1887

Chapter 1 : New Approaches to Microbial Isolation

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

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

New Approaches to Microbial Isolation, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap01-1.gif /docserver/preview/fulltext/10.1128/9781555816827/9781555815127_Chap01-2.gif

Abstract:

Metagenomics approaches promised to provide access to the uncultivated species while bypassing the problem of uncultivability. Significant departures from conventional techniques were clearly in order, and indeed, the new technologies substantially diverged from the cultivation tradition by adopting single-cell and high-throughput strategies, better mimicking the natural milieu and increasing the length of incubation and lowering the concentration of nutrients. This chapter describes the principle of these methods, details their application and the initial results of this application, and summarizes the lessons learned. Cultivation of novel species inside diffusion chambers is a welcome development, but their properties and abilities could be fully studied and utilized only if they could be adapted for growth in vitro. The authors therefore examined whether repetitive cultivation in a series of generations of diffusion chambers facilitated domestication of the grown strains, and discovered a positive correlation between the number of cultivation rounds in situ and the probability of obtaining a variant capable of growth in vitro. In a proof-of-concept study, the authors used the isolation chip (ichip) to grow marine water column and soil microorganisms, recorded the colony count, and compared the rRNA gene diversity of ichip-grown microorganisms and their colony count with microorganisms from parallel incubations in standard petri dishes. A reverse use of the diffusion chamber leads to a different type of cultivation (trap method), which selectively enriches for new and rare filamentous actinomycetes. This makes the trap method particularly useful for the discovery of novel secondary metabolites.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1

Key Concept Ranking

Scanning Electron Microscopy
0.46006474
16s rRNA Sequencing
0.43475854
0.46006474
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Design and application of diffusion chamber (A) and microbial trap (B). Explanations in the text.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

(A) Microcolonies of marine microorganisms grown inside a diffusion chamber incubated in simulated natural environment. Bars, 5 μm. (B) Growth recovery of environmental cells in diffusion chambers plotted as percentage of inoculated cells forming colonies.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Ichip design. Explanations in the text.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Novelty of seawater and soil microbial strains grown in ichip and petri dish. Equation of sequence novelty, in percentage of diversion from the known species, and taxonomic rank of novelty (genus, family level, etc.) is approximate. OTU, operational taxonomic unit.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Prospective ichip to grow oral microorganisms. (A) The assembly of the device is similar to the ichip currently in use ( Fig. 3 ): the central plate is loaded with target (dental plaque) microorganisms; two additional panels with matching through holes press the 0.03-μm-pore-size membranes against the central plate, creating multiple diffusion minichambers. (B) Relative size of the prospective ichip for oral microflora cultivation. (C) Assembled ichip is fastened in the opening of a mold of the volunteer’s upper palate, to be incubated in the mouth in touch with the molar used to sample the plaque.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Bacterial colonies and fungal hyphae (a) and actinomycetes-like colonies (b; scale, 0.1 mm) grown in a trap after 2 weeks of incubation in garden soil.

Citation: Epstein S, Lewis K, Nichols D, Gavrish E. 2010. New Approaches to Microbial Isolation, p 3-12. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555816827.ch01
1. Aas, J. A.,, B. J. Paster,, L. N. Stokes,, I. Olsen, and, F. E. Dewhirst. 2005. Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43:57215732.
2. Amann, J. 1911. Die direkte Zählung der Wasserbakterien mittels des Ultramikroskops. Zentralbl. Bakteriol. 29:381384.
3. Aoi, Y.,, T. Kinoshita,, T. Hata,, H. Ohta,, H. Obokata, and, S. Tsuneda. 2009. Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl. Environ. Microbiol. 75:38263833.
4. Beja, O.,, L. Aravind,, E. V. Koonin,, M. T. Suzuki,, A. Hadd,, L. P. Nguyen,, S. B. Jovanovich,, C. M. Gates,, R. A. Feldman,, J. L. Spudich,, E. N. Spudich, and, E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:19021906.
5. Bollmann, A.,, K. Lewis, and, S. S. Epstein. 2007. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl. Environ. Microbiol. 73:63866390.
6. 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. 68:39783987.
7. Cholodny, N. 1929. Zur Methodik der quantitativen Erforschung des bakteriellen Planktons. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. A 77:179193.
8. Connon, S. A., and, S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:38783885.
9. Davis, K. E.,, S. J. Joseph, and, P. H. Janssen. 2005. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl. Environ. Microbiol. 71:826834.
10. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl, Acad. Sci. USA 89:56855689.
11. DeLong, E. F. 2005. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3:459469.
12. Dojka, M. A.,, J. K. Harris, and, N. R. Pace. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66:16171621.
13. Ferrari, B. C.,, S. J. Binnerup, and, M. Gillings. 2005. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl. Environ. Microbiol. 71:87148720.
14. Fuhrman, J. A.,, K. McCallum, and, A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148149.
15. Gavrish, E.,, A. Bollmann,, S. Epstein, and, K. Lewis. 2008. A trap for in situ cultivation of filamentous actino-bacteria. J. Microbiol. Methods 72:257262.
16. Giovannoni, S. J.,, T. B. Britschgi,, C. L. Moyer, and, K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:6063.
17. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669685.
18. Huber, J. A.,, D. B. Mark Welch,, H. G. Morrison,, S. M. Huse,, P. R. Neal,, D. A. Butterfield, and, M. L. Sogin. 2007. Microbial population structures in the deep marine biosphere. Science 318:97100.
19. Hurst, C. J. 2005. Divining the future of microbiology. ASM News 71:262263.
20. Jannasch, H. W., and, G. E. Jones. 1959. Bacterial populations in seawater as determined by different methods of enumeration. Limnol. Oceanogr. 4:128139.
21. Kaeberlein, T.,, K. Lewis, and, S. S. Epstein. 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296:11271129.
22. Liesack, W., and, E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174:50725078.
23. Marsh, P. D. 2003. Are dental diseases examples of ecological catastrophes? Microbiology 149:279294.
24. Nichols, D.,, K. Lewis,, J. Orjala,, S. Mo,, R. Ortenberg,, P. O’Connor,, C. Zhao,, P. Vouros,, T. Kaeberlein, and, S. S. Epstein. 2008. Short peptide induces an “uncultivable” microorganism to grow in vitro. Appl. Environ. Microbiol. 74:48894897.
25. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace, and, D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337365.
26. Rappe, M. S.,, S. A. Connon,, K. L. Vergin, and, S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630633.
27. Rappe, M. S., and, S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369394.
28. Schloss, P. D., and, J. Handelsman. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68:686691.
29. Sogin, M. L.,, H. G. Morrison,, J. A. Huber,, D. Mark Welch,, S. M. Huse,, P. R. Neal,, J. M. Arrieta, and, G. J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proc. Natl. Acad. Sci. USA 103:1211512120.
30. Staley, J. T., and, A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:321346.
31. Stevenson, B. S.,, S. A. Eichorst,, J. T. Wertz,, T. M. Schmidt, and, J. A. Breznak. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70:47484755.
32. Waksman, S. A., and, M. Hotchkiss. 1937. Viability of bacteria in sea water. J. Bacteriol. 33:389400.
33. Ward, D. M.,, R. Weller, and, M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:6365.
34. Wilson, G. S. 1922. The proportion of viable bacteria in young cultures with especial reference to the technique employed in counting. J. Bacteriol. 7:405446.
35. Winslow,, C.-E. A., and, G. E. Willcomb. 1905. Tests of a method for the direct microscopic enumeration of bacteria. J. Infect. Dis. Suppl. 1:273283.
36. Winterberg, H. 1898. Zur Methodik der Bakterienzahlung. Zeitschr. Hyg. 29:7593.
37. Young, P. 1997. Major microbial diversity initiative recommended. ASM News 63:417421.
38. Zengler, K.,, G. Toledo,, M. Rappe,, J. Elkins,, E. J. Mathur,, J. M. Short, and, M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:1568115686.
39. ZoBell, C. E. 1946. Marine Microbiology: a Monograph on Hydrobacteriology. Chronica Botanica Co., Waltham, MA.

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