Selection of Staphylococcus carnosus strains based on in vitro analysis of technologically relevant physiological activities

Table 2 Conditions and primer sequences for 16S rRNA gene amplification, superoxide dismutase gene amplification and random amplification polymorphism DNA-PCR

Primer	Sequence (5′→3′)	Reference	Additional MgCl₂ [25 mM]	Primer (concentration)	PCR conditions^a	Number of cycles
616V	AGA GTT TGA TYM TGG CTC	Lehner et al. 2004	None	0.5 μl each (10 pmol μl⁻¹)	95 °C, 0.5 min; 58 °C, 1 min; 72 °C, 2 min	30
630R	AAG GAG GTG ATC CAR CC	Sterr et al. 2009	None	0.5 μl each (10 pmol μl⁻¹)	95 °C, 0.5 min; 58 °C, 1 min; 72 °C, 2 min	30
sodA-fwd	CCA TAC GAG TTT GAT GCA TTG	This study	None	0.5 μl each (10 pmol μl⁻¹)	95 °C, 1 min; 54 °C, 1 min; 68 °C, 2 min	30
sodA-rev	AGT AAG CGT GTT CCC AAA CAT	This study	None	0.5 μl each (10 pmol μl⁻¹)	95 °C, 1 min; 54 °C, 1 min; 68 °C, 2 min	30
RAPD1	AGC AGG GTC G	Cocconcelli et al. 1995	2 μl	0.5 μl (100 pmol μl⁻¹)	94 °C, 1 min; 34 °C, 1 min; 68 °C, 2 min	35
RAPD2	AGC AGC GTC G	Cocconcelli et al. 1995	2 μl	0.5 μl (100 pmol μl⁻¹)	94 °C, 1 min; 34 °C, 1 min; 68 °C, 2 min	30
RAPD3	GTA GAC CCG T	Wiese et al. 2004	None	2 μl (12.5 pmol μl⁻¹)	94 °C, 1 min; 36 °C, 1.5 min; 68 °C, 2 min	40
RAPD7	AGC AGC GTG G	Cocconcelli et al. 1995	2 μl	0.5 μl (100 pmol μl⁻¹)	94 °C, 1 min; 36 °C, 1 min; 68 °C, 2 min	37
RAPD8	ACG CGC CCT	Johansson et al. 1995	None	2 μl (12.5 pmol μl⁻¹)	94 °C, 1 min; 36 °C, 1.5 min; 68 °C, 2 min	40
XD9^b	GAA GTC GTC G	Moschetti et al. 1998	3 μl	1 μl (100 pmol μl⁻¹)	94 °C, 1 min; 36 °C, 1 min; 68 °C, 2 min	35
M13	GAG GGT GGC GGT TCT	Huey and Hall 1989	2 μl	0.5 μl (100 pmol μl⁻¹)	94 °C, 1 min; 45 °C, 1 min; 68 °C, 2 min	35

^a16S rRNA gene PCR: initial denaturation: 4 min at 95 °C; final elongation: 5 min at 72 °C; superoxide dismutase gene (sodA): initial denaturation: 5 min at 95 °C; final elongation: 5 min at 68 °C; random amplified polymorphic DNA (RAPD): initial denaturation: 5 min at 94 °C; final elongation: 5 min at 68 °C. Each 25 μl reaction consisted of 2.5 μl 10 × ThermoPol™ reaction buffer, 0.5 μl dNTPs (10 mM each), 0.125 μl Taq Polymerase (5 U μl⁻¹; all New England BioLabs GmbH, Frankfurt, Germany) and 1 μl DNA (50 ng μl⁻¹)
^b2 μl DNA (50 ng μl⁻¹) was used as the template

ISSN: 1869-2044