Impact of the use of wastewater for irrigation of cultivated plots on the soil microbiological quality in semi-arid zone (Tunisia): approaches at the plot and catchment area scales

Affiche, résumé. Session AS: Agricultural Soils: Biodiversity and Functioning; International audience

First molecular detection of mycobacterium bovis in environmental samples from a French region with endemic bovine tuberculosis

Aims The aim of the study was to determine the prevalence of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in environmental matrices within a French region (Cote d'Or) affected by this zoonotic disease. Methods and Results We report here the development and the use of molecular detection assays based on qPCR (double fluorescent dye labelled probe) to monitor the occurrence of Mycobacterium tuberculosis complex (MTBC) or M. bovis in environmental samples collected in pastures where infected cattle and wildlife had been reported. Three qPCR assays targeting members of the MTBC (IS1561’ and Rv3866 loci) or M. bovis (RD4 locus) were developed or refined from existing ass…

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

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

Nodulating symbiotic bacteria and soil quality

Chapitre 9 : Plant microbe interactions and soil quality Partie : 9-2; International audience

New insights into the use of rhizobia to mitigate soil N2O emissions

Agriculture is a major anthropogenic source of the greenhouse gas N2O, which is also involved in stratospheric ozone depletion. While the use of rhizobial inoculants has already been reported as an emerging option for mitigating soil N2O emissions, this study presents an in situ abatement of 70% of soil N2O emission using the strain nosZ+ G49 vs. nosZ− USDA138 in association with soybean. Therefore, we consider that the choice of the inoculant strain of a leguminous crop should take into account the capacity of strains to reduce nitrous oxide in addition to their N fixation capacity. This study also clearly suggests that this mitigation option could be considered not only for soybean but al…

Relation trophique et prévalence de gènes de résistances aux antibiotiques dans les communautés bactériennes de poissons

National audience

Détection de sources animales et environnementales de souches d’E. coli productrices de betalactamases à spectre élargi (BLSE) à l’échelle d’une région française (Bourgogne)

National audience

Knowledge tranfer from fundamental research to practical application in biological nitrogen fixation : prospects and reality

International audience

Distribution de bactéries pathogènes dans les sols évaluée par PCR quantitative en temps réel

National audience

Exposition des eaux souterraines peu profondes à Escherichia coli résistant aux antibiotiques : approche hydrochimique pour identifier les sources et les voies de transfert

L'antibiorésistance est une préoccupation croissante en termes de santé humaine et animale au niveau international. Le but du travail est de suivre l'impact sur la qualité de l'eau dans le bassin versant de l’Ouche et évaluer la capacité des E. coli productrices de BLSE de type CTX-M à se propager et survivre dans les eaux. Une stratégie pour l’échantillonnage des eaux de surface et souterraines a été déployée selon les contextes hydrogéologiques, l'utilisation des terres et les STEP. L’approche hydrochimique s’appuie sur l’analyse des paramètres tels que les nitrates et le bore complétés par l’analyse de Terres rares dont le gadolinium et le suivi de produits pharmaceutiques (caféine, carb…

Ecologie de la santé

Quand l'écologie pose son diagnostic. L'actualité nous le rappelle sans cesse : les maladies comme le paludisme, le Sida, ébola ou zika sont difficiles à combattre, et les maladies chroniques de type cancer, diabète ou maladies cardio-vasculaires toujours plus meurtrières. Pour la première fois de son histoire, l'humanité voit même son espérance de vie diminuer. Pour comprendre les raisons de cette crise sanitaire, l'écologie scientifique pose un autre regard sur la santé qui prend en considération les transformations de l'environnement et l'évolution de nos modes de vie. Cette nouvelle approche évolutive et écologique des problèmes de santé tente d'élucider les mécanismes en jeu dans la tr…

Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes

In this study, we report the cloning and characterization of denitrifying gene clusters of Pseudomonas fluorescens C7R12 containing the narXLDKGHJI, nirPOQSM, norCB and nosRZDFYL genes. While consensus sequences for Fnr-like protein binding sites were identified in the promoter regions of the nar, nir, nor and nos genes, consensus sequences corresponding to the NarL binding sites were identified only upstream the nar genes. Monitoring by mRNA analysis the expression of the narG, nirS, norB and nosZ structural genes suggests a sequential induction of the denitrification system in P. fluorescens.

Survival and change in physiological state of Bradyrhizobium japonicum in soybean (Glycine max L. Merril) liquid inoculants after long-term storage

International audience

Distribution des bacteries pathogènes de l’homme ou commensales dans l’environnement (sol, eau) et les agro-ecosystemes, emergence de resistances aux antibiotiques

Rapid dissemination of Mycobacterium bovis from cattle dung to soil by the earthworm Lumbricus terrestris

International audience; Indirect transmission of Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), between wildlife and livestock is thought to occur by inhalation or ingestion of environmental substrates contaminated through animal shedding. The role of the soil fauna, such as earthworms, in the circulation of M. bovis from contaminated animal feces is of interest in the epidemiology of bTB. The objective of this study was to assess the impact of earthworm activity on M. bovis transfer from animal dung to castings and the surrounding soil. For this purpose, microcosms of soil containing the anecic eathworms Lumbricus terrestris were prepared and covered with cattle fec…

Impact of temperature and soil type on Mycobacterium bovis survival in the environment

Mycobacterium bovis, the causative agent of the bovine tuberculosis (bTB), mainly affects cattle, its natural reservoir, but also a wide range of domestic and wild mammals. Besides direct transmission via contaminated aerosols, indirect transmission of the M. bovis between wildlife and livestock might occur by inhalation or ingestion of environmental substrates contaminated through infected animal shedding. We monitored the survival of M. bovis in two soil samples chosen for their contrasted physical and-chemical properties (i.e. pH, clay content). The population of M. bovis spiked in sterile soils was enumerated by a culture-based method after 14, 30, 60, 90, 120 and 150 days of incubation…

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…

Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils

The capacity of 12 soils to degrade atrazine was studied in laboratory incubations using radiolabelled atrazine. Eight soils showed enhanced degradation of this compound. Twenty-five bacterial strains able to degrade atrazine were isolated by an enrichment method from 10 of these soils. These soils were chosen for their wide range of physico-chemical characteristics. Their history of treatment with atrazine was also variable. The genetic diversity of atrazine degraders was determined by amplified ribosomal restriction analysis (ARDRA) of the 16S rDNA gene with three restriction endonucleases. The 25 bacterial strains were grouped into five ARDRA types. By sequencing and aligning the 16S rDN…

Des bactéries intracellulaires dans le champignon ectomycorhizien Laccaria bicolor

National audience

Physiological characterization of Bradyrhizobium japonicum liquid inoculants stored for many years

National audience

Les particules biotiques (pathogènes ou non)

National audience

Adaptation de Candida albicans dans les tissus humains: du commensalisme à la pathogénicité

National audience; Candida albicans (C. albicans) est un micro-organisme eucaryote appartenant à la flore commensale des muqueuses de l’homme sain. Ce commensalisme résulte d’un équilibre entre la levure et les systèmes de défense de l’hôte. La rupture de cet équilibre chez un patient fragilisé (sujet infecté par le VIH, neutropénique, cancéreux, transplanté ou séjournant en service de réanimation) favorisera une colonisation intense des muqueuses, un envahissement de la barrière digestive et enfin la possibilité de dissémination hématogène. Les candidémies restent des infections graves puisque la mortalité directement attribuable à l’infection est estimée à 38%. Nos travaux ont d’abord por…

Distribution des bactéries pathogènes dans les sols évaluée par PCR quantitative en temps réel

National audience

L'inoculation des légumineuses en France : un exemple de coopération efficace entre l'INRA de Dijon et les fabricants d'inoculants

National audience

Adaptation inattendue de populations de Fusarium oxysporum et F. Dimerum au milieu aquatique urbain des conduites d'eau de bâtiments hospitaliers à Dijon et Nancyξ

National audience; Fusarium oxysporum et F. dimerum sont des champignons d'origine tellurique présents dans de nombreux écosystèmes terrestres mais ils ont été récemment détectés dans les systèmes de distribution d'eau de bâtiments hospitaliers. Une enquête épidémiologique incluant divers bâtiments hospitaliers sur différents sites, des complexes non-hospitaliers et des maisons individuelles a été menée pendant 2 ans dans deux villes françaises Dijon et Nancy. Les champignons ont été détectés seulement dans les canalisations de bâtiments hospitaliers et n'ont pas été détectés dans celles des autres immeubles ni dans l'eau du réseau urbain. Cette distribution surprenante s'explique par une c…

Gestion des microflores bactériennes telluriques bénéfiques et indésirables dans le cadre d'une agriculture durable

Diplôme : HDR

Communication and Autoinduction in the species Listeria monocytogenes

International audience; In order to withstand changes in their environment, bacteria have evolved mechanisms to sense the surrounding environment, integrate these signals and adapt their physiology to thrive under fluctuating conditions. Among these mechanisms, the ability of bacteria to exchange information between cells has become a dynamic field of interest for microbiologists over the past four decades. First described by Nelson et al.,1 this phenomenon often referred as either cell-cell communication, Quorum Sensing and/or AutoInduction involves the synthesis of small signal molecules called autoinducers. These signal molecules may be sensed by the bacterial population in the vicinity …

Plasmid localisation of atrazine-degrading genes in newly described Chelatobacter and Arthrobacter strains

Abstract In a previous study, we isolated a collection of atrazine-degrading bacteria from various soils. The aim of this study was to localise the atrazine-degrading genes in these 25 atrazine-degrading strains. In the case of the Gram-negative strains of Chelatobacter heintzii, six to seven plasmids were observed. The atzABC and trzD genes were located on two or three plasmids with variable molecular masses. For the Gram-positive strains of Arthrobacter crystallopoietes, the atzBC genes were located on a single plasmid of 117 kb. The organisation of atrazine-degrading genes seems to be highly variable between the strains studied. We have shown by a specific PCR the occurrence of IS1071-li…

Effect of natamycin on the enumeration, genetic structure and composition of bacterial community isolated from soils and soybean rhizosphere

Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 degrees C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l(-1). Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming un…

The typology of organic wastes influences dose-response relationships between sulfonamide residues and antibiotic resistance genes in amended soils.

National audience

Genotypic diversity of Sinorhizobium (formerly Rhizobium) meliloti strains isolated directly from a soil and from nodules of alfalfa (Medicago sativa) grown in the same sol

32 ref.; International audience

Evidence of autoinduction heterogeneity via expression of the agr system of listeria monocytogenes at the single-cell level

ABSTRACT To investigate if the primary function of the Agr system of Listeria monocytogenes is to monitor cell density, we followed Agr expression in batch cultures, in which the autoinducer concentration was uniform, and in biofilms. Expression was heterogeneous, suggesting that the primary function of Agr is not to monitor population density.

Occurrence of CTX-M Producing Escherichia coli in Soils, Cattle, and Farm Environment in France (Burgundy Region).

Article en open access; International audience; CTX-M [a major type of extended-spectrum beta-lactamase (ESBU] producing Escherichia coli are increasingly involved in human infections worldwide. The aim of this study was to investigate potential reservoirs for such strains: soils, cattle, and farm environment. The prevalence of bla(CTX-M) genes was determined directly from soil DNA extracts obtained from 120 sites in Burgundy (France) using real-time PCR. bla(CTX-M) targets were found in 20% of the DNA extracts tested. Samples of cattle feces (n = 271) were collected from 182 farms in Burgundy. Thirteen ESBL-producing isolates were obtained from 12 farms and further characterized for the pr…

Impact of soil fertilization with organic amendments on the dissemination of antibiotic resistance in cultivated soils

National audience

Les souches d'E. coli résistantes aux antibiotiques

National audience; Le projet "CIREC" vise à étudier la prévalence et la caractérisation des souches d’E.coli productrices de β-lactamase à spectre élargi (BLSE) de type CTX-M dans les eaux usées et les boues issues d’une quarantaine de stations d’épuration (STEP) de la région Bourgogne. Puis, il s’agira d’identifier et caractériser les voies possibles de transfert de ces souches, les rejets d’effluents traités des STEP dans les rivières pouvant avoir des conséquences sur la contamination de la faune aquatique d’eau douce.

Trends in rhizobial inoculant production and use

International audience

Comment favoriser, à court terme, le passage à l'application des connaissances sur la rhizosphère : des stratégies possibles à mettre en place pour cela ?

National audience

Prévalence et circulation de pathogènes humains et de bactéries résistantes aux antibiotiques dans l'environnement

National audience; Les sols constituent un réservoir important de biodiversité microbienne. Parmi ces microorganismes, certains sont capables d’interactions avec l’Homme (commensalisme) ou d’induire des pathologies (maladies infectieuses aigues ou chroniques). De plus, les bactéries du sol constituent un réservoir important de gènes de résistance aux antibiotiques. Les activités agricoles comme l’élevage et le recyclage de produits résiduaires organiques dans les sols peuvent constituer une source de bactéries pathogènes, résistantes aux antibiotiques ou commensales de l’Homme. Ces pratiques agricoles, qui sont en constante évolution, doivent donc aussi être évaluées en termes de risque san…

Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods

Identifiant HAL : hal-01120618; International audience; Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 104L. monocytogenes per gram of dry soil. Among the …

Dissemination of CTX-M-Producing Escherichia coli in Freshwater Fishes From a French Watershed (Burgundy)

International audience; The burden of extended-spectrum beta-lactamases producing Escherichia coli (ESBL-Ec), has increased over several decades. Freshwater ecosystems are suspected to play an important ecological and evolutionary role in driving the dissemination of antimicrobial resistance. The aim of our study was to decipher the occurrence of ESBL-Ec in a small watershed (Ouche river, Burgundy, France), targeting environmental matrices and fishes. Among cefotaxime resistant E. coli (ctxR Ec) isolates, we detected and characterized 36 ESBL-Ec from water, biofilm and fish guts. ctxR Ec and ESBL-Ec were found in samples from sites near the first small town, located downstream from the wate…

Les sols et la résistance aux antibiotiques

National audience; Les sols renferment des communautés de microorganismes très diversifiées et très abondantes (jusqu’à 1010 bactéries par gramme de sol). La production d’antibiotiques et la résistance aux antibiotiques est un des mécanismes d’interaction entre microorganismes des sols. L’antibiose par production d’antibiotique est un mécanisme très ancien utilisé par les bactéries et les champignons pour limiter le développement de bactéries compétitrices. Les sols sont donc un réservoir potentiel de bactéries résistantes aux antibiotiques (BRA) et de gènes de résistance aux antibiotiques (GRA). Ce pool de gènes de résistance des sols est appelé le résistome des sols, il constitue un réser…

Bioremediation of atrazine-contaminated soil

International audience

Natural soil reservoirs for human pathogenic and fecal indicator bacteria

Prod ? EA UB INRA BIOME; International audience; résumé du livre : Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manuall is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradati…

Prevalence of CTX-M producing E. coli in cattle and soil environment in the Burgundy region

National audience

Distribution and characteristics of Listeria monocytogenes isolates from surface waters of the South Nation River Watershed, Ontario, Canada

ABSTRACT Listeria monocytogenes is a facultative intracellular pathogen thought to be widely distributed in the environment. We investigated the prevalence and characteristics of L. monocytogenes isolates from surface waters derived from catchments within the South Nation River watershed (Ontario, Canada). This watershed is dominated by urban and rural development, livestock and crop production, and wildlife habitats. From June to November 2005, a total of 314 surface water samples were collected biweekly from 22 discrete sampling sites characterized by various upstream land uses. Presumptive Listeria spp. were isolated using a selective enrichment and isolation procedure, and 75 L. monocyt…

High gas pressure survival/reactivation of soil microorganisms

International audience; Deep sea sediments constitute a considerable reserve of microorganisms belonging to different microbial communities. Our researches aimed to better understand cellular mechanisms related to cellular plasticity involved in resistance of such microbial communities to extreme conditions and more particularly to high level of pressure (> 50 MPa). Obviously, the first step is to isolate microorganisms present in deep sea sediments and then cultivate. The comparison of the cultivation of such microorganisms under atmospheric conditions and under pressure conditions will afford a possible reactivation of specific piezotolerants and/or piezophiles organisms from dormancy. Th…

Transfer of knowledge from fundamental research to practical application in biological nitrogen fixation : prospects and reality

International audience

An electrochemical DNA biosensor for the detection of CTX-M extended-spectrum β-lactamase-producing Escherichia coli in soil samples

International audience; An electrochemical hybridization assay involving neutravidin-coated carbon screen-printed electrodes and an HRP-based detection have been shown to provide an effective tool for the genotypic analysis of extended-spectrum beta-lactamase-producing E. coli strains in complex samples such as soil. (c) 2012 Elsevier B.V. All rights reserved.

Genetic diversity of carbofuran-degrading soil bacteria

International audience

Inoculation of an atrazine-degrading strain, Chelobacter heintzii Cit1, in four different soils : effects of different inoculum densities

International audience

Survie et devenir des bactéries résistantes aux antibiotiques dans le sol et les systèmes de culture

National audience; Les sols abritent des communautés de microorganismes extrêmement diversifiées et très abondantes (jusqu’à 1010 bactéries par gramme de sol). La production d’antibiotiques et la résistance aux antibiotiques est un des mécanismes d’interaction entre microorganismes de l’environnement et des sols en particulier. L’antibiose par production d’antibiotique est un mécanisme très ancien utilisé par les bactéries et les champignons pour limiter le développement de bactéries compétitrices. Les sols sont donc un réservoir potentiel de bactéries résistantes aux antibiotiques (BRA) et de gènes de résistance aux antibiotiques (GRA). Ce pool de gènes de résistance des sols est appelé le…

Utiliser les symbiotes des Légumineuses pour favoriser la réduction du gaz à effet de serre N2O dans les sols

Single cell analysis evidence Heterogeneous expression of the Agr communication system of Listeria monocytogenes

http://prodinra.inra.fr/record/271694EAMERSCT3 EJ3; Communication, often referred as Quorum Sensing, is involved in the adaptation of most bacteria to their environment. In the genus Listeria, the agr communication system affects the biology of Listeria monocytogenes during saprophytic life (biofilm formation) and during infection. In the present study, we investigated in situ agr expression of six isolates of L. monocytogenes by combining gfp reporters, flow cytometry and fluorescent microscopy during plantonic growth and dynamic flow cell biofilm set ups. Unexpectedly, during growth in TSB homogenised liquid cultures incubated at 25°C, while auto-inducer concentration was uniform, statist…

Editorial: Antimicrobials in Wildlife and the Environment

2 Pág. Centro de Investigación en Sanidad Animal (CISA)

Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation

ABSTRACT In a recent paper, we demonstrated that inactivation of the Agr system affects the patterns of survival of Listeria monocytogenes (A.-L. Vivant, D. Garmyn, L. Gal, and P. Piveteau, Front Cell Infect Microbiol 4:160, http://dx.doi.org/10.3389/fcimb.2014.00160 ). In this study, we investigated whether the Agr-mediated response is triggered during adaptation in soil, and we compared survival patterns in a set of 10 soils. The fate of the parental strain L. monocytogenes L9 (a rifampin-resistant mutant of L. monocytogenes EGD-e) and that of a Δ agrA deletion mutant were compared in a collection of 10 soil microcosms. The Δ agrA mutant displayed significantly reduced survival in these b…

Réactions non spécifiques aux tests de dépistage ante mortem de la tuberculose bovine : investigations dans un centre de bovins reproducteurs

Conservation of type III secretion system genes inBradyrhizobiumisolated from soybean

International audience; The distribution of rhcRST genes encoding the type III secretion system (T3SS) in a collection of Bradyrhizobium strains was characterized by PCR and Southern blot hybridization. The polymorphism of the corresponding sequences amplified by PCR was characterized by RFLP and sequencing together with those available in the databank. Genomic group I is characterized by the presence of Bradyrhizobium elkanii strains and group II by the presence of B. japonicum and B. liaoningense strains. Highly conserved T3SS-like genes were detected by PCR in all Bradyrhizobium strains isolated from soybean belonging to genomic group II, and in none of the strains belonging to genomic g…

Amperometric detection of extended-spectrum β-lactamase activity : application to the characterization of resistant E.coli strains

EA MERS CT3; International audience; The amperometric detection of extended-spectrum β-lactamase (ESBL) with carbon screen-printed sensors was investigated in the presence of the Nitrocefin, a commercially-available β-lactamase chromogenic cephalosporin substrate. Using an ESBL isolated from a clinical sample, it was shown for the first time that the intensity of a specific anodic pic current (EP = [similar]+0.3 V vs. Ag/AgCl) resulting from the catalytic hydrolysis of the β-lactam ring was proportional to the amount of ESBL. The proof-of-principle of a novel susceptibility assay for the rapid and accurate identification of ESBL- producing bacteria was then demonstrated. The detection schem…

Évaluation des risques relatifs aux mesures de décontamination et de gestion des sous-produits animaux lors des cas de botulisme bovin et aviaire

Le botulisme est une maladie neurologique humaine et animale, le plus souvent d’origine alimentaire, provoquée par l’action de neurotoxines bactériennes (toxines botuliques) produites par la bactérie Clostridium botulinum et qui se manifeste par une paralysie flasque pouvant aller jusqu’à la paralysie respiratoire et l’arrêt cardiaque. Neuf types toxiniques, répartis en une quarantaine de sous-types, sont actuellement connus.En France, le botulisme animal affecte essentiellement les oiseaux (sauvages et domestiques) et les bovins. Chez les volailles, on recense annuellement vingt à trente foyers, majoritairement dus aux types mosaïque C/D (élevages de poulets de chair et de dindes) suivi de…

Diversity of denitrifying community in three soils and ability to reduce nitrous oxide

International audience

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…

Changes in gene expression during adaptation of Listeria monocytogenes to the soil environment

project SEST 009; International audience; Listeria monocytogenes is a ubiquitous opportunistic pathogen responsible for listeriosis. In order to study the processes underlying its ability to adapt to the soil environment, whole-genome arrays were used to analyse transcriptome modifications 15 minutes, 30 minutes and 18 h after inoculation of L. monocytogenes EGD-e in soil extracts. Growth was observed within the first day of incubation and large numbers were still detected in soil extract and soil microcosms one year after the start of the experiment. Major transcriptional reprofiling was observed. Nutrient acquisition mechanisms (phosphoenolpyruvate-dependent phosphotransferase systems and…

Survie et/ou réactivation de microorganismes du sol sous hautes pressions gazeuses

National audience; Le sol constitue une réserve considérable de microorganismes représentatifs de nombreuses communautés cellulaires. Les recherches reposent sur l’hypothèse qu’il existe, dans les échantillons de sol, des communautés microbiennes adaptées à des conditions physiques (pression, température) très différentes de celles rencontrées dans nos laboratoires : soit parce que les conditions de milieu ont changé (sol), soit parce que les conditions de prélèvement sont très différentes des conditions de culture (grands fonds marins). Dans cette optique, l’utilisation des hautes pressions gazeuses (200-1000 bars dans un premier temps) est envisagée afin d’essayer de réactiver des microor…

Extremely rapid acclimation of Escherichia coli to high temperature over a few generations of a fed-batch culture during slow warming

This study aimed to demonstrate that adequate slow heating rate allows two strains of Escherichia coli rapid acclimation to higher temperature than upper growth and survival limits known to be strain-dependent. A laboratory (K12-TG1) and an environmental (DPD3084) strain of E. coli were subjected to rapid (few seconds) or slow warming (1 degrees C 12 h(-1)) in order to (re) evaluate upper survival and growth limits. The slow warming was applied from the ancestral temperature 37 degrees C to total cell death 46-54 degrees C: about 30 generations were propagated. Upper survival and growth limits for rapid warming (46 degrees C) were lower than for slow warming (46-54 degrees C). The thermal l…

Les souches d’Escherichia coli résistantes aux antibiotiques

Parmi les bactéries multi-résistantes, les entérobactéries productrices de β-lactamase à spectre élargi (BLSE) occupent une place croissante. Parmi celles-ci, c’est Escherichia coli (entérobactérie commensale du tube digestif de l’homme et de l’animal) qui est l’espèce la plus concernée par cette production enzymatique. Cependant, il existe peu de données sur l’existence de réservoirs environnementaux pour ces souches, leur capacité à survivre dans l’environnement et en particulier dans les eaux douces et dans les sols. Le projet "CIREC" visait donc à étudier la prévalence et la caractérisation des souches d’E.coli productrices de BLSE de type CTX-M dans les eaux usées et les boues issues d…

Détection et caractérisation moléculaire de souches d’Escherichia coli porteuses de gènes de résistance CTX-M (betalactamases à spectre élargi ou BLSE) et de gènes de virulence dans deux exploitations agricoles

National audience

Long Term Exposure of Agricultural Soil to Veterinary Antibiotics Changes the Population Structure of Symbiotic Nitrogen-Fixing Bacteria Occupying Nodules of Soybeans (Glycine max)

International audience; Antibiotics can be entrained onto agricultural land through the application of animal manures, human biosolids, or recycled wastewater for irrigation. In order to evaluate the impacts on soil microorganisms of exposure to antibiotics, a series of replicated plots were initiated in 1999 at the AAFC research farm in London ON. Every spring a mixture of sulfamethazine, chlortetracycline and tylosin is incorporated directly into the soil to attain concentrations ranging from 0.1 to 10 mg/kg, and these are then seeded with soybeans. In the present study nodules were isolated from soybean plants growing in antibiotic treated and control soils in 2012, after 14 annual treat…

Bacterial community analysis by denaturing gradient gel electrophoresis, second edition

Chapitre 43; absent

16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils

Bacteria capable of denitrification are spread among phylogenetically diverse groups. In the present investigation, molecular methods (amplified ribosomal DNA restriction analysis (ARDRA) and partial 16S rDNA gene sequencing) were used to determine the genetic diversity of culturable denitrifying soil bacteria. The purpose of this work was to study the microbial density and diversity of denitrifying communities isolated from two luvisols and a rendosol. The denitrifying bacterial density was significantly higher in the two luvisols (3x10(6) and 4x10(6) bacteria g(-1) dry soil) than in the rendosol (4x10(5) bacteria g(-1) dry soil). Denitrifying isolates from soils were grouped according to …