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

International audience

Diuron mineralisation in a Mediterranean vineyard soil: impact of moisture content and temperature

BACKGROUND: The diuron-mineralising ability of the microbiota of a Mediterranean vineyard soil exposed each year to this herbicide was measured. The impact of soil moisture and temperature on this microbial activity was assessed. RESULTS: The soil microbiota was shown to mineralise diuron. This mineralising activity was positively correlated with soil moisture content, being negligible at 5% and more than 30% at 20% soil moisture content. According to a double Gaussian model applied to fit the dataset, the optimum temperature/soil moisture conditions were 27.9 °C/19.3% for maximum mineralisation rate and 21.9 °C/18.3% for maximum percentage mineralisation. The impact of temperature and soil…

Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil

Abstract The level of expression of highly conserved, plasmid-borne, and widely dispersed atrazine catabolic genes ( atz ) was studied by RT-qPCR in two telluric atrazine-degrading microbes. RT-qPCR assays, based on the use of real-time PCR, were developed in order to quantify atzABCDEF mRNAs in Pseudomonas sp. ADP and atzABC mRNAs in Chelatobacter heintzii . atz gene expression was expressed as mRNA copy number per 10 6 16S rRNA. In Pseudomonas sp. ADP, atz genes were basally expressed. It confirmed atrazine-degrading kinetics indicating that catabolic activity starts immediately after adding the herbicide. atz gene expression increased transitorily in response to atrazine treatment. This …

Genetic rearrangement of the atzAB atrazine-degrading gene cassette from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2

International audience; We report the characterization of the rearrangement phenomena responsible for the movement of the atrazine-degrading atzA and B genes from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2. Long PCRs and Southern blot analyses revealed that the two genes forming a gene cassette moved in a unique rearrangement event. It also revealed that the boundaries of the plasmid sequence inserted in the chromosome correspond to IS1071or to sequences close to IS1071. It suggests that this genetic rearrangement could result from the transposition of the composite transposon delimited by IS1071 insertion sequences and containing atzA and atzB genes. In addition, for MD1 an…

Caractérisation de populations microbiennes tolérantes au chlordécone à partir de sols contaminés des Antilles

Résistance aux antibiotiques et impact écologique chez les communautés microbiennes benthiques exposées a la contamination urbaine.

National audience

Multiple tools for antibiotics and AMR characterisation in aquatic ecosystems a 2-years monitoring study

International audience

Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions

A collection of 17 atrazine-degrading bacteria isolated from soils was studied to determine the composition of the atrazine-degrading genetic potential (i.e. trzN, trzD and atz) and the presence of IS1071. The characterization of seven new atrazine-degrading bacteria revealed for the first time the trzN-atzBC gene composition in Gram-negative bacteria such as Sinorhizobium sp. or Polaromonas sp. Three main atrazine-degrading gene combinations (i) trzN– atzBC, (ii) atzABC– trzD and (iii) atzABCDEF were observed. The atz and trz genes were often located on plasmids, suggesting that plasmid conjugation could play an important role in their dispersion. In addition, the observation of these gene…

Principaux processus impliqués dans l'atténuation naturelle des pesticides par les sols

Prod 2018-253e EA BIOmE INRA; National audience

Array of microbial indicators, a promise for a better monitoring of pesticide effects on stream biological quality

Visioconférence; National audience; Freshwater contamination by pesticide residues is a major and growing threat to aquatic communities, ecosystem functioning and ultimately human health worldwide. Typical pesticide contamination in agricultural landscapes is characterized by a cocktail of a large number of active compounds and their main transformation products, each of them found at very low and temporally fluctuating concentrations. This makes the quantification of pesticide residues in streams highly challenging and costly by means of grab chemical sampling. Accordingly, it makes also difficult to characterize the chronic exposure of aquatic communities in pesticide-contaminated streams…

Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil

International audience; The plasmid pADP1::Tn5 derived from pADP1[Atr(+)] carrying a TnS transposon conferring kanamycin and streptomycin resistances was constructed and introduced in Agrobacterium tumefaciens St96-4. This genetically modified strain was inoculated (similar to 108 cfu g(-1)) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg(-1)). Bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired pADP1::Tn5. Four transconjugants were isolated from four different soil samples. The estimated transfer frequency of pADP1::Tn5 was 10(-4) per donor. Maize rhizosphere and atrazine treatment had no…

Gene of non-target microorganisms : a new tool to monitor the exposure of soil microbial communities to b-triketone herbicides ?

International audience; β-triketone herbicides are among the most used herbicides in corn crop. These herbicides inhibit the 4-hydroxyphenylpyruvate dioxygenase (4-HPPD), lead to bleaching and prevent the growth of broadleaf weeds. This enzyme is not only found in plants but in all living organisms, including microorganisms where it plays a role in the tyrosine degradation pathway. Thus, microorganisms classified as “non-target organisms” by current EU regulation for pesticide authorization, might be impacted by β-triketones, with consequences on microbial function supporting soil ecosystem services. Since microorganisms have been proposed by EFSA as key-drivers to protect soil ecosystem se…

Influence de la biodégradation bactérienne des antibiotiques sur le devenir de ces substances et la dispersion des antibiorésistances dans les agrosystèmes

National audience; L’exposition environnementale des bactéries aux antibiotiques favorise la dispersion et le développement de capacités de résistance (antibiorésistance), engendrant un risque sanitaire majeur. Par ailleurs, il a récemment été mis en évidence dans des sols traités aux antibiotiques des bactéries capables d’utiliser ces substances pour leur croissance [1]. La dégradation bactérienne des antibiotiques pourrait être un moyen de réduire la pression de sélection positive qu’ils exercent sur la dispersion des antibiorésistances. Ma thèse se propose de vérifier cette hypothèse par l’exploration des scénarii de dispersion des capacités de résistance et de dégradation des antibiotiq…

Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent

Aims:  To characterize an atrazine-degrading bacterial community enriched from the wastewater of a herbicide factory. Methods and Results:  The community mineralized 81·4 ± 1·9% of [14C-ring]atrazine and 31·0 ± 1·8% of [14C-ethyl]atrazine within 6 days of batch cultivation in mineral salts medium containing atrazine as the sole nitrogen source. Degradation activity of the community towards different chloro- and methylthio-substituted s-triazine compounds was also demonstrated. Restriction analysis of amplified 16S rDNA revealed high diversity of bacterial populations forming the community, with Pseudomonas species dominating in the clone library. Atrazine-degrading genetic potential of the …

Sélection artificielle de communautés microbiennes : effet de la diversité génétique et rôle des interactions interspécifiques

National audience; La sélection artificielle, à l'origine des espèces animales et végétales utilisées en agriculture, alongtemps été appliquée à l’échelle de l’individu. Il est possible de transposer cette procéduresur des holobiontes, communautés ou écosystèmes ; toutefois, cela ajoute un niveau decomplexité puisque le phénotype cible de la sélection résulte de la présence de plusieurs espèceset, potentiellement, de leurs interactions. L'ambition de ce projet est i) de déterminer si unediversité génétique microbienne élevée permet d'améliorer l'efficacité de la sélection artificiellede communautés microbiennes et ii) de déterminer si les interactions entre espèces sontimpliquées dans la mi…

Etude des mécanismes à l'origine de la dispersion des gènes codant les enzymes responsables de la minéralisation de l'atrazine au sein de la microflore des sols

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…

A lab-to-field approach to monitor the exposure of soil microbial communities to β-triketone herbicides

International audience; β-triketone herbicides are among the most used herbicides in corn crop. These herbicides inhibit the 4-hydroxyphenylpyruvate dioxygenase (4-HPPD), lead to bleaching and prevent the growth of broadleaf weeds. This enzyme is not only found in plants but in all living organisms, including microorganisms where it plays a role in the tyrosine degradation pathway. Thus, microorganisms classified as “non-target organisms” by current EU regulation for pesticide authorization, might be impacted by β-triketones, with consequences on microbial function supporting soil ecosystem services. Since microorganisms have been proposed by EFSA as key-drivers to protect soil ecosystem se…

Evidence for 2,4-D mineralisation in Mediterranean soils: impact of moisture content and temperature

BACKGROUND: The 2,4-D degradation ability of the microbiota of three arable Mediterranean soils was estimated. The impact of soil moisture and temperature on 2,4-D degradation was investigated. RESULTS: The microbiota of the three soils regularly exposed to 2,4-D were able rapidly to mineralise this herbicide. The half-life of 2,4-D ranged from 8 to 30 days, and maximum mineralisation of 14C-2,4-D ranged from 57 to 71%. Extractable 14C-2,4-D and 14C-bound residues accounted for less than 1 and 15% respectively of the 14C-2,4-D initially added. The highest amounts of 14C-2,4-D bound residues were recorded in the soil with the lowest 2,4-D-mineralising ability. Although all three soils were a…

La nature du sol et la composition floristique comme facteurs de modulation de la diversité et de la fonctionnalité des communautés microbiennes en prairie permanente

National audience; La composition floristique, le mode d’exploitation (fauche, pâturage), l’intensité d’exploitation (chargement, fréquence des coupes, fertilisation) et la pérennité de la couverture végétale sont connus comme étant des facteurs déterminants du fonctionnement des prairies permanentes (Gaujour et al. 2012). Ces pratiques de gestion peuvent modifier les stocks de C directement en modulant les entrées de matières organiques (MO) (litière et/ou effluents d’élevage) et indirectement en orientant la composition et le fonctionnement des communautés végétales ce qui pourrait agir sur le temps de résidence et la localisation de la MO (Hassink et Neeteson 1991). Ce projet a pour obje…

Evaluation de l’impact des pesticides sur des fonctions écosystémiques terrestres

Dans la cadre l’évaluation du risque environnemental menée pour obtenir l’autorisation de mise sur le marché, l’évaluation a prioride l’impact des pesticides sur les microorganismes du sol est estimée par deux tests OCDE mesurant la minéralisation de l’azote et du carbone. Ces deux tests globaux ne rendent pas compte des modifications potentielles d’abondance, de diversité et d’activité de la communauté microbienne des sols exposée aux pesticides. Dans ce contexte, le projet IMPEC visait à développer des indicateurs microbiens pour évaluer l’impact des pesticides sur des fonctions écosystémiques supportées par la communauté microbienne. Cette présentation aura pour objectif de présenter une…

Evaluation of the ecotoxicological impact of pesticides on the diversity and the abundance of soil microorganisms

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…

Taxonomic and functional diversity of atrazine‐degrading bacterial communities enriched from agrochemical factory soil

Aims: To characterize atrazine-degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes. Methods and Results: The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65–80% of 14C ring-labelled atrazine. The presence of trzN-atzBC-trzD, trzN-atzABC-trzD and trzN-atzABCDEF-trzD gene combinations was determined by PCR. In all enriched communities, trzN-atzBC genes were located on a 165-kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restricti…

Fitness drift of an atrazine-degrading population under atrazine selection pressure.

International audience; Pseudomonas sp. ADP harbouring the atrazine catabolic plasmid ADP1 was subcultured in liquid medium containing atrazine as sole source of nitrogen. After approximately 320 generations, a new population evolved which replaced the initial population. This newly evolved population grew faster and degraded atrazine more rapidly than the initial population. Plasmid profiles and Southern blot analyses revealed that the evolved strain, unlike the ancestral strain, presented a tandem duplication of the atzB gene encoding the second enzyme of the atrazine catabolic pathway responsible for the transformation of hydroxyatrazine to N-isopropylammelide. This duplication resulted …

Dynamique des antibiotiques et des antibiorésistances dans les agrosystèmes : Réponse écotoxicologique et adaptation des communautés microbiennes terrestres

National audience; La contamination environnementale par les antibiotiques favorise la dispersion de bactéries antibiorésistantes, ainsi que le développement de bactéries dégradantes pouvant les utiliser pour leur croissance. Propices pour réduire la contamination environnementale et donc la dispersion de l’antibiorésistance, elles représentent toutefois un danger potentiel envers l’efficacité des antibiotiques avec l’éventualité de transmissions de leur capacité aux microorganismes pathogènes. Ainsi, ma thèse a pour but d’explorer les scénarii de dispersion des capacités de résistance et de dégradation dans le contexte agricole de l’épandage de lisier porcin contaminé en antibiotique sulfa…

The impact of urban contamination on antibioresistance in microbial communities from periphyton and sediments

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 an…

Ecotoxicological impact of oxamyl on the abundance and diversity of bacterial communities in an agricultural soil adapted to enhanced degradation

Pesticides are largely applied to crops and end up on soils where they may affect non-target soil microorgan-isms involved in important ecosystem functions. Although in the past two decades microbial-ecology and –ecotoxicology were revolutionized by the incredible developments of molecular methods applied to nucleic acids (both DNA and RNA), within the EU regulation the current evaluation of the ecotoxicological effects of pesticides on soil microorganisms relies on single broad test (i.e. carbon mineralization), non-sensitive enough to detect shifts in diversity and function of microorganisms. Within the framework of the Love-to-Hate IAPP EU project, we tested the interest for combining hi…