New approaches to study the diversity of spore-forming bacteria in natural communities
|Director of thesis||Dr. Pilar Junier, Laboratory of Microbiology, University of Neuchâtel|
|Co-director of thesis|
|Summary of thesis||
Research on bacterial endospores has generally been restricted to medical and food technology domains. By contrast, little is known about the diversity and functioning of spore-forming microorganisms in the natural environment. New species of spore-forming bacteria (i.e. Carboxydothermus hydrogenoformans Z-2901) and new metabolic functions connected to bacterial spore-formers (e.g. metal reduction) have recently been reported. This suggests that both the metabolic and ecological diversity of spore-forming bacteria are not comprehensively assessed. One of the main difficulties when studying spore-forming bacteria in an ecosystem is the inability to specifically target this group within a complex microbial community. Furthermore, spore-forming bacteria are often underrepresented in diversity studies, because DNA extraction from spores is far more challenging than from vegetative cells.
This study follows a new approach by developing a method to first separate the microbial spores from the residual mix of cells and sample matrix, before subjecting only the spore fraction to DNA extraction and high-throughput sequencing. In addition, we investigate the potential for specific molecular markers to study spore-forming bacteria in situ without isolating and cultivating strains in the laboratory. The idea is to identify genes with highly conserved sequence fragments from a selection of genome sequences of spore-forming bacteria retrieved from databases. These fragments are then used as primers for specific in situ targeting of spore-forming bacteria in environmental samples.
|Administrative delay for the defence||la défense publique a eu lieu le 12.12.2013|