TABLE 1.

Oligonucleotides used for FISH in this study and the 16S rRNA sequences of target and nontarget species

Probe, target and nontarget organism(s), or environmental clone(s) (accession no.)a	Target sequenceb	Formamide concn (%)c	NaCl concn (mM)d	Reference
S-*-Tdes-0830-a-A-20	3′ GAGAGACCCGGCTTCGATTG 5′	20	215	This study
NAB12, NAB13, NAB19, NAB20, NAB28	5′ CUCUCUGGGCCGAAGCUAAC 3′
YSd	5′ -------------------- 3′
OPB45 (AF027096)	5′ -------------------- 3′
OPS7 (AF027095)	5′ -------------------- 3′
OPT4, OPT53 (AF027093, AF027094)	5′ -------------------- 3′
DGG19 (AY082369)	5′ -------------------- 3′
SRI-27, SRI-93 (AF255595, AF255596)	5′ -------------------- 3′
Catellatospora ferruginea DSM44099	5′ -------U----C------- 3′
Thermodesulfobacterium commune DSM2178	5′ GC-----U----U------- 3′
S-O-Hydr-0540-a-A-19	3′ CCAGGGCTCGCAACGCGCT 5′	60	4	18
NAB-RT-1, NAB-RT-2	5′ GGUCCCGAGCGUUGCGCGA 3′
Hydrogenobacter thermophilus DSM6534	5′ ------------------- 3′
Aquifex pyrophilus DSM6858	5′ ------------------- 3′
Bacteria	3′ TGAGGATGCCCTCCGTCG 5′	20	215	42
Archaea	3′ TCCTTAACCGCCCCCTCGTG 5′	35	70	42

^aThe S-*-Tdes-0830-a-A-20 sequence is the target sequence for the first group, and the S-O-Hydr-0540-a-A-19 sequence is the target sequence for the second group. The probes for Bacteria and Archaea were S-D-Bact-0338-a-A-18 and S-D-Arch-0915-a-A-20, respectively. Probe nomenclature is based on the oligonucleotide probe database (1).

^bSequence data are from the DDBJ/EMBL/GenBank database. Dashes indicate identical nucleotides, and letters indicate nucleotide differences from the target sequence.

^cFormamide concentration in the hybridization buffer.

^dSodium chloride concentration in the washing buffer.