Three successive extractions reduce quantification bias of microbial communities associated with incomplete DNA recovery in soil

Abstract:

Abstract:［Objective］To assess the quantification bias associated with incomplete extractions of soil microbial DNA and the feasibility of air-dried soil for microbial ecology study． ［Methods］The flooded rice soil and upland wheat soil were used，and multiple extractions of soil microbial DNA was performed by lysing a single sample for 5 successive times． The copy number of 16S rRNA and amoA genes of Archaea and Bacteria was quantified in each DNA extraction by real-time PCR．［Results］Cumulative DNA yields in 3 successive extractions accounted for more than 76% of microbial DNA in soils，and more than 77. 5% of gene copies could be recovered． Air-drying decreased the abundance of bacterial 16S rRNA gene and archaeal 16S rRNA gene by 90. 3% and 12. 5% ，and the abundance of bacterial and archaeal amoA genes showed a decline by 81. 2% and 84. 3% ，respectively． The decline showed similar trend in two soils，suggesting air-dried soil could be of choice for biogeographic survey of microbial communities． ［Conclusion］Three successive extractions of microbial DNA in soil could be of choice for microbial ecology study in order to reduce quantification bias associated with incomplete DNA recovery． Air-dried soil could be employed under certain circumstances，and further investigation is warranted for the underlying mechanism by which microbial communities manage to survive the desiccation of soil．

Key words:Keywords: successive extractions of DNA in soil，air-dry treatment，archaea，bacteria，ammonia oxidizing archaea，ammonia oxidizing bacteria