Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Abstract

Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

“…Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryotes 14 . Despite these advantages of both V4 and V9 regions of 18S rDNA, multiple primer sets have been employed rarely for environmental samples [15][16][17] . Furthermore, only a few specific eukaryotic groups (e.g., Chlorophyta, Trichomonads, Cercozoa, Radiolarians, and Ciliophora) have been elucidated for their diversity and phylogenetic relationship in environmental samples using NGS methods 10,18-21 .…”

Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond

“…The DNA (12 μg) was sequenced using a combination of Roche 454 GS FLX and paired-end Illumina HiSeq2000 platforms at the Genome Quebec and McGill University Innovation Centre, Montreal, Quebec. Quality control and assembly of metagenomic data was performed at the University of Calgary Visual Genomics Center, Calgary, Canada according to previous reports (Saidi-Mehrabad et al, 2013 ; Tan et al, 2013 ; Aguilar et al, 2016 ). Annotation was conducted by submission to the Joint Genome Institute IMG platform (Markowitz et al, 2012 ).…”

Quest of Soil Protists in a New Era

“…Metatranscriptomic exploration also demonstrated the unexpected presence of typically marine and freshwater protists in soils (24). The HTS approaches enabled the surveys of soil protistan communities in remote, harsh, hitherto unsurveyed environments where culture-dependent approaches were not easily applicable (2, 15, 58). Publicly available metagenome data are less used for studying the diversity of soil microeukaryotes but can provide valuable information as they are free from the PCR biases and include the sequences of genes that are not targeted in amplicon-based approaches (34).…”