Dynamic biofilm architecture confers individual and collective mechanisms of viral protection

Abstract

In nature, bacteria primarily live in surface-attached, multicellular communities, termed biofilms1,2,3,4,5,6. In medical settings, biofilms cause devastating damage during chronic and acute infections; indeed, bacteria are often viewed as agents of human disease7. However, bacteria themselves suffer from diseases, most notably in the form of viral pathogens termed bacteriophages8,9,10,11,12, which are the most abundant replicating entities on Earth. Phage–biofilm encounters are undoubtedly common in the environment, but the mechanisms that determine the outcome of these encounters are unknown. Using Escherichia coli biofilms and the lytic phage T7 as models, we discovered that an amyloid fibre network of CsgA (curli polymer) protects biofilms against phage attack via two separate mechanisms. First, collective cell protection results from inhibition of phage transport into the biofilm, which we demonstrate in vivo and in vitro. Second, CsgA fibres protect cells individually by coating their surface and binding phage particles, thereby preventing their attachment to the cell exterior. These insights into biofilm–phage interactions have broad-ranging implications for the design of phage applications in biotechnology, phage therapy and the evolutionary dynamics of phages with their bacterial hosts.

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Fig. 1: Susceptibility of biofilms to phage exposure as a function of biofilm age.
Fig. 2: Phage susceptibility of biofilms depends on extracellular matrix structure and dynamics.
Fig. 3: Phage localization and biofilm architectural properties within wild-type E. coli and mutants lacking major extracellular matrix components.
Fig. 4: Reconstruction of minimal synthetic biofilms recapitulates phage diffusion prevention and phage–cell attachment prevention in vivo.

References

  1. 1.

    Flemming, H.-C. et al. Biofilms: an emergent form of bacterial life. Nat. Rev. Microbiol. 14, 563–575 (2016).

    CAS  Article  Google Scholar 

  2. 2.

    Persat, A. et al. The mechanical world of bacteria. Cell 161, 988–997 (2015).

    CAS  Article  Google Scholar 

  3. 3.

    Hobley, L., Harkins, C., MacPhee, C. E. & Stanley-Wall, N. R. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol. Rev. 39, 649–669 (2015).

    CAS  Article  Google Scholar 

  4. 4.

    Berk, V. et al. Molecular architecture and assembly principles of Vibrio cholerae biofilms. Science 337, 236–239 (2012).

    CAS  Article  Google Scholar 

  5. 5.

    Drescher, K. et al. Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc. Natl Acad. Sci. USA 113, E2066–E2072 (2016).

    CAS  Article  Google Scholar 

  6. 6.

    Nadell, C. D., Drescher, K., Wingreen, N. S. & Bassler, B. L. Extracellular matrix structure governs invasion resistance in bacterial biofilms. ISME J. 9, 1700–1709 (2015).

    Article  Google Scholar 

  7. 7.

    Ochman, H. & Moran, N. A. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292, 1096–1099 (2001).

    CAS  Article  Google Scholar 

  8. 8.

    Samson, J. E., Magadán, A. H., Sabri, M. & Moineau, S. Revenge of the phages: defeating bacterial defences. Nat. Rev. Microbiol. 11, 675–687 (2013).

    CAS  Article  Google Scholar 

  9. 9.

    Zeng, L. et al. Decision making at a subcellular level determines the outcome of bacteriophage infection. Cell 141, 682–691 (2010).

    CAS  Article  Google Scholar 

  10. 10.

    Salmond, G. P. C. & Fineran, P. C. A century of the phage: past, present and future. Nat. Rev. Microbiol. 13, 777–786 (2015).

    CAS  Article  Google Scholar 

  11. 11.

    Rohwer, F. & Segall, A. M. In retrospect: a century of phage lessons. Nature 528, 46–48 (2015).

    CAS  Article  Google Scholar 

  12. 12.

    Hu, B., Margolin, W., Molineux, I. J. & Liu, J. The bacteriophage T7 virion undergoes extensive structural remodeling during infection. Science 339, 576–579 (2013).

    CAS  Article  Google Scholar 

  13. 13.

    Koskella, B. & Brockhurst, M. A. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol. Rev. 38, 916–931 (2014).

    CAS  Article  Google Scholar 

  14. 14.

    Gómez, P. & Buckling, A. Bacteria–phage antagonistic coevolution in soil. Science 332, 106–109 (2011).

    Article  Google Scholar 

  15. 15.

    Weitz, J. S., Hartman, H. & Levin, S. A. Coevolutionary arms races between bacteria and bacteriophage. Proc. Natl Acad. Sci. USA 102, 9535–9540 (2005).

    CAS  Article  Google Scholar 

  16. 16.

    Forde, S. E. et al. Understanding the limits to generalizability of experimental evolutionary models. Nature 455, 220–223 (2008).

    CAS  Article  Google Scholar 

  17. 17.

    Bull, J. J., Otto, G. & Molineux, I. J. In vivo growth rates are poorly correlated with phage therapy success in a mouse infection model. Antimicrob. Agents Chemother. 56, 949–954 (2012).

    CAS  Article  Google Scholar 

  18. 18.

    Chan, B. K. & Abedon, S. T. Bacteriophages and their enzymes in biofilm control. Curr. Pharm. Des. 21, 85–99 (2015).

    CAS  Article  Google Scholar 

  19. 19.

    Doolittle, M. M., Cooney, J. J. & Caldwell, D. E. Tracing the interaction of bacteriophage with bacterial biofilms using fluorescent and chromogenic probes. J. Ind. Microbiol. 16, 331–341 (1996).

    CAS  Article  Google Scholar 

  20. 20.

    Lu, T. K. & Collins, J. J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl Acad. Sci. USA 104, 11197–11202 (2007).

    CAS  Article  Google Scholar 

  21. 21.

    Briandet, R. et al. Fluorescence correlation spectroscopy to study diffusion and reaction of bacteriophages inside biofilms. Appl. Environ. Microbiol. 74, 2135–2143 (2008).

    CAS  Article  Google Scholar 

  22. 22.

    May, T., Tsuruta, K. & Okabe, S. Exposure of conjugative plasmid carrying Escherichia coli biofilms to male-specific bacteriophages. ISME J. 5, 771–775 (2011).

    CAS  Article  Google Scholar 

  23. 23.

    Vilas Boas, D. et al. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH). Biofouling 32, 179–190 (2016).

    CAS  Article  Google Scholar 

  24. 24.

    Serra, D. O., Richter, A. M., Klauck, G., Mika, F. & Hengge, R. Microanatomy at cellular resolution and spatial order of physiological differentiation in a bacterial biofilm. mBio 4, e00103–13 (2013).

    Article  Google Scholar 

  25. 25.

    DePas, W. H. et al. Iron induces bimodal population development by Escherichia coli. Proc. Natl Acad. Sci. USA 110, 2629–2634 (2013).

    CAS  Article  Google Scholar 

  26. 26.

    Grantcharova, N., Peters, V., Monteiro, C., Zakikhany, K. & Römling, U. Bistable expression of CsgD in biofilm development of Salmonella enterica serovar Typhimurium. J. Bacteriol. 192, 456–466 (2010).

    CAS  Article  Google Scholar 

  27. 27.

    Pesavento, C. et al. Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev. 22, 2434–2446 (2008).

    CAS  Article  Google Scholar 

  28. 28.

    Besharova, O., Suchanek, V. M., Hartmann, R., Drescher, K. & Sourjik, V. Diversification of gene expression during formation of static submerged biofilms by Escherichia coli. Front. Microbiol. 7, 1568 (2016).

    Article  Google Scholar 

  29. 29.

    Reyes, A., Semenkovich, N. P., Whiteson, K., Rohwer, F. & Gordon, J. I. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607–617 (2012).

    CAS  Article  Google Scholar 

  30. 30.

    Pires, D. P., Oliveira, H., Melo, L. D. R., Sillankorva, S. & Azeredo, J. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications. Appl. Microbiol. Biotechnol. 100, 2141–2151 (2016).

    CAS  Article  Google Scholar 

  31. 31.

    Arnqvist, A., Olsén, A., Pfeifer, J., Russell, D. G. & Normark, S. The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101. Mol. Microbiol. 6, 2443–2452 (1992).

    CAS  Article  Google Scholar 

  32. 32.

    Olsén, A., Jonsson, A. & Normark, S. Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli. Nature 338, 652–655 (1989).

    Article  Google Scholar 

  33. 33.

    Zhou, Y., Smith, D. R., Hufnagel, D. A. & Chapman, M. R. Experimental manipulation of the microbial functional amyloid called curli. Methods Mol. Biol. 966, 53–75 (2013).

    CAS  Article  Google Scholar 

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Acknowledgements

The authors thank M. Rakwalska-Bange, T. Heimerl and G. Malengo for experimental assistance, R. Hengge and V. Sourjik for strains and N. Rigel and members of the Drescher laboratory for discussions and suggestions. This work was supported by grants from the Max Planck Society, Behrens Weise Foundation, European Research Council (StG-716734), Human Frontier Science Program (CDA00084/2015-C) and Deutsche Forschungsgemeinschaft (SFB987) to K.D., and the Alexander von Humboldt Foundation and Cystic Fibrosis Foundation (STANTO15RO) to C.D.N.

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C.D.N. conceived the topic. C.D.N. and K.D. designed the project. L.V. and P.K.S. generated strains and acquired data. R.H. developed new analytical software. L.V., R.H., C.D.N. and K.D. analysed and interpreted the data. L.V., C.D.N. and K.D. wrote the paper with the help of all authors.

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Correspondence to Carey D. Nadell or Knut Drescher.

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Supplementary Figures 1–10, Supplementary Table 1, Supplementary References.

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Vidakovic, L., Singh, P.K., Hartmann, R. et al. Dynamic biofilm architecture confers individual and collective mechanisms of viral protection. Nat Microbiol 3, 26–31 (2018). https://doi.org/10.1038/s41564-017-0050-1

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