TABLE 3.

Detection by microarrays of biodegradation genes in genomes of reference microorganisms used in this study

Strain	Chemical(s)	gi no.	Gene function	SNR	References
P. putida PpG7	PAH: naphthalene	45703	Catechol 2,3-dioxygenase	13.5 ± 1.5	10, 16, 18, 19, 40
		151379	1,2-Dihydroxynaphthalene dioxygenase	3.2 ± 0.3
		151381	Salicylate hydroxylase	5.4 ± 0.8
		151385	Naphthalene dioxygenase reductase (Fd)	13.4 ± 1.2
		151386	Naphthalene dioxygenase (Fd)	16.5 ± 2.3
		151387	Naphthalene dioxygenase (large subunit)	22.7 ± 2.1
		151388	Naphthalene dioxygenase (small subunit)	6.10 ± 0.5
		551908	Salicylate hydroxylase	5.6 ± 0.6
		4235477	4-Oxalocrotonate decarboxylase	19.0 ± 3.1
		5070351	Dihydroxynaphthalene dehydrogenase	7.2 ± 0.9
		483793	2-Hydroxylchromene2-carboxylate isomerase	12.0 ± 2.0
	Genes not previously reported in strain PpG7a	294344	Protocatechuate 3,4-dioxygenase	10.9 ± 1.3
294357		Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase	7.7 ± 0.9
		595675	4-Oxalocrotonate decarboxylase	10.3 ± 1.6
		1008926	Catechol 1,2-dioxygenase	3.9 ± 0.2
		1255676	Isomerase	10.8 ± 1.7
		2252625	Salicylaldehyde dehydrogenase	20.8 ± 1.9
		3641341	Lactone-specific esterase	3.9 ± 0.5
		4104766	Catechol 2,3-dioxygenase	4.9 ± 0.6
		4235477	4-Oxalocrotonate decarboxylase	19.0 ± 3.2
		11546053	Benzoate dioxygenase	17.8 ± 2.7
		22000712	2-Hydroxymuconic semialdehyde dehydrogenase	5.9 ± 0.5
		22000714	Acetaldehyde dehydrogenase	4.9 ± 0.6
		119911694	4-Chlorobenzoate CoA ligase	5.6 ± 0.4
R. palustris	Monoaromatics: benzoate, toluene	1730295	4-Hydroxybenzoyl-CoA reductase HbaB subunit	13 ± 1.1	11, 15
1730296		4-Hydroxybenzoyl-CoA reductase HbaC subunit	9.5 ± 0.9
		1730297	4-Hydroxybenzoyl-CoA reductase HbaD subunit	14.3 ± 2.0
		2190573	Cyclohex-1-ene-1-carboxylate CoA ligase	24.1 ± 2.1
		2190574	Cyclohexanecarboxyl-CoA dehydrogenase	7.2 ± 0.6
		2190576	2-Hydroxycyclohexanecarboxyl-CoA dehyrogenase	15.8 ± 1.8
		2190579	Benzoyl-CoA reductase subunit	18.0 ± 2.2
		3165396	Benzoyl-CoA reductase subunit	9.6 ± 0.9
		3243085	2-Ketocyclohexanecarboxyl-CoA hydrolase	8.7 ± 0.9
T. aromatica K172	Monoaromatics: benzoate, phenol, toluene	3184130	Benzylsuccinate synthase gamma subunit	11.3 ± 1.0	4, 5, 25, 28, 29
3184131		Benzylsuccinate synthase alpha subunit	4.0 ± 0.5
		3184132	Benzylsuccinate synthase beta subunit	11.4 ± 1.4
		3724166	6-Oxocyclohex-1-ene-1-carbonyl-CoA hydratase	13.4 ± 1.1
		3724167	Cyclohexa-1,5-diene-1-carbonyl-CoA hydratase	10.7 ± 0.8
		3724168	C subunit of benzoyl-CoA reductase	8.9 ± 0.9
		3724169	B subunit of benzoyl-CoA reductase	4.1 ± 0.5
		3724170	A subunit of benzoyl-CoA reductase	9.7 ± 1.3
		3724171	D subunit of benzoyl-CoA reductase	10.3 ± 0.9
		3724172	Ferredoxin	11.3 ± 1.2
		9622531	BbsA; toluene metabolism	3.9 ± 0.5
		9622533	BbsC; toluene metabolism	7.0 ± 0.6
		9622534	BbsD; toluene metabolism	14.4 ± 1.7
		9622535	BbsE; toluene metabolism	9.6 ± 0.8
		9622536	BbsF; toluene metabolism	6.6 ± 0.7
		9622538	E-phenylitaconyl-CoA hydratase; toluene metabolism	15.7 ± 1.3
		9622539	BbsI; toluene metabolism	14.2 ± 1.3
		10697118	Hypothetical protein; phenol metabolism	12.4 ± 1.4
		10697119	Hypothetical protein; phenol metabolism	16.8 ± 1.5
		10697121	Hypothetical protein; phenol metabolism	15.9 ± 1.3
		10697123	Hypothetical protein; phenol metabolism	7.9 ± 0.6
		10697124	Hypothetical protein; phenol metabolism	7.1 ± 0.8
		10697125	Hypothetical protein; phenol metabolism	17.9 ± 1.9
		19571178	2-Oxyglutarate ferredoxin-oxidoreductase beta subunit	33.8 ± 2.8
		19571179	2-Oxoglutarate ferredoxin-oxidoreductase alpha subunit	7.2 ± 0.6
		19571180	6-Hydroxycylohex-1-ene-1-carbonyl-CoA dehydrogenase	4.9 ± 0.4
		12667039	Putative alcohol dehydrogenase	4.2 ± 0.5
		12667041	Putative alcohol dehydrogenase	5.9 ± 0.8
		12667042	Putative acyl-CoA dehydrogenase	15.9 ± 1.4
		12667043	3-Hydroxybenzoate CoA ligase	12.9 ± 1.6
		12667044	Putative hydrolase	21.0 ± 2.3

^aAdditional genes not reported but detected in strain PpG7.