Isolation, Molecular, and Metabolic Profiling of Benzene-Remediating Bacteria Inhabiting the Tannery Industry Soil

Hussain, Nadia; Mohiuddin, Farhan; Muccee, Fatima; Bunny, Saboor Muarij; Al Haddad, Amal H.I.

doi:10.33073/pjm-2025-003

Figures & Tables

Phylogenetic tree constructed for present study bacteria using MEGA11 software.

Growth curve analysis of present study benzene degrading bacteria.

Comparison of FTIR spectra of control and present study benzene degrading bacteria to analyze the variation of the peaks contributed by bacterial benzene degradation.
A) Control, B) Paracoccus aestuarii PUB1, C) Bacillus tropicus PUB2, D) Bacillus albus PUB3, E) Bacillus subtilis PUB4, F) Bacillus cereus PUB6. — Comparison of FTIR spectra of control and present study benzene degrading bacteria to analyze the variation of the peaks contributed by bacterial benzene degradation. A) Control, B) Paracoccus aestuarii PUB1, C) Bacillus tropicus PUB2, D) Bacillus albus PUB3, E) Bacillus subtilis PUB4, F) Bacillus cereus PUB6.

Four pathways of benzene metabolism suggested in benzene-degrading bacteria in the present study based on GC-MS based identification of metabolites.
A1 – benzyl alcohol dehydrogenase, B1 – benzaldehyde dehydrogenase, C1 – benzoate CoA-ligase, D1 – benzoyl-CoA 2,3-dioxygenase, A2 – methyl monooxygenase, B2 – benzoyl alcohol dehydrogenase, C2 – benzaldehyde dehydrogenase, D2 – benzoate 1,2-dioxygenase, E2 – dihydrocyclohexadiene carbohydrate dehydrogenase, A3 – benzoate dioxygenase, B3 – benzoate cis-diol dehydrogenase, A4 – benzene phenol monooxygenase — Four pathways of benzene metabolism suggested in benzene-degrading bacteria in the present study based on GC-MS based identification of metabolites. A1 – benzyl alcohol dehydrogenase, B1 – benzaldehyde dehydrogenase, C1 – benzoate CoA-ligase, D1 – benzoyl-CoA 2,3-dioxygenase, A2 – methyl monooxygenase, B2 – benzoyl alcohol dehydrogenase, C2 – benzaldehyde dehydrogenase, D2 – benzoate 1,2-dioxygenase, E2 – dihydrocyclohexadiene carbohydrate dehydrogenase, A3 – benzoate dioxygenase, B3 – benzoate cis-diol dehydrogenase, A4 – benzene phenol monooxygenase

The β-ketoadipate pathway suggested in the present study benzene degrading bacteria based on GC-MS based identification of metabolites involving this pathway.
a – catechol 1,2-dioxygenase, b – muconate cycloisomerase, c-d – beta-ketoadipate:succinyl CoA transferase, e – succinyl CoA:acetyl CoA C-succinyl transferase, f – succinyl-CoA synthetase, g – succinic dehydrogenase, h – fumarase, i – malate dehydrogenase, j – citrate synthase, k – fatty acid synthase — The β-ketoadipate pathway suggested in the present study benzene degrading bacteria based on GC-MS based identification of metabolites involving this pathway. a – catechol 1,2-dioxygenase, b – muconate cycloisomerase, c-d – beta-ketoadipate:succinyl CoA transferase, e – succinyl CoA:acetyl CoA C-succinyl transferase, f – succinyl-CoA synthetase, g – succinic dehydrogenase, h – fumarase, i – malate dehydrogenase, j – citrate synthase, k – fatty acid synthase

Metabolites identified in the present study bacteria, through comparison of m/z ratios of GC-MS spectra with molecular weights of earlier reported benzene degradation metabolites_

Metabolite identified	Metabolites unidentified	PUB4	PUB1	Fragmentation ion m/z	Molecular weight (M/w)	FTlR spectral peaks (cm⁻¹)
Benzene methylation pathway
Toluene	cis-benzoate dihydrodiol, cis-benzene dihydrodiol	I	I	39,51,65, 77, 91,92	92.14	1452 (aromatic deformation), 2851 and 2920 (=C–H and –C–H)
Benzyl alcohol		I		65, 77, 79,91, 107, 108	108	3427 (OH), 3010 (unsaturated CH), 2900 (saturated CH)
Benzaldehyde		I	I	29, 39,51,52, 77, 78, 105, 106	106	1637–1733 (C=O vibs)
Benzoate		I	I	176, 121,93, 77, 65	121	3427 (OH), 1271 (C-O-C stretching)
Catechol		I	I	81,66, 53, 110	110	3427 (OH), 1658 (C=C), 1250 and 1281 (C-O), 746 and 850 out of plane bending of =C–H bond of aromatic ring
Benzene degradation via benzaldehyde
Benzyl alcohol	benzoate, bcnzoyl-CoA, acetyl CoA	I	I	65, 77, 79,91, 107,108	108	3427 (OH), 3010 (unsaturated CH), 2900 (saturated CH)
Benzaldehyde		I	I	29, 39,51,52, 77, 78, 105, 106	106	1637-1733 (C=O vibs)
Benzene degradation via carboxylation
Benzoate		I	I	176, 121,93, 77, 65	121	3427 (OH), 1271 (C–O–C stretching)
cis-1,6-dihydroxy-2,4-Cyelohexadiene-1-Carboxylie acid		I	I	44, 73, 149	156	2800-3300 (C–H stretch)
Catechol		I	I	81,66, 53	110	Same as above
Benzene degradation via phenol
Phenol		I	I	17, 38, 39, 40, 63, 65, 77, 93, 94	94	3427 (OH), 1650 (C=C stretch)
Catechol		I	1	81,66, 53, 110	110	Same as above
β-ketoadipate pathway
Catechol	3-oxoadiphyl CoA, succinyl CoA, succinate, fumarate	I	I	81,66, 53, 110	110	Same as above
cis,cis-muconate		I	---	77, 106, 122, 126, 138, 171, 195, 228	126	1540–1650 (asymmetric stretch of CO₂^-), 1360–1450 (symmetric stretch of CO₂^-)
3-oxoadipatc enol lactone		I	---			1637–1733 (C=O vibs), 3427 (OH),
3-oxoadipate		I	---	40.44, 73, 84, 87, 101, 114, 115, 160	160	1637–1733 (C=O vibs)
Palmitate		I	I	41,43, 57, 73, 89, 99, 117, 127, 141, 169, 183, 201,215, 229, 239, 257, 271,285,299, 313	255	2848 and 2913 (–CH₃ and –CH₂ vibs), 1695 (C=O), 1464 (–CH₂ and –CH₃), 939 (–OH out plane vibs) and 1299 (–OH in-plane vibs), 723 and 685 (–OH swinging vibs)

Isolation, Molecular, and Metabolic Profiling of Benzene-Remediating Bacteria Inhabiting the Tannery Industry Soil

Figures & Tables

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Fig. 5.

Metabolites identified in the present study bacteria, through comparison of m/z ratios of GC-MS spectra with molecular weights of earlier reported benzene degradation metabolites_

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