Within this project an assessment will be made on the presence of microbial communities inside spent nuclear fuel pools in France (e.g. a few pressurized water reactors of EDF) and Belgium (e.g. BR2 reactor of SCK•CEN). Not only the microbiological population present in planktonic form will be considered, but also special attention will be given to biofilms. As such, this project should result in an inventory of microbial groups present in spent nuclear fuel pools, including a detailed characterization of species abundant in those environments, as well as organisms with potential application in, for example, bioremediation processes.
In a first work package, we will inventory the prokaryotic microorganisms present in each pool using a global metagenomic and metaproteomic approach. The overall microbial populations will be assessed using a 16S and 18S rRNA amplicon sequencing approach. By selectively sequencing marker genes like 16S and 18S rRNA, the type and relative abundance of prokaryotic and eukaryotic microorganisms respectively can be identified. For the most interesting samples, the complete metabolic potential of the microbial community inside those pools will be identified using a shotgun metagenomics approach (i.e. not only sequencing a marker gene, but rather sequence all available DNA). By additionally implementing a metaproteomics approach – performed in collaboration with CEA (France), it will also be possible to identify those parts of the microbial genomes essential for surviving in such harsh environments. For each of the spent nuclear fuel pools where samples are taken, a detailed physicochemical analysis – including gamma spectroscopy for identifying the radionuclides present in water, pH, light intensity, water conductivity – will be performed, in order to correlate the microbial population observed within a specific pool to its physicochemical characteristics. The global radionuclide content in these microbiological populations will be assessed to study a possible relation between microorganisms and their ability to concentrate specific radionuclides.
Next to high-throughput approaches, individual bacterial strains will be isolated from the communities in a second work package, based on the output generated in those 'omics' approaches. Samples originating from each pool will be grown on specific media in various conditions. The consortia and the enrichment degree in these cultures will be assessed using mass spectrometry. The resulting isolates will be subjected to whole-genome sequencing, followed by genome annotation. Particular focus will be given to those parts of the genomes potentially explaining how those isolates can survive in such oligotrophic but highly radioactive environments. Additionally, those organisms will be phenotypically characterized, for example by testing their resistance towards radiation in specialized irradiation facilities (for example, gamma irradiation using BRIGIT at BR2 of SCK•CEN, spent nuclear fuels at Laue Langevin Institute) and resistance towards heavy metals. Combining those tests with transcriptomic approaches (e.g. RNA-seq) will lead to the identification of those gene clusters important for their survival in such extreme environments. This will lead to the identification of species potentially of interest for bioremediation purposes of environments contaminated with radionuclides.
This PhD project is part of collaboration with Commissariat à l'énergie atomique (CEA), more specifically with the group of Dr. Corinne Rivasseau. The PhD candidate will have ample opportunity to exchange experiences and samples with this group, and the PhD includes a one-year (or two times six-months) visit to this laboratory in France.