Table 1.

Sequences, target sites, and specificities of the primers used in this study

PrimeraTarget sitebSequence (5′ to 3′)SpecificityReference
341F-GCc 341-357CCT ACG GGA GGC AGC AGMostBacteria 35
907R907-926CCG TCA ATT CMT TTG AGT TTMost known organisms 37
CYA359F-GC359-378GGG GAA TYT TCC GCA ATG GGCyanobacteria and chloroplasts 39
CYA781R(a)d 781-805GAC TAC TGG GGT ATC TAA TCC CAT TCyanobacteria and chloroplasts 39
CYA781R(b)d 781-805GAC TAC AGG GGT ATC TAA TCC CTT TCyanobacteria and chloroplasts 39
ARC344F-GC344-363ACG GGG YGC AGC AGG CGC GAMostArchaea 49
ARC915R915-934GTG CTC CCC CGC CAA TTC CTMostArchaea 55
  • a F (forward) and R (reverse) indicate the orientation of the primers in relation to the rRNA sequence.

  • b Escherichia coli numbering of Brosius et al. (6).

  • c GC is a 40-nucleotide GC-rich sequence attached to the 5′ end of the primer as described by Muyzer et al. (34). The GC sequence is 5′-CGC CCG CCG CGC CCC GCG CCC GTC CCG CCG CCC CCG CCC G-3′.

  • d Reverse primer CYA781R is an equimolar mixture of CYA781R(a) and CYA781R(b).