Genomic characterization of Pseudomonas wenzhouensis A.M.S.S. isolated from oil-contaminated soil and its metabolic potential for bioremediation
Article Main
Abstract
Petroleum-contaminated soil is useful for environmental bioremediation studies because it contains many different types of microorganisms that can hydrolyze hydrocarbons and degrade sulfur-contaminated environments. This study included the isolation of Pseudomonas wenzhouensis A.M.S.S. from oil-contaminated soil in Mosul, Iraq; its taxonomic status and potential use were determined through extensive whole-genome sequencing. Whole-genome sequencing, Genome Assembly and Annotation, 16S rRNA gene phylogenetic tree, and in silico DNA-DNA Hybridization and Genetic analysis were performed on the isolate to assess its ability to degrade hydrocarbon and sulfur compounds. Genomic analysis showed that the GC content was 61.9 percent, 4.228 projected protein-coding sequences, and 50 tRNA genes, and the 4.65 Mb draft genome produced by de novo assembly demonstrated significant metabolic potential. A.M.S.S. is a unique strain and possibly a new species within the genus, according to anin silico DNA–DNA hybridization value of 60.9%, which is below the 70% species criterion, even though phylogenomic analysis (TYGS) placed the isolate closest to Pseudomonas wenzhouensis A20. A vast gene repertoire for co factor biosynthesis, stress adaptation, and the metabolism of amino acids and carbohydrates was identified through subsystem annotation. Notably, the genome encodes several aromatic compound degradation pathways, and reduction of inorganic sulfate, supporting its ability to catabolize pollutants derived from petroleum and indicating a genomic potential for the breakdown of contaminants produced from petroleum. The study provides important clues about the ecological breadth of this strain and points to its possible use in environmental biotechnology, specifically for the bioremediation of polluted ecosystems.
Article Details
Article Details
Keywords
Aromatic compound degradation, Comparative genomics, Genomic prediction of bioremediation, Sulfur metabolism
References
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Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P. A. & Hugenholtz, P. (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36(10), 996-1004. https://doi.org/10.1038/nbt.4229.
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Parte, A. C. (2014). LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res., 42, D613–D616. https://doi.org/10.1093/nar/gkt1111.
Peix, A., Ramirez-Bahena, M. H. & Velazquez, E. (2009). Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect. Genet. Evol., 9, 1132–1147. https://doi.org/10.1016/j.meegid.2009.08.001.
Pimviriyakul, P., Wongnate, T., Tinikul, R. & Chaiyen, P. (2020). Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microbial Biotechnology, 13(1), 67-86. https://doi.org/10.1111/1751-7915.13488.
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Tamura, K., Stecher, G. & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
Yanagita, H., Kanaly, R. A. & Mori, J. F. (2025). Transcriptomic profiling of Pseudomonas migulae revealed gene regulatory properties during biodegradation of aromatic hydrocarbons under cold stress. Microbial Genomics, 11(9). https://doi.org/10.1099/mgen.0.001470
Zhang, P., Dong, X., Zhou, K., Zhu, T., Liang, J., Shi, W., Gao, M., Feng, C., Li, Q., Zhang, X., Ren, P., Lu, J., Lin, X., Li, K., Zhu, M., Bao, Q. & Zhang, H. (2021). Characterization of a novel chromosome-encoded AmpC βlactamase gene, blaPRC-1, in a newly classified Pseudomonas species, Pseudomonas wenzhouensis A20, isolated from animal farm wastewater. Frontiers in Microbiology, 12, 732932. https://doi.org/10.3389/fmicb.2021.732932.
Al-Sanjary, S. I. H. & Burhan, S.T. (2025). Complete genome sequence of Niallia sp. SS-2023 isolated from oil-contaminated soil in Mosul city, Iraq. Journal of Applied and Natural Science, 17(2), 663 - 670. https://doi.org/10.31018/jans.v17i2.6518
Arias-Barrau, E., Olivera, E. R., Luengo, J. M., Fernández, C., Galán, B., García, J. L., Díaz, E. & Miñambres, B. (2004). The homogentisate pathway: A central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. Journal of Bacteriology, 186(15), 5062–5077. https://doi.org/10.1128/JB.186.15.5062-5077.2004
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M. & Meyer, F. (2008). The RAST Server: rapid
annotations using subsystems technology. BMC Genomics, 9, 1 -15. https://doi.org/10.1186/1471-2164-9-75
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D. & Pyshkin, A.V. (2012).
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19, 455-477. https://doi.org/10.1089/cmb.2012.0021
Chen, Y., Jiang, X., Zhao, J., Yang, M., Chen, Y., Ling, H., Liu, Y., Deng, F. & Wang, Z. (2025). Microbial response under sulfate stress in a sulfur-based autotrophic denitrification system. Frontiers in Microbiology, 16, 1615317. https://doi.org/10.3389/fmicb.2025.1615317
Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X.-W., De Meyer, S. & Trujillo, M. E. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 68(1), 461–466. https://doi.org/10.1099/ijsem.0.002516
Das, N. & Chandran, P. (2021). Microbial degradation of petroleum hydrocarbon contaminants: An overview. Biodegradation, 32(2), 71–88. https://doi.org/10.1007/s10532-020-09910-5
de Sousa, T., Hébraud, M., Enes Dapkevicius, M. L. N., Maltez, L., Pereira, J. E., Capita, R., Alonso-Calleja, C., Igrejas, G. & Poeta, P. (2021). Genomic and metabolic characteristics of the pathogenicity in Pseudomonas aeruginosa. International Journal of Molecular Sciences, 22(23), 12892. https://doi.org/10.3390/ijms222312892
Espinosa-Camacho, L. F., Delgado, G., Cravioto, A. & Morales-Espinosa, R. (2022). Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains. Genes & Genomics, 44(1), 53-77. https://doi.org/10.1007/s13258-021-01155-3.
Gupta, R. S., Patel, S., Saini, N. & Chen, S. (2020). Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the subtilis and Cereus clades of species. Int. J. Syst. Evol. Microbiol., 70, 5753–5798. https://doi.org/10.1099/ijsem.0.004475.
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075. https://doi.org/10.1093/bioinformatics/btt086
Hossain, M. S., Iken, B. & Iyer, R. (2024). Whole genome analysis of 26 bacterial strains reveals aromatic and hydrocarbon degrading enzymes from diverse environmental soil samples. Scientific Reports, 14(1), 30685. https://doi.org/10.1038/s41598-024-78564-3.
Lefort, V., Desper, R. & Gascuel, O. (2015). FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Molecular Biology and Evolution, 32(10), 2798-2800. https://doi.org/10.1093/molbev/msv150.
Meier-Kolthoff, J. P. & Göker, M. (2019). TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications, 10(1), 2182. https://doi.org/10.1038/s41467-019-10210-3
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H.-P. & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60. https://doi.org/10.1186/1471-2105-14-60.
Meier-Kolthoff, J. P., Carbasse, J. S., Peinado-Olarte, R. L. & Göker, M. (2022). TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Research, 50(D1), D801-D807. https://doi.org/10.1093/nar/gkab902.
Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., McNeil,L. K., Paarmann, D., Osterman, A. L., Meyer, F., Formsma, K., Kubal, M., Gerdes, S.,
Glass, E. M., Prjibelski, A. D., Aziz, R. K., DeJongh, M., Ben Zakour, N. L. & Stevens, R. (2014). The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Research, 42, D206-D214. https://doi.org/10.1093/nar/gkt1226
Palleroni, N. J. (2015) Pseudomonas in Bergey’s manual of systematics of archaea and bacteria. Whitman, W.B., Aharal, D.R., Christensen, H., Chuvochina, M., Dedysh, S., Gasparich, G.E., et al. (eds) Hoboken, NJ: John Wiley & Sons, Inc. 1-105.
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P. A. & Hugenholtz, P. (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36(10), 996-1004. https://doi.org/10.1038/nbt.4229.
Parte, A. C., Sardà Carbasse, J., Meier-Kolthoff, J. P., Reimer, L. C. & Göker, M. (2020). List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70(11), 5607-5612. https://doi.org/10.1099/ijsem.0.004332.
Parte, A. C. (2014). LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res., 42, D613–D616. https://doi.org/10.1093/nar/gkt1111.
Peix, A., Ramirez-Bahena, M. H. & Velazquez, E. (2009). Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect. Genet. Evol., 9, 1132–1147. https://doi.org/10.1016/j.meegid.2009.08.001.
Pimviriyakul, P., Wongnate, T., Tinikul, R. & Chaiyen, P. (2020). Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microbial Biotechnology, 13(1), 67-86. https://doi.org/10.1111/1751-7915.13488.
Richter, M. & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences, 106(45), 19126-19131. https://doi.org/10.1073/pnas.0906412106.
Rossi, E., La Rosa, R., Bartell, J. A., Marvig, R. L., Haagensen, J. A., Sommer, L. M. & Johansen, H. K. (2021). Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nature Reviews Microbiology, 19(5), 331-342. https://doi.org/10.1038/s41579-020-00477-5.
Saati-Santamaría, Z., Baroncelli, R., Rivas, R. & García-Fraile, P. (2022). Comparative genomics of the genus Pseudomonas reveals host- and environment-specific evolution. Microbiology Spectrum, 10(6), e0237022. https://doi.org/10.1128/spectrum.02370-22
Safari, M., Yakhchali, B. & Shariati J, V. (2019). Comprehensive genomic analysis of an indigenous Pseudomonas pseudoalcaligenes degrading phenolic compounds. Scientific Reports, 9(1), 12736. https://doi.org/10.1038/s41598-019-49048-6
Sayers, E. W., Agarwala, R., Bolton, E. E., Brister, J. R., Canese, K., Clark, K., Connor, R., Fiorini, N., Funk, K., Hefferon, T., Holmes, J. B., Kim, S., Kimchi, A., Kitts, P. A., Lathrop, S., Lu, Z., Madden, T. L., Marchler-Bauer, A., Phan, L., Schneider, V. A., Schoch, C. L., Pruitt, K. D. & Ostell, J. (2019). Database resources of the national center for biotechnology Information. Nucleic Acids Research, 47(D1), D23–D28. https://doi.org/10.1093/nar/gky1069.
Stothard, P., Grant, J. R. & Van Domselaar, G. (2019). Visualizing and comparing circular genomes using the CGView family of tools. Briefings in Bioinformatics, 20(4), 1576-1582. https://doi.org/10.1093/bib/bbx081.
Tamura, K., Stecher, G. & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
Yanagita, H., Kanaly, R. A. & Mori, J. F. (2025). Transcriptomic profiling of Pseudomonas migulae revealed gene regulatory properties during biodegradation of aromatic hydrocarbons under cold stress. Microbial Genomics, 11(9). https://doi.org/10.1099/mgen.0.001470
Zhang, P., Dong, X., Zhou, K., Zhu, T., Liang, J., Shi, W., Gao, M., Feng, C., Li, Q., Zhang, X., Ren, P., Lu, J., Lin, X., Li, K., Zhu, M., Bao, Q. & Zhang, H. (2021). Characterization of a novel chromosome-encoded AmpC βlactamase gene, blaPRC-1, in a newly classified Pseudomonas species, Pseudomonas wenzhouensis A20, isolated from animal farm wastewater. Frontiers in Microbiology, 12, 732932. https://doi.org/10.3389/fmicb.2021.732932.
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Genomic characterization of Pseudomonas wenzhouensis A.M.S.S. isolated from oil-contaminated soil and its metabolic potential for bioremediation. (2026). Journal of Applied and Natural Science, 18(1), 212-221. https://doi.org/10.31018/jans.v18i1.7208
