Skip to main content
SpringerLink
Log in

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

  • Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Short Original Communication
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

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.

Conclusions

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

References

  • Agnelli A, Ascher J, Corti G, Ceccherini MT, Nannipieri P, Pietramellara G (2004) Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36:859–868

    Article  CAS  Google Scholar 

  • Alef K, Nannipieri P (1995) Methods in applied soil microbiology and biochemistry. Academic Press, London

    Google Scholar 

  • Ascher J, Ceccherini MT, Pantani OL, Agnelli A, Borgogni F, Guerri G, Nannipieri P, Pietramellara G (2009) Sequential extraction and genetic fingerprinting of a forest soil metagenome. Appl Soil Ecol 42:176–181

    Article  Google Scholar 

  • Barnard RL, Osborne CA, Firestone MK (2015) Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate. ISME J 9:946–957

    Article  CAS  Google Scholar 

  • Berendonk TU, Manaia CM, Merlin C, Fatta-Kassinos D, Cytryn E, Walsh F, Burgmann H, Sorum H, Norstrom M, Pons MN, Kreuzinger N, Huovinen P, Stefani S, Schwartz T, Kisand V, Baquero F, Martinez JL (2015) Tackling antibiotic resistance: the environmental framework. Nat Rev Microbiol 13:310–317

    Article  CAS  Google Scholar 

  • Blum SAE, Lorenz MG, Wackernagel W (1997) Mechanism of retarded DNA degradation and prokaryotic origin of DNases in nonsterile soils. Syst Appl Microbiol 20:513–521

    Article  CAS  Google Scholar 

  • Cai P, Huang Q, Zhang X, Chen H (2006) Adsorption of DNA on clay minerals and various colloidal particles from an Alfisol. Soil Biol Biochem 38:471–476

    Article  CAS  Google Scholar 

  • Che RX, Deng YC, Wang F, Wang WJ, Xu ZH, Wang YF, Cui XY (2015) 16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity. J Soils Sediments 15:1987–1990

    Article  CAS  Google Scholar 

  • Che RX, Wang WJ, Zhang J, Nguyen TTN, Tao J, Wang F, Wang YF, Xu ZH, Cui XY (2016) Assessing soil microbial respiration capacity using rDNA- or rRNA-based indices: a review. J Soils Sediments 16:2698–2708

    Article  CAS  Google Scholar 

  • Che RX, Wang F, Wang WJ, Zhang J, Zhao X, Rui YC, Xu ZH, Wang YF, Hao YB, Cui XY (2017) Increase in ammonia-oxidizing microbe abundance during degradation of alpine meadows may lead to greater soil nitrogen loss. Biogeochemistry 136:341–352

    Article  CAS  Google Scholar 

  • Che RX, Deng YC, Wang F, Wang WJ, Xu ZH, Hao YB, Xue K, Zhang B, Tang L, Zhou HK, Cui XY (2018a) Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. Sci Total Environ 639:997–1006

    Article  CAS  Google Scholar 

  • Che RX, Deng YC, Wang WJ, Rui YC, Zhang J, Tahmasbian I, Tang L, Wang SP, Wang YF, Xu ZH, Cui XY (2018b) Long-term warming rather than grazing significantly changed total and active soil procaryotic community structures. Geoderma 316:1–10

    Article  Google Scholar 

  • Che RX, Qin JL, Tahmasbian I, Wang F, Zhou ST, Xu ZH, Cui XY (2018c) Litter amendment rather than phosphorus can dramatically change inorganic nitrogen pools in a degraded grassland soil by affecting nitrogen-cycling microbes. Soil Biol Biochem 120:145–152

    Article  CAS  Google Scholar 

  • Finkel SE, Kolter R (2001) DNA as a nutrient novel role for bacterial competence gene homologs. J Bacteriol 183:6288–6293

    Article  CAS  Google Scholar 

  • Frostegård Å, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65:5409–5420

    Google Scholar 

  • Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2003) Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 43:35–43

    Article  CAS  Google Scholar 

  • Gulden RH, Lerat S, Hart MM, Powell JR, Trevors JT, Pauls KP, Klironomos JN, Swanton CJ (2005) Quantitation of transgenic plant DNA in leachate water: real-time polymerase chain reaction analysis. J Agric Food Chem 53:5858–5865

    Article  CAS  Google Scholar 

  • Hannan S, Ready D, Jasni AS, Rogers M, Pratten J, Roberts AP (2010) Transfer of antibiotic resistance by transformation with eDNA within oral biofilms. FEMS Immunol Med Microbiol 59:345–349

    Article  CAS  Google Scholar 

  • Harris D, Paul EA (1994) Measurement of bacterial growth rates in soil. Appl Soil Ecol 1:277–290

    Article  Google Scholar 

  • Herzog S, Wemheuer F, Wemheuer B, Daniel R (2015) Effects of fertilization and sampling time on composition and diversity of entire and active bacterial communities in German grassland soils. PLoS One 10:e0145575

    Article  CAS  Google Scholar 

  • Hobbie SE, Eddy WC, Buyarski CR, Adair EC, Ogdahl ML, Weisenhorn P (2012) Response of decomposing litter and its microbial community to multiple forms of nitrogen enrichment. Ecol Monogr 82:389–405

    Article  Google Scholar 

  • Kandhavelu M, Vennison SJ (2008) Persistence of plasmid DNA in different soils. Afr J Biotechnol 7:2543–2546

    CAS  Google Scholar 

  • Kunito T, Ihyo Y, Miyahara H, Seta R, Yoshida S, Kubo H, Nagaoka K, Sakai M, Saeki K (2016) Soil properties affecting adsorption of plasmid DNA and its transformation efficiency in Escherichia coli. Biol Fertil Soils 52:223–231

    Article  CAS  Google Scholar 

  • Lim J, Shin SG, Lee S, Hwang S (2011) Design and use of group-specific primers and probes for real-time quantitative PCR. Front Environ Sci Eng 5:28–39

    Article  CAS  Google Scholar 

  • Mao D, Luo Y, Mathieu J, Wang Q, Feng L, Mu Q, Feng C, Alvarez PJ (2014) Persistence of extracellular DNA in river sediment facilitates antibiotic resistance gene propagation. Environ Sci Technol 48:71–78

    Article  CAS  Google Scholar 

  • Mazzoleni S, Carteni F, Bonanomi G, Senatore M, Termolino P, Giannino F, Incerti G, Rietkerk M, Lanzotti V, Chiusano ML (2015) Inhibitory effects of extracellular self-DNA: a general biological process? New Phytol 206:127–132

    Article  CAS  Google Scholar 

  • Mićić M, Whyte JD, Karsten V (2016) High performance bead beating based lysing, homogenization and grinding for DNA, RNA and proteins extraction with FastPrep® systems, sample preparation techniques for soil, plant, and animal samples. Springer Protocols Handbooks. Humana Press, New York, pp 99–116

    Google Scholar 

  • Morrissey EM, McHugh TA, Preteska L, Hayer M, Dijkstra P, Hungate BA, Schwartz E (2015) Dynamics of extracellular DNA decomposition and bacterial community composition in soil. Soil Biol Biochem 86:42–49

    Article  CAS  Google Scholar 

  • Paget E, Monrozier LJ, Simonet P (1992) Adsorption of DNA on clay minerals: protection against DNaseI and influence on gene transfer. FEMS Microbiol Lett 97:31–39

    Article  CAS  Google Scholar 

  • Paget E, Lebrun M, Freyssinet G, Simonet P (1998) The fate of recombinant plant DNA in soil. Eur J Soil Biol 34:81–88

    Article  CAS  Google Scholar 

  • Peng C, Huang QY, Lu YD, Chen WL, Jiang DH, Wei LA (2007) Amplification of plasmid DNA bound on soil colloidal particles and clay minerals by the polymerase chain reaction. J Environ Sci 19:1326–1329

    Article  Google Scholar 

  • Pietramellara G, Ascher J, Ceccherini MT, Nannipieri P, Wenderoth D (2007) Adsorption of pure and dirty bacterial DNA on clay minerals and their transformation frequency. Biol Fertil Soils 43:731–739

    Article  CAS  Google Scholar 

  • Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G, Nannipieri P (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biol Fertil Soils 45:219–235

    Article  CAS  Google Scholar 

  • R Core Team (2018) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna http://www.R-project.org/

    Google Scholar 

  • Romanowski G, Lorenz MG, Sayler G, Wackernagel W (1992) Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl Environ Microbiol 58:3012–3019

    CAS  Google Scholar 

  • Romanowski G, Lorenz MG, Wackernagel W (1993a) Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl Environ Microbiol 59:3438–3446

    CAS  Google Scholar 

  • Romanowski G, Lorenz MG, Wackernagel W (1993b) Plasmid DNA in a groundwater aquifer microcosm-adsorption, DNAase resistance and natural genetic transformation of Bacillus subtilis. Microb Ecol 2:171–181

    CAS  Google Scholar 

  • Trevors JT (1996) Sterilization and inhibition of microbial activity in soil. J Microbiol Methods 26:53–59

    Article  CAS  Google Scholar 

  • Tuominen L, Kairesalo T, Hartikainen H (1994) Comparison of methods for inhibiting bacterial activity in sediment. Appl Environ Microbiol 60:3454–3457

    CAS  Google Scholar 

  • Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J (2014) Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc Natl Acad Sci U S A 111:15202–15207

    Article  CAS  Google Scholar 

  • Vasi F, Travisano M, Lenski RE (1994) Long-term experimental evolution in Escherichia coli. II. Changes in life-history traits adaptation to a seasonal environment. Am Nat 144:432–456

    Article  Google Scholar 

  • Vishnivetskaya TA, Layton AC, Lau MCY, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE, Pfiffner SM, Biggerstaff JP, Stackhouse BT, Phelps TJ, Whyte L, Sayler GS, Onstott TC (2014) Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol 87:217–230

    Article  CAS  Google Scholar 

  • WRB (2006) World reference base for soil resources 2006. FAO/ISRIC/ISSS, Italy

    Google Scholar 

  • Yan H, Wang DD, Dong B, Tang FF, Wang BC, Fang H, Yu YL (2011) Dissipation of carbendazim and chloramphenicol alone and in combination and their effects on soil fungal:bacterial ratios and soil enzyme activities. Chemosphere 84:634–641

    Article  CAS  Google Scholar 

  • Yu WH, Li N, Tong DS, Zhou CH, Lin CX, Xu CY (2013) Adsorption of proteins and nucleic acids on clay minerals and their interactions: a review. Appl Clay Sci 80–81:443–452

    Article  CAS  Google Scholar 

Download references

Funding

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).

Author information

Author notes

  1. Fang Wang and Rongxiao Che contributed equally to this work.

Authors and Affiliations

  1. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China

    Fang Wang, Yanfen Wang & Xiaoyong Cui

  2. Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane, 4111, Australia

    Fang Wang & Zhihong Xu

  3. Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650091, Yunnan, China

    Rongxiao Che

Authors
  1. Fang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rongxiao Che
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhihong Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yanfen Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiaoyong Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaoyong Cui.

Additional information

Responsible editor: Huaiying Yao

Electronic supplementary material

ESM 1

(DOCX 18 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, F., Che, R., Xu, Z. et al. Assessing soil extracellular DNA decomposition dynamics through plasmid amendment coupled with real-time PCR. J Soils Sediments 19, 91–96 (2019). https://doi.org/10.1007/s11368-018-2176-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11368-018-2176-z

Keywords

Search

Navigation