Uncultivated Microorganisms pp 131-159

Part of the Microbiology Monographs book series (MICROMONO, volume 10)

General Model of Microbial Uncultivability

Chapter

Abstract

It has been known for over a century that only a small percent of cells from environmental samples form colonies on standard media (Great Plate Count Anomaly, Staley and Konopka (Annu Rev Microbiol 39:321–346, 1985). This chapter focuses on the causes of this disparity, and describes new cultivation technologies aiming to close the gap. It summarizes the original and literature data on the biology of “uncultivable” species\uncultivable\ species is summarized, and the nature of the restrictions likely limiting the growth of these species is discussed. This analysis leads to a novel model of the microbial life cycle in nature, termed the “scout model.” We argue that if microbial behavior in vivo conforms to the scout model, this will by necessity manifest itself in vitro as the Great Plate Count Anomaly. The scout model also draws connections to other aspects of microbial behavior, such as viability – but not cultivability – of some cells, an apparent slow growth of certain species, seeming ability of microbes to persist in the presence of unfavorable factors, including antibiotics, and latent infections.

References

  1. Aoi Y, Kinoshita T, Hata T, Ohta H, Obokata H, Tsuneda S (2009) Hollow fiber membrane chamber as a device for in situ environmental cultivation. Appl Environ MicrobiolGoogle Scholar
  2. Avery SV (2006) Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 4:577–587PubMedCrossRefGoogle Scholar
  3. Becskei A, Seraphin B, Serrano L (2001) Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J 20:2528–2535PubMedCrossRefGoogle Scholar
  4. Boetius A et al (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626PubMedCrossRefGoogle Scholar
  5. Bogosian G, Bourneuf EV (2001) A matter of bacterial life and death. EMBO Rep 2:770–774PubMedCrossRefGoogle Scholar
  6. Bogosian G, Morris PJ, O'Neil JP (1998) A mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state. Appl Environ Microbiol 64:1736–1742PubMedGoogle Scholar
  7. Bollmann A, Lewis K, Epstein SS (2007) Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73:6386–6390PubMedCrossRefGoogle Scholar
  8. Bollmann A, Palumbo T, Lewis K, Epstein SS (2009) Isolation and characterization of novel bacteria from contaminated subsurface sediments. ISME J Bollmann A, Palumbo T, Lewis K, Epstein SS (2009) Isolation and characterization of novel bacteria from contaminated subsurface sediments. ISME JGoogle Scholar
  9. Bruns A, Cypionka H, Overmann J (2002) Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl Environ Microbiol 68:3978–3987PubMedCrossRefGoogle Scholar
  10. Buchanan RE (1918) Life phases in a bacterial culture. J Infect Dis 23:109–125Google Scholar
  11. Buerger S, Hong S-H, Lucey K, Epstein SS (2008) Single-cell approach to microbial cultivation reveals an unusual growth strategy. In: Abstracts of the 11th International Society for Microbial Ecology Symposium, Cairns, Australia, August 2008Google Scholar
  12. Butkevich NV, Butkevich VS (1936) Multiplication of sea bacteria depending on the composition of the medium and on temperature. Microbiology 5:322–343Google Scholar
  13. Button DK, Schut F, Quang P, Martin R, Robertson BR (1993) Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 59:881–891PubMedGoogle Scholar
  14. Camilli A, Bassler BL (2006) Bacterial small-molecule signaling pathways. Science 311:1113–1116PubMedCrossRefGoogle Scholar
  15. Choi PJ, Cai L, Frieda K, Xie XS (2008) A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322:442–446PubMedCrossRefGoogle Scholar
  16. Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885PubMedCrossRefGoogle Scholar
  17. Davis KE, Joseph SJ, Janssen PH (2005) Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71:826–834PubMedCrossRefGoogle Scholar
  18. Delpy LP, Beranger G, Kaweh M (1956) Method of counting living bacteria. Ann Inst Pasteur 91:112–114Google Scholar
  19. Dubnau D, Losick R (2006) Bistability in bacteria. Mol Microbiol 61:564–572PubMedCrossRefGoogle Scholar
  20. Epstein SS (2009) Microbial awakenings. Nature 457:1083Google Scholar
  21. Ferrari BC, Binnerup SJ, Gillings M (2005) Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 71:8714–8720PubMedCrossRefGoogle Scholar
  22. Ferrell JE Jr (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14:140–148PubMedCrossRefGoogle Scholar
  23. Finkel SE, Kolter R (1999) Evolution of microbial diversity during prolonged starvation. Proc Natl Acad Sci U S A 96:4023–4027PubMedCrossRefGoogle Scholar
  24. Finkel SE, Zinser E, Kolter R (2000) Long-term survival and evolution in stationary phase. In: Storz G, Hengge-Aronis R (eds) Bacterial Stress Responses. ASM, Washington, DC, pp 231–238Google Scholar
  25. Fuqua WC, Winans SC, Greenberg EP (1994) Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 176:269–275PubMedGoogle Scholar
  26. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–342PubMedCrossRefGoogle Scholar
  27. Gray TRG (1976) Survival of vegetative microbes in soil. Symp Soc Gen Microbiol 26:327–364Google Scholar
  28. Huber JA et al (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100PubMedCrossRefGoogle Scholar
  29. Jannasch HW, Jones GE (1959) Bacterial populations in seawater as determined by different methods of enumeration. Limnol Oceanogr 4:128–139CrossRefGoogle Scholar
  30. Kaeberlein T, Lewis K, Epstein SS (2002) Isolating uncultivable microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129PubMedCrossRefGoogle Scholar
  31. Kuznetsov SI, Dubinina GA, Lapteva NA (1979) Biology of oligotrophic bacteria. Annu Rev Microbiol 33:377–387PubMedCrossRefGoogle Scholar
  32. Maamar H, Dubnau D (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 56:615–624PubMedCrossRefGoogle Scholar
  33. McInerney MJ et al (2008) Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann N Y Acad Sci 1125:58–72PubMedCrossRefGoogle Scholar
  34. Nichols D et al (2008) Short peptide induces an uncultivable microorganism to grow in vitro. Appl Environ Microbiol 74:4889–4897PubMedCrossRefGoogle Scholar
  35. Novitsky JA, Morita RY (1976) Morphological characterization of small cells resulting from nutrient starvation of a psychrophilic marine vibrio. Appl Environ Microbiol 32:617–622PubMedGoogle Scholar
  36. Novitsky JA, Morita RY (1978) Possible strategy for the survival of marine bacteria under starvation conditions. Mar Biol 48:289–295CrossRefGoogle Scholar
  37. Nystrom T (2003) Nonculturable bacteria: programmed survival forms or cells at death's door? Bioessays 25:204–211PubMedCrossRefGoogle Scholar
  38. Pedros-Alio C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257–263PubMedCrossRefGoogle Scholar
  39. Postgate JR (1976) Death in macrobes and microbes. In: Gray TRG, Postgate JR (eds) The survival of vegetative microbes. Cambridge University Press, Cambridge, pp 1–19Google Scholar
  40. Postgate JR, Hunter JR (1962) The survival of starved bacteria. J Gen Microbiol 29:233–263PubMedGoogle Scholar
  41. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394PubMedCrossRefGoogle Scholar
  42. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633PubMedCrossRefGoogle Scholar
  43. Santo Domingo JW, Harmon S, Bennett J (2000) Survival of Salmonella species in river water. Curr Microbiol 40:409–417PubMedCrossRefGoogle Scholar
  44. Schink B (2002) Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81:257–261PubMedCrossRefGoogle Scholar
  45. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691PubMedCrossRefGoogle Scholar
  46. Sogin ML et al. (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103:12115–12120PubMedCrossRefGoogle Scholar
  47. Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346PubMedCrossRefGoogle Scholar
  48. Stevenson LH (1978) A case for bacterial dormancy in aquatic systems. Microb Ecol 4:127–133CrossRefGoogle Scholar
  49. Stewart GR, Robertson BD, Young DB (2003) Tuberculosis: a problem with persistence. Nat Rev Microbiol 1:97–105PubMedCrossRefGoogle Scholar
  50. Torrella F, Morita RY (1981) Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl Environ Microbiol 41:518–527PubMedGoogle Scholar
  51. Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346PubMedCrossRefGoogle Scholar
  52. Wilson GS (1922) The proportion of viable bacteria in young cultures with especial reference to the technique employed in counting. J Bacteriol 7:405–446PubMedGoogle Scholar
  53. Winogradsky S (1924) Sur la microflore autochtone de la terre arable. C R Acad Sci 178:1236–1239Google Scholar
  54. Xu H-S, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of non-culturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323CrossRefGoogle Scholar
  55. Zambrano MM, Kolter R (1996) GASPing for life in stationary phase. Cell 86:181–184PubMedCrossRefGoogle Scholar
  56. Zambrano MM, Siegele DA, Almiron M, Tormo A, Kolter R (1993) Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259:1757–1760PubMedCrossRefGoogle Scholar
  57. Zieg J, Silverman M, Hilmen M, Simon M (1977) Recombinational switch for gene expression. Science 196:170–172PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Department of BiologyNortheastern UniversityBostonUSA

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