TABLE 2.

Summary of transcribed genes from pyrosequencing and Illumina sequencing data

Gene(s)	Detected by pyrosequencing in culture with:		Illumina sequencing results			Protein annotation	Function	Pathway
	Benzene	Benzoate	Gene specificitya	Taxon of closest match	% identity or range
bzdA	No	Yes	0.2	Azoarcus	64–87	Benzoate-CoA ligase	Benzoate CoA ligase	Benzoate
bclA	No	No	1.0	Bacteria	77.0	Benzoate-CoA ligase
bzlA	No	No	30	Clostridiales	78–93	Putative benzoate-CoA ligase
bamB	No	No	17	Clostridiales	91	Putative aldehyde ferredoxin oxidoreductase	Benzoyl-CoA reductase (ferredoxin-dependent)	Benzoate
bamC	No	No	55	Clostridiales	88	Putative iron-sulfur binding protein
bamD	Yes	No	ND	Clostridiales	85	Putative NADH oxidoreductase
bamE	Yes	No	101	Clostridiales	74–82	Putative iron-sulfur binding protein
bcrA/badF	No	No	3.0	Proteobacteria	61–86	Benzoyl-CoA reductase, alpha subunit	Benzoyl-CoA reductase (ATP-dependent)	Benzoate
bcrB/badE	No	Yes	3.0	Proteobacteria	67–78	Benzoyl-CoA reductase, beta subunit
bcrC/badD	No	No				Benzoyl-CoA reductase, gamma subunit
bcrD/badG	No	No	3.0	Proteobacteria	71–78	Benzoyl-CoA reductase, delta subunit
bzdN	No	Yes	0.2	Azoarcus	89–100	Benzoyl-CoA reductase, gamma subunit
bzdO	No	Yes	0.3	Azoarcus	88–100	Benzoyl-CoA reductase, beta subunit
bzdP	No	Yes	0.1	Azoarcus	92–96	Benzoyl-CoA reductase, delta subunit
bzdQ	No	Yes	0.1	Azoarcus	98–100	Benzoyl-CoA reductase, alpha subunit
bzdW	Yes	Yes	0.2	Azoarcus	90.0	Cyclohex-1-ene-1-carboxyl-CoA hydratase	Hydratase	Benzoate
bzdX	No	Yes	0.1	Azoarcus	94.0	6-Hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase	Dehydrogenase	Benzoate
had	No	Yes	ND	Proteobacteria	71–73	6-Hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
bzdY	No	Yes	0.1	Azoarcus	89–95	6-Oxocyclohex-1-ene-1-carbonyl-CoA hydrolase	Hydrolase	Benzoate
oah	No	No	4.0	Proteobacteria	73–91	6-Oxocyclohex-1-ene-1-carbonyl-CoA hydrolase
abcA	Yes	No	21	Clostridiales	95–100	Putative anaerobic benzene carboxylase	Putative carboxylases	Unconfirmed pathway
abcD	Yes	No	62	Clostridiales	94–96	Putative anaerobic benzene carboxylase
ppsA	No	No	6.0	Proteobacteria	81–83	Phenylphosphate synthase alpha subunit	Phenyl phosphate synthase	Phenol
ppsB	No	No	12	Proteobacteria	79.17	Phenylphosphate synthase, beta subunit
ppsC	No	No	4.0	Proteobacteria	56.14	Protein stimulating phenylphosphate synthetase activity
ppcB	No	No	72	Deltaproteobacteria	79–87	Phenylphosphate carboxylase subunit beta	Phenylphosphate carboxylase	Phenol
hbcL	No	No	2.0	Azoarcus	39–84	4-Hydroxybenzoate CoA ligase	4-Hydroxybenzoate CoA ligase	Phenol
hcrA	No	No	4.0	Proteobacteria	68	4-Hydroxybenzoyl-CoA reductase alpha subunit	Hydroxybenzoyl-CoA reductase	Phenol
ubiD-like	No	No	14	Clostridiales	89–100	Putative 3-polyprenyl-4-hydroxybenzoate carboxy-lyase	Decarboxylases	Ubiquinoneb
ubiX-like	No	No	21	Clostridiales	91	Putative 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
ubiX	No	No	1.5	Deltaproteobacteria	71–91	3-Octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiX)
ubiX	No	No	0.2	Azoarcus	71–93	3-Octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiX)
ubiD	No	No	0.2	Azoarcus	82–91	3-Polyprenyl-4-hydroxybenzoate carboxy-lyase (UbiD)

^aSpecificity was calculated from the number of reads per contig (see Materials and Methods). ND, not detected in the Illumina sequencing results. A visual representation of the majority of these genes within pathway assignments is presented in Fig. 6. The numbers of reads per gene (and thus gene specificity) were calculated by adding up the number of reads per contig associated with the same gene and also corresponding to microorganisms of the same genus (e.g., Azoarcus) as reported in Table S4 in the supplemental material. Aromatoleum aromaticum EBN1 was renamed Azoarcus, and therefore, genes from this species were considered Azoarcus genes.

^bGenes other than decarboxylase genes from the ubiquinone biosynthesis pathway are shown in Table S10 in the supplemental material.