Journal of Soils and Sediments

, Volume 19, Issue 1, pp 91–96 | Cite as

Assessing soil extracellular DNA decomposition dynamics through plasmid amendment coupled with real-time PCR

  • Fang Wang
  • Rongxiao Che
  • Zhihong Xu
  • Yanfen Wang
  • Xiaoyong CuiEmail author
Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Short Original Communication



Determining soil extracellular DNA decomposition dynamics is essential to assessing lateral gene transfer possibility, nutrient-cycling efficiency, and the reliability of DNA-based methods for examining microbes in soils. The existing methods based on competent cell transformation and stable isotope probes are generally inefficient and not strictly quantitative. Therefore, this study aimed to establish a rigorously quantitative and efficient approach to monitor the decomposition dynamics of the soil extracellular DNA.

Materials and methods

A soil was collected from a Tibetan alpine meadow. Extracellular DNA was simulated by modified exogenous plasmids. The plasmid solution was sprayed onto the fresh soil and thoroughly homogenized. Then, the soil was incubated for 4 weeks, during which they were sampled and immediately stored at − 20 °C on days 0, 0.5, 1, 2, 4, 8, 16, and 28 of the incubation. Finally, the total soil DNA was extracted, and the exogenous plasmid copies remained in the soils were determined using real-time PCR. Additionally, another similar experiment was conducted with a sterilized soil to assess the abiotic influences on the changes in the exogenous plasmid copies.

Results and discussion

In the fresh soil, the exogenous plasmid DNA copies decreased quickly in the first 12 h of the incubation, remained stable in the following 36 h, and gradually dropped to 1.10–5.20% of the initial plasmid copies at sampling time 0 after being incubated for 4 weeks. The variations in the soil plasmid DNA copies fitted well with the modified exponential decay model. As for the sterilized soil, the exogenous plasmid copies remained stable during the 16 day’s incubation. However, they dramatically dropped after being incubated for 28 days, which was probably elicited by the recolonization of microbes in the soil. Collectively, the decrease in the exogenous plasmid DNA copies could be mainly attributed to biological activities.


Extracellular DNA can persist in soil for more than 4 weeks. Exogenous plasmid amendment coupled with real-time PCR provides a convenient and rigorously quantitative approach for monitoring extracellular DNA degradation in soils.


Antibiotic resistance genes DNA degradation Quantitative approach Environmental DNA eDNA 


Funding information

This work was supported by the National Key Research and Development Program of China (2016YFC0501800), the Strategic Priority Research Program (A) of the Chinese Academy of Sciences (XDA20050103), and the National Natural Science Foundation of China (31570518).

Supplementary material

11368_2018_2176_MOESM1_ESM.docx (22 kb)
ESM 1 (DOCX 18 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
  2. 2.Environmental Futures Research Institute, School of Environment and ScienceGriffith UniversityBrisbaneAustralia
  3. 3.Institute of International Rivers and Eco-securityYunnan UniversityKunmingChina

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