Microbial Diversity and Potential for Biogeochemical Cycling in Heavy Metal Contaminated Environments

Abstract

Heavy metal contamination arising from resource extraction and wastes poses a threat to natural ecosystems and public health. Microorganisms influence the mobility and toxicity of metals through various resistance mechanisms and metabolic pathways. This thesis investigates microbial diversity and functional capacity across multiple metal-contaminated systems, integrating environmental sequencing data with experimental observations. The overall objective was to better understand the microbial processes involved in metal cycling, focusing on As, Fe, Cu, Ni, and Pd. Using 16S rRNA amplicon and metagenomic sequencing, I profiled microbial communities from aquifers associated with thermally mobilized arsenic, as well as from mine tailings derived from nickel/copper ores. Sampling across a wide range of spatial and geochemical conditions revealed considerable variation in microbial taxonomic and functional diversity. Although community diversity correlated with many factors, including arsenic (in aquifers) and iron (in tailings) concentrations, metal concentrations alone were not predictive of the abundance and localization of specific populations. Metal resistance genes were widespread in all communities across sites and geochemical conditions, suggesting that metal tolerance is regulated at the gene expression level. In contrast, the distribution of taxa and genes associated with iron- and sulfur- cycling was more closely linked to environmental factors such as redox potential, pH, and/or temperature, where these variables were more selective for specific microbial guilds. Additional results from metaproteomic analyses of tailings samples complemented the metagenomics data by confirming the expression of predicted metal and sulfur-related genes. In both environments, ‘-omics’ approaches identified many uncultivated lineages with the potential for metal and sulfur redox transformations. Sulfate-reducing bacteria were predicted to be especially relevant in heavy metal remediation, due to their ability to precipitate dissolved metals as insoluble sulfides. Building on this insight, I experimentally evaluated the ability of a model sulfate-reducing bacterium, Oleidesulfovibrio alaskensis G20, to selectively recover metals from simulated mining waste. O. alaskensis G20 was shown to form nickel sulfide and palladium nanoparticles from mixed-metal solutions, demonstrating a viable method of biologically mediated metal recovery. Collectively, the research presented in this thesis advances our understanding of microbial diversity and biogeochemical cycling in heavy metal-contaminated environments, and highlights the potential to harness microbe-metal interactions for bioremediation and metal recovery technologies.