Next-Generation Sequencing of Protists as a Measure of Natural Soil Microbial Eukaryotic Community in the Oil Sands Region

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  • Soil plays a central role in the functioning of all terrestrial ecosystems. Among the many ecosystem services to which soil contributes are: purification and storage of water, sequestration of organic matter, nutrient cycling for plant growth, and conservation of healthy faunal and microbial populations. As such, soil quality is a key determinant of land reclamation success. Exploitation of the Athabasca oil sands deposit represents a massive land disturbance in Alberta. To date, over 600 km2 of land has been disturbed by oil sands extraction. Following surface mining, reclamation efforts involve the reconstruction of entire landforms. Salvaged surface soils and near-surface geological materials are placed as a new soil cover on the reconstructed landscapes. The goal of reclamation in Alberta is to achieve land capability equivalent to that which existed prior to disturbance. Soil parameters that are currently used to examine reclamation success include chemical and physical attributes known to limit plant growth. Although it is essential to the functioning of these reconstructed ecosystems, soil biology is not yet included as part of the assessment. This project characterized for the first time the biodiversity of soil microfaunal and mesofaunal populations on natural Athabasca oil sands sites. Specifically, we focused on soil protists and micro-invertebrates, as these largely bacteria-consuming organisms are responsible for much of the nutrient fluxes through the soil food web and have crucial bottom-up impact on animal and plant biodiversity. The report addressed two issues. The first is to pilot the use of Next-Generation Sequencing (NGS) technology to establish an assessment of soil protist and invertebrate biodiversity in undisturbed soils as a starting point to identify bioindicators for future assessments of reclamation success. The second question was to assess the relative merits of using paired end 250 versus paired end 300 kits in the NGS protocol, as a technical note going forward. We found that, for these samples, the paired end 250 kits and the protocols in place to use them were reliable and produced consistent datasets and were sufficient to capture the diversity within our samples. Therefore, the additional cost of the paired end 300 kit was not warranted for our needs and would not be adopted in future NGS studies for these organisms in this particular environment. This first assessment of soil protist biodiversity revealed similar trends to those seen from other NGS studies of soils, with cercozoans and ciliates as obvious components of the biodiversity. Further quantitative analysis is key to making any statements about the numerical abundance of any taxa in our samples. However, there are no obviously comparable samples available, with the closest analysis of boreal forest soil being performed with key differences in NGS technology, and the closest technically comparable sample coming from conifer soils in the southern USA. Although we have made as relevant comparisons as possible, to our knowledge this represents the first report of microbial eukaryotic biodiversity of undisturbed soil in the Athabasca region and is an important first step in assessing downstream efforts for soil reclamation and revegetation.

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    Attribution 3.0 International