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Evaluation of DNA Extraction and Purification Methods for Corn Straw Biogas Slurry

Corn straw biogas slurry always contains humic substances, which poses particular challenges in obtaining PCR-amplifiable DNA for analysis of microbial community. To establish an efficient and reliable DNA extraction method for straw biogas slurry, four approaches: i.e., direct SDS-based method, direct bead-based method, indirect SDS-based method, and indirect bead-based method were evaluated by comparing DNA yield, humic acid contamination, PCR amplifiability, and restriction fragment length polymorphisms (RFLP) of amplified 16S rRNA genes. Direct DNA extraction methods yielded 3-fold higher amounts of DNA than indirect procedures, but its DNA purity was lower. The A260/A230 ratio of DNA from indirect methods (0.8-0.85) were higher than that of DNA from direct methods (0.5-0.6), indicating DNA from direct methods contained high levels of humate contamination. PCR amplification was successful with crude DNA from indirect methods, but not with crude DNA from direct methods. PCR products could also be obtained with purified DNA from direct bead-based method, whereas not direct SDS-based method. Among the four methods, direct bead-based method, indirect SDS-based method and indirect bead-based method could obtain high-quality DNA extracts from corn straw biogas slurry. RFLP analysis further demonstrated the restriction patterns of amplified 16S rRNA genes from three methods were relatively identical microbial diversity.