Identification of microbial communities directly from an Alberta oil sands tailings pond using an in vitro mixed species biofilm dvice and pyrosequencing
Identification of microbial communities directly from an Alberta oil sands tailings pond using an in vitro mixed species biofilm dvice and pyrosequencing
Investigations of the microbial communities present in the environment have traditionally relied on culture based techniques. However, since the majority of microorganisms are not easily grown in the laboratory, only culture-independent approaches can capture the true indigenous microbial diversity. Metagenomics using next-generation pyrosequencing technologies are therefore used for a 16S rRNA gene-based profiling of microbial communities in a variety of environmental samples.The study of natural microbial populations is limited by laboratory culture techniques, as the vast majority of microbes in the environment cannot be recovered in laboratory cultures, placing dependence on molecular methods such as metagenomics instead. Biofilm studies are traditionally conducted by isolating individual planktonic species planktonically from an environmental sample either in a liquid or agar medium, then placing the isolates into a biofilm mode of growth in vitro. In doing so, only a few select organisms are usually recovered and the microbes that prefer the biofilm mode of growth may be selected in contrast to the initial planktonic mode of growthagainst in the initial isolation.  Since environmental biotechnology relies on managing understanding the microbial community structure, it is essential to understand decipher the microbial ecology of the environment first. In order to do so, The aim of this study waswe to isolated and cultured bacteria from oil sands tailings by encouraging them to growing them as a mixed species biofilm rather than single planktonic species planktonically in a broth or culture plates. Biofilm formation was tested under different laboratory culture conditions and populations were compared to each other and the starting original inoculum. Our study demonstrates that a greater representation of the environmental micro-organisms can be cultured if grown directly as a biofilm. This research was supported by funding from Genome Canada, Genome Alberta, the Government of Alberta and Genome BC.
To evaluate the microbial population within an oil sands tailings pond, endogenous mixed species biofilms were isolated from the sediments of an oil sands tailings pond. Biofilms were grown using the Calgary Biofilm Device (CBD) under different growth conditions, with and without different growth media. 454 pyrosequencing revealed unique mixed biofilm populations under a specific growth condition, with the dominant population comprising of fermentative microorganisms capable of reducing nitrate (Pseudomonas, Thauera, Hydrogenophaga, and Acidovorax) or iron (Rhodoferax). Our work uses a different approach compared to the traditional biofilm studies and we could demonstrate that mixed species biofilms can be successfully cultivated and identified directly from oil sands tailings. Interestingly, the cultured population closely represented the endogenous environmental population. Thus, our cultivation technique allows isolation and identification of a representative environmental population of mixed species biofilms under laboratory conditions.