. "S\u00E9diments contamin\u00E9s" . "Diversit\u00E9" . . . . . . . . . . . "Diversit\u00E9 des int\u00E9grons dans des s\u00E9diments estuariens anthropis\u00E9s." . "Diversit\u00E9 des int\u00E9grons dans des s\u00E9diments estuariens anthropis\u00E9s." . . "Contaminants chimiques" . "Th\u00E8ses et \u00E9crits acad\u00E9miques" . . . "2017" . "Estuaire" . "Les int\u00E9grons sont des plateformes g\u00E9n\u00E9tiques bact\u00E9riennes de capture et d'expression de g\u00E8nes. Les int\u00E9grons cliniques sont les principaux responsables de la forte augmentation r\u00E9cente des bact\u00E9ries multir\u00E9sistantes aux antibiotiques. Cependant, dans l\u2019environnement, ils ne repr\u00E9sentent qu\u2019une part minime de l\u2019importante diversit\u00E9 des int\u00E9grons. Ainsi, les objectifs de cette th\u00E8se \u00E9taient (i) d\u2019\u00E9valuer l\u2019\u00E9tendue de la diversit\u00E9 des int\u00E9grons dans l\u2019environnement, (ii) de comprendre les ph\u00E9nom\u00E8nes responsables de la structuration du pool d\u2019int\u00E9grons dans le compartiment s\u00E9dimentaire d\u2019un milieu estuarien anthropis\u00E9 et (iii) de rechercher l\u2019existence potentielle d\u2019int\u00E9grons indicateurs du niveau de contamination chimique.Le suivi des int\u00E9grons de classes 1, 2 et 3 et des populations d\u2019E. coli dans des s\u00E9diments du bassin versant de la Risle impact\u00E9s par des sources de contamination f\u00E9cale bien caract\u00E9ris\u00E9es ont montr\u00E9 qu\u2019en \u00E9tiage, les souches d\u2019E. coli d\u2019origine humaine se diss\u00E9minaient sur de courtes distances. Les int\u00E9grons de classe 1 se diss\u00E9minent sur des distances un peu plus importantes et se maintiennent dans les 12 premiers centim\u00E8tres du compartiment s\u00E9dimentaire au moins.Une m\u00E9thode a \u00E9t\u00E9 d\u00E9velopp\u00E9e permettant, pour la premi\u00E8re fois, l\u2019analyse de la diversit\u00E9 des int\u00E9grons via s\u00E9quen\u00E7age haut-d\u00E9bit. L\u2019application de cette m\u00E9thode sur une carotte s\u00E9dimentaire de 4,8 m de profondeur pr\u00E9lev\u00E9e dans l\u2019estuaire fluvial de la Seine a permis de mettre en \u00E9vidence plusieurs milliers de classes d\u2019int\u00E9grons dont de nombreuses int\u00E9grases encore jamais r\u00E9pertori\u00E9es. La diversit\u00E9 des int\u00E9grons chute fortement avec la profondeur. Les int\u00E9grons de classe 1, majoritaires dans les s\u00E9diments de surface, ont une abondance qui chute fortement avec la profondeur cependant ils r\u00E9pondent plut\u00F4t positivement \u00E0 la contamination chimique renfor\u00E7ant l\u2019id\u00E9e de leur utilisation comme proxy de pollutions anthropiques r\u00E9centes. Trois classes d\u2019int\u00E9grons dominent dans la vase consolid\u00E9e repr\u00E9sentant 38% des s\u00E9quences obtenues dans la carotte s\u00E9dimentaire mais r\u00E9pondant plut\u00F4t n\u00E9gativement \u00E0 la contamination chimique. Enfin, la structure du pool d\u2019int\u00E9grons est fortement corr\u00E9l\u00E9e \u00E0 celle de la communaut\u00E9 bact\u00E9rienne mais semble en partie ind\u00E9pendante de la communaut\u00E9 bact\u00E9rienne dans deux des fractions s\u00E9dimentaires profondes avec la dominance d\u2019une nouvelle classe d\u2019int\u00E9grons qui semble s\u00E9lectionn\u00E9e par les HAP." . "Text" . . "Contamination f\u00E9cale" . "Polluants" . . "Int\u00E9grons" . . "S\u00E9diments" . . "Integrons are bacterial genetic platforms allowing acquisition and expression of genes. Clinical integrons play a major role in the strong increase of antibiotic multi-resistant bacteria recently observed. However, in the environment, they represent only a tiny fraction of the large integron diversity. Therefore, the aims of this thesis were (i) estimating the extent of the integron diversity in the environment, (ii) understanding phenomena responsible for integron pool structure in anthropized estuarine sediments and (iii) looking for integrons potentially proxy of chemical pollution level. The research of class 1, 2 and 3 integrons and the analysis of E. coli populations in sediments from the Risle drainage basin impacted by well-characterized fecal contamination sources show that E. coli strains with human origins were spread on short distances during low water level periods. However, class 1 integrons are spread on slightly longer distances and remain present in the 12 first centimeters of sediments at least. A methodology was developed allowing, for the first time, the analysis of integron diversity by high-throughput sequencing. In this way, the analysis of a 4.8 meter core sediment from the fluvial Seine estuary highlighted several thousands integron classes including many new integrases absent from data bases. Integron diversity decreases along with depth. Class 1 integrons are the majority integrons in surface sediments but their abundance strongly decreases in deep sediments. Class 1 integron abundance rather responds positively to chemical pollutions accentuating the idea that class 1 integrons could be used as proxy of recent anthropogenic pollutions. In the sediment core, three integron classes outshine the whole dataset: they represent 38% of all the sequences from the sediment core. However, abundances of these three majority integron classes rather respond negatively to chemical pollution levels. Integron pool structure is highly correlated to bacterial community diversity but seems to be partially independent to bacterial community diversity within two deep fractions from the sediment core: in these two sediment fractions, a new integron class outshines the rest of integron classes and seems to be specific to these two sediment fractions. Furthermore, this new integron class seems to be selected by PAH." . . "Integron diversity in anthropised estuary sediments" . "Estuaires -- Pollution" .