Bacterial and fungal community structure and diversity in a mining region under long-term metal exposure revealed by metagenomics sequencing

Metals are known to alter soil ecosystem diversity, structure and function. The main objective of the present study is to determine the effects of soil metal contamination on bacterial and fungal biomass, abundance, and diversity based on phospholipid fatty acid (PLFA) and metagenomics (pyrosequencing) analyses. Soil samples from six sites from Northern Ontario (Canada) were analyzed. Chemical analysis showed significant difference between metal contaminated and reference sites for pH, cations exchange capacity (CEC), soil organic carbon (C) and nitrogen (N). Significant differences between metal contaminated and uncontaminated reference sites were observed for total bacteria, arbuscular fungi (AM fungi), other fungi and eukaryotes. Acidobacteria and Proteobacteria were the most dominant bacterial taxonomic groups in all the sites. For fungi, Ascomycota were more prevalent in metal contaminated soils (35.07%) while Basidiomycota represented 59.26% of all fungi in reference areas. Site-specific bacterial and fungal families and genera were identified and characterized. Analysis of bacterial communities revealed Chao1 index values of 232 and 273 for metal contaminated and reference soils, respectively. For fungi, the Chao index values were 23 for metal contaminated and 45 for reference sites. OTUs followed the same trend for both bacteria and fungi. No significant differences were observed for Simpson index, Shannon index and species evenness between two soil groups for bacteria and fungi. Overall, PLFA and metagenomic analyses revealed significant reductions of microbial biomass and abundance in contaminated sites compared to reference soil type. No significant variations in microbial diversity were observed when all the sites were compared.