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Chapter 1 : Does Cultivation Still Matter?

Author: Karsten Zengler1
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Affiliations: 1: Department of Bioengineering, University of California—San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0412
Content Type: Monograph
Publication Year: 2008

Category: Genomics and Bioinformatics; Environmental Microbiology

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Abstract:

Recently several advances have been made to overcome cultivation biases and have spurred renewed interest in classical microbiology as well as in innovative isolation techniques. Researchers have discovered many clades of so far uncultivated microorganisms while analyzing the genetic information obtained from analyzing soil samples by various methods. This chapter focuses on aspects that are often not considered during cultivation, such as salt components of the medium, the choice of gelling agents and glassware, the size of sample and inoculum, the time of incubation, and how colonies are being detected. It provides detailed and resourceful advice for successful cultivation approaches. The goal of studies focusing on expressed gene products, such as RNA profiling and metaproteome, is not only to determine the genetic potential of an environment but to find out which genes are expressed at a certain moment in time under certain conditions. It is likely that not all microbes can be accessible as defined cultures in the laboratory by using current technology. Therefore, the development and combination of innovative techniques to study uncultivated microorganisms, ideally in their natural environment, is essential to advance the understanding of microbial physiology and ecology, and shed light on these most diverse creatures on our planet.

Citation: Zengler K. 2008. Does Cultivation Still Matter?, p 3-10. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch1
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References

/content/book/10.1128/9781555815509.ch01
1. Ashby, M. N.,, J. Rine,, E. F. Mongodin,, K. E. Nelson, and, D. Dimster-Denk. 2007. Serial analysis of ribosomal DNA and the unexpected dominance of rare members of microbial communities. Appl. Environ. Microbiol. 73: 4532– 4542.
2. Beijerinck, W. M. 1895. Über Spirillum desulfuricans als Ursache von Sulfatreduktion. Z entralblatt Bakteriol. 1: 1– 9, 49– 59, and 104– 114.
3. Breitbart, M.,, L. R. Thompson,, C. A. Suttle, and, M. B. Sullivan. 2007. Exploring the vast diversity of marine viruses. Oceanography 20: 135– 139.
4. Casas, V., and, F. Rohwer. 20007. Phage metagenomics. Methods Enzymol. 421: 259– 268.
5. Cash, H. L.,, C. V. Whitham,, C. L. Behrendt, and, L. V. Hooper. 2006. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313: 1126– 1130.
6. Cohn, F. 1875. Untersuchungen über Bakterien. Beitr. Biol. Pflanz. 1: 127– 224.
7. Conn, H. J. 1918. The microscopic study of bacteria and fungi in soil. N. Y. Agr. Exp. Sta., Tech. Bull. 64: 3– 20.
8. Cooper, T. F.,, D. E. Rozen, and, R. E. Lenski. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. USA 100: 1072– 1077.
9. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick,, R. D. Fleischmann,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenney,, G. Sutton,, W., FritzHugh, C. Fields, and, J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496– 512.
10. Gest, H. 2007. Fresh views of the 17th-century discoveries by Hooke and van Leeuwenhoek. Microbe 2: 483– 488.
11. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669– 685.
12. Herring, C. D.,, A. Raghunathan,, C. Honisch,, T. Patel,, M. K. Applebee,, A. J. Joyce,, T. J. Albert,, F. R. Blattner,, D. van den Boom,, C. R. Cantor, and, B. Ø. Palsson. 2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 38: 1406– 1412.
13. Huber, J. A.,, D. B. M. 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: 97– 100.
14. Keller, M., and, K. Zengler. 2004. Tapping into microbial diversity. Nat. Rev. Microbiol. 2: 141– 150.
15. Koch, R. 1877. Untersuchungen über Bakterien VI. Verfahren zur Untersuchung, zum Conservieren und Photographieren. Beitr. Biol. Pflanz. 2: 399– 434.
16. Konstantinidis, K. T.,, A. Ramette, and, J. M. Tiedje. 2006. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl. Environ. Microbiol. 72: 7286– 7293.
17. Lartigue, C.,, J. I. Glass,, N. Alperovich,, R. Pieper,, P. P. Parmar,, C. A. Hutchison III,, H. O. Smith, and, J. C. Venter. 2007. Genome transplantation in bacteria: changing one species to another. Science 317: 632– 638.
18. Lechene, C.,, F. Hillion,, G. McMahon,, D. Benson,, A. M. Kleinfeld,, J. P. Kampf,, D. Distel,, Y. Luyten,, J. Bonventre,, D. Hentschel,, K. M. Park,, S. Ito,, M. Schwartz,, G. Benichou, and, G. Slodzian. 2006. High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J. Biol. 5: 20.
19. Maron, P. A.,, L. Ranjard,, C. Mougel, and, P. Lemanceau. 2007. Metaproteomics: a new approach for studying functional microbial ecology. Microb. Ecol. 53: 486– 493.
20. Muβmann, M.,, F. Z. Hu,, M. Richter,, D. de Beer,, A. Preisler,, B. B, Jørgensen,, M. Huntemann,, F. O. Glöckner,, R. Amann,, W. J. H. Koopman,, R. S. Lasken,, B. Janto,, J. Hogg,, P. Stoodley,, R. Boissy, and, G. D. Ehrlich. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol. 5: e230.
21. Orphan, V. J.,, C. H. House,, K.-U. Hinrichs,, K. D. McKeegan, and, E. F. DeLong. 2001. Methane-consuming Archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484– 487.
22. Ouverney, C. C., and, J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65: 1746– 1752.
23. Peña, A.,, M. Valens,, F. Santos,, S. Buczolits,, J. Antón,, P. Kämpfer,, H. J. Busse,, R. Amann, and, R. Rosselló-Mora. 2005. Intraspecific comparative analysis of the species Salinibacter ruber. Extremophiles 9: 151– 161.
24. Rosselló-Mora, R., and, R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25: 39– 67.
25. Suttle, C. A. 2007. Marine viruses—major players in the global ecosystem. Nat. Rev. Microbiol. 5: 801– 812.
26. Tyson, G. W.,, I. Lo,, B. J. Baker,, E. E. Allen,, P. Hugenholtz, and, J. F. Banfield. 2005. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl. Environ. Microbiol. 71: 6319– 6324.
27. van Niel, C. B. 1949. The “Delft School” and the rise of general microbiology. Microbiol. Mol. Biol. Rev. 13: 161– 174.
28. Wagner, M.,, H. Smidt,, A. Loy, and, J. Zhou. 2007. Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb. Ecol. 53: 498– 506.
29. Winogradsky, S. 1887. Über Schwefelbacterien. Botanische Zeitung 45: 489– 507, 513– 523, 529– 539, 545– 559, 569– 576, 585– 594, and 606– 610.

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