A microbial community description of a heavy metal contaminated soil site

Abstract

Tui mine area, with extremely low pH (2.9-3.3) values and high-metal concentrations, is one of the most contaminated sites in NZ. The structure of the microbial community in different soil layers (Top, Middle and Bottom) of the Tui mine tailing was investigated using culture-based and molecular approaches. The zinc resistance of an Acidocella strain, isolated previously, was determined by culturing methods. Growth curves of Acidocella indicated that it could grow at up to 250mM ZnSO₄, and in the presence of 250mM MgSO₄, both growth and Zn²⁺ resistance were greatly enhanced with tolerance up to 750mM Zn²⁺. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be related to Actinobacteridae and Gammaproteobacteria. By contrast, cloning and pyrosequencing analysis of the 16S rRNA genes revealed that Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans were the most common strains that occurred in the soil environment in all layers. From a clone library of the Top layer DNA, 69 out of 118 clone sequences were phylogenetically affiliated with the iron-oxidizing Leptospirillum ferrooxidans within the Nitrospira and 16 with Acidithiobacillus ferrooxidans within the Proteobacteria. A broadly similar result was obtained from pyrosequencing analysis. The most abundant OTU (21.9%) was affiliated with Leptospirillum ferrooxidans and the second most abundant (8.4%) affiliated with Acidithiobacillus ferrivorans. With the Bottom layer soil, 61.5% of the amplicons sequences in the pyrosequencing run had the closest match with Leptospirillum ferrooxidans and the second most abundant OTU (27.2% of sequences) were affiliated with Acidithiobacillus ferrivorans SS3. Both molecular approaches indicate that a diverse population of bacterial species (128 different species from pyrosequencing) exist in the Top layer soil with the Bottom layer soil having a lower in diversity (49 different species from pyrosequencing).