New approaches to study the diversity of spore-forming bacteria in natural communities

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.