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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.

Bow echoes (BEs) are bow-shaped lines of convective cells that are often associated with swaths of damaging straight-line winds and small tornadoes. This paper describes a convolutional neural network (CNN) able to detect BEs directly from French kilometer-scale model outputs in order to facilitate and accelerate the operational forecasting of BEs. The detections are only based on the maximum pseudoreflectivity field predictor (“pseudo” because it is expressed in mm h−1 and not in dBZ). A preprocessing of the training database is carried out in order to reduce imbalance issues between the two classes (inside or outside bow echoes). A CNN sensitivity analysis against a set of hyperparameters is done. The selected CNN configuration has a hit rate of 86% and a false alarm rate of 39%. The strengths and weaknesses of this CNN are then emphasized with an object-oriented evaluation. The BE largest pseudoreflectivities are correctly detected by the CNN, which tends to underestimate the size of BEs. Detected BE objects have wind gusts similar to the hand-labeled BE. Most of the time, false alarm objects and missed objects are rather small (e.g., 2). Based on a cooperation with forecasters, synthesis plots are proposed that summarize the BE detections in French kilometer-scale models. A subjective evaluation of the CNN performances is also reported. The overall positive feedback from forecasters is in good agreement with the object-oriented evaluation. Forecasters perceive these products as relevant and potentially useful to handle the large amount of available data from numerical weather prediction models.

Background Microbes typically live in communities where individuals can interact with each other in numerous ways. However, knowledge on the importance of these interactions is limited and derives mainly from studies using a limited number of species grown in coculture. Here, we manipulated soil microbial communities to assess the contribution of interactions between microorganisms for assembly of the soil microbiome. Results By combining experimental removal (taxa depletion in the community) and coalescence (mixing of manipulated and control communities) approaches, we demonstrated that interactions between microorganisms can play a key role in determining their fitness during soil recolonization. The coalescence approach not only revealed the importance of density-dependent interactions in microbial community assembly but also allowed to restore partly or fully community diversity and soil functions. Microbial community manipulation resulted in shifts in both inorganic nitrogen pools and soil pH, which were related to the proportion of ammonia-oxidizing bacteria. Conclusions Our work provides new insights into the understanding of the importance of microbial interactions in soil. Our top-down approach combining removal and coalescence manipulation also allowed linking community structure and ecosystem functions. Furthermore, these results highlight the potential of manipulating microbial communities for the restoration of soil ecosystems.

In previous two-tier experiments designed to test agronomical (treated wastewater) and worst-case scenario (wastewater spiked with a mixture of 14 pharmaceuticals and personal care products (PPCPs) at 10 and 100μg/L), 14 different wastewater-borne PPCPs accumulated in soil, lettuce roots, and leaves leading to a significant ecotoxicological impact on soil and root-associated bacteria. Here, we assessed the effects of wastewater irrigation on the arbuscular mycorrhizal fungal (AMF) colonization, diversity, and composition in lettuce roots. Neither the wastewater nor the concentration of spiked PPCPs had an impact on the colonization, alpha-diversity indices (Chao1, PD whole tree, Simpson reciprocal, and Shannon), and composition of root-associated AMF communities. Taxonomical analysis of the fungi revealed the presence of 14 major phylotypes, 13 of which belonged to the Glomeromycota division. As for the alpha and beta diversity indices, none of the phylotypes was affected by either the wastewater or the PPCPs. This indicates that under both agronomical and worst-case scenario, the irrigation of lettuce with wastewater had no effect on the root-associated AMF community.

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; Hexoses and disaccharides are the key carbon sources for essentially all physiological processes across kingdoms. In plants, sucrose, and in some cases raffinose and stachyose, are transported from the site of synthesis in leaves, the sources, to all other organs that depend on import, the sinks. Sugars also play key roles in interactions with beneficial and pathogenic microbes. Sugar transport is mediated by transport proteins that fall into super-families. Sugar transporter (ST) activity is tuned at different levels, including transcriptional and posttranslational levels. Understanding the ST interactome has a great potential to uncover important players in biologically and physiologically relevant processes, including, but not limited to Arabidopsis thaliana. Here, we combined ST interactions and coexpression studies to identify potentially relevant interaction networks.

National audience; β-triketone herbicides are among the most used herbicides in corn crop to control broadleaf weeds.These herbicides inhibit the 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) and lead to bleaching anddeath of weeds. This enzyme is not only found in plants but in all living organisms, includingmicroorganisms where it takes part to the tyrosine degradation pathway. Thus, microorganismsclassified as “non-target organisms” by current EU regulation for pesticide authorization, might beimpacted by β-triketones, with possible domino effect on microbial functions supporting soilecosystem services (Thiour-Mauprivez et al. 2019). Since microorganisms have been proposed by EFSAas key-drivers to be monitored to better protect soil ecosystem services, we tested the hypothesis thathppd bacterial community can constitute a biomarker of exposure to β-triketones. Within this context,we developed a toolbox to monitor the abundance, the diversity and the activity of the hppd bacterialcommunity.Abundance and diversity of hppd bacterial community were tested in a lab-to-field experimentaldesign following the tiered-approach recommended by EFSA to conduct pesticide environmental riskassessment (ERA). Under lab conditions, soil microcosms not exposed (control) or exposed to x1 or x10times the agronomical dose of sulcotrione (active ingredient) or Decano® (one of the commercialformulation of sulcotrione) were studied. Under field conditions, samples were collected in corn cropexposed to β-triketones or not (control). Analytical chemistry was applied to all samples to study thedissipation of β-triketone, search for residues and estimate the scenario of exposure of soilmicroorganisms. Nucleic acids (DNA/RNA) were extracted from soil samples. Home-made degeneratedprimers, specific to the hppd gene of soil bacteria, allowed us to measure the abundance (quantitativePCR), the composition (α-diversity) and the diversity (β-diversity) (NGS) of the hppd bacterialcommunity (Thiour-Mauprivez et al. 2020). Finally, the inhibition of the activity of the 4-HPPD wasassessed on pure bacterial strains under wet lab conditions to measure EC50 of β-triketones.Our poster will be presented to the audience with the aim to identify the better proxy of the hppdbacterial community that could be used as a biomarker to reflect the exposure of soil microbialcommunity to β-triketone residues. As a perspective my work might be extended to other pesticidestargeting other enzymes that are also present in so call non-target organisms such as sulfonylureasinhibiting acetohydroxy acid synthase (AHAS).

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizospherecore microbiota4,5of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced acore networkof the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how thesecore microbiotaandcore networkcontribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

National audience; The present work aimed to design a degenerate primer pair to target a large part of the hppd soil bacterial community, possibly affected by herbicides. We validated these primers by qPCR and high-throughput sequencing analysis of soil samples.

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.

Nitric oxide (NO) is a ubiquitous signalling molecule with widespread distribution in prokaryotes and eukaryotes where it is involved in countless physiological processes. While the mechanisms governing nitric oxide (NO) synthesis and signalling are well established in animals, the situation is less clear in the green lineage. Recent investigations have shown that NO synthase, the major enzymatic source for NO in animals, is absent in land plants but present in a limited number of algae. The first detailed analysis highlighted that these new NO synthases are functional but display specific structural features and probably original catalytic activities. Completing this picture, analyses were undertaken in order to investigate whether major components of the prototypic NO/cyclic GMP signalling cascades mediating many physiological effects of NO in animals were also present in plants. Only a few homologues of soluble guanylate cyclases, cGMP-dependent protein kinases, cyclic nucleotide-gated channels, and cGMP-regulated phosphodiesterases were identified in some algal species and their presence did not correlate with that of NO synthases. In contrast, S-nitrosoglutathione reductase, a critical regulator of S-nitrosothiols, was recurrently found. Overall, these findings highlight that plants do not mediate NO signalling through the classical NO/cGMP signalling module and support the concept that S-nitrosation is a ubiquitous NO-dependent signalling mechanism.

International audience; The evolutionally conserved chaperone-like protein CDC48 (cell division cycle 48) is a major component of ubiquitin-dependent protein degradation pathways in animal and yeast and, more generally, of the protein quality control machinery. In plants, CDC48 plays essential regulatory functions in development and the possibly that it contributes to protein degradation through the ubiquitin-proteasome system (UPS) and the endoplasmic reticulum-associated protein degradation (ERAD) system has been reported. In this review we described recent findings highlighting a role for CDC48 in plant immunity. First data indicated that CDC48 is S-nitrosylated in plant cells undergoing an immune response, regulates the turnover of immune receptors and mediates the degradation of viral proteins. Furthermore its overexpression was associated to an exacerbated hypersensitive-like cell death. We also designed and reported here the first CDC48 interactome. The corresponding data confirm the closed interaction of CDC48 with components of the UPS and shed light on its putative regulatory function of S-adenosyl-methionine synthesis and metabolism. More generally, these investigations further support the concept that plant cells facing pathogen attack finely regulate the protein quality control machinery.

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.

International audience; The core microbiota concept has been proposed to describe the subset of a microbiota (e.g. the rhizosphere microbial community) associated with a given host (e.g. a plant) going beyond macroenvironment differences (e.g. soil type), and characterized by taxonomic markers (e.g. 16S rRNA gene sequences). Its existence has been questioned by geographical studies, showing the overruling soil type effect in shaping microbial communities. As far as biotic determinants are concerned, several “hosts” or macroorganisms are impacting a given habitat and its specific microbial community. In soils, there is an overlap between the so-called rhizosphere and the drilosphere, defined as the functional domains under the influence of plant roots and earthworms respectively. Plants and earthworms have been sharing the same soils over geological times, thus microbial communities living at the congruence of rhizosphere and drilosphere could be specific of plant-earthworm interaction, as a consequence of their coevolution. Here we tested the hypothesis of a specific core microbiota at the interface of two interacting macroorganisms, in three different soils. We grew barley in microcosms in the presence/absence of the endogeic earthworm Aporrectodea caliginosa. We investigated the structure of microbial communities and quantified their abundance. Because interactions between earthworms and plants have been proposed tobe mediated through the mineralization of organic matter and the release of nutrients, we also studied the abundance of genes involved in nitrogen cycling in different micro environments (bulk soil, rhizosphere and earthworm casts). 16S rRNA gene amplicon sequencing revealed the presence of microsites core microbiota over the three soil types. Despite an expected strong influence of soil type on microbial community composition (59% of explained variance), significant effects of both microsites (13%) and macro-organisms presence (7%) were observed. Many genes of the nitrogen cycle were influenced by soil type, whereas earthworms were only responsible for an increase in the abundance of the ureC gene. The interaction between plant and soil type was modifying the abundance of nosZ, nifH and narG, in the rhizosphere suggesting a strong control of the nitrogen cycle by the plant dependent on soil fertility. A refined analysis on each soil separately revealed a significant interaction between plant and earthworm presence on the structure of the rhizosphere and drilosphere microbiota. This suggests that assembly of microbial community in plant rhizospheres and earthworm casts was dependent on the mutual presence of earthworm and plant respectively. Several bacterial species were significantly enriched at the interface of plant rhizosphere and earthworm casts, suggesting that direct/indirect relationships between macroorganisms associated microbiota resulted in recruiting and promoting specific members.

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.

We report here the 7,259,392-bp draft genome of Pseudomonas sp. strain ADP. This is a bacterial strain that was first isolated in the 1990s from soil for its ability to mineralize the herbicide atrazine. It has extensively been studied as a model to understand the atrazine biodegradation pathway. This genome will be used as a reference and compared to evolved populations obtained by experimental evolution conducted on this strain under atrazine selection pressure.

Fusarium species are ubiquitous in soil. They cause plant and human diseases and can produce mycotoxins. Surveys of Fusarium species diversity in environmental samples usually rely on laborious culture-based methods. In the present study, we have developed a molecular method to analyze Fusarium diversity directly from soil DNA. We designed primers targeting the translation elongation factor 1-alpha (EF-1 alpha) gene and demonstrated their specificity toward Fusarium using a large collection of fungi. We used the specific primers to construct a clone library from three contrasting soils. Sequence analysis confirmed the specificity of the assay, with 750 clones identified as Fusarium and distributed among eight species or species complexes. The Fusarium oxysporum species complex (FOSC) was the most abundant one in the three soils, followed by the Fusarium solani species complex (FSSC). We then compared our molecular approach results with those obtained by isolating Fusarium colonies on two culture media and identifying species by sequencing part of the EF-1 alpha gene. The 750 isolates were distributed into eight species or species complexes, with the same dominant species as with the cloning method. Sequence diversity was much higher in the clone library than in the isolate collection. The molecular approach proved to be a valuable tool to assess Fusarium diversity in environmental samples. Combined with high throughput sequencing, it will allow for in-depth analysis of large numbers of samples

International audience; Arbuscular mycorrhizal (AM) symbiosis that associates roots of most land plants with soil-borne fungi (Glomeromycota), is characterized by reciprocal nutritional benefits. Fungal colonization of plant roots induces massive changes in cortical cells where the fungus differentiates an arbuscule, which drives proliferation of the plasma membrane. Despite the recognized importance of membrane proteins in sustaining AM symbiosis, the root microsomal proteome elicited upon mycorrhiza still remains to be explored. In this study, we first examined the qualitative composition of the root membrane proteome of Medicago truncatula after microsome enrichment and subsequent in depth analysis by GeLC-MS/MS. The results obtained highlighted the identification of 1226 root membrane protein candidates whose cellular and functional classifications predispose plastids and protein synthesis as prevalent organelle and function, respectively. Changes at the protein abundance level between the membrane proteomes of mycorrhizal and nonmycorrhizal roots were further monitored by spectral counting, which retrieved a total of 96 proteins that displayed a differential accumulation upon AM symbiosis. Besides the canonical markers of the periarbuscular membrane, new candidates supporting the importance of membrane trafficking events during mycorrhiza establishment/functioning were identified, including flotillin-like proteins. The data have been deposited to the ProteomeXchange with identifier PXD000875. Biological significance During arbuscular mycorrhizal symbiosis, one of the most widespread mutualistic associations in nature, the endomembrane system of plant roots is believed to undergo qualitative and quantitative changes in order to sustain both the accommodation process of the AM fungus within cortical cells and the exchange of nutrients between symbionts. Large-scale GeLC-MS/MS proteomic analysis of the membrane fractions from mycorrhizal and nonmycorrhizal roots of M. truncatula coupled to spectral counting retrieved around one hundred proteins that displayed changes in abundance upon mycorrhizal establishment. The symbiosis-related membrane proteins that were identified mostly function in signaling/membrane trafficking and nutrient uptake regulation. Besides extending the coverage of the root membrane proteome of M. truncatula, new candidates involved in the symbiotic program emerged from the current study, which pointed out a dynamic reorganization of microsomal proteins during the accommodation of AM fungi within cortical cells

Background Membrane microdomains are defined as highly dynamic, sterol- and sphingolipid-enriched domains that resist to solubilization by non-ionic detergents. In plants, these so-called Detergent Insoluble Membrane (DIM) fractions have been isolated from plasma membrane by using conventional ultracentrifugation on density gradient (G). In animals, a rapid (R) protocol, based on sedimentation at low speed, which avoids the time-consuming sucrose gradient, has also been developed to recover DIMs from microsomes as starting material. In the current study, we sought to compare the ability of the Rapid protocol versus the Gradient one for isolating DIMs directly from microsomes of M. truncatula roots. For that purpose, Triton X-100 detergent-insoluble fractions recovered with the two methods were analyzed and compared for their sterol/sphingolipid content and proteome profiles. Results Inferred from sterol enrichment, presence of typical sphingolipid long-chain bases from plants and canonical DIM protein markers, the possibility to prepare DIMs from M. truncatula root microsomes was confirmed both for the Rapid and Gradient protocols. Contrary to sphingolipids, the sterol and protein profiles of DIMs were found to depend on the method used. Namely, DIM fractions were differentially enriched in spinasterol and only shared 39% of common proteins as assessed by GeLC-MS/MS profiling. Quantitative analysis of protein indicated that each purification procedure generated a specific subset of DIM-enriched proteins from Medicago root microsomes. Remarkably, these two proteomes were found to display specific cellular localizations and biological functions. In silico analysis of membrane-associative features within R- and G-enriched proteins, relative to microsomes, showed that the most noticeable difference between the two proteomes corresponded to an increase in the proportion of predicted signal peptide-containing proteins after sedimentation (R) compared to its decrease after floatation (G), suggesting that secreted proteins likely contribute to the specificity of the R-DIM proteome. Conclusions Even though microsomes were used as initial material, we showed that the protein composition of the G-DIM fraction still mostly mirrored that of plasmalemma-originating DIMs conventionally retrieved by floatation. In parallel, the possibility to isolate by low speed sedimentation DIM fractions that seem to target the late secretory pathway supports the existence of plant microdomains in other organelles. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0255-x) contains supplementary material, which is available to authorized users.

11 pages; International audience; Truffles, i.e. tree root-associated fungal fruiting bodies, clearly range among the world's most exclusive delicacies. Despite the quite restricted natural geographic occurrence of one of the most renowned fungal species, namely Tuber melanosporum, the development of inoculation procedures in the late 1960s made it possible to enlarge its production area in different countries. This was achieved by planting orchards with host tree seedlings colonized by the fungus. In the present work, we investigate the behavior of one of the earliest T. melanosporum orchards planted in Burgundy (France) over a longterm scale (more than 30 years). A picture of the orchard evolution was obtained by recording truffle yields and fungal morphotypes over the seasons and relating them to host-tree development and climate data. The most relevant results include the timedelayed, but rather fast replacement of inoculated T. melanosporum by naturally occurring T. aestivum and the key role of climate in the inter-annual variability of truffle production.

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.

International audience; The complexity of Multi-Agent Systems is constantly increasing. With the growth of the number of agents, interactions between them draw complexan d huge conversations, i.e. sequences of messages exchanged inside the system. In this paper, we present a knowledge discovery process, mining those conversations to infer their underlying models, using stochastic grammatical inference techniques. We present some experiments that show the process we design is a good candidate to observe the interactions between the agents and infer the conversation models they build together.

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).