Applying genomics to monitor plant-microbe symbiosis during land reclamation at a gold mine

CIM Vancouver 2016
Mr Charles W.Greer (National Research Council Canada), Mr Damase Khasa (Centre d’étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval), Mr Sébastien Roy (Centre SÈVE, Département de biologie, Université de Sherbrooke), Mrs Guylaine Bois (Integra Gold Corp), Mrs Katrina Callender (National Research Council Canada)
The remediation of contaminated sites and the revegetation and reclamation of land disturbed by industrial activity are significant societal challenges in terms of scale and cost. The development and deployment of technologies that can efficiently and cost-effectively address these challenges is the objective of many groups working to improve human and environmental health and reduce the liability on industry and society as a whole. Plants and microbes establish complex mutually beneficial relationships on and inside plants that involve nutrient exchange, disease suppression and enable plants to expand their growth ranges into harsh and inhospitable environments. This symbiotic relationship is being exploited on disturbed lands in the mining sector to facilitate plant development, improve soil quality, ultimately leading to a restored, healthy ecosystem.
Alders are pioneer actinorhizal tree and shrub species that form symbiotic associations with the N2-fixing Actinobacteria Frankia spp., ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) fungi. These associations were explored on an active gold mine in Val d’Or, Quebec to phytostabilize and revegetate waste rock. The two native alder species (Alnus viridis ssp. crispa [A. crispa] and A. incana ssp. rugosa [A. rugosa]) survived and established in the mine waste rock without the need for amendments or fertilizer. After two (2) years of growth A. crispa had greater biomass production than A. rugosa suggesting that it may be better suited for use in the phytostabilization of alkaline metal-mine residues. Alders had similar, positive effects on soil quality, restoring the soil pH to neutral and reducing extractable metals by up to 50%. Acetate mineralization and most probable number (MPN) assays revealed that alder revegetation positively stimulated soil microbial communities, increasing microbial density and activity. High throughput pyrosequencing showed that alder revegetation positively stimulated soil microbial communities, increasing microbial diversity (Shannon index) and the abundance of key bacterial species involved in N2-fixation, contaminant degradation and metal sequestration. Although there were no discernible trends in fungal population dynamics, significant shifts in the bacterial community structure from Betaproteobacteria dominated to Alphaproteobacteria and Actinobacteria dominated populations were observed during reclamation, indicating the importance of these bacteria in soil quality improvement and remediation. The application of genomics tools provides a deeper understanding of the importance of plant-microbial interactions and how they can be exploited to improve overall reclamation and remediation efficiency.
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