Table 1 PCR primers and cycling conditions used for quantification of the different phyla

Acidobacteria

Acid31

GAT CCT GGC TCA GAA TC

Barns et al. [27]

Acidobacterium capsulatum

Acid31

2 µL

95 °C

15 min

×1

Eub518

2 µL

95 °C

15 s

×35

Sybr Green

10 µL

55 °C

30 s

Eub518

ATT ACC GCG GCT GCT GG

Muyzer et al. [28]

DEPC H2O

2 µL

72 °C

30 s

DNA

4 µL

80 °C

30 s

60–95 °C

×1

Actinobacteria

Actino235

CGC GGC CTA TCA GCT TGT TG

Stach et al. [29]

Arthrobacter crystallopoietes

Actino235

1.5 µL

95 °C

15 min

×1

Eub518

1.5 µL

95 °C

15 s

×35

Sybr Green

10 µL

60 °C

30 s

Eub518

ATT ACC GCG GCT GCT GG

Muyzer et al. [28]

BSA 3%

0.4 µL

72 °C

30 s

DEPC H2O

2.6 µL

80 °C

30 s

DNA

4 µL

60–95 °C

×1

α-Proteobacteria

α682F

CNA GTG TAG AGG TGA AAT T

De Gregoris et al. [31]

Bradyrhizobium japonicum

α682F

2 µL

95 °C

15 min

×1

908αR

2 µL

95 °C

15 s

×35

Sybr Green

10 µL

61.5 °C

15 s

908αR

CCC CGT CAA TTC CTT TGA GTT

DEPC H2O

2 µL

72 °C

20 s

DNA

4 µL

60–95 °C

×1

Bacteroidetes

Cfb319

GTA CTG AGA CAC GGA CCA

Manz et al. [30]

Flavobacterium aquatile

Cfb319

2 µL

95 °C

15 min

×1

Eub518

2 µL

95 °C

15 s

×35

Sybr Green

10 µL

60 °C

30 s

Eub518

ATT ACC GCG GCT GCT GG

Muyzer et al. [28]

DEPC H2O

2 µL

72 °C

30 s

DNA

4 µL

80 °C

30 s

60–95 °C

×1

β-Proteobacteria

Eub338

ACT CCT ACG GGA GGC AGC AG

Overmann et al. [32]

Alcaligenes faecalis

Bet680

2 µL

95 °C

15 min

×1

Eub338

2 µL

95 °C

15 s

×35

Sybr Green

10 µL

55 °C

30 s

Bet680

TCA CTG CTA CAC GYG

Lane [33]

DEPC H2O

2 µL

72 °C

30 s

DNS

4 µL

80 °C

30 s

60–95 °C

×1