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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.

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Maize cultivators often use β-triketone herbicides to prevent the growth of weeds in their fields. These herbicides target the 4-HPPD enzyme of dicotyledons. This enzyme, encoded by the hppd gene, is widespread among all living organisms including soil bacteria, which are considered as “non-target organisms” by the legislation. Within the framework of the pesticide registration process, the ecotoxicological impact of herbicides on soil microorganisms is solely based on carbon and nitrogen mineralization tests. In this study, we used more extensive approaches to assess with a lab-to-field experiment the risk of β-triketone on the abundance and the diversity of both total and hppd soil bacterial communities. Soil microcosms were exposed, under lab conditions, to 1× or 10× the recommended dose of sulcotrione or its commercial product, Decano®. Whatever the treatment applied, sulcotrione was fully dissipated from soil after 42 days post-treatment. The abundance and the diversity of both the total and the hppd bacterial communities were not affected by the herbicide treatments all along the experiment. Same measurements were led in real agronomical conditions, on three different fields located in the same area cropped with maize: one not exposed to any plant protection products, another one exposed to a series of plant protection products (PPPs) comprising mesotrione, and a last one exposed to different PPPs including mesotrione and tembotrione, two β-triketones. In this latter, the abundance of the hppd community varied over time. The diversity of the total and the hppd communities evolved over time independently from the treatment received. Only slight but significant transient effects on the abundance of the hppd community in one of the tested soil were observed. Our results showed that tested β-triketones have no visible impact toward both total and hppd soil bacteria communities.

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.

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.

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.

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

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 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.