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Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.

International audience; The standard techniques for diagnosis of human filariasis are the microscopic examination of blood smears or skin biopsies, which are relatively invasive and poorly sensitive at low levels of infection. Recently, filarial DNA has been detected in fecal samples from non-human primates in Central Africa. The aim of this study was to demonstrate proof-of-concept of a non-invasive molecular diagnosis technique for human filariasis by targeting fragments of 12S rDNA, Cox1, ITS1 and LL20-15kDa ladder antigen-gene by conventional PCR in DNA extracted from stool samples of 52 people infected with Mansonella perstans and/or Loa loa . Of these, 10 patients were infected with soil-transmitted helminths ( Trichuris trichiura and/or Ascaris lumbricoides ), and none were positive for Necator americanus . Interestingly, no filarial gene fragments were detected in the stools of any of the 52 patients. Future studies should evaluate whether a co-infection with soil-transmitted helminths causing gastrointestinal bleeding and likely allowing (micro)filaria exit into the digestive tract, may facilitate the molecular detection of filarial DNA fragments in stool samples.; Les techniques standards de diagnostic des filarioses humaines (examen microscopique de gouttes épaisses ou de biopsies cutanées) sont relativement invasives et peu sensibles à de faibles niveaux d’infection. De l’ADN de filaires a été récemment détecté dans des échantillons de fèces de primates non-humains en Afrique centrale. L’objectif de cette étude était de démontrer la preuve de concept d’un diagnostic moléculaire non invasif des filarioses chez l’homme en ciblant des fragments d’ADNr 12S, Cox1, ITS1 et l’antigène LL20-15kDa par PCR classique. L’ADN a été extrait d’échantillons de selles de 52 personnes infectées par Mansonella perstans et/ou Loa loa . Parmi ces patients, dix étaient infectés par des géohelminthes ( Trichuris trichiura et/ou Ascaris lumbricoides ) et aucun n’était positif pour Necator americanus . De manière intéressante, aucun fragment de gène de filaires n’a été détecté dans les selles des 52 patients. Des études futures devraient être menées pour évaluer si une coinfection avec des géohelminthes (provoquant des hémorragies gastro-intestinales et permettant probablement l’effraction de (micro)filaires dans le tube digestif) facilite la détection moléculaire de fragments d’ADN de filaires dans les selles.

The standard techniques for diagnosis of human filariasis are the microscopic examination of blood smears or skin biopsies, which are relatively invasive and poorly sensitive at low levels of infection. Recently, filarial DNA has been detected in fecal samples from non-human primates in Central Africa. The aim of this study was to demonstrate proof-of-concept of a non-invasive molecular diagnosis technique for human filariasis by targeting fragments of 12S rDNA, Cox1, ITS1 and LL20-15kDa ladder antigen-gene by conventional PCR in DNA extracted from stool samples of 52 people infected with Mansonella perstans and/or Loa loa . Of these, 10 patients were infected with soil-transmitted helminths ( Trichuris trichiura and/or Ascaris lumbricoides ), and none were positive for Necator americanus . Interestingly, no filarial gene fragments were detected in the stools of any of the 52 patients. Future studies should evaluate whether a co-infection with soil-transmitted helminths causing gastrointestinal bleeding and likely allowing (micro)filaria exit into the digestive tract, may facilitate the molecular detection of filarial DNA fragments in stool samples., Les techniques standards de diagnostic des filarioses humaines (examen microscopique de gouttes épaisses ou de biopsies cutanées) sont relativement invasives et peu sensibles à de faibles niveaux d’infection. De l’ADN de filaires a été récemment détecté dans des échantillons de fèces de primates non-humains en Afrique centrale. L’objectif de cette étude était de démontrer la preuve de concept d’un diagnostic moléculaire non invasif des filarioses chez l’homme en ciblant des fragments d’ADNr 12S, Cox1, ITS1 et l’antigène LL20-15kDa par PCR classique. L’ADN a été extrait d’échantillons de selles de 52 personnes infectées par Mansonella perstans et/ou Loa loa . Parmi ces patients, dix étaient infectés par des géohelminthes ( Trichuris trichiura et/ou Ascaris lumbricoides ) et aucun n’était positif pour Necator americanus . De manière intéressante, aucun fragment de gène de filaires n’a été détecté dans les selles des 52 patients. Des études futures devraient être menées pour évaluer si une coinfection avec des géohelminthes (provoquant des hémorragies gastro-intestinales et permettant probablement l’effraction de (micro)filaires dans le tube digestif) facilite la détection moléculaire de fragments d’ADN de filaires dans les selles.

International audience; Per- and polyfluoroalkyl substances (PFASs) are utilized in specific firefighting foams. The objectives of this study were i) to map PFAS distribution in the soil and groundwater of a firefighter training site active for more than 3 decades, ii) to locate the main points of entry of PFASs into the aquifer and iii) to identify which PFASs seeped most deeply into the soil. A total of 44 soil cores and 17 groundwater samples were collected. Perfluorooctane sulfonate (PFOS), 6:2 fluorotelomer sulfonic acid (6:2 FTSA) and 6:2 Fluorotelomer sulfonamide alkylbetaine (6:2 FTAB) were the most predominant PFASs in surface soil. The highest total PFAS concentrations (up to 357 μg/g) were measured in two areas. Both areas were considered as potential points of entry of PFASs into the aquifer since PFASs were detected in soil 15 m below the surface, despite the presence of clay layers. The highest total PFAS concentrations were recorded in the monitoring wells located in the perimeter of the firefighter training site and in the spring located downgradient in the direction of groundwater flow. They ranged from 300 to 8300 ng/L. The fluorotelomer 6:2 FTAB was quantified in 6 monitoring wells, suggesting that this FT can reach a water table 20 m below the ground's surface.

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub-continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd

International audience; Although soil characteristics modulate metal mobility and bioavailability to organisms, they are often ignored in the risk assessment of metal transfer. This paper aims to determine the ability of chemical methods to assess and predict cadmium (Cd), lead (Pb) and zinc (Zn) environmental bioavailability to the land snail Cantareus aspersus. Snails were exposed in the laboratory for 28 days to 17 soils from around a former smelter. The soils were selected for their range of pH, organic matter, clay content, and Cd, Pb and Zn concentrations. The influence of soil properties on environmental availability (estimated using HF-HClO(4), EDTA, CaCl(2), NH(4)NO(3), NaNO(3), free ion activity and total dissolved metal concentration in soil solution) and on environmental bioavailability (modelled using accumulation kinetics) was identified. Among the seven chemical methods, only the EDTA and the total soil concentration can be used to assess Cd and Pb environmental bioavailability to snails (r²(adj)=0.67 and 0.77, respectively). For Zn, none of the chemical methods were suitable. Taking into account the influence of the soil characteristics (pH and CEC) allows a better prediction of Cd and Pb environmental bioavailability (r²(adj)=0.82 and 0.83, respectively). Even though alone none of the chemical methods tested could assess Zn environmental bioavailability to snails, the addition of pH, iron and aluminium oxides allowed the variation of assimilation fluxes to be predicted. A conceptual and practical method to use soil characteristics for risk assessment is proposed based on these results. We conclude that as yet there is no universal chemical method to predict metal environmental bioavailability to snails, and that the soil factors having the greatest impact depend on the metal considered.

International audience; Under temperate climates and in cultivated soils, nitrate is the most important source of nitrogen (N) available for crops and, before its reduction and assimilation into amino acids, must enter the root cells and then move in the whole plant. The aim of this review is to provide an overall picture of the numerous membrane proteins that achieve these processes by being localized in different compartments and in different tissues. Nitrate transporters (NRT) from the NRT1 and NRT2 families ensure the capacity of root cells to take up nitrate, through high- and low-affinity systems (HATS and LATS) depending on nitrate concentrations in the soil solution. Other members of the NRT1 family are involved subsequently in loading and unloading of nitrate to and from the xylem vessels, allowing its distribution to aerial organs or its remobilization from old leaves. Once in the cell, nitrate can be stored in the vacuole by passing through the tonoplast, a step that involves chloride channels (CLC) or a NRT2 member. Finally, with the exception of one NRT1 member, the transport of nitrite towards the chloroplast is still largely unknown. All these fluxes are controlled by key factors, the 'major tour operators' like the internal nutritional status of the plant but also by external abiotic factors.

International audience; Increased expression of vascular endothelial growth factor (VEGF) contributes to the growth of many tumors by increasing angiogenesis. Although hypoxia is a potent inducer of VEGF, we previously showed that epidermal growth factor receptor amplification and loss of PTEN, both of which can increase phosphatidylinositol-3-kinase (PI3K) activity, increase VEGF expression. Using both adenoviral vectors and a cell line permanently expressing constitutively active myristoylated Akt (myrAkt), we show that activation of Akt, which is downstream of PI3K, increases VEGF expression in vitro and increases angiogenesis in a Matrigel plug assay. Transient transfection experiments using reporter constructs containing the VEGF promoter showed that up-regulation of VEGF by Akt is mediated through Sp1 binding sites located in the proximal promoter. Small interfering RNA directed against Sp1 prevented the induction of VEGF mRNA in response to myrAkt but not to hypoxia. Expression of myrAkt is associated with increased phosphorylation of Sp1 and its increased binding to a probe corresponding to the -88/-66 promoter region. In conclusion, our results indicate that Sp1 is required for transactivation of the VEGF by Akt. Others have proposed that the PI3K/Akt pathway can increase VEGF expression via the hypoxia-inducible factor 1 (HIF-1); however, our results suggest an alternative mechanism can also operate.

International audience; Spatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa-area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered ~5.3 × 10(5) km(2)) and developing an innovative evaluation of the habitat-area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro- and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services.

International audience; Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops.

International audience; This study investigates the relevance of several soil chemical extractions (calcium chloride, acetic acid, citric acid and a four-step sequential procedure) and predicted free metal ion activities in the soil solution to characterise the transfer of trace metals (Cd, Pb, and Zn) from soil to snail soft tissues over a large smelter-impacted area (Metaleurop Nord, Nord-Pas-de-Calais, France). The study was first performed on six snail species together and then specifically on Cepaea sp. and Oxychilus draparnaudi. When the six species were considered together, the accumulation of metals depended mostly on the species. When significant, total or extractable metal concentrations, or the predicted free ion activities, accounted for less than 7% of the variation of the metal concentrations in the snail tissues. Species-specific analyses showed that extractable concentrations explained approximately 25% of the variation of the metal concentrations in O. draparnaudi, and up to 8% in Cepaea snails. When using total soil concentrations and soil properties as explanatory variables, the models were generally slightly better, explaining up to 42% of the variance. The soil extraction procedures and predicted free ion activities used in this study did not accurately estimate the metal transfer from soil to snails and could not be used in risk assessment.

International audience; Field investigations in 361 liver fluke infected cattle- or sheep-breeding farms on acid soil were carried out during thirty years in March and April to record indicator plants in relation to the category of site colonized by the intermediate host of liver fluke, the snail Galba truncatula. Seven types of snail zones and six species of indicator plants were recorded in the 7709 positive sites studied. The most frequent habitats were located at the peripheral extremities of open drainage furrows. Juncus acutiflorus, Juncus effusus, Glyceria fluitans, and Agrostis stolonifera were the indicator plants. Plant indicators were highly efficient (38-80% of variance explained) when used with the size of site area within a hydrographical zone. The identification of positive sites for G. truncatula is a key for controlling the intermediate host on pastures through biological control with predatory molluscs. The positive sites may be detected using a two-step method including first categorization of hydrographical zones and then, within a zone, use of one or several indicator plants (frequently J. acutiflorus).

International audience; In urban areas, there may be a high local risk of zoonosis due to high densities of stray cat populations. In this study, soil contamination by oocysts of Toxoplasma gondii was searched for, and its spatial distribution was analysed in relation to defecation behaviour of cats living in a high-density population present in one area of Lyon (France). Sixteen defecation sites were first identified. Cats were then repeatedly fed with marked food and the marked faeces were searched for in the defecation sites. Of 260 markers, 72 were recovered from 24 different cats. Defecation sites were frequented by up to 15 individuals. Soil samples were also examined in order to detect the presence of T. gondii using real-time PCR. The entire study area was then sampled according to cat density and vegetation cover type. Only three of 55 samples were positive and all came from defecation sites. In a second series of observations, 16 defecation sites were sampled. Eight of 62 samples tested positive, originating in five defecation sites. Laboratory experiments using experimental seeding of soil showed that the inoculated dose that can be detected in 50% of assays equals 100-1000oocysts/g, depending on the strain. This study shows that high concentrations of oocysts can be detected in soil samples using molecular methods and suggests that spatial distribution of contamination areas is highly heterogeneous. Positive samples were only found in some of the defecation sites, signifying that at-risk points for human and animal infection may be very localised.

6 pages; International audience; The fate of organic herbicides applied to agricultural fields may be affected by other soil amendments, such as copper applied as a fungicide. The effect of copper on the leaching of diuron and glyphosate through a granitic and a calcareous soil was studied in the laboratory using sieved-soil columns. Each soil was enriched with copper sulfate to obtain soil copper concentrations of 125, 250, 500, and 1000 mg kg(-1). Glyphosate leaching was influenced by soil pH and copper concentration, whereas diuron leaching was not. In the calcareous soil, glyphosate leaching decreased as copper levels increased from 17 mg kg(-1) (background) to 500 mg kg(-1). In the granitic soil, glyphosate leaching increased as copper levels increased from 34 mg kg(-1) (background) to 500 mg kg(-1). The shapes of the copper elution curves in presence of glyphosate were similar to shapes of the glyphosate curves, suggesting the formation of Cu-glyphosate complexes that leach through the soil. Soil copper concentration does not influence diuron leaching. In contrast, increasing copper concentrations reduces glyphosate leaching through calcareous soils, and conversely, increases glyphosate leaching through granitic soils. Our findings suggest that the risk of groundwater contamination by glyphosate increases in granitic soils with elevated copper concentrations.

International audience; The present study investigated the possible influence of the earthworm Aporrectodea tuberculata on the transfer of cesium-137 ((137)Cs) from a contaminated (130 Bq/kg) deciduous forest soil to the lettuce Lactuca sativa and to the snail Cantareus aspersus (formerly Helix aspersa) in two laboratory experiments. In the first experiment, the International Organization for Standardization 15952 test was used to expose snails for five weeks to contaminated soil with or without earthworms. In these conditions, the presence of earthworms caused a two- to threefold increase in (137)Cs concentrations in snails. Transfer was low in earthworms as well as in snails, with transfer factors (TFs) lower than 3.7 x 10(-2). Activity concentrations were higher in earthworms (2.8- 4.8 Bq/kg dry mass) than in snails (

International audience; The International Standardization Organization recently launched a soil toxicity test with snails (Helix aspersa). We assessed the sensitivity of this test for seven polycyclic aromatic compounds. Control animals had 100% survival and low variability for growth measurements. Maximum exposure concentrations of 2,800 mg/kg (4,000 mg/kg for acridine) had no effect on survival. Similarly, growth (biomass and shell size) was not affected by pyrene, fluoranthene, fluorene, carbazole, phenanthrene, or acridine, whereas dibenzothiophene gave a 10% effect concentration of 1,600 mg/kg. Measured internal concentrations of carbazole, dibenzothiophene, and acridine increased with increasing soil concentrations, but biota-soil accumulation factors were low (0.002-0.1). Compared to previously tested organisms, with all being exposed in the same soil type and under similar test conditions, the H. aspersa test was relatively insensitive to all substances.

International audience; Among soil invertebrates, terrestrial snails are herbivorous and detritivorous organisms exposed to polluted soils by both digestive and cutaneous routes. Using laboratory-reared snails (Helix aspersa aspersa), we describe how the effects of contaminants on survival and growth of snails can be evaluated in laboratory bioassays. A national ring test was performed to assess the effect of Cd added to the soil or to the food. The ecotoxicity of sewage sludge also was evaluated. The present results demonstrate that toxicity depends on both the pollutants and the exposure route. Cadmium was sixfold more toxic for snails exposed via food contamination (median effective concentration [EC50], 68-139 microg/g) than via soil contamination (EC50, 534-877 microg/g), whereas the opposite occurred with the sewage sludge (EC50, 55% of sludge in the food and 10% of waste in the soil). A logistic relationship linked growth inhibition and internal Cd concentrations, which can reach 2,000 microg/g in the viscera of snails exposed to 626 microg/g in the food. No clear trend was found between Cu, Zn, Pb, Cr, and Ni concentrations in the sludge and in snail tissues. These data enabled the development of an international standard, which should enhance the use of terrestrial gastropods for both fundamental research and routine risk assessment in the terrestrial environment.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The transfer of Cd, Cu, Ni, Ph, and Zn was evaluated in a soil-plant (lettuce, Lactuca sativa)-invertebrate (snail, Helix aspersa) food chain during a microcosm experiment. Two agricultural soils, polluted and unpolluted, were studied. Lettuce was cultivated for eight weeks before introduction of snails into the microcosms (M-snails). In a parallel experiment, snails were exposed to lettuce only (i.e., without soil) in simpler exposure devices called containers (C-snails). Snail exposure duration was eight weeks for both M- and C-snails. No effects on snail survival were found. Both M- and C-snails exposed to polluted soil showed a growth reduction, but only after two weeks of exposure. Time-dependent accumulation in M-snails exposed to the polluted environment showed a regular increase of Cd and Zn concentrations over time and a rapid increase of Ph concentrations within the first two weeks, which then remained stable. Copper and Ni concentrations did not increase during any of the experiments. Concentrations in M- and C-snails were compared to estimate the relative contribution of soil and plant to the total bioaccumulation. The results suggest that the soil contribution may be higher than 80% for Pb, from 30 to 60% for Zn, and from 2 to 40% for Cd

Controlling gene expression during plant development is an efficient tool to explore gene function. In this paper, we describe a gene expression system driven by a heat-shock gene promoter (HSP18.2), to trigger the expression of an intron-containing inverted-repeat. RNA interference became a powerful way for gene functional analysis by reverse genetic approaches. However, constitutive gene silencing cannot be used with genes involved in fundamental processes such as embryo viability. Inducible promoters provide an alternative approach for temporal and spatial gene expression control and we described here a new system, complementary to those using chemical gene inducers. To evaluate the efficiency of this system, RNA corresponding to the phytoene desaturase gene of Arabidopsis thaliana was used as a reporter gene in transgenic plants and a comparative study was performed using either the CaMV35S constitutive promoter or the HSP18.2 inducible promoter.

Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.