Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities

• Published in: Journal of fungi (Basel) Vol. 8; no. 5; p. 419
• Main Authors: Nkuna, Rosina, Ijoma, Grace N, Matambo, Tonderayi S
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 20.04.2022; MDPI
• Subjects: bioleaching; Chelating agents; Criminal investigations; Deoxyribonucleic acid; DNA; DNA extraction; DNA sequencing; Edetic acid; ethylene diamine tetraacetic acid (EDTA); fungi; Heavy metal content; Iron; Laboratories; Magnesium; Metagenomics; Metal ions; mine tailing; Sulfur; South Africa; ethylene diamine tetraacetic acid (EDTA); DNA extraction; mine tailing; bioleaching; fungi
• ISSN: 2309-608X; 2309-608X
• DOI: 10.3390/jof8050419

The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4-13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include , , , , and ; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.