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Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria Cover

Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria

Polish Journal of Microbiology
Volume 74 (2025): Issue 2 (June 2025)
By: ,  ,  ,  ,  ,   and    
Open Access
|Jun 2025
Figures & tables

Figures & Tables

Fig. 1.

Total bases, GC and AT contents, and Q20 and Q30 ratios of total reads calculated during WGS analysis.

Fig. 2.

Krona image of taxonomic assignments to metagenomic contigs by Kraken.

Fig. 3.

Pathways associated with aromatic compound metabolism, with their respective abundances, explored in a bacterial consortium using whole genome sequencing.

BD – benzoate degradation, ABD – aminobenzoate degradation, FBD – fluorobenzoate degradation, CLAD – chloroalkane and chloroalkene degradation, CLHD – chlorocyclohexane and chlorobenzene degradation, TD – toluene degradation, XD – xylene degradation, SD – styrene degradation, AD – atrazine degradation, CD – caprolactam degradation, DD – dioxin degradation, ND – naphthalene degradation, PAHD – polycyclic aromatic hydrocarbon degradation, SD – steroid degradation, MP450 – metabolism of xenobiotics by cytochrome P450

Table I

Stoichiometry of reactions involved in benzene, xylene and toluene degradation identified in the current study bacteria based on WGS.

No. of reactionStoichiometry of reactions
ReactantsProducts
Benzene degradation pathway
IC6H6 + H2 + CO2 benzeneC7H8O + [O-]
benzyl alcohol
IIC7H8OC7H6O + H2
benzaldehyde
IIIC7H6O + [O-]C7H6O2
benzoate
IVC7H6O2 + [O-] + H2OC7H8O4
cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
VC7H8O4C6H6O2
catechol
VIC6H6O2 + 2 [H+]C6H5O4- + 3 [H+]
cis, cis-muconate
VIIC6H5O4-C6H6O4
muconolactone
VIIIC6H6O4C6H5O4+ [H+]
3-oxoadipate enol lactone
IXC6H5O4C6H5O52-
3-oxoadipate
XC6H5O52- + [H+] + C21H36N7O16P3SC27H42N7O20P3S + [O]
3-oxoadipyl-CoA
XIC27H42N7O20P3S + 5H2OC23H38N7O17P3S + 4CO2+ 7H2O
acetyl-CoA
p-Xylene degradation pathway
IC8H10 + [O-] p-xyleneC8H10O
4-methylbenzyl alcohol
IIC8H10O + CO2C9H10O2 + [O-]
p-methylbenzoate
IIIC9H10O2 + 2O2C8H9O4 + CO2 + [H+]
cis-1-2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate
IVC8H9O4C7H8O2 + CO2 + [H+]
4-methylcatechol
VC7H8O2 + O2C7H8O4
2-hydroxyl-5-methyl-cis, cis-muconic semialdehyde
VIC7H8O4 + [O]C7H8O5
2-hydroxyl-5-methyl-cis, cis-muconate
VIIC7H8O5C7H8O5
2-oxo-5-methyl-cis-muconate
VIIIC7H8O5C6H8O3 + CO2
2-hydroxyl-cis-hexa-2,4-dienoate
IXC6H8O3 + H2OC6H10O4
4-hydroxyl-2-oxohexanoate
XC6H10O4 + 2O2 + H2O3CO2+ C3H3O3- + H2O
pyruvate
m-Xylene degradation pathway
IC8H10+ [O] m-xyleneC8H10O
3-methylbenzyl alcohol
IIC8H10OC8H8O + H2
3-methylbenzaldehyde
IIIC8H8O + CO2+ H2C9H10O2 + H2O
m-methylbenzoate
IVC9H10O2 + CO2C8H8O4 + H2
1,2-dihydroxy-3-methylcyclohexa-3,5-dienecarboxylate
o-Xylene degradation pathway
IC8H10 + [O-] o-xyleneC8H10O
2-methylbenzyl alcohol
IIC8H10OC8H8O + H2
2-methylbenzaldehyde
IIIC8H8O + CO2 + H2C9H10O2 + [O]
o-methylbenzoate
IVC9H10O + CO2C8H10O4
1,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate
VC8H10O4C7H8O2 + CO2 + H2
3-methylcatechol
VIC7H8O2 + O2C7H8O4
cis, cis-2-hydroxyl-6-oxohept-2,4-dienoate
VIIC7H8O4 + [O-]C5H6O3 + 2CO2 + H2
cis-2-hydroxy penta-2,4-dienoate
VIIIC5H6O3 + H2OC5H7O4- + [H+]
4-hydroxyl-2-oxopentanoate
IXC5H7O4- + [O-]C3H3O3- + 2CO2 + 2H2 pyruvate
Toluene degradation pathway
IC6H5CH3 + [O] tolueneC6H5CH2OH
benzyl alcohol
IIC6H5CH2OH benzyl alcoholC6H5CHO + H2
benzaldehyde
IIIC6H5CHO + [O] benzaldehydeC7H5O2 + [H]
benzoate
Table II

Statistics of contigs produced by the metaSPAdes program.

No.Quast quality parametersStatistics (bp)
1Contigs > 10,000 bp4,992
2Contigs ≥ 5,000 bp940
3Contigs ≥ 10,000 bp431
4Contigs ≥ 25,000 bp169
5Contigs ≥ 50,000 bp76
6Largest contig469,435
7Total length30,570,959
8Total length ≥ 1,000 bp27,559,880
9Total length ≥ 5,000 bp19,294,370
10Total length ≥ 10,000 bp15,759,083
11Total length ≥ 25,000 bp11,859,173
12Total length ≥ 50,000 bp8,511,336
13N5010,938
Table III

Functional annotation of genes associated with aromatic compound degradation via the KEGG database.

No.Associated biochemical pathwayGenes identified
1Xylene degradation pathwaytoluene methyl-monooxygenase [EC:1.14.15.26],
aryl-alcohol dehydrogenase [EC:1.1.1.90],
benzaldehyde dehydrogenase (NAD) [EC:1.2.1.28],
benzoate/toluate 1,2-dioxygenase subunit α [EC:1.14.12.-],
dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.-, 1.3.1.67, 1.3.1.68],
catechol 2,3-dioxygenase [EC:1.13.11.2],
2-hydroxymuconate-semialdehyde hydrolase [EC:3.7.1.9],
2-oxopent-4-enoate/cis-2-oxohex-4-enoate hydratase [EC:4.2.1.80, 4.2.1.132],
4-hydroxy-2-oxovalerate/4-hydroxy-2-oxohexanoate aldolase [EC:4.1.3.39 4.1.3.43],
acetaldehyde/propanal dehydrogenase [EC:1.2.1.10, 1.2.1.87],
aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde
dehydrogenase [EC:1.2.1.32 1.2.1.85],
4-oxalocrotonate tautomerase [EC:5.3.2.6],
2-oxo-3-hexenedioate decarboxylase [EC:4.1.1.77],
2-keto-4-pentenoate hydratase [EC:4.2.1.80],
4-hydroxy 2-oxovalerate aldolase [EC:4.1.3.39],
acetaldehyde dehydrogenase [EC:1.2.1.10]
2Toluene degradation pathwaytoluene methyl-monooxygenase [EC:1.14.15.26],
aryl-alcohol dehydrogenase [EC:1.1.1.90],
benzaldehyde dehydrogenase (NAD) [EC:1.2.1.28]
3Benzenebenzoate/toluate 1,2-dioxygenase subunit alpha [EC:1.14.12.10], dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.25],
catechol 1,2-dioxygenase [EC:1.13.11.1],
muconate cycloisomerase [EC:5.5.1.1],
muconolactone D-isomerase [EC:5.3.3.4],
3-oxoadipate enol-lactonase [EC:3.1.1.24],
3-oxoadipate CoA-transferase, alpha subunit [EC:2.8.3.6],
acetyl-CoA acyltransferase [EC:2.3.1.16],
3-oxoadipyl-CoA thiolase [EC:2.3.1.174],
catechol 2,3-dioxygenase [EC:1.13.11.2],
2-hydroxymuconate-semialdehyde hydrolase [EC:3.7.1.9],
2-keto-4-pentenoate hydratase [EC:4.2.1.80],
4-hydroxy 2-oxovalerate aldolase [EC:4.1.3.39],
acetaldehyde dehydrogenase [EC:1.2.1.10],
protocatechuate 3,4-dioxygenase, alpha subunit [EC:1.13.11.3],
3-carboxy-cis, cis-muconate cycloisomerase [EC:5.5.1.2],
4-carboxymuconolactone decarboxylase [EC:4.1.1.44],
3-hydroxybenzoate 6-monooxygenase [EC:1.14.13.24]
3Aminobenzoate degradation pathwaybenzaldehyde dehydrogenase (NAD) [EC:1.2.1.28],
amidase [EC:3.5.1.4],
4-hydroxybenzoate decarboxylase subunit C [EC:4.1.1.61]
4Fluorobenzoate degradation pathwaybenzoate/toluate 1,2-dioxygenase subunit alpha [EC:1.14.12.10],
dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.25],
catechol 1,2-dioxygenase [EC:1.13.11.1],
muconate cycloisomerase [EC:5.5.1.1]
Fig. 4.

Reconstruction of ortho, meta and para-xylene degradation pathways based on whole genome shotgun functional annotation.

Fig. 5.

Reconstruction of benzene, 3-aminobenzene sulfonate, toluene and 2-, 3- and 4-fluorobenzoate degradation pathways based on whole genome shotgun functional annotation.

Fig. 6.

Reactions of benzene and xylene metabolism catalyzed by bacterial enzymes identified in the current study using whole genome shotgun functional annotation.

DOI: https://doi.org/10.33073/pjm-2025-020 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 244 - 261
Submitted on: Apr 7, 2025
Accepted on: May 11, 2025
Published on: Jun 18, 2025
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
metagenome,
Bacillus,
taxonomic profiling,
bioremediation,
benzene,
xylene
Related subjects:
Life sciences,
Microbiology and virology

© 2025 FATIMA MUCCEE, FARHAN MOHIUDDIN, AANSA SHAHAB, ALI ALMAJWAL, TAYYABA AFSAR, HOUDA AMOR, SUHAIL RAZAK, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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