Table 1.

Summary of RNA isolation protocols used in this studya

RNA isolation protocol (reference)Soil vol (g)Method of cell disruptionbNucleic acid separation solutioncNucleic acid precipitation solutiondSpeed to performe
Solution and equipmentBead-beating time(s) and speed(s)
Bürgmann et al. (3)0.50.2% CTAB, 0.75 g of 0.1-mm silica beads45 s at 6 m s−1PCI20% PEG+
FastRNA Pro Soil-Direct kit (Bio101)0.51 ml RNApro soil lysis solution (proprietary solution); lysing matrix tube40 s at 6 m s−1PC0.6 vol isopropanol++
Griffiths et al. (8)0.5Lysing matrix E (Qbiogene); 5% CTAB30 s at 5.5 m s−1CI30% PEG++
Hurt et al. (9), as modified by Gomes et al. (7)0.51% CTAB, 2% SDS; 0.4 g of 0.1-mm glass beads60 s at 5.5 m s−1CI0.6 vol isopropanol+
Mo Bio RNA PowerSoil Total RNA isolation kit (MoBio)2.0Solution SR1 (proprietary; contains SDS); bead tube; vortex adaptorVortex at maximum speed for 15 minPCI5 ml isopropanol (with column purification)++
Peršoh et al. (14)0.50.4 M LiCl; 0.5 g of 0.5-mm, 0.3 g of 0.1-mm, and 1 4-mm glass bead; freeze-thaw cycles30 s at 4 m s−1 and 60 s at 5.5 m s−1PCI0.7 vol isopropanol+++
  • a The final volume eluted for all protocols was 100 μl. The Griffiths et al. and Peršoh et al. protocols, which normally elute RNA in 50 μl, were set to 100 μl. The RNeasy mini kit (Qiagen) was used with the Griffiths et al. and Hurt et al. protocols, as is recommended for protocols that require an additional purification step.

  • b Total bead-beating times are displayed and can consist of multiple bead-beating rounds. The bead beater used in all protocols was a FastPrep instrument (Bio101). CTAB, cetyltrimethylammonium bromide.

  • c PCI, phenol-chloroform-isoamyl alcohol (25:24:1); PC, phenol-chloroform (1:1); CI, chloroform-isoamyl alcohol (24:1).

  • d PEG, polyethylene glycol.

  • e Comparison of times required to perform RNA isolation from 4 samples in parallel. + indicates less than 4 h, ++ indicates between 4 and 8 h, and +++ indicates over 8 h.