Characterization of rhizosphere, soil and endophytic microbial communities of native vegetation on a disturbed alpine/tundra mine site


Katrina Callender, National Research Council Canada (NRC); Charles Greer, National Research Council Canada; Jessica Wasserscheid, National Research Council Canada; Damase Khasa, Institute of integrative biology & systems at Université Laval; Martin Nadeau, Viridis Terra Innovations; Stephane Boudreau, Department of Biology at Université Laval; Sabine Martin, LRSV; Marius Poulain, National Research Council Canada; Charlotte Begouen-Dumeaux, National Research Council Canada; Stephanie Messina-Pacheco, National Research Council Canada; Loic Didillon, Tata Steel Minerals Canada ; Qinhong Cai, National Research Council Canada; Hugo T. Thibaudeau Robitaille, M.

Mining activities result in considerable land disturbance, producing large volumes of tailings and waste rock, some of which may be contaminated with heavy metals and organic and inorganic compounds. Waste rock and tailings dumps are not aesthetic and can contribute environmental pollutants to the air and groundwater. A cost-effective approach to address this issue is to revegetate tailings and rock dumps to reduce the mobility of contaminants, eventually leading to ecosystem recovery. In view of the nature of these disturbed sites, plant establishment and growth is very challenging. The purpose of this study was to evaluate the microbial community structure in native plants encroaching on these dump sites, with the objective of identifying plant beneficial bacteria and fungi that could play an important role in helping plants grow in these environments. Native plants growing on the Schefferville iron mining facility were harvested in alpine and tundra, disturbed and undisturbed sites in August 2016 and 2017. Bulk soil, rhizosphere and root endophytic microbial communities were analyzed via high throughput amplicon sequencing of total DNA extracted from different species of representative plants growing on site. Ecological data analysis, including multivariate and statistical analyses, was then performed specifically targeting microorganisms that were associated with plants growing on the disturbed sites. Rhizosphere and endophytic bacterial communities from plants growing in disturbed and undisturbed sites were found to be significantly different. Amongst dominant bacterial and fungal taxa, some were observed to be solely present in roots and rhizospheres originating from disturbed sites. These included species implicated in iron oxide reduction, metal sequestration and heavy metal resistance such as Geobacter, Polaromonas and Cyanobacteria. These microorganisms may enable plants to better tolerate and thrive in harsh environments and could potentially be used as plant inocula to increase the efficiency of mine rehabilitation.
Keywords: environmental microbiology, genomics, biological processes, mine restoration, waste management