Impact of repeated treatments of the pesticides chlorpyrifos or tebuconazole on soil microorganisms using alternative methods

International audience

Biotic and abiotic soil properties influence survival of Listeria monocytogenes in soil

International audience; Listeria monocytogenes is a food-borne pathogen responsible for the potentially fatal disease listeriosis and terrestrial ecosystems have been hypothesized to be its natural reservoir. Therefore, identifying the key edaphic factors that influence its survival in soil is critical. We measured the survival of L. monocytogenes in a set of 100 soil samples belonging to the French Soil Quality Monitoring Network. This soil collection is meant to be representative of the pedology and land use of the whole French territory. The population of L. monocytogenes in inoculated microcosms was enumerated by plate count after 7, 14 and 84 days of incubation. Analysis of survival pr…

Depth matters : Effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

International audience; Climate change is predicted to affect not only the amount but also the temporal distribution of rain. Changes in frequency and amplitude of rain events, i.e. precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used 18O stable isotope probing (SIP) to investigate bacterial and fungal communities that actively grew or not upon rewetting, at three different depths in plant-soil mesocosms previously subjected to frequent or infrequent watering for 12 weeks (equal total water input). Phylogenetic marker genes for bacteria and fungi were sequenced after rewetting,…

Effects of precipitation regime on soil bacterial and fungal activity upon rewetting of a plant-soil system using 18O-SIP: depth matters

EASPEBIOmEDOCT INRA; Climate change is predicted to affect not only the amount but also the temporal distribution of rain. Changes in frequency and amplitude of rain events, likely shape the activity of plants and soil microbes. Fluctuating water conditions will differ with soil depth between precipitation patterns, affecting plant growth and may result in differential microbial response upon rewetting. Our objective was to investigate, in plant-soil systems, the response of the metabolically active microbial communities to a rewetting event and to which extent this was modulated by 1) soil depth and 2) precipitation legacy. Wheat planted in soil mesocosms were subjected to frequent or infr…

Evolution expérimentale

National audience

Technosols to reclaim industrial wastelands: depth distribution of abundance and activity of N-cycling microbial communities

International audience; Construction of Technosols through assemblage of treated soil and recycled wastes is an innovative option for the restoration of degraded lands and re-use of industrial wastes. Recent studies have evidenced that Technosols could support soil functions such as primary production but the knowledge about other ecosystemic services, such as nutrient cycling, is limited. In this work, we investigated the abundance and the activity of microbial communities involved in N-cycling in different horizons (0–15, 15–35, 35–70 cm) of two types of Technosols constructed to reclaim an industrial wasteland. The estimation by real-time PCR of the abundances of the different microbial …

Mitigation of N2O emissions in agroecosystems: the role of N2O-reducers

CT3 ; EnjS4 ; Département EA; Mitigation of N2O emissions in agroecosystems: the role of N2O-reducers. 16. International Symposium on Microbial Ecology - ISME16

Génétique et amélioration des plantes au sein du réseau PhytoMic

National audience

Shifts in microbial diversity through land use intensity as drivers of carbon mineralization in soil

10 pages; International audience; Land use practices alter the biomass and structure of soil microbial communities. However, the impact of land management intensity on soil microbial diversity (i.e. richness and evenness) and consequences for functioning is still poorly understood. Here, we addressed this question by coupling molecular characterization of microbial diversity with measurements of carbon (C) mineralization in soils obtained from three locations across Europe, each representing a gradient of land management intensity under different soil and environmental conditions. Bacterial and fungal diversity were characterized by high throughput sequencing of ribosomal genes. Carbon cycl…

Deciphering biotic interactions and their role in soil microbial community assembly

National audience; Soil microbial communities play key roles in ecosystem functioning. Yet, little is known aboutthe importance of microbe-microbe interactions in soil microbial community assembly andfunctions. To address this knowledge gap, the objective of my thesis is to assess the role ofinteractions between micro-organisms in soil microbial communities. For this purpose, we willmanipulate the interactions between microorganisms within complex soil microbialcommunities by (i) removing different members of the soil community, (ii) adding microbialtaxa to the soil community and (iii) increasing the physical distance between members of thesoil community. How shifts in microbial interaction…

Unraveling biotic interactions determining soil microbial community assembly and functioning

National audience; Microbial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial …

Predicting pesticide biodegradation potential from microbial community composition: new tools for bioremediation

Bioaugmentation is receiving increasing attention as a green technology to treat contaminatedareas by inoculating specific biodegrading microorganisms. However, our understanding of therole of microbial community composition and structure in the expression of contaminantdegradation potential is yet to improve. It could help making wise choice for microorganisms –community or specific strain – to be inoculated in contaminated soils with consideration to theirindigeneous microbiota.Here we tried to predict the microbial degradation of two herbicides, glyphosate andisoproturon by means of penalized regression and machine learning methods routinely used ingenomic selection. To this end, we cond…

Microbial metacommunity: a METABAR coding approach

Microbial metacommunity: a METABAR coding approach. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)

Loss in microbial diversity affects nitrogen cycling in soil

International audience; Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 s…

Effets des interactions entre diversité végétale inter et intraspécifique et communautés microbiennes du sol sur les propriétés de l’écosystème - Candidature à la bourse Phytomic

National audience; Le lien entre diversité et fonctionnement d’un écosystème ainsi que les mécanismes sous-jacents sont très étudiés en génétique des populations et en écologie des communautés et des écosystèmes. La première s’attèle à décrire les effets de la variabilité génétique intraspécifique sur différentes propriétés écosystémiques tandis que la deuxième s’intéresse aux interactions écologiques au niveau interspécifique. Notre objectif est de faire le lien entre ces deux champs disciplinaires par l’étude des effets conjoints d’une mobilisation de la diversité végétale intra et interspécifique et de la diversité microbienne sur les propriétés de l’écosystème. Nous avons mesuré différe…

Le partage des tâches favorise la coexistence dans les communautés bactériennes dégradant l’atrazine

National audience; Les communautés microbiennes exercent un rôle primordial dans la dégradation des xénobiotiques1, et en particulier des pesticides. Dans le cas de l’herbicide atrazine, plusieurs études ont démontré que sa dégradation faisait intervenir un consortium, plutôt qu’une espèce isolée2,3,4. Cependant, on ne sait pas comment la mise en place de ces consortiums dégradants se fait dans la nature. La théorie de la Reine Noire formalise les conditions nécessaires pour le mise en place de dépendance entre espèces5 : un membre de la communauté, appelé « helper », fournit un bien commun à la communauté par la dégradation d’un composé complexe, alors que les autres, appelés « beneficiari…

Predicting pesticide biodegradation potential from microbial community composition : new tools for bioremediation

Bioaugmentation is receiving increasing attention as a green technology to treat contaminated areas by inoculating specific biodegrading microorganisms. However, our understanding of the role of microbial community composition and structure in the expression of contaminant degradation potential is yet to improve. It could help making wise choice for microorganisms – community or specific strain – to be inoculated in contaminated soils with consideration to their indigeneous microbiota. Here we tried to predict the microbial degradation of two herbicides, glyphosate and isoproturon by means of penalized regression and machine learning methods routinely used in genomic selection. To this end,…

Recurrent inoculation: a strategy for a better survival of Pseudomonas fluorescens strain in soil

A growing interest is shown for microbial inoculants as a promising alternative to agrochemicals for sustainable agricultural. However, biotic and abiotic stresses are known to affect their establishment and effectiveness, leading to inconsistent performance in field conditions. At the same time, a poor survival of the strain is often observed, which constitutes a main hamper for bacterial inoculant development. We hypothesize that recurrent inoculations would improve the survival of the strain in soil. For this purpose, we tested different scenarios of inoculation of the plant growth promoting rhizobacteria Pseudomonas fluorescens in soil microcosms: a single inoculation, two inoculations …

Artificial selection of rhizosphere microbiota associated to phenotypical changes in plant functions

International audience; Artificial selection applied at community level is an important, but still growing topic at the interface of ecology and evolution. Its recent implementation to microbial communities holds appealing promises not only in terms of fundamental knowledge about selection itself and the levels at which it may be used, but also in terms of relevant applications to our societies, including bioremediation and agroecology. In this experimental evolution study, we performed an artificial selection of rhizosphere microbial communities inducing relevant phenotypic changes in plants. In total, we grew more than 2200 Brachypodium distachyon plants, consisting in ten consecutive gen…

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils—Case of Sulfamethazine-Degrading Microbacterium sp. C448

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, Micro…

Bacterial hppd: a biomarker of exposure of soils to beta-triketone herbicides?

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-d…

Effet de la diversité génétique sur l’efficacité de la sélection artificielle au niveau de la communauté : comment sélectionner des communautés microbiennes qui maximisent la fourniture d’azote aux plantes ?

National audience; La sélection artificielle, à l’origine des espèces animales et végétales d’intérêt agronomique, est classiquement exercée au niveau de l’individu, voire des gènes. Cependant, appliquer cette sélection au niveau supra-individuel permet l’accès à des sources de variation phénotypique supplémentaires introduites par les interactions inter-individuelles. Dans les procédures de sélection artificielle au niveau des communautés, comme dans les procédures classiques, la diversité tend à s’éroder au cours du temps ce qui peut altérer l’efficacité de la sélection. L’objectif de ma thèse est de déterminer comment la diversité génétique influence l’efficacité de la sélection artifici…

Recurrent inoculation: a strategy for a better survival of Pseudomonas fluorescens strain in soil

A growing interest is shown for microbial inoculants as a promising alternative to agrochemicals for sustainable agricultural. However, biotic and abiotic stresses are known to affect their establishment and effectiveness, leading to inconsistent performance in field conditions. At the same time, a poor survival of the strain is often observed, which constitutes a main hamper for bacterial inoculant development. We hypothesize that recurrent inoculations would improve the survival of the strain in soil. For this purpose, we tested different scenarios of inoculation of the plant growth promoting rhizobacteria Pseudomonas fluorescens in soil microcosms: a single inoculation, two inoculations …

Antibiotics favor the establishment of antibiotrophic bacteria in agricultural soil microbial communities, but are not always sufficient to enhance antibiotic-degradation: manure spreading can help.

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 …

Evidence of a core microbiota shaped by plant and earthworm interactions across soils

Prod 2018-139a EA AGROSUP INRA BIOME IPM; International audience; While having distinct niches, plants and earthworms have occupied soils over geological times, mutually influencing each-others. These macroorganisms are considered “ecosystem engineers”, actively modifying soil physical structure, which notably provides specific habitats for microorganisms: the rhizosphere and the drilosphere (casts/burrows produced by earthworms). In this study, we aimed to disentangle the relative importance of both macroorganisms in shaping microbial community assembly in different soil types, and determine the extent and modalities of how rhizosphere and drilosphere communities may coalesce with each-oth…

Sélection artificielle de microbiote rhizosphériques associés à des changements phénotypiques de traits de plante

International audience; La sélection artificielle appliquée au niveau des communautés est un sujet grandissant à l’interface de l’écologie et de l’évolution. Son implémentation relativement récente à l’écologie microbienne s’avère prometteuse non seulement en termes de connaissance fondamentale sur le principe de sélection en luimême, mais aussi en termes de potentiel d’application, notamment en bioremédiation et en agroécologie.Nous avons utilisé l’évolution expérimentale afin de sélectionner artificiellement des communautés microbiennes rhyzosphériques induisant des changements phénotypiques chez leurs hôtes. Durant dix générations consécutives, nous avons fait pousser plusieurs lignées d…

Impact of land use, pesticide application and agricultural management practices on the phosphorus foraging capacity of mycorrhizal fungi in 217 european agricultural soils

More than 80% of vascular plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Several studies have shown the potential of AMF to provide plants with phosphorus (P) via their hyphal network. Most of these studies have been performed in the greenhouse under controlled conditions using standardized soil mixtures. However, few studies have investigated hyphal P transfer in natural soils, severely limiting our understanding of the main drivers of P transfer by AMF in real agricultural soils. As a consequence, the potential of using AMF as a tool to increase crop yield remains a mystery. Using agricultural soils from a large field observation study in Europe, we aimed at a…

Loss in microbial diversity affects nitrogen cycling in soil

National audience; Microbial communities have a central role in ecosystem processes by driving the Earth’s biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequen…

A core microbiota of plant and earthworm interaction? Phylogenetic and functional aspects

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…

Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils

International audience; Introduction Agriculture is the main source of terrestrial N2O emissions, a potent greenhouse gas and the main cause of ozone depletion ((Hu et al., 2015). The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers (nosZII) was related to the potential capacity of the soil to act as a N2O sink (see Hallin et al., 2017 and references therein). However little is known about how this group responds to different agricultural practices. Here, we investigated how N2O-producers and N2O-reducers were …

Evolution expérimentale

EA SPE GESTAD BIOME; L'évolution expérimentale consiste à tenter de mener en laboratoire le processus d’évolution afin d’en étudier les règles de fonctionnement sous-jacentes. Les sources de variation dans la réponse sont analysées au cours d’expériences exécutées et répliquées en conditions contrôlées. Cette approche dynamique de l’évolution complète les études habituelles analysant l’évolution a posteriori au moyen de méthodes comparatives ou en étudiant des fossiles. Elle constitue également un pont entre les études conduites dans les conditions naturelles et les simulations réalisées par modélisation mathématique.

Assemblage, structuration et évolution des communautés microbiennes terrestres