Pb, Cd, and Zn soil contamination: Monitoring functional and structural impacts on the microbiome

Heavy metals (HM) contamination in soils due to anthropogenic activities is a serious environmental problem. In this study, we investigated the impact of Pb, Cd and Zn at soil pollution levels on soil organisms, with special attentions to microbiota. We monitored by Illumina MiSeq technology and bioinformatics analysis the functional and structural evolution of the HM-exposed soil microbiome after different exposure times (0-160 days). Ecotoxicological tests showed 100% acute toxicity of HMs towards the nematode Caenorhabditis elegans and a significant decrease in the metabolic activity of bacteria. Firmicutes was the most resistant phylum, which selectively displaced other bacterial phyla (Proteobacteria, Actinobacteria and Verrucomicrobia). This was likely related to its capability to form endospores under stressed environment. A bioinformatics analysis using PICRUSt showed that HM exposure had a strong effect on metabolic pathways, specifically, genetic information processing (transcription factors), metabolism (glycan biosynthesis and energy metabolism), and environmental information processing (transporters and ABC transporters), particularly after 55 days of exposure. The assessment of functional and structural development of a HM-exposed soil allowed evaluation on the cellular adaptive responses to the tested environmental stresses, and provided valuable information to assist developing effective remediation strategies of HMs polluted soils using bacteria as the remediator.