Doctor of Philosophy / Department of Biological & Agricultural Engineering / Kyle R. Mankin / The overall goal of this study was to evaluate and apply the Soil and Water Assessment Tool (SWAT) model for fecal bacteria modeling. Methods were developed to characterize fecal coliform bacteria (FCB) from livestock, human, and wildlife sources to use as input in the model. Model sensitivity to predict FCB concentration was evaluated for the model parameters and input parameters using both SWAT 2000 and 2005 versions. Sensitivity of input parameters generally, ranked as Bacteria concentration ≥ TBACT > Wildlife source loads > Livestock stocking rate ≥ Livestock manure production rate > BACTKDQ for SWAT 2000 whereas it was ranked as BACTKDQ > TBACT > Bacteria concentration > WDLPQ > WDLPS for SWAT 2005. Sensitivity of model and input parameters were found changed from SWAT 2000. The SWAT (2005) model was calibrated and validated for daily flow, sediment, and fecal bacteria concentration using one year of measured data (January to December, 2004). The SWAT model predicted results with poor to very good agreement when compared with measured data with coefficient of determination (R2) and Nash-Sutcliffe Efficiency Index (E) range of 0.10 to 0.89 for daily flows, sediment, total phosphorus, total nitrogen and total FCB concentration. More extensive in-stream data are needed for more comprehensive model assessment. The SWAT model (2005) was evaluated for source-specific FCB modeling using three years (2004-2006) of observed modified deterministic probability of bacteria source tracking (BST) data. The FCB sources were modeled with three combinations (livestock and human, livestock and wildlife, wildlife and human) and each single source to evaluate the source-specific FCB concentrations. The SWAT model determined poor to good agreement for the combined source of FCB (R2, E range from -2.92 to 0.71) but determined generally decreased agreement for each single source of bacteria (R2, E range from -5.03 to 0.39) potentially due to BST uncertainty, spatial variability and source characterization. The SWAT model identified critical sub-watersheds in the watershed where implementing vegetative filter strips (VFS) could be most effective to abate fecal bacteria pollution. The targeting method of VFS application to the watershed sub-basins was found to be more effective in reducing both FCB (60% vs. 42%) and sediment yield (63% vs. 33%) as compared to a random approach. The FCB source characterization methods for modeling developed in this study are general and have the potential to be extended to other watersheds. The results of this study demonstrate that the SWAT model can be used to characterize the distribution of bacteria sources within a bacteria impaired watershed and assist with developing total maximum daily loads (TMDLs) and watershed restoration strategies.

Microbial contamination of drinking water poses an important health risk which causes severe illnesses and epidemics. In order to improve surface and drinking water quality, the understanding of fecal pathogen contamination processes including their prevention and control needs to be enhanced. The watershed model soil water assessment tool (SWAT) is commonly used to simulate the complex hydrological, meteorological, erosion, land management and pollution processes within river basins. In recent years, it has been increasingly applied to simulate microbial contamination transport at the watershed scale. SWAT is used in this study to simulate Escherichia coli (E.coli) and fecal coliform densities for the agriculturally dominated Payne River Basin in Ontario, Canada. Unprecedented extensive monitoring data that consist of 30 years of daily hydrological data and 5 years of bi-weekly nutrient data have been used to calibrate and validate the presented model here. The calibration and validation of the streamflow and nutrients indicate that the model represent these processes well. The model performs well for periods of lower E. coli and fecal coliform loadings. On the other hand, frequency and magnitude of higher microbial loads are not always accurately represented by the model.

Dans le cadre de l’évaluation du risque immunotoxique de composés glycolypidiques d’origine bactérienne, cette thèse a portée sur l’évaluation de toxicité d’endotoxines d’E.coli de deux sérotype différents : LPS O55:B5 utilisé couramment en comme immunostimulant et le LPS O157:H7 dont la réalité environnementale a soulevé notre questionnement scientifique quant à son impact sur le système immunitaire du poisson et son caractère potentiellement pro-inflammatoire. Les différents procédés employés ont compris l’évaluation des paramètres cellulaires (production d’espèces réactives d’oxygène et phagocytose) ainsi que la caractérisation et la quantification de l’expression de gènes de cytokines (TGFβ et IL-10) et facteurs immuno-associés (MARCO, HSP60 et vitellogénine) chez le modèle gardon (Rutilus rutilus).Les approches expérimentales se sont déroulées tout d’abord en ex vivo sur des leucocytes isolés d’organes lymphoïdes (Rein antérieur, rate et sang) de gardon et ont montré une tolérance endotoxique vis-à-vis de ces LPS à de 1µg/mL même combinés au diclofénac à 0,1 µM. ce travaill a été suivi par une évaluation du risque potentiel d’autres composés glycolipidiques d’origine bactérienne (rhamnolipides).Les approches in vivo qui ont suivies ont été réalisées sur : (i) sur modèle poisson-zèbre (Danio rerio) au laboratoire et (ii) sur modèle gardon par encagement sur terrain. Les résultats obtenus sur danios au laboratoire ont montré une toxicité du sérotype O157 :H7 et une influence sur les paramètres comportementaux par les LPS (Sickness behaviour). Sur terrain, l’approche in vivo par encagement a révélé – au niveau de la rate et du rein antérieur – des réponses cellulaires et moléculaires, sérotype, organe et sexe dépendante avec une immunomodulation prédominante chez les mâles d’autant plus que la période d’étude s’est déroulée durant la maturation sexuelle des gardons. Ce travail fait état du caractère inflammatoire et toxique du LPS peu étudié d’E.coli O157 :H7, évalué par des immunomarqueurs cellulaires bien maitrisés et moléculaires néo-développés. / In the context of immunotoxic risk evaluation of glycolypidic compounds of bacterial origin, this thesis focused on the evaluation of E.coli endotoxin toxicity of two different serotypes: LPS O55: B5 commonly used as an immunostimulant et LPS O157: H7, whose environmental reality has raised our scientific questioning about its impact on the fish's immune system et its potentially pro-inflammatory nature. The various methods used included the evaluation of cellular parameters (production of reactive oxygen species et phagocytosis) as well as the characterization of cytokines (TGFβ et IL-10) et immune-realted factors (MARCO, HSP60 et vitellogenin) genes et the quantification of their expression in the roach model (Rutilus rutilus).The experimental approaches were first carried out ex vivo on leukocytes isolated from lymphoid organs (anterior kidney, spleen et blood) roach et showed an endotoxic tolerance at 1μg / mL even combined with 0.1 μM diclofenac. This work was followed by an evaluation of the potential risk of other glycolipidic compounds of bacterial origin (rhamnolipids).The in vivo approaches that followed were performed on: (i) zebrafish (Danio rerio) model in the laboratory et (ii) on roach model by field caging. The results obtained on danios in the laboratory showed a toxicity of the serotype O157: H7 et an influence on the behavioral parameters by the LPS (Sickness behavior). On the field, the caging approach revealed - at spleen et the anterior kidney level - cellular et molecular responses, serotype, organ et sex-dependent with a predominant immunomodulation in males, especially since the study period took place during the sexual maturation of roaches. This work reports the inflammatory et toxic nature of the less studied E.coli O157: H7 LPS serotype, evaluated by well-mastered cellular et neo-developed molecular immunomarkers.

The composition of the gut microbiome can be affected by environmental factors, such as diet. The Western dietary pattern is associated with microbiome dysbiosis and adverse health outcomes, including obesity and metabolic disorders. The objective of this study was to examine the effect of gut microbiota from lean or obese human donors on metabolism and weight gain in recipient mice fed one of three basal diets: 1) the standard AIN93G diet, which promotes rodent health; 2) the total Western diet (TWD), which mimics the American dietary pattern and promotes inflammation-associated colorectal carcinogenesis; and 3) a 45% high fat diet-induced obesity (DIO) diet, which promotes excessive weight gain and symptoms of metabolic syndrome. We hypothesized that fecal microbiome transfer (FMT)from obese human donors would lead to an obese phenotype with symptoms of metabolic syndrome in recipient mice, and that consumption of TWD or DIO diets would further exacerbate the metabolic syndrome phenotype. The experiment design consisted of two main factors: body type of the human donor (obese or lean) and experimental diet (AIN, DIO or TWD), which was fed to mice for 22 weeks. Prior to FMT, the resident gut microbiome in mice was depleted using an established broad spectrum antibiotic/antifugal oral dosing regimen. Interestingly, human donor body type did not significantly affect final body weight or body composition in recipient

La préservation de la richesse aquatique est devenue un souci majeur d'ordre mondial suite au risque de pénurie en eau. Au Liban, les rejets anthropiques incontrôlés et incontrôlables au bord des rivières menacent la qualité de ses eaux de surface. Pour cela, quatre cours d'eau libanais ont été choisis comme cadre d'étude : la rivière Damour, la rivière Kadisha-Abou Ali, la rivière Ibrahim et la rivière Oronte.Les différents paramètres physico-chimiques et microbiologiques étudiés ont permis dans un premier temps la construction d'une base de données de chacune de ces rivières. Une seule analyse spatio-temporelle des paramètres séparément n'aide pas à définir l'état trophique des rivières. Partant de l'idée des corrélations que peuvent exister entre certains paramètres, l'Analyse en Composante Principale (ACP) retenant la totalité de l'information sera utilisée en dépit des méthodes classiques. Cet outil statistique a permis de classer les rivières par niveau de pollution. Il a aussi aidé à observer l'impact des apports des polluants sur les différentes stations de rivières étudiées.Pour suivre le devenir des coliformes fécaux dans les eaux, l'ACP des variables microbiologiques a montré la persistance des colonies bactériennes dans les eaux malgré les conditions climatiques diverses et le régime méditerranéen torrentiel des rivières. En effet, les sédiments constituent des réservoirs potentiels de microorganismes pathogènes. Le décrochage bactérien des agrégats sédimentaires et la remise en suspension dans l'eau pose un problème alarmant de santé publique. / Preservation of aquatic wealth has worldwide become a major concern due to the risk of water shortage. In Lebanon, uncontrolled and uncontrollable anthropogenic rejections along rivers threaten the quality of its surface waters. Four Lebanese rivers were selected as study framework: The Damour river, Kadisha-Abu Ali river, Ibrahim river and Orontes river. The physico-chemical and microbiological parameters analyzed has formed a large database of these rivers. The spatio-temporal analysis of separate parameters did not help defining the trophic status of rivers. The assumption that correlations exist between certain parameters, guides us to use the Principal Component Analysis (PCA) in spite of conventional methods. This statistical tool was used to define the pollution levels in rivers. It also leads to observe the impact of pollutants inflows on different sites studied. To follow the fate of fecal coliform in water, the ACP of microbiological variables showed the persistence of bacterial colonies in water despite the various climatic conditions and the Mediterranean flow rate. Indeed, sediments are potential reservoirs of pathogenic microorganisms. The bacteria aggregated to the sediment can be present again in water column causing an alarming public health problem.