Indicator organisms (IOs) such as Escherichia coli and Enterococcus spp. are used to predict the presence of pathogens in waters. Determining the relationships between environmental factors, IOs, and pathogens is a key to assessing water quality and ensuring public health, yet certain strains of E. coli and Enterococcus spp. survive for long periods in natural waters. Molecular subtyping, using repetitive extragenic palindromic DNA sequences (BOX-PCR), has been used to discriminate among environmental E. coli and Enterococcus spp. isolates. The reproducibility of BOX-PCR patterns varies with DNA purification methods; therefore, it is important to develop a standardized, rapid, high throughput DNA purification protocol for population biology studies. I have compared the effects of DNA purification methods on the reproducibility, cost, and speed of producing BOX-PCR patterns using three methods: a commercially available Qiagen kit (Qiagen DNeasy tissue), a whole cell method requiring no pre-treatment, and a method developed in-house using the MacConnell Mini-prep 96 (mini-prep) instrument. The whole cell method was the least expensive, but demonstrated the least precision (reproducibility). The Qiagen kit and the Mini-prep 96 showed high reproducibility (90-95%); however, the Mini-prep 96 is less expensive and very rapid, allowing processing of up to 192 isolates/day. Water and sediment from a Florida river were placed in an outdoor flume that maintained turbulent flow and oxic conditions in the water column (~11 mg/L). The flume was inoculated with seven E. coli strains and nine Enterococcus spp. of distinct BOX-PCR phylotypes. Putative "survivor" strains previously isolated from mesocosms and disinfected wastewater effluent and control laboratory strains were chosen to test the hypothesis of differential survival of strains under hydrodynamically active conditions. IO strains isolated each day were typed by BOX-PCR (n=100 isolates/day), revealing differential survival of certain E. coli and Enterococcus strains. Ultimately, a better understanding of the effect of hydrodynamic regime and phylotype distribution on IO survival in water will allow more accurate modeling of the fate of these organisms in aquatic environments. This will in turn lead to a better understanding of the organisms we use as indicators of pollution. This is necessary to ensure the health and safety of all recreational water users.

La diversité fongique des meules de plusieurs espèces de Macrotermitinae a été analysée au niveau taxinomique, fonctionnel et génétique à l’aide d’une approche polyphasique associant plusieurs techniques complémentaires. L’objectif étant d’évaluer la spécificité des taxons fongiques associés aux meules ainsi que les relations qu’ils entretiennent avec les termites champignonnistes. Une grande variété de phylotypes cultivables appartenant majoritairement au phylum des Ascomycètes a été obtenue par isolement et séquençage des ITS fongiques, et peu de séquences se sont révélées être spécifiques à un genre de Macrotermitinae particulier. Les profils physiologiques obtenus ont mis en évidence la nature saprophytique de la majorité des phylotypes et confirmé l’absence de taxons spécifiques. Par PCR-DGGE de l’ADN total de meules, 100% des phylotypes ITS et 28S fongiques identifiés étaient affiliés au genre Termitomyces. La technique Suicide Polymerase Endonuclease Restriction (SuPER) a été adaptée à la mycoflore des meules pour limiter l’impact de l’ADN majoritaire du Termitomyces symbiotique. Celle-ci a permis la détection de plusieurs autres populations fongiques. Les analyses phylogénétiques ont montré d’une part la spécificité des Xylaria associés aux meules de Macrotermitinae bien qu’aucune co-évolution n’ait été observée avec les termites hôtes et d’autre part leur affiliation dans un sous-genre spécifique. Une analyse préliminaire des facteurs d’inhibition a également révélé l’implication des termites dans la régulation des communautés fongiques des meules. Dans leur ensemble, nos résultats illustrent clairement l’influence des Macrotermitinae sur les communautés fongiques telluriques pendant leurs différentes activités. / Fungal diversity of several Macrotermitinae fungus combs was analyzed at taxonomic, functional and genetic levels using a polyphasic approach. The aim of this thesis was to evaluate the specificity of fungal strains from combs and to elucidate their relationship with fungus-growing termites. A large variety of culturable phylotypes mainly belonging to Ascomycota phylum was retrieved using conventional isolation techniques followed by sequencing of ITS1-5.8S-ITS2 region. Based on the obtained results, there is evidence for any speciesspecificity between these taxa and a given genus of Macrotermitinae. This finding was supported by the physiological profile of some representative phylotypes which revealed the saprophytic nature of most of the isolates. By PCR-DGGE analysis of fungal ITS and LSU, all of the sequences were belonged to Termitomyces genus. The Suicide Polymerase Endonuclease Restriction method was adapted to the analysis of comb mycoflora for restricting the impact of the dominant Termitomyces DNA. As expected, this latter technique revealed non-Termitomyces fungal populations. Phylogenetic analysis also showed the specificity of termiteassociated Xylaria although they do not evolved with termite hosts, and also their affiliation to a new genus or at least a specific sub-genus. Preliminary investigation revealed the implication of termite workers in fungal regulation in fungus combs. All in one, our results clearly underline the great impact of fungus-growing termite species on soil fungal community during their activities.