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Agroecology: biodiversity in agroecosystems to regulate pests and diseases?Agriculture is currently facing yield stability and is causing a negative environmental impact. These two elements call into question the ever increasing use of synthetic inputs. In order to make agroecosystems resilient and autonomous with regard to synthetic inputs, one of the bets of agroecology is to mobilize biodiversity to promote biological regulation. In short, it aims to design agroecosystems capable of self-regulation while remaining sufficiently productive. We will begin by presenting the different meanings of agroecology and our own positioning. Then we will show how leveraging biodiversity is possible by illustrating it at different scales from organ to landscape. Thirdly, we will question the limits or unknowns of these effects and the compromises with respect to other services expected from agroecosystems. In conclusion, we will put these elements in a context of global change and in particular of climate change.; Agroécologie : la biodiversité dans les agroécosystèmes pour réguler les bioagresseurs ?L’agriculture fait actuellement face à une stabilité des rendements et est source d’un impact environnemental négatif. Ces deux éléments remettent en cause l’usage toujours en augmentation des intrants de synthèse. Afin de rendre les agroécosystèmes résilients et autonomes vis-à-vis des intrants de synthèse, un des paris de l’agroécologie est de mobiliser la biodiversité pour favoriser les régulations biologiques. En somme elle vise à concevoir des agroécosystèmes capables de s’autoréguler tout en restant suffisamment productifs. Nous commencerons par présenter les différentes acceptions de l’agroécologie et notre propre positionnement. Puis nous montrerons comment l’utilisation du levier que représente la biodiversité est possible en l’illustrant à différentes échelles depuis l’organe jusqu’au paysage. Dans un troisième temps, nous questionnerons les limites voire les inconnus de ces effets et les compromis vis à vis des autres services attendus des agroécosystèmes. En conclusion nous replacerons ces éléments dans un contexte de changement global et en particulier de changement climatique.

Diversification in pathogen control methods to reduce the severity of economically important foliar diseases such as Zymoseptoria tritici on wheat is needed. One way is to identify plant physiological and architectural traits that influence disease development and that can be selected in the process of crop breeding. Such traits may be used for improving tolerance or disease escape. Traits favoring disease escape, the focus of our work, may significantly decrease crop epidemics (Robert et al., 2018). However, understanding the role of such traits in crop-pathogen interactions is a daunting task because the interactions are multiple and dynamic in time. To characterize and quantify crop-pathogen interactions, an innovative trait-based and resource-based modeling framework was developed (Precigout et al., 2017). In this framework, the pathosystem is assumed to respond dynamically to both architecture and physiological status of the host canopy. A canopy consists of plenty of small patches, i.e. small functional and infectable units of leaf tissue. Production of new patches, for canopy growth and renewal of photosynthetically active plant tissues, is a function of the available resources produced by the other patches. Pathogen spores can contaminate nearby healthy patches. The definition of patch proximity depends on dispersal abilities of the pathogen and canopy architecture. We used and adapted this modeling framework to quantify the effects of several plant traits on Zymoseptoria tritici epidemics for varied climate scenarios. The complex infection cycle of Z. tritici characterized by a long symptomless incubation period was implemented in the model. We studied plant architectural traits such as leaf size or stem height, and plant physiological traits such as leaf lifespan or leaf metabolite contents. In our simulations, these traits impacted the epidemics dynamics though their effects on pathogen dispersal and on the amount of resources available for the pathogen. Sensitivity analyses showed how disease severity depended on plant traits and pathogen virulence. The importance of several plant and pathogen traits could be linked to the pathogen’s ability to manage the race for the colonization of the canopy in the face of canopy growth. Playing on host traits also made it possible to simulate different wheat varieties - with contrasted heights, pathogen resistance or precocity - to characterize the behavior of the pathosystem of interest for different host ideotypes. We argue that this kind of trait-based modeling approach is a valuable tool to identify plant traits promoting more resilient agroecosystems in particular for crop breeding in a context of innovative and sustainable crop protection.

Crop pathogens are known to rapidly adapt to agricultural practices. Although cultivar resistance breakdown and resistance to pesticides have been broadly studied, little is known about the adaptation of crop pathogens to more quantitative traits such as quantitative resistance. Quantitative resistance could be more sustainable than gene for gene resistance because it exerts a lower selective pressure on pathogens and relies on a variety of plant traits (and probably genes) rather than on a single one. Using a modelling approach, in this study we address the epidemiological and evolutionary responses of the pathogen to changes in several plant traits that impact epidemic development. With the model, we study life history evolution of biotrophic fungal pathogens of wheat. We focus on a single pathogen life history trait, the latent period, which directly determines the amount of resource allocated to growth and reproduction alongside the speed of canopy colonization. We investigate the evolutionary response of pathogens to changing several plant traits such as leaf metabolite concentration, leaf dimension and leaf lifespan. These plant traits impact epidemic development: disease severity is predicted to increase with metabolite content and leaf lifespan. We compare predictions of latent period evolution based on different “empirical” fitness measures such as annual spore production or within-season exponential growth rate, with predictions based on the more rigorous concept of invasion fitness from adaptive dynamics theory. For each of the studied plant traits, we use pairwise invisibility plots to identify evolutionarily stable strategies of the latent period (ESS). The ESS latent period responds differently to the different plant traits: it is longer on plants with long-lasting leaves and shorter on plants with bigger leaves leading to denser canopies. Our results further reveal that early canopy colonization during crop development might be a critical factor determining the issue of between-strain competition and shaping pathogen adaptation in the context of plant quantitative resistance. Finally, we argue that landscape-level heterogeneity may induce maladaptation of the pathogen that may be useful in stalling the evolutionary breakdown of quantitative resistance

Epidemiologists and pathologists for addressing topical questions about, for example, the efficiency of agroecological solutions to mitigating crop diseases or their impact on pathogen evolution. We propose here to showcase two modeling approaches that our team is currently using in this context. Firstly, based on the framework of physiologically structured population models and its numerical implementation (referred to as the EBTtool) we represent a (multi-) seasonally growing crop canopy as a dynamic collection of small infectable patches of leaf tissue with intrinsic and dynamic properties (e.g. age, position in the canopy, nutrient content, infection status). Dynamics of predicted disease epidemics depend on the dynamic properties of all the patches over time. Secondly, the agent-based modeling environment NetLogo provides a conceptual framework to model spatially extended dynamics of disease progression in explicit landscapes with different spatial arrangements of crops that are not necessarily static over the cropping seasons. We are using these two modeling approaches to study resource dynamics at the canopy and landscape scales as a way to explore the potential of regulating crop pathogens by reducing or diversifying nitrogen fertilization practices in the pathosystems wheat/rusts and wheat/septoria tritici blotch. These modeling approaches offer the opportunity to (1) predict short and long term epidemiological dynamics based on assumptions on the consumer-resource interactions at the lesion scale, (2) to reveal pathogen trade-offs (transmission, virulence, aggressiveness) that emerge from the interactions between the pathogen and ecophysiological and morphological dynamics of the crop canopy, (3) to study the effect of spatial resource heterogeneity on pathogen dynamics, adaptation and maladaptation.

Diversification in pathogen control methods to reduce the severity of economically important foliar diseases such as Zymoseptoria tritici on wheat is needed. One way is to identify plant physiological and architectural traits that influence disease development and that can be selected in the process of crop breeding. Such traits may be used for improving tolerance or disease escape. Traits favoring disease escape, the focus of our work, may significantly decrease crop epidemics (Robert et al., 2018). However, understanding the role of such traits in crop-pathogen interactions is a daunting task because the interactions are multiple and dynamic in time. To characterize and quantify crop-pathogen interactions, an innovative trait-based and resource-based modeling framework was developed (Precigout et al., 2017). In this framework, the pathosystem is assumed to respond dynamically to both architecture and physiological status of the host canopy. A canopy consists of plenty of small patches, i.e. small functional and infectable units of leaf tissue. Production of new patches, for canopy growth and renewal of photosynthetically active plant tissues, is a function of the available resources produced by the other patches. Pathogen spores can contaminate nearby healthy patches. The definition of patch proximity depends on dispersal abilities of the pathogen and canopy architecture. We used and adapted this modeling framework to quantify the effects of several plant traits on Zymoseptoria tritici epidemics for varied climate scenarios. The complex infection cycle of Z. tritici characterized by a long symptomless incubation period was implemented in the model. We studied plant architectural traits such as leaf size or stem height, and plant physiological traits such as leaf lifespan or leaf metabolite contents. In our simulations, these traits impacted the epidemics dynamics though their effects on pathogen dispersal and on the amount of resources available for the pathogen. Sensitivity analyses showed how disease severity depended on plant traits and pathogen virulence. The importance of several plant and pathogen traits could be linked to the pathogen's ability to manage the race for the colonization of the canopy in the face of canopy growth. Playing on host traits also made it possible to simulate different wheat varieties - with contrasted heights, pathogen resistance or precocity - to characterize the behavior of the pathosystem of interest for different host ideotypes. We argue that this kind of trait-based modeling approach is a valuable tool to identify plant traits promoting more resilient agroecosystems in particular for crop breeding in a context of innovative and sustainable crop protection.

Epidemiologists and pathologists for addressing topical questions about, for example, the efficiency of agroecological solutions to mitigating crop diseases or their impact on pathogen evolution. We propose here to showcase two modeling approaches that our team is currently using in this context. Firstly, based on the framework of physiologically structured population models and its numerical implementation (referred to as the EBTtool) we represent a (multi-) seasonally growing crop canopy as a dynamic collection of small infectable patches of leaf tissue with intrinsic and dynamic properties (e.g. age, position in the canopy, nutrient content, infection status). Dynamics of predicted disease epidemics depend on the dynamic properties of all the patches over time. Secondly, the agent-based modeling environment NetLogo provides a conceptual framework to model spatially extended dynamics of disease progression in explicit landscapes with different spatial arrangements of crops that are not necessarily static over the cropping seasons. We are using these two modeling approaches to study resource dynamics at the canopy and landscape scales as a way to explore the potential of regulating crop pathogens by reducing or diversifying nitrogen fertilization practices in the pathosystems wheat/rusts and wheat/septoria tritici blotch. These modeling approaches offer the opportunity to (1) predict short and long term epidemiological dynamics based on assumptions on the consumer-resource interactions at the lesion scale, (2) to reveal pathogen trade-offs (transmission, virulence, aggressiveness) that emerge from the interactions between the pathogen and ecophysiological and morphological dynamics of the crop canopy, (3) to study the effect of spatial resource heterogeneity on pathogen dynamics, adaptation and maladaptation.

Agroécologie : la biodiversité dans les agroécosystèmes pour réguler les bioagresseurs ? L’agriculture fait actuellement face à une stabilité des rendements et est source d’un impact environnemental négatif. Ces deux éléments remettent en cause l’usage toujours en augmentation des intrants de synthèse. Afin de rendre les agroécosystèmes résilients et autonomes vis-à-vis des intrants de synthèse, un des paris de l’agroécologie est de mobiliser la biodiversité pour favoriser les régulations biologiques. En somme elle vise à concevoir des agroécosystèmes capables de s’autoréguler tout en restant suffisamment productifs. Nous commencerons par présenter les différentes acceptions de l’agroécologie et notre propre positionnement. Puis nous montrerons comment l’utilisation du levier que représente la biodiversité est possible en l’illustrant à différentes échelles depuis l’organe jusqu’au paysage. Dans un troisième temps, nous questionnerons les limites voire les inconnus de ces effets et les compromis vis à vis des autres services attendus des agroécosystèmes. En conclusion nous replacerons ces éléments dans un contexte de changement global et en particulier de changement climatique., Agroecology: biodiversity in agroecosystems to regulate pests and diseases? Agriculture is currently facing yield stability and is causing a negative environmental impact. These two elements call into question the ever increasing use of synthetic inputs. In order to make agroecosystems resilient and autonomous with regard to synthetic inputs, one of the bets of agroecology is to mobilize biodiversity to promote biological regulation. In short, it aims to design agroecosystems capable of self-regulation while remaining sufficiently productive. We will begin by presenting the different meanings of agroecology and our own positioning. Then we will show how leveraging biodiversity is possible by illustrating it at different scales from organ to landscape. Thirdly, we will question the limits or unknowns of these effects and the compromises with respect to other services expected from agroecosystems. In conclusion, we will put these elements in a context of global change and in particular of climate change.

Diversification in pathogen control methods to reduce the severity of economically important foliar diseases such as Zymoseptoria tritici on wheat is needed. One way is to identify plant physiological and architectural traits that influence disease development and that can be selected in the process of crop breeding. Such traits may be used for improving tolerance or disease escape. Traits favoring disease escape, the focus of our work, may significantly decrease crop epidemics (Robert et al., 2018). However, understanding the role of such traits in crop-pathogen interactions is a daunting task because the interactions are multiple and dynamic in time. To characterize and quantify crop-pathogen interactions, an innovative trait-based and resource-based modeling framework was developed (Precigout et al., 2017). In this framework, the pathosystem is assumed to respond dynamically to both architecture and physiological status of the host canopy. A canopy consists of plenty of small patches, i.e. small functional and infectable units of leaf tissue. Production of new patches, for canopy growth and renewal of photosynthetically active plant tissues, is a function of the available resources produced by the other patches. Pathogen spores can contaminate nearby healthy patches. The definition of patch proximity depends on dispersal abilities of the pathogen and canopy architecture. We used and adapted this modeling framework to quantify the effects of several plant traits on Zymoseptoria tritici epidemics for varied climate scenarios. The complex infection cycle of Z. tritici characterized by a long symptomless incubation period was implemented in the model. We studied plant architectural traits such as leaf size or stem height, and plant physiological traits such as leaf lifespan or leaf metabolite contents. In our simulations, these traits impacted the epidemics dynamics though their effects on pathogen dispersal and on the amount of resources available for the pathogen. Sensitivity analyses showed how disease severity depended on plant traits and pathogen virulence. The importance of several plant and pathogen traits could be linked to the pathogen’s ability to manage the race for the colonization of the canopy in the face of canopy growth. Playing on host traits also made it possible to simulate different wheat varieties - with contrasted heights, pathogen resistance or precocity - to characterize the behavior of the pathosystem of interest for different host ideotypes. We argue that this kind of trait-based modeling approach is a valuable tool to identify plant traits promoting more resilient agroecosystems in particular for crop breeding in a context of innovative and sustainable crop protection.

Crop pathogens are known to rapidly adapt to agricultural practices. Although cultivar resistance breakdown and resistance to pesticides have been broadly studied, little is known about the adaptation of crop pathogens to more quantitative traits such as quantitative resistance. Quantitative resistance could be more sustainable than gene for gene resistance because it exerts a lower selective pressure on pathogens and relies on a variety of plant traits (and probably genes) rather than on a single one. Using a modelling approach, in this study we address the epidemiological and evolutionary responses of the pathogen to changes in several plant traits that impact epidemic development. With the model, we study life history evolution of biotrophic fungal pathogens of wheat. We focus on a single pathogen life history trait, the latent period, which directly determines the amount of resource allocated to growth and reproduction alongside the speed of canopy colonization. We investigate the evolutionary response of pathogens to changing several plant traits such as leaf metabolite concentration, leaf dimension and leaf lifespan. These plant traits impact epidemic development: disease severity is predicted to increase with metabolite content and leaf lifespan. We compare predictions of latent period evolution based on different “empirical” fitness measures such as annual spore production or within-season exponential growth rate, with predictions based on the more rigorous concept of invasion fitness from adaptive dynamics theory. For each of the studied plant traits, we use pairwise invisibility plots to identify evolutionarily stable strategies of the latent period (ESS). The ESS latent period responds differently to the different plant traits: it is longer on plants with long-lasting leaves and shorter on plants with bigger leaves leading to denser canopies. Our results further reveal that early canopy colonization during crop development might be a critical factor determining the issue of between-strain competition and shaping pathogen adaptation in the context of plant quantitative resistance. Finally, we argue that landscape-level heterogeneity may induce maladaptation of the pathogen that may be useful in stalling the evolutionary breakdown of quantitative resistance

poster abstract; Crop canopy architecture affects the dispersal of airborne fungal spores of plant diseases, in particular in the case of septoria tritici blotch (STB) which is an important wheat disease mainly spread by rain splash. Therefore, the characteristics of canopy architecture (medium of dispersal of the pathogenic agent) can be taken into account to implement alternative disease control methods in order to slow down the vertical dispersal of STB in the field. And for the particular case of cultivar mixtures, different plant architectural traits can be used to improve the “barrier” effect on spore dispersal, which is provided by the most resistant components in the mixtures (see Vidal et al. in this issue). We investigated, by the mean of experiments under controlled conditions and modelling, the effects of the canopy architecture on one dispersal cycle of spores of Zymoseptoria tritici. The experiment was performed using a simulator of artificial rains on micro-canopies of wheat (1 m2), which were grown in a controlled greenhouse environment. A linear inoculum source of spores suspension was exposed to a simulated and calibrated rainfall event in order to get reproducible splash-dispersal towards four types of canopy differing by their architectures characterized by their leaf area densities (LAD). Splash droplets of the suspension were collected at different locations within the canopies to quantify spore fluxes and the resulting disease severity and incidence were assessed after the latency period. Based on a mechanistic modelling of spore dispersal and a 3D numerical reconstruction of the canopies, we quantified strong effects of the canopy structure on the spore dispersal. Denser canopies (i.e. with higher LAD) had a higher rate of spore interception that led, (i) for susceptible cultivars, to a higher disease severity, and (ii) for the resistant cultivars, to a higher spore trapping rate and therefore to a better “barrier” effect in the case of cultivar mixtures.

poster abstract; International audience; The upper leaves of wheat are the main sources of assimilate for grain production. As such, they are a specific target for fungicide treatments. The efficacy of a treatment can be assessed by the quantity of fungicide deposited on target leaves relative to the spraying application rate per unit area. For a given spraying system and under favorable meteorological conditions, foliar deposit depends on the individual areas and spatial arrangement of leaves within the canopy, which determine the interception of the spray; and on the physio-chemical characteristics of the product, which determine its fate on leaf surfaces. The objectives of this study are to model the deposition of pesticide on the upper leaves of wheat and to identify the plant architectural traits that influence the foliar deposit as the plant develops. For this we couple a 3D architectural model of wheat (ADEL-Wheat), which captures the dynamics of the spatial arrangement of individual leaves at different stages of plant development, with the projection algorithm of the Caribu light interception model that allows estimating the deposit of fungicide within the canopy. A three-year experiment was performed (ECHAP project), with detailed assessments of plant architecture for three genotypes, and of tracer-deposit (tartrazine) on the four upper leaves, for two spraying dates. The architectural measurements were used to calibrate the wheat model that was tested against the foliar deposit data. We used the model to further analyse the origin of the differences of deposit between leaves and between treatment dates observed in the experiments. The analyses reveal that the dynamics of leaf bending, assumed to be a function of leaf age, has a strong influence in spraying efficacy, especially for the upper two leaves. We therefore propose that optimal application strategy could be reasoned not only by considering the degree of expansion of targeted leaves, but also their dynamic of bending.

Book of abstracts-posters; It is urgent for agriculture to adopt new methods of crop protection that use less pesticide. In the perspective of agroecology, a solution is to regulate the pathogen populations via the properties of plant canopies. Here, we focus on the effects of plant architecture on foliar fungal epidemics. Combined FSPM-epidemic models are potential good tools to simulate these effects and to identify the most influential plant traits on epidemics. In wheat, the main fungal foliar diseases are septoria and brown rust. Both diseases develop lesions on leaves but the symptoms, the infection cycles and the dispersal types are different. Zymoseptoria tritici is a hemi-biotrophic fungus with sporulation occurring on necrotic leaf tissue after a biotrophic colonization phase, and it is mainly dispersed by rain-splash. Puccinia triticina is a strictly biotrophic fungus that grows and sporulates only on living tissues and spores are mainly dispersed by wind. The effects of architecture may depend on the dispersal strategy and infection cycle. This raises questions on the influence of plant architecture on these varied types of foliar fungi: do architectural traits impact their epidemics in the same way? Are there plant traits with opposite effects on the diseases? Answering these questions is crucial in the perspective of controlling fungi complexes on the same host. Several wheat architectural traits, such as stem height and plant development rate, are known to influence septoria. However, only very few studies are available on leaf rust. Our objective is to compare the effects of wheat architecture on epidemics of septoria and brown rust. For this, two FSPM models (Wheat-septoria and Wheat-brown rust) were developed and used to compare the effects of wheat properties on epidemics. The tested plant traits are phenology, organ growth rates (stems and leaves), organ dimensions, leaf curvature, and timing of leaf senescence. The outputs compared are the disease severity on each leaf rank of the canopy. The analysis is done for different climates. The results show that the two pathogens are impacted differently by plant architectural traits, even if they are both very sensitive to leaf green life span. The interaction with climate is also different. This work is an important step in developing methods to study varied pathosystems using FSPMs. This is also a first step to establish a more generic understanding of how different types of fungus are influenced by plant architecture

oral communication abstract; The upper leaves of wheat are the main sources of assimilate for grain production. As such, they are a specific target for fungicide treatments. The efficacy of a treatment can be assessed by the quantity of fungicide deposited on target leaves relative to the spraying application rate per unit area. For a given spraying system and under favorable meteorological conditions, foliar deposit depends on the individual areas and spatial arrangement of leaves within the canopy, which determine the interception of the spray; and on the physio-chemical characteristics of the product, which determine its fate on leaf surfaces. The objectives of this study are to model the deposition of pesticide on the upper leaves of wheat and to identify the plant architectural traits that influence the foliar deposit as the plant develops. For this we couple a 3D architectural model of wheat (ADEL-Wheat), which captures the dynamics of the spatial arrangement of individual leaves at different stages of plant development, with the projection algorithm of the Caribu light interception model that allows estimating the deposit of fungicide within the canopy. A three-year experiment was performed (ECHAP project), with detailed assessments of plant architecture for three genotypes, and of tracer-deposit (tartrazine) on the four upper leaves, for two spraying dates. The architectural measurements were used to calibrate the wheat model that was tested against the foliar deposit data. We used the model to further analyse the origin of the differences of deposit between leaves and between treatment dates observed in the experiments. The analyses reveal that the dynamics of leaf bending, assumed to be a function of leaf age, has a strong influence in spraying efficacy, especially for the upper two leaves. We therefore propose that optimal application strategy could be reasoned not only by considering the degree of expansion of targeted leaves, but also their dynamic of bending.

L’objectif du projet ECHAP est d’identifier les possibilités de réduction de traitements fongicides via l’utilisation de l’architecture des couverts. Le projet a tout d’abord apporté des connaissances qui ont levé des verrous sur les mécanismes d’interaction. Il combine également 3 expérimentations opérationnelles au champ et un travail de modélisation du système. Les expérimentations au champ confirment l’effet de l’architecture sur le développement épidémique ainsi que l’effet marqué sur l’interception des fongicides et qui s’exprime clairement entre les variétés. Un modèle innovant et original simulant le système « architecture–épidémie-fongicide », septo3dfongi, a été développé. Il est opérationnel et permet de simuler et de raisonner des stratégies de traitements. Des critères d’évaluation multicritères des stratégies ont été également proposés.

ECHAP : un projet pour identifier les possibilités de réduction de l'utilisation des fongicides en utilisant l'architecture des couverts. 45e Congrès du Groupe Français des Pesticides Devenir et impact des pesticides : verrous à lever et nouveaux enjeux

National audience

La pulvérisation en grandes cultures se résume, le plus souvent, à un choix de buse, un volume de bouillie et une dose de produit associé. Le dépôt des fongicides sur les organes ciblés est un sujet aujourd’hui peu connu.Sa compréhension est pourtant capitale pour améliorer l’efficacité des traitements et réduire l’impact environnemental.