La contamination des équipements d’alimentation des veaux en pré-sevrage est une préoccupation de santé importante dans l’industrie laitière, et peut être associée à une augmentation des taux de morbidité et de mortalité. Les producteurs laitiers et intervenants ont donc besoin d’un outil pratique, rapide et fiable pour évaluer la propreté des équipements, compte tenu que l’évaluation visuelle seule est insuffisante. Les objectifs de cette étude sont de développer une méthode standardisée pour évaluer la propreté de plusieurs équipements grâce à la luminométrie, d’estimer la prévalence de contamination et décrire les pratiques de gestion recommandées pour le nettoyage. Un total de 7 troupeaux laitiers du Québec a été choisi par convenance. Après l’évaluation visuelle de l’hygiène, la propreté des équipements a été évaluée par écouvillonnage direct pour les seaux et les tétines avec des écouvillons Hygiena UltraSnap®. Une technique de rinçage a été utilisée pour les tubes à gaver, les biberons et les distributrices automatiques de lait (AMF) avec des écouvillons UltraSnap®, AquaSnap® et MicroSnap®. Pour valider la technique d’écouvillonnage direct des seaux, une étape avec le même opérateur et entre plusieurs opérateurs a été réalisée, ainsi qu’une culture bactérienne conventionnelle. Au total, 519 écouvillons ont été prélevés sur 201 équipements. La contamination médiane (intervalle interquartile) en RLU pour le biberon, le tube à gaver, l’AMF, le seau et la tétine est de 2 (1;6), 2 (0;12), 52 (19;269), 886 (128;7,230) et 899 (142;6 928), respectivement. La technique d’écouvillonnage direct, qui consiste à écouvillonner directement la surface d’un équipement, a montré une excellente corrélation pour la fidélité intra-opérateur (corrélation intra-classe (ICC) = 0,93; IC95%: 0,88-0,96). La fidélité inter-opérateur (2 sessions avec 3 opérateurs différents) a montré une corrélation élevée (ICC = 0,88; IC95%: 0,78-0,94 pour la 1ère session et ICC = 0,89; IC95%: 0,79-0,95 pour la 2e). Le score visuel (qui grade de 1 à 4 la propreté des équipements selon la quantité de matières organiques) des tubes à gaver, de l’AMF et des seaux a été positivement associé aux valeurs du luminomètre. Une corrélation positive entre la culture bactérienne et l’écouvillonnage direct des seaux a été trouvée pour l’UltraSnap (rho de Spearman (rs) = 0,653; IC95%: 0,283-0,873; P = 0,0003) et le MicroSnap (rs = 0,569; IC95%: 0,309-0,765; P = 0,002). Cette étude décrit une technique standardisée d’écouvillonnage à la ferme pour évaluer le statut hygiénique des équipements par luminométrie, qui peut être intégrée dans la gestion des problèmes de santé des veaux laitiers en pré-sevrage. / The contamination of equipment used to feed pre-weaned calves is an important health issue for the dairy industry, which can be associated with increased morbidity and mortality rates. Therefore, dairy producers and consultants need a practical, quick, and reliable tool to assess equipment cleanliness, since visual assessment alone is insufficient. The objectives of this cross-sectional study are to develop a standardized robust method to evaluate the cleanliness of several types of feeding equipment on-farm by using luminometry, with special emphasis on a direct swabbing technique to sample buckets, and to estimate the prevalence of contamination and the recommended management practices for cleaning and describing equipment. A total of 7 Quebec commercial dairy herds were selected conveniently. Following visual hygiene scoring, the cleanliness of available piece of feeding equipment was assessed using direct surface swabbing for buckets and nipples with Hygiena Ultra-Snap® swabs. A liquid rinsing technique was used for esophageal feeders, bottles, and automatic milk feeders (AMF) with UltraSnap®, AquaSnap®, and MicroSnap® swabs. To validate the direct swabbing technique of buckets, a comparison within and between operators was realized, as well as a conventional bacterial culture. A total of 519 swab samples were obtained from 201 pieces of equipment. The median (interquartile range) contamination in RLU for a bottle, esophageal feeder, AMF, bucket and nipple was 2 (1;6), 2 (0;12), 52 (19;269), 886 (128;7,230) and 899 (142;6,928), respectively. The direct swabbing technique, which consists in swabbing directly the surface of an equipment, showed an excellent correlation for inter-rater reliability (intraclass correlation (ICC) = 0.93; 95%CI: 0.88–0.96). The inter-operator (2 sessions with 3 different operators) reliability showed high correlation (ICC = 0.88; 95%CI: 0.78–0.94 for the 1st session, and ICC = 0.89; 95%CI: 0.79–0.95 for the 2nd session). The visual score (who ranks equipment cleanliness from 1 to 4 according to the quantity of organic matter) of esophageal feeders, AMF and buckets was positively associated with luminometer values. A positive correlation between bacterial culture and direct swabbing of buckets was found for the UltraSnap (Spearman’s rho (rs) = 0.653; 95%CI: 0.283–0.873; P = 0.0003) and MicroSnap (rs = 0.569, 95%CI: 0.309–0.765; P = 0.002). This study describes a standardized and practical on-farm swabbing technique for assessing the hygienic status of feeding equipment by luminometry, which can be integrated in the investigation of preweaning dairy calves’ health problems.

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Thesis (M. Tech. Environmental health) -- Central University of technology, Free State, 2011 / In nature microorganisms do not exist alone, but in association with one another. These kinds of associations can also be found in food industries, where cells of the same or different species can attach to pipes (biofilm formation) and a variety of surfaces in food processing environments and in food product such as yoghurt which can contain both yeast and bacteria originating from the starter culture as well as fruit. To control food spoilage organisms and food-borne pathogens preventative measures such as good manufacturing processes, the use of sanitizers and preservatives as well as hazard analysis critical control points (HACCP) are crucial in food industries. Sanitation of the working surface, floors, pipes, containers and equipment is a stepwise application of a detergent, acid or alkali rinse, a disinfectant treatment followed by final rinsing. If rinsing of the sanitizer is not done properly it may end up in the product in sub-lethal doses. In this study the influence of Liquid Hypochlorite (LH) and Liquid Iodophore (LI) sanitizers on organism growth and toxicity was evaluated. The organisms investigated included Escherichia coli 0113, Escherichia coli 026 and Zygosaccharomyces bailii Y-1535 in yeast malt broth, which was supplemented with LH and LI at sub-lethal concentrations 0.05% LH, 0.2% LH and 0.075% LI. Subsequently, bacterial and yeast growth responses as pure cultures and in combination (E. coli + Z. bailii) were measured as colony forming units and optical density values. Incorporation of the sanitizers in the growth media resulted in different levels of growth inhibition. Z. bailii proved more robust and the growth rate was not influence significantly by the addition of sanitizers or communal growth with either E. coli strains. The growth rate of both E. coli strains decreased where grown in combination with Z. bailii as well as in the presence of sanitizers, with the most influence exerted by LH. Changes in endotoxicity following the growth of the test samples (stressed cells) and the control (unstressed) were measured by the limulus amoebocyte lysate (LAL) and porcine IL-6 ELISA methods. Where E. coli strains were cultured together with Z. bailii the toxicity of tire mixture showed a decrease over time when measured with the limulus amoebocyte assay method. Interestingly the communal growth of the E. coli strains and Z bailii produced different toxicity profiles when the IL-6 porcine method was used, hi both cases, where E. coli strains were cultured together with Z. bailii the toxicity of the mixture showed an increase over tune when measured by this assay. Other than a similar toxicity profile for E. coli 0113 grown in pure culture, the comparison between results obtained using the LAL or porcine IL-6 methods yielded no correlation in determined toxicity. It was established that LH and LI sanitizers as well as communal growth had an influence in the toxicity of LPS/EPS and the method used to determine such toxicity should be carefully considered.

Thesis (D. Tech. Environmental health) -- Central University of technology, Free State, 2011 / Apart from being the primary food source of many cultures around the world, fish contains notable amounts of essential fatty acids that are required by the human body, thus making fish a vital part of the human diet. In South Africa Cape hake is a well-known and highly consumed local fish species, which is transported from coastal areas countrywide where the fresh fish are displayed on ice in various retail stores. Fish is known to be highly susceptible to spoilage and, as a result, the maintenance of the cold-chain in related products is of particular importance. Additionally, recent trends showing a decline in natural fish resources have instigated growing concerns about the sustainability and optimal utilisation of fish as a food source. Against this backdrop, this study aimed at determining the influence of storage parameters on selected triglycerides and their possible metabolic pathways. Also applying prediction modelling of fatty acids and volatiles as instruments to assess exposure of Cape hake fillets to excessive microbial contamination and, in effect, be indicative of the environmental parameters (for example temperature) that may influence such contamination. Randomly selected juvenile hakes were filleted and stored under various simulated retail storage conditions, under either controlled or uncontrolled environmental conditions. For each hake filleted, one fillet was inoculated with an increased load of autochthonous microbiota, and the corresponding fillet was kept at similar temperature conditions. All fillets were monitored over a ten day period, during which fatty acid and volatile samples were collected and analysed. From the resulting triglycerides a selection of fatty acids were profiled and their possible metabolic pathways investigated. Fish maturity, the distribution of the fatty acids and the implication thereof in the nutritional value were also assessed. Conventional chemometric methods utilising mathematical expressions were subsequently utilised in order to predict contamination and whether the cold chain was sustained, while an artificial neural network (ANNs) were designed to predict excessive microbial contamination in the fillets. The results showed that the nutritional value of fish differs notably with its maturity and size. Mathematical equations were furthermore found to be effective assessment instruments to indicate the percentage differences in storage temperature, as well as consequent microbial influences. Thus, this approach may introduce mathematical prediction modelling as a promising mechanism to assess Cape hake spoilage. An artificial neural network (ANN) was successfully designed, that succeeded in distinguishing between Cape hake fillets displayed and stored on ice that have been exposed to excessive contamination and those that have not been exposed. In the latter case, the selected variable was a fatty acid, hexadecanoic acid, used as biochemical indicator. This modulating approach may provide a platform for future shelf-life studies on related muscle tissue. Ultimately, the study endeavoured to add to the body of knowledge regarding the biochemical and microbiological changes related to Cape hake storage, the prediction thereof via contemporary methods and contributing to the safety and effective utilization of this unique and declining South African nutritional resource.

Thesis (M. Tech. (Environmental Health)) - Central University of Technology, Free State, 2014 / In the battle to sustain and produce quality food that is safe and affordable, the limited legislative and regulatory environment continues to allow opportunities for food to become contaminated during processing. The degree of contamination distributed over the final food product (including meat products) depends upon several factors that include knowledge and behaviour of the food handlers, equipment, the hygiene habits of personnel, and the monitoring that takes place at food processing plants (including butcheries). The current study was conducted in five selected butcheries (forming 15% of the registered butcheries at the time the study was conducted) in the Mangaung Metropolitan municipal area, purposely targeting the ones registered with the municipality. The hygiene practices of meat handlers were assessed (through self-administered questionnaires) because meat is a perishable product that requires labour intensive processing for production of quality products. Thus, mishandling by food handlers may create and maintain conditions favourable to microbial contamination. Furthermore, the study assessed and characterised microbial contamination on working surfaces and utensils through swabs as well as bioluminescence instrument [Adenosine Tri-phosphate (ATP) Hygiena] for cleanness of the working environment. Concomitant to the above, meat handlers’ hands and aprons were also assessed for possible microbial contamination as well as their characterisation. Lastly, aerosolised microbes [through an air sampler (Surface Air System) SAS Super 90] were also collected for iv quantification and identification during working hours as airborne microbes can settle on working surfaces and/or utensils as a result of movement of workers and other related working processes. Statistical points such as correlations, standard deviations, group standard deviations as well as significant differences were captured per respective chapter where necessary. Data reported in this study is over 3 month period with two weeks intervals during sampling and thus reported as either weekly or rounds between sampling periods. The results of the current study indicate that the food safety objectives are negligibly achieved, indicating a need for proper food safety training which is audit based. On administration of a questionnaire, food handlers showed poor knowledge of food safety awareness coupled with poor attitude and behaviour in terms of food safety. The five butchery premises were further examined regarding the airborne and surface microbial loads, as well as that of the food handlers’ hands, during processing. The microbial loads in the air appeared to comply with the suggested limits at all the sampled butcheries. Microbial loads on meat contact surfaces showed levels conforming to the South African standard or guideline of 1 × 102 cfu.m-2. Total Coliforms on hands and on aprons were compared to the general microbial target value of <2.5 cfu.m-2 as suggested by literature. In this study, Matrix Laser Desorption Time of Flight Mass Spectrophotometer (MALDI-TOF MS) was found to be an accurate, rapid and cost effective method towards v identifying of foodborne pathogens and spoilage bacteria including yeast. Moreover, in recent years South Africa’s meat scandals have increased consumer awareness and the demand for food safety. Section 11 of the Meat Safety Act (Act no. 40 of 2000) stipulates that every abattoir must utilize an independent inspection service appointed by the department of agriculture to ensure that meat of high quality and wholesomeness is produced. However, once the meat and meat products leave the abattoir, they are under the jurisdiction of the local authorities who rely only on visual assessment as opposed to microbiological inspection in the maintenance of their hygiene and quality. Despite the high incidence of foodborne illnesses in both developed and developing countries; South African data on foodborne illness incidents is still insufficient. This could be attributed to the fact that in South Africa, legislation governing the acceptable standards of the levels of microbiota in the air and on food handlers’ hands is still inadequate. Additionally, lack of obligatory usage of Hazard Analysis Critical Control Point (HACCP) procedures in the meat premises poses a risk for economic productivity. In conclusion, the identification of airborne bacteria in the butcheries strongly suggests that in the planning of the existing establishments, the building layout, control of the traffic flow of personnel, the durability and imperviousness of floors, the ventilation system and the placement of the equipment were not carefully considered. This may play a role in the prevalence and proliferation of airborne microbes as the resulting establishments provide an environment conducive to the breeding of microbes. vi In regard to swabs, it was concluded that floors may present a high point of contamination possibly through aerosolization of microbial communities. Moreover, cleaning materials and hygiene practices need to be reviewed. The results of the administered questionnaire showed that food handlers should be sufficiently trained with regard to food quality management tools such as Good Manufacturing Practices (GMP), Hazard Analysis and Critical Control Point (HACCP) systems and food safety. The evaluation of meat contact surfaces for organic soils to determine their cleanliness using the rapid ATP bioluminescence testing can be convenient for everyone involved in the food chain since visual and touch inspection cannot be conclusive enough to meet regulatory requirements in terms of microbial counts.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The presence of mineral oils in dry foodstuff was found to originate from the packaging materials, namely, paperboard manufactured from recovered fibres, and these oils subsequently migrate to the foodstuff via the vapour phase. The presence of mineral oils in food is of concern as it originates from the use of paper products not originally intended for food contact applications, i.e., before the paper is subjected to a suitable recycling process. These mineral oils consist of technical grade compounds which may contain aromatic compounds and other components with unknown toxicological effects. Although the related authorities are currently considering the safe and legal limits of these contaminants in foodstuffs, as well as establishing a standardised test method for monitoring mineral oils in food and packaging materials, paperboard manufacturers wish to ensure that their products are safe for food contact applications. Since recycling is unavoidable, particularly from an ecological and economical point of view, one of the proposed solutions the industry is focussing on is the use of a functional barrier towards mineral oils – be it an inner bag as a direct food-contact surface, or a barrier coating directly applied on the inner side of the paperboard. In this study, a permeation test method was established, and developed, to evaluate the transmission rate of a volatile organic compound, acting as a mineral oil simulant, through model paper and plastic packaging materials. This was correlated to the transmission rate of actual mineral oil through the packaging materials, and therefore used as a highly accelerated tool to characterise packaging materials in relation to their barrier properties. The test method, referred to as the “heptane vapour transmission rate,” was subsequently used to derive the required transport parameters’ characteristics of each of the tested materials, which enabled an evaluation of the potential shelf-life of the packaged product. This research demonstrated that barrier-coated paperboards have the ability to behave in the same way as, and often even better than, commercial plastic films, towards the migration of mineral oil. Detailed information on the interaction between the packaging materials and mineral oil simulant, n-heptane, was acquired from gravimetric sorption. Insight was obtained into a material’s ability to function as a mineral oil barrier. It was established that the quick and easy permeation method was sufficient for evaluating packaging materials as potential mineral oil barriers, and resulted in the determination of transport parameters that were higher than that obtained by sorption. The obtained transport parameters could therefore be considered a worst case scenario when predicting the package content shelf-life. / AFRIKAANSE OPSOMMING: Daar is voorheen bevind dat die teenwoordigheid van mineraalolies in droë voedsel afkomstig is van die verpakkingsmateriaal, naamlik karton, wat vervaardig is van herwonne papierprodukte, en daarna migreer die olies na die voedsel deur die gasfase. Die teenwoordigheid van hierdie mineraalolies in kos wek groot kommer aangesien dit afkomstig is van papierprodukte wat nie oorspronklik bedoel is vir voedselkontak voor die herwinningsproses nie. Die olies bestaan uit industriële graad mineraalolies wat moontlik aromatiese verbindings asook ander komponente bevat waarvan die toksiekologiese effekte onbekend is. Terwyl die betrokke owerhede tans besig is om die veilige en wettige grense van hierdie kontaminante in voedsel te oorweeg, asook die vestigting van 'n gestandaardiseerde toetsmetode vir die kontrole van mineraalolies in die voedsel-verpakkingsmateriaal-kombinasie, wil karton- en papiervervaardigers graag verseker dat hul produkte veilig is vir voedselkontak. Siende dat herwinning onvermydelik is vanuit 'n ekologiese en ekonomiese oogpunt, is een van die voorgestelde oplossings in die bedryf om te fokus op die gebruik van 'n funksionele keerfilm ten opsigte van mineraalolies, wat ‘n sakkie binne-in die karton, wat dien as die direkte kos-kontakoppervlak, of 'n keerlaag, wat direk aangewend word op die binnekant van die karton, kan behels. Hierdie studie ondersoek die daarstel en deursypelingsontwikkeling van 'n toetsmetode om die oordragtempo van 'n vlugtige organiese verbinding, wat optree as 'n mineraalolie simulant, deur middel van model papier- en plastiekverpakkingsmateriale, te evalueer. Dit stem ooreen met die oordragtempo van werklike mineraalolies deur die verpakkingsmateriaal en kan dus gebruik word as 'n hoogs versnelde instrument om verpakkingsmateriale te karakteriseer met betrekking tot hul keereienskappe. Die toetsmetode, die sogenaamde "heptaangasoordragtempo," is vervolgens gebruik om die vereiste oordragparameters af te lei wat kenmerkend is van elk van die geëvalueerde verpakkingsmateriale en wat sodoende gebruik kon word om die potensiële raklewe van die verpakte produk te bepaal. Hierdie navorsing het getoon dat kartonprodukte met ‘n keerlaag die vermoë het om dieselfde op te tree as kommersiële plastiekfilms en dikwels selfs beter, ten opsigte van die migrasie van mineraalolies. Gedetailleerde inligting oor die interaksie tussen die verpakkingsmateriale en mineraalolie simulant, n-heptaan, is verkry vanaf gravimetriese sorpsie. Dit gee insig in 'n materiaal se vermoë om te funksioneer as 'n mineraalolie-keermiddel. Daar is vasgestel dat die vinnige en maklike deurwerking metode voldoende is vir die evaluering van verpakkingsmateriale as potensiële mineraalolie-keermiddels, en verleen oordragparameters wat hoër is as dié verkry deur sorpsie. Hierdie oordragparameters kan dus as 'n ergste scenario vir die voorspelling van die raklewe van ‘n verpakte produk beskou word.

L’objectif général de cette thèse est de caractériser la dynamique des transferts des bactéries fécales à l’aide d’une modélisation spatio-temporelle, à l’échelle du bassin versant (BV) dans une région agricole et à l’échelle événementielle. Ce projet vise à mieux comprendre l'influence des processus hydrologiques, les facteurs environnementaux et temporels impliqués dans l’explication des épisodes de contamination microbienne des eaux récréatives. Premièrement, un modèle bayésien hiérarchique a été développé pour quantifier et cartographier les niveaux de probabilité des eaux à être contaminées par des effluents agricoles, sur la base des données spectrales et des variables géomorphologiques. Par cette méthode, nous avons pu calculer les relations pondérées entre les concentrations d’Escherichia coli et la distribution de l’ensemble des paramètres agro-pédo-climatiques qui régissent sa propagation. Les résultats ont montré que le modèle bayésien développé peut être utilisé en mode prédictif de la contamination microbienne des eaux récréatives. Ce modèle avec un taux de succès de 71 % a mis en évidence le rôle significatif joué par la pluie qui est la cause principale du transport des polluants. Deuxièmement, le modèle bayésien a fait l’objet d'une analyse de sensibilité liée aux paramètres spatiaux, en utilisant les indices de Sobol. Cette démarche a permis (i) la quantification des incertitudes sur les variables pédologiques, d’occupation du sol et de la distance et (2) la propagation de ces incertitudes dans le modèle probabiliste c'est-à-dire le calcul de l’erreur induite dans la sortie par les incertitudes des entrées spatiales. Enfin, une analyse de sensibilité des simulations aux différentes sources d’incertitude a été effectuée pour évaluer la contribution de chaque facteur sur l’incertitude globale en prenant en compte leurs interactions. Il apparaît que sur l’ensemble des scénarios, l’incertitude de la contamination microbienne dépend directement de la variabilité des sols argileux. Les indices de premier ordre de l’analyse de Sobol ont montré que parmi les facteurs les plus susceptibles d’influer la contamination microbienne, la superficie des zones agricoles est le premier facteur important dans l'évaluation du taux de coliformes. C’est donc sur ce paramètre que l’attention devra se porter dans le contexte de prévision d'une contamination microbienne. Ensuite, la deuxième variable la plus importante est la zone urbaine avec des parts de sensibilité d’environ 30 %. Par ailleurs, les estimations des indices totaux sont meilleures que celles des indices de premier ordre, ce qui signifie que l’impact des interactions paramétriques est nettement significatif pour la modélisation de la contamination microbienne Enfin, troisièmement, nous proposons de mettre en œuvre une modélisation de la variabilité temporelle de la contamination microbiologique du bassin versant du lac Massawippi, à partir du modèle AVSWAT. Il s'agit d'une modélisation couplant les composantes temporelles et spatiales qui caractérisent la dynamique des coliformes. La synthèse des principaux résultats démontrent que les concentrations de coliformes dans différents sous-bassins versants se révèlent influencées par l’intensité de pluie. La recherche a également permis de conclure que les meilleures performances en calage sont obtenues au niveau de l'optimisation multi-objective. Les résultats de ces travaux ouvrent des perspectives encourageantes sur le plan opérationnel en fournissant une compréhension globale de la dynamique de la contamination microbienne des eaux de surface. / Abstract : The aim of this study was to predict water faecal contamination from a bayesian probabilistic model, on a watershed scale in a farming area and on a factual scale. This project aims to better understand the influence of hydrological, environmental and temporal factors involved in the explanation of microbial contamination episodes of recreational waters. First, a bayesian probabilistic model: Weight of Evidence was developed to identify and map the probability of water levels to be contaminated by agricultural effluents, on the basis of spectrals data and geomorphologic variables. By this method, we were able to calculate weighted relationships between concentrations of Escherichia coli and distribution of key agronomic, pedologic and climatic parameters that influence the spread of these microorganisms. The results showed that the Bayesian model that was developed can be used as a prediction of microbial contamination of recreational waters. This model, with a success rate of 71%, highlighted the significant role played by the rain, which is the main cause of pollution transport. Secondly, the Bayesian probabilistic model has been the subject of a sensitivity analysis related to spatial parameters, using Sobol indications. This allowed (1) quantification of uncertainties on soil variables, land use and distance and (2) the spread of these uncertainties in the probabilistic model that is to say, the calculation of induced error in the output by the uncertainties of spatial inputs. Lastly, simulation sensitivity analysis to the various sources of uncertainty was performed to assess the contribution of each factor on the overall uncertainty taking into account their interactions. It appears that of all the scenarios, the uncertainty of the microbial contamination is directly dependent on the variability of clay soils. Sobol prime indications analysis showed that among the most likely to influence the microbial factors, the area of farmland is the first important factor in assessing the coliforms. Importance must be given on this parameter in the context of preparation for microbial contamination. Then, the second most important variable is the urban area with sensitivity shares of approximately 30%. Furthermore, estimates of the total indications are better than those of the first order, which means that the impact of parametric interaction is clearly significant for the modeling of microbial contamination. Thirdly, we propose to implement a temporal variability model of microbiological contamination on the watershed of Lake Massawippi, based on the AVSWAT model. This is a model that couples the temporal and spatial components that characterize the dynamics of coliforms. The synthesis of the main results shows that concentrations of Escherichia coli in different sub-watersheds are influenced by rain intensity. Research also concluded that best performance is obtained by multi-objective optimization. The results of these studies show the prospective of operationally providing a comprehensive understanding of the dynamics of microbial contamination of surface water.

Les champignons endophytes sont des organismes qui vivent à l’intérieur de plantes sans causer de symptômes de maladie apparents. Ils sont trouvés dans virtuellement toutes plante, et la nature des interactions peut aller de mutualiste à pathogène dépendant des conditions. La diversité et la structure des communautés des champignons endophytes dans les plantes poussant en milieu extrêmement pollué, ainsi que leur rôle potentiel pour améliorer la phytorémédiation, demeurent peu compris. Dans cette étude, nous nous sommes intéressés aux communautés de champignons endophytes de racines de deux espèces de plantes (Eleocharis erythropoda et Populus sp.). Ces espèces poussaient de manière spontanée dans trois bassins de sédimentation d’un ancienne usine pétro-chimique ayant des niveaux de contaminations différents, en utilisant à la fois une approche d’isolation d’organisme ainsi que des analyses de pyroséquençage de l’ITS d’ADN ribosomal. Nos résultats indiquent que les niveaux de contamination ont un effet significatif sur la composition taxonomique des champignons endophytes des racines de E. erythropoda. Une majorité des données de séquences appartiennent à la classe des Dothideomycetes dans les échantillons de forte concentration en hydrocarbures pétroliers, dont une majorité appartient au genre Alternaria. La comparaison des données d’isolation et de pyroséquençage suggère que l’isolation de souches ne permet pas l’obtention des souches les plus représentées dans les données de pyroséquençage. Ces résultats pourront potentiellement aider à l’élaboration de stratégies pour améliorer la phytorémédiation en utilisant les champignons endophytes. / Endophytic fungi are organisms that live inside plant tissues without any apparent disease symptoms. They are found in virtually all plant species and their interactions can vary widely from mutualism to parasitism depending chiefly on environmental conditions and stresses. The diversity and community structure of fungal endophytes in extremely polluted sites and their role in phytoremediation remain largely unexplored. In this study we investigated the community structure of endophytic fungi in roots of two plant species (Eleocharis eryhtropoda and Populus sp.) growing spontaneously in three petroleum-contaminated sedimentation basins of a former petro-chemical plant with different contamination levels. We used both a culture-dependent method of strain isolation as well as a culture-independent method of pyrosequencing of ITS ribosomal DNA. Our results indicate that levels of contamination shape the taxonomic composition of endophytic fungi in E. erythropoda roots. A majority of the reads belonged to the Dothydeomycetes class in smaples from high petroleum-hydrocarbon levels, with the Alternaria genus accounting for the majority of these reads. In addition comparison between culture-dependent and -independent methods showed that strain isolation does not promote the most abundant species found in pyrosequencing. This could help to develop strategies for improving phytoremediation using fungal endophytes.