Table 1.

Probe sequences used in this study

Probe rRNA positionsaSequence (5′-3′) % FormamidebTarget(s) Accession no.c
ALF1-645645–663 CTC ACA CTC AAG ACA TCC 35 DGGE sequence ALF1
Isolate A1a
Caulobacter sp. strain  FWC14d M83800
BET3-447447–464 AGC GCA GAC CGT TTC TTC 40 DGGE sequence BETA3
CF1-853 853–873 TAA TGC TTT CGC TCA GAC AC 35DGGE sequence CF1
Isolate CF1
Flavobacterium ferrugineum M28237
Flexibacter elegans M58782
Flexibacter sancti M28057
Cytophaga arvensicola D12657
Ac1-847 847–865 TTA GCT GCG TCG CAC AAA C 20 DGGE sequence Ac1
  • a Escherichia coli numbering (3).

  • b Indicates the appropriate formamide concentration in hybridization buffer for each probe.

  • c GenBank accession numbers from the National Center for Biotechnology Information.

  • d Sequence similarity of >99% to DGGE sequence ALF1.