Comparative evaluation of DNA extraction from rice’s root-associated bacterial consortium for population structure study

¹ Department of Chemical and Process Engineering, The Sirindhorn International Thai-German Graduate School of Engineering (TGGS), King Mongkut’s University of Technology North Bangkok (KMUTNB), Bangkok, Thailand
² Department of Biomedical Sciences, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT) Vellore, Tamilnadu, India
³ Department of Biology, Faculty of Science, Mahasarakam University, Mahasarakam, Thailand
⁴ Department of Biotechnology, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok (KMUTNB), Bangkok, Thailand
⁵ Department of Biology, Faculty of Science, Burapha University, Chonburi, Thailand
⁶ Biorefinery and Process Automation Engineering Center (BPAEC), King Mongkut’s University of Technology North Bangkok (KMUTNB), Bangkok, Thailand

^* Corresponding author: macintous@gmail.com

Abstract

Understanding in population structure of a plant’s root-associated microbiome is applied in good practices in agricultural activities to improve production yields and enhance plant immune responses. The molecular analysis of bacterial populations inhabited in soil faces difficulties in obtaining high yield and high purity of DNA, and different commercial DNA extraction kits have been developed for this purpose. This study focuses on the comparison of DNA extraction of six different rice root-associated bacterial consortium using three commercial kits with two key technologies, spin-column adsorption and magnetic bead adsorption. The quality and quantity of genomic DNA obtained from these extraction methods were analyzed and compared based on DNA concentration, DNA purity and efficiency to be used as a template for 16sRNA amplification. The results showed that the extraction kit with magnetic bead adsorption technology showed the highest concentration (101.32 ng/μl) compared to other DNA extraction kits (32.67 and 1.89 ng/μl). The purity values (A260/A280) were assessed by using Nano-drop spectrophotometer and resulted in purities of nucleic acids in the range of 1.4-1.7. Thus, it was concluded that the extracted DNA obtained from the extraction kit with magnetic bead adsorption technology can be valuable for molecular analysis of microbial communities present in the soil.