Membre du comité d'organisation logistique et scientifique

visioconférence, France, 6-9 octobre 2020; 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…

Estimation of the density of the protocatechuate-degrading bacterial community in soil by real-time PCR

Summary The β-ketoadipate pathway is the major route for degradation of aromatic compounds by various soil microorganisms. Protocatechuate 3,4-dioxygenase, a key enzyme of this pathway and which is encoded by pcaGH genes, catalyses the ring cleavage of protocatechuate. Microorganisms harbouring pcaGH genes are widely distributed in the environment but little is known about their relative abundance within the total microflora. Hence, this paper reports the development of a real-time PCR assay to quantify the bacterial pcaH sequence that encodes the β sub-unit of the protocatechuate 3,4-dioxygenase. This real-time PCR assay was linear over seven orders of magnitude with a calculated efficienc…

Biotic control of atrazine degradation in soils: functional diversity of degradation and macrofauna effects.

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Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR.

Abstract Denitrification, the reduction of nitrate to nitrous oxide or dinitrogen, is the major biological mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Microorganisms capable of denitrification are widely distributed in the environment but little is known about their abundance since quantification is performed using fastidious and time-consuming MPN-based approaches. We used real-time PCR to quantify the denitrifying nitrite reductase gene (nirK), a key enzyme of the denitrifying pathway catalyzing the reduction of soluble nitrogen oxide to gaseous form. The real-time PCR assay was linear over 7 orders of magnitude and sensitive down to 102 copies by assa…

Natural products for biocontrol: Fate in the environment and impact on biodiversity

In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: Evidence for the selective loss of a 47kb region on the plasmid ADP1 containing the atzA, B and C genes

International audience; The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original on…

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 …

Retour sur les journées d’écotoxicologie microbienne

National audience; Les Journées d’Écotoxicologie Microbienne, organisées à Lyon du 20 au 22 mars 2013, avaient pour objectifs de réunir pour la première fois les chercheurs traitant de cette thématique afin i) de dresser un état des lieux des forces en présence dans ce domaine à l’échelle nationale, et ii) d’engager une réflexion collective quant à ses évolutions futures. Rassemblant une quarantaine de chercheurs représentant plus de 25 laboratoires répartis sur toute la France, elles ont permis, à partir d’une enquête web menée au préalable auprès des chercheurs, d’une étude bibliométrique et d’une démarche participative innovante (de type «world café»), d'identifier dans un premier temps …

Adaptation des communautés microbiennes aux polluants chimiques

L’Homme au travers des activités industrielles, agricoles,…, qu’il développe, exerce une pression de plus en plus prégnante sur l’environnement et sur les organismes qui y vivent. La pression anthropique est quasi-généralisée à la surface du globe terrestre. Elle se caractérise par le relargage et la dispersion de nombreux polluants organiques et métalliques, conduisant des scientifiques à proposer que l’humanité était entrée, depuis la révolution industrielle, dans l’anthropocène, une nouvelle époque géologique. Les sols arables qui nourrissent l’humanité ne sont pas indemnes de contaminations. Ils sont fréquemment exposés aux intrants chimiques et organiques employés dans les itinéraires …

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…

Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation.

International audience; Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of th…

Bilan 2019 des activités du réseau ECOTOX

Rapport final du projet Antibiotools - Des outils pour caractériser et suivre les antibiotiques et antibiorésistances dans les écosystèmes aquatique (PNREST Anses, 2017/3 ABR/22)

Transcriptomic and proteomic responses of Microbacterium sp. C448 exposed to sulfamethazine antibiotic

International audience; The Microbacterium sp. C448 was isolated from a soil regularly exposed to sulfamethazine(SMZ), for its ability to partly mineralise this antibiotic and other related sulfonamides.The aim of our study was to explore its metabolic adaptation towards exposure to SMZenvironmental (10 mg/L) and medicinal (250 mg/L) concentrations. Its transcriptomic andproteomic responses were analysed by focusing on the degradation regulon (sad genes) andresistance genes (folP and sul1).The transcriptomic and proteomic results were essentially congruent whatever theconcentrations tested. In culture conditions, exposure to the highest concentration of SMZ led tothe highest sad expression …

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

Solutions de biocontrôle : Devenir dans l'environnement et impacts écotoxicologiques

51 ème congrès du Groupe Français de Recherches sur les Pesticides 31 mai-1 er juin 2023, Paris

Nouvelles tendances pour les recherches en écotoxicologie terrestre

L’écotoxicologie fait aujourd’hui face à des enjeux qui concernent une meilleure connaissance des effets différés dans le temps et l’espace de mélanges de composés en faibles doses, sur des communautés d’organismes non cibles. Des approches classiquement basées sur l’abondance, a diversité et l’activité des organismes montrent des limites d’interprétation, car souvent soumises à des facteurs confondants ou à des interactions dans un contexte de changements globaux. C’est notamment le cas dans les agroécosystèmes où les pratiques agricoles, la couverture du sol peuvent masquer des effets spécifiques liés à l’apport de contaminants. Nous présentons ici quelques approches en émergence en écoto…

Utilisation des mécanismes d'adaptation microbienne pour caractériser les conséquences écologiques de l'interdiction d'utilisation du diuron en zone viticole

National audience

Intérêt de la normalisation de méthodes pour la recherche publique et la société

Biocontrôle : impacts écologiques et durabilité

Evidence for the adaptation of bacterial populations to antibiotics degradation in agricultural soils

A recent study has reported accelerated biodegradation of antibiotics in agricultural soils repeatedly amended with sewage manure contaminated by veterinary antibiotics. This pioneer work carried out by the research team directed by Dr E Topp (Agriculture and Agri-Food Canada) led to the characterization of sail microbial communities able to degrade sulfamethazine, an antibiotic belonging to sulphonamides. They showed that up to 30% of 14C0

Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example

ABSTRACT We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.

Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis.

The ability of facultative anerobes to respire nitrate has been ascribed mainly to the activity of a membrane-bound nitrate reductase encoded by the narGHJI operon. Respiratory nitrate reduction is the first step of the denitrification pathway, which is considered as an important soil process since it contributes to the global cycling of nitrogen. In this study, we employed direct PCR, cloning, and sequencing of narG gene fragments to determine the diversity of nitrate-reducing bacteria occurring in soil and in the maize rhizosphere. Libraries containing 727 clones in total were screened by restriction fragment analysis. Phylogenetic analysis of 128 narG sequences separated the clone famili…

Explorer les impacts des débris plastiques sur la santé des sols et la productivité agricole : le projet MINAGRIS

Bien que les quantités de plastiques qui pénètrent dans les sols soient égales, voire supérieures, à celles qui atteignent nos rivières, nos mers et nos océans, l'impact des débris plastiques sur la santé des sols est largement méconnu. MINAGRIS, projet financé par l'UE et démarré en septembre 2021, va étudier comment les débris plastiques affectent la biodiversité des sols, leurs fonctions, les services écosystémiques associés et la productivité agricole.

Effect of primary mild stresses on resilience and resistance of the nitrate reducer community to a subsequent severe stress

International audience; The factors regulating soil microbial stability (e.g. resistance and resilience) are poorly understood, even though microorganisms are essential for ecosystem functioning. In this study, we tested whether a functional microbial community subjected to different primary mild stresses was equally resistant or resilient to a subsequent severe stress. The nitrate reducers were selected as model community and analysed in terms of nitrate reduction rates and genetic structure by narG PCR-restriction fragment length polymorphism fingerprinting. Heat, copper and atrazine were used as primary stresses and mercury at a high concentration as a severe stress. None of the primary …

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

National audience

Developing and evaluating tools for assessing the impact of low-dose herbicide nicosulfuron on soil microbial diversity and functioning

Today's conventinal agriculture still relies on the general use of pesticides. Even thought this guarantees production capabilities it also causes environmental pollution having impact on non-targeted organisms. Agricultural practices have been recognized by "The European Soil Framework Directive" as a major threat for soil biodiversity. However, without taking into consideration. recent methodological advances in microbiology, pesticide regulation at EU level relying solely on simple C and N mineralization tè-sts•. ln order to cope with this ECOFUN­-MICROBIODIV project .aim to develop and evaluate tools to estimate the impact of herbicide nicosulfuron on the function and population dynamic…

Regulating role of lumbricid macrofauna in Atrazine biodegradation in temperate cropped soil.

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Soil Microbial ecotoxicology towards the standardization

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 …

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

International audience

Evaluation du risque des intrants chimiques sur les microorganismes des sols agricoles

International audience; Les sols agricoles ne sont pas uniquement le support inerte des productions végétales et animales mises en place pour nourrir une population humaine toujours grandissante. Les sols constituent une niche écologique qui héberge de nombreux organismes (macro-, meso- et micro-faune, microorganismes) qui accomplissent de nombreuses fonctions et jouent un rôle important dans la santé des cultures, mais aussi plus globalement des écosystèmes. Toutefois, les sols sont en danger, car comme les autres composantes de l’environnement, ils sont soumis aux changements climatiques mais aussi à de nombreuses pressions anthropiques qui altèrent ses composantes abiotiques et biotiques…

Development of a new functional marker for β-triketone herbicides exposure in agricultural soils

The β-triketone herbicides are maize selective herbicides that have been largely applied in replacement of atrazine, banned in Europe in 2003. Their mode of action lays on the inhibition of the p-hydroxyphenylpyruvate dioxygenase (HPPD), a key enzyme of the carotenoid biosynthesis. In recent studies, we showed that within the soil bacterial community, many microorganisms possess a functional HPPD enzyme involved in tyrosine metabolism. These “non-target organisms” harbor the target of the β-triketone herbicides and consequently may be affected in response to its exposure. Within this context, the objective of our work is to check for the interest of hppd bacterial community as a marker of e…

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of physicochemical and microbiological soil parameters, 411-417

International audience

Impact of maize mucilage on atrazine mineralization andatzC abundance

Soil was amended with maize mucilage, a major rhizodeposit, to study its role on the number of culturable soil micro-organisms, the structure of the bacterial community, atrazine mineralization and atzC abundance. The maximal percentage of atrazine mineralization was lower for mucilage-amended than for water-amended soil. Total culturable soil bacteria and 16S rDNA copy number, measured by RT-PCR, presented similar values and were not significantly (P < 0.05) different among treatments. Mucilage applied at a rate of 70 mu g C g(-1) dry soil day(-1) over two weeks did not modify the abundance of the total soil microflora. Global structure of soil bacterial communities revealed by RISA analys…

Evaluation de l’impact écotoxicologique des pesticides sur les microorganismes du sol

Arbuscular mycorrhizal symbiosis: a key actor in the soil for water quality preservation processes

National audience

Assessment of the effect of pesticides on soil microorganisms

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…

Les microorganismes dégradants des composés chimiques, moteur de la bioremédiation des sols pollués ? Exemples d’essai en conditions contrôlées de biostimulation, de bioaugmentation et de bioprophylaxie

Assessment of ecotoxicological impact of pesticides on microbial functions in agroecosystems: how to define suitable indicators and for what purposes?

Assessment of ecotoxicological impact of pesticides on microbial functions in agroecosystems: how to define suitable indicators and for what purposes?. 7th edition of the International Conference on Pesticide Behaviour in Soils, Water and Air

Biotic control of Atrazine degradation in soils: Impacts of earthworms on atrazine-degrading bacterial communities.

PosterFR2116Poster

Prediction of the fate of pesticides in the environment from their molecular properties

Manuela Cigolini, M. ,Luzzani, G., Sacchettini, G. (eds)Manuela Cigolini, M. ,Luzzani, G., Sacchettini, G. (eds); Prediction of the fate of pesticides in the environment from their molecular properties. XV Symposium in Pesticide Chemistry “Environmental risk assessment and management

Soil microorganisms for the environmental risk assessment of pesticides: where are we and where are we going? Keynote conference

Soils host a tremendous biodiversity among which microorganisms which are accomplishing a wide range of functions supporting soil ecosystem services. Arable soils are threatened by agricultural practices which are still highly dependent on pesticide use. Within this context this talk will exposed how microorganisms can be better implemented in the environmental risk assessment of pesticides to better protect soils

ECOFUN-MICROBIODIV : an FP7 European project to estimate the ecotoxicological impact of low dose pesticide application in agriculture on soil functional microbial diversity

Soil is hosting a tremendous microbial diversity playing a key-role in a number of soil ecosystemic services including nutrient cycling and filtering. ln the European Soil Framework Directive pesticides are clearly marked as one of the major threats for soil biodiversity and functioning. ln orcier to guarantee minimum effects of pesticide application on soil microbes, pesticicleregistration at EU level (Regulation 2006/388) consiclers the toxicity of pesticides ontci non targefsoil microbes by relying on carbon- and nitrcigen-mineralization tests (OECO 216, 217). However tnese tests do not provicle a comprehensive assessment of pesticides onto soil microbes.-ECOFUN-MICROBIODIV was a project…

Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils

ABSTRACT Microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. The diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. The narG gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. The use of narG is of special interest because the phylogeny of the narG gene closely reflects the 16S ribosomal DNA phylogeny. Therefore, targeting the narG gene provided for the first time a unique insight into the taxonomic composition of the nitrate-reducing community in planted an…

Evolution of genetic degradation potential of pesticide-degrading bacterial communities

International audience

Towards the identification and quantification of candidate metabolites of tebuconazole fungicide

International audience; Tebuconazole belongs to the family of triazole fungicides, used for crop protection and human health applications. In the environment, the dissipation of the parent molecule leads to the formation of metabolites that are of unknown identity or toxicity. In order to identify and determine the putative identity of those metabolites and their po- tential toxicity, a quadrupole time-of-flight (Q-TOF) approach is often used. Q-SAR approaches help to predict their toxicity by comparing them to a known database of molecules with known properties. All together the information on the candidate by-products may help to select relevant sub-set of metabolites for further quantifi…

Role of microbes in sustaining the health of soil ecosystems: pesticide soil microbial ecotoxicology as a study case

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…

L’écotoxicologie microbienne au service de l’évaluation du risque écotoxicologique des pesticides pour les sols

Genomic approach to search for IPU degrading gene: catA as a possible gene target responsible for 4- isopropyl aniline degradation

Affiche, résumé étendu; Genomic approach to search for IPU degrading gene: catA as a possible gene target responsible for 4- isopropyl aniline degradation

Assessment of pesticides ecotoxicology on soil microorganism

National audience

Ecotoxicological impact of pesticides on natural microbial communities responsible for pesticide biodegradation in river sediments

International audience; The general use of pesticides in various crops allows ensuring the quality of the crop production but has environmental impact, pesticide residues being often found in water resources, notably river in the agrosystems. As a result of repeated exposure to pesticides microorganisms can adapt to their degradation being responsible for enhanced degradation, an environmental friendly process diminishing the persistence of pesticide residues in the environment. This process can occur in the soil but also in the sediment of the river regularly exposed to pesticide contamination. To our best knowledge the ecotoxicological impact of multiple pesticides contamination on the de…

Effect of inoculation with selected Bradyrhizobium spp. on the survival and growth of Acacia mangium saplings after 20 months in the field

This work was designed to test the long-term effect of the inoculation of #Acacia mangium# seedlings with 10 selected strains of #Bradyrhizobium spp.#. The percentage of survival of seedlings inoculated with any of the #Bradyrhizobium# strains was increased by 10% as compared to the control plants. However, out of the 10 #Bradyrhizobium# strains tested, only 3 strains, Aust l3c, Lu 4 and Tel 8, belonging to the phylogenelic group 1, significandy enhanced the growth of #A. mangium# after 20 months in the field. For the first time, inoculation with indigenous Malaysian strains #Bradyrhizobium# such as Tel 8 and Lu 4 at the seedling stage is reported to produce enhanced and sustained growth an…

Potential for microbial diuron mineralisation in a small wine-growing watershed: from treated plots to lotic receiver hydrosystem

BACKGROUND: Since biological degradation processes are known to be a major driver of the natural attenuation of pesticide residues in the environment, microbial communities adapted to pesticide biodegradation are likely to play a key environmental role in reducing pesticide exposure in contaminated ecosystems. The aim of this study was to assess the diuron-mineralising potential of microbial communities at a small-scale watershed level, including a diuron-treated vineyard (pollution source), its associated grass buffer strip (as a river protection area against pesticide runoff) and the lotic receiver hydrosystem (sediments and epilithon), by using radiorespirometry. RESULTS: Comparison of r…

Table Ronde : Focus sur l’expertise - Relation Entreprises / Recherche Académique

Bilan 2020 des activités du réseau ECOTOX

pas de résumé

Evidence for the interest of suspect screening metabolomics to identify known and unkown pesticide metabolites in soil

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…

International ring test for evaluating method for direct soil DNA extraction

Importance of genetic plasticity for microbial adaptation to pesticide biodegradation: in vitro evolution of Pseudomonas sp. ADP under atrazine or cyanuric acid selection pressure as case studies

International audience

L’holobionte vigne, un levier biologique pour lutter contre les dépérissements ?

National audience

RNA and degradation enzyme gene expression

Relevance of different soil fauna and microflora groups in the monitoring of soil biodiversity: RMQS-Biodiv, a French pilot area experience.

PosterFR2116Poster

Qualité du Sol - Méthode pour extraire directement l'ADN d'échantillons de sol (Norme française - internationale)

La présente Norme internationale spécifie une méthode pour extraire directement l'ADN d'échantillons de sol en vue d'analyser la structure globale et l'abondance des communautés microbiennes du sol en utilisant des techniques de PCR. Cette méthode est principalement destinée aux sols agricoles et forestiers. Cette méthode peut ne pas être appropriée aux sols riches en matières organiques (par exemple sols de tourbières) ou aux sols très pollués par des polluants organiques ou des métaux lourds. L'extraction directe de l'ADN d'échantillons de sol fournit des informations précieuses sur l'abondance et la structure des communautés microbiennes qui sont des paramètres clés pour estimer la biodi…

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality -- Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Genetic plasticity of atrazine-degrader: evidence for the deletion of atzABC genes in pseudomonas sp. adp in response to cyanuric acid selection pressure

International audience; Several bacterial strains are known to metabolize s-triazines herbicides among which atrazine reported worldwidel to contaminate soil and water resources. The complete mineralization of atrazine to carbon dioxide and ammonium is catalyzed by 6 hydrolytic enzymes encoded by atzABCDEF genes located on the plasmid pADP1 in Pseudomonas ADP. The atzABC genes code for the upper pathway transforming atrazine to cyanuric acid, while the atzDEF genes code for the lower pathway transforming cyanuric acid to simple compounds. In order to study the genetic plasticity of the atrazine catabolic pathway, we performed an in vitro evolution study consisting in applying a continuous s…

Herbicide degradation in temperate soils : effects of earthworms interaction with indigenous and atrazine degrading bacterial communities

poster

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…

Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil

FR2116; In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s- triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atr…

Interactions biotiques entre macrofaune lombricienne et les communautés microbiennes, indigènes et bioaugmentées, dégradant l'atrazine en sol tempéré.

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Soil quality - Method to directly extract DNA from Soil Samples. ISO/ DIS 11063

DNA (deoxy ribonucleic acids) is an essential component of any living organisms coding for enzymes responsible for any biological activities. The study of DNA sequences from DNA sources extracted from different matrixes, by means of numerous molecular approaches, provides molecular markers that can be used to sharply distinguish and identify different organisms (bacteria, archaea and eucaryotes). Up to now, most of the studies aiming to develop microbial soil quality indicators applicable to complex environment, such as soil, were biased by the unculturability of many microorganisms and the lack of sensitivity of traditional microbiological methods. The recent development of numerous molecu…

Développement d'indicateurs microbiens pour l'évaluation de l'impact des pesticides sur des fonctions écosystémiques terrestres et aquatiques

National audience

Ecologie des communautés microbiennes dégradant des pesticides dans l’environnement

Regulation of bacterial and fungal MCPA degradation at the soil–litter interface

Abstract Much is known about mechanisms and regulation of phenoxy acid herbicide degradation at the organism level, whereas the effects of environmental factors on the performance of the phenoxy acid degrading communities in soils are much less clear. In a microcosm experiment we investigated the small-scale effect of litter addition on the functioning of the MCPA degrading communities. 14 C labelled MCPA was applied and the functional genes tfdA and tfdAα were quantified to characterise bacterial MCPA degradation. We identify the transport of litter compounds as an important process that probably regulates the activity of the MCPA degrading community at the soil–litter interface. Two possi…

Biodégradation de molécules xénobiotiques par la microflore du sol

Microcosm assessment of the dissipation and soil microbial ecotoxicity of chlorpyrifos and tebuconazole using standardized advanced molecular tools

International audience

Biodiversity-based agroecological system experiments to test agroecological weed management at various temporal and spatial scales: The CA-SYS and ABY platforms

Functional metagenomics on biobed systems : Evolutionary mechanisms of known and isolation of novel pesticide biocatalytic enzymes

Ecotoxicological impact of low dose herbicide nicosulfuron on soil microbial biodiversity and functioning

[div]Long-term dynamics of the atrazine mineralization potential in surface and subsurface soil in an agricultural field as a response to atrazine applications[/div]

Abstract The dynamics of the atrazine mineralization potential in agricultural soil was studied in two soil layers (topsoil and at 35–45 cm depth) in a 3 years field trial to examine the long term response of atrazine mineralizing soil populations to atrazine application and intermittent periods without atrazine and the effect of manure treatment on those processes. In topsoil samples, 14 C-atrazine mineralization lag times decreased after atrazine application and increased with increasing time after atrazine application, suggesting that atrazine application resulted into the proliferation of atrazine mineralizing microbial populations which decayed when atrazine application stopped. Decay …

Do crop genotypes have residual effects on Glomeromycota communities in agro-systems

International audience

Comment les sols atténuent-ils naturellement les pesticides ?

prod 2018-138 BIOmE INRA; National audience

Evidence de l'adaptation des communautés microbiennes sédimentaires de rivière à la minéralisation du diuron: influence du ruissellement et de l'érosion des sols

International audience; Purpose Surface runoff and erosion are major drivers of pesticide transport from soils to rivers draining vineyard watersheds. A recent study showed that applications of diuron on vineyards and diuron dispersal could lead to microbial adaptation to diuron biodegradation from treated soils to the receiving hydrosystem. Given the limited knowledge on microbial adaptation to pesticide degradation in aquatic environments, we conducted a microcosm study designed to assess the impact of runoff and erosion processes on the adaptation of riverine-sediment microbial communities to diuron mineralization. Materials and methods The experimental laboratory set-up consisted in aqu…

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 …

How to manage and analyse a large biodiversity data set: the case of the regional ‘RMQS Biodiv' experience

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New approach to identify and categorize pesticide metabolites in soil combining suspect screening metabolomics with in silico molecular typology. 5th International Conference on Environmental Pollution and Remediation (ICEPR)

New approach to identify and categorize pesticide metabolites in soil combining suspect screening metabolomics with in silico molecular typology. 5th International Conference on Environmental Pollution and Remediation (ICEPR). 5th International Conference on Environmental Pollution and Remediation (ICEPR)

Do we need a new regulatory framework for assessing the soil microbial ecotoxicity of pesticides?

International audience

Molecular analysis of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHs

International audience; A PCR-based molecular tool was developed to estimate the diversity of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHS. A degenerate primer pair specific to catA sequences was designed by multiple alignment of known sequences coding a key intermediate of the β-ketoadiapate pathway degrading catechol, namely catechol 1,2-dioxygenase. The specificity of this primer pair was assessed in 21 pure strains by PCR and sequencing. Comparison of the 16S rDNA and catA phylogenies revealed an absence of congruence between these two genes. The primer set was able to amplify catA sequences in DNA extracts from an industrial soil highly …

Isolation and characterisation of an isoproturon-mineralisingMethylopilasp. TES from French agricultural soil

Using enrichment culture three isoproturon (IPU) mineralising bacterial isolates were isolated from a French agricultural soil mineralising up to 50% of the initially added 14C-ring labelled IPU within only eight days. These isolates showed similar metabolic (BIOLOG GN) and amplified rDNA restriction (ARDRA) profiles. Partial 16S rDNA sequencing revealed that they were identical and identified as Methylopila sp TES. This strain harbours a large plasmid (220 kb) putatively bearing essential IPU-degrading genes as demonstrated by a curing experiment. Methylopila sp. TES transformed IPU and its known metabolites to CO2 and biomass but did not degrade chlorotoluron, monolinuron, diuron and linu…

Response of soil bacterial and hppd communities to tembotrione herbicide

Herbicides used in agriculture aim to prevent weed growth but are known to end up in contactwith soil microorganisms, thus defined as non-target organisms. Tembotrione, a recentlymarketed β-triketone herbicide, is known to inhibit the 4-HydroxyPhenylPyruvateDioxygenase(4-HPPD) in weeds. This enzyme is also found in numerous soil microorganisms, such as somePGPR and symbiotic bacteria, that play a key role in maintenance of ecosystem services.In this study, one of the major concerns is to assess whether tembotrione could have toxiceffects on soil microorganisms and could disturb soil microbial community dynamic andstructure. To investigate the possible impacts of this herbicide on these comm…

Use of PCAH as a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in soil environment

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling. The pcaH gene encoding a key ring-cleaving enzyme of the β -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two soils. The RFLP screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70 % identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This gene constitutes a suitable molecular marker to study the diversity of this functional group.

Evaluation of the environmental fate and ecotoxicological impact of the pesticide chlorpyrifos in soil for improvement of its environmental risk assessment

EABIOMEUBINRA; Pesticides protect crops from various pests but can also harm nontarget organisms. To minimize risks for the environment and human health, a huge amount of studies are carried out and evaluated during the authorization process of each pesticide. However, the prediction of the environmental fate and ecotoxicological impact of a pesticide remains difficult. Several 100 formerly used pesticides are now banned because unexpected risks emerged decades after their authorization. Risk assessment documents of the organophosphate insecticide chlorpyrifos (CHL) particularly lack information about its degradation and potential transformation products in soil, and its impact on non-targe…

Indicateurs pour l'évaluation de l'impact de produits phytosanitaires sur la composante microbienne de la qualité biologique des sols

National audience

Devenir et impacts écotoxicologiques des produits phytosanitaires dans les sols

How pesticides are affecting soil microorganisms?

Ecologie microbienne appliquée et dépollution - Les micro-organismes acteurs majeurs de l'élimination des pollutions qui affectent l'environnement

Chapitre 16; National audience

Antibiotrophie : une fonction émergente favorisant l’implantation des bactéries antibiorésistantes dans les sols

National audience; La fonction antibiotrophique, permettant l’utilisation d’antibiotiques comme source nutritive, arécemment été découverte chez des bactéries antibiorésistantes environnementales. Pourvérifier si leur avantage sélectif en environnements pollués s’en trouvait augmenté, nous avonsconduit une expérience en microcosmes dans laquelle Microbacterium sp. C448 (C448),présentant des capacités de résistance et de dégradation vis-à-vis des sulfamides, a été inoculéedans quatre sols supplémentés ou non par l’antibiotique sulfaméthazine (SMZ) et/ou du lisier.Après un mois d’incubation, C448 n’a été détectée que dans les sols traités avec la SMZ,indiquant une faible compétitivité de la s…

Membres du comité d’organisation scientifique

EA BIOME INRA; National audience

Impact of a new bio-pesticide produced by Paenibacillus sp. strain B2 on the genetic structure and density of soil bacterial communities

The effect of paenimyxin, a new biopesticide produced by Paenibacillus sp. strain B2, on the density of soil bacterial communities was assessed by colony counting and by 16S rDNA and nirK quantitative polymerase chain reaction (PCR). Paenimyxin had a negative effect on the bacterial colony-forming unit (CFU) number, which was significantly reduced 2 and 4 days after treatment. The effect of paenimyxin on cultivatable bacteria was negligible 7 days after treatment. Approximately 107 16S rDNA sequences per gram of soil (dry weight) were detected by quantitative PCR in all samples. Paenimyxin did not affect the quantification of 16S rDNA or of the denitrifying bacterial community. In addition,…

Développement d’indicateurs microbiens pour l’évaluation de l’impact des pesticides sur des fonctions écosystémiques terrestres et aquatiques

Les dernières évolutions réglementaires incitent les agriculteurs à diminuer le recours aux pesticides mais les pratiques agricoles en dépendent encore largement. Les conséquences environnementales de l’application de pesticides sont constatées par la détérioration de la qualité des masses d’eau. L’impact de la contamination des agrosystèmes par des résidus chimiques sur les fonctions remplies par la biodiversité reste peu décrit. Le projet IMPEC vise à développer des méthodes pour évaluer l’impact produit par des pesticides sur les communautés microbiennes terrestres et aquatiques ainsi que sur les fonctions écosystémiques qu’elles assurent.

Biodegradation of pesticides by soil microflora

Pesticides, microorganismes des sols et qualité de l'environnement

Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR

Abstract Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR® Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08×108 and 1.12×1011 copies per gram of dry weight of environmental sample. Environmental real-…

Understanding the microbiological and physicochemical influence of alperujo vermicompost on diuron behaviour and soil quality

Vermicompost as soil organic amendment increase the yield crops because improve the soil structure, the water retention capacity, the microbial biodiversity and thereby its metabolic activity. Vermicompost is also thought to reduce the pesticide pollution. The vermicompost selected was composed of “alperujo” which is largest organic residue in olive oil production. Agricultural soil was 5% amended twice and incubated for 3 months. A 3µg g-1 agricultural dosage of Diuron was applied to amended and unamended soils. The effect of alperujo vermicompost on dehydrogenase activity, the biodiversity and estimated bacterial density, the density of protocathechuate-degrading bacterial community and d…

Impact of phosphate fertilization and arbuscular mycorrhiza on the development, nutrition and quality of micropropagated walnut rootstocks.

The English walnut (Juglans regia L.) is the main species cultivated for the production of edible nuts. Due to heterozygosis, the characteristics of agronomical interest of walnut cultivars are not inherited via seed propagation. In vitro plant tissue culture thus plays a key role in mass propagation of high-quality walnut rootstocks. Micropropagation of walnut explants needs an ex vitro acclimatization phase to repair the in vitro induced abnormalities, and further requires a post-acclimatization growth in greenhouse conditions when plantlets become photoautotrophic. However, poor survival and slow growth rates are common difficulties encountered in nurseries when establishing micropropaga…

Etude du devenir du chlordécone dans les sols Antillais

National audience

Plant beneficiating from arbuscular mycorrhizal symbiosis: impact of fungal diversity and soil fertilization

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…

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,…

Corrigendum to “Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR” [J. Microbiol. Methods 59 (2004) 327–335]

Enhanced isoproturon mineralisation in a clay silt loam agricultural soil

International audience; 14C-ring-labelled isoproturon mineralisation was investigated in a French agricultural soil previously exposed to isoproturon. 50 different soil samples collected every 2 m along a transect of 100 m in length were treated one or two times with isoproturon under laboratory conditions and analysed by radiorespirometry. 94% of the soil samples showed a high ability to mineralise isoproturon with a relatively low variability in the cumulative percentage of mineralisation ranging from 30 to 51% of the initially added radioactivity for the samples treated once with the herbicide. About 45 to 67% of the initially added radioactivity was transformed into 14CO2 in soil sample…

Nouveaux outils en bioremédiation : prédiction du potentiel de dégradation d’une communauté à partir de sa composition et création de communautés multidégradantes par coalescence

En bioremédiation, la bioaugmentation consiste en l’introduction de microorganismes dans un milieu contaminé afin d’augmenter et/ou de suppléer la population bactérienne en place, dans l’objectif de le dépolluer. Cette approche est cependant limitée par la difficulté de choisir des microorganismes efficients - communauté ou souche spécifique – à inoculer, en lien avec les conditions abiotiques et les microorganismes indigènes du milieu pollué.Dans ce travail nous avons cherché à prédire le potentiel microbien de dégradation de deux pesticides, le glyphosate et l’isoproturon, de communautés microbiennes telluriques en utilisant des méthodes statistiques issues de la prédiction génomique. Pou…

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…

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

Sucrose amendment enhances phytoaccumulation of the herbicide atrazine in Arabidopsis thaliana.

International audience; Growth in the presence of sucrose was shown to confer to Arabidopsis thaliana (thale cress or mustard weed) seedlings, under conditions of in vitro culture, a high level of tolerance to the herbicide atrazine and to other photosynthesis inhibitors. This tolerance was associated with root-to-shoot transfer and accumulation of atrazine in shoots, which resulted in significant decrease of herbicide levels in the growth medium. In soil microcosms, application of exogenous sucrose was found to confer tolerance and capacity to accumulate atrazine in Arabidopsis thaliana plants grown on atrazine-contaminated soil, and resulted in enhanced decontamination of the soil. Applic…

Characterization of an isoproturon mineralizing bacterial culture enriched from a French agricultural soil.

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to IPU. Molecular analysis of the bacterial culture by DNA fingerprinting, cloning and sequencing of the 16S rRNA genes revealed that it consisted of six different members among whom the dominant was related to Sphingomonas sp. Six bacterial strains belonging to genera Ancylobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Variovorax and Agrobacterium were isolated from the IPU-degrading culture. None of these were able to degrade IPU in pure culture and only the intact culture sustained th…

TyPol : un outil opérationnel permettant de cartographier et choisir des molécules « modèles » pour des études en écodynamique et en écotoxicologie des pesticides

Characterization of the biodegradation, bioremediation and detoxification capacity of a bacterial consortium able to degrade the fungicide thiabendazole

Thiabendazole (TBZ) is a persistent fungicide used in the post-harvest treatment of fruits. Its application results in the production of contaminated effluents which should be treated before their environmental discharge. In the absence of efficient treatment methods in place, biological systems based on microbial inocula with specialized degrading capacities against TBZ could be a feasible treatment approach. Only recently the first bacterial consortium able to rapidly transform TBZ was isolated. This study aimed to characterize its biodegradation, bioremediation and detoxification potential. The capacity of the consortium to mineralize 14C-benzyl-ring labelled TBZ was initially assessed. …

Molecular approaches to study microbial mechanisms involved in pesticide biodegradation: atrazine as a case study

atzgene expressions during atrazine degradation in the soil drilosphere

One of the various ecosystemic services sustained by soil is pollutant degradation mediated by adapted soil bacteria. The pathways of atrazine biodegradation have been elucidated but in situ expression of the genes involved in atrazine degradation has yet to be demonstrated in soil. Expression of the atzA and atzD genes involved in atrazine dechlorination and s-triazine ring cleavage, respectively, was investigated during in situ degradation of atrazine in the soil drilosphere and bulked samples from two agricultural soils that differed in their ability to mineralize atrazine. Interestingly, expression of the atzA gene, although present in both soils, was not detected. Atrazine mineralizati…

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

Le chlordécone (CLD), un insecticide organochloré utilisé en Martinique et en Guadeloupe pendant 20 ans afin de lutter contre le charançon du bananier, contamine des sols agricoles des Antilles posant un problème environnemental qui est devenu un problème majeur de santé publique. Il n’existe que très peu d’évidence rapportant la biodégradation de cet insecticide, classé depuis 2009 comme polluant organique persistant (POP) par la convention de Stockholm. L’objectif de ce travail est de rechercher des éléments indiquant la biotransformation du CLD dans les sols contaminés des Antilles. Des cultures par enrichissement ont été établies à partir d’échantillons de sols contaminés pour isoler de…

Exposure of benthic microbial communities to pharmaceuticals and resulting adaptation including tolerance, biodegradation and antibiotic resistance: advances and challenges

International audience; Since the early 1920’s, pharmaceuticals, including antibiotics, have been massively producedand consumed for the benefit of both human and animal health. Pharmaceuticals residues havethen reached the aquatic environment through diffuse and point (wastewater) sources. Amongthe pharmaceutical residues, the ubiquitous presence of antibiotics could exert a selectivepressure on microbial communities leading to the acquisition and dissemination of antibioticresistance in the environment.We present here the synthesis of recent research projects (e.g. PANDORE, Antibio-tools,Antibiotox, PharmaTox...) investigating the dissemination of pharmaceuticals, includingantibiotics, in…

Ecology of pesticide-degrading microbes: from agricultural field to microbial gene dynamics

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…

A tiered-based approach to study the dissipation and adsorption of isoproturon, tebuconazole and chlorpyrifos in soil

Rôle des micro-organismes dans la dégradation des produits phytosanitaires

Processes involved in adaptation of soil microbes to accelerated pesticide biodegradation

Membres du comité d'organisation scientifique

Présentation du projet ANTIBIO-TOOLS

Présentation du projet ANTIBIO-TOOLS au comité de gestion de SIPIBEL (Site Pilote de Bellecombe)

Mapping field-scale spatial patterns of size and activity of the denitrifier community

International audience; There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6–16 m) and mapped the dis…

Mapping spatial patterns of denitrifiers for bridging community ecology and microbial processes along environmental gradients

International audience; While there is ample evidence that microbial processes can exhibit large variations at a field scale, very little is known about the spatial distribution of the communities mediating these processes. The objective of this study was to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We used geostatistical modeling to map the distribution of size and activity of the denitrifier community in the pasture. Size of the denitrifier community was estimated by PCR quantification of the denitrification gene copy numbers while its activity w…

Bioremediation of atrazine-contaminated soil

International audience

Analysis of atz gene expressions during atrazine degradation in various soil microsites.

communication orale et affichée

Biodegradation of synthetic β-triketone herbicide

Les épandages de déchets modifient-ils la qualité biologique des sols agricoles à long terme ? Résultats du programme VADEBIO

EA EcolDur CT3; National audience

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 …

Ecotoxicology at the era of biocontrol expansion

MECANO: mieux produire et valoriser les services environnementaux nécessaires dans la durée du fonctionnement des agrosystèmes

Biogeochemical characterization of soils affected by more than 100 years of lead mining activity.

&amp;lt;p&amp;gt;Mining has an adverse effect on soil quality as it is a source of heavy metal environmental pollution with direct consequences on its ecosystem services, especially those related to microbial activity. The magnitude and diversity of the impact produced by pollution is linked to the complexity and diversity of mining processes that share the same mining area. The soil will be modified, not only in the physicochemical characteristics but also physical alterations of varied typology will occur. All these changes and alterations related to mining activity are accompanied by changes in the composition, diversity and activity of soil microorganisms..&amp;lt;br&amp;gt;A study was…

Evidence of atrazine mineralization in a soil from the Nile Delta: Isolation of Arthrobacter sp. TES6, an atrazine-degrading strain

International audience; The s-triazine herbicide atrazine was rapidly mineralized (i.e., about 60% of C-14-ring-labelled atrazine released as (CO2)-C-14 within 21 days) by an agricultural soil from the Nile Delta (Egypt) that had been cropped with corn and periodically treated with this herbicide. Seven strains able to degrade atrazine were isolated by enrichment cultures of this soil. DNA fingerprint and phylogenetic studies based on 165 rRNA analysis showed that the seven strains were identical and belonged to the phylogeny of the genus Arthrobacter (99% similarity with Arthrobacter sp. AD38, EU710554). One strain, designated Arthrobacter sp. strain TES6, degraded atrazine and mineralized…

Response of the PCB-contaminated soil bacterial community to applied bioremediation treatments

For full field implementation of the bioremediation as a strategy for cleaning PCB-contaminated soils, the impact of the applied treatment on the microbial community needs to be clarified. An ideal bioremediation should have positive effects on PCB-removal but should pose no treats to the health of the soil ecosystem. Microbes, playing an essential role in maintenance of the soil ecosystem, are the first indicators of a negative impact of soil manipulation to ecosystem. A small-scale bioremediation experiment was conducted in order to get insight into behavior of the microbial community during bioremediation of PCB-contaminated soil, targeting both functional PCB-degrading community (by bph…

Microalgae community structure analysis based on 18S rDNA amplification from DNA extracted directly from soil as a potential soil bioindicator

International audience; Soil algae are photosynthetically active microorganisms showing changeable community structure, depending on the soil type, the agricultural practices and the application of pesticides. To characterise algal community structure, molecular approaches complementary to classical microbiological approaches based on the isolation and the culture of soil algae are required. Our study describes a polymerase chain reaction (PCR) approach targeting algal 18S rDNA sequences of desoxyribonucleic acid (DNA) samples extracted either from unialgal eukaryotic microalgae culture, complex assemblages of microalgae populations or natural soil communities. Our first results showed that…

Mapping field-scale spatial distribution patterns of size and activity of the denitrifier community

International audience

DNA extraction from soils: old bias for new microbial diversity analysis methods.

ABSTRACT The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure o…

Fate, biodegradation and ecotoxicological impact of the bioherbicide leptospermone on soil bacterial community

International audience

Chemical pollution and microbiomes responses

Adaptation des communautés microbiennes autotrophes et hétérotrophes aux changements spatio-temporels d'exposition aux pesticides en cours d'eau

National audience

Microbial communities as ecological indicators of ecosystem recovery following chemical pollution

International audience; ‘Ecosystem recovery’ is a concept that emerged from the need to preserve our environment against increasing contamination from human activity. However, ecological indicators of ecosystem recovery remain scarce, and it is still difficult to assess recovery of ecological processes at relevant spatial and temporal scales. Microbial communities hold key relevance as indicators of ecosystem recovery as they are ubiquitous among diverse ecosystems, respond rapidly to environmental changes, and support many ecosystem functions and services through taxonomic and functional biodiversity. This chapter summarizes the state-of-the-art in knowledge on the processes driving the st…

Accelerated mineralisation of atrazine in maize rhizosphere soil

International audience; The mineralisation rate of atrazine measured in soil pre-treated with this herbicide, was significantly higher in the maize rhizosphere than in bulk soil. Maize rhizosphere was also shown to significantly increase microbial biomass C as compared with bulk soil. Ribosomal intergenic spacer analysis conducted on nucleic acids extracted directly from soil samples revealed that the structure of microbial communities observed in the rhizosphere was slightly different from that of bulk soil. The quantification of the relative amount of the gene atzC, which encodes an enzyme involved in atrazine mineralisation, was carried out on soil nucleic acids by using quantitative-com…

Isolement de champignons d’un andosol de Guadeloupe contaminé à la chlordécone : caractérisation de leurs tolérances

Approches moléculaires pour l’étude de la diversité taxonomique et fonctionnelle microbienne

Towards a French network on microbial ecotoxicology

National audience; Les Journées d’Ecotoxicologie Microbienne, organisées à Lyon du 20 au 22 mars 2013, avaient pour objectifs de réunir pour la première fois les chercheurs traitant de cette thématique afin i) de dresser un état des lieux des forces en présence dans ce domaine à l’échelle nationale, et ii) d’engager une réflexion collective quant à ses évolutions futures. Rassemblant une quarantaine de chercheurs représentant plus de 25 laboratoires répartis sur toute la France, elles ont permis, à partir d’une enquête web menée au préalable auprès des chercheurs, d’une étude bibliométrique et d’une démarche participative innovante (de type «world café»), d'identifier dans un premier temps …

Biodégradation de l'atrazine en sols tempérés : rôle régulateur d'un modèle d'interaction biotique macrofaune/bactérie.

communication orale

Degradation of simazine by microorganisms isolated from soils of Spanish olive fields.

Special Issue: Pesticides, Microbial Functions and Biodiversity in Soil; The capability of the microbial flora isolated from an olive field soil from Andalusia to mineralize simazine has been analyzed. From this soil, a group of bacteria capable of degrading 60 mg simazine litre-1 in less than a week has been isolated. These microorganisms showed a low capacity for degrading this herbicide to carbon dioxide. When total DNA was isolated from this group of bacteria, we were able to detect by PCR the presence of only the atzC and the trzN genes. Some components of this bacterial population have been identified by sequencing of specific fragments from bacterial 16S rDNA, including Variovorax sp…

Isolation and characterisation of a bacterial strain degrading the herbicide sulcotrione from an agricultural soil

BACKGROUND: The dissipation kinetics of the herbicide sulcotrione sprayed 4 times on a French soil was studied using a laboratory microcosm approach. An advanced cultivation-based method was then used to isolate the bacteria responsible for biotransformation of sulcotrione. Chromatographic methods were employed as complementary tools to define its metabolic pathway. RESULTS: Soil microflora was able quickly to biotransform the herbicide (DT50 ≈ 8 days). 2-Chloro-4-mesylbenzoic acid, one of its main metabolites, was clearly detected. However, no accelerated biodegradation process was observed. Eight pure sulcotrione-resistant strains were isolated, but only one (1OP) was capable of degrading…

Qualité des sols - Méthode pour extraire directement l'ADN d'échantillons de sol. Norme AFNOR

La présente Norme internationale spécifie une méthode pour extraire directement l'ADN d'échantillons de sol en vue d'analyser la structure globale et l'abondance des communautés microbiennes du sol en utilisant des techniques de PCR. Cette méthode est principalement destinée aux sols agricoles et forestiers. Cette méthode peut ne pas être appropriée aux sols riches en matières organiques (par exemple sols de tourbières) ou aux sols très pollués par des polluants organiques ou des métaux lourds. L'extraction directe de l'ADN d'échantillons de sol fournit des informations précieuses sur l'abondance et la structure des communautés microbiennes qui sont des paramètres clés pour estimer la biodi…

NF ISO 14239 - Qualité du Sol - Systèmes d’incubation de laboratoire destinés à la mesure de la minéralisation de produits chimiques organiques dans le sol en conditions aérobies (Norme française - internationale)

EA BIOME INRA; Le présent document spécifie les étapes principales d’une méthode d’amplification par réaction de polymérisation en chaîne (PCR) quantitative (qPCR) permettant de mesurer Domaine d'application Le présent document définit six systèmes d'incubation appropriés permettant de mesurer les vitesses et l'étendue de la minéralisation de composés organiques dans le sol par mesurage du dégagement de dioxyde de carbone (CO2) . Tous les systèmes d'incubation peuvent être utilisés avec des composés solubles ou insolubles, mais le choix du système dépend des objectifs globaux de l'étude. Le présent document ne s'applique pas à l'utilisation desdits systèmes pour les bilans de masse, qui son…

Metabolic response of Microbacterium sp. C448 exposed to environmental and medicinal concentrations of sulfamethazine antibiotic

International audience

Identification of the hcb gene operon encoding a multicomponent monoxygenase catalyzing the aerobic dechlorination of hexachlorobenzene in Nocardioides sp. Strain PD653

EA BIOME; International audience

Direct Soil DNA Extraction from Soil: toward an ISO standard

Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil

In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s-triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atrazine-deg…

Je t’aime moi non plus’ ou les relations complexes qu’entretiennent les microorganismes du sol avec les pesticides et vice-versa

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

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…

Changes in the glomeromycota community in soils treated with a mix of pesticides

International audience

Multiple-scale distribution and function of soil microorganisms

Approches typologiques basées sur l’utilisation des QSAR - TyPol : un outil opérationnel permettant de cartographier et choisir des molécules « modèles » pour des études en écodynamique et en écotoxicologie

National audience

Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils

Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA revealed significant chang…

Présentation des métiers de l’Institut National de la Recherche Agronomique (INRA)

National audience

2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic…

Sensitive measure of prevalence and parasitaemia of haemosporidia from European blackbird (Turdus merula) populations: value of PCR-RFLP and quantitative PCR.

8 pages; International audience; Haemosporidian parasites are common in birds in which they act as an important selective pressure. While most studies so far have focused on the effect of their prevalence on host life-history traits, no study has measured the effect of parasitaemia. We developed molecular methods to detect, identify and quantify haemosporidia in 2 natural populations of the Blackbird Turdus merula. Three different parasite genotypes were found - 1 Haemoproteus and 2 Plasmodium. A PCR-RFLP screening revealed that only approximately 3% of blackbirds were free of parasites, compared to the 34% of uninfected birds estimated by blood smear screening. A quantitative PCR (q-PCR) a…

Impact écotoxicologique de pesticides sur les communautés microbiennes naturelles responsables de la biodégradation de pesticides dans les sédiments de rivière

National audience; L’utilisation quasi généralisée de pesticides dans de nombreuses cultures permet d’assurer une certaine qualité de la production végétale mais elle a des conséquences environnementales causant la contamination des eaux de surface, notamment les rivières circulant dans les agrosystèmes. Suite à l’exposition répétée aux pesticides, une fraction de la microflore est capable de s’adapter pour les dégrader conduisant à la mise en place de la biodégradation accélérée, un processus intéressant du point de vue environnemental parce qu’il diminue la persistance des pesticides dans l’environnement. La biodégradation accélérée peut avoir lieu dans les sols mais également dans les sé…

Mécanismes d'évolution de pseudomonas sp. adp sous pression de sélection exercée par l'atrazine

L’atrazine est un pesticide qui est largement utilisé dans le monde depuis une quarantaine d’années. Son application répétée aaboutit non seulement à la contamination des eaux mais également à l’apparition de bactéries telluriques capables d’utiliserce xénobiotique comme source d’azote pour leur croissance. La caractérisation des gènes atz responsables de la dégradationde cette molécule a révélé qu’ils étaient largement dispersés et très conservés au sein du monde bactérien traduisant ainsid’une évolution et d’une dispersion récente de ces gènes, probablement concomitantes avec l’application d’atrazine dansl’environnement

Développement d’indicateurs microbiens pour l’évaluation de l’impact des pesticides sur des fonctions écosystémiques terrestres et aquatiques (acronyme : IMPEC)

Développement d’indicateurs microbiens pour l’évaluation de l’impact des pesticides sur des fonctions écosystémiques terrestres et aquatiques (acronyme : IMPEC)

SCAR-based real time PCR to identify a biocontrol strain (T1) of Trichoderma atroviride and study its population dynamics in soils.

Strains of Trichoderma spp. are known for their antagonistic properties against plant pathogens, some are already on the market, others are under development. In order to launch a strain on the market its perfect identification at the species and strain levels is needed. The aim of this study is to (i) design a SCAR marker for specific identification of strain T1 of Trichoderma atroviride and (ii) monitor population dynamics of this strain in soil by real time PCR. A primer pair targeting a 141-bp fragment enabled specific detection of this strain without cross detection of autochthonous populations of Trichoderma in several field soils. In two soils, population dynamics assessed by real ti…

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…

Estimation of atrazine-degrading genetic potential and activity in three French agricultural soils

The impact of organic amendment (sewage sludge or waste water) used to fertilize agricultural soils was estimated on the atrazine-degrading activity, the atrazine-degrading genetic potential and the bacterial community structure of soils continuously cropped with corn. Long-term application of organic amendment did not modify atrazine-mineralizing activity, which was found to essentially depend on the soil type. It also did not modify atrazine-degrading genetic potential estimated by quantitative PCR targeting atzA, B and C genes, which was shown to depend on soil type. The structure of soil bacterial community determined by RISA fingerprinting was significantly affected by organic amendmen…

Freshwater sediment pesticide biodegradation potential as an ecological indicator of microbial recovery following a decrease in chronic pesticide exposure

International audience; Water resources and aquatic ecosystems are an essential concern of any policy for sustainable development. In the context of the European Water Framework Directive, which aims to achieve good chemical and ecological status of waters, the herbicide diuron was banned in France in December 2008. In lotic ecosystems, benthic microbial assemblages are considered as useful potential indicators of ecological status because they integrate the effects of multiple anthropogenic disturbances and have strong capacities to adapt to novel environmental conditions. Field studies have thus revealed that in situ diuron exposure can induce microbial adaptation leading to an increase i…

Studies on the response of soil microflora to the application of the fungicide fenhexamid

The aim of this work was to evaluate the impact of the fungicide fenhexamid (FEX) on the genetic structure of soil bacterial communities using the Ribosomal Intergenic Spacer Analysis molecular technique. Using real-time PCR, we also tried to quantify the pcaH sequences which encode the dioxygenases involved in the degradation process of a variety of aromatic compounds. Soil taken from a vineyard in the Etna Park (Sicily, Italy) was treated with FEX in the ratio 2 µg g-1 soil every 7 days, the process being repeated four times. The analyses were carried out before treatment and 7 days after each further application of FEX. At the same time, the degradation rate was evaluated. The use of FEX…

Monitoring of atrazine treatment on soil bacterial, fungal and atrazine-degrading communities by quantitative competitive PCR

We report the development of quantitative competitive (QC) PCR assays for quantifying the 16S, 18S ribosomal and atzC genes in nucleic acids directly extracted from soil. QC-PCR assays were standardised, calibrated and evaluated with an experimental study aiming to evaluate the impact of atrazine application on soil microflora. Comparison of QC-PCR 16S and 18S results with those of soil microbial biomass showed that, following atrazine application, the microbial biomass was not affected and that the amount of 16S rDNA gene representing 'bacteria' increased transitorily, while the amount of 18S rDNA gene representing fungi decreased in soil. In addition, comparison of atzC QC-PCR results wit…

pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pai…

Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil

International audience; We report the characterisation of Nocardioides sp. SP12, an atrazine-degrading bacteria isolated from atrazine-treated bulk- and maize rhizosphere soil. Based on 16S rDNA alignment, strain SP12 showed close phylogenic relationships with Nocardioides sp. C157 and Nocardioides simplex. Internal transcribed spacer (ITS) sequences of strain SP12 were longer than those of other Nocardioides sp. and present Ala- and Ile-tRNA unlike Actinomycetales. Nocardioides sp. SP12 presents a novel atrazine catabolic pathway combining trzN with atzB and atzC. Atrazine biodegradation ends in a metabolite that co-eluted in HPLC with cyanuric acid. This metabolite shows an absorption spe…

. Chimie théorique et étude du devenir de composés organiques dans l'environnement grâce à l'outil TyPol

Le nombre et la diversité des composés organiques (pesticides, hydrocarbures aromatiques polycycliques HAP, polychlorobiphényles PCB, médicaments...) susceptibles d’être pré-sents dans l’environnement étant très élevés, il est impossible de réaliser des expériences pour117caractériser pour chacun d’entre eux leur devenir et leurs impacts. Ainsi, des méthodes de pré-diction se développent depuis de nombreuses années et, parmi elles, des méthodes basées surl’hypothèse que la structure des molécules conditionne leurs propriétés physico-chimiques, etpar voie de conséquence leurs effets biologiques et leur comportement dans l’environnement.Dans le cadre du réseau d’animation scientifique «Ecodyn…

Combined metabolic activity within an atrazine-mineralizing community enriched from agrochemical factory soil

Abstract The main objective of this work was to characterize an atrazine-mineralizing community originating from agrochemical factory soil, especially to elucidate the catabolic pathway and individual metabolic and genetic potentials of culturable members. A stable four-member bacterial community, characterized by colony morphology and 16S rDNA sequencing, was rapidly able to mineralize atrazine to CO 2 and NH 3 . Two primary organisms were identified as Arthrobacter species (ATZ1 and ATZ2) and two secondary organisms (CA1 and CA2) belonged to the genera Ochrobactrum and Pseudomonas, respectively. PCR assessment of atrazine-degrading genetic potential of the community, revealed the presence…

Development and dissemination to operational stakeholders of integrative tools for chemical and biological measurements in watercourses to monitor the impact of pesticides according to agricultural practices and their evolution

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 …

Long-term impact of 19 years' farmyard manure or sewage sludge application on the structure, diversity and density of the protocatechuate-degrading bacterial community

International audience; Impact of long-term biosolids application on soil-living micro-organisms key players of ecosystemic services is scarcely reported. Here, the impact of the 19 year-long application of farmyard manure (FM) and sewage sludge (SS) organic fertilisation regimes on the protocatechuate-degrading bacterial (pca) community was estimated by comparison to a mineral fertilisation regime (U). The structure, diversity and density of the pca community were determined using pcaH, a gene encoding the protocatechuate 3,4-dioxygenase. Ten years after the last application, the structure of the pca community in soils amended with 55100 (100 t/ha/2 years) and to a lesser extent with FM (1…

Effets de l’apport de composts sur la biodiversité des sols

National audience; Les sols remplissent des services écosystémiques indispensables à la vie humaine parmi lesquels celui d’approvisionnement en aliments et de régulation, par le stockage, la transformation et le transfert, de l’eau et des éléments tels que le carbone, l’azote, etc.. La matière organique est un élément déterminant du maintien de ces services de par son incidence sur la structure physique des sols, leurs caractéristiques chimiques et leur activité biologique. De fait, si le retour au sol de la matière organique issue du compostage des déchets et des produits résiduaires organiques est une pratique ancestrale, son intérêt ressurgit aujourd’hui face aux défis démographiques, al…

Microbial degradation of chemicals, the engine of soil bioremediation? Examples of biostimulation, bioaugmentation and bioprophylaxic study cases

Processes involved in the adaptation of soil microbiota to enhance biodegradation of pesticides: atrazine-degrading community as a study case

International audience

L’expertise académique à destination des entreprises dans les domaines de l’Environnement et de la Santé

Fiche thématique; L'expertise académique à destination des entreprises dans les domaines de l'Environnement et de la Santé Ce texte rapporte des éléments de discussion abordés lors de la table-ronde « L'expertise académique au service des entreprises » qui s'est tenue dans le cadre de la journée de la Fondation Rovaltain du 15 novembre 2019 à Alixan. Cette table-ronde, focalisée sur l'expertise académique à destination du monde de l'entreprise, a mobilisé des intervenants des deux secteurs pour un regard croisé sur les avantages et les limitations rencontrées dans ce cadre de collaboration.

7ème séminaire du Réseau d’Ecotoxicologie terrestre et aquatique, programme et livre des résumés

Impact of Leptospermone, a Natural β-Triketone Herbicide, on the Fungal Composition and Diversity of Two Arable Soils

International audience; Impact of leptospermone, a β-triketone bioherbicide, was investigated on the fungal community which supports important soil ecological functions such as decomposition of organic matter and nutrients recycling. This study was done in a microcosm experiment using two French soils, Perpignan (P) and Saint-Jean-de-Fos (SJF), differing in their physicochemical properties and history treatment with synthetic β-triketones. Soil microcosms were treated with leptospermone at recommended dose and incubated under controlled conditions for 45 days. Untreated microcosms were used as control. Illumina MiSeq sequencing of the internal transcribed spacer region of the fungal rRNA re…

Effect of cropping cycles and repeated herbicide applications on the degradation of diclofop-methyl, bentazone, diuron, isoproturon and pendimethalin in soil.

A greenhouse study was conducted to investigate the ability of four crops (wheat, corn, oilseed rape and soybean) to influence the degradation of bentazone, diclofop-methyl, diuron, isoproturon and pendimethalin in soil. The present study showed that microbial biomass-carbon was significantly higher in planted soils than in bulk soil, especially with wheat and corn, after several cropping cycles. The biomass in corn and soybean planted soils was adversely affected by bentazone but recovered after three cropping cycles. In wheat-planted soils, diclofop-methyl application resulted in persistent increase of the amount of microbial biomass. Bentazone did not show accelerated degradation even af…