Michael Hemkemeyer, Geertje J. Pronk, Katja Heister, Ingrid Kogel-Knabner, Rainer Martens & Christoph C. Tebbe.

Overview

  • Key words: Artificial soils; soil minerals; soil particle size fractions; soil microbial diversity; terminal restriction fragment length polymorphism
  • Aim of the study: Analyse the importance of different mineral compositions for the diversity of soil microorganisms
    application quantitative PCR
  • Sample name: Artificial soil
  • Material: FastPrep-24™ instrument, FastDNA™ Spin Kit for Soil containing Lysing Matrix E
  • Buffer: Sodium Phosphate buffer and MT buffer supplied with the FastDNA™ Spin Kit for Soil

Protocols & Parameters

DNA was extracted with the FastDNA™ Spin Kit for Soil using the FastPrep-24™ 5G instrument according to the manufacturer's instructions, using following modifications:


  1. Volumes of sodium phosphate buffer and supplied 'MT-buffer' were adjusted to 950 and 120 μL, respectively.
  2. Bead-beating was run twice for 45 s at a speed of 6.5 m/s.
  3. The samples were then centrifuged for 5 min at 14,000 x g and room temperature.
  4. The DNA bound to the binding matrix of the FastDNA™ Spin Kit was washed twice with 1 mL 5.5 M guanidinthiocyanate to remove coextracted contaminants.
  5. After elution of DNA with 100 μL distilled water, this step was repeated using the eluate.

Conclusion

  • The combination of FastDNA™ Spin Kit for Soil and the FastPrep-24™ 5G instrument provide a high quality of gDNA.
  • The qPCR results revealed that the mineral composition and the particle size fractions have specific and different selective effects on soil samples