Microbial DNA profiling by multiplex terminal restriction fragment length polymorphism for forensic comparison of soil and the influence of sample condition

J Appl Microbiol. 2008 Sep;105(3):813-21. doi: 10.1111/j.1365-2672.2008.03819.x. Epub 2008 Apr 19.


Aims: To evaluate: (i) the impact of air-drying on bacterial, archaeal and fungal soil DNA profiles and (ii) the potential use of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) as a tool for forensic comparison of soil.

Methods and results: An M-TRFLP approach was used to profile bacterial, archaeal and fungal DNA profiles from five different soil sites. Air-drying soil significantly reduced the quantity of DNA but the number of operational taxanomic units (OTU) was unaffected. The impact of air-drying on soil DNA profiles was dependent on soil site and microbial primers. Fungal profiles were altered the least by air-drying. For prokaryotic profiles, air-drying altered the relative similarity/dissimilarity between soil sites. The M-TRFLP approach was more discriminatory compared with soil colour and single-taxa profiling, but did not significantly improve resolution between two similar soils.

Conclusions: Of those tested, soil fungi were potentially the more robust target for application to soil forensic studies as they were altered less by air-drying and provided clear discrimination of soils from different sites. The M-TRFLP method demonstrated potential to achieve greater resolution, discriminating the soil sites based on both bacterial and fungal components.

Significance and impact of the study: Soil DNA profiling has potential as a forensic tool, but sample condition and the appropriate selection of microbial target taxa must be considered.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Color
  • DNA Fingerprinting / methods*
  • DNA, Bacterial / genetics*
  • DNA, Fungal / genetics*
  • Discriminant Analysis
  • Forensic Sciences / methods*
  • Humans
  • Polymorphism, Restriction Fragment Length
  • Soil Microbiology*
  • Specimen Handling / standards


  • DNA, Bacterial
  • DNA, Fungal