TABLE 5.

Genes detected in soil microcosm incubated with naphthalene

Gene (gi no.)	Gene function	Microorganism	Log mean signal ratioa	SNRb
1477920	2,4-DNT dioxygenase ferredoxin oxidoreductase	Burkholderia sp. strain RASC	1.64 ± 0.18	3.23 ± 0.45
1477923	2,4-DNT dioxygenase large subunit	Burkholderia sp. strain RASC	2.02 ± 0.23	3.42 ± 0.62
1773277	2-NT oxygenase large subunit	Pseudomonas sp.	1.98 ± 0.23	6.32 ± 0.43
2828015	Salicylate-5-hydroxylase large subunit	Ralstonia sp. strain U2	1.26 ± 0.13	13.94 ± 1.03
2828016	Salicylate-5-hydroxylase small subunit	Ralstonia sp. strain U2	1.94 ± 0.22	15.02 ± 0.75
2828018	Naphthalene 1,2-dioxygenase large subunit	Ralstonia sp. strain U2	1.34 ± 0.14	3.77 ± 0.27
3337416	Salicylaldehyde dehydrogenase	Ralstonia sp. strain U2	1.49 ± 0.16	4.33 ± 0.24
3894249	Phenol hydroxylase	Unidentified bacterium rN5	1.32 ± 0.14	6.85 ± 0.45
4220429	Putative aldolase	Ralstonia sp. strain U2	1.74 ± 0.19	3.99 ± 0.12
4220432	Glutathione S-transferase protein	Ralstonia sp. strain U2	1.65 ± 0.18	6.62 ± 0.67
4220433	Gentisate 1,2-dioxygenase	Ralstonia sp. strain U2	2.12 ± 0.26	10.63 ± 0.45
4220434	Fumarylpyruvate hydrolase	Ralstonia sp. strain U2	2.34 ± 0.28	8.14 ± 0.27
4220435	Maleylpyruvate isomerase	Ralstonia sp. strain U2	2.27 ± 0.27	7.74 ± 0.56
4234963	Naphthalene dioxygenase	Uncultured bacterium D1b	1.95 ± 0.22	9.58 ± 0.88
4234998	Naphthalene dioxygenase	Uncultured bacterium U3b	1.64 ± 0.18	5.62 ± 0.59
8118285	Polyaromatic hydrocarbon dioxygenase large subunit	Comamonas testosteroni	1.22 ± 0.13	3.94 ± 0.45
8118287	cis-Naphthalene dihydrodiol dehydrogenase	C. testosteroni	1.63 ± 0.18	13.96 ± 1.22
16943679	Cyclopentanone 1,2-monooxygenase	C. testosteroni	0.77 ± 0.08	13.92 ± 1.73
17863951	Naphthalene dioxygenase	Burkholderia sp. strain S1-17	1.72 ± 0.19	5.13 ± 0.76
17942397	2,4-DNT oxygenase Fe-S protein	Burkholderia cepacia	2.04 ± 0.24	11.93 ± 0.35
18307552	Naphthalene dioxygenase Fe-S protein	Ralstonia sp. strain NI1	2.32 ± 0.28	7.88 ± 0.67
18643025	Nitrobenzene dioxygenase alpha subunit	Comamonas sp. strain JS765	1.12 ± 0.12	8.53 ± 0.34

^aHybridization signal ratios (log mean ± standard deviation from six replicates) of the naphthalene-spiked TFD soil to the control TFD soil. The hybridization signals of 40 genes were significantly different (P = 0.05), but only the genes with >3-fold difference are listed.

^bMean ± standard deviation of six replicate Cy5 signals from treated samples.