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International audience; Preservation of biodiversity and ecosystem services is critical for sustainable development and human well-being. However, an unprecedented erosion of biodiversity is observed and the use of plant protection products (PPP) has been identified as one of its main causes. In this context, at the request of the French Ministries responsible for the Environment, for Agriculture and for Research, a panel of 46 scientific experts ran a nearly 2-year-long (2020-2022) collective scientific assessment (CSA) of international scientific knowledge relating to the impacts of PPP on biodiversity and ecosystem services. The scope of this CSA covered the terrestrial, atmospheric, freshwater, and marine environments (with the exception of groundwater) in their continuity from the site of PPP application to the ocean, in France and French overseas territories, based on international knowledge produced on or transposable to this type of context (climate, PPP used, biodiversity present, etc.). Here, we provide a brief summary of the CSA's main conclusions, which were drawn from about 4500 international publications. Our analysis finds that PPP contaminate all environmental matrices, including biota, and cause direct and indirect ecotoxicological effects that unequivocally contribute to the decline of certain biological groups and alter certain ecosystem functions and services. Levers for action to limit PPP-driven pollution and effects on environmental compartments include local measures from plot to landscape scales and regulatory improvements. However, there are still significant gaps in knowledge regarding environmental contamination by PPPs and its effect on biodiversity and ecosystem functions and services. Perspectives and research needs are proposed to address these gaps.

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.

Important mineralization of 14C-chlorpyrifos was found in a Tunisian soil exposed repeatedly to this insecticide. A bacterial strain able to grow in minimal salt medium (MSM) supplemented with 25 mg L− 1 of chlorpyrifos was isolated from this soil. It was characterized as Serratia rubidaea strain ABS 10 using morphological and biochemical analyses, as well as 16S rRNA sequencing. In liquid culture S. rubidaea stain ABS 10 was able to almost entirely dissipate chlorpyrifos within 48 hours of incubation. Although, S. rubidaea strain ABS 10 was able to grow on MSM supplemented with chlorpyrifos and to dissipate it in liquid culture, it was not able to mineralize 14C-chlorpyrifos. Therefore, one can conclude that the dissipation capability of this bacteria might be attributed to its capacity to adsorb CHL. In both non-sterile and sterile soil inoculated with S. rubidaea strain ABS 10, chlorpyrifos was more rapidly dissipated than in respective controls.

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.

The English walnut (Juglans regiaL.) is the main species cultivated for the production of edible nuts.In vitromicropropagation of walnut explants, necessary for mass propagation of high-quality walnut rootstocks, needs anex vitroacclimatization phase followed by apost-acclimatization growth in greenhouse when plantlets become photoautotrophic. However, poor survival and slow growth rates are common difficulties encountered in nurseries when establishing micropropagated walnut saplings. As many other fruit and nut bearing trees, walnut exhibits a high dependency on symbiotic soil-borne arbuscular mycorrhizal fungi for better soil nutrient acquisition and development due to a coarse root architecture that notably limits soil inorganic phosphate (Pi) uptake. In the context of rootstock production, we investigated the establishment of seven walnut rootstocks of economic interest (RG2, RG6, R17, RX1, VLACH, VX211, and WIP3) inoculated or not withRhizophagus irregularisunder two contrasting Pi fertilization regimes. We demonstrated that inoculation withR. irregularisdecreases micropropagated walnut rootstock dependency on Pi fertilization both at the acclimatization andpost-acclimatization stages, together with improving quality, sapling biomass production and nutrition of walnut rootstocks. We also showed that these benefits are rootstock-dependent, indicating that walnut mycorrhizal dependency for Pi nutrition varies between cultivars.

International audience; The transfer of pesticides from agricultural soils to food and drinking water is a major health issue. There are actually few robust methods to identify, characterize and quantify the dissipation of pesticides in complex media such as soils, waters and sediments. Here, we review multi-elemental compound-specific isotope analysis to study sources and transformations of pesticides in agricultural soils. First, we discuss advanced extraction and purification techniques for pesticides in soils. Then, analytical techniques for reliable measurements of the stable isotope composition of the pesticides are presented. We report a unique dataset of 547 isotopic compositions of 71 active molecules produced by various pesticide manufacturers, for the following isotopes: 13C, 15N, 37Cl, and 2H. We also report 270 isotope fractionation values for 33 compounds, which might help to elucidate the mechanisms of pesticide transformation by biodegradation, photodegradation and other abiotic processes. Compounds include legacy pesticides such as atrazine, lindane, dichlorodiphenyltrichloroethane, chlordecone and organophosphorus compounds. Transformation processes may be identified and quantified using the Rayleigh concept for isotope fractionation during reaction.

Prod 2020-50 EA BIOmE INRA; International audience; The activity of microorganisms in soil is important for a robust functioning of soil and related ecosystem services. Hence, there is a necessity to identify the composition, diversity, and function of the soil microbiome in order to determine its natural properties, functioning, and operating range as well as to assess ecotoxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of these methods are standardised. Consequently, there is a need to identify the most promising non-standardised methods for assessing soil quality and to transform them into standards. In agreement with the “Ecosystem Service Approach”, new methods should focus more on soil microbial functions, including nutrient cycling and greenhouse gas emission, pest control and plant growth promotion, carbon cycling and sequestration, as well as soil structure development and filter function. The few existing standardised methods available that focus on the function of the soil microbiome mostly include measurements, like basal respiration, enzyme activities, and biodegradation of organic matter, under well-defined conditions in the lab. This paper sets out to summarise and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality – Biological Characterization sub-committee (ISO TC 190/SC 4), where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality, going beyond the existing test systems. Of particular note is the current evolution of molecular methods in microbial ecology that use quantitative real-time PCR (qPCR) to produce a large number of new functional endpoints which are more sensitive as compared to “classical” methods. Quantitative PCR assesses the abundance of microbes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways based on the assessment of marker gene sequences that drive the related processes. In the assessment of soil quality methods, it was found that most methods focus on bacteria and related endpoints. Techniques to describe fungal communities as well as their functional traits are far less represented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods 18 S. Thiele-Bruhn et al.: Identification of new microbial functional standards for soil quality assessment indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. However, it is obvious that with increasing developments in high throughput sequencing technologies and big data analyses, including metagenomics analysis, it will be possible to implement these technologies into the standardisation process for assessing the functions of the soil microbiome. Overall, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.

4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.

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 implementation of the new Water Reuse regulation in the European Union brings to the forefront the need to evaluate the risks of using wastewater for crop irrigation. Here, a two-tier ecotoxicological risk assessment was performed to evaluate the fate of wastewater-borne micropollutants in soil and their ecotoxicological impact on plants and soil microorganisms. To this end, two successive cultivation campaigns of lettuces were irrigated with wastewater (at agronomical dose (not spiked) and spiked with a mixture of 14 pharmaceuticals at 10 and 100 µg/L each) in a controlled greenhouse experiment. Over the two cultivation campaigns, an accumulation of PPCPs was observed in soil microcosms irrigated with wastewater spiked with 100 μg/L of PPCPs with the highest concentrations detected for clarithromycin, hydrochlorothiazide, citalopram, climbazole and carbamazepine. The abundance of bacterial and fungal communities remained stable over the two cultivation campaigns and was not affected by any of the irrigation regimes applied. Similarly, no changes were observed in the abundance of ammonium oxidizing archaea (AOA) and bacteria (AOB), nor in clade A of commamox no matter the cultivation campaign or the irrigation regime considered. Only a slight increase was detected in clade B of commamox bacteria after the second cultivation campaign. Sulfamethoxazole-resistant and -degrading bacteria were not impacted either. The irrigation regimes had only a limited effect on the bacterial evenness. However, in response to wastewater irrigation the structure of soil bacterial community significantly changed the relative abundance of Acidobacteria, Chloroflexi, Verrucomicrobia, Beta-, Gamma- and Deltaprotebacteria. Twenty-eight operational taxonomic units (OTUs) were identified as responsible for the changes observed within the bacterial communities of soils irrigated with wastewater or with water. Interestingly, the relative abundance of these OTUs was similar in soils irrigated with either spiked or non-spiked irrigation solutions. This indicates that under both agronomical and worst-case scenario the mixture of fourteen PPCPs had no effect on soil bacterial community., This study has been financially supported by the European Union through the WaterJPI-2015 AWARE project (PCIN-2017-067) within the Water Challenges for a Changing World Joint Programming Initiative. The authors thank Damià Barceló, Sandra Pérez and Serge Chiron for having invited us to participate to the AWARE project. The authors also acknowledge SCIEX for loaning the instrument LC/HRMS QTOF X500R. The EU is not liable for any use that may be made of the information contained therein. The authors would also like to thank Marie Christine Breuil for measuring the inorganic nitrogen pools.

The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these two herbicides (i.e. dissipation and formation of transformation products) was monitored to assess the scenario of exposure of soil microorganisms to natural and synthetic herbicides. Ecotoxicological impact of both herbicides was explored by monitoring soil bacterial diversity and activity using next-generation sequencing of 16S rRNA gene amplicons and soil metabolomics. Both leptospermone and sulcotrione fully dissipated over the incubation period. During their dissipation, transformation products of natural and synthetic β-triketone were detected. Hydroxy-leptospermone was almost completely dissipated by the end of the experiment, while CMBA, the major metabolite of sulcotrione, remained in soil microcosms. After 8 days of exposure, the diversity and structure of the soil bacterial community treated with leptospermone was significantly modified, while less significant changes were observed for sulcotrione. For both herbicides, the diversity of the soil bacterial community was still not completely recovered by the end of the experiment (45 days). The combined use of next-generation sequencing and metabolomic approaches allowed us to assess the ecotoxicological impact of natural and synthetic pesticides on non-target soil microorganisms and to detect potential biomarkers of soil exposure to β-triketones.

The reuse of water for agricultural practices becomes progressively more important due to increasing demands for a transition to a circular economy. Treated wastewater can be an alternative option of blue water used for the irrigation of crops but its risks need to be evaluated. This study assesses the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) derived from treated wastewater into lettuce as well as the impact on root-associated bacteria under a realistic and worst-case scenario. Lettuce was grown in a controlled greenhouse and irrigated with water or treated wastewater spiked with and without a mixture of fourteen different PPCPs at 10 μg/L or 100 μg/L. After harvesting the plants, the same soil was reused for a consecutive cultivation campaign to test for the accumulation of PPCPs. Twelve out of fourteen spiked PPCPs were detected in lettuce roots, and thirteen in leaves. In roots, highest concentrations were measured for sucralose, sulfamethoxazole and citalopram, while sucralose, acesulfame and carbamazepine were the highest in leaves. Higher PPCP concentrations were found in lettuce roots irrigated with spiked treated wastewater than in those irrigated with spiked water. The absolute bacterial abundance remained stable over both cultivation campaigns and was not affected by any of the treatments (type of irrigation water (water vs. wastewater) nor concentration of PPCPs). However, the irrigation of lettuce with treated wastewater had a significant effect on the microbial α-diversity indices at the end of the second cultivation campaign, and modified the structure and community composition of root-associated bacteria at the end of both campaigns. Five and fourteen bacterial families were shown to be responsible for the observed changes at the end of the first and second cultivation campaign, respectively. Relative abundance of Haliangium and the clade Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was significantly affected in response to PCPPs exposure. Caulobacter, Cellvibrio, Hydrogenophaga and Rhizobacter were significantly affected in microcosms irrigated with wastewater., This study has been financially supported by the EU through the WaterJPI-2015 AWARE project (PCIN-2017-067) within the Water Challenges for a Changing World Joint Programming Initiative. We would like to thank Prof. Damià Barceló the coordinator for raising the AWARE (Assessing the fate of pesticides and water-borne contaminants in agricultural crops and their environmental risks) project, and the German Federal Office for Agriculture and Food (Deutsches Bundesamt für Landwirtschaft und Ernährung BLE. Grant number: 2816ERA04W). The authors also acknowledge SCIEX for loaning the instrument LC/HRMS QTOF X500R. Additionally, the authors would like to kindly thank Miljenka Vuko and Akane Chiba for their statistical advices.

The results of the Impact-CE project highlight the specific contribution of various integrative tools to have a more complete vision of the chemical and biological impact of pesticides on watercourses. In addition to grabe sampling, which gives a quantitative and instantaneous view of contamination, these tools provide more representative information over time, which makes them better tools for prioritising basins that contribute to contamination. They are also more robust for reporting interannual changes in agricultural practices, even if it may remain difficult to dissociate the effect of limited changes in practices from that of significant climatic variations. The results also confirm that, thanks to their accumulation capacity, passive samplers can reveal trace substances that are not seen by grabe measurements, such as degradation products, or that are only mobilised during floods. They also show the added value of both chemical and biological information in order to refine the impact diagnosis, highlight possible causes and provide additional information in terms of biodiversity and functioning of ecosystems. Interviews conducted with operational actors during the project show that it is essential that these tools be better known and appropriated by field managers, through training and support., Les résultats du projet Impact-CE mettent en évidence l’apport spécifique de divers outils intégratifs pour d’obtenir une vision plus complète de l’impact chimique et biologique des produits phytosanitaires sur les cours d’eau. En complément de l'échantillonnage ponctuel qui donne une vision quantitative et instantanée de la contamination, ces outils apportent des informations plus représentatives dans le temps ce qui en fait de meilleurs outils pour hiérarchiser des bassins contributifs à la contamination. Ils sont également plus robustes pour rendre compte d’évolutions interannuelles de pratiques, même s’il peut rester délicat de dissocier l’effet de changements limités de pratiques de celui de variations climatiques importantes. Les résultats confirment également que, grâce à leur capacité d’accumulation, les échantillonneurs passifs peuvent mettre en évidence des substances non vues par les mesures ponctuelles car présentes en très faible quantité, comme des produits de dégradation, ou seulement mobilisées de manière fugace, lors des crues. Ils montrent également la plus-value de mettre en regard des informations chimiques et biologiques pour affiner le diagnostic d’impact, en asseoir la pertinence en termes de causes possibles et apporter des informations complémentaires en termes de qualité et de bon fonctionnement des écosystèmes. Des entretiens réalisés auprès d'acteur opérationnels au cours du projet montrent qu'il est essentiel que ces outils puissent être mieux connus et appropriés par les gestionnaires de terrain, par le biais de formations mais aussi d’un accompagnement approprié.

The insecticide

We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.

We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.

International audience; The effect of wastewater irrigation on the diversity and composition of bacterial communities of soil mesocosms planted with lettuces was studied over an experiment made of five cultivation campaigns. A limited effect of irrigation with either raw or treated wastewater was observed in both alpha-diversity and beta-diversity of soil bacterial communities. However, the irrigation with wastewater fortified with a complex mixture of fourteen relevant chemicals at 10 mu g/L each, including pharmaceutical, biocide, and pesticide active substances, led to a drift in the composition of soil bacterial community. One hundred operational taxonomic units (OTUs) were identified as responsible for changes between treated and fortified wastewater irrigation treatments. Our findings indicate that under a realistic agronomical scenario, the irrigation of vegetables with domestic (treated or raw) wastewater has no effect on soil bacterial communities. Nevertheless, under the worst-case scenario tested here (i.e., wastewater fortified with a mixture of chemicals), non-resilient changes were observed suggesting that continuous/repeated irrigation with wastewater could lead to the accumulation of contaminants in soil and induce changes in bacterial communities with unknown functional consequences.

International audience; The use of reclaimed water in crop irrigation helps to mitigate water shortage. The fertilization of arable soils with sewage sludge, biosolids, or livestock manure reduces extensive application of synthetic fertilizers. However, both practices lead to the introduction of pharmaceutical active compounds (PhACs) in arable soil, known to host a wide range of living organisms, including microorganisms which are supporting numerous ecosystem services. In soils, the fate of PhACs is governed by different abiotic and biotic processes. Among them, soil sorption and microbial transformation are the most important ones and determine the fate, occurrence, and dispersion of PhACs into the different compartments of the environment. The presence of PhACs in soils can compromise the abundance, diversity, and activity of the soil microbial community which is one of the key players in a range of soil ecosystem services. This chapter reviews the current knowledge of the effects of PhACs, commonly found in wastewater effluents and derived organic fertilizers, on the soil microbial community.

International audience; Pesticides are applied in large quantities to agroecosystems worldwide. To date, few studies assessed the occurrence of pesticides in organically managed agricultural soils, and it is unresolved whether these pesticide residues affect soil life. We screened 100 fields under organic and conventional management with an analytical method containing 46 pesticides (16 herbicides, 8 herbicide transformation products, 17 fungicides, seven insecticides). Pesticides were found in all sites, including 40 organic fields. The number of pesticide residues was two times and the concentration nine times higher in conventional compared to organic fields. Pesticide number and concentrations significantly decreased with the duration of organic management. Even after 20 years of organic agriculture, up to 16 different pesticide residues were present. Microbial biomass and specifically the abundance of arbuscular mycorrhizal fungi, a widespread group of beneficial plant symbionts, were significantly negatively linked to the amount of pesticide residues in soil. This indicates that pesticide residues, in addition to abiotic factors such as pH, are a key factor determining microbial soil life in agroecosystems. This comprehensive study demonstrates that pesticides are a hidden reality in agricultural soils, and our results suggest that they have harmful effects on beneficial soil life.

Walnut trees are among the most important hardwood species in the northern hemisphere, ecologically and economically. They are mainly cultivated for timber and nut production but are also attractive ornamental trees in parks. Establishing walnut orchards is difficult because seedlings have a coarse root architecture and few of them survive to transplanting. Planting success is mainly determined by the root system morphology and the nutrient status of the seedlings, so that rhizosphere conditions are critical for plant performance. Walnut trees can associate with soil-borne arbuscular mycorrhizal fungi, which are obligate biotrophs. In this association, plant-produced carbon compounds are traded against fungus-acquired soil mineral nutrients. The beneficial effect of arbuscular mycorrhizal symbiosis on hardwood seedling quality and field performance has long been known, but an integrated view is lacking about the effects of arbuscular mycorrhizas on walnut cropping. Therefore, we surveyed the literature published over the last 40 years to provide up-to-date knowledge on the relationships between arbuscular mycorrhizas and walnut trees. Our review outlines the major following points: (1) the arbuscular-mycorrhiza-mediated nutrient uptake capacity of walnut trees is associated with first- to third-order roots, and fibrous tip-ended roots are dependent on arbuscular mycorrhizal fungi, whereas pioneer roots are not; (2) early inoculation with arbuscular mycorrhizal fungi improves the survival and seedling performance attributes of transplanted walnut trees: biotization enhances walnut transplant success by increasing the number of lateral roots and plant P uptake, but these benefits are fungus- and host-dependent; (3) in the context of walnut agroforestry, deeply rooted walnut trees play a role as reservoirs of arbuscular mycorrhizal fungal propagules for the surrounding vegetation, but tree shade and soluble phosphate availability decrease walnut mycorrhizal dependency; and (4) the arbuscular mycorrhizal mycelium mediates the transport of juglone and thus plays a role in walnut tree allelopathy.

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).

International audience; Since the early 20's antibiotics have been massively produced and consumed for the benefit of bothhuman and animal health. Nevertheless, antibiotics have also reached the aquatic environmentthrough diffuse sources (e.g. veterinary treatment, contaminated manure application...) and throughwastewater. Consequently, antibiotics concentrations between the ng/L and μg/L range are regularlydetected in surface water and those molecules have also been found in sediments and aquatic biota.The ubiquitous presence of antibiotics exerts a selective pressure on microbial communities leading tothe acquisition and dissemination of antibioresistance in the environment. While both antibiotics andantibioresistance have been found in different aquatic compartments, more investigation is requiredto better understand their distribution and to identify hot spots of accumulation.In this context, we investigated the repartition of antibiotics and antibioresistance in different aquaticcompartments on 4 stations belonging to regional observatories and presenting contrasting levels ofpharmaceuticals: 2 on the Arve river belonging to Sipibel observatory and 2 on Lake Geneva belongingto the Observatory on Lakes. On the Arve river, the 2 stations were located up- and down- stream thedischarge place of a wastewater treatment plant (WWTP) collecting both urban and hospitalwastewaters. On Lake Geneva, one station was located in a relatively pristine area while the secondwas close to the discharge of an urban WWTP. To better identify a potential temporal dynamic ofantibiotics and antibioresistances over seasons, 6 samplings were conducted during 1.5 year. On eachsampling campaign, the following parameters were determined: (i) antibiotics levels in water,sediments and periphyton; (ii) antibioresistance in periphyton and sediments using various techniques:detection of resistance genes, integrons quantification, detection of tolerance acquisition via a PICT(Pollution Induced Community Tolerance) approach; (iii) antibiotics biodegradation potential ofmicrobial community from sediments (by radiorespirometric measurement); (iv) diversity of bacteriaand diatoms in periphyton and sediments; (v) physico-chemical parameters and (vi) metalliccontamination in sediments.While microbial resistance to antibiotics is commonly assessed by quantifying resistance genes orisolating antibiotic resistant bacteria, antibiotic resistance can also be estimated by measuring theacquisition of antibiotics tolerance at community level, following a PICT approach. In our study,periphytic microbial communities from the Arve river were found to have a higher tolerance to thetested antibiotics (ciprofloxacin, ofloxacin, sulfamethazine and erythromycin) than communities fromLake Geneva, in agreement with the expected levels of contamination. In addition, in some cases, ahigher tolerance was also found at stations close to WWTP effluents than in upstream/protectedstations. For example, periphytic microbial communities collected downstream the WWTP on the Arveriver were generally found to have a higher tolerance to ciprofloxacin than the upstream communities.Comparing whole community tolerance to other classical indicators of antibioresistance and toantibiotics levels in the aquatic ecosystems allows us to better understand the interconnectionbetween pharmaceutical exposure, in situ tolerance and genetic potential for antibioresistance.

International audience; Mining activities frequently leave a legacy of residues that remain in the area for long periods causing the pollution of surroundings. We studied on a 100 year-old mine, the behavior of potentially toxic elements (PTEs) and their ecotoxicological impact on activity and diversity of microorganisms. The PTEs contamination assessment allowed the classification of the materials as highly (reference- and contaminated-samples) and very highly polluted (illegal spill of olive mill wastes (OMW), tailings, and dumps). OMW presented the lowest enzymatic activities while tailings and dumps had low dehydrogenase and arylsulfatase activities. All the beta-diversity indices studied were negatively impacted in dumps. Tailings had lower Chao1 and PD whole tree values as compared to those of reference-samples. beta-diversity analysis showed similar bacterial community composition for referenceand contaminated-samples, significantly differing from that of tailings and dumps. The relative abundance of Gemmatimonadetes, Bacteroidetes, and Verrucomicrobia was lower in OMW, tailings, and dumps as compared to reference-samples. Fifty-seven operational taxonomic units were selected as responsible for the changes observed between samples. This study highlights that assessing the relationship between physicochemical properties and microbial diversity and activity gives clues about ongoing regulating processes that can be helpful for stakeholders to define an appropriate management strategy.

International audience; The scientific knowledge produced by academic research can be valued in all sectors of human activity, including private sector. The ROVALTAIN Foundation organized a round-table during its scientific day in 2019. It crossed the points of view of academic scientists and industrial partners, addressing five main topics. The first one concerned the validation of a common definition of the academic research/private partners interface. Then, the group discussed the place for academic expertise in the corporate world; the advantages of involving academic researchers in expertise for the private sector; and the limits of this model. To conclude, the need of a third party, like the ROVALTAIN Foundation, as a catalyzer in building the interface between academic research and private partners has been discussed.

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

International audience

International audience; Standard tests have been used in soil ecotoxicology for about 40 years, but there is still room for improvement, such as (1) increased use of such tests because of regulatory requirements, in particular for the risk assessment of chemicals (mainly pesticides) and, to a lesser extent, of contaminated soils; (2) increased efforts regarding the standardization of ecotoxicological methods, handled either by OECD (Organization for Economic Cooperation and Development) prospectively for individual chemicals or by ISO (International Organization for Standardization) retrospectively for contaminated soils; (3) increased inclusion of ecological aspects, i.e., by performing higher-tier tests under semi-field and field conditions. However, until quite recently, nominal concentrations of the stressors are used, meaning that their bioavailability was not taken into account. We are providing an overview on currently required and/or proposed ecotoxicological effect tests, covering OECD and ISO methods for main soil organism groups (microbes, invertebrates, and plants). Based on this overview, we discuss how the current set of test methods could be improved, trying to capture ecological reality by addressing issues such as different soils, species, endpoints, and exposure (i.e., bioavailable instead of nominal/total concentrations). The TRIAD approach is highlighted as an example how bioavailability could be implemented in soil quality regulations.

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.

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon. IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

International audience; During the past decades, environmental concentrations of antibiotics have largely increased,resulting in a risk of ecosystem disturbance. However, because their composition is often rich innitrogen and carbon, antibiotics are of nutritional interest for microorganisms, as long as theirbiocidal character is not considered. Antibiotic-degrading bacteria have therefore emerged amongststrains that were resistant to antibiotics. Called antibiotrophs, they are able to use selectedantibiotics as nutritive sources for their growth. While several antibiotrophs have been isolated fromdifferent agroecosystems, little is known about their ecology. In particular, their dispersal capacity ispoorly evaluated, even though manure spreading is a suspected source of antibiotrophs foragroecosystems. Also, their antibiotic degradation ability in complex agricultural soil communitiesremains insufficiently studied.In this context, a microcosm experiment was set up by inoculating the sulfonamide-degrading andresistant bacterium, Microbacterium sp. C448, in four different soil types supplied or not withsulfamethazine and/or swine manure. After one month of incubation, qPCR analyses and 16S rDNAsequencing were performed to respectively quantify the inoculated strain, its antibiotrophic genesadA, and to characterize the structure of bacterial communities. In parallel, a similar experimentwas carried out with the addition of radiolabeled sulfamethazine, in order to monitoredantibiotrophy activity during incubation by radiorespirometry.Quantitative PCR results showed an effective establishment of the strain and its sulfamethazinedegradinggene (sadA) only under sulfamethazine selection pressure. This reflects the lowcompetitiveness of the strain, which possesses a low invasion potential under non-antibioticcontaminated conditions. Sulfamethazine treated soils differed in their capacity to mineralize theantibiotic. Indeed, in absence of manure and despite the presence of Microbacterium sp. C448, onlyone of the four tested soils exhibited slight mineralization capacities. Whatever the soil type,radiorespirometry analyses showed that manure addition significantly enhanced sulfamethazinemineralization. These results confirm that the presence of functional genes does not necessarilyensure functionality. Moreover, they suggest that sulfamethazine does not necessarily confer aselective advantage to the degrading strain, as a nutritional source. In addition, 16S rDNA sequencinganalyses strongly suggest that sulfamethazine has released trophic niches by biocidal action.Accordingly, manure-originating bacteria and/or Microbacterium sp C448 could have access to lowcompetition or competition-free trophic niches. However, simultaneous inputs of manure and of thestrain could induce detrimental competition for Microbacterium sp. C448, thus forcing it to usesulfamethazine as a nutritional source. Altogether, these results suggest that the studiedantibiotrophic strain can modulate its sulfamethazine-degradation function depending on microbialcompetition and resource accessibility, to establish in an agricultural soil. Most importantly, this workhighlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, asantibiotics can not only release existing trophic niches but also constitute new ones.