TABLE 2.

Conditions for PCR amplifications

Oligonucleotide class	Bacterial group/strain specificity	Gene (size, bp)	Oligonucleotide name	Oligonucleotide type	Oligonucleotide sequence	PCR conditions
						Initial step	Amplification (35 cycles)	Final step
Generic	Rhizobiales	nifH (95)	nifH_UN_FW	Forward	CGGGCGTCGGNTGYGCNGG	15 s at 95°C	2 s at 98°C, 2 s at 65°C and 2 s at 60°C, 5 s at 72°C	25 s at 72°C
			nifH_UN_R	Reverse	CAAAGCCACCGCANACNACRTCNCC
		nifH (350)a	KAD	Forward	CATCTTGTGGCGACCGCGATCTC	15 s at 95°C	2 s at 98°C, 2 s at 58°C and 2 s at 55°C, 20 s at 72°C	25 s at 72°C
			GEM	Reverse	ATSGCCATCATYTCRCCGGA
	Rhizobium, Sinorhizobium, and Mesorhizobium	rpoB (786)	rpoB_RSM_FW	Forward	ACCCGCGATATTCCGAAYGTHTC	15 s at 95°C	2 s at 98°C, 2 s at 68°C and 2 s at 65°C, 25 s at 72°C	30 s at 72°C
			rpoB_RSM_RV	Reverse	GTTCAGAACGACGTCGACRTG
	Rhizobiales	nodC (384 bp)	nodC_FW_UNi2	Forward	GATATGGAGTACTGGCTSGCNTG	15 s at 95°C	2 s at 98°C, 2 s at 65°C and 2 s at 60°C, 10 s at 72°C	30 s at 72°C
			nodC_RV_UNi2	Reverse	GTTCTGTCCGACGACGTCGAGCGTVAGRAASCG
	Alphaproteobacteria	rpoB (740–752)b	Br3200F	Forward	TGAAGATGGTCAAGGTCTTCGT	15 s at 95°C	2 s at 98°C, 2 s at 60°C and 2 s at 55°C, 25 s at 72°C	30 s at 72°C
			Br3950R	Reverse	GTCCGACTTSACHGTCAGCAT
	Bacteria	16S rRNA (1,300)c	63F	Forward	CAGGCCTAACACATGCAAGTC	15 s at 95°C	2 s at 98°C, 2 s at 57°C and 2 s at 54°C, 30 s at 72°C	30 s at 72°C
			L1401	Reverse	GCGTGTGTACAAGACCC
Specific	S. americanum CCGM7	rpoB (264)	rpoB_CCGM7_F2	Forward	CTCGAGGCCTACCACGAGAGC	15 s at 95°C	2 s at 98°C, 2 s at 65°C and 2 s at 60°C, 10 s at 72°C	30 s at 72°C
			rpoB_CCGM7_R2	Reverse	CGTCGCCTGTACGTCCGTCG
	R. phaseoli CCGM1	rpoB (290)	rpoB_CCGM1_FW	Forward	GATGTAGCCCACCGTGACC	15 s at 95°C	2 s at 98°C, 2 s at 65°C and 2 s at 60°C, 10 s at 72°C	30 s at 72°C
			rpoB_CCGM1_RV	Reverse	CTTACAAGGCGAATGGCAAC

^aSee reference 59.

^bSee reference 60.

^cSee reference 61.