Table 1.

Real time PCR primers used for the quantification of microbial population

Target gene	Primer sequence	Length	Initial denaturation	Denaturation	Annealing	Extension	Cycles	Reference
General bacteria								Denman and McSweeney (2006)
F sequence (5′-3′)	CGGCAACGAGCGCAACCC	130	95 °C 2 min	95 °C 15 s	60 °C 60 s	72 °C 30 s	40
R sequence (5′-3′)	CCATTGTAGCACGTGTGTAGCC
General anaerobic fungi
F sequence (5′-3′)	GAGGAAGTAAAAGTCGTAACAAGGTTTC	120	95 °C 2 min	95 °C 15 s	60 °C 60 s	72 °C 30 s	40
R sequence (5′-3′)	CAAATTCACAAAGGGTAGGATGATT
Methanogens
F sequence (5′-3′)	TTCGGTGGATCDCARAGRGC	140	95 °C 2 min	95 °C 15 s	60 °C 60 s	72 °C 30 s	40
R sequence (5′-3′)	GBARGTCGWAWCCGTAGAATCC
Fibrobacter succinogenes
F sequence (5′-3′)	GTTCGGAATTACTGGGCGTAAA	121	95 °C 2 min	95 °C 15 s	60 °C 60 s	72 °C 30 s	40
R sequence (5′-3′)	CGCCTGCCCCTGAACTATC
Ruminococcus flavefaciens
F sequence (5′-3′)	CGAACGGAGATAATTTGAGTTTACTTAGG	132	95 °C 2 min	95 °C 15 s	60 °C 60 s	72 °C 30 s	40
R sequence (5′-3′)	CGGTCTCTGTATGTTATGAGGTATTACC