TABLE 1.

Oligonucleotide probes used in this study

ProbeSpecificityProbe sequence (5′-3′)Target site 16S or 23S rRNA position (nucleotide)% FAaSource or reference
NON338ACTCCTACGGGAGGCAGC16S (338-355)064
EUB338BacteriaGCTGCCTCCCGTAGGAGT16S (338-355)352
ALF968α-ProteobacteriaGGTAAGGTTCTGCGCGTT16S (968-985)2049
    SPH120Sphingomonas spp.GGGCAGATTCCCACGCGT16S (120-137)3049
    ROSEO536Roseobacter cladeCAACGCTAACCCCCTCCG16S (536-553)2016
        ODB1021Octadecabacter spp.GCGTCCCCTAAGGGAACT16S (1021-1038)15This study
    RSHP995Roseobacter sp. strain Shippagan groupCTCGGATTGTCCAGGCAT16S (995-1012)10This study
BET42aβ-ProteobacteriaGCCTTCCCACTTCGTTT23S (1027-1043)3544
GAM42aγ-ProteobacteriaGCCTTCCCACATCGTTT23S (1027-1043)3544
    ALT1413Alteromonas-ColwelliaTTTGCATCCCACTCCCAT16S (1413-1430)4023
    PSA184Pseudoalteromonas-ColwelliaCCCCTTTGGTCCGTAGAC16S (184-210)3023
        GPU622Glaciecola puniceaCTAAAAGGCCTTCCCACG16S (622-639)17This study
        GVstr214bGlaciecola sp. strain GVstr214.6CTAAATGCTATTCCCAGG16S (622-639)12This study
        GVstr214cCompetitor for GVstr214CCAAATGCTATTCCCAGG16S (622-639)12This study
    NOR2-1453Psychromonas spp.GGTCATCGCCATCCCC16S (1453-1468)3023
    SF825Shewanella frigidimarinaAAGTCACCAAACTCCGAG16S (825-842)10This study
    PSYB476Psychrobacter spp.CTGCAGCTAATGTCATCG16S (476-493)10This study
    MB-IC022bMarinobacter sp. strain IC022 groupGTTTCCGCCCGACTTGCA16S (55-72)25This study
    MB-IC022cCompetitor for MB-IC022GTTTCCGCTCGACTTGCA16S (55-72)25This study
    G VVibrio spp.AGGCCACAACCTCCAAGTAG16S (822-841)3026
    OCE232Oceanospirillum spp.AGCTAATCTCACGCAGGC16S (232-249)4023
    PS56aTrue Pseudomonas spp.GCTGGCCTAGCCTTC23S (1432-1446)055
CF319aCF groupTGGTCCGTGTCTCAGTAC16S (319-336)3543
    PB223bPolaribacter spp.GGACGCATAGCCATCTTT16S (223-240)15This study
    PB223cCompetitor for PB223GAACGCATAGCCATCTTT16S (223-240)15This study
HGC69aGram positive (Actinobacteria)TATAGTTACCACCGCCGT23S (1901-1918)2553
PLA46PlanctomycetalesGACTTGCATGCCTAATCC16S (46-63)3050
ARCH915ArchaeaGTGCTCCCCCGCCAATTCCT16S (915-934)2059
  • a Values represent percent formamide in the hybridization buffer.

  • b Probes GVstr214, MB-IC022, and PB223 were used with competitors GVstr214c, MBIC022c, and PB223c, respectively.