References
- Abate TA, Desta AF, Love NG. Evaluating tannery wastewater treatment performance based on physicochemical and microbiological characteristics: An Ethiopian case study. Water Environ Res. 2021 May;93(5):658–669. https://doi.org/10.1002/wer.1364
- Albokari M, Arishi A, Essa A. Molecular analysis of the bacterial communities from tannery contaminated sites in Riyadh, Saudi Arabia. Res J Biotech. 2018 Mar;13(3):46–53.
- Aparicio JD, Raimondo EE, Saez JM, Costa-Gutierrez SB, Ál-varez A, Benimeli CS, Polti MA. The current approach to soil remediation: A review of physicochemical and biological technologies, and the potential of their strategic combination. J Environ Chem Eng. 2022 Apr;10(2):107141. https://doi.org/10.1016/j.jece.2022.107141
- Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020 Apr;36(7):2251–2252. https://doi.org/10.1093/bioinfor-matics/btz859
- Bacosa HP, Mabuhay-Omar JA, Balisco RAT, Omar DM Jr, Inoue C. Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): Insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates. World J Microbiol Biotechnol. 2021 Jun;37(7):122. https://doi.org/10.1007/s11274-021-03093-4
- Banerjee S, Bedics A, Harkai P, Kriszt B, Alpula N, Táncsics A. Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: Uncovering the role of Hydrogenophaga strains in xylene degradation. Environ Sci Pollut Res Int. 2022a Apr;29(19):28431–28445. https://doi.org/10.1007/s11356-021-18300-w
- Banerjee S, Bedics A, Tóth E, Kriszt B, Soares AR, Bóka K, Tánc-sics A. Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m-and p-xylene under microaerobic conditions. Front Microbiol. 2022b Sep;13:929128. https://doi.org/10.3389/fmicb.2022.929128
- Bedics A, Táncsics A, Tóth E, Banerjee S, Harkai P, Kovács B, Bóka K, Kriszt B. Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie Van Leeuwenhoek. 2022 Sep;115(9):1113–1128. https://doi.org/10.1007/s10482-022-01759-z
- Biswas R, Halder U, Kabiraj A, Mondal A, Bandopadhyay R. Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria. Arch Microbiol. 2021 Aug;203(6):2761–2770. https://doi.org/10.1007/s00203-021-02275-w
- Blair JM, Richmond GE, Piddock LJ. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol. 2014;9(10):1165–1177. https://doi.org/10.2217/fmb.14.66
- Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug;30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
- Brewster JD. A simple micro-growth assay for enumerating bacteria. J Microbiol Methods. 2003 Apr;53(1):77–86. https://doi.org/10.1016/s0167-7012(02)00226-9
- Caron-Beaudoin É, Whyte KP, Bouchard MF, Chevrier J, Haddad S, Copes R, Frohlich KL, Dokkie D; Treaty 8 Tribal Association; Juul S, et al. Volatile organic compounds (VOCs) in indoor air and tap water samples in residences of pregnant women living in an area of unconventional natural gas operations: Findings from the EXPERIVA study. Sci Total Environ. 2022 Jan;805:150242. https://doi.org/10.1016/j.scitotenv.2021.150242
- Chettri D, Verma AK, Chirania M, Verma AK. Metagenomic approaches in bioremediation of environmental pollutants. Environ Pollut. 2024 Dec;363(Pt_2):125297. https://doi.org/10.1016/j.en-vpol.2024.125297
- Chicca I, Becarelli S, Dartiahl C, La China S, De Kievit T, Petroni G, Di Gregorio S, Levin DB. Degradation of BTEX mixture by a new Pseudomonas putida strain: Role of the quorum sensing in the modulation of the upper BTEX oxidative pathway. Environ Sci Pol-lut Res Int. 2020 Oct;27(29):36203–36214. https://doi.org/10.1007/s11356-020-09650-y
- Cunningham CJ, Kuyukina MS, Ivshina IB, Konev AI, Peshkur TA, Knapp CW. Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils. Environ Sci Processes Impacts. 2020 May;22(5):1110–1124. https://doi.org/10.1039/c9em00606k
- Dairawan M, Shetty PJ. The evolution of DNA extraction methods. Am J Biomed Sci Res. 2020 Feb;8(1);39–45. https://doi.org/10.34297/AJBSR.2020.08.001234
- Devanadera A, Vejarano F, Zhai Y, Suzuki-Minakuchi C, Oht-subo Y, Tsuda M, Kasai Y, Takahata Y, Okada K, Nojiri H. Complete genome sequence of an anaerobic benzene-degrading bacterium, Azoarcus sp. strain DN11. Microbiol Resour Announc. 2019 Mar;8(11):e01699-18. https://doi.org/10.1128/MRA.01699-18
- Doley R, Barthakur M. Biodegradation of monoaromatic hydrocarbons toluene and xylene through native bacterial strain Bacillus subtilis RD20. Research Square. 2022. https://doi.org/10.21203/rs.3.rs-1974378/v2
- Dou J, Ding A, Liu X, Du Y, Deng D, Wang J. Anaerobic benzene biodegradation by a pure bacterial culture of Bacillus cereus under nitrate reducing conditions. J Environ Sci. 2010;22(5):709–715. https://doi.org/10.1016/s1001-0742(09)60167-4
- Evangelista AT, Truant AL, Bourbeau PP. Rapid systems and instruments for the identification of bacteria. In: Truant AL, editor. Manual of commercial methods in clinical microbiology. Washington (USA): ASM Press; 2001. p. 22–49. https://doi.org/10.1128/9781555817961.ch3
- Eze MO. Metagenome analysis of a hydrocarbon-degrading bacterial consortium reveals the specific roles of BTEX biodegraders. Genes. 2021 Jan;12(1):98. https://doi.org/10.3390/genes12010098
- Francisco P Jr, Ogawa N, Suzuki K, Miyashita K. The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates. Microbiology. 2001 Jan;147(Pt_1):121–133. https://doi.org/10.1099/00221287-147-1-121
- Ganesh A, Lin J. Diesel degradation and biosurfactant production by Gram-positive isolates. Afr J Biotechnol. 2009 Nov;8(21):5847–5854. https://doi.org/10.5897/AJB09.811
- Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr;29(8):1072–1075. https://doi.org/10.1093/bioinformatics/btt086
- Ha BN, Tan TN. Integration of bioremediation and physico-chemical methods for wastewater treatment and resource recovery. In: Srivastav AL, Zinicovscaia I, Cepoi L, editors. Biotechnologies for wastewater treatment and resource recovery. Amsterdam (The Netherlands): Elsevier Inc.; 2025. p. 109–122. https://doi.org/10.1016/B978-0-443-27376-6.00002-5
- Handayani S, Safitri R, Surono W, Astika H, Damayanti R, Agung M, Rukiah. Biodegradation of BTEX by indigenous microorganisms isolated from UCG project area, South Sumatra. IOP Conf Ser Earth Environ Sci. 2019;308:012017. https://doi.org/10.1088/1755-1315/308/1/012017
- Hidde Boersma F, Colin McRoberts W, Cobb SL, Murphy CD. A 19F NMR study of fluorobenzoate biodegradation by Sphingomonas sp. HB-1. FEMS Microbiol Lett. 2004 Aug;237(2):355–361. https://doi.org/10.1111/j.1574-6968.2004.tb09717.x
- Hossain MS, Iken B, Iyer R. Whole genome analysis of 26 bacterial strains reveals aromatic and hydrocarbon degrading enzymes from diverse environmental soil samples. Sci Rep. 2024 Dec;14(1):30685. https://doi.org/10.1038/s41598-024-78564-3
- Hussain N, Mohiuddin F, Muccee F, Bunny SM, Al Haddad AHI. Isolation, molecular, and metabolic profiling of benzene-remediat-ing bacteria inhabiting the tannery industry soil. Pol J Microbiol. 2025 Mar;74(1):33–47. https://doi.org/10.33073/pjm-2025-003
- Jin A, Tursun D, Tan L, Yang Z, Duo Z, Qin Y, Zhang R. Whole genome sequencing and analysis of benzo(a)pyrene-degrading bacteria Bacillus cereus M72-4. Genome. 2025 Jan;68:1–9. https://doi.org/10.1139/gen-2024-0114
- Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019 Jul;7:e7359. https://doi.org/10.7717/peerj.7359
- Kannan P, Verma I, Banerjee B, Saleena LM. Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: A metagenomic approach. Arch Microbiol. 2023 Dec;206(1):27. https://doi.org/10.1007/s00203-023-03765-9
- Kaur G, Lecka J, Krol M, Brar SK. Novel BTEX-degrading strains from subsurface soil: Isolation, identification and growth evaluation. Environ Pollut. 2023 Oct;335:122303. https://doi.org/10.1016/j.envpol.2023.122303
- Kaur G, Sood P. Significance of biological approaches/bioremediation of wastewater treatment over physicochemical methods: a comparative analysis. In: Srivastav AL, Zinicovscaia I, Cepoi L, editors. Biotechnologies for wastewater treatment and resource recovery. Amsterdam (The Netherlands): Elsevier; 2025. p. 211-225. https://doi.org/10.1016/B978-0-443-27376-6.00027-X
- Kaur G, Verma S, Krol M, Brar SK. Analysis of benzene, toluene, ethylbenzene, xylene(s) biodegradation under anoxic conditions using response surface methodology. Int Biodeterior Biodegrad. 2025 Feb;198:105973. https://doi.org/10.1016/j.ibiod.2024.105973
- Kesavan S, Inamdar MG, Muthunarayanan V. Concentration of benzene, toluene, napthalene and acenaphthene on selected bacterial species. Mater Today Proc. 2021;37:273–279. https://doi.org/10.1016/j.matpr.2020.05.241
- Kumar L, Chugh M, Kumar S, Kumar K, Sharma J, Bharadvaja N. Remediation of petrorefinery wastewater contaminants: A review on physicochemical and bioremediation strategies. Process Saf Environ Prot. 2022 Mar;159:362–375. https://doi.org/10.1016/j.psep.2022.01.009
- Kuppan N, Padman M, Mahadeva M, Srinivasan S, Devarajan R. A comprehensive review of sustainable bioremediation techniques: Eco friendly solutions for waste and pollution management. Waste Manage Bull. 2024 Sep;2(3):154–171. https://doi.org/10.1016/j.wmb.2024.07.005
- Lee SH, Jin HM, Lee HJ, Kim JM, Jeon CO. Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59. J Bacteriol. 2012 Jan;194(2):544. https://doi.org/10.1128/JB.06436-11
- Lee Y, Lee Y, Jeon CO. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci Rep. 2019 Jan;9(1):860. https://doi.org/10.1038/s41598-018-36165-x
- Li AJ, Pal VK, Kannan K. A review of environmental occurrence, toxicity, biotransformation and biomonitoring of volatile organic compounds. Environ Chem Ecotoxicol. 2021;3;91–116. https://doi.org/10.1016/j.enceco.2021.01.001
- Li F, Wang B, Zhu B. Occupational health risk assessment and risk monetization based on xylene exposure. Ecotoxicol Environ Saf. 2025 Jan;290:117562. https://doi.org/10.1016/j.ecoenv.2024.117562
- Liaqat I, Sabri AN. Analysis of cell wall constituents of biocide-resistant isolates from dental-unit water line biofilms. Curr Microbiol. 2008 Oct;57(4):340–347. https://doi.org/10.1007/s00284-008-9200-2
- Lopez ES, Elufisan TO, Bustos P, Charles CPM, Mendoza-Herrera A, Guo X. Complete genome report of a hydrocarbon-degrading Sphingobium yanoikuyae S72. Appl Sci. 2022 Jun; 12(12):6201. https://doi.org/10.3390/app12126201
- Matheson S, Fleck R, Irga PJ, Torpy FR. Phytoremediation for the indoor environment: A state-of-the-art review. Rev Environ Sci Biotechnol. 2023;22(1):249–280. https://doi.org/10.1007/s11157-023-09644-5
- Mayz J, Manzi L, Lárez A. Isolation, characterization and identification of hydrocarbonoclastic Pseudomonas species inhabiting the rhizosphere of Crotalaria micans Link. Eur J Exp Biol. 2013;3(5):313–332.
- Mazzeo DEC, Levy CE, de Angelis Dde F, Marin-Morales MA. BTEX biodegradation by bacteria from effluents of petroleum refinery. Sci Total Environ. 2010 Sep;408(20):4334–4340. https://doi.org/10.1016/j.scitotenv.2010.07.004
- Miri S, Rasooli A, Brar SK, Rouissi T, Martel R. Biodegradation of p-xylene – a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression. Environ Sci Pollut Res Int. 2022 Mar;29(15):21465–21479. https://doi.org/10.1007/s11356-021-17387-5
- Mohamed MA, Jaafar J, Ismail AF, Othman MHD, Rahman MA. Fourier transform infrared (FTIR) spectroscopy. In: Hilal N, Ismail AF, Matsuura T, Oatley-Radcliffe D, editors. Membrane characterization. Amsterdam (The Netherlands): Elsevier; 2017. p. 3–29. https://doi.org/10.1016/B978-0-444-63776-5.00001-2
- Mohammadpour H, Shahriarinour M, Yousefi R. Benzene degradation by free and immobilized Bacillus glycinifermantans strain GO-13T using GO sheets. Pol J Environ Stud. 2020;29(4):2783–2793. https://doi.org/10.15244/pjoes/111512
- Nagda A, Meena M, Shah MP. Bioremediation of industrial effluents: A synergistic approach. J Basic Microbiol. 2022 Mar;62(3-4):395–414. https://doi.org/10.1002/jobm.202100225
- Nanda M, Kumar V, Sharma DK. Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to ‘clean-up’ heavy metal contaminants from water. Aquat Toxicol. 2019 Jul;212:1–10. https://doi.org/10.1016/j.aquatox.2019.04.011
- Neely CJ, Graham ED, Tully BJ. MetaSanity: An integrated microbial genome evaluation and annotation pipeline. Bioinformatics. 2020 Aug;36(15):4341–4344. https://doi.org/10.1093/bioinformat-ics/btaa512
- Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: A new versatile metagenomic assembler. Genome Res. 2017 May;27(5):824–834. https://doi.org/10.1101/gr.213959.116
- Ortega-González DK, Zaragoza D, Aguirre-Garrido J, Ramírez-Saad H, Hernández-Rodríguez C, Jan-Roblero J. Degradation of benzene, toluene, and xylene isomers by a bacterial consortium obtained from rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated area. Folia Microbiol. 2013 Nov;58(6):569–577. https://doi.org/10.1007/s12223-013-0248-4
- Oruko RO, Odiyo JO, Edokpayi JN. The role of leather microbes in human health. In: Chauhan NS, editor. Role of microbes in human health and diseases. London (UK): IntechOpen; 2019. https://doi.org/10.5772/intechopen.81125
- Oyewusi HA, Wahab RA, Huyop F. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Mol Biol Rep. 2021 Mar;48(3):2687–2701. https://doi.org/10.1007/s11033-021-06239-7
- Raju KS, Kumar DN. Review of approaches for selection and en-sembling of GCMs. J Water Clim Change. 2020 Sep;11(3);577–599. https://doi.org/10.2166/wcc.2020.128
- Révész F, Farkas M, Kriszt B, Szoboszlay S, Benedek T, Táncsics A. Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: Enrichment, isolation and whole-genome analysis. Environ Sci Pollut Res Int. 2020 Sep;27(25):31130–31142. https://doi.org/10.1007/s11356-020-09277-z
- Sales da Silva IG, Gomes de Almeida FC, Padilha da Rocha e Silva NM, Casazza AA, Converti A, Asfora Sarubbo L. Soil bioremediation: Overview of technologies and trends. Energies 2020;13(18):4664. https://doi.org/10.3390/en13184664
- Sathesh-Prabu C, Woo J, Kim Y, Kim SM, Lee SB, Jeon CO, Kim D, Lee SK. Comparative genomic analysis and BTEX degradation pathways of a thermotolerant Cupriavidus cauae PHS1. J Microbiol Biotechnol. 2023 Jul;33(7):875–885. https://doi.org/10.4014/jmb.2301.01011
- Schad L. Polychlorinated biphenyl (PCB) pollution of the Hudson River: Social policy and health considerations. Honors Theses. 2016:208. [cited 2025 Jan 20]. Available from https://digitalworks.union.edu/theses/208
- Schumann P, Pukall R. The discriminatory power of ribotyping as automatable technique for differentiation of bacteria. Syst Appl Microbiol. 2013 Sep;36(6):369–375. https://doi.org/10.1016/j.syapm.2013.05.003
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul;30(14):2068-9. https://doi.org/10.1093/bioin-formatics/btu153
- Sornaly HH, Ahmed S, Titin KF, Islam MN, Parvin A, Islam MA, Faruquee HM, Biswas KK, Islam R, Paul DK. The utility of bioremediation approach over physicochemical methods to detoxify dyes discharges from textile effluents: A comprehensive review study. Sustainable Chem Pharm. 2024 Jum;39:101538. https://doi.org/10.1016/j.scp.2024.101538
- Surendra SV, Mahalingam BL, Velan M. Degradation of monoaromatics by Bacillus pumilus MVSV3. Braz Arch Biol Technol. 2017;60:e16160319. https://doi.org/10.1590/1678-4324-2017160319
- Tabakova T. State of the art and challenges in complete benzene oxidation: A review. Molecules. 2024 Nov;29(22):5484. https://doi.org/10.3390/molecules29225484
- Táncsics A, Farkas M, Horváth B, Maróti G, Bradford LM, Lueders T, Kriszt B. Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT. Arch Microbiol. 2020 Mar;202(2):421–426. https://doi.org/10.1007/s00203-019-01743-8
- Undugoda L, Kandisa R, Kannangara S, Sirisena D. Plasmid encoded toluene and xylene degradation by phyllosphere bacteria. J Environ Anal Toxicol. 2018;8(2):1000559. https://doi.org/10.4172/2161-0525.1000559
- Unegg MC, Steininger KW, Ramsauer C, Rivera-Aguilar M. Assessing the environmental impact of waste management: A comparative study of CO2 emissions with a focus on recycling and incineration. J Cleaner Prod. 2023 Aug;415:137745. https://doi.org/10.1016/j.jclepro.2023.137745
- Weelink SA, Van Eekert MH, Stams AJ. Degradation of BTEX by anaerobic bacteria: Physiology and application. Rev Environ Sci Bio-technol. 2010;9:359–385. https://doi.org/10.1007/s11157-010-9219-2
- Wongbunmak A, Khiawjan S, Suphantharika M, Pongtha-rangkul T. BTEX biodegradation by Bacillus amyloliquefaciens subsp. plantarum W1 and its proposed BTEX biodegradation pathways. Sci Rep. 2020 Oct;10(1):17408. https://doi.org/10.1038/s41598-020-74570-3
- Wood DE, Salzberg SL. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014 Mar;15(3):R46. https://doi.org/10.1186/gb-2014-15-3-r46
- Wu S, Zhong J, Lei Q, Song H, Chen SF, Wahla AQ, Bhatt K, Chen S. New roles for Bacillus thuringiensis in the removal of environmental pollutants. Environ Res. 2023 Nov;236(Pt_1):116699 https://doi.org/10.1016/j.envres.2023.116699
- You J, Du M, Chen H, Zhang X, Zhang S, Chen J, Cheng Z, Chen D, Ye J. BTEX degradation by a newly isolated bacterium: Performance, kinetics, and mechanism. Int Biodeterior Biodegrad. 2018 Apr;129;202–208. https://doi.org/10.1016/j.ibiod.2018.02.012
- You L, Li Y, Huang G, Zhang J. Modeling regional ecosystem development under uncertainty – A case study for New Binhai District of Tianjin. Ecol Modell. 2014 Sep;288:127–142. https://doi.org/10.1016/j.ecolmodel.2014.06.008
- Zhang R, Ye Z, Guo X, Yang Y, Li G. Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater. Environ Int. 2024 Jun;188:108755. https://doi.org/10.1016/j.envint.2024.108755