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Table T8. PCR primers used during Expedition 337.

Primer Gene Target Tm (°C) Sequence (5'–3') Reference
General domain specific:
8Fmod 16S Bacteria 60 AGA GTT TGA TYM TGG CTC AG Modified from Loy et al., 2002
27F 16S Bacteria 55 AGA GTT TGA TCM TGG CTC AG Lane, 1991
338Rabc 16S Bacteria 60 ACW CCT ACG GGW GGC WGC Daims et al., 1999
Bac806R 16S Bacteria 60 GG ACT ACC AGG GTA TCT AAT CCT GTT Nadkarni et al., 2002
Bac806F 16S Bacteria 60 AAC AGG ATT AGA TAC CCT GGT AGT CC Nadkarni et al., 2002
Bac908F 16S Bacteria 60 AAC TCA AAK GAA TTG ACG GG M. Lever, unpubl. data
Bac908R 16S Bacteria 60 CCC GTC AAT TCM TTT GAG TT M. Lever, unpubl. data
926R 16S Bacteria 55 CCG TCA ATT CCT TTR AGT TT Muyzer et al.,1993
Bac1075R 16S Bacteria 60 CAC GAG CTG ACG ACA RCC M. Lever, unpubl. data
21F 16S Archaea 55 TTC CGG TTG ATC CYG CCG GA DeLong, 1992
806F 16S Archaea 55 ATTAGATACCCSBGTAGTCC Takai and Horikoshi, 2000
915Rmod 16S Archaea 55 GTG CTC CCC CGC CAA TT Modified from Stahl and Amann, 1991
915Fmod 16S Archaea 55 AAT TGG CGG GGG AGC AC Modified from Stahl and Amann, 1991
958R 16S Archaea 55 YCC GGC GTT GAM TCC AAT T DeLong, 1992
1059R 16S Archaea 55 GCC ATG CAC CWC CTC T Yu et al., 2005
Medlin A 18S Eukarya 60 AACCTGGTTGATCCTGCCAGT Medlin et al., 1988
Medlin B 18S Eukarya 60 GATCCTTCTGCAGGTTCACCTAC Medlin et al., 1988
Euk 570R 18S Eukarya 60 GCTATTGGAGCTGGAATTAC Elwood et al., 1985
Group specific:
Bif-16S-F* 16S Bifidobacterium 55 CCA TCG CTT AAC GGT GGA T M. Lever, unpubl. data
Bif-16S-R* 16S Bifidobacterium 55 CCA CAT CCA GCA TCC ACC M. Lever, unpubl. data
Blau-16S-F* 16S Blautia 55 CGG TAT GTA AAC TTC TAT CAG CA M. Lever, unpubl. data
Blau-16S-R* 16S Blautia 55 CAG TTT CCA ATG CAG TCC M. Lever, unpubl. data
Xanth-16S-F* 16S Xanthomonas TBD GGA AAG AAA AGC AGT CGG TT M. Lever, unpubl. data
Xanth-16S-R* 16S Xanthomonas TBD AGT GAC CCA GTA TCC ACT GC M. Lever, unpubl. data
Halo-16S-F* 16S Halomonas TBD GAT AAG CCG GTT GTG AAA GC M. Lever, unpubl. data
Halo-16S-R* 16S Halomonas TBD TCA GTG TCA GTC CAG AAG GC M. Lever, unpubl. data
SAR11-16S-F* 16S SAR 11 55 AAG GTC CGG CTA ACT TCG T M. Lever, unpubl. data
SAR11-16S-R* 16S SAR 11 55 AAT CCT CTT CGC TAC CCA TG M. Lever, unpubl. data
MGI-16S-F* 16S Marine Group I Archaea 60 TAA AAC CAG CAC CTC AAG TGG M. Lever, unpubl. data
MGI-16S-R* 16S Marine Group I Archaea 60 TCG RAC GTG TTC TGG TAG ACC M. Lever, unpubl. data
Mbb arb-mcrI-F* mcrA Methanobrevibacter TBD TTT GGA ATA TGT GAA GCT CCA AA M. Lever, unpubl. data
Mbb arb-mcrI-R* mcrA Methanobrevibacter TBD AGT AGC GAA AGC TGT TGC ACA A M. Lever, unpubl. data
mcrIRD F mcrA Methanogens and methanotrophs 55 TWYGACCARATMTGGYT Lever, 2008
mcrIRD R mcrA Methanogens and methanotrophs 55 ACRTTCATBGCRTARTT Lever, 2008
ANME-1-mcrI F mcrA ANME-1 Archaea 63 GACCAGTTGTGGTTCGGAAC Lever, 2008
ANME-1-mcrI R mcrA ANME-1 Archaea 63 ATCTCGAATGGCATTCCCTC Lever, 2008
fhs F fhs Acetogens and other C1 metabolizers 60 GAT GAT CGA CAA CCA CRT CTA Lever et al., 2010
fhs R fhs Acetogens and other C1 metabolizers 60 GGC ACT TGA TGT CGA AGA A Lever et al., 2010
dsrB F1a dsrB All dsrB except xenologous Firmicutes 56 CAC ACC CAG GGC TGG Lever et al., 2013
dsrB F1b dsrB All dsrB except xenologous Firmicutes 56 CAT ACT CAG GGC TGG Lever et al., 2013
dsrB F1c dsrB All dsrB except xenologous Firmicutes 56 CAT ACC CAG GGC TGG Lever et al., 2013
dsrB F1d dsrB All dsrB except xenologous Firmicutes 56 CAC ACT CAA GGT TGG Lever et al., 2013
dsrB F1e dsrB All dsrB except xenologous Firmicutes 56 CAC ACA CAG GGA TGG Lever et al., 2013
dsrB F1f dsrB All dsrB except xenologous Firmicutes 56 CAC ACG CAG GGA TGG Lever et al., 2013
dsrB F1g dsrB All dsrB except xenologous Firmicutes 56 CAC ACG CAG GGG TGG Lever et al., 2013
dsrB F1h dsrB All dsrB except xenologous Firmicutes 56 CAT ACG CAA GGT TGG Lever et al., 2013
dsrB F2a dsrB Xenologous Firmicutes 56 CGT CCA CAC CCA GGG Lever et al., 2013
dsrB F2b dsrB Xenologous Firmicutes 56 TGT GCA TAC CCA GGG Lever et al., 2013
dsrB F2c dsrB Xenologous Firmicutes 56 CAT TCA TAC CCA GGG Lever et al., 2013
dsrB F2d dsrB Xenologous Firmicutes 56 TGT TCA CAC CCA GGG Lever et al., 2013
dsrB F2e dsrB Xenologous Firmicutes 56 CGT GCA CAC GCA GGG Lever et al., 2013
dsrB F2f dsrB Xenologous Firmicutes 56 CGT TCA TAC ACA GGG Lever et al., 2013
dsrB F2g dsrB Xenologous Firmicutes 56 TGT CCA CAC TCA GGG Lever et al., 2013
dsrB F2h dsrB Xenologous Firmicutes 56 CGT GCA TAC GCA GGG Lever et al., 2013
dsrB F2i dsrB Xenologous Firmicutes 56 CAT CCA TAC TCA GGG Lever et al., 2013
dsrB 4RSI1a dsrB All dsrB except xenologous Firmicutes 56 CAG TTA CCG CAG TAC AT Lever et al., 2013
dsrB 4RSI1b dsrB All dsrB 56 CAG TTA CCG CAG AAC AT Lever et al., 2013
dsrB 4RSI1c dsrB All dsrB except xenologous Firmicutes 56 CAG TTG CCG CAG TAC AT Lever et al., 2013
dsrB 4RSI1d dsrB All dsrB except xenologous Firmicutes 56 CAG TTT CCG CAG TAC AT Lever et al., 2013
dsrB 4RSI1e dsrB All dsrB 56 CAG TTG CCG CAG AAC AT Lever et al., 2013
dsrB 4RSI1f dsrB All dsrB except xenologous Firmicutes 56 CAG TTT CCA CAG AAC AT Lever et al., 2013

* = used for DNA contamination tests only. For dissimilatory sulfate-reducing microbesa mixture consisting of dsrB F1a–h and 4RSIa–f was used to target all sulfate reducers, except for xenologous Firmicutes. To target the latter, a different primer mixture, consisting of dsrB F2a–i and 4RSIb and e was used. TBD = to be determined.

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