset allows for crossdisciplinary reuse in agronomy, ecology, and entomology to explore pest-enemy interactions, edge effects, and the influence of landscape and climate on crop-pest dynamics.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Cayetano Herrera) 12 Jun 2026
https://hal.inrae.fr/hal-05652738v2
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[hal-05840935] Change in farming systems and their expression at the territorial scale: The case of crop succession as an indicator of change.
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ano.nymous@ccsd.cnrs.fr.invalid (Elise Ygaunin) 27 Oct 2026
https://hal.inrae.fr/hal-05840935v1
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[hal-05796718] Methods for evaluating the efficacy of microbial biocontrol agents against Botrytis cinerea on tomato plant
Botrytis cinerea, the causal agent of gray mold, is a highly adaptable necrotrophic fungus that causes significant losses in economically important crops such as tomatoes. Increasing resistance to fungicides and environmental concerns have stimulated interest in microbial biocontrol agents as part of integrated pest management strategies. This chapter presents standardized protocols for evaluating the efficacy of microbial biocontrol agents against B. cinerea on tomato plants under controlled conditions. Methods include preparation of pathogen and biocontrol inoculum, production of healthy plants, and bioassays on whole plants, detached stems, and detached leaves, with quantitative disease assessment. These protocols aim to ensure reproducibility and comparability while facilitating mechanistic studies and optimization of biocontrol strategies prior to field application.
ano.nymous@ccsd.cnrs.fr.invalid (Jean-François Bourgeay) 13 Oct 2026
https://hal.inrae.fr/hal-05796718v1
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[hal-05838785] Biodiversity Economics in the Field: The Values of Crop Diversity for Farmers
Conservation of biodiversity in agricultural landscapes is often framed as an externality problem in which biodiversity is valued for benefits provided to agents outside the agricultural sector. This review develops a complementary perspective, where farmers may conserve biodiversity in order to self-internalize biodiversity-related services serving as inputs in the agricultural technology. After formalizing this mechanism in a microeconomic model and discussing biodiversity measurement through habitat indices, we organize the empirical literature around three values of biodiversity for agriculture: its productive value (increasing output), cost-saving value (reducing costs), and insurance value (stabilizing production). Evidence from observational data suggests that these values are overwhelmingly positive, but highly heterogeneous across contexts. The review also examines the dynamic and spatial dimensions of biodiversity, as well as the policy instruments that can exploit its technical properties when external values beyond private benefits justify intervention.
ano.nymous@ccsd.cnrs.fr.invalid (François Bareille) 26 Oct 2026
https://hal.inrae.fr/hal-05838785v1
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[hal-05839758] Intercropping chickpea with oat combined with inter-row mowing reduces ascochyta blight severity along the main axis and alters the shoot architecture
Chickpea is a key species for the agroecological and dietary transitions. Yet, its adoption is hindered by yield fluctuations, notably due to weeds and ascochyta blight (Ascochyta rabiei). Service plants can provide weed and disease regulation in low-input cropping systems (Moreau et al., 2025). Still, regulating them may be necessary, for example via mowing, to avoid high yield reductions in the cash crop (Guy et al., 2026). In this study, we investigated the effect of these practices on chickpea’s shoot architecture, pod production, and ascochyta blight severity. A two-year field experiment (2023, 2024) was conducted near Angers (France). Chickpea was grown as a sole crop or in intercrop with oat sown in the middle of the inter-rows. Chickpea’s inter-rows were either not mowed or mowed once at early flowering. In 2024, a treatment with an additional earlier mowing was tested in the intercrop. At grain-filling, plant biomass (chickpea, oat, weeds) was measured, chickpea’s shoot architecture was described, and ascochyta blight severity on leaves was assessed at each node on the main axis using a 0-4 scale. The two years were very contrasted, with a much higher weed and disease pressure in 2024 than in 2023. Ascochyta blight was always lower in the intercrop, especially under high disease pressure, with visible effects from the first basal nodes. Still, in 2023, introducing oat decreased branching, pod production, and node number, while mowing had no effect. By contrast, in 2024, intercropping had a limited effect on the shoot architecture, while mowing increased branching by 78% on both the sole and intercropped chickpea. In 2024, adding an earlier mowing before flowering in the intercrop doubled pod production, while maintaining the same level of disease control than the intercrops with 0 or 1 mowing. This work underlines the relevance of mowed intercropping systems for reducing disease severity, while limiting competition with the cash crop. References Guy et al., 2026. Eur. J. Agron., 178. Moreau et al., 2025. Agron. Sustain. Dev., 45.
ano.nymous@ccsd.cnrs.fr.invalid (Margaux Guy) 26 Oct 2026
https://hal.science/hal-05839758v1
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[hal-05750044] Effect of service plant intercropping and inter-row mowing on plant growth, architecture, and yield components of chickpea
Service plants are crops that are grown in intercropping with cash crops to provide services without being harvested (Gardarin et al., 2022). The use of this practice is becoming increasingly popular and can contribute to providing a diversity of services including weed, disease or pest regulation and nitrogen provision (Moreau et al., 2025; Gardarin et al., 2022). However, the competition of service plants with cash crops can be too strong and needs to be managed to ensure the success the practice (Bousselin et al. 2024; Verret et al. 2017). Recent work has focused on the use of service plant mowing to reduce the impact of service plants sown in inter-rows of a cash crop (Guy et al. 2025). The implementation of such practice needs to rely on a good understanding of the dynamics of plant-plant interactions, which includes the impact of this practice on plant architecture and yield components. To address this problem, a field experiment comparing different service plants intercropped with chickpea in Western France (Oceanic climate, clay loam soil) for two consecutive years (2023 and 2024). Chickpea was chosen as it is highly sensitive to competition. In this trial different service plant species were tested including oat, Berseem clover, and faba bean. The service plants were sown in the inter-rows of chickpea or grown alone. Each of these treatments was implemented both with no mowing or with a mowing of chickpea’s inter-rows at early flowering stage. The mowing led to an almost total destruction of the service plant in both years. These treatments were arranged following a randomized complete block design (n=4). For each treatment, the plant biomass, its N content, N2 fixation, architecture and yield components were measured. Among the service plant species tested, only oat decreased weed biomass in both years from the beginning of flowering to the grain filling stage (p&lt;0.05). This species also significantly reduced by more than 50% the intensity of ascochyta blight symptoms in 2024 (p&lt;0.05). In 2023, intercropping with oat reduced the branching and pod production by more by 38% (p&lt;0.05), and 58% (p&lt;0.05) respectively, while mowing had no significant effect. In intercropping system, internodes length was also modified. In 2024, the weed pressure and the precipitations were unusually high. Intercropping had a limited effect on chickpeas’ architecture, but mowing increased branching by more than 70% (p&lt;0.05). This year, both the mowing and the intercropping with oat increased the pod production from 1.9 pods per plant to 12 to 25 pods per plant (p&lt;0.01). Despite this result, none of the plots has harvested in 2024 due to disease pressure. These results suggest that mowing a competitive service plant like oat is an efficient strategy for both limiting its impact on cash crops and providing services. However, its impact on plant architecture and yield components suggests that an earlier mowing would be more beneficial for the cash crop. References Bousselin et al. 2024. Eur. J. Agron. 154, 12797. https://doi.org/10.1016/j.eja.2024.127097 Gardarin et al. 2022. Agron. Sustain. Dev. 42, 39. https://doi.org/10.1007/s13593-022-00771-x Guy et al. 2025. Preprint SSRN. 5436278. http://dx.doi.org/10.2139/ssrn.5436278 Moreau et al. 2025. Agron. Sustain. Dev. 45, 38. https://doi.org/10.1007/s13593-025-01031-4 Verret et al. 2017. Field Crops Res. 204, 158-168. https://doi.org/10.1016/j.fcr.2017.01.010
ano.nymous@ccsd.cnrs.fr.invalid (Margaux Guy) 15 Sep 2026
https://hal.science/hal-05750044v1
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[hal-03557439] Yeast and Filamentous Fungi Microbial Communities in Organic Red Grape Juice: Effect of Vintage, Maturity Stage, SO2, and Bioprotection
Changes are currently being made to winemaking processes to reduce chemical inputs [particularly sulfur dioxide (SO 2 )] and adapt to consumer demand. In this study, yeast growth and fungal diversity were investigated in merlot during the prefermentary stages of a winemaking process without addition of SO 2 . Different factors were considered, in a two-year study: vintage, maturity level and bioprotection by the adding yeast as an alternative to SO 2 . The population of the target species was monitored by quantitative-PCR, and yeast and filamentous fungi diversity was determined by 18S rDNA metabarcoding. A gradual decrease of the α-diversity during the maceration process was highlighted. Maturity level played a significant role in yeast and fungal abundance, which was lower at advanced maturity, while vintage had a strong impact on Hanseniaspora spp. population level and abundance. The presence of SO 2 altered the abundance of yeast and filamentous fungi, but not their nature. The absence of sulfiting led to an unexpected reduction in diversity compared to the presence of SO 2 , which might result from the occupation of the niche by certain dominant species, namely Hanseniaspora spp. Inoculation of the grape juice with non- Saccharomyces yeast resulted in a decrease in the abundance of filamentous fungi generally associated with a decline in grape must quality. Lower abundance and niche occupation by bioprotection agents were observed at the overripened stage, thus suggesting that doses applied should be reconsidered at advanced maturity. Our study confirmed the bioprotective role of Metschnikowia pulcherrima and Torulaspora delbrueckii in a context of vinification without sulfites.
ano.nymous@ccsd.cnrs.fr.invalid (Sara Windholtz) 04 Feb 2022
https://hal.inrae.fr/hal-03557439v1
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[hal-05690913] Biocontrol of grapevine downy mildew: A Synthetic Microbial Community (SynCom) approach
Culturomic approaches, involving the use of a range of different culture conditions coupled with a high-throughput method of identification, are recommended to isolate and identify microorganisms in environmental samples. In the case of plant samples, a number of studies have shown that microorganism cultivability can be increased by using plant-based culture media rather than conventional media that contain chemically synthesized or animalbased extracts. Being able to access this microbial biodiversity is crucial to the development of microbial biocontrol for plant diseases. Particularly in vineyards, where the majority of fungicide treatments target two major pathogens, the oomycete Plasmopara viticola that causes downy mildew and the fungus Erysiphe necator that causes powdery mildew, the development of new microbial biocontrol products is expected to reduce fungicide use. Tapping into the existing reservoir of naturally occurring disease biocontrol agents and growth-promoting microorganisms associated with grapevines is the first step to formulate effective biocontrol products and move towards more sustainable viticulture.<p>This study aimed to use a culturomic approach to build a collection of grapevine foliar microorganisms which can subsequently be used to assemble Synthetic Microbial Communities (SynComs) for biocontrol of downy mildew. Alongside three conventional culture media, we developed a grapevine leaf-based culture medium to cultivate epiphytic and endophytic bacteria, yeast and filamentous fungi. Overall, we isolated 1090 microorganisms, including 543 bacteria, 243 yeast/yeast-like fungi and 304 filamentous fungi. Using MALDI-TOF MS and Sanger sequencing, we were able to identify 88 % of the isolates with 91 total genera identified across the 4 culture media used. Using the grapevine leaf-based culture medium enabled the cultivation of 4 genera of bacteria, 1 yeast genus and 12 genera of filamentous fungi that were not seen on the other media. We proceeded to build a SynCom of 42 isolates, selecting candidates from the collection that were either known to be representative of the natural grapevine leaf microbiota or to have biocontrol activity against downy mildew or other plant diseases. In vitro confrontation tests on leaf discs revealed that the SynCom significantly reduced downy mildew symptoms. Over a hundred subsets of the whole SynCom were then tested against Plasmopara viticola to test hypotheses on the effect of community diversity and composition on leaf colonization as well as resistance to invasion by the pathogen. These findings could be useful in informing the design of eventual commercial multi-strain biocontrol products.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Aarti D Jaswa) 13 Jul 2026
https://hal.science/hal-05690913v1
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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-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-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-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-05545557] Multiple, simultaneous abiotic stresses differentially impact downy mildew infection in grapevine
Grapevine health and resilience under climate change demand an understanding of how multiple stress interact. Climate change has led to more frequent and intense droughts and heat waves, which often occur together and may affect disease pressure. Here, we explored a complex multi-stress framework by combining drought and heat stress with downy mildew infection in grapevine, determining their possible interactions (synergistic or antagonistic) on pathogenesis, and detailing their effects on grapevine leaf physiology. We subjected grapevines to drought, heat stress, or a combination of both, subsequently inoculating leaves with Plasmopara viticola. In these same leaves we quantified their physiological responses and changes in defense-related metabolite (H2O2 and phenols) concentrations. Our results revealed common and distinct responses to the multi-stress interactions. Drought and drought-heat treatments led to low stomatal conductance (a reduction in stomatal aperture), which acted as a biophysical mechanism restricting P. viticola entry and resulting in a lower P. viticola sporulation rate. Defense-related metabolites were differentially regulated according to the stress combination and suggesting a role in the biochemical mechanism against the P. viticola infection. Stilbene concentration increased by 36, 57 and 113% in response to drought, heat, and drought-heat, respectively. Flavonoids and phenolic acids exhibited distinct patterns in response to different stress treatments. These results shed light on the mechanisms that drive complex interactions between abiotic and biotic stressors, enhancing our understanding of multi-stress resilience and allowing us to better predict how grapevines will respond to the changing climate.
ano.nymous@ccsd.cnrs.fr.invalid (Ana Clara Fanton) 10 Mar 2026
https://hal.inrae.fr/hal-05545557v1
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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-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-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-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-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-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-03697249] Estimating consensus proteomes and metabolic functions from taxonomic affiliations
Purpose: Metabarcoding, and metagenomic sequencing have enabled the characterization of highly diverse environmental communities. The challenge of estimating the metabolic functions carried out by these communities has led to the development of several state-of-the-art methods, most of which are tailored to a specific gene marker. However, the increasing diversity of approaches resulting from advances in sequencing technologies drives the need for methods capable of handling heterogeneous microbial community data. Moreover, predictions often depend on their internal analysis pipelines and are influenced by the underlying databases, which link marker genes to specific functional annotations. This limits users' ability to evaluate the quality of predictions by tracing internal data and processes. Finally, users are constrained by the specific annotations provided by these methods (e.g. EC numbers), limiting their ability to conduct further specialized analyses based on intermediate results. Methods: EsMeCaTa predicts consensus proteomes and their associated functions from taxonomic affiliations. A key feature of EsMeCaTa is its explainability and flexibility. To support the flexible integration of heterogeneous sequencing data, EsMeCaTa utilizes taxonomic affiliations obtained through analyses of diverse sequencing datasets. To provide insight into the knowledge available for each taxonomic affiliation and to interpret the relevance of predicted functions, EsMeCaTa identifies a taxonomic rank within a given affiliation that is sufficiently represented by documented proteomes in the UniProt database. The proteins of the UniProt proteomes are clustered and filtered according to a threshold to create consensus proteomes. These consensus proteomes are automatically annotated with functional information (e.g., EC numbers, GO terms) but they are also designed to be used in further customized annotation workflows. Functional annotations are reported in a functional table, which can be enriched with taxon abundances to generate comprehensive functional profiles. Results: EsMeCaTa predictions have been validated using multiple datasets and compared to a state-of-the-art method. Additionally, it was applied to a novel metabarcoding dataset from a methanogenic reactor, characterizing the microbial community and biogas production across different time points and intake condition. Our results demonstrate the link between biogas production, intake condition and the dynamics of the metabolic functions predicted by EsMeCaTa in the microbial communities.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Belcour) 07 Jan 2025
https://hal.science/hal-03697249v2
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[hal-05567423] Video of the presentation at LREC conference: EPOP: A benchmark corpus for Assessing NLP Models on Structured Information Extraction in Plant Health
This video presents the work published in LREC conference proceedings in 2026. In this presentation, we introduce the EPOP (Epidemiomonitoring of Plants) corpus, a new annotated resource for structured information extraction in the domain of plant health epidemiology. The corpus consists of translated news reports that reflect real-world phytosanitary monitoring scenarios. It includes annotations for named entities (e.g. Plant, Pest, Vector, Disease, Dissemination Pathway), identity coreferences, and both binary and complex n-ary relations that represent key events such as Transmits or Causes, along with their modalities. A distinctive feature of EPOP is its normalization layer where mentions of species and geographical locations are linked to canonical identifiers in the NCBI Taxonomy and GeoNames, enabling semantic disambiguation and integration with external knowledge bases. As the first publicly available corpus of its kind, EPOP presents a realistic and challenging benchmark, with high linguistic variability, entity role ambiguity, and long-distance relations. We report baseline results on core tasks (named entity recognition, normalization (entity-linking), and relation extraction) using both fine-tuned BERT-based models and hard-prompted large language models. These experiments demonstrate the utility of EPOP while also identifying areas for improvement, particularly in the extraction of complex relations. The corpus is released under an open license, to support research in environmental NLP, crop protection, and knowledge graph enrichment.
ano.nymous@ccsd.cnrs.fr.invalid (Claire Nédellec) 25 Mar 2026
https://hal.inrae.fr/hal-05567423v1
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[hal-04074159] Les légumineuses dans les produits agroalimentaires
L’Institut national de recherche pour l’agriculture, l’alimentation et l’environnement INRAE a mené une analyse des produits alimentaires nouvellement commercialisés dans le monde, à partir de la base de données MINTEL-GNPD, afin d’apprécier la progression d’usage des ingrédients à base de légumineuses dans les grandes régions du monde, dont l’Europe.
ano.nymous@ccsd.cnrs.fr.invalid (Tristan Salord) 19 Apr 2023
https://hal.inrae.fr/hal-04074159v1
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[hal-03358998] Functional–Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures
Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Blanc) 07 Oct 2021
https://inria.hal.science/hal-03358998v1
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[hal-05290797] Mining microbiota data to identify antagonists of grapevine downy mildew.
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ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 06 Oct 2025
https://hal.science/hal-05290797v1
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[hal-05084268] Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology
This report was shared with the winegrowers who made their plots available for my PhD project. It presents the methodology used, the main results, and future research perspectives. The aim of the study was to identify microorganisms capable of protecting grapevines against Plasmopara viticola, the causal agent of downy mildew, in order to reduce reliance on chemical fungicides. Over a two-year period, leaf and soil samples were collected in the spring from 14 vineyard plots in the Bordeaux region. These plots were selected based on long-term records showing contrasting levels of downy mildew incidence and severity. Sampling focused on young leaves and the top few centimeters of soil. Molecular biology analyses (DNA extraction, PCR, and sequencing) were then carried out to characterize the microorganisms (bacteria and fungi) present in these plots. Several hypotheses were explored. The main one, presented in this report, is that plots with low levels of downy mildew symptoms harbor a higher abundance of microorganisms potentially involved in regulating the pathogen. Source : Fournier, P., Pellan, L., Jaswa, A., Cambon, M. C., Chataigner, A., Bonnard, O., Raynal, M., Debord, C., Poeydebat, C., Labarthe, S., Delmotte, F., This, P., &amp; Vacher, C. (2025). Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology. Environmental Microbiome, 20(1), 37. https://doi.org/10.1186/s40793-025-00691-9
ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 26 May 2025
https://hal.science/hal-05084268v1
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[hal-05655335] The Value of Seed Quality Certification in Integrated Supply Chains
The Value of Seed Quality Certification in Integrated Supply Chains.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655335v1
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[hal-05687897] On the external validity of risk attitudes
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ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687897v1
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[hal-04478362] Évolutions réglementaires et adaptations en grandes cultures
L’utilisation de mélanges, qu’ils soient de variétés ou d’espèces, pose des questions en termes de réglementation, mais aussi de sélection, d’évaluation ou encore de commercialisation.
ano.nymous@ccsd.cnrs.fr.invalid (Virginie Bertoux) 26 Feb 2024
https://hal.science/hal-04478362v1
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[hal-05687889] Eliciting beliefs when the distribution matters: a horse race of elicitation interfaces
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ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687889v1
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[hal-05045420] Meso-institutions to reduce uncertainties on seed mixtures quality: Role and Emerging process
Meso-institutions to reduce uncertainties on seed mixtures quality: Role and Emerging process.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 24 Apr 2025
https://hal.science/hal-05045420v1
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[hal-04732725] Multiple agricultural risks and insurance—issues, perspectives, and illustration for wine-growing
Agricultural producers face multiple risks, including climatic, disease, and market risks, that make crop insurance especially valuable to them. However, risk interactions raise specific issues: The value of prevention efforts in a multiple risk context, risk correlation, and compounded effects (whereby the realization of a risk makes it difficult to prevent another one) all affect the design and effectiveness of insurance. In contrast to the US, the EU-subsidized crop insurance creates different financial conditions for climate and pest risks and increases expertise costs. We discuss how this affects input use and disproportionately disadvantages organic producers because of compounded effects. We report on an experiment bundling a real pest insurance contract with an agronomic protocol aiming at reducing treatments, for vine-growing in the South-West of France. The experiment highlighted the costs to separating risks in insurance contracts, as well as the need for insurance to help transition to greener practices.
ano.nymous@ccsd.cnrs.fr.invalid (Cécile Aubert) 15 Oct 2024
https://hal.inrae.fr/hal-04732725v1
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[hal-04263759] Comparing input interfaces to elicit belief distributions
This paper introduces a new software interface to elicit belief distributions of any shape: Click-and-Drag . The interface was tested against the state of the art in the experimental literature—a text-based interface and multiple sliders—and in the online forecasting industry—a distribution-manipulation interface similar to the one used by the most popular crowd-forecasting website. By means of a pre-registered experiment on Amazon Mechanical Turk, quantitative data on the accuracy of reported beliefs in a series of induced-value scenarios varying by granularity, shape, and time constraints, as well as subjective data on user experience were collected. Click-and-Drag outperformed all other interfaces by accuracy and speed, and was self-reported as being more intuitive and less frustrating, confirming the pre-registered hypothesis. Aside of the pre-registered results, Click-and-Drag generated the least drop-out rate from the task, and scored best in a sentiment analysis of an open-ended general question. Further, the interface was used to collect homegrown predictions on temperature in New York City in 2022 and 2042. Click-and-Drag elicited distributions were smoother with less idiosyncratic spikes. Free and open source, ready to use oTree, Qualtrics and Limesurvey plugins for Click-and-Drag, and all other tested interfaces are available at https://beliefelicitation.github.io/ .
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 11 Oct 2024
https://hal.science/hal-04263759v1
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[hal-05687885] Eliciting beliefs when the distribution matters: a horse race of elicitation interfaces
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ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687885v1
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[hal-05671803] Social Learning to Reduce Pesticides: Evidence from a French Agricultural Extension Programme
Social learning is likely to play a crucial role in disseminating new agricultural technologies and driving the agroecological transition in European countries. We evaluated a French pesticide reduction programme designed to train farmers and promote practices through demonstration days on participating farms. Using pseudo-panel data from surveys conducted before and after the programme’s launch, we found evidence of decreased pesticide use among cohorts linked to farms attending demonstration days. Our analysis, supported by a placebo test and various robustness checks, suggests that peer-sharing in training programmes can scale up effectively at no additional cost.
ano.nymous@ccsd.cnrs.fr.invalid (Rose Deperrois) 27 Jun 2026
https://hal.science/hal-05671803v1
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[hal-05671801] Early Adopters and the Diffusion of Agroecological Knowledge in Peer Groups
Peer-to-peer knowledge diffusion is increasingly recognized as a key mechanism in various economic contexts and may play a crucial role in fostering the adoption of agroecological practices among farmers. However, the conditions for effective peer learning remain poorly understood, particularly regarding the role of the injection point -- the first individual to receive information -- within a peer group. This study examines whether the profile of the injection point affects the diffusion of agroecological knowledge. We conduct a randomized controlled trial (RCT) with roughly 850 voluntary French farmers, randomly assigned to peer groups on a digital communication platform. Over an 18-month period, only one farmer per treated group receives information on agroecology, serving as the injection point for diffusion. Treatment varies according to whether the injection point is an early adopter of agroecology or an ordinary peer. A benchmark group receives direct broadcasting of the information to all members. The experiment began in January 2025 and will run until June 2026, with data collection ongoing.
ano.nymous@ccsd.cnrs.fr.invalid (Rose Deperrois) 27 Jun 2026
https://hal.science/hal-05671801v1
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[hal-05386837] Réduire l’usage des pesticides : Quand les agriculteurs s’inspirent de leurs pairs
S’inspirer de ses semblables et changer ainsi ses habitudes, c’est quelque chose qui s’observe souvent pour tout type de comportement. C’est aussi un levier d’action non négligeable pour réduire les pesticides, quand les injonctions perçues comme « venant d’en haut » font parfois freiner des quatre fers les premiers concernés.
ano.nymous@ccsd.cnrs.fr.invalid (Rose Deperrois) 28 Nov 2025
https://hal.science/hal-05386837v1
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[hal-03612024] Les leviers politiques et organisationnels
Les chapitres précédents ont montré qu’il existe aujourd’hui des connaissances et savoir-faire permettant de transformer les systèmes agricoles afin de développer de nouvelles manières de protéger les cultures contre les bioagresseurs. De nouvelles pistes de recherche visant à aller jusqu’au bout du chemin vers une agriculture sans pesticides ont également été identifiées. Mais les solutions techniques seules ne suffisent pas et, pour être adoptées par le plus grand nombre d’agriculteurs, doivent être accompagnées de solutions à la fois politiques et organisationnelles. Les solutions politiques font référence à l’ensemble des moyens dont disposent les pouvoirs publics pour soutenir l’effort de transition. Les solutions organisationnelles, quant à elles, incluent les initiatives privées qui, sans s’opposer aux initiatives publiques, émanent directement des acteurs de la transition implantés dans les territoires.
ano.nymous@ccsd.cnrs.fr.invalid (Pascale Bazoche) 17 Mar 2022
https://hal.inrae.fr/hal-03612024v1
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[hal-05772007] Mélanges de semences prêt-à-l’emploi : la création d’un nouveau segment sur le marché des semences
Les mélanges de semences prêt-à-l’emploi répondent à une demande de certains agriculteurs souhaitant bénéficier des avantages de la culture en mélange mais manquant de temps ou de technicité pour réaliser eux-mêmes leur mélange. L’objectif de cet article est de décrire le marché pour ces mélanges prêt-à-l’emploi et les contraintes pesant sur son développement. L’analyse s’appuie sur des entretiens semi-directifs menés auprès d’acteurs intervenant sur les mélanges variétaux de blé tendre, de maïs fourrage et les mélanges d’espèces fourragères. Si les mélanges de semences peuvent présenter des intérêts pour les agriculteurs et pour limiter l’usage des produits phytosanitaires, les productions qui en sont issues ne sont pas toujours acceptées en aval de la filière. Les mélanges de semences prêt-à-l’emploi se caractérisent en outre par une conception, une production et une commercialisation plus complexes que celles des semences de variétés pures. Un certain nombre de freins à la production et la diffusion d’informations sur la performance de ces mélanges prêt-à-l’emploi peuvent également limiter leur diffusion.
ano.nymous@ccsd.cnrs.fr.invalid (Aline Fugeray-Scarbel) 30 Sep 2026
https://hal.science/hal-05772007v1
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[hal-03172917] Économie et réglementation de la qualité sur le marché des semences de grandes cultures
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ano.nymous@ccsd.cnrs.fr.invalid (Aline Fugeray-Scarbel) 22 Mar 2021
https://hal.science/hal-03172917v1
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[hal-05440369] Learning about best management practices: Theory and experimentation under the umbrella of crop insurance
Decision Support Systems (DSS) with embedded best management practices help reduce pesticide use. However, costly experimentation is necessary to learn about the quality of their data processing and recommendation models. We study farmers’ choices to try such a DSS. Due to order effects, learning can be inefficient and stop after inadequate recommendations, leading to crop losses. Subsidizing crop insurance conditional on DSS use is a cost-effective policy to foster experimentation. A 4-year living lab on-farm experiment involving French wine cooperatives, an insurer, and researchers supports our theoretical results on learning dynamics and provides additional insight into information requirements for subsidized green insurance.
ano.nymous@ccsd.cnrs.fr.invalid (Cécile Aubert) 05 Jan 2026
https://hal.inrae.fr/hal-05440369v1
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[hal-05655305] Seed mixtures development and their impact on farmers' surplus
Seed mixtures development and their impact on farmers' surplus.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655305v1
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[hal-05444215] Incentives for Meso-Institutional Quality Evaluation: The Seed Mixtures Market Case
Incentives for Meso-Institutional Quality Evaluation: The Seed Mixtures Market Case.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 06 Jan 2026
https://hal.science/hal-05444215v1
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[hal-04081107] MoBiDiv - MObilizing and Breeding Intra and inter-specific crop DIVersity for a systemic change towards pesticide-free agriculture
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ano.nymous@ccsd.cnrs.fr.invalid (Aline Fugeray-Scarbel) 25 Apr 2023
https://hal.inrae.fr/hal-04081107v1
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[hal-04080918] Freins et leviers à la diffusion des mélanges de variétés de blé (France) et d'orge (Danemark)
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ano.nymous@ccsd.cnrs.fr.invalid (Aline Fugeray-Scarbel) 25 Apr 2023
https://hal.science/hal-04080918v1
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[hal-05045433] Quelles conditions pour la mise en place de méso-institutions d’évaluation de la qualité ? : Cas du marché des mélanges de semences
Quelles conditions pour la mise en place de méso-institutions d’évaluation de la qualité ? : Cas du marché des mélanges de semences.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 24 Apr 2025
https://hal.science/hal-05045433v1
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[hal-03172168] MoBiDiv -Mobiliser et Sélectionner la diversité cultivée intra et inter spécifique pour un changement systémique vers une agriculture zéro-pesticide
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ano.nymous@ccsd.cnrs.fr.invalid (Jérôme Enjalbert) 22 Mar 2021
https://hal.science/hal-03172168v1
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[hal-05655317] The value and quality of private labels on the agricultural seed mixtures market. A mixed method approach
The value and quality of private labels on the agricultural seed mixtures market. A mixed method approach.
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655317v1
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[hal-04478335] Des projets engagés dans la diversification végétale
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ano.nymous@ccsd.cnrs.fr.invalid (Jérôme Enjalbert) 26 Feb 2024
https://hal.science/hal-04478335v1
