What are we missing? Optimising DNA extraction from allophanic soils

Allophanic soils are so named because of the presence of the clay allophane, and, in Aotearoa New Zealand, are predominantly found in the North Island. They make up 5% of New Zealand soils. Due to their different physical and chemical properties to other soils, these clay-rich soils are difficult to extract DNA from. This study was conducted to maximize DNA extraction from allophanic soils for microbiota assessments. Soil samples were collected from five Aotearoa regions, and DNA was extracted using skim milk and casein. Following findings from this work, further testing using different rates of casein was carried out to maximize DNA concentration, and hence, diversity. Amplicon sequencing of the bacterial (16S) and fungal (ITS) marker genes was performed on DNA extracts, and resulting amplicon sequence variants were analyzed to determine any effects the modified extraction method had on apparent microbial biodiversity. Amending extraction protocol with either skim milk or casein significantly increased the amount of DNA extracted from high-clay soils, with skim milk returning higher DNA concentrations than casein. However, with reference to diversity, casein-amended DNA extracts confirmed higher 16S and ITS diversity compared to skim milk extracts.