. 2011 Aug 17;4(5):585–602. doi: 10.1111/j.1751-7915.2010.00239.x

Table 3.

Examples of oligonucleotide primer sets for PCR‐based analyses for methanogens.

Type of sample	Application	Target gene	Target group	Probe set (forward/reverse/probe)^a	Reference
Anaerobic process	qPCR	16S rRNA	Methanomicrobiales	MMB282F/MMB832R/MMB749F	Yu et al. (2005)
			Methanosarcinales	MSL812F/MSL1159R/MSL860F
			Methanobacteriales	MBT857F/MBT1196R/MBT929F
			Methanococcales	MCC495F/MCC832R/MCC686F
			Methanosarcinaceae	Msc380F/Msc828R/Msc492F
			Methanosaeta	Mst702F/Mst862R/Mst753F
	qPCR	mcrA	Methanocorpusculaceae	mlas/mcrA‐rev/mcp	Steinberg and Regan (2009)
			Methanospirillaceae	mlas/mcrA‐rev/msp
			Methanosaetaceae	mlas/mcrA‐rev/msa
			Methanobacteriaceae	mlas/mcrA‐rev/mbac‐mcrA
			Methanobacteriaceae	mlas/mcrA‐rev/mrtA
			Methanoregula	mlas/mcrA‐rev/Fen
			Methanosarcina	mlas/mcrA‐rev/msar
	qPCR	16S rRNA	Methanoculleus	298F/586R	Franke‐Whittle et al. (2009a)
			Methanosarcina	240F/589R
			Methanothermobacter	410F/667R
	qPCR	16S rRNA	Methanoculleus thermophilus	Mc412f/Mc578r	Hori et al. (2006)
			Methanosaeta thermophila	Ms413f/Ms578r
			Methanothermobacter	Mt392f/Mt578r
	qPCR	16S rRNA	Methanosaeta	MS1b/SAE835R/SAE761TAQ	Shigematsu et al. (2003)
			Methanosarcina	MB1b/SAR835R/SAR761TAQ
			Methanoculleus	AR934F/MG1200b/MCU1023TAQ
	qPCR	mcrA	Methanosaeta	ME1/ME2b/SAE716TAQ	Shigematsu et al. (2004)
			Methanosarcina	ME1/ME2b/SAR716TAQ
			Methanoculleus	ME1/ME2b/MCU716TAQ
	qPCR	16S rRNA	Methanosaeta	S‐F‐Msaet‐0387‐S‐a‐21/S‐F‐Msaet‐0540‐A‐a‐31/S‐F‐Msaet‐0573‐A‐a‐17	Sawayama et al. (2004)
	qPCR	16S rRNA	Methanosarcina	S‐G‐Msar‐0450‐S‐a‐19/S‐P‐Msar‐0540‐A‐a‐31/S‐G‐Msar‐0589‐S‐a‐20	Sawayama et al. (2006)
			Methanobacterium	S‐F‐Mbac‐0398‐S‐a‐20/S‐G‐Mbac‐0526‐A‐a‐33/S‐G‐Mbac‐0578‐A‐a‐22
			Methanothermobacter	S‐F‐Mbac‐0398‐S‐a‐20/S‐G‐Mthb‐0549‐S‐a‐32/S‐G‐Mthb‐0589‐A‐a‐25
	qPCR	16S rRNA	Methanospirillum	AR934F/MG1200b/MSP1025TAQ	Tang et al. (2005)
	qPCR	16S rRNA	Methanolinea	NOBI109f/NOBI633	Imachi et al. (2008)
	PCR‐cloning	16S rRNA	Most methanogens	109f/UNIV1492r^b	Narihiro et al. (2009a)
	PCR‐cloning	16S rRNA	Most methanogens	25f/1391r	Ariesyady et al. (2007)
				25f/UNIV1492r^b
				109f/UNIV1492r^b
Anaerobic process, wetland	PCR‐cloning	mcrA	Most methanogens	mlas/mcrA‐rev	Steinberg and Regan (2008)
Wetland	PCR‐cloning	mcrA	Most methanogens	ME1/ME2	Hales et al. (1996)
Wetland	qPCR	16S rRNA	Methanolobus psychrophilus	R15F/R15R	Zhang et al. (2008a)
Rumen	qPCR, DGGE	16S rRNA	Most methanogens	Met630F/Met803R	Hook et al. (2009)
	PCR, DGGE	16S rRNA	Most methanogens	A357f/A693r	Yu et al. (2008)
				A24f/A329r
				A24f/A348r
	PCR‐typing	16S rRNA	Most methanogens	Arch f2/Arch r1386	Skillman et al. (2004)
			Methanosarcinales	Arch f2/MSr r859
			Methanobacteriales	Mbac f331/Arch r1386
			Methanobacterium	fMbium/Arch r1386
			Methanococcales	Arch f2/Mcc r
			Methanobrevibacter	fMbb1/Arch r1386
	qPCR	16S rRNA	Methanobrevibacter smithii	forward/reverse/probe	Armougom et al. (2009)
Gastrointestinal tract	PCR‐cloning	mcrA	Most methanogens	MrtA_for/MrtA_rev	Scanlan et al. (2008)
Deep sea sediments	PCR‐cloning	16S rRNA	Most methanogens	146f/1324r	Marchesi et al. (2001)
	qPCR	mcrA	Most methanogens	METH‐f/METH‐r	Colwell et al. (2008)
	qPCR	mcrA	Most methanogens	ME3MF and ME3MF‐e/ME2r'	Nunoura et al. (2008)
Lake sediment	PCR‐cloning	16S rRNA	Methanomicrobia	355F^c/1068R	Banning et al. (2005)
			Methanobacteriales	109f/1401R
			Methanococcales	344F^d/1202R
Sulfurous lake	PCR, DGGE	16S rRNA	Most methanogens	ARC344f/ARC915	Casamayor et al. (2001)
Landfill	PCR‐cloning	mcrA	Most methanogens	MLf/MLr	Luton et al. (2002)
Ciliate endosymbiont	PCR, DGGE	16S rRNA	Most methanogens	A1f/A1100r	Embley et al. (1992)
Rice paddy soil	PCR, DGGE	16S rRNA	Most methanogens	109f/ARC915	Grosskopf et al. (1998)
Pure cultures	PCR‐ribotyping	16S rRNA	Most methanogens	Met83F (or Met86F)/Met1340R	Wright and Pimm (2003)
Pure cultures	PCR‐cloning	mcrA	Most methanogens	MCRf/MCRr	Springer et al. (1995)

^a.

The primer sequences were shown in Tables 1 and 2.

^b.

UNIV1492r reverse primer was originally referred from Lane (1991) as an universal primer.

^c.

355F forward primer was originally referred as M(SA/MI)355 probe developed by Ovreås et al. (1997) as shown in Table 1.

^d.

344F forward primer was originally referred as ARC344 probe developed by Raskin and colleagues (1994b) as shown in Table 1.