TABLE 2.

Primers used for Archaea-specific PCR-DGGE targeting rrs genes

Primer	Sequence (5′→3′)	Annealing positionsa	Targeted V region(s)	Amplicon length (bp)b	Annealing temp (°C)	MgCl2 concn (mM)	Reference(s)
A2Fa	TTC CGG TTG ATC CYG CCR GA	7-27	V1-V2	343	56	3.0	5, 11, 19
GC-A348rc	CCC CRT AGG GCC YGG	335-349
GC-A24fc	TCY GKT TGA TCC YGS CRG A	8-26	V1-V2	306	56	3.0	3
A329r	TGT CTC AGG TTC CAT CTC CG	310-329					This study
A24f	TCY GKT TGA TCC YGS CRG A	8-26	V1-V2	342	56	3.0	3
GC-A348rc	CCC CRT AGG GCC YGG	335-249
GC-ARC344fc	ACG GGG YGC AGC AGG CGC GA	344-363	V3	191	56	1.75	4, 15
519r	GWA TTA CCG CGG CKG CTG	519-534
GC-A357fc	CCC TAC GGG GCG CAG CAG	340-357	V3-V4	372	53	3.0
A693r	GGA TTA CAR GAT TTC	693-707					This study
GC-ARC344fc	ACG GGG YGC AGC AGG CGC GA	344-363	V3-V5	591	56	1.75	4, 7, 23
ARC915r	GTG CTC CCC CGC CAA TTC CT	915-934
GC-ARCH915c	AGG AAT TGG CGG GGG AGC AC	915-934	V6-V8	492	65	1.75	12
UNI-b-rev	GAC GGG CGG TGT GTR CAA	1390-1407
A1040f	GAG AGG WGG TGC ATG GCC	1043-1060	V7	171	56	1.75	3, 25
GC-UA1204rc	TTM GGG GCA TRC IKA CCT	1196-1213

^aEscherichia coli rrs gene numbering.

^bCalculated using the rrs genes of E. coli.

^cPrimer with a 40-bp GC clamp (CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G) attached to the 5′ end.