Table 2.

Oligonucleotide primers and PCR conditions used in this study

				Cycle
Primer name and amplified region	Primer sequence
		Cycles	Hot start	Denaturation	Annealing	Extension	Final extension
16S rRNA**	IF 5′-AGA GTT TGA TCM TGG CTC AG-3′		94 °C	94 °C	49 °C	72 °C	72 °C
	4R 5′-AGG CCT TCT TCA TAC ACG CG-3′	25	2 min	15 s	15 s	15 s	7 min
16S rRNA**	2F 5′-GCA AGC CTG ATG CAG CCA TG-3′		94 °C	94 °C	49 °C	72 °C	72 °C
	3R 5′-ATC GTT TAC GGC GTG GAC TA-3′	25	2 min	15 s	15 s	15 s	7 min
16S rRNA**	3F 5′-AAA CAG GAT TAG ATA CCC TG-3′		94 °C	94 °C	49 °C	72 °C	72 °C
	2R 5′-CTG GTC GTA AGG GCC ATG AT-3′	25	2 min	15 s	15 s	15 s	7 min
16S rRNA**	4F 5′-AGG TGG GGA TGA CGT CAA GT-3′		94 °C	94 °C	49 °C	72 °C	72 °C
	1R 5′-AAG GAG GTG WTC CAR CC-3′	25	2 min	15 s	15 s	15 s	7 min
luxA-specific*	F 5′-GTTCTTAGTTGGATTATTGG-3’		94 °C	94 °C	44 °C	72 °C	72 °C
Positions 568–995	R 5′-TCAGTTCCCATTAGCTTCAAATCC-3’	29–33	2 min	15 s	30 s	30 s	7 min
1st luxA†	F 5′-CAGAATCACCAAAAAGGAATAGGT-3’	30	94 °C	94 °C	55 °C	72 °C	72 °C
Positions 1–590	R 5′-CAATTTCATTATAGAGTTCCATCTGTG-3’		2 min	15 s	30 s	30 s	7 min
2nd luxA†	F 5′-GTTCTTAGTTGGATTATTGGTA-3’	26–30	94 °C	94 °C	50 °C	72 °C	72 °C
Positions 450–1068	R 5′-AACTTGTTCCTTATTATCTCTAGTAT-3’		2 min	15 s	30 s	30 s	7 min
luxA 1–569†	F 5′-GCGAAGATTAAGAAATAAAA-3’	25–30	94 °C	94 °C	47 °C	72 °C	72 °C
Positions 1–569	R 5′-TTCTTTAGAGTACTTTGTTGG-3’		2 min	15 s	30 s	30 s	7 min
luxA 400–1168†	F 5′-ATTTAATTTTGGTGTTGTTA-3’	25–30	94 °C	94 °C	43 °C	72 °C	72 °C
Positions (400–1168)	R 5′-TTATTTTTGAGGTTCTTTTA-3’		2 min	15 s	30 s	30 s	7 min
luxA 401–11686	F 5′-TTTAATTTTGGTGTTGTT-3’	25–30	94 °C	94 °C	43 °C	72 °C	72 °C
Positions 401–1168	R 5′-TTATTTTTGAGGTTCTTTT-3’		2 min	15 s	30 s	30 s	7 min
luxA ext†	F 5′-AATTTATTTAGGTTCTTTTAAG-3’	28	94 °C	94 °C	42.5 °C	72 °C	72 °C
	R 5′-AAYATTTRTTTTTCGTATCA-3’		2 min	15 sec	30 s	30 s	7 min
luxA intl†	F 5′-CTATAATCAACACGTCGATTS-3’	28	94 °C	94 °C	48.4 °C	72 °C	72 °C
	R 5′-CAATGGTWCTTAGTTGGATTAT-3’		2 min	15 s	30 s	30 s	7 min
luxA int2†	F 5′-CCATYTGTGYTTTTTTYTCATT-3’	28	94 °C	94 °C	48.5 °C	72 °C	72 °C
	R 5′-KTTTGATACATATTGGACSTT-3’		2 min	15 s	30 sec	30 s	7 min
luxA int3†	F 5′-TGATAATCRTAACCWCGAGT-3’	28	94 °C	94 °C	47.5 °C	72 °C	72 °C
	R 5′-AAGGTCGWTTTAATTTTGG-3’		2 min	15 s	30 s	30 s	7 min
Pleiogleiog A‡	F 5′-GTTTAAGATCAACTGTCTAAAGGRCG-3’	25–30	94 °C	94 °C	56 °C	72 °C	72 °C
	R 5′-TCAGAACCATTCGCTTCAAATCCAAC-3’		2 min	15 s	30 s	30 s	7 min
Pleiogleiog AB‡	F 5′-CGTCGCCGACTTGATTACAGTAACG-3’	25–30	94 °C	94 °C	60 °C	72 °C	72 °C
	R 5′-ATCCTTTTCTTGCTGCCCATTCAACC-3’		2 min	15 s	30 s	30 s	7 min
Pphosp A‡	F 5′-CTTTTAGATCCAATGTCAAAAGGCCG-3’	25–30	94 °C	94 °C	58 °C	72 °C	72 °C
	R 5′-TCAGAGCCATTTGCTTCGAAACCAAG-3’		2 min	15 s	30 s	30 s	7 min
Pphosp AB‡	F 5′-AAACGTCGTGTTGATTATAGCAACG-3’	25–30	94 °C	94 °C	55.4 °C	72 °C	72 °C
	R 5′-TCCAACGATATGTTAGTGGAAGC-3’		2 min	15 s	30 s	30 s	7 min
luxAl27§	F 5′-GANCANCANTTNACNGAGTTTGG-3’	30	94 °C	94 °C	58 °C	72 °C	72 °C
	R 5′-ATTTCNTCTTCAGNNCCATTNGCTTCAAANCC-3’		5 min	30 s	30 s	90 s	7 min
luxAf Wimpee¶	F 5′-CTACTGGATCAAATGTCAAAAGGA-3’	30	94 °C	94 °C	56 °C	72 °C	72 °C
	R 5′-TCAGAACCGTTTGCTTCAAAACC-3’		5 min	1.5 min	30s	2 min	7 min
gapA**	F 5′-GTG TAC TTC GAG CGT TAT AC-3′	29	95 °C	95 °C	40 °C	70 °C	70 °C
	5′-GCC CAT TAC TCA CCC TTG TT-3′		5 min	15 s	15 s	1 min	7 min

^*Lee and Ruby, 1995.

^†Oligonucleotide primers designed in this study.

^‡Ast and Dunlap, 2004.

^§Modified from Budsberg et al., 2003.

^¶Wimpee et al., 1991.

^**Nishiguchi and Nair, 2003.