Bacterial degradation of aromatic compounds

Abstract

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Keywords: Bioremediation; PAHs; biodegradation; polycyclic aromatic hydrocarbons.

Scheme 1.

Proposed catabolic pathways of naphthalene by bacteria [–27, 33].

Scheme 2.

Proposed catabolic pathways of fluorene by bacteria [26, 40, 41, 43, 45, 46]. Compound designations: 1, fluorene; 2, fluorene-1,2-diol; 3, 2-hydroxy-4-(2-oxo-indan-1-ylidene)-2-butenoic acid; 4, 1-formyl- 2-indanone; 5, 2-indanone-1-carboxylic acid; 6, 2-indanone; 7, 3-chromanone; 8, 9-fluorenol; 9, 9-fluorenone; 10, 3,4-dihydroxy-9-fluorenone; 11, 4-hydroxy-9-fluorenone; 12, 2’,3’-dihydroxy-biphenyl-2-carboxylic acid; 13, 8-hydroxy-3,4-benzocoumarin; 14, phthalate; 15, protocatechuic acid; 16, 4-carboxy-2-hydroxymuconate- 6-semialdehyde; 17, 2-pyrone-4,6-dicarboxylic acid; 18, 4-carboxy-2-hydroxymuconic acid; 19, fluorene-3,4-diol; 20, 2-hydroxy-4-(1-oxo-indan-2-ylidene)-2-butenoic acid; 21, 2-formyl-1-indanone; 22, 1-indanone-2-carboxylic acid; 23, 1-indanone; 24, 3-hydroxy- 1-indanone; 25, 2-chromanone; 26, 3-(2-hydroxy-phenyl)-propionic acid; 27, salicylic acid.

Scheme 3.

Proposed catabolic pathways of phenanthrene by bacteria [24, 49, 55, 57, 58, 63, 139, 150]. Compound designations: 1, phenanthrene; 2, cis-1,2-dihydroxy-1,2-dihydrophenanthrene; 3, 1,2- dihydroxyphenanthrene; 4, 3-hydroxy-3H-benzo[f]chromene-3-carboxylic acid; 5, 4-(2-hydroxy-naphthalen-1-yl)-2-oxo-but-3-enoic acid; 6, 2-hydroxy-naphthalene-1-carbaldehyde; 7, 2-hydroxy-1-naphthoic acid; 8, 5,6-benzocoumarin; 9, cis-9,10-dihydroxy-9,10-dihydrophenanthrene; 10, 9,10-dihydroxyphenanthrene; 11, 2,2’-diphenic acid; 12, cis-3,4-dihydroxy-3,4-dihydrophenanthrene; 13, 3,4-dihydroxyphenanthrene; 14, 2-hydroxy-2H-benzo[h]chromene-2-carboxylic acid; 15, 4-(1-hydroxynaphthalen-2-yl)-2-oxo-but-3-enoic acid; 16, 1-hydroxy-naphthalene-2-carbaldehyde; 17, 1-hydroxy-2-naphthoic acid; 18, 7,8-benzocoumarin; 19, 1-(2-carboxy-vinyl)-naphthalene-2-carboxylic acid; 20, 2-(2-carboxy-vinyl)-naphthalene-1-carboxylic acid; 21, naphthalene-1,2-dicarboxylic acid; 22, naphthalene-1,2-diol; 23, 2-hydroxybenzalpyruvic acid; 24, salicylic aldehyde; 25, salicylic acid; 26, gentisic acid; 27, coumarin; 28, 2-carboxycinnamic acid; 29, 2-formylbenzoic acid; 30, phthalic acid; 31, 3,4-dihydroxyphthalic acid; 32, protocatechuic acid; 33, trans-2,3-dioxo-5-(2’-hydroxyphenyl)-pent-4-enoic acid.

Scheme 4.

Proposed catabolic pathways of fluoranthene by bacteria [, –70, 85, 147]. Compound designations: 1, fluoranthene; 2, cis-7,8-fluoranthene dihydrodiol; 3, 7,8-dihydroxy-fluoranthene; 4, 7,8-dimethoxyfluoranthene; 5, 2-hydroxy-4-(2-oxo-2H-acenaphthylen-1-ylidene)-but-2-enoic acid; 6, 2-oxo-acenaphthene-1-carboxylic acid; 7, 2-hydroxylmethyl-2H-acenaphthylen-1-one; 8, 1-acenaphthenone; 9, 3-hydroxymethyl-3H-benzo[de] chromen-2-one; 10, 2-hydroxymethyl-acenaphthylen-1-ol; 11, cis-1,2-fluoranthene dihydrodiol; 12, 1,2-dihydroxy-fluoranthene; 13, 1,2-dimethoxyfluoranthene; 14, 9-fluorenone-1-(carboxy-2-hydroxy-1-propenol); 15, 9-fluorenol-1-carboxy-3-propenyl-2-one; 16, 9-fluorenone-1-carboxylic acid; 17, 9-fluorenol-1-carboxylic acid; 18, 9-fluorenone; 19, 9-fluorenol; 20, 2’,3’-dihydroxybiphenyl-2,3-dicarboxylic acid; 21, benzene-1,2,3-tricarboxylic acid; 22, cis-8,9-fluoranthene dihydrodiol; 23, 8,9-dihydroxy-fluoranthene; 24, 8,9-dimethoxyfluoranthene; 25, naphthalene-1,8-dicarboxylic acid; 26, cis-2,3-fluoranthene dihydrodiol; 27, 2,3-dihydroxy-fluoranthene; 28, 2,3-dimethoxyfluoranthene; 29, 9-carboxymethylene-9H-fluorene-1-carboxylic acid; 30, cis-1,9a-dihydroxy-1-hydrofluorene-9-one-8-carboxylic acid; 31, 4-hydroxybenzochromene-6-one-7-carboxylic acid.

Scheme 5.

Proposed catabolic pathways of pyrene by bacteria [3, 9, 61, 76, 78, 82, 85, 86, 91, 139]. Compound designations: 1, pyrene; 2, pyrene-cis-1,2-dihydrodiol; 3, pyrene-1,2-diol; 4, 2-hydroxy-3-(perinaphthenone-9-yl)-propenic acid; 5, 2-hydroxy-2H-1-oxa-pyrene-2-carboxylic acid; 6, 4-hydroxyperinaphthenone; 7, 1,2-dimethoxypyrene; 8, pyrene-trans-4,5-dihydrodiol; 9, pyrene-cis-4,5-dihydrodiol; 10, pyrene-4,5-diol; 11, phenanthrene-4,5-dicarboxylic acid; 12, 4-carboxyphenanthrene-5-ol; 13, 4-carboxy-5-hydroxy-phenanthrene-9,10-dihydrodiol; 14, 4-carboxyphenanthrene-5,9,10-triol; 15, 2,6,6’-tricarboxy-2’-hydroxybiphenyl; 16, 2,2’-dicarboxy-6,6’-dihydroxybiphenyl; 17, phthalic acid; 18, 4-phenantroic acid; 19, 3,4-dihydroxy-3,4-dihydro-phenanthrene-4-carboxylic acid; 20, phenanthrene-3,4-diol; 21, 4-phenanthroic acid methyl ester; 22, 4-hydroxyphenanthrene; 23, 7,8-benzocoumarin; 24, 2-hydroxy-2-(phenanthrene-5-one-4-enyl)-acetic acid; 25, 5-hydroxy-5H-4-oxa-pyrene-5-carboxylic acid; 26, pyrene-4,5-dione; 27, 4-oxa-pyrene-5-one.

Scheme 6.

Proposed catabolic pathways of benzo[a]pyrene by bacteria [79, 99, 100]. Compound designations: 1, benzo[a]pyrene; 2, benzo[a]pyrene-11,12-epoxide; 3, benzo[a]pyrene trans-11,12-dihydrodiol; 4, benzo[a]pyrene cis-11,12-dihydrodiol; 5, 11,12-dihydroxybenzo[a]pyrene; 6, hydroxymethoxybenzo[a]pyrene; 7, dimethoxybenzo[a]pyrene; 8, benzo[a]pyrene cis-4,5-dihydrodiol; 9, 4,5-dihydroxybenzo[a]pyrene; 10, 4-formylchrysene-5-carboxylic acid; 11, 4,5-chrysene-dicarboxylic acid; 12, chrysene-4 or 5-carboxylic acid; 13, benzo[a]pyrene cis-7,8-dihydrodiol; 14, 7,8-dihydroxybenzo[a]pyrene; 15, cis-4-(7-hydroxypyrene-8-yl)-2-oxobut-3-enoic acid; 16, pyrene-7-hydroxy-8-carboxylic acid; 17, 7,8-dihydro-pyrene-8-carboxylic acid; 18, benzo[a]pyrene cis-9,10-dihydrodiol; 19, 9,10-dihydroxybenzo[a]pyrene; 20, cis-4-(8-hydroxypyrene-7-yl)-2-oxobut-3-enoic acid; 21, pyrene-8-hydroxy-7-carboxylic acid; 22, 7,8-dihydro-pyrene-7-carboxylic acid; 23, 10-oxabenzo[def]chrysene-9-one.

Scheme 7.

Simplified bacterial catabolic pathways of dibenzofuran (X= O) and carbazole (X = S).

Scheme 8.

Bacterial catabolic pathways of dibenzo-p-dioxin.

Scheme 9.

Bacterial catabolic pathways of dibenzothiophene.

Scheme 10.

Catabolism of naphthalene, methylnaphthalene, and tetralin by anaerobic bacteria [–131].