Optimizing DNA extraction from allophanic soils using casein, and implications for apparent microbial community composition

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 12.5% of New Zealand soils and are often found in highly productive agricultural regions. Due to their distinct physical and chemical properties, extracting microbial DNA from these clay-rich soils is extremely challenging using standard extraction kits. Casein blocks DNA adsorption by allophane particles, freeing it to be successfully extracted. However, excess casein promotes DNA adsorption by humic acids in addition to casein itself adsorbing DNA molecules. This study was conducted to optimise microbial DNA extraction from allophanic soils using a casein additive and assess impacts of the modified protocol on microbial composition and diversity. Soil with varying allophane levels, determined by percentage phosphate (P) retention, were collected from different sites across NZ, and DNA was extracted using the PowerSoil Pro kit with casein added in the first step. Illumina MiSeq sequencing of 16S and ITS rRNA was used to determine the impact of the casein additive on apparent bacterial and fungal community composition. Amending the extraction protocol with casein gave successful DNA extraction from high-clay soils, significantly increasing yield. The optimal casein rate for soils with percent P retention >85% fell between 1–2 mg per extraction to achieve the highest DNA yield. Impacts of casein addition on apparent microbial communities will also be presented.