Collection HAL

[hal-04971434] Political and organisational levers

The preceding chapters have shown that knowledge and know-how now exist to transform agricultural systems and develop new ways of protecting crops against pests. New avenues of research have also been identified with a view to completing the road to pesticide-free agriculture. But technical solutions alone are not enough and, if they are to be adopted by as many farmers as possible, they need to be supported by both political and organisational solutions. Political solutions refer to all the means available to public authorities to support transition efforts. In contrast, organisational solutions, include private initiatives which, while not in opposition to public initiatives, emanate directly from local actors involved in transitions. Agricultural development and training policies: how to provide farmers with the keys to alternative approaches?The development of pesticide-free systems presupposes the development of a coherent set of agroecological practices that make the most of natural regulations. This complex objective means that actors in the agricultural world have the skills

ano.nymous@ccsd.cnrs.fr.invalid (Pascale Bazoche) 28 Feb 2025

https://hal.inrae.fr/hal-04971434v1

[hal-04644219] Reducing chemical inputs in agriculture requires a system change

Many countries have implemented policies to reduce the use of chemical inputs in agriculture. However, these policies face many obstacles that limit their effectiveness. The purpose of this paper is to review the main challenges associated with reducing chemical inputs in agriculture and to propose potential solutions. Our analysis, based on a literature review linking agronomy and economics, shows that several agronomic options have proven effective in reducing chemical inputs or mitigating their negative impacts. We argue that the organization of the agri-food system itself is a major barrier to their implementation. Involving all stakeholders, from the chemical input industry to consumers, and designing appropriate policy frameworks are key to address this issue. We recommend combining different policy instruments, such as standards, taxes and subsidies, in a simplified and coherent way to increase effectiveness and ensure better coordination in the adoption of sustainable practices.

ano.nymous@ccsd.cnrs.fr.invalid (Thierry Brunelle) 11 Jul 2024

https://hal.science/hal-04644219v1

[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

[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

[hal-05146900] Potential of service plants for regulating multiple pests while limiting disservices in agroecosystems. A review

Service plants are primarily used in agroecosystems to provide ecosystem services that are not directly marketable. They are a promising option to promote biological pest regulation. Past studies have demonstrated their usefulness for regulating one pest category (either pathogens/parasites, herbivores or weeds). However, a multi-pest view of the role of service plants, including the potential disservices (negative impacts) that they may generate, is lacking. Such an overview is essential to meet the challenge of agroecology. This paper aims to fill this gap. Here, a trait-based approach was used to provide an overview of the potentialities of service plants, (inserted either in intercropping, in rotation with the crops, or in field edges) for regulating multiple pests, while limiting disservices. For that purpose, we first laid the foundation of a conceptual framework by synthesizing the mechanisms and service plant traits involved in the regulation of each pest category and in the mitigation of each disservice. On this basis, we analyzed (1) the compatibility in the regulation of the different pests by service plants, and (2) the compatibility between multi-pest regulation vs disservice mitigation. Our main conclusions are: (1) Despite knowledge gaps, there is good potential of service plants for multi-pest regulation; (2) The challenge lies at least as much to mitigate disservices that service plants may cause as to promote multi-pest regulation; (3) The level of incompatibility between promoting multi-pest regulation vs mitigating disservices varies with the mode of insertion of service plants, increasing with interactions with crop plants. This review shows how a trait-based approach can be used to synthesize knowledge from different disciplines and provides a tool for cross-disciplinary dialogue. It identifies priority research actions that are needed to increase synergy, genericity and adaptation of service plants to local conditions, and provides foundations for the design of service-plant based agroecosystems.

ano.nymous@ccsd.cnrs.fr.invalid (Delphine Moreau) 07 Jul 2025

https://hal.science/hal-05146900v1

[hal-05458576] Valoriser la production fruitière écologique du Pilat un projet de recherche-action

Ces travaux décrivent les démarches de co-conception d'un territoire de production fruitière, visant à valoriser le caractère écologique de la production fruitière, permettant de bien rémunérer les agriculteurs et de leur offrir des bonnes conditions de travail tout en favorisant les biodiversité et préservant les ressources naturelles et en participant à la sécurité alimentaire des bassins de vie.

ano.nymous@ccsd.cnrs.fr.invalid (Muriel Valantin-Morison) 14 Jan 2026

https://hal.science/hal-05458576v1

[hal-05615322] Strategic free-riding in pest control: Theory and evidence in organic-conventional mixed landscapes

Organic and conventional farmers face the same pests but differ in technologies and economic incentives to control them. This paper theoretically and empirically characterizes the strategic interactions for pest control between these two types of farmers within mixed organic-conventional landscapes. Our non-cooperative game model shows that each farmer type is expected to strategically free-ride on the other’s control efforts when managing a sufficiently small share of the landscape, and that the extent of free-riding increases with lower pest pressure, higher relative treatment costs, and lower treatment efficacy. Using exhaustive French postcode-level data on insecticide purchases against the vector of a vine disease (Flavescence dorée), we provide empirical support for all our theoretical propositions. Our preferred estimates indicate that organic farmers free-ride on conventional farmers’ efforts until they reach about 8% of the landscape. Beyond this threshold, organic treatments only partially substitute for reduced conventional treatments, up to a point where conventional farmers may eventually free-ride if the organic landscape share becomes large enough. Consistent with the model’s predictions, high pest pressure substantially reduces the scope for free-riding, while differences in relative treatment costs and treatment efficacy also affect its extent, though to a lesser degree.

ano.nymous@ccsd.cnrs.fr.invalid (François Bareille) 07 May 2026

https://hal.inrae.fr/hal-05615322v1

[hal-05587920] Pesticide-free fields under minimum tillage and flower strips enhance carabid beetles and spiders through increased overwintering and spill over processes

Enhancing generalist arthropod predators in arable farming can contribute to pest control and pesticide use reduction, and be achieved through a diversity of management options at field and farm scales. Most studies however link management options to densities of circulating adults, which gives little insight into potential source-sinks dynamics and the occurrence of ‘source’ habitats enabling overwintering. In this study, we assessed the assemblages of emerging and circulating ground-dwelling carabids and spiders during four months in a continuous mosaic of pesticide-free winter-sown crops under contrasted tillage regimes (minimum vs. conventional tillage) and sown flower strips bordering fields. We detected clear patterns, with high in-field carabid and spider overwintering densities than in adjacent flower strips, which were rarely a preferred overwintering habitat. Our results nevertheless indicate that within both taxa, different species exhibit different responses and source-sink dynamics. Our results also demonstrate the key role of pesticide-free fields under minimum tillage, acting both as a high-quality overwintering site for some dominant carabid species and as a source habitat, as several predator species activity-density responded positively to the increased area of minimum tillage fields in the surroundings. We detected a comparable positive effect of the area of flower strips in the surrounding for some species, suggesting that these linear features could also act as a temporary refuge and source. These findings highlight that sustaining diverse communities of carabid beetles and spiders probably requires adopting several and complementary management options and that in-field farming practice represent a powerful lever to foster natural enemies populations.

ano.nymous@ccsd.cnrs.fr.invalid (Paul Bannwart) 10 Apr 2026

https://hal.inrae.fr/hal-05587920v1

[hal-05613501] From Concept to Perspective: Digital Twins of Microbial Systems

Digital twins (DTs) are increasingly recognized across diverse sectors for their capacity to enhance the control, efficiency, and comprehension of the physical or biological systems they represent. For microbial systems, DTs could allow model-guided improvements of the services provided by the microbial communities in the agrifood chain. While DTs definitions are generally built on the same core idea of bi-directional exchanges between digital and physical counterparts, where realtime data feeds digital models and model-driven insights guide the real system, a wide variety of definitions of what is a DT still co-exist across domains. This variability underscores the need for a clear, system-specific definition of DTs for microbial ecosystems. In this perspective paper, we propose a conceptual framework for microbial system digital twins (MSDTs), defined as a collection of models dynamically linked to the microbiological system through in-line, at-line or off-line data and control flows. We illustrate this framework with examples spanning environmental, bioprocess, plant, animal, food, and human microbial systems, in a One Health perspective. For each ecosystem, we explore the potential applications of MSDTs. We also identify the scientific challenges that remain in experiments, bioinformatics, data science, modeling, control and microbial ecosystem engineering to build accurate MSDTs. We advocate for the development of MSDT in laboratory settings, as a catalyst for interdisciplinary sciences, and we stress practical and ethical issues preventing the generalization of MSDT for large-scale applications. However, high-tech MSDTs in laboratory environments may pave the way for low-tech, generalizable microbial solutions for improved ecosystemic microbial services.

ano.nymous@ccsd.cnrs.fr.invalid (Simon Labarthe) 06 May 2026

https://hal.inrae.fr/hal-05613501v1

[hal-04207320] Biodiversity conservation, ecosystem services and organic viticulture: A glass half-full

Organic farming is a promising but still debated option to ensure sustainable agriculture. However, whether organic farming fosters synergies or mitigates tradeoffs between biodiversity, ecosystem services and crop production has rarely been quantified. Here, we investigate relationships between multitrophic diversity (14 taxa above and belowground), yield, natural pest control and soil quality (14 proxies of ecosystem services) in organic and conventional vineyards along a landscape gradient. Organic farming enhanced biodiversity and pest control, but decreased wine production. Compared to conventional systems, multitrophic diversity was 15 % higher, and pest control services were 9 % higher in organic systems, while wine production was 11 % lower. Regardless of management type, we found a strong tradeoff between wine production and pest control, but not between wine production and biodiversity. The landscape context was not a strong moderator of organic farming effects across taxa groups and ecosystem services, but affected specific taxa and ecosystem services, especially natural pest control. Our study reveals that wine production and biodiversity conservation do not necessarily exclude each other, which implies the existence of a safe operating space where biodiversity and wine production can be combined. We conclude that organic farming can contribute to improve the sustainability of viticulture, but needs to be complemented by management options at the local and landscape scales in order to fully balance biodiversity conservation with the simultaneous provision of multiple ecosystem services.

ano.nymous@ccsd.cnrs.fr.invalid (Léa Beaumelle) 14 Sep 2023

https://hal.inrae.fr/hal-04207320v1

[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

[hal-05100639] Opportunities and Challenges in Combining Optical Sensing and Epidemiological Modelling

Plant diseases impair yield and quality of crops and threaten the health of natural plant communities. Epidemiological models can predict disease and inform management. However, data are scarce, since traditional methods to measure plant diseases are resource intensive and this often limits model performance. Optical sensing offers a methodology to acquire detailed data on plant diseases across various spatial and temporal scales. Key technologies include multispectral, hyperspectral and thermal imaging, and light detection and ranging; the associated sensors can be installed on ground-based platforms, uncrewed aerial vehicles, aeroplanes and satellites. However, despite enormous potential for synergy, optical sensing and epidemiological modelling have rarely been integrated. To address this gap, we first review the state-of-the-art to develop a common language accessible to both research communities. We then explore the opportunities and challenges in combining optical sensing with epidemiological modelling. We discuss how optical sensing can inform epidemiological modelling by improving model selection and parameterisation and providing accurate maps of host plants. Epidemiological modelling can inform optical sensing by boosting measurement accuracy, improving data interpretation and optimising sensor deployment. We consider outstanding challenges in: A) identifying particular diseases; B) data availability, quality and resolution, C) linking optical sensing and epidemiological modelling, and D) emerging diseases. We conclude with recommendations to motivate and shape research and practice in both fields. Among other suggestions, we propose to standardise methods and protocols for optical sensing of plant health and develop open access databases including both optical sensing data and epidemiological models to foster cross-disciplinary work.

ano.nymous@ccsd.cnrs.fr.invalid (Alexey Mikaberidze) 18 Jun 2025

https://hal.science/hal-05100639v1

[hal-05606391] Quantifying Species‐ and Community‐Level Predation by Carabids on Pests and Beneficials in Wheat and Beet Fields

In this study, we apply a hierarchical Bayesian model to quantify predation by carabid beetles at species and community levels across three cropping contexts: fodder beet, sugar beet, and winter wheat. Prey includes pests (aphids and slugs) and beneficial organisms (earthworms, springtails, and spiders). Model predictions indicate higher overall predation pressure in wheat than in beet. However, the median diet composition contains a larger share of pests in beet fields, whereas consumption of earthworms and spiders is greater in wheat. The strongest diet shifts among cropping contexts occur in smaller carabids (genera Bembidion Latreille, 1802 [Carabidae: Bembidiini] and Trechus Clairville, 1806 [Carabidae: Trechini]), whereas larger species (Pterostichus melanarius [Illiger, 1798] [Carabidae: Pterostichini], Pseudoophonus rufipes [De Geer, 1774] [Carabidae: Harpalini], and Poecilus cupreus [Linnaeus, 1758] [Carabidae: Pterostichini]) show more stable diets. Although community structure (species and relative abundances) differs markedly between wheat and beet, it does not appear to be the main driver of the community-level predation indicator. Overall, our results support a higher potential for aphid biocontrol by carabid communities in sugar beet, with a lower collateral impact on earthworms and spiders.

ano.nymous@ccsd.cnrs.fr.invalid (Marion Rosec) 29 Apr 2026

https://institut-agro-rennes-angers.hal.science/hal-05606391v1

[hal-04966935] Co-GWAS unveils the genetic architecture of inter-individual epistasis affecting biomass and disease severity in wheat binary mixtures

Identifying the genetic determinants underlying plant-plant interactions is key for understanding plant community dynamics, both in natural and agronomical systems. This report unveils the complex genetic architecture of plant-plant interaction effects on aerial biomass and septoria tritici blotch severity in varietal mixtures of wheat, using co-genome-wide association study. Fifty-four signi cant allelic interactions between distinct loci were identi ed, with half involving hub loci. Some inter-individual epistasis might be related to the shade-avoidance syndrome. Our results underscore the critical role of allelic interactions between inter-individual loci in shaping plant phenotypes and community dynamics, offering new perspectives to optimize varietal mixtures.

ano.nymous@ccsd.cnrs.fr.invalid (Laura Mathieu) 26 Feb 2025

https://hal.science/hal-04966935v1

[hal-04145269] A workflow for processing global datasets: application to intercropping

Field experiments are a key source of data and knowledge in agricultural research. An emerging practice is to compile the measurements and results of these experiments (rather than the results of publications, as in meta-analysis) into global datasets. Our aim in the present study was to provide several methodological paths related to the design of global datasets. We considered 37 field experiments as the use case for designing a global dataset and illustrated how tidying and disseminating the data are the first steps towards open science practices. We developed a method to identify complete factorial designs within global datasets using tools from graph theory. We discuss the position of global datasets in the continuum between data and knowledge, compared to other approaches such as meta-analysis. We advocate using global datasets more widely in agricultural research.

ano.nymous@ccsd.cnrs.fr.invalid (Rémi Mahmoud) 27 Mar 2024

https://hal.inrae.fr/hal-04145269v4

[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

[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

[hal-05453887] A method to estimate absolute odorant concentration of olfactory stimuli

The accurate quantification and delivery of odorant concentrations remain a significant challenge. Traditional methods estimate stimulus intensity based on the amount of odorant in the source, but this does not reflect the actual concentration sent due to variable evaporation rates and delivery devices. This leads to inconsistencies in stimulus delivery, complicating cross-laboratory comparisons, threshold evaluations, and the replication of natural olfactory conditions in the lab. To address this, we present a model based on mass transfer theory to predict the concentration of odorants delivered by a simple and versatile odor delivery system commonly used in insect electrophysiological experiments. The present model, built with adaptable compartments, accounts for airflow, source size, and the physicochemical properties of odorants. It helps to better design and use odor delivery systems, especially for stimuli required to mimic natural odor environments. Calibration uses known partition coefficients. The model also considers the dynamic shape of odor stimuli, which affects neuronal responses and must be carefully interpreted, especially when using tools like photoionisation detectors (PID). This approach was applied to study the impact of a plant volatile known to activate pheromone-sensitive neurons, (Z)-3-hexenyl acetate, on pheromone detection in Agrotis ipsilon moths. While interference occurs in laboratory conditions at 160 ppb, such concentrations are unlikely in natural settings, suggesting these effects are less relevant ecologically.

ano.nymous@ccsd.cnrs.fr.invalid (Lucie Conchou) 12 Jan 2026

https://hal.science/hal-05453887v1

[hal-05361550] A La Carte Seed Harvesting: Messor barbarus Ants Select Durum Wheat Genotypes

<div>Biotic interactions between plants and insects can drive key evolutionary processes. In Mediterranean agroecosystems, the harvester ants Messor barbarus (Hymenoptera: Formicidae) frequently collect seeds, including those of cultivated cereals. Yet their potential role in shaping crop traits remains poorly understood. This study investigates whether harvester ant seed predation is driven by genetic and phenotypic variation in durum wheat (Triticum turgidum ssp. durum), a major Mediterranean crop derived from wild emmer (T. turgidum ssp. dicoccoides). Using a panel of 180 genetically diverse durum wheat inbred lines grown in a field experiment, we visually recorded spike predation and performed a genome-wide association study (GWAS) using SNP markers to assess the genetic architecture of susceptibility to seed predation by M. barbarus. We identified a significant quantitative trait loci (QTL) on chromosome 2A explaining 21% of the variation in predation rate. This region contains a 3.6 Mb chromosomal inversion and 46 candidate genes, including a MYB transcription factor potentially involved in regulating cuticle and chemical traits. To validate these genetic findings, we conducted a cafeteria experiment with 208 spikes from 26 genotypes, placed at the entrances of eight ant nests. Ants preferentially removed spikes from genotypes carrying the allele identified in the GWAS. Additionally, shorter spikes were more likely to be harvested. However, unlike previous studies on wild plants, seed morphology and protein content did not significantly affect ant preference. Synthesis. Our results demonstrate that M. barbarus exhibits genotype-specific preferences in durum wheat, associated with a major QTL, and is influenced by spike traits. This study provides the first evidence of ant-mediated selective pressure in a cereal crop and opens new perspectives on plant-insect dynamics in agroecosystems and the role of plant-insect interactions in the evolutionary history of crop species.</div>

ano.nymous@ccsd.cnrs.fr.invalid (Clément Plessis) 12 Nov 2025

https://hal.inrae.fr/hal-05361550v1

[hal-05369425] A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola

A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.

ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 17 Nov 2025

https://hal.science/hal-05369425v1

[hal-05293171] Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv. campestris 8004

Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. Despite their critical importance, the molecular mechanisms driving intermicrobial competition within the seed microbiome remain poorly understood, limiting the potential to optimize seed inoculation strategies. In this study, we evaluated the inhibitory potential of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP13502 as a potent inhibitor of Xcc8004, mediated by exometabolites specifically induced in the presence of Lysobacterales (formerly Xanthomonadales). Transcriptomic analysis of CFBP13502 revealed upregulation of a gene cluster involved in the biosynthesis of a lipopeptide siderophore biosynthesis. Gene deletion confirmed that this cluster is essential for the growth inhibition of Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, providing strong evidence for the role of iron chelation. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, which we named lactuchelins, produced by CFBP13502. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.

ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 01 Oct 2025

https://hal.science/hal-05293171v1

[hal-05166317] Unifying antimicrobial peptide datasets for robust deep learning-based classification

Leguminous crops are vital to sustainable agriculture due to their ability to fix atmospheric nitrogen, improving soil fertility and reducing the need for synthetic fertilizers. Additionally, they are an excellent source of protein for both human consumption and animal feed. Antimicrobial peptides (AMPs), found in various leguminous seeds, exhibit broad-spectrum antimicrobial activity through diverse mechanisms, including interaction with microbial cell membranes and interference with cellular processes, making them valuable for enhancing crop resilience and food safety. In the field of plant sciences, computational biology methods have been instrumental in the discovery and optimization of AMPs. These methods enable rapid exploration of sequence space and the prediction of AMPs using deep learning technologies. Optimizing AMP annotations through computational design offers a strategic approach to enhance efficacy and minimize potential side effects, providing a viable alternative to conventional antimicrobial agents. However, the presence of overlapping sequences across multiple databases poses a challenge for creating a reliable dataset for AMP prediction. To address this, we conducted a comprehensive analysis of sequence redundancy across various AMP databases. These databases encompass a wide range of AMPs from different sources and with specific functions, including both naturally occurring and artificially synthesized AMPs. Our analysis revealed significant overlap, underscoring the need for a non-redundant AMP sequence database. We present the development of a new database that consolidates unique AMP sequences derived from leguminous seeds, aiming to create a more refined dataset for the binary classification and prediction of plant-derived AMPs. This database will support the advancement of sustainable agricultural practices by enhancing the use of plant-based AMPs in agroecology, contributing to improved crop protection and food security.

ano.nymous@ccsd.cnrs.fr.invalid (Shuang Peng) 10 Sep 2025

https://hal.science/hal-05166317v1

[hal-05147982] Origin, divergence and migration routes of psyllids of the Cacopsylla pruni complex (Hemiptera: Psylloidea) inferred by approximate bayesian computation methods

Aim: Population genetics is essential to decipher the evolutionary history of pests and insect vectors from both a theoretical point of view and to predict and mitigate the future of epidemics. We attempt to shed light on the evolutionary history and phylogeography of two cryptic psyllid species (namely, A and B) of the Cacopsylla pruni complex, vectors of ‘C andidatus Phytoplasma prunorum’. The bacterium is known to cause the European stone fruit yellows (ESFY), a disease affecting Prunus trees and causing significant crop losses. Analyses were conducted to decipher the origin, order and time of divergence, as well as the migration routes of the species complex on the scale of their current distribution area. Location: Western Palearctic. Time Period: Late Tertiary (i.e., the Neogene: 23.030–2.588 Mya) to today. Taxon: Psyllids, jumping plantlice. Methods: Our study was conducted on a dataset of 97 geolocated sampling points, representing a total of 1245 individuals from all across the Western Palearctic. We used mitochondrial and nuclear gene data to infer the population genetic diversity and structure of the complex and to reconstruct a dated phylogenetic tree of the Psyllinae family in order to subsequently perform Approximate Bayesian Computation analyses. Results: Both species have diverged in what is now France from a common ancestor, around 20.19 Mya, before expanding into Spain around 6.61 Mya for species A and Eastern Europe around 6.36 Mya for species B. Then species B seems to have moved to Corsica during the Messinian salinity crisis (5.96–5.33 Mya) from French or Italian B populations. Main Conclusions: No apparent admixture was found between both species after their divergence from France, which would indicate an absence of gene flow between them at the point when they recolonised common ecological niches. This strong genetic differentiation confirms previous work on reproductive barriers between the two species.

ano.nymous@ccsd.cnrs.fr.invalid (Margaux Darnis) 19 Aug 2025

https://hal.inrae.fr/hal-05147982v1

[hal-05192190] Powdery mildew caused by Leveillula taurica (Synonym: Phyllactinia taurica): A global challenge for pepper production

Background Pepper powdery mildew, caused by the obligate fungal pathogen Leveillula taurica (asexual stage: Oidiopsis taurica (Lév.) Salmon 1906, synonym: Oidiopsis sicula Scalia 1902), poses a significant threat to pepper ( Capsicum spp.) cultivation worldwide. This review delves into the taxonomy, geographical distribution, host range, disease symptoms, and life cycle of L. taurica and discusses strategies for managing its epidemics, with a focus on plant genetic immunity. Taxonomy Phylum: Ascomycota ; Class: Leotiomycetes ; Order: Helotiales ; Family: Erysiphaceae; Tribe: Phyllactinieae; Genus and species: Leveillula taurica (Lév.) Arnaud 1921. Synonym: Erysiphe taurica Léveillé 1851; in 2025, the species Leveillula taurica was renamed Phyllactinia taurica . Host Range and Distribution Leveillula taurica exhibits a broad host range, infecting monocotyledonous and dicotyledonous plants of around 200 genera across 60 families, including both herbaceous plants and trees. It causes substantial agricultural losses, particularly in pepper crops. The pathogen is distributed globally, occurring on all continents except Antarctica. Disease Symptoms Initial symptoms include chlorotic spots on the upper leaf surface, which may coalesce and turn necrotic over time. A white mycelial coating (conidia and conidiophores) appears on the lower leaf surface beneath these spots. Severe infections can lead to leaf curling, defoliation, sunburned fruits and reduced yield and quality. The disease is particularly destructive in greenhouses and regions with hot, dry days alternating with cool, humid nights. Disease Control The hemi‐endophytic lifestyle of L. taurica complicates disease management. Effective management of L. taurica involves integrated strategies: regular crop monitoring for early detection, cultural practices to limit fungal development, biocontrol agents, and chemical treatments to prevent or eradicate infections, and the use of resistant plant varieties. Sulphur‐based fungicides, commonly used in organic farming, as well as demethylation inhibitors and quinone outside inhibitor (QoI) fungicides, have demonstrated efficacy; however, the emergence of QoI‐resistant isolates necessitates cautious use. Additionally, biocontrol agents, such as Trichoderma spp. and other mycoparasitic fungi, provide alternative tools by inhibiting fungal growth. Breeding and deploying resistant varieties provide a sustainable approach to managing this disease.

ano.nymous@ccsd.cnrs.fr.invalid (Anne Massire) 30 Jul 2025

https://hal.inrae.fr/hal-05192190v1

[hal-05166334] A mass spectrometry-based peptidomic dataset of the spermosphere in common bean (Phaseolus vulgaris L.) seeds

Abstract The spermosphere, a dynamic microenvironment surrounding germinating seeds, is shaped by the complex interactions between natural compounds exuded by seeds and seed-associated microbial communities. While peptides exuded by plants are known to influence microbiota diversity, little is known about those specifically exuded by seeds. In this study, we characterised the peptidome profile of the spermosphere for the first time using seeds from eight genotypes of common bean ( Phaseolus vulgaris ) grown in two contrasting production regions. An untargeted LC-MS/MS peptidomic analysis revealed 3,258 peptides derived from 414 precursor proteins of common bean in the spermosphere. This comprehensive peptidomic dataset provides valuable insights into the characteristics of peptides exuded by common bean seeds in the spermosphere. It can be used to identify peptides with potential antimicrobial or other biological activities, advancing our understanding of the functional roles of seed-exuded peptides in the spermosphere.

ano.nymous@ccsd.cnrs.fr.invalid (Chandrodhay Saccaram) 17 Jul 2025

https://hal.science/hal-05166334v1

[hal-05099666] Lucerne genetic diversity for living mulch: identifying key traits and evaluating their impacts on wheat development

Context Lucerne (Medicago sativa) can offer ecosystem services as a perennial living mulch, supporting annual cash crops through weed suppression and nitrogen fixation. However, trials with wheat have shown that current lucerne varieties are excessively competitive, leading to reduced wheat yields. Aims This study aimed to analyse the diversity within the M. sativa complex to identify traits that enhance lucerne effectiveness as a living mulch, focusing on the competition for light and nitrogen among lucerne, wheat and weeds. Methods Thirty diverse lucerne accessions were cultivated as living mulch with a winter wheat, over 2 years. Lucerne dormancy and growth habit effects were evaluated on wheat relative dominance during the early stages and on weed abundance. In later stages, the effects of lucerne height and lodging on wheat biomass and nitrogen status were also assessed. Key results Results indicated that lucerne dormancy and growth habit influenced wheat growth during early stages, with dormant and prostrate lucerne accessions reducing competition and enhancing wheat dominance. However, non-dormant and erect lucerne accessions effectively suppressed weeds but competed intensely with wheat. Tall and erect lucerne accessions supported wheat nitrogen status in the second year only. Lucerne lodging affected wheat growth, with tall lucerne reducing wheat biomass in the first year. Conclusions Lucerne should exhibit slow growth, moderate height, and low lodging to optimise its benefits. No variety in our panel exhibited all these desirable traits. Implications These findings highlight the need for breeding programs to combine lucerne beneficial traits as a living mulch into new varieties.

ano.nymous@ccsd.cnrs.fr.invalid (Zineb El Ghazzal) 05 Jun 2025

https://hal.inrae.fr/hal-05099666v1

[hal-05069503] Metabolomic datasets of an apple progeny carrying resistance quantitative trait loci to apple scab before or after inoculation of the pathogen Venturia inaequalis

Phytosanitary treatments are massively used in orchards to fight apple scab, a disease caused by the fungus Venturia inaequalis (Vi). To reduce these treatments, resistant varieties are largely deployed but their effectiveness can decrease over time. The combination of complementary molecular mechanisms within new varieties could enhance the durability of genetic resistance however, the underlying resistance mechanisms remain poorly understood. An apple pseudo-F1 progeny was previously widely investigated for its quantitative trait loci (QTL) controlling resistance to scab and at least three of them seem to act complementarily; notably, one of them is specific to some Vi isolates while the others have a broader spectra of action. The aim of this approach is to better understand the underlying molecular mechanisms and metabolites associated with resistance alleles by exploring apple leaf specialized metabolism. A total of three experiments was conducted: one experiment included non-inoculated leaves whereas in the two other experiments, leaf samples were collected five days after inoculation with two different Vi isolates, including one known to overcome one QTL. Metabolic content was extracted in aqueous methanol before performing an untargeted metabolomic analysis using an Orbitrap IDXTM mass spectrometer, allowing high-resolution mass spectrometry (HRMS) detection. This approach without a priori enables the detection of potentially new chemical families involved in resistance to apple scab. The current data article includes 1) the protocol of plant sample production with a table summarizing key elements of the experimental designs, 2) overview of the raw metabolomic profiles from all three experiments and 3) assessment of metabolic feature reproducibility between replicates in each dataset through Principal Component Analysis. The raw data files are available on the recherche.data.gouv repository (10.57745/XJBD8V). These datasets are valuable resources to further investigate the molecular mechanisms underlying genetic resistance to apple scab, with a focus on specialized metabolism. In the long term, it should improve apple breeding strategies by informing on how to combine appropriate genetic and biochemical factors in new varieties to ensure a more durable resistance.

ano.nymous@ccsd.cnrs.fr.invalid (Romane Lapous) 19 May 2025

https://hal.inrae.fr/hal-05069503v1

[hal-05031294] Cost vector effects in forced-choice discrete choice experiments: Assessing the acceptability of future glyphosate policies

One way to evaluate future policies that significantly deviate from the status quo is through discrete choice experiments (DCEs) with a reference policy featuring a positive cost and no opt-out option. This study examines how the design of the cost vector, particularly the cost assigned to the reference policy, influences DCE outcomes in this context. Focusing on glyphosate phase-out policies in France, we compare a strict ban (used as the reference policy) with taxation alternatives. Using a split-sample design with two groups of 500 individuals, we analyze how variations in the ban’s cost and the associated cost range affect welfare estimates. Our findings reveal that while overall preference rankings remain consistent across samples, willingness-to-pay for some attributes increases when the reference policy’s cost rises. We explore potential drivers of this effect, including the inability to choke off demand for the ban, strategic biases, attribute non-attendance, relative evaluation, and anchoring bias. The results suggest that relative evaluation and anchoring bias are the most likely explanations for the observed differences. These findings provide methodological insights for addressing cost vector effects in DCEs.

ano.nymous@ccsd.cnrs.fr.invalid (Vincent Martinet) 11 Apr 2025

https://hal.inrae.fr/hal-05031294v1

[hal-05025610] Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology

Background: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and longterm epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola. Results: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease. Conclusion: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.

ano.nymous@ccsd.cnrs.fr.invalid (Paola Fournier) 08 Apr 2025

https://hal.inrae.fr/hal-05025610v1

[hal-04948208] Deep-learning-ready RGB-depth images of seedling development

In the era of machine learning-driven plant imaging, the production of annotated datasets is a very important contribution. In this data paper, a unique annotated dataset of seedling emergence kinetics is proposed. It is composed of almost 70,000 RGB-depth frames and more than 700,000 plant annotations. The dataset is shown valuable for training deep learning models and performing high-throughput phenotyping by imaging. The ability of such models to generalize to several species and outperform the state-of-the-art owing to the delivered dataset is demonstrated. We also discuss how this dataset raises new questions in plant phenotyping.

ano.nymous@ccsd.cnrs.fr.invalid (Félix Mercier) 14 Feb 2025

https://hal.science/hal-04948208v1

[hal-04906415] Do semi-natural habitats enhance overwintering of generalist predators in arable cropping systems? A meta-analysis

Highlights• Overwintering preferences of carabid and spider between SNH and crops were analysed.• SNH harbored higher densities of overwintering spiders than the adjacent crop. • Carabid overwintering densities were higher in linear SNH but not in patches of SNH. • Carabid overwintering densities were higher in SNH adjacent to a spring-sown crop.

ano.nymous@ccsd.cnrs.fr.invalid (Paul Bannwart) 22 Jan 2025

https://agroparistech.hal.science/hal-04906415v1

[hal-04881001] Environmental and bioclimatic data for epidemiological analysis over French Mediterranean areas

Risk-based surveillance is now a well-established paradigm in epidemiology, involving the distribution of sampling efforts differentially in time, space, and within populations, based on multiple risk factors. To assess and map the risk of the presence of the bacterium Xylella fastidiosa, we have compiled a dataset that includes factors influencing plant development and thus the spread of such harmful organism. To this end, we have collected, preprocessed, and gathered information and data related to land types, soil compositions, and climatic conditions to predict and assess the probability of risk associated with X. fastidiosa in relation to environmental features. This resource can be of interest to researchers conducting analyses on X. fastidiosa and, more generally, to researchers working on geospatial modeling of risk related to plant infectious diseases.

ano.nymous@ccsd.cnrs.fr.invalid (Camille Portes) 13 Jan 2025

https://hal.science/hal-04881001v1

[hal-04380787] Bayesian joint-regression analysis of unbalanced series of on-farm trials

Participatory plant breeding (PPB) is aimed at developing varieties adapted to agroecologically-based systems. In PPB, selection is decentralized in the target environments, and relies on collaboration between farmers, farmers' organisations and researchers. By doing so, evaluation of new genotypes takes genotype x environment (GxE) interactions into account to select for specific adaptation. In many cases, there is little overlap among genotypes assessed from farm to farm because the farmers participating in a PPB project choose which ones to assess on their farm. In addition, on-farm trials can often generate more extreme observations than trials carried out on research stations. These features make the estimation of genotype, environment and interaction effects more difficult. This challenge is not unique to PPB, as many breeding programs use sparse testing or incomplete block designs to evaluate more genotypes, however in PPB genotypes are not always assigned randomly to environments. To explore methods of overcoming these challenges, this article tests various data analysis scenarios using a Bayesian approach with different models and a real wheat PPB dataset over 11 years. Four morpho-agronomic traits were studied, representing over 1000 GxE combinations from 189 on-farm trials. This dataset was severely unbalanced with more than 90% of GxE combinations missing. We compared various Bayesian Finlay-Wilkinson models and found that placing hierarchical distributions on model parameters and modelling residuals using a Student's t distribution jointly improved the estimates of main effects and interactions. Environment effects were the most important and explained more than 50% of the variance of observations. This statistical framework allowed us to estimate two indicators of genotype stability (one static and one dynamic) despite the high disequilibrium of the data. We found differences in mean and stability as between genotype categories, with registred varieties consistently shorter (-30 cm) and containing less protein (-0.3%) than other types of varieties. The methods developed could be used for evaluation and/or selection within networks of various stakeholders such as farmers, gardeners, plant breeders or managers of genetic resource centres.

ano.nymous@ccsd.cnrs.fr.invalid (Michel Turbet Delof) 06 Jan 2025

https://hal.science/hal-04380787v4

[hal-04827822] Quantitative assessment and spatial distribution of Plasmopara viticola oospores in vineyard soil

Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. While primary inoculum plays a decisive role in disease epidemics, we still know very little about the abundance and the distribution of oospores, which are the overwintering forms of the pathogen resulting from sexual reproduction. In this study, we used ddPCR to describe the spatial distribution of P. viticola inoculum in a vineyard soil at the onset of the growing season. We found P. viticola oospores in all soil samples except one. The distribution of primary inoculum at the field scale was not random but characterized by 25 m-diameter patches of concentrically increasing oospore concentration. There was a positive coregionalization between soil inoculum and soil moisture spatial distributions, possibly mediated by disease incidence. The results indicated that oospores accumulated 5 times more in the ridge of soil below the vine stocks than in the inter-row. We conducted a leaf disc bioassay to assess soil infectious potential on a subset of samples collected in the field. Soil infectious potential estimated through infected leaf-disc area was positively correlated with our DNA-based quantification of oospores. Overall, the quantitative and spatially explicit survey of primary inoculum reservoir gained from these molecular and biological methods will contribute to the design of management strategies aimed at preventing primary inoculum accumulation in the vineyard from one season to the next.

ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Poeydebat) 09 Dec 2024

https://hal.inrae.fr/hal-04827822v1

[hal-04744299] Guidelines for the annotation of the corpus Epidemiomonitoring Of Plant (EPOP)

This document details the instructions for manual annotation of the EPOP Epidemiomonitoring Of Plant) corpus of documents. It is intended for the experts who annotate these documents and for the evaluation and development of methods that automatically predict these annotations. It is divided into three parts, dedicated to entity annotation and normalization, and relationship annotation. Each instruction is detailed and illustrated with examples.

ano.nymous@ccsd.cnrs.fr.invalid (Claire Nédellec) 27 Nov 2024

https://hal.science/hal-04744299v2

[hal-04717658] Impact of intraspecific genetic variation on interspecific competition: a theoretical case study of forage binary mixtures

Introduction Increasing intraspecific genetic variation (IV) has been identified as a potential factor to improve productivity and stabilise botanical composition in plant communities. In grasslands systems, this could offer a lever to manage uncertainties of production and variability in the harvested species balance. However, little is known about the conditions to favour IV impact and the mechanisms at play. Methods The dependency of IV impact on traits holding it and environmental stressors were analysed using a spatially-explicit individual-based model (IBM) of grassland communities. Sixty-three binary mixtures were defined to reflect a gradient of functional divergence between species regarding light and nitrogen (N) acquisition. The growth and dynamics of these communities were simulated for one year with three possible IV levels under two environments contrasting in terms of soil N fertility. Results and discussion The model predicted a positive impact of moderate and high IV levels on maintaining the species balance over time, but no marked effects on mixture productivity. This stabilising effect increased at higher IV levels and under low soil N fertility. It also tended to be more pronounced in communities with intermediate functional divergence offering a significant overlap between light and N acquisition parameter values of both species. The major traits involved in the plant response to neighbours differed depending on the most contested resource, as indicated by the within-population selection of individuals with favourable N-related parameters under low N and light-related parameters under high N environments. The hypothesis that IV favours a complementarity of resource use between species was not supported. Rather, a greater spatial heterogeneity in competitive interactions was demonstrated, leading to a higher probability of growth and survival for individuals within the subordinate species. These results highlight the potential usefulness of IV to design forage mixtures with improved stability and resilience.

ano.nymous@ccsd.cnrs.fr.invalid (Béatrice Wolff) 02 Oct 2024

https://hal.inrae.fr/hal-04717658v1

[hal-04669546] Pherosensor-toolbox: a Python package for Biology-Informed Data Assimilation

Insect pests are a major threat for agricultural systems, leading to an intensive use of pesticide for crop protection with non-sustainable drawbacks on environment, biodiversity and human health. Most of insects produce pheromones for conspecific communication, making pheromone sensors a good tool for early specific detection of pests, in order to reduce pesticide use in a precision agriculture context. `Pheromone-toolbox` is a Python package containing numerical tools for pheromone sensor data assimilation to infer the position of emitting pest insects. It contains specific tools to model pheromone propagation and solve the corresponding inverse problem to determinate emitters position taking into account the environmental context (wind, landscape, vegetation...). A specific focus is put on the integration of biological knowledge of pest behavior during inference.

ano.nymous@ccsd.cnrs.fr.invalid (Thibault Malou) 26 Sep 2024

https://hal.inrae.fr/hal-04669546v2

[hal-03641417] Weed suppression in cover crop mixtures under contrasted levels of resource availability

Cover crop (CC) mixtures appear as a promising agroecological tool for weed management. Although CC supress weed growth by competing for resources, their suppressive effect under contrasting levels of soil resource availability remains poorly documented. A two field:year experiment was conducted to investigate the weed suppressive effect of four CC mixtures. They were composed of 2 or 8 species including or not legume species and compared to a bare soil control. The experiment included two levels of irrigation and nitrogen fertilisation at CC sowing. The objectives were to assess (i) weed and CC aboveground biomass response to CC mixtures and resource availability, (ii) the weed suppressive effect of CC mixtures across a gradient of CC biomass and (iii) weed community response to CC mixtures and resource availability. CC and weed biomass were mainly influenced by interactions between CC mixtures and fertilisation and between CC mixtures and irrigation, with contrasted effects between field:years. Nitrogen fertilisation increased biomass of non-legume based CC mixtures but this only resulted into a further reduction of weed biomass of little biological relevance. Legume-based CC mixtures suppressed weeds to a greater extent without nitrogen fertilisation in year 2 but not in year 1, possibly due to contrasted initial soil nitrogen availability (lower in year 2). Weed biomass generally benefited more from irrigation than CC mixtures. Among the 33 weed species recorded, weed communities in each plot were dominated by wheat volunteers, Geranium dissectum, Veronica persica and Echinochloa crus-galli, whose biomass varied depending on the interaction between year, CC mixture and resource availability. Our results revealed that competitive outcomes between CC mixtures and weed species were driven by a complex interaction between resource availability and species traits. Further experiments focusing on plant traits should improve our understanding of weed:CC competitive outcomes under various levels of resource availability.

ano.nymous@ccsd.cnrs.fr.invalid (Alicia Rouge) 22 Jul 2024

https://institut-agro-dijon.hal.science/hal-03641417v1

[hal-04633322] Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew

Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. &amp; M. A. Curtis; Berl. &amp; De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.

ano.nymous@ccsd.cnrs.fr.invalid (Manon Paineau) 03 Jul 2024

https://hal.inrae.fr/hal-04633322v1

[hal-04052344] Carry-over effects of cover crops on weeds and crop productivity in no-till systems

The carry-over effect of cover crops on weeds and crop productivity in the subsequent crops has been related to cover crop composition and cover crop termination methods but their interaction with soil resource availability remains poorly documented, as well as the relative importance of each of these factors. This study investigated the effect of cover crop management (i.e. cover crop mixture, fertilisation, irrigation, termination method and their combinations) on weed biomass and crop productivity in two subsequent crops (spring barley followed by winter linseed). We hypothesised that cover crop management could affect productivity of the subsequent crops through both weed suppression and nitrogen supply. Two experiments spanning a duration of two years were set-up, on two different fields in two different years, to investigate the effect of cover crop mixture (2 or 8 species including or not legume species, plus a bare soil control), water and nitrogen availability at cover crop sowing and cover crop termination methods (rolling, herbicide-use and winter-kill control) on weed biomass and crop productivity of the two subsequent unweeded, unfertilised and directly seeded crops. Weed biomass and crop productivity in both subsequent crops were affected by multiple interactions between cover crop mixture, soil resource availability, cover crop termination method and experiment. In experiment 1, combinations of cover crop management alternative to the reference (i.e. bare soil, without fertilisation and irrigation, winter-killed) mainly showed beneficial carry-over effects (i.e. lower weed biomass and higher crop productivity) in the subsequent spring barley while having no effect in winter linseed. In experiment 2, alternative combinations of cover crop management mainly showed no effects or detrimental carry-over effects (i.e. higher weed biomass and lower crop productivity) in spring barley while having some positive effects in winter linseed (i.e. only when cover crops were terminated with herbicide-use). Crop productivity was mainly affected by weed biomass which was significantly reduced almost only when cover crops were terminated with herbicide-use. Crop productivity was also affected but to a lesser extent by cover crop soil-mediated effects (e.g. nitrogen supply). These results highlight complex interactions between cover crop management and environmental conditions on the carry-over effects of cover crops in the subsequent crops. Cover crops may not play an essential role for weed management in no-till and herbicide-free systems, particularly at low levels of cover crop biomass production.

ano.nymous@ccsd.cnrs.fr.invalid (Alicia Rouge) 13 Mar 2024

https://hal.inrae.fr/hal-04052344v1

[hal-04092957] A tale of two copies: Evolutionary trajectories of moth pheromone receptors

Pheromone communication is an essential component of reproductive isolation in animals. As such, evolution of pheromone signaling can be linked to speciation. For example, the evolution of sex pheromones is thought to have played a major role in the diversification of moths. In the crop pests Spodoptera littoralis and S. litura , the major component of the sex pheromone blend is ( Z , E )-9,11-tetradecadienyl acetate, which is lacking in other Spodoptera species. It indicates that a major shift occurred in their common ancestor. It has been shown recently in S. littoralis that this compound is detected with high specificity by an atypical pheromone receptor, named SlitOR5. Here, we studied its evolutionary history through functional characterization of receptors from different Spodoptera species. SlitOR5 orthologs in S. exigua and S. frugiperda exhibited a broad tuning to several pheromone compounds. We evidenced a duplication of OR5 in a common ancestor of S. littoralis and S. litura and found that in these two species, one duplicate is also broadly tuned while the other is specific to ( Z , E )-9,11-tetradecadienyl acetate. By using ancestral gene resurrection, we confirmed that this narrow tuning evolved only in one of the two copies issued from the OR5 duplication. Finally, we identified eight amino acid positions in the binding pocket of these receptors whose evolution has been responsible for narrowing the response spectrum to a single ligand. The evolution of OR5 is a clear case of subfunctionalization that could have had a determinant impact in the speciation process in Spodoptera species.

ano.nymous@ccsd.cnrs.fr.invalid (Zibo Li) 12 Feb 2024

https://hal.inrae.fr/hal-04092957v1

[hal-04195817] SNEToolkit: Spatial named entities disambiguation toolkit

‘‘Can you tell me where San Jose is located?’’ ‘‘Uh! Do you know that there are more than 1700 locations named San Jose in the world?’’ The official name of a location is often not the name with which we are familiar. Spatial named entity (SNE) disambiguation is the process of identifying and assigning precise coordinates to a place name that can be identified in a text. This task is not always straightforward, especially when the place name in question is ambiguous for various reasons. In this context, we are interested in the disambiguation of spatial named entities that can be identified in a textual document on a country level. The solution that we propose is based on a set of techniques that allow us to disambiguate the spatial entity considering the context in which it is mentioned from a certain number of characteristics that are specific to it. The solution uses as input a textual document and extricates the named entities identified therein while associating them with the correct coordinates. SNE disambiguation is designed to support the process of fast exploration of spatiotemporal data analysis, most often for event tracking. The proposed approach was tested on 1360 SNEs extracted from the GeoVirus dataset. The results show that SNEToolkit outperformed the baseline, the standard Geonames geocoder, with a recall value of 0.911 against a recall value of 0.871 for the baseline. A flexible Python package is provided for end users.

ano.nymous@ccsd.cnrs.fr.invalid (Rodrique Kafando) 04 Sep 2023

https://hal.inrae.fr/hal-04195817v1

[hal-04071365] Arabidopsis transcriptome dataset of the response of imbibed wild-type and glucosinolate-deficient seeds to nitrogen-containing compounds

The presented RNAseq data were obtained from Arabidopsis seeds dry and 6h imbibed to describe, in wild-type and glucosinolate (GSL)-deficient genotypes, the response at the RNA level to nitrogen compounds, i.e., potassium nitrate (KNO3, 10mM), potassium thiocyanate (KSCN, 8µM). The cyp79B2 cyp79B3 (cyp79B2/B3) double mutant deficient in Indole GSL, the myb28 myb29 (myb28/29) double mutant deficient in aliphatic GSL, the quadruple mutant cyp79B2 cyp79B3 myb28 myb29 (qko) deficient in total GSL in the seed and the WT reference genotype in Col-0 background were used for the transcriptomic analysis. Total ARN was extracted using NucleoSpin® RNA Plant and Fungi kit. Library construction and sequencing were performed with DNBseq™ technology at Beijing Genomics Institute. FastQC was used to check reads quality and mapping analysis were made using a quasi-mapping alignment from Salmon. Gene expression changes in mutant seeds compared to WT were calculated using DESeq2 algorithms. This comparison with the qko, cyp79B2/B3 and myb28/29 mutants made it possible to identify 30220, 36885 and 23807 differentially expressed genes (DEGs), respectively. Mapping rate result was merge into a single report using MultiQC; graphic results were illustrated through Veen diagrams and volcano plots. Fastq raw data and count files from 45 samples are available in the repository Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) and can be consulted with the data identification number GSE221567 at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221567.

ano.nymous@ccsd.cnrs.fr.invalid (Mailen Ortega-Cuadros) 17 Apr 2023

https://univ-angers.hal.science/hal-04071365v1

[hal-04051555] Modelling the spatialisation of pesticide sales to monitor environmental policies in France

Environmental policy monitoring requires data with suitable spatial and temporal resolutions. We present a new method of spatialising pesticide sales in France to monitor environmental policies on a territorial scale. Data on pesticide sales in France are available yearly at a postal code resolution. Our spatialisation model combines parcel-scale land use data with information on pesticide types and applied doses, based on legal authorisations for pesticide use in France. We compared the performance of our new model with that of a simple surface fraction model in two distinct territories: Bourville (830 ha, Normandy), a small catchment composed of two small postal code fractions with available ground truth data about pesticide application, and Pleine-Fougères (12,007 ha, Britany), a larger area with a single postal code comprising seven municipalities with contrasting inter-municipal land uses and no ground truth information about pesticide application. For the Bourville site, due to homogeneous land use, the new model was no better than the simple model for global pesticide use, but it performed better when the results were analysed by crop type. For the Pleine-Fougères site, the new model was effective in distinguishing the use of pesticides by municipality, whereas the simple model was not. Our results demonstrate that our new model improves pesticide use quantification at a territorial level and can provide valid support for monitoring public policies regarding water quality and pesticide use over time and space.

ano.nymous@ccsd.cnrs.fr.invalid (Philippe Martin) 30 Mar 2023

https://hal.inrae.fr/hal-04051555v1

[hal-04059021] Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and Vitis vinifera ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (Erysiphe necator) Under Drought Conditions

The increasing needs of humanity for food supply, the need to reduce fertilizer and pesticide use to protect human and environmental health, and the threats of climate change and disease emergence all provide incentives to use microorganisms to promote crop growth and health (Busby et al. 2017; D'Hondt et al. 2021; Toju et al. 2018). One of the challenges currently facing us is discovering and identifying microbial strains or consortia capable of alleviating biotic and abiotic stresses, and integrating them into crop management (Berg et al. 2017; Poudel et al. 2016). Addressing this challenge is crucial in the case of European cultivated grapevine (Vitis vinifera L.) because this emblematic crop is a very heavy user of phytosanitary products (mainly copper, sulfur and synthetic chemical fungicides targeting leaf diseases). Strengthening microbial biocontrol of grapevine leaf diseases by stimulating the microbiota naturally present in vineyards or by inoculating new microorganisms (Bartoli et al. 2020) could reduce viticulture reliance on chemical fungicides. However, this nature-based solution (Maes and Jacobs 2017) will only be effective and sustainable if microbial antagonisms are resilient to microclimatic and climatic variations and associated changes in vine physiology. This is why vine-pathogen-microbiota interactions should be studied under a range of abiotic conditions. Powdery mildew is one of the grapevine leaf diseases for which the use of chemical fungicides must be reduced. It is caused by the ascomycete fungus Erysiphe necator

ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 05 Apr 2023

https://hal.science/hal-04059021v1

[hal-04059014] Leaf microbiome data for European cultivated grapevine (Vitis vinifera L.) during downy mildew (Plasmopara viticola) epidemics in three wine-producing regions in France

Grapevine downy mildew (Plasmopara viticola) is a major disease of European cultivated grapevine (Vitis vinifera L.) against which a large amount of synthetic pesticides are used. Developing microbial biocontrol of P. viticola could reduce the use of pesticides in viticulture and preserve human and environmental health. To achieve this goal, the ecological interactions that develop during infection between P. viticola and the vine foliar microbiome need to be explored. Here, we present metabarcoding datasets describing the bacterial and fungal communities of pairs of symptomatic and asymptomatic leaf samples collected during downy mildew epidemics in three major wine-producing regions of France. Fungal and bacterial communities were sequenced on a MiSeq Illumina platform, and the abundance of the oomycete P. viticola was quantified using qPCR. We provide the raw metabarcoding datasets, the amplicon sequence variant tables obtained after bioinformatic processing, the metadata describing sampling sites and tissue health conditions, and the code used for bioinformatic analysis. These datasets will enable microbiome comparison within pairs of symptomatic and asymptomatic samples collected at the same time on the same leaf. Such a comparison could help describe the ecological interactions between P. viticola and the grapevine foliar microbiome.

ano.nymous@ccsd.cnrs.fr.invalid (Didac Barroso-Bergadà) 05 Apr 2023

https://hal.science/hal-04059014v1

[hal-03910388] Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs

The fungus Botrytis cinerea is a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have been characterized as virulence factors, their roles in host specialization remain unknown. The aim of this study was to identify the genomic correlates of host-specialization in populations of B. cinerea associated with grapevine and tomato. Using PacBio sequencing, we produced complete assemblies of the genomes of strains Sl3 and Vv3 that represent the French populations T and G1 of B. cinerea, specialized on tomato and grapevine, respectively. Both assemblies revealed 16 core chromosomes that were highly syntenic with chromosomes of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes, especially the chromosome BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like element was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the accessory chromosome BCIN19 and the small RNAs producing retrotransposons Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that accessory chromosomes, repertoires of transposons and their derived small RNAs differ between populations of B. cinerea specialized on different hosts. The genomic data characterized in our study pave the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen.

ano.nymous@ccsd.cnrs.fr.invalid (Adeline Simon) 22 Dec 2022

https://hal.science/hal-03910388v1

[hal-05533608] Elucidating the interplay between metabolites and microorganisms in the spermosphere of common bean (Phaseolus vulgaris L.) seeds

The spermosphere, the dynamic interface surrounding germinating seeds, is shaped by the intricate interplay between seed-exuded natural compounds and seed-associated microbial communities. In this work, we provide the first comprehensive metabolomic and microbiome characterization of common bean ( Phaseolus vulgaris ) spermosphere of eight genotypes produced in two contrasted production regions. Through an integrated approach, we explored the metabolomic and microbiota composition in the spermosphere of germinating common bean seeds and elucidated their environmental and genotype regulation. We detected and analyzed 2,467 metabolite features (Mf) through untargeted metabolomics categorized into fourteen metabolic categories, highlighting the prevalence of amino acids, flavonoids, and terpenoids. Genotype was the key factor influencing the chemical composition of the spermosphere. Furthermore, we identified 19 bacterial families and 23 fungal families inhabiting the spermosphere, with both genotype and seed production location exerting varying degrees of influence on microbial community composition. Through a multiscale integrated approach, we revealed specific associations between metabolites and microorganisms, such as negative correlation between flavonoids and Bacillus spp., emphasizing the genotype-dependent nature of these interactions. This comprehensive investigation sheds light on the mechanisms underlying seed germination and the complex interactions between plant genotypes, seed exudates, environmental conditions, and microbial communities in the spermosphere. These findings provide a framework for developing innovative strategies to promote seed health and sustainable crop production. IMPORTANCE The spermosphere, the dynamic interface around germinating seeds, is shaped by the intricate interplay between seed-exuded compounds and microbial communities. Despite the importance of these interactions for eventual seedling emergence and health, little knowledge is available on the subject. We are the first to comprehensively analyze the chemical and microbial diversity of the spermosphere of Phaseolus vulgaris (common bean). We identified thousands of primary and specialized metabolites, highlighting their diversity but largely unknown roles in germinating seed-environment interactions. We revealed significant genotype-driven differences in the chemical composition as well as the influence of both genotype and seed production location on microbial community structure in the spermosphere. Our metabolome-microbiome integrative analysis suggests that common bean shapes the spermosphere microbiome through specific seed exudates. This research advances our understanding of the metabolic capabilities and ecological roles of seed microbiota within the spermosphere, contributing to our understanding of seed health and vigor.

ano.nymous@ccsd.cnrs.fr.invalid (Chandrodhay Saccaram) 02 Mar 2026

https://hal.science/hal-05533608v1

[hal-05261852] Figurative representation tools to support the participatory design process of an agrifood system

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ano.nymous@ccsd.cnrs.fr.invalid (Aliénor Morvan) 15 Sep 2025

https://hal.inrae.fr/hal-05261852v1

[hal-05155592] Differences in growth features between species are driving cereal-legume intercrop yield: A statistical learning approach based on aggregated dataset

Increasing crop diversification is crucial for developing more sustainable agricultural systems, and cereal-legume intercropping is a promising strategy. This study investigates the factors influencing the yield of cereal-legume intercrops using data from six field experiments in southwestern France, where durum wheat was intercropped with either faba bean or pea. We assessed how differences in plant traits (e.g., height or biomass growth rates) between the associated species were related to the intercrop productivity. Additionally, we developed a novel modeling approach, combining machine learning and mixed-effects models, to identify the key drivers of intercrop performance based on variable importance. Our results showed that interspecific differences in plant traits within intercrops, particularly in biomass accumulation rate, maximum leaf area index, and elongation rates, were the most important factors explaining intercrop yield. These traits and their differences mainly suggest that competitive processes shape the outcome of a mixture and highlight the importance of dynamic measurements in agronomic experiments. The relationship between species yield and trait differences was symmetric for both intercropped species. Furthermore, these relationships were scale-dependent, with trends observed at the aggregate level not always consistent at the level of individual experiments. Our study highlights the importance of considering trade-offs when designing intercropping systems for practical applications and demonstrates the value of combining machine learning with ecological knowledge to gain insights into complex agricultural systems from aggregated datasets.

ano.nymous@ccsd.cnrs.fr.invalid (Rémi Mahmoud) 10 Jul 2025

https://hal.science/hal-05155592v1

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