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 CrenarchaeotaTTAGGCCCAATAATCMTCCT20554-573176
EURY-806GII EuryarchaeotaCACAGCGTTTACACCTAG20806-823296
ROS-537Roseobacter clade (Alphaproteobacteria)CAACGCTAACCCCCTCC55537-55463
SAR11-441SAR11 clade (Alphaproteobacteria)TACAGTCATTTTCTTCCCCGAC45441-462188
SAR116/1-447Cluster 1 of SAR116 clade (Alphaproteobacteria)GCTACCGTCATCATCTTC65447-46471
SAR116/2-436Cluster 2 of SAR116 clade (Alphaproteobacteria)CATCTTCACCAGTGAAAG45436-45271
OM43-162OM43 clade (Betaproteobacteria)ATGCGGCATTAGCTAACC55162-179262
SAR86-1245SAR86 cluster (Gammaproteobacteria)TTAGCGTCCGTCTGTAT551245-1262325
NOR5-730NOR5 subcluster of OM60 clade (Gammaproteobacteria)TCGAGCCAGGAGGCCGCC55730-74763
ALT-1413Alteromonas spp., Colwellia spp. (Gammaproteobacteria)TTTGCATCCCACTCCCAT501413-143062
GV-841Vibrio spp. (Gammaproteobacteria)AGGCCACAACCTCCAAGTAG50841-82262
PSA184Pseudoalteromonas spp., Colwellia spp. (Gammaproteobacteria)CCCCTTTGGTCCGTAGAC50184-21062
CF6-1267DE cluster 2 (Cytophaga-Flavobacterium)GAAGATTCGCTCCTCCTC401267-1284144
SAR406-97SAR406 cluster (Chlorobium-Fibrobacter)CACCCGTTCGCCAGTTTA6597-11471
SAR202-104SAR202 clade (Chloroflexus)GTTACTCAGCCGTCTGCC104-131189
FreshwaterR-BT065Beta I lineage of limnic BetaproteobacteriaGTTGCCCCCTCTACCGTT5565-72278
Bet2-870Beta II lineage of limnic BetaproteobacteriaCCCAGGCGGCTGACTTCA55870-88135
SOL-852SOL cluster (filamentous Saprospiraceae)ACGCTTTCGCTTGGACAC852-869255
LD2-739LD2 clade (subgroup of SOL cluster)GCGTCAATACAGATCCAG55739-757223
HAL-844Haliscomenobacter cluster (subgroup of SOL cluster)CGCTTGGACACTCACTCC844-861255
Acl-1214acl lineage of limnic ActinobacteriaCATGCGTGCAGCCCAAGACA551214-1233310
Acl-840-1sub-group 1 of acl lineageTCGCACAAACCGTGGAAG30840-857310
Acl-840-2sub-group 2 of acl lineageTCGCAGAAACCGTGGAAG30840-857310
Acl-840-3sub-group 3 of acl lineageTCGCAGAGACCGTGGAAG30840-857310
Acl-840-H1unlabeled helper for Acl-840 probescCTAGYGCCCAYCGTTTACGG30810-82991
Acl-840-H2unlabeled helper for Acl-840 probescGTTCSCACAACTAGYGCCCA30820-83991
Acl-840-H3unlabeled helper for Acl-840 probescGGGGCRCTTAATGCGTTAGCTG30859-88091
  • 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.