1887

Chapter 8 : Culture-Dependent Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Culture-Dependent Microbiology, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap08-2.gif

Abstract:

This chapter concentrates on some examples of the latest techniques being successfully exploited for isolating dominant but uncultured bacteria from a variety of habitats. Regardless of what isolation method is used, the choice of an appropriate medium is crucial when culturing bacteria in nature. The most successful isolation approaches for numerically abundant types of bacteria by plating on solid media use very-low-nutrient media (5 to 80 mg of organic components per liter) incubated for up to 84 days. Plating has also been used to isolate new, abundant bacteria from some extreme environments. Enrichment has been especially successful at isolating naturally abundant thermophiles in the from a hot-subsurface aquifer from a gold mine. Micromanipulation can also be a valuable aid for isolating target bacteria, especially when fluorescent in situ hybridization (FISH) with phylogenetic probes is used to visualize the target bacteria. Finally, the chapter describes the extinction culture, which is also called dilution culture and dilution to extinction. It involves diluting water samples with filter-sterilized water until only a few bacteria remain and then growing the cells in either the unamended water or by adding small amounts of organic substrates to culture them.

Citation: Fry J. 2004. Culture-Dependent Microbiology, p 80-87. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch8

Key Concept Ranking

Anoxic Rice Field Soils
0.42744374
0.42744374
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555817770.chap8
1. Anton, J.,, A. Oren,, S. Beniloch,, F. Rodriguez-Valera,, R. Amann,, and R. Rossello-Mora. 2002. Salinibacter ruber gen. nov., sp nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int. J. Syst. Evol. Microbiol. 52: 485 491.
2. Atlas, R. M. 1995. Handbook of Media for Environmental Microbiology. CRC Press, Boca Raton, Fla.
3. Austin, B. (ed.). 1988. Methods in Aquatic Bacteriology. John Wiley, Chichester, United Kingdom.
4. Balows, A.,, H. G. Truper,, W. H. Dworkin,, and K.-H. Schleifer (ed.). 1992. The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed, vol. 1-4. Springer-Verlag, Berlin, Germany.
5. Bartscht, K.,, H. Cypionka,, and J. Overmann. 1999. Evaluation of cell activity and of methods for the cultivation of bacteria from a natural lake community. FEMS Microbiol. Ecol. 28: 249 259.
6. Bockelmann, U.,, W. Manz,, T. R. Neu,, and U. Szewzyk. 2000. Characterization of the microbial community of lotic organic aggregates ("river snow") in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33: 157 170.
7. Breznak, J. A. 2002. A need to retrieve the not-yet-cultured majority. Environ. Microbiol. 4: 4 5.
8. Bruns, A.,, H. Cypionka,, and J. Overmann. 2002. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68: 3978 3987.
9. Bull, A. T.,, and J. H. Slater (ed.). 1982. Microbial Interactions and Communities, vol. 1. Academic Press, London, United Kingdom.
10. Button, D.,, F. Schut,, P. Quang,, R. Martin,, and B. Robertson. 1993. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl. Environ. Microbiol. 59: 881 891.
11. Button, D.F., , B. R. Robertson,, P. W. Lepp,, and T. M. Schmidt. 1998. A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl. Environ. Microbiol. 64: 4467 4476.
12. Button, D.F., , B. R. Robertson,, and P. Quang,. 2001. Isolation of oligobacteria, p. 161 173. In J. H. Paul (ed.), Marine Microbiology, Methods in Microbiology, vol. 30. Academic Press, San Diego, Calif.
13. Chin, K. J.,, D. Hahn,, U. Hengstmann,, W. Liesack,, and P. H. Janssen. 1999. Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl. Environ. Microbiol. 65: 5042 5049.
14. DeLong, E. E.,, and N. R. Pace. 2001. Environmental diversity of Bacteria and Archaea. Syst. Biol. 50: 470 478.
15. Eguchi, M.,, M. Ostrowski,, F. Fegatella,, J. Bowman,, D. Nichols,, T. Nishino,, and R. Cavicchioli. 2001. Sphingomonas alaskensis strain AFOl, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl. Environ. Microbiol. 67: 4945 4954.
16. Eilers, H.,, J. Pernthaler,, F. O. Glockner,, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66: 3044 3051.
17. Eilers, H.,, J. Pernthaler,, J. Peplies,, F. O. Glockner,, G. Gerdts,, and R. Amann. 2001. Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 67: 5134 5142.
18. Fry, J. C., 1987. Functional roles of major groups of bacteria associated with detritus, p. 83 122. In D. J. W. Moriarty, and R. S. V. Pullin (ed.), Detritus and Microbial Ecology in Aquaculture, vol. 14, ICLARM Conference Proceedings. International Centre for Living Aquatic Resources Management, Manila, Philippines.
19. Fry, J. C., 1990. Oligotrophs, p. 93 116. In C. Edwards (ed.), Microbiology of Extreme Environments. Open University Press, Milton Keynes, United Kingdom.
20. Fry, J.C., , and T. Zia. 1982. Viability of heterotrophic bacteria in fresh-water. J. Gen. Microbiol. 128: 2841 2850.
21. Garrity, G.M., , M. Winters,, A. W. Kuo,, and D. B. Searles. 2002. Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology. Release 2, 2nd ed. Springer-Verlag, New York, N.Y.
22. Giovannoni, S. J.,, and M. S. Rappé,. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes, p. 47 84. In D. L. Kirchmann (ed.), Microbial Ecology of the Oceans. Wiley, New York, N.Y.
23. Gonzalez, J. M.,, and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63: 4237 4242.
24. Grigorova, R.,, and J. R. Norris (ed.). 1990. Techniques in microbial ecology p. 627. In Methods in Microbiology, vol. 22. Academic Press, London, United Kingdom.
25. Holt, J. G. (ed.). 1994. Bergey's Manual of Determinative Bacteriology, 9th ed., p. 787. Williams & Wilkins, Baltimore, Md.
26. Huber, R.,, S. Burggraf,, T. Mayer,, S. M. Barns,, P. Rossnagel,, and K. O. Stetter. 1995. Isolation of a hyperthermophilic archaeum predicted by in-situ RNA analysis. Nature 376: 57 58.
27. Hugenholtz, P.,, B. M. Goebel,, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765 4774.
28. Janssen, P. H.,, P. S. Yates, B. E. Grinton, P. M. Taylor, and M. Sait. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions. Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68: 2391 2396.
29. Kampfer, P. 1997. Detection and cultivation of filamentous bacteria from activated sludge. FEMS Microbiol. Ecol. 23: 169 181.
30. Paul, J. H. (ed.). 2001. Marine microbiology, p. 666. In Methods in Microbiology, vol. 30. Academic Press, San Diego, Calif.
31. Pinhassi, J.,, U. L. Zweifel,, and A. Hagstrom. 1997. Dominant marine bacterioplankton species found among colony-forming bacteria. Appl. Environ. Microbiol. 63: 3359 3366.
32. Rappé, M. S.,, S. A. Connon,, K. L. Vergin,, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterio-plankton clade. Nature 418: 630 633.
33. Saul, D. J.,, R. A. Reeves,, H. W. Morgan,, and P. L. Bergquist. 1999. Thermus diversity and strain loss during enrichment. FEMS Microbiol. Ecol. 30: 157 162.
34. Schut, F.,, E. de Vries,, J. Gottschal,, B. Robertson,, W. Harder,, R. Prins,, and D. Button. 1993. Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions. Appl. Environ. Microbiol. 59: 2150 2160.
35. Sekiguchi, Y.,, H. Takahashi,, Y. Kamagata,, A. Ohashi,, and H. Harada. 2001. In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the Green Non-Sulfur Bacteria, subdivision I. Appl. Environ. Microbiol 67: 5740 5749.
36. Stackebrandt, E.,, and B. J. Tindall. 2000. Appreciating microbial diversity: rediscovering the importance of isolation and characterization of microorganisms. Environ. Microbiol. 2: 9 10.
37. Suzuki, M. T.,, M. S. Rappé,, Z. W. Haimberger,, H. Winfield,, N. Adair,, J. Strobel,, and S.J. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63: 983 989.
38. Takai, K.,, H. Hirayama,, Y. Sakihama,, F. Inagaki,, Y. Yamato,, and K. Horikoshi. 2002. Isolation and metabolic characteristics of previously uncultured members of the order Aquificales in a subsurface gold mine. Appl. Environ. Microbiol. 68: 3046 3054.
39. Vancanneyt, M.,, F. Schut,, C. Snauwaert,, J. Goris,, J. Swings,, and J. Gottschal. 2001. Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int. J. Syst. Evol. Microbiol. 51: 73 79.
40. Wery, N.,, M.-A. Cambon-Bonavita,, F. Lesongeur,, and G. Barbier. 2002. Diversity of anaerobic heterotrophic thermophiles isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. FEMS Microbiol. Ecol. 41: 105 114.
41. Zinder, S. H. 2002. The future for culturing environmental organisms: a golden era ahead? Environ. Microbiol. 4: 14 15.

Tables

Generic image for table
Table 1

Some examples of methods used for the isolation of abundant from natural habitats

Citation: Fry J. 2004. Culture-Dependent Microbiology, p 80-87. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch8

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error