[en] The Prototype repository is an international project to build and study a full-scale model of the planned Swedish final repository for spent nuclear fuel. The Prototype consists of two sections with four and two full-scale copper canisters, respectively. In 2011, the outer section with two canisters (nos. 5 and 6) was excavated. Groundwater surrounding the Prototype has been demonstrated to include microorganisms such as iron-reducing bacteria (IRB) and sulphate-reducing bacteria (SRB) with the ability to affect the repository through reduction of structural Fe(III) in the buffer or by the production of sulphide, respectively. During excavation, samples were taken for microbiological and molecular biological analysis from backfill, buffer, and canister surfaces and analysed with an emphasis on microbial presence and number. The underground environment is anaerobic, but the construction of a repository will raise the oxygen levels. Oxygen is not favourable for the longevity of the copper canister, but oxygen levels will decrease over time, partly due to microbial activity that consumes oxygen. Therefore, evaluating the presence and numbers of the heterotrophic aerobic bacteria that consume oxygen as well as monitoring the oxygen levels are important. The oxygen content of the bentonite itself is also a primary concern, and a method for measuring how the oxygen diffuses through the clay has long been needed. In the work reported here, we performed two pilot studies to address this need. One of these studies tested a method for differentiating between oxygen saturation in aerobic versus anaerobic bentonite; this method has potential for further development. The tunnel above the Prototype canisters was backfilled with a mixture of bentonite and crushed rock. Sixty-three randomly chosen samples from a cross-section through the backfill were analysed for culturable heterotrophic aerobic bacteria. All but one exhibited growth, with four samples exhibiting numbers over 106 colony-forming units per gram wet weight (CFU gww-1). These four samples were all taken near the tunnel ceiling, supporting the possibility of an influx of nutrients from surrounding groundwater. This milieu seems to favour SRB over IRB, according to the most probable number (MPN) results for these samples. Microbial numbers in buffer and on canister surfaces seem to be low judging from the present results. However, from samples from buffer areas with high water saturation and low density, i.e. three samples from buffer ring 5 in deposition hole 6, we were able to grow up to 1.3 X 104 cells gww-1 in IRB medium. DNA from these samples was extracted and then sequenced to obtain information about the species cultivated. Alignment indicated that species of anaerobic thermophilic bacteria, such as Thermacetogenium phaeum, and other aerobic bacteria with the potential to form spores, such as Thermaerobacter subterraneus, could be found in the buffer. These bacteria must have been dormant since the formation of the bentonite blocks, but are obviously still viable when given appropriate growing conditions. Molecular biology methods were also able to find traces of SRB on canister surfaces, though these bacteria were not viable and could not be cultivated