TABLE 1.

A description of the group-specific primers used for the qPCR assaysa

DomainTarget groupPrimer sequence (5′-3′)Primer nameReference
Bacteria All groupsACT CCT ACG GGA GGC AGC AGEub338 13
All groupsATT ACC GCG GCT GCT GGEub518 18
α-ProteobacteriabTCT ACG RAT TTC ACC YCT ACAlf685 13
β-ProteobacteriabTCA CTG CTA CAC GYGBet680 21
Actinobacteria c CGC GGC CTA TCA GCT TGT TGActino235 26
Firmicutes d GCA GTA GGG AAT CTT CCGLgc353 17
Bacteroidetes e GTA CTG AGA CAC GGA CCACfb319 15
Acidobacteria GAT CCT GGC TCA GAA TCAcid31 2
Eucarya (Fungi)All groupsTCC GTA GGT GAA CCT GCG GITS1f 7
All groupsCGC TGC GTT CTT CAT CG5.8s 31
Basidiomycota CAG GAG ACT TGT ACA CGG TCC AGITS4b 7
Basidiomycota TCG ATG AAG AAC GCA GCG5.8sr 31
  • a The bacterial taxonomy follows that described in the latest edition of Bergey's Manual of Systematic Bacteriology.

  • b This class is within the phylum Proteobacteria.

  • c Commonly labeled the Actinomycete or high-GC-content gram-positive group.

  • d Commonly labeled the low-GC-content gram-positive group.

  • e Commonly labeled the Cytophaga-Flavobacteria or Cytophaga-Flexibacteria-Bacteroides group.