Microbial communities in sediments of the Kamniška Bistrica river and frequency of conjugation

Escherichia coli je bakterija, ki je del črevesne mikrobiote ljudi in živali s stalno telesno temperaturo ter pri zdravih ljudeh običajno ne povzroča bolezni. Iz črevesja se E. coli z iztrebki izloča v naravo, kjer lahko preživi in se pod določenimi pogoji tudi razmnožuje. Bakterijski sevi, ki v naravnem okolju preživijo, se morajo zaradi selekcijskega pritiska hitro prilagajati na spreminjajoče se okolje, vključno na prisotnost antibiotikov. To jim med drugim omogočajo tudi konjugacija ter drugi horizontalni prenosi genov. Cilj magistrskega dela je bil ugotoviti, ali je E. coli zmožna konjugacijskega prenosa plazmida pKJK5 v rečnih sedimentih Kamniške Bistrice. Prav tako nas je zanimalo, kakšna je sestava mikrobne združbe sedimentov reke Kamniške Bistrice. Frekvenco konjugacijskega prenosa smo ugotavljali na trdnih bakterijskih gojiščih in v sedimentih v prisotnosti in odsotnosti hranil ter pri različnih temperaturah. Ugotovili smo, da frekvenca konjugacije pada s temperaturo in je še posebej pri nižjih temperaturah odvisna od prisotnosti hranil. Mikrobno združbo sedimentov reke Kamniške Bistrice smo določali z metodo sekvenciranja naslednje generacije (tarčno sekvenciranje PCR - pomnožkov gena za 16S rRNA). Ugotovili smo, da največji delež mikrobne združbe spada v debla Proteobacteria, Nitrospirae, Bacteroidetes in Cyanobacteria.Escherichia coli is a bacterium that is part of the gut microbiota of humans and other warm blooded animals and usually does not cause disease in healthy people. With faeces E. coli is excreted from the gut into the natural environment, where it can survive and under certain conditions even reproduce. Bacterial strains that are able to survive outside the intestine have to quickly adapt to the changing environment, including the presence of antibiotics. This adaption can be due to conjugation and other types of horizontal gene transfer. The aim of this Master Thesis was to determine whether E. coli is capable of conjugal transfer of the pKJK5 plasmid in Kamniška Bistrica river sediments. Further, our goal was also to determine the structure of the microbial communities in the sediments of the Kamniška Bistrica River. The conjugal transfer frequency was determined on solid medium and in sediments in the presence and absence of nutrients at different temperatures. Our results showed that with decreasing temperature the conjugation frequency is also decreasing and that the conjugation frequency is dependent on the presence of nutrients, especially at lower temperatures. The structure of the microbial community in the sediments was determined using next-generation sequencing (targeted amplicon sequencing of the 16S ribosomal RNA gene). The majority of microorganisms in the microbial community belonged to phyla Proteobacteria, Nitrospirae, Bacteroidetes and Cyanobacteria