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

Table 1.

Oligonucleotide probes and primers targeting the 16S rRNA gene of methanogens.

Target group Probe name Probe sequence (5′–3′)a Application Probe length (mer) Reference
Most methanogens Arch f2b TTCYGGTTGATCCYGCCRGA PCR (forward) 20 Skillman et al. (2004)
Arch r1386 GCGGTGTGTGCAAGGAGC PCR (reverse) 18 Skillman et al. (2004)
A1f TCYGKTTGATCCYGSCRGAG PCR (forward), DGGE 20 Embley et al. (1992)
A1100r TGGGTCTCGCTCGTTG PCR (forward), DGGE 16 Embley et al. (1992)
Met83F ACKGCTCAGTAACAC PCR (forward) 15 Wright and Pimm (2003)
Met86F GCTCAGTAACACGTGG PCR (forward) 16 Wright and Pimm (2003)
Met448F GGTGCCAGCCGCCGC sequencing 15 Wright and Pimm (2003)
Met1027F GTCAGGCAACGAGCGAGACC sequencing 20 Wright and Pimm (2003)
Met1340R CGGTGTGTGCAAGGAG PCR (reverse) 16 Wright and Pimm (2003)
109f ACKGCTCAGTAACACGT PCR (forward) 17 Grosskopf et al. (1998)
146f GGSATAACCYCGGGAAAC PCR (forward) 18 Marchesi et al. (2001)
1324r GCGAGTTACAGCCCWCRA PCR (reverse) 18 Marchesi et al. (2001)
ARC344f ACGGGGYGCAGCAGGCGCGA PCR (forward), DGGE 20 Casamayor et al. (2001)
25f CYGGTYGATYCTGCCRG PCR (forward) 17 Dojka et al. (1998)
1391r GACGGGCGGTGTGTRCA PCR (reverse) 17 Barns et al. (1994)
A24f TCYGKTTGATCCYGSCRGA PCR (forward), DGGE 19 Yu et al. (2008)
A357f CCCTACGGGGCGCAGCAG PCR (forward), DGGE 18 Yu et al. (2008)
A329r TGTCTCAGGTTCCATCTCCG PCR (reverse), DGGE 20 Yu et al. (2008)
A348r CCCCRTAGGGCCYGG PCR (reverse), DGGE 15 Yu et al. (2008)
A693r GGATTACARGATTTC PCR (reverse), DGGE 15 Yu et al. (2008)
Met630F GGATTAGATACCCSGGTAGT qPCR (forward), DGGE 20 Hook et al. (2009)
Met803R GTTGARTCCAATTAAACCGCA qPCR (reverse), DGGE 21 Hook et al. (2009)
A1040f GAGAGGWGGTGCATGGCC PCR (forward), DGGE 18 Reysenbach and Pace (1995)
ARC344 TCGCGCCTGCTGCICCCCGT MH 20 Raskin et al. (1994b)
ARC915 GTGCTCCCCCGCCAATTCCT PCR (reverse), DGGE, MH, FISH 20 Raskin et al. (1994b)
MER1 GGGCACGGGTCTCGCT PCR (reverse) 16 Hales et al. (1996)
Class Methanomicrobia 1068R ATGCTTCACAGTACGAAC PCR (reverse) 18 Banning et al. (2005)
CMSMM1068m GGATGCTTCACAGTACGAAC RNase H 20 Narihiro et al. (2009b)
Order Methanocellales
Family Methanocellaceae
Genus Methanocella SANAE1136 GTGTACTCGCCCTCCTCG FISH 18 Sakai et al. (2007)
Order Methanomicrobiales MG1200 CGGATAATTCGGGGCATGCTG MH, FISH 21 Raskin et al. (1994b)
MG1200m CCGGATAATTCGGGGCATGCTG RNase H 22 Narihiro et al. (2009b)
M(SA/MI)355 GTAAAGTTTTCGCGCCTG MH 18 Ovreås et al. (1997)
MMB282F ATCGRTACGGGTTGTGGG qPCR (forward) 18 Yu et al. (2005)
MMB749F TYCGACAGTGAGGRACGAAAGCTG qPCR (probe) 24 Yu et al. (2005)
MMB832R CACCTAACGCRCATHGTTTAC qPCR (reverse) 21 Yu et al. (2005)
Family Methanomicrobiaceae
Genus Methanoculleus 298F GGAGCAAGAGCCCGGAGT qPCR (forward) 18 Franke‐Whittle et al. (2009a)
586R CCAAGAGACTTAACAACCCA qPCR (reverse) 20 Franke‐Whittle et al. (2009a)
F2SC668 TCCTACCCCCGAAGTACCCCTC RNase H 22 Narihiro et al. (2009b)
F2SC732 TCGAAGCCGTTCTGGTGAGGCG RNase H 22 Narihiro et al. (2009b)
AR934F AGGAATTGGCGGGGGAGCAC qPCR (forward) 20 Shigematsu et al. (2003)
MCU1023TAQ GAATGATTGCCGGGCTGAAGACTC qPCR (probe) 24 Shigematsu et al. (2003)
MG1200b CCGGATAATTCGGGGCATGCTG qPCR (reverse) 22 Shigematsu et al. (2003)
Species M. thermophilus Mc412f CTGGGTGTCTAAAACACACCCAA qPCR (forward) 23 Hori et al. (2006)
Mc578r ATTGCCAGTATCTCTTAG qPCR (reverse) 18 Hori et al. (2006)
SMCUT1253 GCCTTTCGGCGTCGATACCC RNase H 20 Narihiro et al. (2009b)
Genus Methanofollis F3SC984 CATATCGCTGTCCTACCCGG RNase H 20 Narihiro et al. (2009b)
Genus Methanogenium GMG1128 CGTTCCGGAGAACAAGCTAG RNase H 20 Narihiro et al. (2009b)
Genus Methanomicrobium GMM829 CTCGTAGTTACAGGCACACC FISH, RNase H 20 Yanagita et al. (2000)
Genus Methanoplanus
Species M. limicola SMPL623c TTCTCTTAAACGCCTGCAGG RNase H 20 Narihiro et al. (2009b)
Species M. endosynbiosus SMPL623c TTCTCTTAAACGCCTGCAGG RNase H 20 Narihiro et al. (2009b)
Species M. petrolearius SMPP1252d CTTCTCAGTGTCGTTGCTCA RNase H 20 Narihiro et al. (2009b)
Genus Methanolacinia SMPP1252d CTTCTCAGTGTCGTTGCTCA RNase H 20 Narihiro et al. (2009b)
Family Methanospirillaceae
Genus Methanospirillum F7SC1260 TATCCTCACCTCTCGGTGTC RNase H 20 Narihiro et al. (2009b)
MSP1025TAQ GAATGATAGTCGGGATGAAGACTCTA qPCR (probe) 26 Tang et al. (2005)
Genus Methanosphaerula
Genus Methanolinea NOBI109f ACTGCTCAGTAACACGT qPCR (forward) 17 Imachi et al. (2008)
NOBI633 GATTGCCAGTTTCTCCTG qPCR (reverse), FISH 18 Imachi et al. (2008)
Family Methanocorpusculaceae
Genus Methanocorpusculum F6SC393e GACAGGCACTCAGGGTTTCC RNase H 20 Narihiro et al. (2009b)
GMCP489 GCCCTGCCCTTTCTTCACAT RNase H 20 Narihiro et al. (2009b)
Family incertae sedis
Genus Methanocalculus F6SC393e GACAGGCACTCAGGGTTTCC RNase H 20 Narihiro et al. (2009b)
GMCL488 CCCCGCCCTTTCTCCTGGTG RNase H 20 Narihiro et al. (2009b)
Genus Methanoregula
Species M. boonei 6A8 644 TCTTCCGGTCCCTAGCCTGCCA FISH 22 Bräuer et al. (2006)
Species M. formicica SMSP129 TATCCCCTTCCATAGGGTAGATT FISH 23 Yashiro et al. (2009)
Order Methanosarcinales MSMX860 GGCTCGCTTCACGGCTTCCCT MH 21 Raskin et al. (1994b)
MSSH859 TCGCTTCACGGCTTCCCT FISH 18 Boetius et al. (2000)
MSr r859 TCGCTTCACGGCTTCCCTG PCR (reverse) 19 Skillman et al. (2004)
MSMX860m GCTCGCTTCACGGCTTCCCT RNase H 20 Narihiro et al. (2009b)
MSL812F GTAAACGATRYTCGCTAGGT qPCR (forward) 20 Yu et al. (2005)
MSL860F AGGGAAGCCGTGAAGCGARCC qPCR (probe) 21 Yu et al. (2005)
MSL1159R GGTCCCCACAGWGTACC qPCR (reverse) 17 Yu et al. (2005)
Family Methanosaetaceae
Genus Methanosaeta MX825 TCGCACCGTGGCCGACACCTAGC MH, FISH 23 Raskin et al. (1994b)
MX825mix TCGCACCGTGGCYGACACCTAGC RNase H 23 Narihiro et al. (2009b)
MX1361 ACGTATTCACCGCGTTCTGT FISH 20 Crocetti et al. (2006)
S‐G‐Msae‐0332‐a‐A‐22 TTAGGTCCGGGATGCXCCACGT MH, FISH 22 Zheng and Raskin (2000)
Mst702F TAATC CTYGA RGGAC CACCA qPCR (forward) 20 Yu et al. (2005)
Mst753F ACGGC AAGGG ACGAA AGCTA GG qPCR (probe) 22 Yu et al. (2005)
Mst862R CCTAC GGCAC CRACM AC qPCR (reverse) 17 Yu et al. (2005)
MS1b CCGGCCGGATAAGTCTCTTGA qPCR (forward) 21 Shigematsu et al. (2003)
SAE761TAQ ACCAGAACGGACCTGACGGCAAGG qPCR (probe) 24 Shigematsu et al. (2003)
SAE835R GACAACGGTCGCACCGTGGCC qPCR (reverse) 21 Shigematsu et al. (2003)
S‐F‐Msaet‐0387‐S‐a‐21 GATAAGGGRAYCTCGAGTGCY qPCR (forward) 21 Sawayama et al. (2004)
S‐F‐Msaet‐0540‐A‐a‐31 AGACCCAATAAHARCGGTTACCACTCGRGCC qPCR (probe) 31 Sawayama et al. (2004)
S‐F‐Msaet‐0573‐A‐a‐17 GGCCGRCTACAGACCCT qPCR (reverse) 17 Sawayama et al. (2004)
Species M. concilii Rotcl1 CTCCCGGCCTCGAGCCAGAC FISH 20 Zepp Falz et al. (1999)
MS1 CCGGATAAGTCTCTTGA MH 17 Rocheleau et al. (1999)
MS2 CTGAATGAGAGCGCTTTCTTT MH 21 Rocheleau et al. (1999)
MS5 GGCCACGGTGCGACCGTTGTCG MH, FISH 22 Rocheleau et al. (1999)
MMX1273 GGTTTTAGGAGATTCCCGTC RNase H 20 Narihiro et al. (2009b)
GTMS393m ACCCAGCACTCGAGGTCCCC RNase H 20 Narihiro et al. (2009b)
Species M. thermophila Ms413f CAGATGTGTAAAATACATCTGTT qPCR (forward) 23 Hori et al. (2006)
Ms578r TCTGGCAGTATCCACCGA qPCR (reverse) 18 Hori et al. (2006)
TMX745 CCCTTGCCGTCGGATCCGTT RNase H 20 Narihiro et al. (2009b)
Family Methanosarcinaceae MS1414 CTCACCCATACCTCACTCGGG MH, FISH 21 Raskin et al. (1994b)
EelMS240f CTATCAGGTTGTAGTGGG FISH 18 Boetius et al. (2000)
Msc380F GAAACCGYGATAAGGGGA qPCR (forward) 18 Yu et al. (2005)
Msc492F TTAGCAAGGGCCGGGCAA qPCR (probe) 18 Yu et al. (2005)
Msc828R TAGCGARCATCGTTTACG qPCR (reverse) 18 Yu et al. (2005)
R15Fg GCTACACGCGGGCTACAATGA qPCR (forward) 21 Zhang et al. (2008a)
FMSC394 ATGCTGGCACTCGGTGTCCC RNase H 20 Narihiro et al. (2009b)
MS821mh GCCATGCCTGACACCTAGCG RNase H 20 Narihiro et al. (2009b)
Genus Methanimicrococcus GMIB1254 CACCTTTCGGTGTAGTTGCC RNase H 20 Narihiro et al. (2009b)
Genus Methanosarcina MS821 CGCCATGCCTGACACCTAGCGAGC MH, FISH 24 Raskin et al. (1994b)
SARCI551 GACCCAATAATCACGATCAC FISH 20 Sorensen and Ahring (1997)
SARCI645 TCCCGGTTCCAAGTCTGGC FISH 19 Sorensen and Ahring (1997)
MB1 TTTGGTCAGTCCTCCGG MH 17 Rocheleau et al. (1999)
MB3 CCAGACTTGGAACCG MH 15 Rocheleau et al. (1999)
MB4 TTTATGCGTAAAATGGATT MH, FISH 19 Rocheleau et al. (1999)
240F CCTATCAGGTAGTAGTGGGTGTAAT qPCR (forward) 25 Franke‐Whittle et al. (2009a)
589R CCCGGAGGACTGACCAAA qPCR (reverse) 18 Franke‐Whittle et al. (2009a)
MB1b CGGTTTGGTCAGTCCTCCGG qPCR (forward) 20 Shigematsu et al. (2003)
SAR761TAQ ACCAGAACGGGTTCGACGGTGAGG qPCR (probe) 24 Shigematsu et al. (2003)
SAR835R AGACACGGTCGCGCCATGCCT qPCR (reverse) 21 Shigematsu et al. (2003)
S‐G‐Msar‐0450‐S‐a‐19 TAGCAAGGGCCGGGCAAGA qPCR (forward) 19 Sawayama et al. (2006)
S‐P‐Msar‐0540‐A‐a‐31 AGACCCAATAATCACGATCACCACTCGGGCC qPCR (probe) 31 Sawayama et al. (2006)
S‐G‐Msar‐0589‐S‐a‐20 ATCCCGGAGGACTGACCAAA qPCR (reverse) 20 Sawayama et al. (2006)
Genus Methanococcoides GMCO441 ACATGCCGTTTACACATGTG RNase H 20 Narihiro et al. (2009b)
Genus Methanohalobium GMHB842 TCGGCACTAGGAACGGCCGT RNase H 20 Narihiro et al. (2009b)
Genus Methanohalophilus GMHP1258 CCGTCACTTTTCAGTGTAGG RNase H 20 Narihiro et al. (2009b)
Genus Methanolobus GMLB834 TGAAACGGTCGCACCGTCCCAG RNase H 22 Narihiro et al. (2009b)
Species M. psychrophilus R15F GCTACACGCGGGCTACAATGA qPCR (forward) 21 Zhang et al. (2008a)
R15R AATTTAGGTTCGAACACGGCATGAA qPCR (reverse) 25 Zhang et al. (2008a)
Genus Methanomethylovorans
Genus Methanosalsum GMSS261 GTCGGCTAGCAGGTACCTTG RNase H 20 Narihiro et al. (2009b)
Family Methermicoccaceae
Genus Methermicoccus
Class Methanobacteria
Order Methanobacteriales MB310 CTTGTCTCAGGTTCCATCTCCG MH 22 Raskin et al. (1994b)
MB311 ACCTTGTCTCAGGTTCCATCTCC FISH 23 Crocetti et al. (2006)
Mbac f331 CTTGTCTCAGGTTCCATCTC PCR 20 Skillman et al. (2004)
MB1174 TACCGTCGTCCACTCCTTCCTC MH, FISH 22 Raskin et al. (1994b)
MBT857F CGWAGGGAAGCTGTTAAGT qPCR (forward) 19 Yu et al. (2005)
MBT929F AGCACCACAACGCGTGGA qPCR (probe) 18 Yu et al. (2005)
MBT1196R TACCGTCGTCCACTCCTT qPCR (reverse) 18 Yu et al. (2005)
1401R KTTTGGGTGGYGTGACGGGC PCR (reverse) 20 Banning et al. (2005)
Family Methanobacteriaceae MB1175m CCGTCGTCCACTCCTTCCTC RNase H 20 Narihiro et al. (2009b)
MEB859 AGGGAAGCTGTTAAGTCC FISH 18 Boetius et al. (2000)
Genus Methanobrevibacter fMbb1 CTCCGCAATGTGAGAAATCG PCR 20 Skillman et al. (2004)
GMB406 GCCATCCCGTTAAGAATGGC RNase H 20 Narihiro et al. (2009b)
Species M. ruminantium MBR1001 TCAGCCTGGTAATCATACA FISH 19 Yanagita et al. (2000)
Species M. smithii Forward CCGGGTATCTAATCCGGTTC qPCR (forward) 20 Armougom et al. (2009)
Reverse CTCCCAGGGTAGAGGTGAAA qPCR (reverse) 20 Armougom et al. (2009)
Probe CCGTCAGAATCGTTCCAGTCAG qPCR (probe) 22 Armougom et al. (2009)
Genus Methanobacterium fMbium CGTTCGTAGCCGGCYTGA PCR 18 Skillman et al. (2004)
GMBA755 TGGCTTTCGTTACTCACC RNase H 18 Narihiro et al. (2009b)
S‐F‐Mbac‐0398‐S‐a‐20 CCCAAGTGCCACTCTTAACG qPCR (forward) 20 Sawayama et al. (2006)
S‐G‐Mbac‐0526‐A‐a‐33 AAYGGCCACCACTTGAGCTGCCGGTGTTACCGC qPCR (reverse) 33 Sawayama et al. (2006)
S‐G‐Mbac‐0578‐A‐a‐22 AGACTTATCAARCCGGCTACGA qPCR (probe) 22 Sawayama et al. (2006)
Genus Methanosphaera GMSP838 CCGGAACAACTCGAGGCCAT RNase H 20 Narihiro et al. (2009b)
Genus Methanothermobacter Mt392f ACTCTTAACGGGGTGGCTTTT qPCR (forward) 21 Hori et al. (2006)
Mt578r TCATGATAGTATCTCCAGC qPCR (reverse) 19 Hori et al. (2006)
410F CTCTTAACGGGGTGGCTTTT qPCR (forward) 20 Franke‐Whittle et al. (2009a)
667R CCCTGGGAGTACCTCCAGC qPCR (reverse) 19 Franke‐Whittle et al. (2009a)
GMTB541 AAAAGCGGCTACCACTTGAGCT RNase H 22 Narihiro et al. (2009b)
S‐F‐Mbac‐0398‐S‐a‐20 CCCAAGTGCCACTCTTAACG qPCR (forward) 20 Sawayama et al. (2006)
S‐G‐Mthb‐0549‐S‐a‐32 CGGACGCTTTAGGCCCAATAAAAGCGGCTACC qPCR (probe) 32 Sawayama et al. (2006)
S‐G‐Mthb‐0589‐A‐a‐25 GGGATTTCACCAGAGACTTATCAG qPCR (reverse) 25 Sawayama et al. (2006)
Family Methanothermaceae
Genus Methanothermus FMTH1183 TACGGACCTACCGTCGCCCGCA RNase H 22 Narihiro et al. (2009b)
Class Methanococci
Order Methanococcales M(CO/BA)377 CCCCCGTCGCACTTKCGTG MH 19 Ovreås et al. (1997)
Mcc r WASTVGCAACATAGGGCACGG PCR (reverse) 21 Skillman et al. (2004)
MCC495F TAAGGGCTGGGCAAGT qPCR (forward) 16 Yu et al. (2005)
MCC686F TAGCGGTGRAATGYGTTGATCC qPCR (probe) 22 Yu et al. (2005)
MCC832R CACCTAGTYCGCARAGTTTA qPCR (reverse) 20 Yu et al. (2005)
1202R CCAGGRGATTCGGGGCATGC PCR (reverse) 20 Banning et al. (2005)
Family Methanocaldococcaceae S‐F‐Mcc‐1109‐b‐A‐20 GCAACATGGGGCRCGGGTCT MH 20 Nercessian et al. (2004)
MC504 GGCTGCTGGCACCGGACTTGCCCA FISH 24 Crocetti et al. (2006)
FMCMT1044i GTCAACCTGGCCTTCATCCTGC RNase H 22 Narihiro et al. (2009b)
Genus Methanocaldococcus
Genus Methanotorris
Family Methanococcaceae MC1109 GCAACATAGGGCACGGGTCT MH 20 Raskin et al. (1994b)
Genus Methanococcus GMC728 ACCCGTTCCAGACAAGTGCCTT RNase H 22 Narihiro et al. (2009b)
GMC231 ACTACCTAATCGAGCGCAGTCC RNase H 22 Narihiro et al. (2009b)
GMC416 TTGATAAAAGCCCATGCTGTGC RNase H 22 Narihiro et al. (2009b)
Genus Methanothermococcus GMTL416 TAGAAAAGCCTACGCAGTGC RNase H 20 Narihiro et al. (2009b)
Class Methanopyri
Order Methanopyrales
Family Methanopyraceae
Genus Methanopyrus FMCMT1044i GTCAACCTGGCCTTCATCCTGC RNase H 22 Narihiro et al. (2009b)
S‐G‐Mp‐0431‐a‐A‐20 TTACACCCCGGTACAGCCGC MH 20 Nercessian et al. (2004)
GMPK1331 GGTTACTACCGATTCCACCTTC RNase H 22 Narihiro et al. (2009b)
a.

IUPAC Ambiguity Codes: Y = C or T, R = A or G, K = G or T, S = C or G, W = A or T, M = A or C, H = A or C or T, V = A or C or G

b.

Arch f2 probe covers members of the orders Methanomicrobiales, Methanosarcinales and Methanococcales.

c.

SMPL623 probe covers members of the Methanoplanus limicola and M. endosynbiosus.

d.

SMPP1252 probe covers members of the Methanoplanus petrolearius and Methanolacinia.

e.

F6SC393 probe covers members of the genera Methanocorpusculum and Methanocalculus.

f.

EelMS240 probe targets for members of the genera Methanolobus, Methanohalophilus, Methanococcoides and Methanomethylovorans.

g.

R15F probe covers members of the genera Methanomethylovorans and Methanosarcina and Methanolobus psychrophilus.

h.

MS821m probe covers members of the genera Methanimicrococcus and Methanosarcina.

i.

FMCMT1044 probe covers members of the family Methanocaldococcaceae and genus Methanopyrus.

MH, membrane hybridization.