The phenomenon of microbial uncultivability

Current Opinion in Microbiology

Volumn 16, Issue 5, 2013, Pages 636-642

  Epstein, S S ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SIDEROPHORE;

BACTERIUM CULTURE; DIFFUSION CHAMBER; DORMANCY; GENE REPRESSION; MICROBIAL DIVERSITY; MICROBIAL GROWTH; NONHUMAN; NUTRIENT CONCENTRATION; PETRI DISH; REVIEW; STATISTICS;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; ENVIRONMENTAL MICROBIOLOGY; MICROBIOLOGICAL TECHNIQUES;

EID: 84887626254     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2013.08.003     Document Type: Review

References (46)

1. Pedros-Alio C. The rare bacterial biosphere. Annu Rev Mar Sci 2012, 4:449-466.
2. Rappe M.S., Giovannoni S.J. The uncultured microbial majority. Annu Rev Microbiol 2003, 57:369-394.
3. Staley J.T., Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 1985, 39:321-346.
4. Winterberg H. Zur Methodik der Bakterienzahlung. Zeitschr Hyg 1898, 29:75-93.
5. Jannasch H.W., Jones G.E. Bacterial populations in seawater as determined by different methods of enumeration. Limnol Oceanogr 1959, 4:128-139.
6. Waksman S.A., Hotchkiss M. Viability of bacteria in sea water. J Bacteriol 1937, 33:389-400.
7. ZoBell C.E. Marine Microbiology: A Monograph on Hydrobacteriology 1946, Chronica Botanica Co, Waltham, MA, USA.
8. Lewis K., Epstein S., D'Onofrio A., Ling L.L. Uncultured microorganisms as a source of secondary metabolites. J Antibiotics 2010, 63:468-476.
9. Hurst C.J. Divining the future of microbiology. ASM News 2005, 71:262-263.
10. Achtman M., Wagner M. Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 2008, 6:431-440.
11. Rappe M.S., Connon S.A., Vergin K.L., Giovannoni S.J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 2002, 418:630-633.
12. Button D.K., Schut F., Quang P., Martin R., Robertson B.R. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 1993, 59:881-891.
13. Connon S.A., Giovannoni S.J. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 2002, 68:3878-3885.
14. Song J., Oh H.M., Cho J.C. Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean. FEMS Microbiol Lett 2009, 295:141-147.
15. Zengler K., Toledo G., Rappe M., Elkins J., Mathur E.J., Short J.M., Keller M. Cultivating the uncultured. Proc Natl Acad Sci U S A 2002, 99:15681-15686.
16. Davis K.E., Joseph S.J., Janssen P.H. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 2005, 71:826-834.
17. Bruns A., Cypionka H., Overmann J. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl Environ Microbiol 2002, 68:3978-3987.
18. Schink B. Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 2002, 81:257-261.
19. D'Onofrio A., Crawford J.M., Stewart E.J., Witt K., Gavrish E., Epstein S., Clardy J., Lewis K. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol 2010, 17:254-264.
20. Aoi Y., Kinoshita T., Hata T., Ohta H., Obokata H., Tsuneda S. Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl Environ Microbiol 2009, 75:3826-3833.
21. Ben-Dov E., Kramarsky-Winter E., Kushmaro A. An in situ method for cultivating microorganisms using a double encapsulation technique. FEMS Microbiol Ecol 2009, 68:363-371.
22. Ferrari B.C., Binnerup S.J., Gillings M. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl Environ Microbiol 2005, 71:8714-8720.
23. Gavrish E., Bollmann A., Epstein S., Lewis K. A trap for in situ cultivation of filamentous actinobacteria. J Microbiol Methods 2008, 72:257-262.
24. Kaeberlein T., Lewis K., Epstein S.S. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 2002, 296:1127-1129.
25. Nichols D., Cahoon N., Trakhtenberg E.M., Pham L., Mehta A., Belanger A., Kanigan T., Lewis K., Epstein S.S. Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol 2010, 76:2445-2450.
26. Sizova M.V., Hohmann T., Hazen A., Paster B.J., Halem S.R., Murphy C.M., Panikov N.S., Epstein S.S. New approaches for isolation of previously uncultivated oral bacteria. Appl Environ Microbiol 2012, 78:194-203.
27. Epstein S.S., Lewis K., Nichols D., Gavrish E. New approaches to microbial isolation. Manual of Industrial Microbiology and Biotechnology 2010, ASM. edn 3. R.H. Baltz, J.E. Davies, A. Demain (Eds.).
28. Bollmann A., Lewis K., Epstein S.S. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 2007, 73:6386-6390.
29. Bollmann A., Palumbo A.V., Lewis K., Epstein S.S. Isolation and physiology of bacteria from contaminated subsurface sediments. Appl Environ Microbiol 2010, 76:7413-7419.
30. Nichols D., Lewis K., Orjala J., Mo S., Ortenberg R., O'Connor P., Zhao C., Vouros P., Kaeberlein T., Epstein S.S. Short peptide induces an "uncultivable" microorganism to grow in vitro. Appl Environ Microbiol 2008, 74:4889-4897.
31. Sangwan P., Kovac S., Davis K.E., Sait M., Janssen P.H. Detection and cultivation of soil verrucomicrobia. Appl Environ Microbiol 2005, 71:8402-8410.
32. Oliver J.D. Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev 2010, 34:415-425.
33. Epstein S.S. Microbial awakenings. Nature 2009, 457:1083.
34. Epstein S.S. General model of microbial uncultivability. Uncultivated Microorganisms 2009, 131-150. Spinger. S.S. Epstein (Ed.).
35. Avery S.V. Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 2006, 4:577-587.
36. Choi P.J., Cai L., Frieda K., Xie X.S. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 2008, 322:442-446.
37. Dubnau D., Losick R. Bistability in bacteria. Mol Microbiol 2006, 61:564-572.
38. Maamar H., Dubnau D. Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 2005, 56:615-624.
39. Maamar H., Raj A., Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 2007, 317:526-529.
40. Fuqua W.C., Winans S.C., Greenberg E.P. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol 1994, 176:269-275.
41. Mukamolova G.V., Kaprelyants A.S., Young D.I., Young M., Kell D.B. A bacterial cytokine. Proc Natl Acad Sci U S A 1998, 95:8916-8921.
42. Mukamolova G.V., Murzin A.G., Salina E.G., Demina G.R., Kell D.B., Kaprelyants A.S., Young M. Muralytic activity of Micrococcus luteus Rpf and its relationship to physiological activity in promoting bacterial growth and resuscitation. Mol Microbiol 2006, 59:84-98.
43. Shah I.M., Laaberki M.H., Popham D.L., Dworkin J. A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments. Cell 2008, 135:486-496.
44. Buerger S., Spoering A., Gavrish E., Leslin C., Ling L., Epstein S.S. Microbial scout hypothesis, stochastic exit from dormancy, and the nature of slow growers. Appl Environ Microbiol 2012, 78:3221-3228.
45. Buerger S., Spoering A., Gavrish E., Leslin C., Ling L., Epstein S.S. Microbial scout hypothesis and microbial discovery. Appl Environ Microbiol 2012, 78:3229-3233.
46. Xu H.-S., Roberts N., Singleton F.L., Attwell R.W., Grimes D.J., Colwell R.R. Survival and viability of non-culturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 1982, 8:313-323.