Characterisation of microbial communities and chemical contaminants of an acid mine drainage site

Abstract

With mining being a strong part of the world’s history, and the need to continue mining for industrial and economic growth, it is important to monitor the health of both operating and legacy mine sites. Acid Mine Drainage (AMD) is a severe environmental issue that can lead to biodiversity and ecological loss and negatively impact environmental health. Despite this, there are a range of microbial communities, both prokaryotic and eukaryotic, that are able to survive through a range of adapted ecological functions, including heavy metal resistance and biosynthesis of compounds inferring survival in AMD habitats. This thesis utilised 16S and 18S rRNA and metabolic pathway analysis, in conjunction with ICP-OES analysis, to investigate potential links between microbial communities and chemical contaminants in the context an of Australian mine site. Following an analysis of current literature regarding AMD (Chapter One), the methodology of characterising an affected mine site (Captains Flat Mine, NSW) was conducted, sampling a range of sites within the mine over two time points (April and July) (Chapter Two). The resulting water and sediment samples underwent microbial (DNA extraction) and chemical analyses (ICP-OES), in order to isolate the dominant prokaryotic and eukaryotic communities, and contaminants, respectively. Community DNA was sent for further microbiome analysis (16/18S rDNA, NGS WSU), and QIIME2 was used to evaluate and characterise the results produced, in conjunction with chemical contamination concentrations produced via ICP-OES analysis (Chapters Three and Four). Samples were further analysed for metabolic pathways using PICRUSt2, and the MetaCyc Database (Chapter Five). It was from these analyses that prokaryotes and eukaryotes within Captains Flat Mine were determined to have dynamic and heterogenous microbial communities with minimum crossover between sites and time points (field trips) and low dissimilarity between profile clusters, and thus variation in metabolic potential. ICP-OES analysis, determined Cd, Cu, Pb, and Zn to be the main contaminants across all sites (exhibiting results above the ANZECC guidelines), indicating the value of this site as a model system for AMD microbial ecology. Finally, this thesis concludes with a discussion of key findings and recommendations for future branches of research (Chapter Six).

Date of Award	2023
Original language	English
Awarding Institution	Western Sydney University
Supervisor	Thomas Jeffries (Supervisor)