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Volume 73, Issue 9

sp. nov., isolated from soil, exhibiting high-efficiency degradation of benzo(a)pyrene Open Access

Abstract

A Gram-negative, yellow-pigmented, aerobic and rod-shaped bacterium, designated as strain BaP3, was isolated from the soil. Strain BaP3 grew at 16–37℃ (optimum, 30 °C) and pH 6.0–8.0 (optimum, pH 7.0). Additionally, strain BaP3 could tolerate NaCl concentrations in the range 0–6 % (optimum, 1%). Moreover, strain BaP3 was motile by flagella. The phylogenetic analysis of 16S rRNA sequences showed that strain BaP3 belonged to the genus , and the sequence was most closely related to CGMCC 1.3392 and DSM 15758, with 99.66 % sequence similarity. RY24 was the next closely related species, exhibiting 99.38 % 16S rRNA gene sequence similarity. The DNA–DNA hybridization and average nucleotide identity values between strain BaP3 and its closely related types were below 50 and 92 %, respectively. Both results were below the cut-off for species distinction. The genomic DNA G+C content of strain BaP3 was 65.30 mol%. The predominant quinone in strain BaP3 was identified as ubiquinone Q-9. The major cellular fatty acids were summed feature 8 (C 7 and/or C 6), summed feature 3 (C 7 and/or C 6) and C. These results indicated that strain BaP3 represents a novel species in the genus . The type strain is BaP3 (CCTCC AB 2022379=JCM 35914), for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): benzo(a)pyrene , biodegradation , PAHs and Pseudomonas benzopyrenica
Funding
This study was supported by the:
  • National Infrastructure of Natural Resources for Science and Technology Program of China (Award NIMR-2022-8)
    • Principle Award Recipient: ZhixiongXie
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-09-19
2024-05-08
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References

  1. Migula W. Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
     [Google Scholar]
  2. Kim CM, Jeong JW, Lee DH, Kim SB. Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2021; 71:11 [View Article] [PubMed]
     [Google Scholar]
  3. Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic analyses of the genus Pseudomonas lead to the rearrangement of several species and the definition of new genera. Biology 2021; 10:782 [View Article] [PubMed]
     [Google Scholar]
  4. Lalucat J, Gomila M, Mulet M, Zaruma A, García-Valdés E. Past, present and future of the boundaries of the Pseudomonas genus: proposal of Stutzerimonas gen. nov. Syst Appl Microbiol 2022; 45:126289 [View Article] [PubMed]
     [Google Scholar]
  5. Gross H, Loper JE. Genomics of secondary metabolite production by Pseudomonas spp. Nat Prod Rep 2009; 26:1408–1446 [View Article] [PubMed]
     [Google Scholar]
  6. Jiang Y, Huang H, Wu M, Yu X, Chen Y et al. Pseudomonas sp. LZ-Q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system. Biophys Rep 2015; 1:156–167 [View Article] [PubMed]
     [Google Scholar]
  7. Prabhu Y, Phale PS. Biodegradation of phenanthrene by Pseudomonas sp. strain PP2: novel metabolic pathway, role of biosurfactant and cell surface hydrophobicity in hydrocarbon assimilation. Appl Microbiol Biotechnol 2003; 61:342–351 [View Article] [PubMed]
     [Google Scholar]
  8. Wang W, Wang L, Shao Z. Polycyclic aromatic hydrocarbon (PAH) degradation pathways of the obligate marine PAH degrader Cycloclasticus sp. strain P1. Appl Environ Microbiol 2018; 84:e01261-18 [View Article] [PubMed]
     [Google Scholar]
  9. Sivaram AK, Logeshwaran P, Lockington R, Naidu R, Megharaj M. Impact of plant photosystems in the remediation of benzo[a]pyrene and pyrene spiked soils. Chemosphere 2018; 193:625–634 [View Article] [PubMed]
     [Google Scholar]
  10. Lu Q, Chen K, Long Y, Liang X, He B et al. Benzo(a)pyrene degradation by cytochrome P450 hydroxylase and the functional metabolism network of Bacillus thuringiensis. J Hazard Mater 2019; 366:329–337 [View Article] [PubMed]
     [Google Scholar]
  11. Kadri T, Rouissi T, Kaur Brar S, Cledon M, Sarma S et al. Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: a review. J Environ Sci 2017; 51:52–74 [View Article] [PubMed]
     [Google Scholar]
  12. Ridgway HF, Safarik J, Phipps D, Carl P, Clark D. Identification and catabolic activity of well-derived gasoline-degrading bacteria from a contaminated aquifer. Appl Environ Microbiol 1990; 56:3565–3575 [View Article] [PubMed]
     [Google Scholar]
  13. Xue SW, Tian YX, Pan JC, Liu YN, Ma YL. Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1. Sci Rep 2021; 11:21317 [View Article] [PubMed]
     [Google Scholar]
  14. Mawad AMM, Abdel-Mageed WS, Hesham AE-L. Quantification of naphthalene dioxygenase (NahAC) and catechol dioxygenase (C23O) catabolic genes produced by phenanthrene-degrading Pseudomonas fluorescens AH-40. Curr Genomics 2020; 21:111–118 [View Article] [PubMed]
     [Google Scholar]
  15. Qin R, Xu T, Jia X. Engineering Pseudomonas putida to produce rhamnolipid biosurfactants for promoting phenanthrene biodegradation by a two-species microbial consortium. Microbiol Spectr 2022; 10:e0091022 [View Article] [PubMed]
     [Google Scholar]
  16. Oyehan TA, Al-Thukair AA. Isolation and characterization of PAH-degrading bacteria from the Eastern Province, Saudi Arabia. Mar Pollut Bull 2017; 115:39–46 [View Article] [PubMed]
     [Google Scholar]
  17. Amy PS, Hiatt HD. Survival and detection of bacteria in an aquatic environment. Appl Environ Microbiol 1989; 55:788–793 [View Article] [PubMed]
     [Google Scholar]
  18. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  25. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12:59–60 [View Article] [PubMed]
     [Google Scholar]
  26. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  29. Zhang D-F, Cui X-W, Zhao Z, Zhang A-H, Huang J-K et al. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie van Leeuwenhoek 2020; 113:1523–1530 [View Article] [PubMed]
     [Google Scholar]
  30. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  31. Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in bacterial taxonomy: impact on the genus Pseudomonas. Genes 2020; 11:139 [View Article] [PubMed]
     [Google Scholar]
  32. Hauser E, Kämpfer P, Busse HJ. Pseudomonas psychrotolerans sp. nov. Int J Syst Evol Microbiol 2004; 54:1633–1637 [View Article] [PubMed]
     [Google Scholar]
  33. Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of changes in taxonomic opinion no. 35. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  34. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 2014; 42:D231–9 [View Article] [PubMed]
     [Google Scholar]
  35. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2019; 362251–2252 [View Article]
     [Google Scholar]
  36. Liang C, Huang Y, Wang H. pahE, a functional marker gene for polycyclic aromatic hydrocarbon-degrading bacteria. Appl Environ Microbiol 2019; 85:e02399-18 [View Article] [PubMed]
     [Google Scholar]
  37. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  38. Sedkova N, Tao L, Rouvière PE, Cheng Q. Diversity of carotenoid synthesis gene clusters from environmental Enterobacteriaceae strains. Appl Environ Microbiol 2005; 71:8141–8146 [View Article] [PubMed]
     [Google Scholar]
  39. Gao J, Xie G, Peng F, Xie Z. Pseudomonas donghuensis sp. nov., exhibiting high-yields of siderophore. Antonie van Leeuwenhoek 2015; 107:83–94 [View Article] [PubMed]
     [Google Scholar]
  40. Huq MA. Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden. Arch Microbiol 2018; 200:343–348 [View Article] [PubMed]
     [Google Scholar]
  41. Wang X, He S, Guo H-B, Thin KK, Gao J et al. Pseudomonas rhizoryzae sp. nov., isolated from rice. Int J Syst Evol Microbiol 2020; 70:944–950 [View Article]
     [Google Scholar]
  42. Cappuccino J, Sherman N. Microbiology: A Laboratory Manual: International Edition 2010
     [Google Scholar]
  43. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  44. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article] [PubMed]
     [Google Scholar]
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Pseudomonas benzopyrenica sp. nov., isolated from soil, exhibiting high-efficiency degradation of benzo(a)pyrene
Int J Syst Evol Microbiol 73, 006034 (2023); https://doi.org/10.1099/ijsem.0.006034
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