Skip to content
2000
  1. Home
  2. A-Z Publications
  3. Current Genomics
  4. Fast Track Articles
  5. Fast Track Article
image of Characterization and Genomic Analysis of Arthrobacter sp. SF27: A Promising Dibutyl Phthalate-degrading Strain

Abstract

Background

Phthalic acid esters (PAEs) are widely used chemical compounds in various industries. However, PAEs are also a major source of pollution in soil and aquatic ecosystems, posing a significant environmental threat. Microbial degradation is a very effective way to remove phthalic acid esters from a polluted environment.

Objectives

The aims of this study were to investigate the ability of the strain sp. SF27 (=VKM Ac-2063) to degrade PAEs (specifically, dibutyl phthalate (DBF)); to annotate the complete genome of the strain SF27 (GenBank accession number GCA_012952295); to identify genes (gene clusters) potentially involved in the degradation of DBF and its major degradation product, phthalic acid (PA).

Methods

The ability of the strain SF27 to use DBP as the only source of carbon and energy was determined by cultivating it on a mineral medium containing 0.5–4 g/L DBP. The evaluation of the bacterial decomposition of DBP was carried out by GC-MS. The genome was annotated using the JGI Microbial Genome Annotation Pipeline (MGAP) (https://jgi.doe.gov/). Functional annotation was performed using various databases: KEGG, COG, NCBI, and GO. The Mauve program was used to compare the strain SF27 genome and the genomes of the closest DBP-degrading strains.

Results

The strain sp. SF27 is capable of growing on DBP as the sole source of carbon and energy at high concentrations (up to 4 g/L). The strain was able to degrade 60% of DBP (initial concentration of 1 g/L) and 20% of DBP (initial concentration of 3 g/L) within 72 hours. The genome analysis of the strain SF27 (GenBank accession number GCA_012952295) identified genes encoding hydrolases potentially involved in the initial stages of DBP degradation, leading to the formation of PA. Additionally, a cluster of genes encoding enzymes that are responsible for the transformation of PA into protocatechuic acid (PCA) has been identified and described in the genome. Based on genome analysis and cultural experiments, a complete pathway for the degradation of PA by the strain sp. SF27 into basal metabolic compounds of the cell has been proposed.

Conclusion

Based on the conducted research, it can be stated that the strain sp. SF27 is an efficient of , promising for the development of biotechnologies aimed at the restoration of ecosystems contaminated with DBP.

© 2025 Bentham Science Publishers
Loading

Article metrics loading...

/content/journals/cg/10.2174/0113892029343036250210044540
2025-03-14
2025-05-13

  • From This Site

    /content/journals/cg/10.2174/0113892029343036250210044540
    dcterms_title,dcterms_subject,pub_keyword
    -contentType:Contributor -contentType:Concept -contentType:Institution
    10
    5
Loading full text...

Full text loading...

References

  1. Naveen K.V. Saravanakumar K. Zhang X. Sathiyaseelan A. Wang M.H. Impact of environmental phthalate on human health and their bioremediation strategies using fungal cell factory- A review. Environ. Res. 2022 214 Pt 1 113781 10.1016/j.envres.2022.113781 35780847
    [Google Scholar]
  2. Liu Y. Chen Z. Shen J. Occurrence and removal characteristics of phthalate esters from typical water sources in northeast china. J. Anal. Methods Chem. 2013 2013 1 8 10.1155/2013/419349 23577281
    [Google Scholar]
  3. Staples C.A. Parkerton T.F. Peterson D.R. A risk assessment of selected phthalate esters in North American and Western European surface waters. Chemosphere 2000 40 8 885 891 10.1016/S0045‑6535(99)00315‑X 10718582
    [Google Scholar]
  4. Benjamin S. Masai E. Kamimura N. Takahashi K. Anderson R.C. Faisal P.A. Phthalates impact human health: Epidemiological evidences and plausible mechanism of action. J. Hazard. Mater. 2017 340 360 383 10.1016/j.jhazmat.2017.06.036 28800814
    [Google Scholar]
  5. Yang T. Ren L. Jia Y. Fan S. Wang J. Wang J. Nahurira R. Wang H. Yan Y. Biodegradation of di-(2-ethylhexyl) phthalate by Rhodococcus ruber YC-YT1 in contaminated water and soil. Int. J. Environ. Res. Public Health 2018 15 5 964 10.3390/ijerph15050964 29751654
    [Google Scholar]
  6. Gadupudi C.K. Rice L. Xiao L. Kantamaneni K. Endocrine disrupting compounds removal methods from wastewater in the United Kingdom: a review. Sci 2021 3 1 11 10.3390/sci3010011
    [Google Scholar]
  7. Roccuzzo S. Beckerman A.P. Trögl J. New perspectives on the bioremediation of endocrine disrupting compounds from wastewater using algae-, bacteria- and fungi-based technologies. Int. J. Environ. Sci. Technol. 2021 18 1 89 106 10.1007/s13762‑020‑02691‑3
    [Google Scholar]
  8. Liang D.W. Zhang T. Fang H.H.P. He J. Phthalates biodegradation in the environment. Appl. Microbiol. Biotechnol. 2008 80 2 183 198 10.1007/s00253‑008‑1548‑5 18592233
    [Google Scholar]
  9. Cheng J. Liu Y. Wan Q. Yuan L. Yu X. Degradation of dibutyl phthalate in two contrasting agricultural soils and its long-term effects on soil microbial community. Sci. Total Environ. 2018 640-641 821 829 10.1016/j.scitotenv.2018.05.336 29879668
    [Google Scholar]
  10. Feng N.X. Feng Y.X. Liang Q.F. Chen X. Xiang L. Zhao H.M. Liu B.L. Cao G. Li Y.W. Li H. Cai Q.Y. Mo C.H. Wong M.H. Complete biodegradation of di-n-butyl phthalate (DBP) by a novel Pseudomonas sp. YJB6. Sci. Total Environ. 2021 761 761 143208 10.1016/j.scitotenv.2020.143208 33162130
    [Google Scholar]
  11. Yastrebova O.V. Pyankova A.A. Plotnikova E.G. Phthalate-degrading bacteria isolated from an industrial mining area and the processing of potassium and magnesium salts. Appl. Biochem. Microbiol. 2019 55 4 397 404 10.1134/S000368381904015X
    [Google Scholar]
  12. Patil N.K. Karegoudar T.B. Parametric studies on batch degradation of a plasticizer di-n-butylphthalate by immobilized Bacillus sp. World J. Microbiol. Biotechnol. 2005 21 8-9 1493 1498 10.1007/s11274‑005‑7369‑0
    [Google Scholar]
  13. Fan S. Li C. Guo J. Johansen A. Liu Y. Feng Y. Xue J. Li Z. Biodegradation of phthalic acid esters (PAEs) by Bacillus sp. LUNF1 and characterization of a novel hydrolase capable of catalyzing PAEs. Environ. Technol. Innov. 2023 32 103269 10.1016/j.eti.2023.103269
    [Google Scholar]
  14. Xu Y. Liu X. Zhao J. Huang H. Wu M. Li X. Li W. Sun X. Sun B. An efficient phthalate ester-degrading Bacillus subtilis: Degradation kinetics, metabolic pathway, and catalytic mechanism of the key enzyme. Environ. Pollut. 2021 273 116461 10.1016/j.envpol.2021.116461 33485001
    [Google Scholar]
  15. Shariati S. Ebenau-Jehle C. Pourbabaee A.A. Alikhani H.A. Rodriguez-Franco M. Agne M. Jacoby M. Geiger R. Shariati F. Boll M. Degradation of dibutyl phthalate by Paenarthrobacter sp. Shss isolated from Saravan landfill, Hyrcanian Forests, Iran. Biodegradation 2022 33 1 59 70 10.1007/s10532‑021‑09966‑7 34751871
    [Google Scholar]
  16. Li C. Liu C. Li R. Liu Y. Xie J. Li B. Biodegradation of dibutyl phthalate by the New Strain Acinetobacter baumannii DP-2. Toxics 2022 10 9 532 10.3390/toxics10090532 36136497
    [Google Scholar]
  17. Jin D. Kong X. Liu H. Wang X. Deng Y. Jia M. Yu X. Characterization and cenomic analysis of a highly efficient dibutyl phthalate-degrading bacterium Gordonia sp. strain QH-12. Int. J. Mol. Sci. 2016 17 7 1012 10.3390/ijms17071012 27347943
    [Google Scholar]
  18. Liu T. Li J. Qiu L. Zhang F. Linhardt R.J. Zhong W. Combined genomic and transcriptomic analysis of the dibutyl phthalate metabolic pathway in Arthrobacter sp. ZJUTW. Biotechnol. Bioeng. 2020 117 12 3712 3726 10.1002/bit.27524 32740909
    [Google Scholar]
  19. Nandi M. Paul T. Kanaujiya D.K. Baskaran D. Pakshirajan K. Pugazhenthi G. Biodegradation of benzyl butyl phthalate and dibutyl phthalate by Arthrobacter sp. via micellar solubilization in a surfactant-aided system. Water Sci. Technol. Water Supply 2021 21 5 2084 2098 10.2166/ws.2020.347
    [Google Scholar]
  20. Wang Y. Miao B. Hou D. Wu X. Peng B. Biodegradation of di-n-butyl phthalate and expression of the 3,4-phthalate dioxygenase gene in Arthrobacter sp. ZH2 strain. Process Biochem. 2012 47 6 936 940 10.1016/j.procbio.2012.02.027
    [Google Scholar]
  21. Wen Z.D. Gao D.W. Wu W.M. Biodegradation and kinetic analysis of phthalates by an Arthrobacter strain isolated from constructed wetland soil. Appl. Microbiol. Biotechnol. 2014 98 10 4683 4690 10.1007/s00253‑014‑5568‑z 24522730
    [Google Scholar]
  22. Hu T. Yang C. Hou Z. Liu T. Mei X. Zheng L. Zhong W. Phthalate esters metabolic strain Gordonia sp. GZ-YC7, a potential soil degrader for high concentration di-(2-ethylhexyl) phthalate. Microorganisms 2022 10 3 641 10.3390/microorganisms10030641 35336217
    [Google Scholar]
  23. Ren L. Lin Z. Liu H. Hu H. Bacteria-mediated phthalic acid esters degradation and related molecular mechanisms. Appl. Microbiol. Biotechnol. 2018 102 3 1085 1096 10.1007/s00253‑017‑8687‑5 29238874
    [Google Scholar]
  24. Eaton R.W. Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J. Bacteriol. 2001 183 12 3689 3703 10.1128/JB.183.12.3689‑3703.2001 11371533
    [Google Scholar]
  25. Stanislauskienė R. Rudenkov M. Karvelis L. Gasparavičiūtė R. Meškienė R. Časaitė V. Meškys R. Analysis of phthalate degradation operon from Arthrobacter sp. 68b. Biologija (Vilnius) 2011 57 2 45 54 10.6001/biologija.v57i2.1828
    [Google Scholar]
  26. Plotnikova E.G. Altyntseva O.V. Kosheleva I.A. Puntus I.F. Filonov A.E. Gavrish E.Y. Demakov V.A. Boronin A.M. Bacterial degraders of polycyclic aromatic hydrocarbons isolated from salt-contaminated soils and bottom sediments in salt mining areas. Microbiology 2001 70 1 51 58 10.1023/A:1004892804670 11338837
    [Google Scholar]
  27. Plotnikova E.G. Yastrebova O.V. Anan’ina L.N. Dorofeeva L.V. Lysanskaya V.Y. Demakov V.A. Halotolerant bacteria of the genus Arthrobacter degrading polycyclic aromatic hydrocarbons. Russ. J. Ecol. 2011 42 6 502 509 10.1134/S1067413611060130
    [Google Scholar]
  28. Yastrebova O.V. Korsakova E.S. Plotnikova E.G. Characteristics of bacteria of Micrococcaceae family, isolated from different biotopes of salt mining area (Perm region). Izvestia of RAS SamSC(Russia) 2018 20 5 300 306
    [Google Scholar]
  29. Raymond R.L. Microbial oxidation of n-paraffinic hydrocarbons. Dev. Ind. Microbiol. 1961 2 23 32
    [Google Scholar]
  30. Yastrebova O.V. Malysheva A.A. Plotnikova E.G. Halotolerant terephthalic acid-degrading bacteria of the genus Glutamicibacter. Appl. Biochem. Microbiol. 2022 58 5 590 597 10.1134/S0003683822050167
    [Google Scholar]
  31. Gerhardt P. Murray R. G. E. Costilow R. N. Nester E. W. Wood W. A. Krieg N. R. Phillips G. Manual of methods for general bacteriology Amer. Soci. microbiol. 1981 1 21 33 10.1136/jcp.34.9.1069‑c
    [Google Scholar]
  32. Wilson K. Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol. 2001 Chapter 2 4 18265184
    [Google Scholar]
  33. Andrews S. FastQC: A quality control tool for high throughput sequence data. 2010 Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    [Google Scholar]
  34. Bolger A.M. Lohse M. Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014 30 15 2114 2120 10.1093/bioinformatics/btu170 24695404
    [Google Scholar]
  35. 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. Sirotkin A.V. Vyahhi N. Tesler G. Alekseyev M.A. Pevzner P.A. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012 19 5 455 477 10.1089/cmb.2012.0021 22506599
    [Google Scholar]
  36. Mavromatis K. Ivanova N.N. Chen I.M.A. Szeto E. Markowitz V.M. Kyrpides N.C. The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand. Genomic Sci. 2009 1 1 63 67 10.4056/sigs.632 21304638
    [Google Scholar]
  37. Chen F. Chen Y. Chen C. Feng L. Dong Y. Chen J. Lan J. Hou H. High-efficiency degradation of phthalic acid esters (PAEs) by Pseudarthrobacter defluvii E5: Performance, degradative pathway, and key genes. Sci. Total Environ. 2021 794 148719 10.1016/j.scitotenv.2021.148719 34214821
    [Google Scholar]
  38. Kumar V. Sharma N. Maitra S.S. Comparative study on the degradation of dibutyl phthalate by two newly isolated Pseudomonas sp. V21b and Comamonas sp. 51F. Biotechnol. Rep. 2017 15 1 10 10.1016/j.btre.2017.04.002 28580302
    [Google Scholar]
  39. Vandera E. Samiotaki M. Parapouli M. Panayotou G. Koukkou A.I. Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose. J. Proteomics 2015 113 73 89 10.1016/j.jprot.2014.08.018
    [Google Scholar]
/content/journals/cg/10.2174/0113892029343036250210044540
Loading
Characterization and Genomic Analysis of Arthrobacter sp. SF27: A Promising Dibutyl Phthalate-degrading Strain
Bentham Science Publishers ; https://doi.org/10.2174/0113892029343036250210044540
/content/journals/cg/10.2174/0113892029343036250210044540
/content/journals/cg/10.2174/0113892029343036250210044540
Loading

Data & Media loading...

Supplements

Supplementary material is available on the publisher's website along with the published article.

file format download Download

  • Article Type:     Research Article
Keywords: degradation ; Phthalic acid esters ; genome ; dibutyl phthalate ; Arthrobacter

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test