Table 1.

Summary of primer specificity tests by three-step end-point PCR

DomainGroupaSubgroupbOrganism or clonecAmplificationdwith the following primer set (annealing temp, °C):
BACT1 (59)ARCH1 (59)BACT2 (56)ARCHGI (59)ARCHGII (59)PHPICO (60)
BacteriaVerMB11A01++
HgcMB11A03++
CyaSynMB11A04+++
CyaSynMB11E08+++
CyaSynMB11E09+++
CyaSynMB11F02+++
CyaSynSynechococcus sp. strain WH7803+++
CyaSynSynechococcus sp. strain WH7805++
CyaSynSynechococcus sp. strain WH8103++
CyaPlastidsMB11B05++
AlpSar11MB11B07++
AlpRosStrain R2A57++
AlpSar116MB11B03++
GamEscherichia coliDH10B++
GamSar86MB11B08++
GamMB11B11++
LgcBacillus subtilis++
FbcStrain R2A10++
ArchaeaCreDesulfurococcus ambivalens+
CreGISBAR12+
CreGISBAR5+±
CreGI2i±e+±+
EurHaloferax mediterranei+
EurHaloferax volcanii+
EurHalococcus salinarum+
EurSulfolobus acidocaldarius+
EurMethanobacterium thermoautotrophicum+
EurMethanococcus jannaschii+
EurThermoplasma acidophilum+
EurGIISBAR16+
EurGIISBAR1A+
EurGIIWHARN+
EurGIISB95-71+
EurGIISB95-72+
EurGIISB95-74+
  • a Ver, Verrucomicrobiales; Hgc, high-G+C-content gram-positive bacteria; Cya,Cyanobacteria; Alp, α-Proteobacteria; Gam, γ-Proteobacteria; Lgc, low-G+C-content gram-positive bacteria; Fbc, Flexibacter, Bacteroides, andCytophaga; Cre, Crenarchaeota; Eur,Euryarchaeota.

  • b Syn, Synechococcus; Ros,Roseobacter; GI, group I marine Archaea; GII, group II marine Archaea. Sar11, Sar116, and Sar86 are groups according to reference 16b.

  • c Boldfacing indicates organisms or clones used as standards in the 5′-nuclease assays.

  • d +, strong amplification; ±, weak amplification; −, no amplification; ∗, clone does not include a priming site.

  • e Likely due to contamination with E. coli genomic DNA.