TABLE 2

Probes and hybridization conditions applied for CARD-FISH

ProbeTarget organismSequence (5′ → 3 ′)FA concna (%)NaCl concnb (mM)Reference
ARCH915ArchaeaGTGCTCCCCCGCCAATTCCT358055
EUB338BacteriaGCTGCCTCCCGTAGGAGT358056
EUB338-IISupplement to EUB338GCAGCCACCCGTAGGTGT358057
EUB338-IIISupplement to EUB338GCTGCCACCCGTAGGTGT358057
NON338ControlACTCCTACGGGAGGCAGC358058
CF319aBacteroidetesTGGTCCGTGTCTCAGTAC358059
SAR202-312RSAR202 cladeTGTCTCAGTCCCCCTCTG405660
CYA664CyanobacteriaGGAATTCCCTCTGCCCC61
SAR406-97SAR406 cladeCACCCGTTCGCCAGTTTA405662
ROS537RoseobacterCAACGCTAACCCCCTCC358063
SAR11-152RcSAR11 cladeATTAGCACAAGTTTCCYCGTGT2515943
SAR11-441R(ori)cTACAGTCATTTTCTTCCCCGAC43
SAR11-441R(mod)cTACCGTCATTTTCTTCCCCGAC43
SAR11-487(mod)cCGGACCTTCTTATTCGGG41
SAR11-542RcTCCGAACTACGCTAGGTC43
SAR11-732RcGTCAGTAATGATCCAGAAAGYTG43
SAR324-1412SAR324 cladeGCCCCTGTCAACTCCCAT358041
GAM42adGammaproteobacteriaGCCTTCCCACATCGTTT358064
SAR86-1245SAR86 cladeTTAGCGTCCGTCTGTAT358065
  • a FA, formamide concentration (vol/vol) in CARD-FISH hybridization buffer.

  • b NaCl concentration in washing buffer.

  • c A mixture of 6 probes, including an unlabeled helper, SAR11-487-h3 (5′-CGGCTGCTGGCACGAAGTTAGC-3′), was used to detect the SAR11 clade.

  • d Including an unlabeled competitor probe, Bet42a (5′-GCCTTCCCACTTCGTTT-3′) (64).