TABLE 1.

Newly designed FISH probes specific for Polynucleobacter bacteriaa

ProbeSequenceLength (nt)TargetPositionbFormamide concnc (%)SpecificityNo. of unspecific matchesd
PnecABD-4455′-GAG CTG CTG TTT CTT CCC-3′1816S rRNA445-46335Subclusters A, B, and D0
PnecC-16S-4455′-GAG CCG GTG TTT CTT CCC-3′1816S rRNA445-46335Subcluster C (PnecC)1f
PnecC-23S-1665′-GTT CGC TTC TCA TAC CCT-3′1823S rRNA166-18235Subcluster C (PnecC)0
PnecD1-1815′-TTT CCC CCT AAG GGA TT-3′1716S rRNA181-19715Part of subcluster De1g
PnecD2-1815′-TTT CCC CCT TAG GGA TT-3′1716S rRNA181-19715Other part of subcluster De3h
  • a Information on the division of the Polynucleobacter cluster in four subclusters (A to D) can be found elsewhere (23).

  • b E. coli numbering.

  • c Concentration in hybridization buffer.

  • d Number of known sequences which match the probes but do not belong to the target group.

  • e Sequences of isolate MWH-CaK1 (AJ550667) and clone 27 (AF361194) are not targeted by these probes (both belong to subcluster D).

  • f Uncultured Cytophagales bacterium clone LiUU-1-2B (AF550604). Sequence was published by Eilers et al. (13).

  • g Environmental sequence (AY592152) was obtained by Heijs et al. (unpublished data) from an anaerobic marine site.

  • h Two Beggiatoa sequences (AF110273, AF110274) and one alphaproteobacterial sequence from a hot spring (AF445716).