Next Generation Sequencing of Protists as a Measure of Microbial Community in Oil Sands Tailings Ponds: Amplicon Versus Metagenomic Approaches

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  • The Alberta oil sands provide a major benefit to the province as an economic driver. At the same time, their responsible exploitation, particularly in mitigating the environmental impact of oil extraction stands as a significant challenge to be addressed. One of the most contentious aspects is the reclamation of tailings ponds, vast reservoirs of post-processing water and solids mixed with a variety of industrial compounds. Microbiological processes from bacteria and archaea have been previously shown to be at play in the tailings ponds and are factored into plans for their reclamation. However, the impact of microbial eukaryotes, known in all other environments to play a role in the food web, has been relatively poorly addressed. This will be important to know, particularly in light of end pit lake plans for reclamation moving forward. To better understand the microbial communities in the tailings ponds for improved reclamation planning, we have begun using next generation sequencing (NGS) methods to understand the microbial eukaryotic communities present in tailings. We also compare results from two different NGS strategies, metagenomic versus amplicon based, to assess a productive strategy for analyses going forward. Metagenomic data sequenced using the Illumina platform from a tailings sample were obtained via the Hydrocarbon Metagenomics project. Amplicon data were generated in the lab from extracted genomic DNA from the same environmental sample that generated the metagenome data and sequenced using the Illumina platform. Informatic analyses of these datasets were run to obtain ecological measures (rank abundances, diversity indices, taxonomic affiliation). Both the metagenomic and amplicon datasets confirmed the presence of a diverse community of microbial eukaryotes in the tailings. The overall taxonomic affiliations of the sequences were broadly consistent. However, the amplicon-based study gave vastly more data than the metagenomic one, showing a large additional set of low abundance organisms present in the sample. The community of microbial eukaryotes in the tailings pond is real, non-trivial and diverse. The breadth of the community within different ponds, at different spatial distributions and seasons should be explored to better understand the extent of what is present and how it changes periodically through the year so as to better plan reclamation efforts. The amplicon-based analysis gave ~1,600x more data and revealed a much more complex picture of eukaryotic diversity. While metagenomic approaches give a broader picture of all genes from all microbes in the environment, for the specific question of assessing eukaryotic diversity an amplicon based approach is recommended at the present time.

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    Attribution 3.0 International