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The plant plasma membrane (PM) plays a key role in nutrition, cell homeostasis, perception of environmental signals, and set-up of appropriate adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is thus necessary to understand how its individual components, the way they are organized and interact together, allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome fromArabidopsis thalianasuspension cell culture. We identified a core set of 2,165 proteins (406 of which had not been shown associated to PM previously), which is by far the largest set of available data concerning the plant PM proteome. Using the same samples, we combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 405 molecular species of lipids. We showed that the different classes of lipids (sterols, phospholipids, and sphingolipids) were present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were then determined, allowing us to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids (for instance fatty acyl chain length and saturation according to the polar head). Results obtained are consistent with plant PM being an ordered mosaic of domains and point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport or signaling have been identified and put in perspective of the lipids with which they are associated. All these results provide an overall view of both the organization and the functioning of the PM.

Under agroforestry practices, inter-specific facilitation between tree rows and cultivated alleys occurs when plants increase the growth of their neighbours especially under nutrient limitation. Due to a coarse roots architecture limiting soil inorganic phosphate (Pi) uptake, walnut trees (Juglansspp.) exhibit dependency on soil-borne symbiotic arbuscular mycorrhizal fungi that extend extra-radical hyphae beyond the root Pi depletion zone. To investigate the benefits of mycorrhizal walnuts in alley cropping, we experimentally simulated an agroforestry system in which walnut rootstocks RX1 (J. regiaxJ. microcarpa) were connected or not by a common mycelial network (CMN) to maize plants grown under two contrasting Pi levels. Mycorrhizal colonization parameters showed that the inoculum reservoir formed by inoculated walnut donor saplings allowed the mycorrhization of maize recipient roots. Relative to non-mycorrhizal plants and whatever the Pi supply, CMN enabled walnut saplings to access maize Pi fertilization residues according to significant increases in biomass, stem diameter and expression ofJrPHT1;1andJrPHT1;2, two mycorrhiza-inducible phosphate transporter candidates here identified by phylogenic inference of orthologs. In the lowest Pi supply, stem height, leaf Pi concentration and biomass of RX1 were significantly higher than in non-mycorrhizal controls, showing that mycorrhizal connections between walnut and maize roots alleviated Pi deficiency in the mycorrhizal RX1 donor plant. Under Pi limitation, maize recipient plants also benefited from mycorrhization relative to controls, as inferred from larger stem diameter and height, biomass, leaf number, N content and Pi concentration. Mycorrhization-induced Pi uptake generated a higher carbon cost for donor walnut plants than for maize plants by increasing walnut plant photosynthesis to provide the AM fungus with carbon assimilate. Here we show for the first time that CMN alleviates Pi deficiency in co-cultivated walnut and maize plants, and may therefore contribute to limit the use of chemical P fertilizers in agroforestry systems.

Abiotic factors have long been recognised as important factors in structuring microbial diversity and species associations, among which topography and hydro-geomorphic flows have an impact from plot to large scale. These factors are deeply involved in the dynamics of climate change. However, the actual impact of topography on microbial communities in spatially defined habitats remains unclear and, needing further development, represents a promising branch to investigate microbiological assets in the environment. In this study, we analysed a parcel in continental France which revealed a combined action of hydro-geomorphic fluxes and topography in structuring microbial assemblages. Species-habitat occurrence seems to respond to the effective energy locally displayed by fluxes. Largest richness and microbial variety occurred where fluxes are small such as on limited slope or reduced runoff concentrations. Species dominance was higher in zones with higher fluxes suggesting: 1) an impoverishment of the more sensible species, or 2) a selective adaptation of the most resistant species. This differentiation was evidenced by analysing the potential impact of topography and cumulated fluxes for runoff and sediments (i.e., WTI, LS RUSLE indexes) on microbial richness, dominance, and abondance at Phylum and Class levels.

The use of ensemble prediction systems (EPS) is challenging because of the huge information it provides. Forecasts from ensemble prediction systems (EPS) are often summarised by statistical quantities (ie quantiles maps). Although such mathematical representation is efficient for capturing the ensemble distribution, it lacks physical consistency, which raises issues for many applications of EPS in an operational context. In order to provide a physically-consistent synthesis of the French convection-permitting AROME-EPS forecasts, we propose to automatically draw a few scenarios that are representative of the different possible outcomes. Each scenario is a reduced set of EPS members.To design a scenario synthesis, the procedure can be divided into two parts. A first step aims at extracting relevant features in each EPS member in order to reduce the problem dimensionality. Then, a clustering is done based on these features.The originality of our work is to leverage the capacities of deep learning for the features extraction. For that purpose, we use a convolutional autoencodeur (CAE) to learn an optimal low-dimensional representation (also called latent space representation) of the input forecast field. In this work, the algorithm is developed to work on 1h-accumulated rainfall from AROME-EPS, with a focus on convective cases.The CAE is trained on around 150 000 forecasts and its performance is evaluated based on the quality of the reconstructed input fields from the latent space. To examine the reconstruction quality, an object-oriented approach is used. CAE is also compared with the commonly-used principal component analysis (PCA). In a second part, different clustering methods (kmeans, HDBSCAN, …) are applied to EPS members in the latent space and evaluated using subjective and objective diagnostics.

International audience; Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations. Crop domestication events led to spectacular modifications of plant traits increasing their suitability to human requirements. Cereals and especially wheat have been domesticated in the Middle East 1. Domestication process led to dramatic phenotypic changes in cultivated species in relation to cultivation conditions and human needs. The Domestication syndrome 2 refers to the whole set of phenotypic changes occurred during this process, including: loss of dormancy, increasing seed size, modifying seed dispersal mode and apical dominance as well photoperiod sensitivity. open

Native arbuscular mycorrhizal fungi (AMF) associated to cassava (Manihot esculenta), a globally important food crop have been shown to enhance its growth, nutrition and productivity. In order to better characterize levels of AMF diversity and identify species relevant to cassava productivity, deeper sequencing depth of cassava field soils is needed. In this paper, we hypothesise that community composition could be linked to specific edaphic factors within contrasted soils. The arbuscular mycorrhizal fungi (AMF) communities of Manihot esculenta rhizosphere soils was investigated by Illumina MiSeq technology. We analyzed the possible correlation between soil characteristics and AMF community composition in cassava field soils within three different agro-ecological zones. Principal Coordinate Analysis (PCoA) and Permutational Multivariate Analysis of Variance were used to test the relative contribution of each agro-ecological zone in explaining the variation in AMF community composition within cassava field soils. Pearson correlations were used to identify the soil properties that significantly explained AMF community compositions within the three zones. The results have shown that despite the fact that the three zones exhibited contrasted soils, AMF community in cassava field soils was dominated by Glomeraceae (Rhizophagus, Glomus, Funneliformis and Septoglomus), with Rhizophagus as the most dominant core genus. Soil type determined the distribution of AMF communities in cassava field soils, and this effect was attributed to soil properties related to organic matter, three micronutrients (available phosphorus, Ca2+, Mg2+), V% and clay. It was shown that high available phosphorus contents (50-100ppm) reduce diversity but did not affect the dominance of the genus Rhizophagus.

During arbuscular mycorrhizal symbiosis, arbuscule-containing root cortex cells display a proliferation of plastids, a feature usually ascribed to an increased plant anabolism despite the lack of studies focusing on purified root plastids. In this study, we investigated mycorrhiza-induced changes in plastidic pathways by performing a label-free comparative subcellular quantitative proteomic analysis targeted on plastid-enriched fractions isolated from Medicago truncatula roots, coupled to a cytological analysis of plastid structure. We identified 490 root plastid protein candidates, among which 79 changed in abundance upon mycorrhization, as inferred from spectral counting. According to cross-species sequence homology searches, the mycorrhiza-responsive proteome was enriched in proteins experimentally localized in thylakoids, whereas it was depleted of proteins ascribed predominantly to amyloplasts. Consistently, the analysis of plastid morphology using transmission electron microscopy indicated that starch depletion associated with the proliferation of membrane-free and tubular membrane-containing plastids was a feature specific to arbusculated cells. The loss of enzymes involved in carbon/nitrogen assimilation and provision of reducing power, coupled to macromolecule degradation events in the plastid-enriched fraction of mycorrhizal roots that paralleled lack of starch accumulation in arbusculated cells, lead us to propose that arbuscule functioning elicits a nutrient starvation and an oxidative stress signature that may prime arbuscule breakdown.

SPE IPM INRA UB; International audience; In arbuscular mycorrhizal (AM) roots, the plasma membrane (PM) of the host plant is involved in all developmental stages of the symbiotic interaction, from initial recognition to intracellular accommodation of intra-radical hyphae and arbuscules. Although the role of the PM as the agent for cellular morphogenesis and nutrient exchange is especially accentuated in endosymbiosis, very little is known regarding the PM protein composition of mycorrhizal roots. To obtain a global overview at the proteome level of the host PM proteins as modified by symbiosis, we performed a comparative protein profiling of PM fractions from Medicago truncatula roots either inoculated or not with the AM fungus Rhizophagus irregularis. PM proteins were isolated from root microsomes using an optimized discontinuous sucrose gradient; their subsequent analysis by liquid chromatography followed by mass spectrometry (MS) identified 674 proteins. Cross-species sequence homology searches combined with MS-based quantification clearly confirmed enrichment in PM-associated proteins and depletion of major microsomal contaminants. Changes in protein amounts between the PM proteomes of mycorrhizal and non-mycorrhizal roots were monitored further by spectral counting. This workflow identified a set of 82 mycorrhiza-responsive proteins that provided insights into the plant PM response to mycorrhizal symbiosis. Among them, the association of one third of the mycorrhiza-responsive proteins with detergent-resistant membranes pointed at partitioning to PM microdomains. The PM-associated proteins responsive to mycorrhization also supported host plant control of sugar uptake to limit fungal colonization, and lipid turnover events in the PM fraction of symbiotic roots. Because of the depletion upon symbiosis of proteins mediating the replacement of phospholipids by phosphorus-free lipids in the plasmalemma, we propose a role of phosphate nutrition in the PM composition of mycorrhizal roots.

International audience; The complexity of Multi-Agent Systems is constantly increasing. With the growth of the number of agents, interactions between them draw complex and huge conversations. In this paper, we present a knowledge discovery process based on conversation mining and used to infer conversation models. Conversations are made up of sequences of messages exchanged inside the system. In order to discover the underlying conversation models that agents use while interacting with each other, we apply stochastic grammatical inference techniques on the conversations. We present some experiments that show the process we design is a good candidate to equip agents with the capacity to learn to interact.

Dans le cadre du projet Holoviti (Plan National Dépérissement du Vignoble), l’holobionte vigne est étudié, dans le continuum sol - racines - parties aériennes (SRP), chez des ceps symptomatiques (S) ou asymptomatiques (AS) de la forme lente d’esca (tigrures foliaires). Ces recherches ont été réalisées sur une parcelle du château de Marsannay, située sur la commune de Couchey en Côte d’Or (21). Celle-ci a été choisie car elle présente simultanément trois types de dépérissements : deux liés à des agents pathogènes, respectivement viraux (agent du court-noué) et fongiques (agents de l’esca), et un lié à des dysfonctionnements physiologiques (porte-greffe 161-49C). Cette parcelle a été cartographiée et suivie cep à cep en 2019 et 2020. Le prélèvement des échantillons des différents compartiments a été réalisé en septembre, à l’apparition des symptômes d’esca, sur 8 couples de ceps (AS et S) de même âge. Les ceps AS et S de chaque couple sont voisins (même environnement) et les différents couples sont dispersés au sein de la parcelle. Quatre analyses complémentaires ont été réalisées : (i) de la métagénomique, pour mettre en évidence de évènements de co-occurence ou de co-exclusion de certaines espèces selon que les ceps sont AS ou S ; (ii) de la transcriptomique, pour définir comment les communautés répondent à leur environnement ; (iii) de la métabolomique, indicateur le plus direct de la santé des plantes ; ainsi que (iv) des dosages enzymatiques, pour évaluer l’état de stress (notamment oxydatif) de la vigne. Dans le cadre de l’analyse métagénomique (ciblée), les amorces choisies ont visé les communautés bactériennes, fongiques (avec pour le compartiment racinaire un focus sur les communautés mycorhiziennes) et les oomycètes. Les résultats de l’analyse des communautés bactériennes dans le continuum SRP pour le millésime 2019 révèlent une baisse de la diversité spécifique (Indice de Shannon) le long de ce dernier. On retrouve une trentaine d’embranchements de bactéries répartis sur l’ensemble des compartiments. Les compartiments « sol », « racines » et « feuilles » apparaissent différents entre eux mais cette première analyse ne permet pas de discriminer les ceps AS des individus S. Pour les compartiments « bois de greffon » et « sarments » l’étude de l’abondance des communautés bactériennes révèle des tendances (des communautés plus ou moins abondantes, voire absentes chez les ceps S), qui seront à confirmer sur le millésime 2020.Ces premiers résultats, devront également être complétés par l’analyse des autres microbiotes (champignons et oomycètes). De plus, dans l’objectif d’appréhender le fonctionnement (ou dysfonctionnement) de l’holobionte vigne, ils devront également être rapportés aux indicateurs de fonctionnement de la plante (analysés conjointement).