Table 1.

Primers, conditions, and bacterial strains used to generate the standard for qPCR and genes amplified and conditions used for PCR-DGGE

Gene	qPCR				PCR-DGGE
	Primer	Conditions	Control strain used to generate standard	Reference(s)	PCR annealing temp (°C)	% UF denaturant	Reference(s)
Bacterial 16S rRNA gene	Eub338/Eub518	60°C; 40 cycles	Burkholderia terrae BS001	27	Touchdown, 60 to 55	40–65	32
Oxalobacteraceae, 16S rRNA gene	Ox225Fw/Ox656Rev	65°C; 40 cycles	Janthinobacterium lividum	18, 28	65	20–60	18
Actinobacteria, 16S rRNA gene	Actino235/Eub518	62°C; 40 cycles	Streptomyces griseus	27	63	40–60	33
Bacterial chitinase, chiA	GA1F/GA1R	57°C; 40 cycles	Streptomyces griseus	29, 30	57	40–50	21
Fungal ITS	5.8S/ITS1f	53°C; 40 cycles	Rhizoctonia solani	27	57	20–55	34, 35, 61