TABLE 1.

Some oligonucleotide probes targeted to clades of marine and freshwater heterotrophic picoplankton

Plankton typeProbe nameTarget groupSequence (5′-3′)FAa(%)Escherichia coli 16S rRNA positionbReference or source
MarineCREN-554GI CrenarchaeotaTTAGGCCCAATAATCMTCCT20554-573 176
EURY-806GII EuryarchaeotaCACAGCGTTTACACCTAG20806-823 296
ROS-537 Roseobacter clade (Alphaproteobacteria)CAACGCTAACCCCCTCC55537-554 63
SAR11-441SAR11 clade (Alphaproteobacteria)TACAGTCATTTTCTTCCCCGAC45441-462 188
SAR116/1-447Cluster 1 of SAR116 clade (Alphaproteobacteria)GCTACCGTCATCATCTTC65447-464 71
SAR116/2-436Cluster 2 of SAR116 clade (Alphaproteobacteria)CATCTTCACCAGTGAAAG45436-452 71
OM43-162OM43 clade (Betaproteobacteria)ATGCGGCATTAGCTAACC55162-179 262
SAR86-1245SAR86 cluster (Gammaproteobacteria)TTAGCGTCCGTCTGTAT551245-1262 325
NOR5-730NOR5 subcluster of OM60 clade (Gammaproteobacteria)TCGAGCCAGGAGGCCGCC55730-747 63
ALT-1413 Alteromonas spp., Colwellia spp. (Gammaproteobacteria)TTTGCATCCCACTCCCAT501413-1430 62
GV-841 Vibrio spp. (Gammaproteobacteria)AGGCCACAACCTCCAAGTAG50841-822 62
PSA184 Pseudoalteromonas spp., Colwellia spp. (Gammaproteobacteria)CCCCTTTGGTCCGTAGAC50184-210 62
CF6-1267DE cluster 2 (Cytophaga-Flavobacterium)GAAGATTCGCTCCTCCTC401267-1284 144
SAR406-97SAR406 cluster (Chlorobium-Fibrobacter)CACCCGTTCGCCAGTTTA6597-114 71
SAR202-104SAR202 clade (Chloroflexus)GTTACTCAGCCGTCTGCC104-131 189
FreshwaterR-BT065Beta I lineage of limnic BetaproteobacteriaGTTGCCCCCTCTACCGTT5565-72 278
Bet2-870Beta II lineage of limnic BetaproteobacteriaCCCAGGCGGCTGACTTCA55870-881 35
SOL-852SOL cluster (filamentous Saprospiraceae)ACGCTTTCGCTTGGACAC852-869 255
LD2-739LD2 clade (subgroup of SOL cluster)GCGTCAATACAGATCCAG55739-757 223
HAL-844 Haliscomenobacter cluster (subgroup of SOL cluster)CGCTTGGACACTCACTCC844-861 255
Acl-1214acl lineage of limnic ActinobacteriaCATGCGTGCAGCCCAAGACA551214-1233 310
Acl-840-1sub-group 1 of acl lineageTCGCACAAACCGTGGAAG30840-857 310
Acl-840-2sub-group 2 of acl lineageTCGCAGAAACCGTGGAAG30840-857 310
Acl-840-3sub-group 3 of acl lineageTCGCAGAGACCGTGGAAG30840-857 310
Acl-840-H1unlabeled helper for Acl-840 probescCTAGYGCCCAYCGTTTACGG30810-829 91
Acl-840-H2unlabeled helper for Acl-840 probescGTTCSCACAACTAGYGCCCA30820-839 91
Acl-840-H3unlabeled helper for Acl-840 probescGGGGCRCTTAATGCGTTAGCTG30859-880 91
  • a If available, stringent conditions for hybridization (% of formamide [FA] in the wash buffer) are given for CARD-FISH as described (211).

  • b Probe target position according to reference 33.

  • c Unlabeled helper oligonucleotides are added at a 1:1 concentration to hybridization mixes according to reference 70.