TABLE 1.

Primers used for PCR amplification for library construction and real-time quantification

Target gene and corresponding primer pair(s)PositionSequence (5′-3′)ApplicationReference(s)
Archaea
    16S rRNA
        519F (DQ831586)a519-533cCAGCMGCCGCGGTAAQuantification61, 83
        727R712-727cGCTTTCRTCCCTCACCGT
        arch20F2-20cTTCCGGTTGATCCYGCCRGClone library23
        arch958R958-976cTCCGGCGTTGAMTCCAATT
        ITS 51R (with arch20F)51-71cTCGCAGCTTRSCACGYCCTTCClone library28
    amoA
        amoAF (EF534487)a217-237bGCTCTAATTATGACAGTATACQuantification61
        amoAR399-422bAYCATGTTGAAYAATGGTAATGAC
        FamoAF19-38gSTAATGGTCTGGCTTAGACGClone library26
        FamoAR582-601gACATACAGATGGATGGCCGC
    4-Hydroxylbutyl-CoA dehydratase
        Budh-3F (FJ656518)a3-25bGCATCAAATACAAGCACATTACCQuantification and cloneThis study
        Budh-500R500-525bCATATTTGTCATCTGAATATTTGTA    library
    Acetyl-CoA carboxylase
        ACA-490F (FJ656668)a498-517bGCAAGTATWGGWCCTTCTGCQuantificationThis study
        ACA-841R842-868bGATAATWTCTTTCATWTCATAWGGTTG
        ACA-385F385-517bAYTCWGGWGGTGCAMGAATClone library
        ACA-1100R1090-1109bGAACCWGGCATGTTACCWGG
    Methylmalonyl-CoA epimerasef
        MMN-323F323-348bCGATATGCRTTTTGYTTTTGYCTWATQuantification and cloneThis study
        MMN-1073R1073-1092bCAAAATGAYATHYTMAAAGA    library
Bacteria
    16S rRNA
        Bac518F (FJ656473)a518-534cCCAGCAGCCGCGGTAATQuantification6, 55
        Bac786R786-803cCTACCAGGGTATCTAATC
        27F8-27cAGAGTTTGATCMTGGCTCAGClone library
        1492R1510-1492cTACGGYTACCTTGTTACGACTT
        227R (with 27F)227-244cATGGTCCGCGAACTCATCQuantification (Nitrospina clade)70
        NCC214NF (with 1492R)214-231cAGCTCGCACCGATGGATGPCR (Nitrococcus clade)f
        NIT3_1035R (with 27F)1035-1048cCCTGCGCTCCATGCTCCGPCR (Nitrobacter clade)f54
    amoA
        amoA1F (EF617305)a332-349dGGGGTTTCTACTGGTGGTQuantification and PCR66
        amoA2R820-822dCCCCTCKGSAAAGCCTTCTTC
        A189Ff172-189eGGNGACTGGGACTTCTGGPCR56
        A682R665-682eGAASGCNGAGAAGAASGC
    amoA-amoBf
        amoA3F295-310eGGTGAGTGGGYTAACMGPCR64
        amoB4R30-44eGCTAGCCACTTTCTGG
Eukarya
    18S rRNAf
        82F82-98cGAAACTGCGAATGGCTCPCR60
        1520R1505-1520CYGCAGGTTCACCTAC
  • a Primer and reference gene sequence used for real-time PCR.

  • b Numbering of the positions for this gene is based on the gene of “Ca. Nitrosopumilus maritimus” SCM1 (NC 010085).

  • c Numbering of the positions is based on the 16S rRNA gene of Escherichia coli and 18S rRNA gene of Gracilariopsis sp. (M33639).

  • d Numbering of the positions is based on bacterial amoA of Nitrosomonas europaea (L08050).

  • e Numbering is based on bacterial amoA of Nitrosococcus oceani (AF047705).

  • f Target genes could not be amplified from our cultures using the primer set.

  • g Numbering of the positions for this gene is based on the gene of a metagenomic clone from the Sargasso Sea (AACY01435967).