Skip to main content
SpringerLink
Log in

Identification and Genetic Characterization of Phenol-Degrading Bacteria from Leaf Microbial Communities

  • Original Article
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Microbial communities on aerial plant leaves may contribute to the degradation of organic air pollutants such as phenol. Epiphytic bacteria capable of phenol degradation were isolated from the leaves of green ash trees grown at a site rich in airborne pollutants. Bacteria from these communities were subjected, in parallel, to serial enrichments with increasing concentrations of phenol and to direct plating followed by a colony autoradiography screen in the presence of radiolabeled phenol. Ten isolates capable of phenol mineralization were identified. Based on 16S rDNA sequence analysis, these isolates included members of the genera Acinetobacter, Alcaligenes, and Rhodococcus. The sequences of the genes encoding the large subunit of a multicomponent phenol hydroxylase (mPH) in these isolates indicated that the mPHs of the gram-negative isolates belonged to a single kinetic class, and that is one with a moderate affinity for phenol; this affinity was consistent with the predicted phenol levels in the phyllosphere. PCR amplification of genes for catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) in combination with a functional assay for C23O activity provided evidence that the gram-negative strains had the C12O−, but not the C23O−, phenol catabolic pathway. Similarly, the Rhodococcus isolates lacked C23O activity, although consensus primers to the C12O and C23O genes of Rhodococcus could not be identified. Collectively, these results demonstrate that these leaf surface communities contained several taxonomically distinct phenol-degrading bacteria that exhibited diversity in their mPH genes but little diversity in the catabolic pathways they employ for phenol degradation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. Abd-El-Haleem D, Moawad H, Zaki EA, Zaki S (2002) Molecular characterization of phenol-degrading bacteria isolated from different Egyptian ecosystems. Microb Ecol 43:217–224

    Article  PubMed  CAS  Google Scholar 

  2. Arutchelvan V, Kanakasabai V, Nagarajan S, Muralikrishnan V (2005) Isolation and identification of novel high strength phenol degrading bacterial strains from phenol-formaldehyde resin manufacturing industrial wastewater. J Hazard Mater 127:238–243

    Article  PubMed  CAS  Google Scholar 

  3. Agency for Toxic Substances and Disease Registry (ATSDR) (1998) Toxicological profile for phenol. In: U. S. Department of Health and Human Services, Public Health Service, Atlanta, GA

  4. Barac T, Taghavi S, Borremans B, Provoost A, Oeyen L, Colpaert JV, Vangronsveld J, van der Lelie D (2004) Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotechnol 22:583–588

    Article  PubMed  CAS  Google Scholar 

  5. Barbe V, Vallenet D, Fonknechten N, Kreimeyer A, Oztas S, Labarre L, Cruveiller S, Robert C, Duprat S, Wincker P, Ornston LN, Weissenbach J, Marliere P, Cohen GN, Medigue C (2004) Unique features revealed by the genome sequence of Acinetobacter sp ADP1, a versatile and naturally transformation competent bacterium. Nucl Acids Res 32:5766–5779

    Article  PubMed  CAS  Google Scholar 

  6. Basile LA, Erijman L (2008) Quantitative assessment of phenol hydroxylase diversity in bioreactors using a functional gene analysis. Appl Microbiol Biotechnol 78:863–872

    Article  PubMed  CAS  Google Scholar 

  7. Chen CL, Wu JH, Liu WT (2008) Identification of important microbial populations in the mesophilic and thermophilic phenol-degrading methanogenic consortia. Water Res 42:1963–1976

    Article  PubMed  CAS  Google Scholar 

  8. Cohen MF, Meziane T, Yamasaki H (2004) A photocarotogenic Rhodococcus sp. isolated from the symbiotic fern Azolla. Endocytobiosis Cell Res 15:350–355

    Google Scholar 

  9. De Kempeneer L, Sercu B, Vanbrabant W, Van Langenhove H, Verstraete W (2004) Bioaugmentation of the phyllosphere for the removal of toluene from indoor air. Appl Microbiol Biotechnol 64:284–288

    Article  PubMed  CAS  Google Scholar 

  10. DeRito CM, Pumphrey GM, Madsen EL (2005) Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol 71:7858–7865

    Article  PubMed  CAS  Google Scholar 

  11. El-Sayed WS, Ibrahim MK, Abu-Shady M, El-Beih F, Ohmura N, Saiki H, Ando A (2003) Isolation and characterization of phenol-catabolizing bacteria from a coking plant. Biosci Biotechnol Biochem 67:2026–2029

    Article  PubMed  CAS  Google Scholar 

  12. Filonov AE, Duetz WA, Karpov AV, Gaiazov RR, Kosheleva IA, Breure AM, Filonova IF, van Andel JG, Boronin AM (1997) Competition of plasmid-bearing Pseudomonas putida strains catabolizing naphthalene via various pathways in chemostat culture. Appl Microbiol Biotechnol 48:493–498

    Article  PubMed  CAS  Google Scholar 

  13. Futamata H, Harayama S, Watanabe K (2001) Diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria. Appl Microbiol Biotechnol 55:248–253

    Article  PubMed  CAS  Google Scholar 

  14. Futamata H, Harayama S, Watanabe K (2001) Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. Appl Environ Microbiol 67:4671–4677

    Article  PubMed  CAS  Google Scholar 

  15. Garcia MT, Ventosa A, Mellado E (2005) Catabolic versatility of aromatic compound-degrading halophilic bacteria. FEMS Microbiol Ecol 54:97–109

    Article  PubMed  CAS  Google Scholar 

  16. Heinaru E, Truu J, Stottmeister U, Heinaru A (2000) Three types of phenol and p-cresol catabolism in phenol- and p-cresol-degrading bacteria isolated from river water continuously polluted with phenolic compounds. FEMS Microbiol Ecol 31:195–205

    Article  PubMed  CAS  Google Scholar 

  17. Ilori MO, Amund OO, Ezeani CK, Omoijiahina S, Adebusoye SA (2006) Occurrence and growth potentials of hydrocarbon degrading bacteria on the phylloplane of some tropical plants. Afric J Biotechnol 5:542–545

    CAS  Google Scholar 

  18. Jiang HL, Tay STL, Maszenan AM, Tay JH (2006) Physiological traits of bacterial strains isolated from phenol-degrading aerobic granules. FEMS Microbiol Ecol 57:182–191

    Article  PubMed  CAS  Google Scholar 

  19. Jiang Y, Wen JP, Li HM, Yang SL, Hu ZD (2005) The biodegradation of phenol at high initial concentration by the yeast Candida tropicalis. Biochem Eng J 24:243–247

    Article  CAS  Google Scholar 

  20. Jurkevitch EJ, Shapira G (2000) Structure and colonization dynamics of epiphytic bacterial communities and of selected component strains on tomato (Lycopersicon esculentum) leaves. Microb Ecol 40:300–308

    PubMed  Google Scholar 

  21. Kadivar H, Stapleton AE (2003) Ultraviolet radiation alters maize phyllosphere bacterial diversity. Microb Ecol 45:353–361

    Article  PubMed  CAS  Google Scholar 

  22. Larkin MJ, Kulakov LA, Allen CCR (2005) Biodegradation and Rhodococcus—masters of catabolic versatility. Curr Opin Biotechnol 16:282–290

    Article  PubMed  CAS  Google Scholar 

  23. Lin CW, Lai CY, Chen LH, Chiang WF (2007) Microbial community structure during oxygen-stimulated bioremediation in phenol-contaminated groundwater. J Hazard Mater 140:221–229

    Article  PubMed  CAS  Google Scholar 

  24. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucl Acids Res 29:173–174

    Article  PubMed  CAS  Google Scholar 

  25. Mandri T, Lin J (2007) Isolation and characterization of engine oil degrading indigenous microrganisms in Kwazulu-Natal, South Africa. Afric J Biotechnol 6:23–27

    CAS  Google Scholar 

  26. Muller RH, Babel W (1996) Growth rate-dependent expression of phenol-assimilation pathways in Alcaligenes eutrophus JMP134-the influence of formate as an auxiliary energy source on phenol conversion characteristics. Appl Microbiol Biotechnol 46:156–162

    Article  Google Scholar 

  27. O’ Brien RD, Lindow SE (1989) Effects of plant species and environmental conditions on epiphytic population sizes of Pseudomonas syringae and other bacteria. Phytopathology 79:619–627

    Article  Google Scholar 

  28. Paller G, Hommel RK, Kleber HP (1995) Phenol degradation by Acinetobacter calcoaceticus Ncib-8250. J Basic Microbiol 35:325–335

    Article  PubMed  CAS  Google Scholar 

  29. Pankhurst ES (1965) A spot test for catechol 2:3-oxygenase in bacteria. J Appl Bacteriol 28:309–315

    PubMed  CAS  Google Scholar 

  30. Parvanov D, Topalova Y (2008) Biodegradation potential of phenol-resistant bacteria localized in different stream habitats. Biotechnol Biotechnol Equip 22:709–715

    CAS  Google Scholar 

  31. Rivas R, Garcia-Fraile P, Mateos PF, Martinez-Molina E, Velazquez E (2007) Characterization of xylanolytic bacteria present in the bract phyllosphere of the date palm Phoenix dactylifera. Lett Appl Microbiol 44:181–187

    Article  PubMed  CAS  Google Scholar 

  32. Saadoun I (2002) Isolation and characterization of bacteria from crude petroleum oil contaminated soil and their potential to degrade diesel fuel. J Basic Microbiol 42:420–428

    Article  PubMed  Google Scholar 

  33. Sandhu A, Halverson LJ, Beattie GA (2007) Bacterial degradation of airborne phenol in the phyllosphere. Environ Microbiol 9:383–392

    Article  PubMed  CAS  Google Scholar 

  34. Sei K, Inoue D, Wada K, Mori K, Ike M, Kohno T, Fujita M (2004) Monitoring behaviour of catabolic genes and change of microbial community structures in seawater microcosms during aromatic compound degradation. Water Res 38:4405–4414

    Article  PubMed  CAS  Google Scholar 

  35. Shashirekha S, Uma L, Subramanian G (1997) Phenol degradation by the marine cyanobacterium Phormidium valderianum BDU 30501. J Indust Microbiol Biotechnol 19:130–133

    Article  CAS  Google Scholar 

  36. Song JM, Sung JH, Kim YM, Zylstra GJ, Kim E (2000) Roles of the meta- and the ortho-cleavage pathways for the efficient utilization of aromatic hydrocarbons by Sphingomonas yanoikuyae B1. J Microbiol 38:245–249

    CAS  Google Scholar 

  37. Tay ST, Moy BY, Maszenan AM, Tay JH (2005) Comparing activated sludge and aerobic granules as microbial inocula for phenol biodegradation. Appl Microbiol Biotechnol 67:708–713

    Article  PubMed  CAS  Google Scholar 

  38. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W: improving the sensitivity of progressive multiple Sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  39. Van Aken B, Yoon JM, Schnoor JL (2004) Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine by a phytosymbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoides x nigra DN34). Appl Environ Microbiol 70:508–517

    Article  PubMed  CAS  Google Scholar 

  40. van der Geize R, Dijkhuizen L (2004) Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr Opin Microbiol 7:255–261

    Article  PubMed  CAS  Google Scholar 

  41. Wang YJ, Xiao M, Geng XL, Liu JY, Chen J (2007) Horizontal transfer of genetic determinants for degradation of phenol between the bacteria living in plant and its rhizosphere. Appl Microbiol Biotechnol 77:733–739

    Article  PubMed  CAS  Google Scholar 

  42. Watanabe K, Teramoto M, Futamata H, Harayama S (1998) Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol 64:4396–4402

    PubMed  CAS  Google Scholar 

  43. Wei GH, Yu JF, Zhu YH, Chen WM, Wang L (2008) Characterization of phenol degradation by Rhizobium sp CCNWTB 701 isolated from Astragalus chrysopteru in mining tailing region. J Hazard Mater 151:111–117

    Article  PubMed  CAS  Google Scholar 

  44. Whiteley AS, Wiles S, Lilley AK, Philp J, Bailey MJ (2001) Ecological and physiological analyses of Pseudomonad species within a phenol remediation system. J Microbiol Meth 44:79–88

    Article  CAS  Google Scholar 

  45. Xu Y, Zhang W, Chen M, Lin M, Li JM, Fang XJ (2000) Isolation and identification of a phenol-degrading bacterial strain. Acta Sci Circumstantiae 20:450–455

    CAS  Google Scholar 

  46. Yang CH, Crowley DE, Borneman J, Noel TK (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci U S A 98:3889–3894

    Article  PubMed  CAS  Google Scholar 

  47. Zahn JA, DiSpirito AA, Do YS, Brooks BE, Cooper EE, Hatfield JL (2001) Correlation of human olfactory responses to airborne concentrations of malodorous volatile organic compounds emitted from swine effluent. J Environ Qual 30:624–634

    PubMed  CAS  Google Scholar 

  48. Zahn JA, Hatfield JL, Do YS, DiSpirito AA, Laird DA, Pfeiffer RL (1997) Characterization of volatile organic emissions and wastes from a swine production facility. J Environ Qual 26:1687–1696

    Article  CAS  Google Scholar 

  49. Zhang X, Gao P, Chao Q, Wang L, Senior E, Zhao L (2004) Microdiversity of phenol hydroxylase genes among phenol-degrading isolates of Alcaligenes sp. from an activated sludge system. FEMS Microbiol Lett 237:369–375

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Dr. Janice Thompson, Troy Bowman, and Iowa Select farms for their assistance in obtaining the green ash leaf samples. The work was supported by funds from the Iowa Space Grant Consortium, Department of Agronomy Endowment and the College of Agriculture and Life Sciences at Iowa State University.

Author information

Authors and Affiliations

  1. Department of Plant Pathology and Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011, USA

    Amarjyoti Sandhu, Larry J. Halverson & Gwyn A. Beattie

  2. Department of Plant Pathology, Iowa State University, 207 Science I, Ames, IA, 50011, USA

    Gwyn A. Beattie

Authors
  1. Amarjyoti Sandhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Larry J. Halverson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gwyn A. Beattie
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gwyn A. Beattie.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sandhu, A., Halverson, L.J. & Beattie, G.A. Identification and Genetic Characterization of Phenol-Degrading Bacteria from Leaf Microbial Communities. Microb Ecol 57, 276–285 (2009). https://doi.org/10.1007/s00248-008-9473-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-008-9473-9

Keywords

Search

Navigation