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Updated: May 17, 2026
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
[Three successive extractions reduce quantification bias of microbial communities associated with incomplete DNA
Yun Guo1, Yucheng Wu, Xiangui Lin
1School of Geography Science, Nanjing Normal University, Nanjing 210046, China. guoyun@issas.ac.cn
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.
