Table 1.

Primers and probes used in the present study.

Target name	Primer/probe name	Primer/probe sequence (5′–3′)	Size (bp)	T (°C)	Reference
Sul1	SulF1	CTGAACGATATCCAAGGATTYCC	245	50	Heuer and Smalla (2007)
	SulR1	AAAAATCCCATCCCCGGRTC	245	50
Sul2	SulF2	CTCAATGATATTCGCGGTTTYCC	245	50
	SulR2	AAAAACCCCATGCCGGGRTC	245	50
Sul3	SulF3	ATTAATGATATTCAAGGTTTYCC	245	50
	SulR3	AAGAAGCCCATACCCGGRTC	245	50
Sul1	qSUL653f	CCGTTGGCCTTCCTGTAAAG
	qSUL719r	TTGCCGATCGCGTGAAGT	67	60
	tpSUL1	FAM-CAGCGAGCCTTGCGGCGG-TAMRA
	qSUL2_595f	CGGCTGCGCTTCGATT			Modified from Heuer et al. (2008)
Sul2	qSUL2_654r	CGCGCGCAGAAAGGATT	60	60
	tpSUL2_614	FAM-CGGTGCTTCTGTCTGTTTCGCGC-TAMRA
16S rRNA	27f	AGAGTTTGATCMTGGCTCAG	1465	55	Lane (1991)
	1492r	GGCTACCTTGTTACGACTT
16S rRNA	1369F	CGGTGAATACGTTCYCGG	124	56/60	Suzuki et al. (2000), Newcombe et al. (2005)
	1492R	GGWTACCTTGTTACGACT
	TM1389F	CTTGTACACACCGCCCGTC
IncP1α,β	trfA2 1	CGAAATTCRTRTGGGAGAAGTA	241	57	Gotz et al. (1996)
	trfA2 2	CGYTTGCAATGCACCAGGTC
IncP7	rep1	CCCTATCTCACGATGCTGTA	524	52	Levchuk et al. (2006)
	rep2	GCACAAACGGTCGTCAG
InqQ	oriT1	TTCGCGCTCGTTGTTCTTCGAGC	191	57	Gotz et al. (1996)
	oriT2	GCCGTTAGGCCAGTTTCTCG
IncW	IncW_f	CCTAAGAACAACAAAGCCCCCG	242	64	Carattoli et al. (2005)
	IncW_r	GGTGCGCGGCATAGAACCGT
IncN	IncN-f	GTCTAACGAGCTTACCGAAG	559	55
	incN_r	GTTTCAACTCTGCCAAGTTC