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International audience; Travelling waves (TW) are among the most striking ecological phenomena emerging in oscillating populations. Despite much theory, understanding how real-world TW arise remains a challenge for ecology. Herein, we analyse 16-year time series of cyclic vole populations collected at 314 localities covering 2500 km² in France. We found evidence for a linear front TW spreading at a speed of 7.4 km year(-1) along a north-west/south-east direction and radiating away from a major landscape discontinuity as predicted by recent theory. The spatial signature of vole dispersal was assessed using genetic data collected at 14 localities. Both data sets were handled using similar autocorrelation approaches. Our results revealed a remarkable congruence of the spatial extent and direction of anisotropy of both demographic and genetic structures. Our results constitute the first empirical evidence that effective dispersal is limited in the direction of TW while most of the individual exchanges occur along the wave front.

Outdoor field measurements of bioaerosols are performed within a wide range of basic and applied scientific disciplines, each with its own goals, assumptions, and terminology. This article contains brief reviews of outdoor field bioaerosol research from these diverse interests, with emphasis on perspectives from the atmospheric sciences. The focus is on a high-level discussion of pressing scientific questions, grand challenges, and needs for cross-disciplinary collaboration. The research topics, in which bioaerosol field measurement is important, include (i) atmospheric physics, clouds, climate, and hydrological cycle; (ii) atmospheric chemistry; (iii) airborne allergen-containing particles; (iv) airborne human pathogens and national security; (v) airborne livestock and crop pathogens; and (vi) biogeography and biodiversity. We concisely review bioaerosol impacts and discuss properties that distinguish bioaerosols from abiological aerosols. We give extra focus to regions of specific interest, i.e., forests, polar regions, marine and coastal environments, deserts, urban and rural areas, and summarize key considerations related to bioaerosol measurements, such as of fluxes, of long-range transport, and of sampling from both stationary and vessel-driven platforms. Keeping in mind a series of key scientific questions posed within the diverse communities, we suggest that pressing scientific questions include the following: (i) emission sources and flux estimates; (ii) spatial distribution; (iii) changes in distribution; (iv) atmospheric aging; (v) metabolic activity; (vi) urbanization of allergies; (vii) transport of human pathogens; and (viii) climate-relevant properties.

International audience; In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.

A growing body of circumstantial evidence suggests that ice nucleation active (Ice(+)) bacteria contribute to the initiation of precipitation by heterologous freezing of super-cooled water in clouds. However, little is known about the concentration of Ice(+) bacteria in precipitation, their genetic and phenotypic diversity, and their relationship to air mass trajectories and precipitation chemistry. In this study, 23 precipitation events were collected over 15 months in Virginia, USA. Air mass trajectories and water chemistry were determined and 33 134 isolates were screened for ice nucleation activity (INA) at -8 °C. Of 1144 isolates that tested positive during initial screening, 593 had confirmed INA at -8 °C in repeated tests. Concentrations of Ice(+) strains in precipitation were found to range from 0 to 13 219 colony forming units per liter, with a mean of 384±147. Most Ice(+) bacteria were identified as members of known and unknown Ice(+) species in the Pseudomonadaceae, Enterobacteriaceae and Xanthomonadaceae families, which nucleate ice employing the well-characterized membrane-bound INA protein. Two Ice(+) strains, however, were identified as Lysinibacillus, a Gram-positive genus not previously known to include Ice(+) bacteria. INA of the Lysinibacillus strains is due to a nanometer-sized molecule that is heat resistant, lysozyme and proteinase resistant, and secreted. Ice(+) bacteria and the INA mechanisms they employ are thus more diverse than expected. We discuss to what extent the concentration of culturable Ice(+) bacteria in precipitation and the identification of a new heat-resistant biological INA mechanism support a role for Ice(+) bacteria in the initiation of precipitation.

We thank the staff of the INRAE Experimental facilities of the Plant Pathology research unit (IEPV, https://doi.org/10.15454/8DGF-QF70) for their involvement in field experiments; International audience; Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.

Plant qualitative resistances to viruses are natural exhaustible resources that can be impaired by the emergence of resistance-breaking (RB) virus variants. Mathematical modelling can help determine optimal strategies for resistance durability by a rational deployment of resistance in agroecosystems. Here, we propose an innovative approach, built up from our previous empirical studies, based on plant cultivars combining qualitative resistance with quantitative resistance narrowing population bottlenecks exerted on viruses during host-to-host transmission and/or within-host infection. Narrow bottlenecks are expected to slow down virus adaptation to plant qualitative resistance. To study the effect of bottleneck size on yield, we developed a stochastic epidemic model with mixtures of susceptible and resistant plants, relying on continuous-time Markov chain processes. Overall, narrow bottlenecks are beneficial when the fitness cost of RB virus variants in susceptible plants is intermediate. In such cases, they could provide up to 95 additional percentage points of yield compared with deploying a qualitative resistance alone. As we have shown in previous works that virus population bottlenecks are at least partly heritable plant traits, our results suggest that breeding and deploying plant varieties exposing virus populations to narrowed bottlenecks will increase yield and delay the emergence of RB variants. This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.

Published in Rimbaud, L., Dallot, S., Bruchou, C., Thoyer, S., Jacquot, E., Soubeyrand, S., Thébaud, G. (2019). Improving management strategies of plant diseases using sequential sensitivity analyses. Phytopathology, 109, 1184-1197. DOI:10.1094/PHYTO-06-18-0196-R; Improvement of management strategies of epidemics is often hampered by constraints on experiments at large spatiotemporal scales. A promising approach consists of modelling the biological epidemic process and human interventions, which both impact disease spread. However, few methods enable the simultaneous optimisation of the numerous parameters of sophisticated control strategies. To do so, we propose a heuristic approach (i.e., a practical improvement method approximating an optimal solution) based on sequential sensitivity analyses. In addition, we use an economic improvement criterion, based on the net present value, accounting for both the cost of the different control measures and the benefit generated by disease suppression. This work is motivated by sharka (caused by Plum pox virus ), a vector-borne disease of prunus trees (especially apricot, peach and plum) whose management in orchards is mainly based on surveillance and tree removal. We identified the key parameters of a spatiotemporal model simulating sharka spread and control, and approximated optimal values for these parameters. The results indicate that the current French management of sharka efficiently controls the disease, but can be economically improved using alternative strategies that are identified and discussed. The general approach should help policymakers to design sustainable and cost-effective strategies for disease management.

This article has an erratum: https://doi.org/10.1051/e3sconf/20198802003Présentation d'une communication à la conférence internationale i-DUST 2018 – Inter-Disciplinary Underground Science & Technology (2018/06/04-05), Avignon (FRA); International audience; Groundwater is a major source of water for irrigation of vegetables, especially in the Mediterranean basin. Contamination of aquifer by pathogens has been responsible for numerous disease outbreaks worldwide. Several studies reported that groundwater dissolved organic matter (DOM) can serve as a source of carbon and energy for heterotrophic metabolism of pathogens. In this study, we aimed to investigate the DOM composition of groundwater collected at Avignon. Six liters of groundwater were filtered (0.2 µm) and freeze-dried following appropriate cleaning procedure. The bulk analyses of powder sample were performed using 1D and 2D nuclear magnetic resonance spectroscopy and liquid chromatography coupled with mass spectroscopy. Several components were found at concentrations around 1 µM and comprise : (i) humic and fulvic acids originated from land-derived material or soils and, (ii) various acids, esters and alcohols of different sizes including acetate, lactate and formate, these may result from microbial metabolism. In conclusion, the Avignon groundwater DOM contains a heterogeneous mixture of dissolved organic components with a rather low potential bioreactivity based on the low level of labile biogeochemicals such as carbohydrates.

Cucumber vein yellowing virus (CVYV) is emerging throughout the Mediterranean Basin, where it causes important damages on cucumber and melon crops. It has been suggested that CVYV originated from the Middle East and has spread only recently to other areas. In this work, an isolate from Sudan was characterized and surveys performed in that country between 1992 and 2012 revealed a long‐term presence of CVYV with a high molecular variability, showing that the virus has long been endemic in Sub‐Saharan Africa. Comparison of the full‐length sequences of 11 CVYV isolates from different geographic origins revealed recombination events in CVYV populations from the Mediterranean Basin and the Middle East, and evidence for different selection pressures along the genome. These results shed a new light on the evolution of CVYV.

Previous studies have shown that rosemary (Rosmarinus officinalis L.) can serve as a companion plant to control Myzus persicae (Sulzer) because of the repellent effect of certain volatile organic compounds (VOCs) that it emits. In the present study, we investigated which of five clones of rosemary may reveal a repellent effect on M. persicae and aimed to determine the possible VOCs involved. Analyses of the mixtures of VOCs released by the different clones revealed the presence of 15 main components. However, each clone was characterized by a specific volatile profile showing the existence of marked chemical variability. By testing the identified VOCs individually, using a dual‐choice olfactometer, we observed that five volatiles had a significant repulsive effect on M. persicae: bornyl acetate, camphor, α‐terpineol, terpinene‐4‐ol and geranyl acetone. In addition, only one clone of rosemary elicited a significant repulsive action. Nevertheless, all of the tested clones released compounds that are repellent to the aphid when tested individually. Therefore, the emission of individual volatiles by a rosemary plant is not sufficient to elicit a repellent effect. The concentration, proportion and even the association/synergy of VOCs in the released olfactory bouquets can probably explain these contrasting results and are worthy of additional exploration in future studies.

Understanding soil fertility and leaf nutrients provides the basis for optimizing fertilization for fruit crop production. However, for central Shaanxi province of China, the largest kiwifruit-producing region in the world, limited information is available on soil fertility and leaf nutrients of these orchards. Here, we assessed 17 soil fertility parameters and 12 leaf elements for 116 kiwifruit orchards in central Shaanxi. The investigated region included five locations: Zhouzhi, Mei, Yangling, Wugong and Qishan. The soils in this region had an average pH of 7.54 and exchangeable Ca of 5.68 g/kg, indicating that the soils were calcareous. Over a quarter of the orchards were deficient in soil organic matter. Although over 50% of the soils were excessive in NO3–-N and over 25% both deficient and excessive in P and K, more than 65.0% of the orchards were deficient in leaf N, P and K, implying the low NPK use efficiency in central Shaanxi. Moreover, Cl and Zn deficiencies as well as Cu and Ca excesses were found in both soil and leaf diagnosis. Analysis of variance showed that, among the study locations, Zhouzhi was characterized by low soil pH, low soil/leaf Ca and high soil/leaf N, whereas Wugong was featured by high soil/leaf Na. Correlation analysis indicated that soil pH positively correlated with soil Ca, and both parameters negatively correlated with soil N, P, Fe, Mn, Cu and Cl (P < 0.01). Additionally, soil N, Ca, Mn and Cl positively correlated with the corresponding leaf elements (P < 0.001). These results could be used to guide the sustainable nutrient management of kiwifruit production in central Shaanxi.

Strategies to manage plant disease—from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences—all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant–microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum—more so than the separation of discrete pathotypes—and that host jumps are common. By setting the mechanisms of plant–pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.

Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.

International audience; A recommendation – based on reviews by Benoît Moury and ananonymous reviewer – of : Suffert F, Goyeau H, Sache I, Carpentier F, Gelisse S, Morais D, Delestre G. 2017.Epidemiological trade-off between intra- and interannual scales in the evolution ofaggressiveness in a local plant pathogen population. bioRxiv, 151068, ver. 3 of 12thNovember 2017. doi: 10.1101/151068

12 pages; International audience; Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.

Certain amino acids induce inhibitory effects in plant growth due to feedback inhibition of metabolic pathways. The inhibition patterns depend on plant species and the plant developmental stage. Those amino acids with inhibitory action on specific weeds could be utilized as herbicides, however, their use for weed control has not been put into practice. Orobanche minor is a weed that parasitizes red clover. O. minor germination is stimulated by clover root exudates. The subsequent seedling is an obligated parasite that must attach quickly to the clover root to withdraw its nutrients. Early development of O. minor is vulnerable to amino acid inhibition and therefore, a series of in vitro, rhizotron, and field experiments were conducted to investigate the potential of amino acids to inhibit O. minor parasitism. In in vitro experiments it was found that among a collection of 20 protein amino acids, lysine, methionine and tryptophan strongly interfere with O. minor early development. Field research confirmed their inhibitory effect but revealed that methionine was more effective than lysine and tryptophan, and that two successive methionine applications at 308 and 543 growing degree days inhibited O. minor emergence in red clover up to 67%. We investigated additional effects with potential to influence the practical use of amino acids against broomrape weeds, whether the herbicidal effect may be reversible by other amino acids exuded by host plants or may be amplified by inducing host resistance barriers against O. minor penetration. This paper suggests that amino acids may have the potential to be integrated into biorational programs of broomrape management., This work was funded by INRA ‘Division Santé des Plantes et Environnement. Appel à projets scientifiques 2015. Catégorie Biocontrôle’. MF-A was supported by the Marie-Curie FP7 COFUND People Programme, through the award of an AgreenSkills fellowship (under grant agreement n° PCOFUND-GA-2010-267196).

During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.

© 2017 The Author(s) Forest-driven water and energy cycles are poorly integrated into regional, national, continental and global decision-making on climate change adaptation, mitigation, land use and water management. This constrains humanity's ability to protect our planet's climate and life-sustaining functions. The substantial body of research we review reveals that forest, water and energy interactions provide the foundations for carbon storage, for cooling terrestrial surfaces and for distributing water resources. Forests and trees must be recognized as prime regulators within the water, energy and carbon cycles. If these functions are ignored, planners will be unable to assess, adapt to or mitigate the impacts of changing land cover and climate. Our call to action targets a reversal of paradigms, from a carbon-centric model to one that treats the hydrologic and climate-cooling effects of trees and forests as the first order of priority. For reasons of sustainability, carbon storage must remain a secondary, though valuable, by-product. The effects of tree cover on climate at local, regional and continental scales offer benefits that demand wider recognition. The forest- and tree-centered research insights we review and analyze provide a knowledge-base for improving plans, policies and actions. Our understanding of how trees and forests influence water, energy and carbon cycles has important implications, both for the structure of planning, management and governance institutions, as well as for how trees and forests might be used to improve sustainability, adaptation and mitigation efforts. publisher: Elsevier articletitle: Trees, forests and water: Cool insights for a hot world journaltitle: Global Environmental Change articlelink: http://dx.doi.org/10.1016/j.gloenvcha.2017.01.002 content_type: article copyright: © 2017 The Author(s). Published by Elsevier Ltd. ispartof: Global Environmental Change vol:43 pages:51-61 status: published

Plant pathogens can play a role in the competitive interactions between plant species and have been understudied in native prairies, which are declining globally, and in Conservation Reserve Program (CRP) lands in the United States. Barley/Cereal yellow dwarf virus (B/CYDV) are among the most economically important disease-causing agents of small grain cereal crops, such as wheat, and are known to infect over 150 Poaceae species, including many of the grass species present in prairies and CRP lands. Field surveys of Poaceae species were conducted in endangered Palouse Prairie and CRP habitats of southeastern Washington and adjacent northern Idaho, USA from 2010 to 2012 to examine for the presence of B/CYDV among plant hosts and aphid vectors. Viral species were identified via cloning and sequencing. Landscape, soil and climate data were retrieved from USDA-NASS and USDA-NRCS databases. Analyses were conducted to examine effects of diverse agroecological and environmental factors on virus prevalence. A total of 2271 grass samples representing 30 species were collected; 28 of these were infected with BYDV in at least one location. BYDV infection was detected at every CRP and prairie remnant sampled, with an overall infection of 46%. BYDV-SGV and BYDV-PAV were the only two B/CYDV species encountered, with BYDV-SGV being more prevalent. Sampling time (season) and host plant identity were the main variables explaining variation in virus prevalence among sites. BYDV was more prevalent in perennial compared to annual grass species. Aphids were encountered only once suggesting non-colonizing aphids, potentially from neighboring cereal fields, are responsible for disease spread in these habitats. BYDV prevalence increased in sampled habitats as cereal crop cover increased within a 1-km radius of a habitat patch. Results demonstrate moderate to high and persistent prevalence of BYDV in an endangered grassland habitat. Species composition and susceptibility to pathogens should be considered when creating seed mixes for CRP sites, especially in relation to agricultural crops and diseases in a region. Future work exploring host abundance, competence and habitat utilization by vectors is required to fully elucidate BYDV ecology and epidemiology in grassland habitats.

BGPI : équipe 5; The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining if there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally-intensive testing procedure, namely the Generalized Monte Carlo Plug-In test with Calibration (GMCPIC test), which is implemented in an R package available at http://dx.doi.org/10.5281/zenodo.53996. A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

Streptomyces is a genus known for its ability to protect plants against many pathogens and various strains of this bacteria have been used as biological control agents. In this study, the efficacy of Streptomyces philanthi RM-1-138, S. philanthi RL-1-178, and Streptomyce mycarofaciens SS-2-243 to control various strains of Botrytis cinerea was evaluated both in vitro and in vivo. In vitro studies using confrontation tests on PDA plates indicated that the three strains of Streptomyces spp. inhibited the growth of 41 strains of B. cinerea. Volatile compounds produced by Streptomyces spp. had an influence on the growth of ten strains of B. cinerea while its culture filtrate at low concentration (diluted at 10−3) showed a complete inhibition (100%) of spore germination of B. cinerea strain BC1. A significant protection efficacy of tomato against B. cinerea was observed on both whole plant test (57.4%) and detached leaf test (60.1%) with S. philanti RM-1-138. Moreover, this antagonistic strain had a preventive and a curative effect. These results indicated that S. philanthi RM-1-138 may have the potential to control gray mold caused by B. cinerea on tomato but further work is required to enhance its efficacy and its survival in planta.

Background and aims Plant soluble sugars, as main components of primary metabolism, are thought to be implicated in defence against pathogenic fungi. However, the function of sucrose and hexoses remains unclear. This study aimed to identify robust patterns in the dynamics of soluble sugars in sink tissues of tomato plants during the course of infection by the necrotrophic fungus Botrytis cinerea. Distinct roles for glucose and fructose in defence against B. cinerea were hypothesized. [br/] Methods We examined sugar contents and defence hormonal markers in tomato stem tissues before and after infection by B. cinerea, in a range of abiotic environments created by various nitrogen and water supplies.[br/] Key Results Limited nitrogen or water supplies increased tomato stem susceptibility to B. cinerea. Glucose and fructose contents of tissues surrounding infection sites evolved differently after inoculation. The fructose content never decreased after inoculation with B. cinerea, while that of glucose showed either positive or negative variation, depending on the abiotic environment. An increase in the relative fructose content (defined as the proportion of fructose in the soluble sugar pool) was observed in the absence of glucose accumulation and was associated with lower susceptibility. A lower expression of the salicylic acid marker PR1a, and a lower repression of a jasmonate marker COI1 were associated with reduced susceptibility. Accordingly, COI1 expression was positively correlated with the relative fructose contents 7 d after infection. [br/] Conclusions Small variations of fructose content among the sugar pool are unlikely to affect intrinsic pathogen growth. Our results highlight distinct use of host glucose and fructose after infection by B. cinerea and suggest strongly that adjustment of the relative fructose content is required for enhanced plant defence.

Post-harvest applications of UV-C radiation have proven very efficient in reducing the development of post-harvest diseases in many species including lettuce (Lactuca sativa L.). Several studies suggest that UV-C radiation is effective not only because of its disinfecting effect but also because it may stimulate plant defenses. Pre-harvest treatment with UV-C radiation may thus offer an interesting potential for lettuce protection, provided that application doses are effective while excluding any harmful effects on the plants. Here we provide evidence that 0.85 kJ m−2 and 1.70 kJ m−2 represent doses of UV-C radiation that are not deleterious for lettuce plants. We used several criteria to evaluated the effect of UV-C radiation on the plant, including histological observations; the concentration of malondialdehyde, an indicator of membrane integrity, as well as parameters derived from measurements of chlorophyll fluorescence, such as maximal efficiency of photosystem II (Fv/Fm) and the Performance Index of Strasser. We observed that a single dose of 0.85 kJ m−2 slightly increased plant resistance to grey mould (Botrytis cinerea L.) while a single dose of 1.70 kJ m−2 had the opposite effect. When a 0.85 kJ m−2 dose was applied 4 times, at two-day intervals, there was an increase in the total phenol content of leaves, and in PAL, CAT, and MDAHR activities. Leaves inoculated 2 days after the latter UV-C treatment showed significantly decreased sensitivity (−30%) when compared to the control.

Potato virus Y (PVY) is one of the rare members of the genus Potyvirus for which the genetic diversity is structured by the plant species of origin. This structure has been explained by the occurrence in some crop species of barriers to infection by PVY isolates originating from other plant species. A particularly strong barrier to infection has been shown between PVY isolates from pepper (Capsicum spp.) and potato (Solanum tuberosum). PVY isolates from potato belong mainly to clades N and O and are poorly or not infectious at all in pepper. By contrast, PVY isolates from pepper belong mainly to clade C1 and are poorly or not infectious at all in potato. Recent surveys and genetic analyses, however, have revealed that PVY isolates of clades N and/or O can be quite frequent in pepper crops. Conversely, PVY isolates of clade C1 are almost absent in potato crops. However, we showed that PVY isolates of clade C1 from pepper are infectious in a potato cultivar devoid of the resistance gene Nc tbr . It has also been shown that, among pepper, tomato and tobacco genotypes carrying eIF4E-mediated recessive resistances, PVY evolution in one crop species could favour its future adaptation to other species. Altogether, these results suggest a lack of strong barriers to PVY host change between solanaceous crops. The contrast with older studies could be due to a range of factors, including an insufficient sampling effort in previous studies (too few isolates collected and characterised, too few plant genotypes assayed), to recent changes among PVY populations and/or to the contrasted behaviour of different genotypes within a plant species upon PVY inoculation.

Camelina [i](Camelina sativa[/i] (L.) Crantz) is a re-emergent oilseed crop that is also becoming important as a model for applied projects based on studies in[i] Arabidopsis thaliana[/i], since the two species are closely related members of the tribe [i]Camelineae[/i] of the Brassicaeae. Since camelina can be transformed genetically by floral dip, genetically modified (GM) camelina is being created in many laboratories, and small-scale field trials are already being conducted in the US and Canada. Although camelina does not cross-fertilize [i]Brassica[/i] crop species, such as oilseed rape, nothing was known about its ability to cross with other members of the tribe Camelineae, which in addition to arabidopsis includes the widespread weed, shepherd's purse ([i]Capsella bursa-pastoris[/i]). We have tested the ability of camelina to cross with arabidopsis and [i]C. bursa-pastoris[/i], as well as with the more distantly related Cardamine hirsuta, tribe cardamineae. No seeds were produced in crosses with arabidopsis, and a few seeds were obtained in crosses with [i]C. hirsuta[/i], but the embryos aborted at an early stage of development. A few seeds were also obtained in crosses with[i] C. bursa-pastoris[/i], which germinated to produce plants of a phenotype intermediate to that of the parents, but the hybrids were both male and female sterile. Therefore, the likelihood of pollen-mediated gene flow from camelina to these related species is low.

We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster. The role of these polymorphisms in plant aphid/interactions remains unclear. The Vat gene structure suggests a functioning with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced during cell puncture by the aphid. A few hours later, several miRNAs are upregulated in Vat plants. Peroxidase activity increases, and callose and lignin are deposited in the walls of the cells adjacent to the stylet path, disturbing aphid behavior. In aphids feeding on Vat plants, Piwi-interacting RNA-like sequences are abundant and the levels of other miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). Resistance to viruses is qualitative and local.Durability of NLR genes is highly variable. A. gossypii clones are adapted to Vat resistance, either by introducing a new effector that interferes with the deployment of plant defenses, or by adapting to the defenses it triggered. Viruses transmitted in a non-persistent manner cannot adapt to Vat resistance. At population level, Vat reduces aphid density and genetic diversity. The durability of Vat resistance to A. gossypii populations depends strongly on the agro-ecosystem, including, in particular, the presence of other cucurbit crops serving as alternative hosts for adapted clones in fall and winter. At the crop level, Vat resistance decreases the intensity of Cucumber Mosaic Virus (CMV) and Cucurbit aphid-borne yellows virus (CABYV) epidemics. The durability of resistance to CABYV could potentially be increased if combined with Vat resistance.

International audience; Induced chemical defence is a cost-efficient protective strategy, whereby plants induce the biosynthesis of defence-related compounds only in the case of pest attack. Plant responses that are pathogen specific lower the cost of defence, compared to constitutive defence. As nitrogen availability (N) in the root zone is one of the levers mediating the concentration of defence-related compounds in plants, we investigated its influence on response traits of tomato to two pathogenic bacteria, growing plants hydroponically at low or high N supply. Using two sets of plants for each level of N supply, we inoculated one leaf of one set of plants with Pseudomonas syringae, and inoculated the stem of other set of plants with Pseudomonas corrugata. Tomato response traits (growth, metabolites) were investigated one and twelve days after inoculation. In infected areas, P. syringae decreased carbohydrate concentrations whereas they were increased by P. corrugata. P. syringae mediated a redistribution of carbon within the phenylpropanoid pathway, regardless of N supply: phenolamides, especially caffeoylputrescine, were stimulated, impairing defence-related compounds such as chlorogenic acid. Inoculation of P. syringae produced strong and sustainable systemic responses. By contrast, inoculation of P. corrugata induced local and transient responses. The effects of pathogens on plant growth and leaf gas exchanges appeared to be independant of N supply. This work shows that the same genus of plant pathogens with different infection strategies can mediate contrasted plant responses.

Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.

1.Visualisation of spatial networks based on pairwise metrics such as (dis)similarity coefficients provides direct information on spatial organization of biological systems. However, for large networks, graphical representations are often unreadable as nodes (samples), and edges (links between samples) strongly overlap. We present a new method, MAPI (Mapping Averaged Pairwise Information), allowing translation from spatial networks to variation surfaces.[br/] 2.MAPI relies on i) a spatial network in which samples are linked by ellipses and, ii) a grid of hexagonal cells encompassing the study area. Pairwise metric values are attributed to ellipses and averaged within the cells they intersect. The resulting surface of variation can be displayed as a colour map in Geographical Information System (GIS), along with other relevant layers, such as land cover. The method also allows the identification of significant discontinuity in grid cell values through a nonparametric randomisation procedure.[br/] 3.The interest of MAPI is here demonstrated in the field of spatial and landscape genetics. Using simulated test datasets, as well as observed data from three biological models, we show that MAPI is i) relatively insensitive to confounding effects resulting from isolation-by-distance (i.e. over-structuring), ii) efficient in detecting barriers when they are not too permeable to gene flow and, iii) useful to explore relationships between spatial genetic patterns and landscape features.[br/] 4.MAPI is freely provided as a PostgreSQL/PostGIS database extension allowing easy interaction with GIS or the R software and other programming languages. Although developed for spatial and landscape genetics, the method can also be useful to visualise spatial organisation from other kinds of data from which pairwise metrics can be computed.

Brown rot (BR) caused by Monilinia spp., has been an economic problem for the stone fruit market due to the dramatic losses, with the biggest losses mainly during the postharvest period. There is much literature about basic aspects of Monilinia spp. infection, which indicates that environment significantly influences its occurrence in the orchard. However, progress is needed to sustainably limit this disease: the pathogen is able to develop resistance to pesticides and most of BR resistance research programs in plant models perish. Solving this problem becomes important due to the need to decrease chemical treatments and reduce residues on fruit. Thus, research has recently increased, exploring a wide range of disease control strategies (e.g. genetic, chemical, physical). Summarizing this information is difficult, as studies evaluate different Monilinia and Prunus model species, with diverse strategies and protocols. Thus, the purpose of this review is to present the diversity and distribution of agents causing BR, focusing on the biochemical mechanisms of Monilinia spp. infection both of the fungi and of the fruit, and report on the resistance sources in Prunus germplasm. In this review, we comprehensively compile the information currently available to better understand mechanisms related to BR resistance.

International audience; Human population migrations, as well as long-distance trade activities, have been responsible for the spread of many invasive organisms. The black rat, Rattus rattus, has colonized most of the world following ship-mediated trade. Owing to its tight association with human infrastructures, this species has been able to survive in unfavourable environments, such as Sahelian Africa. In this work, we combined interview-based and population genetic surveys to investigate the processes underlying the ongoing invasion of southwestern Niger by black rats, with special emphasis on the capital city, Niamey. Our trapping and interview data are quite congruent, and all together point towards a patchy, but rather widespread, current distribution of R. rattus. Genetic data strongly suggest that road network development for truck-based commercial flow from/to international harbours located in neighbouring countries (Benin, Togo, and Nigeria) facilitates the passive dispersal of black rats over a long distance through unfavourable landscapes. Another potentially, more ancient, invasion route may be associated with boat transport along the Niger River. Human-mediated dispersal thus probably allows the foundation of persisting populations within highly anthropized areas while population dynamics may be more unstable in remote areas and mostly depends on propagule pressure.

During a survey conducted in Sudan in 2012, a virus with spherical particles was isolated from a squash plant showing chlorotic leaf spots. The virus was transmitted mechanically and by two whitefly species, but not by aphids. RT-PCR with generic torradovirus primers yielded a band of expected size from total RNA of a symptomatic plant. Next-generation sequencing confirmed that this is tentatively a new torradovirus, for which we propose the name 'squash chlorotic leaf spot virus'. Using specific RT-PCR primers, the virus was detected in cucurbit samples collected since 1992 at different locations in Sudan.

International audience; Botrytis cinerea is able to build-up resistance to pyrrolnitrin, an antibiotic produced by diverse biocontrol agents, possibly compromising the durability of this method of disease control. The development of two near-isogenic lines of B. cinerea differing in their level of resistance to pyrrolnitrin was compared in tomato plants and on PDA medium. In tomato plants, significant differences in the percentage of infected petioles 1 day after inoculation and in symptom progression on petioles and stems were observed between the resistant mutant and the sensitive wild-type parent, suggesting a difference in their level of aggressiveness. Cytohistological investigations revealed that conidia of both near-isogenic lines germinated 6 h after inoculation and mycelium developed within petiole tissues 12 h after inoculation. However, while the wild-type parent isolate spread throughout the petiole and rapidly invaded the stem tissues via the leaf-abscission zone 72 h after inoculation, the pyrrolnitrin-resistant mutant failed to extend beyond petiole tissues to invade the stem. Moreover, 72 h after inoculation, the mycelial development of the pyrrolnitrin-resistant mutant was accompanied by abnormal glycogen accumulation and chlamydospore-like cell formation. In contrast, wild-type parent mycelium was normally structured with intensive colonization of stem tissues. Additionally, on PDA medium the mycelium of the pyrrolnitrin-resistant mutant was less vigorous than the wild-type isolate. These results suggest that the acquisition of pyrrolnitrin-resistance in B. cinerea is accompanied by changes in mycelial structure and reduction in mycelial growth, leading to a noticeable loss of aggressiveness on tomato plants.

In the evaluation of the potential impacts of first-generation genetically modified (GM) crops, one of the most complex issues has been whether the expression of viral sequences would lead to the emergence of novel viruses, which could occur through recombination between transgene mRNA and that of an infecting non-target virus. Here, we examine this issue, focusing on Cucumber mosaic virus (CMV), which is a particularly pertinent choice, as it is both a major plant pathogen and also the virus with which this question has been studied in the most detail. Using recent results on recombination in CMV, we employ a novel framework giving particular prominence to the formulation of the risk hypothesis and to hypothesis testing via examination of the potential pathway to harm. This allows us to conclude with greater certainty that the likelihood of this potential harm, the emergence of novel viruses, is low.

Grey mould is a worldwide disease on many economically important crops. It is caused by two fungal species, [i]Botrytis cinerea[/i] and[i] B. pseudocinerea[/i], which are mainly airborne dispersed. Although several studies have considered the abundance of airborne inoculum of [i]B. cinerea[/i] in models forecasting the risk of grey mould epidemics, the genetic characteristics of this inoculum are poorly known. In the present study, airborne inoculum of [i]B. cinerea[/i] and [i]B. pseudocinerea[/i] was collected on 29 dates over a 2.5-year period on a site in south-eastern France. The 683 sampled isolates were genotyped with nine microsatellites markers, and 616 were identified as [i]B. cinerea[/i]. The genetic structure of[i] B. cinerea[/i] airborne inoculum was inferred with Bayesian assignment tests. Eight genetic clusters were identified. Cluster abundance showed temporal variation and was statistically linked to the season (P = 0.0009) and the origin of air masses (P < 0.0001). The proportion of isolates belonging to the species[i] B. pseudocinerea[/i] was equal to 9.8 % on average, but it showed temporal variation; it tended to be higher in winter. This study is the first to provide information about the genetic characteristics of airborne inoculum of[i] B. cinerea[/i] and [i]B. pseudocinerea[/i] and to bring evidence of relationship with seasons, meteorological parameters and with the origin of air masses.

Communication orale non invitée à la conférence : 2. International Symposium on Organic Greenhouse Horticulture, Avignon, France, 28-31/10/2013; International audience; The environment of greenhouses is commonly modified to reduce the pressure of pests and diseases, but it can also be exploited to stimulate natural defences of plants. In addition to genetic influences, several agronomic factors can be used as levers to increase the concentrations of secondary metabolites involved in the defence of fruit and vegetable crops. Many secondary metabolites involved in plant defences are also phytonutrients, i.e. compounds that have beneficial effects on human health, including protection against cardiovascular diseases, cancers, and metabolic or neurodegenerative diseases. Nitrogen deprivation, photooxidative stress and exposure to specific wavelengths such as those supplied by UV radiations are well known for stimulating the production of secondary metabolites in a large range of plants. We propose here a review of factors meeting the specifications of organic farming, which are both effective and applicable in greenhouse conditions. Among all these factors, mild stress and innovative covering materials emerge as especially promising.

UMR 1334 AGAP : Equipe AFEF ‘Architecture et fonctionnement des espèces fruitières’ ; Team AFFS ‘Architecture and Functioning of Fruit Species’; Current commercial apple growing is highly dependent on off-farm inputs and it is urgent to develop new strategies to remedy this situation. The challenge for the future is to achieve lower-input apple orchards, whether under Integrated Fruit Production (IFP) or Organic Fruit Production (OFP) systems. This paper analyses the different agronomic factors that play key roles both in the current and future ‘More Sustainable Orchard’, with particular attention on plant protection. Firstly, the concept of ‘ideotype’ is developed, emphasizing the most important characteristics of optimal ideotypes for apple. Secondly, current knowledge on the relationships between genotype, cultural practices and the environment is presented and discussed. This paper deals with properties that need to be combined at plant material and orchard levels to optimise the IFP and OFP low-input systems. The focus is on: (a) the main characteristics of apple ideotypes; (b) breeding strategies; and (c) adapted cultural practices and control measures in the orchards.

Background: In order to select for quantitative plant resistance to pathogens, high throughput approaches that can precisely quantify disease severity are needed. Automation and use of calibrated image analysis should provide more accurate, objective and faster analyses than visual assessments. In contrast to conventional visible imaging, chlorophyll fluorescence imaging is not sensitive to environmental light variations and provides single-channel images prone to a segmentation analysis by simple thresholding approaches. Among the various parameters used in chlorophyll fluorescence imaging, the maximum quantum yield of photosystem II photochemistry (Fv/Fm) is well adapted to phenotyping disease severity. Fv/Fm is an indicator of plant stress that displays a robust contrast between infected and healthy tissues. In the present paper, we aimed at the segmentation of Fv/Fm images to quantify disease severity., Results: Based on the Fv/Fm values of each pixel of the image, a thresholding approach was developed to delimit diseased areas. A first step consisted in setting up thresholds to reproduce visual observations by trained raters of symptoms caused by Xanthomonas fuscans subsp. fuscans (Xff) CFBP4834-R on Phaseolus vulgaris cv. Flavert. In order to develop a thresholding approach valuable on any cultivars or species, a second step was based on modeling pixel-wise Fv/Fm-distributions as mixtures of Gaussian distributions. Such a modeling may discriminate various stages of the symptom development but over-weights artifacts that can occur on mock-inoculated samples. Therefore, we developed a thresholding approach based on the probability of misclassification of a healthy pixel. Then, a clustering step is performed on the diseased areas to discriminate between various stages of alteration of plant tissues. Notably, the use of chlorophyll fluorescence imaging could detect pre-symptomatic area. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R., Conclusions: In this paper, we describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R downloadable at http://www.r-project.org/. The R script is available at http://lisa.univ-angers.fr/PHENOTIC/telechargements.html.

International audience; Cucumber mosaic virus is one of the most prevalent viruses in Tunisian pepper crops, where it has been detected in 68% of plants developing mosaic symptoms, making it essential to characterize the molecular and biological properties of local CMV populations. Two hundred and seventy-eight isolates collected in the late 1990s, 2006 and 2008–2010 were characterized genetically. Isolates belonging to the three phylogenetic subgroups of CMV (IA, IB and II) were detected, but surprisingly, 90% of the isolates were reassortants between subgroups IA and IB, with two predominant haplotypes, IB-IA-IA and IB-IA-IB (nomenclature according to the subgrouping of the three genomic RNAs). The IB-IA-IA haplotype was present in all regions surveyed, while IB-IA-IB was observed only in northern Tunisia. This situation was unexpected, because CMV reassortants were previously thought to be counterselected in nature, and this raises the questions of the origin of IB strains in Tunisia and of the widespread distribution of these two reassortant types. Phylogenetic studies revealed low diversity within haplotypes, whatever the locality or the year of sampling. However, analysis of haplotype frequencies revealed a high genetic differentiation between CMV populations, which was better explained by the localities of sampling than by years. Geographic distances affected the differentiation of CMV populations, mainly between north and central Tunisia. When tested against a polygenic resistance to CMV movement in pepper, 55 of 57 isolates tested were able to break the resistance, indicating that this resistance would not be useful for controlling CMV in Tunisian pepper fields.

Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts., Author Summary Natural selection and genetic drift drive the evolution of virus populations within their hosts and therefore influence strongly virus emergences. To help predict future virus emergences, we developed a model that estimates simultaneously genetic drift and selection intensities using high-throughput sequence data representing the within-host population dynamics of Potato virus Y variants differing at most by two substitutions involved in pathogenicity properties. The competitiveness costs induced by these mutations as well as the mathematical expressions of the competition coefficients of virus variants were derived from Lotka–Volterra equations. High genetic differentiation of virus populations between hosts was evidenced as well as its hump-shaped behaviour with time. The modelling framework proposed here was intended to help design control strategies aiming to prevent virus emergences.

Many studies from the last decades have shown that airborne microorganisms can be intrinsically linked to atmospheric processes. Certain bacteria may constitute the most active ice nuclei found in the atmosphere and might have some influence on the formation of ice crystals in clouds. This study deals with the ice nucleation activity of Pseudomonas syringae inside of thunderstorms through numerical simulations using BRAMS (Brazilian Regional Atmospheric Model System). The numerical simulations were developed in order to investigate the effect on the total amount of rainwater as a function of ice nuclei (IN) P. syringae concentrations with different scenarios (classified as S2 to S4 scenarios) corresponding to a maximum of 102 to 104 IN bacteria per liter of cloud water plus the BRAMS default (classified as S5 scenario). Additionally, two other scenarios were included without any IN (S1) and the sum of RAMS default and S4 scenario (classified as S6). The chosen radiosonde data is for 3 March 2003, typical summertime in São Paulo City which presents a strong convective cell. The objective of the simulations was to analyze the effect of the IN concentrations on the BRAMS modeled cloud properties and precipitation. The simulated electrification of the cloud permitted analysis of the total flashes estimated from precipitable and non-precipitable ice mass fluxes in two different lightning frequencies. Among all scenarios, only S4 and S6 presented a tendency to decrease the total cloud water, and all bacteria scenarios presented a tendency to decrease the total amount of rain (−8%), corroborating other reports in the literature. All bacteria scenarios also present higher precipitable ice concentrations compared to S5 scenario, the RAMS default. The main results present the total flash number per simulation as well. From the results, the total flash numbers, from both lightning frequencies, in S4 and S6 scenarios, are from 3.1 to 3.7 higher than the BRAMS default. Even the lower bacterial concentrations (scenarios S2 and S3) produced 3 time higher number of flashes, compared to S5 scenario. This result is a function of the hydrometeors in each simulation. In conclusion, IN bacteria could affect directly the thunderstorm structure and lightning formation with many other microphysical implications.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Adaptation of populations to new environments is frequently costly due to trade-offs between life history traits, and consequently, parasites are expected to be locally adapted to sympatric hosts. Also, during adaptation to the host, an increase in parasite fitness could have direct consequences on its aggressiveness (i.e. the quantity of damages caused to the host by the virus). These two phenomena have been observed in the context of pathogen adaptation to host's qualitative and monogenic resistances. However, the ability of pathogens to adapt to quantitative polygenic plant resistances and the consequences of these potential adaptations on other pathogen life history traits remain to be evaluated. Potato virus Y and two pepper genotypes (one susceptible and one with quantitative resistance) were used, and experimental evolutions showed that adaptation to a quantitative resistance was possible and resulted in resistance breakdown. This adaptation was associated to a fitness cost on the susceptible cultivar, but had no consequence either in terms of aggressiveness, which could be explained by a high tolerance level, or in terms of aphid transmission efficiency. We concluded that quantitative resistances are not necessarily durable but management strategies mixing susceptible and resistant cultivars in space and/or in time should be useful to preserve their efficiency.

International audience; The deployment of resistant crops often leads to the emergence of resistance-breaking pathogens that suppress the yield benefit provided by the resistance. Here, we theoretically explored how farmers' main leverages (resistant cultivar choice, resistance deployment strategy, landscape planning and cultural practices) can be best combined to achieve resistance durability while minimizing yield losses as a result of plant viruses. Assuming a gene-for-gene type of interaction, virus epidemics are modelled in a landscape composed of a mosaic of resistant and susceptible fields, subjected to seasonality, and a reservoir hosting viruses year-round. The model links the genetic and the epidemiological processes, shaping at nested scales the demogenetic dynamics of viruses. The choice of the resistance gene (characterized by the equilibrium frequency of the resistance-breaking virus at mutation-selection balance in a susceptible plant) is the most influential leverage of action. Our results showed that optimal strategies of resistance deployment range from 'mixture' (where susceptible and resistant cultivars coexist) to 'pure' strategies (with only resistant cultivar) depending on the resistance characteristics and the epidemiological context (epidemic incidence and landscape connectivity). We demonstrate and discuss gaps concerning virus epidemiology across the agro-ecological interface that must be filled to achieve sustainable disease management.

To establish a baseline sensitivity of Botrytis cinerea to pyrrolnitrin, an antibiotic produced by several biological control agents, 204 isolates were tested for sensitivity to pyrrolnitrin using a spore germination assay. The results showed that the isolates exhibited a wide range of sensitivity to pyrrolnitrin, with an 8.4-fold difference in EC50 (effective concentration to reduce spore germination by 50% comparing to the control) values between the least and the most sensitive isolates. The model-based clustering analysis indicates that the distribution of the EC50 values best fit a normal mixture model with three components and unequal variance. The less sensitive isolates were also multidrug resistant isolates. The efficacy of the pyrrolnitrin-producing Pseudomonas chlororaphis ChPhzS24 strain was tested in vitro and on tomato plants with isolates of B. cinerea having different EC50 values. Whatever the EC50 value of the isolates tested, no significant differences in sensitivity were observed towards this bacterium indicating an absence of resistance to this biological control agent within B. cinerea isolates and suggesting also that additional mechanisms of action are probably operated by this biological control agent.

Étude menée par l’Inra à la demande du ministère de l’Écologie, de l’Énergie, du Développement durable et de la Mer et du ministère de l’Alimentation, de l’Agriculture et de la Pêche; La loi de programmation relative au Grenelle de l’environnement fixe l’objectif de réduire de moitié les usages des produits phytopharmaceutiques en 10 ans en accélérant la diffusion de méthodes alternatives sous réserve de leur mise au point. Dès 2007, à la demande des ministères en charge de l’environnement et de l’agriculture, l’Inra a lancé une étude sur les itinéraires culturaux économes en pesticides. Quatre filières ont été prises en compte : grandes cultures, arboriculture fruitière, viticulture et cultures légumières. Pour chacune d’elles, différentes stratégies de limitation du recours aux produits phytosanitaires ont été analysées, au vu des connaissances disponibles. L’impact économique et environnemental du recours à ces stratégies a été évalué, au niveau national (en France métropolitaine), pour différents scénarios. L’étude comporte également une analyse des jeux d’acteurs en amont et en aval des filières agricoles face à la réduction d’usage des pesticides. L'étude a par ailleurs défini les modalités de conception d’un réseau d’acquisition et de diffusion de références agronomiques. Ces résultats seront mobilisés pour la mise en place du réseau de fermes de références, d’expérimentation et de démonstration prévu par le plan ministériel Ecophyto 2018. Ecophyto R&D a mobilisé une centaine d’experts issus de plus de 30 organismes, parmi lesquels l'Inra, des établissement d'enseignement supérieur, des orgnaismes de développement agricole, les services techniques des ministère, etc. Les résultats ont pour fonction d'éclairer la décision publique et d'identifier des moyens pour la mettre en oeuvre. Ils ne constituent pas une source directement utilisable pour piloter des changements techniques au niveau local ou au niveau d'une exploitation agricole.

The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of Snomax™ were investigated in the temperature range between −5 and −15°C. Water suspensions of these bacteria were directly sprayed into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of −5.7°C. At this temperature, about 1% of the Snomax™ cells induced immersion freezing of the spray droplets before the droplets evaporated in the cloud chamber. The living cells didn't induce any detectable immersion freezing in the spray droplets at −5.7°C. After evaporation of the spray droplets the bacterial cells remained as aerosol particles in the cloud chamber and were exposed to typical cloud formation conditions in experiments with expansion cooling to about −11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets. Then, only a minor fraction of the cells acted as heterogeneous ice nuclei either in the condensation or the immersion mode. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between −7 and −11°C with an ice nucleation (IN) active fraction of the order of 10−4. In agreement to previous literature results, the ice nucleation efficiency of Snomax™ cells was much larger with an IN active fraction of 0.2 at temperatures around −8°C.

A cloud modeling framework is described to simulate ice nucleation by biogenic aerosol particles, as represented by airborne ice-nucleation active (INA) bacteria. It includes the empirical parameterization of heterogeneous ice nucleation. The formation of cloud liquid by soluble material coated on such insoluble aerosols is represented and determines their partial removal from deep convective clouds by accretion onto precipitation. Preliminary simulations are performed for a case of deep convection over Oklahoma. If present at high enough concentrations, as might occur in proximity to land sources, INA bacteria are found to influence significantly: – (1) the average numbers and sizes of crystals in the clouds; (2) the horizontal cloud coverage in the free troposphere; and (3) precipitation and incident solar insolation at the surface, which influence rates of bacterial growth. At lower concentrations, the corresponding responses of cloud fields appear much lower or are ambiguous. In nature, the growth rates of INA bacteria on leaves prior to emission into the atmosphere are known to be highly dependent on temperature, precipitation and plant species. Consequently, the open question emerges of whether emissions of such ice-nucleating biogenic particles can then be modified by their own effects on clouds and atmospheric conditions, forming a weak feedback in climate or microclimate systems.

For the past 200 years, the field of aerobiology has explored the abundance, diversity, survival and transport of micro-organisms in the atmosphere. Micro-organisms have been explored as passive and severely stressed riders of atmospheric transport systems. Recently, an interest in the active roles of these micro-organisms has emerged along with proposals that the atmosphere is a global biome for microbial metabolic activity and perhaps even multiplication. As part of a series of papers on the sources, distribution and roles in atmospheric processes of biological particles in the atmosphere, here we describe the pertinence of questions relating to the potential roles that air-borne micro-organisms might play in meteorological phenomena. For the upcoming era of research on the role of air-borne micro-organisms in meteorological phenomena, one important challenge is to go beyond descriptions of abundance of micro-organisms in the atmosphere toward an understanding of their dynamics in terms of both biological and physico-chemical properties and of the relevant transport processes at different scales. Another challenge is to develop this understanding under contexts pertinent to their potential role in processes related to atmospheric chemistry, the formation of clouds, precipitation and radiative forcing. This will require truly interdisciplinary approaches involving collaborators from the biological and physical sciences, from disciplines as disparate as agronomy, microbial genetics and atmosphere physics, for example.

Dicarboximides and phenylpyrroles are commonly used fungicides against plant pathogenic ascomycetes. Although their effect on fungal osmosensing systems has been shown in many studies, their modes-of-action still remain unclear. Laboratory- or field-mutants of fungi resistant to either or both fungicide categories generally harbour point mutations in the sensor histidine kinase of the osmotic signal transduction cascade. In the present study we compared the mechanisms of resistance to the dicarboximide iprodione and to pyrrolnitrin, a structural analogue of phenylpyrrole fungicides, in Botrytis cinerea. Pyrrolnitrin-induced mutants and iprodione-induced mutants of B. cinerea were produced in vitro. For the pyrrolnitrin-induced mutants, a high level of resistance to pyrrolnitrin was associated with a high level of resistance to iprodione. For the iprodione-induced mutants, the high level of resistance to iprodione generated variable levels of resistance to pyrrolnitrin and phenylpyrroles. All selected mutants showed hypersensitivity to high osmolarity and regardless of their resistance levels to phenylpyrroles, they showed strongly reduced fitness parameters (sporulation, mycelial growth, aggressiveness on plants) compared to the parental phenotypes. Most of the mutants presented modifications in the osmosensing class III histidine kinase affecting the HAMP domains. Site directed mutagenesis of the bos1 gene was applied to validate eight of the identified mutations. Structure modelling of the HAMP domains revealed that the replacements of hydrophobic residues within the HAMP domains generally affected their helical structure, probably abolishing signal transduction. Comparing mutant phenotypes to the HAMP structures, our study suggests that mutations perturbing helical structures of HAMP2-4 abolish signal-transduction leading to loss-of-function phenotype. The mutation of residues E529, M427, and T581, without consequences on HAMP structure, highlighted their involvement in signal transduction. E529 and M427 seem to be principally involved in osmotic signal transduction.