TABLE 1.

A list of sequences and hybridization conditions of oligonucleotide probes used in this study

Probe	Sequence (5′ to 3′)	Specificity	FAa (%)	Reference(s)
EUB338	GCTGCCTCCCGTAGGAGT	Most bacteria		4
EUB338 II	GCAGCCACCCGTAGGTGT	Planctomycetales		8
EUB338 III	GCTGCCACCCGTAGGTGT	Verrucomicrobiales		8
ARC915	GTGCTCCCCCGCCAATTCCT	Archaea	35	41
ALF1b	CGTTCG(C/T)TCTGAGCCAG	Alphaproteobacteria, some Deltaproteobacteria, Spirochaetes	20	24
BET42a	GCCTTCCCACTTCGTTT	Betaproteobacteria	35	24
GAM42a	GCCTTCCCACATCGTTT	Gammaproteobacteria	35	24
G123T	CCTTCCGATCTCTATGCA	Thiothrix eikelboomii, T. nivea, T. unzii, T. fructosivorans, T. defluvii, Eikelboom type 021N groups I, II, and III	40	19
21N	TCCCTCTCCCAAATTCTA	Eikelboom type 021N strain II-26	35	45
Thio820	ACCAAACATCTAGTATTCATCG	Acidithiobacillus thiooxidans, Acidithiobacillus ferrooxidans	30	15, 34
S-S-T.int-0442-a-A-18	TCGATATTTCGCCCCCGC	Thiomonas intermedia	10	This study
S-S-T.plum-450-a-A-18	ATTAGCCTCAACTGTTTC	Thiobacillus plumbophilus	20	This study
S-S-H.neap-635-a-A-19	TAGAATCCCAGTATCCAAT	Halothiobacillus neapolitanus	35	This study
Ntspa712	CGCCTTCGCCACCGGCCTTCC	Most members of the Nitrospirae phylum	50	9
LF655	CGCTTCCCTCTCCCAGCCT	Leptospirillum groups I, II, and III	35	5
ACD840	CGACACTGAAGTGCTAAGC	Acidiphilium genus	10	5
HGC69A	TATAGTTACCACCGCCGT	Actinobacteria (high G+C gram-positive bacteria)	20	37
LGC354a	TGGAAGATTCCCTACTGC	Firmicutes (gram-positive bacteria with low G+C content)	35	25
LGC354b	CGGAAGATTCCCTACTGC	Firmicutes (gram-positive bacteria with low G+C content)	35	25
LGC354c	CCGAAGATTCCCTACTGC	Firmicutes (gram-positive bacteria with low G+C content)	35	25

^aFA, formamide concentration.