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Interaction between copper and extracellular nucleic acids in the EPS of unsaturated Pseudomonas putida CZ1 biofilm

Abstract

The role of extracellular DNA (eDNA) in biofilm in heavy metal complexation has been little reported. In this study, the interaction between the extracellular fraction of unsaturated biofilms and Cu2+ was studied using random amplified polymorphic DNA (RAPD) and synchrotron-based X-ray absorption spectroscopy (XAS) analyses. Under Cu2+ stress, the amount of eDNA was about 10-fold higher than the treatment without Cu2+ stress, which was substantially more than the amount of intracellular DNA (iDNA) present in the biofilm. The eDNA content increased significantly under Cu2+ stress and higher eDNA contents were found in colloidal extracellular polymeric substances (EPS) than in capsular EPS in Luria-Bertani medium. It was found that the composition of eDNA was distinctly changed under conditions of Cu2+ stress compared with the treatments without Cu2+ treatments, with specific eDNA bands appearing under Cu2+ treatments as revealed by RAPD analyses. X-ray absorption fine structure (XAFS) analysis assessing the molecular speciation of copper showed that copper in the secreted eDNA mainly existed as species resembling Cu3(PO4)2, followed by Cu-citrate species. This study investigated the interaction between copper and eDNA in unsaturated Pseudomonas putida CZ1 biofilms. Potential function of eDNA in biofilms under Cu2+ stress was found.

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References

  1. Auerbach ID, Sorensen C, Hansma HG, Holden PA (2000) Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms. J Bacteriol 182(13): 3809–3815.

    Article  CAS  Google Scholar 

  2. Aguilera A, Souza-Egipsy V, Martin-Uriz PS, Amils R (2008) Extraction of extracellular polymeric substances from extreme acidic microbial biofilms. Appl Microbiol Biotechnol 78(6):1079–1088

    Article  CAS  Google Scholar 

  3. Chen XC, Shi JY, Chen YX, Xu XH, Xu SY, Wang YP (2006) Tolerance and biosorption of copper and zinc by Pseudomonas putida CZ1 isolated from metal-polluted soil. Can J Microbiol 52:308–316

    Article  CAS  Google Scholar 

  4. Chen GC, Chen XC, Yang YQ, Hay AG, Yu XH, Chen YX (2011a) Sorption and distribution of copper in unsaturated Pseudomonas putida CZ1 biofilms as determined by X-ray fluorescence microscopy. Appl Environ Microbiol 77(14):4719–4727

    Article  CAS  Google Scholar 

  5. Chen XC, Chen GC, Chen LG, Chen YX, Lehmann J, McBride MB (2011b) Adsorption of copper and zinc by biochars produced from pyrolysis of hardwood and corn straw in aqueous solution. Bioresour Technol 102:8877–8884.

    Article  CAS  Google Scholar 

  6. Chen GC, Lin HR, Chen XC (2016) Spatial pattern of copper phosphate precipitation involves in copper accumulation and resistance of unsaturated Pseudomonas putida CZ1 biofilm. J Microbiol Biotechnol 26:2116–2126.

    Article  CAS  Google Scholar 

  7. Clerc A, Manceau C, Nesme X (1998) Comparison of randomly amplified polymorphic DNA with amplified fragment length polymorphism to assess genetic diversity and genetic relatedness within genospecies III of Pseudomonas syringae. Appl Environ Microbiol 64(4):1180–1187.

    CAS  Google Scholar 

  8. Costerton JW, Cheng KJ, Geesey GG, Ladd TI, Nickel JC, Dasgupta M, Marrie TJ (1987) Bacterial biofilms in nature and disease. Annu Rev Microbiol 41:435–464

    Article  CAS  Google Scholar 

  9. Dengler V, Foulston L, DeFrancesco AS, Losick R (2015) An electrostatic net model for the role of extracellular DNA in biofilm formation by Staphylococcus aureus. J Bacteriol 197(24):3779–3787

    Article  CAS  Google Scholar 

  10. Fang LC, Wei X, Cai P, Huang QY, Chen H, Liang W, Rong XM (2011) Role of extracellular polymeric substances in Cu(II) adsorption on Bacillus subtilis and Pseudomonas putida. Bioresour Technol 102(2):1137–1141

    Article  CAS  Google Scholar 

  11. Flemming HC, Wingender J (2001) Relevance of microbial extracellular polymeric substances (EPSs)—part I: structural and ecological aspects. Water Sci Technol 43(6):1–8

    Article  CAS  Google Scholar 

  12. Flemming HC, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8(9):623–633

    Article  CAS  Google Scholar 

  13. Gadd GM (2000) Bioremedial potential of microbial mechanisms of metal mobilization and immobilization. Curr Opin Biotechnol 11(3):271–279

    Article  CAS  Google Scholar 

  14. Hao LK, Guo Y, Byrne JM, Zeitvogel F, Schmid G, Ingino P, Li JL, Neu TR, Swanner ED, Kappler A, Obst M (2016) Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores. Geochim Cosmochim Acta 180:66–96

    Article  CAS  Google Scholar 

  15. Harrison JJ, Rabiei M, Turner RJ, Badry EA, Sproule KM, Ceri H (2006) Metal resistance in Candida biofilms. FEMS Microbiol Ecol 55(3):479–491

    Article  CAS  Google Scholar 

  16. Harrison JJ, Ceri H, Turner RJ (2007) Multimetal resistance and tolerance in microbial biofilms. Nat Rev Microbiol 5(12):928–938

    Article  CAS  Google Scholar 

  17. Hong FS, Wu C, Liu C, Wang L, Gao FQ, Yang F, Xu JH, Liu T, Xie YN, Li XZ (2007) Direct evidence for interaction between lead ions and kidney DNA from silver crucian carp. Chemosphere 68(8):1442–1446

    Article  CAS  Google Scholar 

  18. Jakubovics NS, Burgess JG (2015) Extracellular DNA in oral microbial biofilms. Microbes Infect 17(7):531–537

    Article  CAS  Google Scholar 

  19. Jakubovics NS, Shields RC, Rajarajan N, Burgess JG (2013) Life after death: the critical role of extracellular DNA in microbial biofilms. Lett Appl Microbiol 57:467–475

    Article  CAS  Google Scholar 

  20. Lin HR, Zhu X, Wang YX, Yu X (2017) Effect of sodium hypochlorite on typical biofilms formed in drinking water distribution systems. J Water Health 15(2):218–227

    Article  Google Scholar 

  21. MacNaughton JB, Yablonskikh MV, Hunt AH, Kurmaev EZ, Lee JS, Wettig SD, Moewes A (2006a) Solid versus solution: examining the electronic structure of metallic DNA with soft X-ray spectroscopy. Phys Rev B 74(12)

  22. MacNaughton JB, Kurmaev EZ, Finkelstein LD, Lee JS, Wettig SD, Moewes A (2006b) Electronic structure and charge carriers in metallic DNA investigated by soft X-ray spectroscopy. Phys Rev B 73(20)

  23. Mulcahy H, Charron-Mazenod L, Lewenza S (2008) Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms. PLoS Pathog 4(11):e1000213

    Article  CAS  Google Scholar 

  24. Okshevsky M, Meyer RL (2013) The role of extracellular DNA in the establishment, maintenance and pertubation of bacterial biofilms. Crit Rev Microbiol 41(3):341–352

    Article  CAS  Google Scholar 

  25. Okshevsky M, Regina VR, Meyer RL (2015) Extracellular DNA as a target for biofilm control. Curr Opin Biotechnol 33:73–80

    Article  CAS  Google Scholar 

  26. Pal A, Paul AK (2008) Microbial extracellular polymeric substances: central elements in heavy metal bioremediation. Indian J Microbiol 48(1):49–64

    Article  CAS  Google Scholar 

  27. Priester JH, Olson SG, Webb SM, Neu MP, Hersman LE, Holden PA (2006) Enhanced exopolymer production and chromium stabilization in Pseudomonas putida unsaturated biofilms. Appl Environ Microbiol 72(3):1988–1996

    Article  CAS  Google Scholar 

  28. Randrianjatovo-Gbalou I, Rouquette P, Lefebvre D, Girbal-Neuhauser E, Marcato-Romain CE (2017) In situ analysis of Bacillus licheniformis biofilms: amyloid-like polymers and eDNA are involved in the adherence and aggregation of the extracellular matrix. J Appl Microbiol 122(5):1262–1274

    Article  CAS  Google Scholar 

  29. Shi JY, Wu B, Yuan XF, Cao YY, Chen XC, Chen YX, Hu TD (2008) An X-ray absorption spectroscopy investigation of speciation and biotransformation of copper in Elsholtzia splendens. Plant Soil 302(1–2):163–174

    Article  CAS  Google Scholar 

  30. Steinberger RE, Holden PA (2005) Extracellular DNA in single- and multiple-species unsaturated biofilms. Appl Environ Microbiol 71(9):5404–5410

    Article  CAS  Google Scholar 

  31. van Hullebusch ED, Zandvoort MH, Lens PNL (2003) Metal immobilisation by biofilms: mechanisms and analytical tools. Rev Environ Sci Biotechnol 2(1):9–33

    Article  Google Scholar 

  32. Webb SM (2005) SIXpack: a graphical user interface for XAS analysis using IFEFFIT. Phys Scr T115:1011–1014

    Article  CAS  Google Scholar 

  33. Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS (2002) Extracellular DNA required for bacterial biofilm formation. Science 295(5559):1487–1487

    Article  CAS  Google Scholar 

  34. Wu JF, Xi CW (2009) Evaluation of different methods for extracting extracellular DNA from the biofilm matrix. Appl Environ Microbiol 75(16):5390–5395

    Article  CAS  Google Scholar 

  35. Xue Z, Sendamangalam VR, Gruden CL, Seo Y (2012) Multiple roles of extracellular polymeric substances on resistance of biofilm and detached clusters. Environ Sci Technol 46(24):13212–13219

    Article  CAS  Google Scholar 

  36. Zaharik ML, Finlay BB (2004) Mn2+ and bacterial pathogenesis. Front Biosci 9:1035–1042

    Article  CAS  Google Scholar 

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Acknowledgements

We gratefully thank the staff at the Shanghai Synchrotron Radiation Facility and the Beijing Synchrotron Radiation Facility for their help during data collection.

Funding

The work was supported by the National Natural Science Foundation of China (No. 21778070 40701161).

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Correspondence to Guangcun Chen.

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The authors declare that they have no conflict of interest.

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Responsible editor: Diane Purchase

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Lin, H., Wang, C., Zhao, H. et al. Interaction between copper and extracellular nucleic acids in the EPS of unsaturated Pseudomonas putida CZ1 biofilm. Environ Sci Pollut Res 25, 24172–24180 (2018). https://doi.org/10.1007/s11356-018-2473-5

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Keywords

  • Pseudomonas putida CZ1
  • Unsaturated biofilm
  • Extracellular polymeric substances
  • Extracellular DNA
  • Molecular speciation