TABLE 2.

Primer sets used for this study

Primer pair	Protein or gene targeted	Sequences (5′-3′)	PCR annealing temp (°C)	Amplicon size (bp)	Reference
TBMD-F/TBMD-R	Subfamily 1 of α-subunit of hydroxylase component of multicomponent mono-oxygenases	GCCTGACCATGGATGC(C/G)TACTGG, CGCCAGAACCACTTGTC(A/G)(A/G)TCCA	65.5	640	17
(GC-)TMOA-F/TMOA-Ra	Subfamily 2 of α-subunit of hydroxylase component of multicomponent mono-oxygenases	CGAAACCGGCTT(C/T)ACCAA(C/T)ATG, ACCGGGATATTT(C/T)TCTTC(C/G)AGCCA	61.2	505	17
TOL-F/TOL-R	Subfamily 5 of hydroxylase component of two-component side chain mono-oxygenases	TGAGGCTGAAACTTTACGTAGA, CTCACCTGGAGTTGCGTAC	55	475	3
XYLA-F/XYLA-R	Electron transfer component of two-component side chain mono-oxygenases	CCAGGTGGAATTTTCAGTGGTTGG, AATTAACTCGAAGCGCCCACCCCA	64	291	17
TODC1-F/TODC1-R	Subfamilies D.1.B, D.1.C, D.2.A, D.2.B, and D.2.C of α-subunits of type D iron-sulfur multicomponent aromatic dioxygenases	CAGTGCCGCCA(C/T)CGTGG(C/T)ATG, GCCACTTCCATG(C/T)CC(A/G)CCCCA	66	510	17
XYLE-F/XYLE-R	Subfamily 1.2.A of catechol extradiol dioxygenases	CCGCCGACCTGATC(A/T)(C/G)CATG, TCAGGTCA(G/T)CACGGTCA(G/T)GA	61.5	242	17
XYLE2-F/XYLE2-R	Subfamily 1.2.B of catechol extradiol dioxygenases	GTAATTCGCCCTGGCTA(C/T)GTICA, GGTGTTCACCGTCATGAAGCG(C/G/T)TC	64	906	17
CDO-F/CDO-R	Cdo (U01826) of subfamily 1.2.C of catechol extradiol dioxygenases	CATGTCAACATGCGCGTAATG, CATGTCTGTGTTGAAGCCGTA	58	255	17
TBUE-F/TBUE-R	TbuE (U20258) of subfamily 1.2.C of catechol extradiol dioxygenases	CTGGATCATGCCCTGTTGATG, CCACAGCTTGTCTTCACTCCA	60	444	17
TODE-F/TODE-R	TodE (Y18245), TodE (Y18245), and TobE (AF180147) of subfamily 1.3.B of catechol extradiol dioxygenases	GGATTTCAAACTGGAGACCAG, GCCATTAGCTTGCAGCATGAA	58	246	17
(GC-)63F/518Ra	Eubacterial 16S rRNA gene	CAGGCCTAACACATGCAAGTC, TTACCGCGGCTGCTGG	55	455	11

^aA 40-bp GC clamp (5′-CGCCCGCCGCGCGCGGCGGGCGGGGCGGGGGCACGGGGGG-3′) was attached to the 5′ end of forward primers TMOA-F and 63F (47).