난배양 미생물의 배양

목차

1. Abstract

2. Introduction

3. 난배양성 미생물의 기능 분석 방법
3.1. FISH (fluorescent in situ hybridization) - MAR (microautoradiography)
3.2. Stable-isotope probing (SIP)
3.3. Isotope array

4. 난배양 미생물을 성장시키는 방법

5. 난배양 미생물의 배양과 가축화

6. 성장 요인

7. 결론 및 전망

8. References

본문내용

1. Abstract
대다수의 미생물 종은 '배양되지 않고'는 실험실에서 자라지 않는다. 이 때문에 모조의 자연 환경에서 유기체를 배양하는 여러 가지 방법이 개발되었다. 이 방법들로는 자연 환경에서 화합물을 확산시킬 수 있는 공간(chamber)에 세포를 두는 방법, 균사(발목균, 미세 균류)를 형성하는 유기체들을 특정적으로 잡아둘 수 있는 다공성 막으로 된 트랩 및 배양하도록 도움을 주는 종의 아래에서 성장시키는 방법 등이 있다. in situ에서의 반복적인 배양은 시험관의 일반적인 배지에서 자랄 수 있는 길들여진 변종을 생산하고 이차 대사산물의 생산을 위해 확장 될 수 있다. 공동 배양 접근법은 배양되지 않은 박테리아인 iron-chelating siderophore의 성장 인자의 첫 번째 부류를 밝혀냈다. 다양한 분류학적 그룹의 많은 난배양된 생물체는 siderophore를 생성하는 능력을 상실했으며, 성장을 위해 인접한 종에 의존하고 있는 것으로 보인다. 새로운 배양법은 이전에는 접근 할 수 없었던 미생물의 2차대사산물 잠재력의 개발을 가능하게 한다.

2. Introduction
주어진 환경의 모든 박테리아가 실험실 배지에서 자라는 것은 아니라는 최초의 증거는 현미경 검사에서 나왔다. 현미경으로 관찰된 세포의 수는 페트리 접시에서 자라는 콜로니의 수보다 훨씬 많다. 이러한 사례로 112 주년을 맞이한 Great Plate Count Anomaly는 아마도 가장 오래된 미해결 미생물 현상일 것이다. 오스트리아의 미생물학자인 Heinrich Winterberg는 1898년에 흥미로운 관찰을 했다. 그의 샘플에 있는 미생물 세포의 수는 영양 배지에서 형성된 콜로니의 수와 일치하지 않았다. 약 10년 후 J Amann은 이 불일치를 비 배양 세포가 배양 가능한 세포보다 거의 150배 많다는 걸 정량화하여 보였다.(1911) 이 논문은 오늘날 Great Plate Count Anomaly로 알려진 중요한 현상을 발견하기 위한 초기 연구 단계 중 일부를 의미한다.

참고자료

· Winterberg, H. Zur Methodik der Bakterienzahlung. Zeitschr. f. Hyg. 29, 75–93 (1898).
· Amann, J. Die direkte Za ¨hlung der Wasserbakterien mittels des Ultramikroskops. Centralbl. f. Bakteriol. 29, 381–384 (1911).
· Staley, J. T. & Konopka, A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39, 321–346 (1985).
· Butkevich, N. V. & Butkevich, A. V. S. Multiplication of sea bacteria depending on the composition of the medium and on temperature. Microbiology (Moscow) 5, 322–343 (1936).
· Butkevich, V. S. Zu ¨r Methodik der bakterioloschen Meeresuntersuchungen und einige Angaben u ¨ber die Verteilung der Bakterien im Wasser und in den Bu ¨den des Barents Meeres. Trans. Oceanogr. Inst. Moscow (in Russian with German summary). 2, 5–39 (1932).
· Cholodny, N. Zur Methodik der quantitativen Erforschung des bakteriellen Planktons. Zentralbl. Bakteriol. Parasitenkd. Infektionskr. Hyg. A. 77, 179–193 (1929).
· Jannasch, H. W. & Jones, G. E. Bacterial populations in seawater as determined by different methods of enumeration. Limnol. Oceanogr. 4, 128–139 (1959).
· Waksman, S. A. & Hotchkiss, M. Viability of bacteria in sea water. J. Bacteriol. 33, 389–400 (1937).
· ZoBell, C. E. Marine Microbiology: A Monograph on Hydrobacteriology, Chronica Botanica: Waltham, MA, USA, (1946).
· Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R. & Stahl, D. A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986).
· Barns, S. M., Fundyga, R. E., Jeffries, M. W. & Pace, N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl Acad. Sci. USA 91, 1609–1613 (1994).
· DeLong, E. F. Archaea in coastal marine environments. Proc. Natl Acad. Sci. USA 89, 5685–5689 (1992).
· Dojka, M. A., Harris, J. K. & Pace, N. R. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66, 1617–1621 (2000).
· Fuhrman, J. A., McCallum, K. & Davis, A. A. Novel major archaebacterial group from marine plankton. Nature 356, 148–149 (1992).
· Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60–63 (1990).
· Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765–4774 (1998).
· Liesack, W. & Stackebrandt, E. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174, 5072–5078 (1992).
· Ravenschlag, K., Sahm, K., Pernthaler, J. & Amann, R. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65, 3982–3989 (1999).
· Ward, D. M., Weller, R. & Bateson, M. M. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63–65 (1990).
· Allsopp, D., Colwell, R. R. & Hawksworth, D. L. Microbial Diversity and Ecosystem Function, CAB International: Wallingford, UK, (1995). 21 Tiedje, J. M. Microbial diversity: of value to whom? ASM News 60, 524–525 (1994).
· Staley, J. T., Bryant, M. P., Pfennig, N. & Holt, J. G. (eds). Bergey’s Manual of Systematic Bacteriology. 1st edn, Vol. 3, 2185–2190 (The Williams & Wilkins Co., Baltimore, 1989).
· Rappe, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394 (2003).
· Schloss, P. D. & Handelsman, J. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68, 686–691 (2004).
· Colwell, R. R. & Grimes, D. J. Nonculturable Microorganisms in the Environment, (ASM Press: Washington, DC, 2000).
· Osburne, M. S., Grossman, T. H., August, P. R. & MacNeil, I. A. Tapping into microbial diversity for natural products drug discovery. ASM News 66, 411–417 (2000).
· Hurst, C. J. Divining the future of microbiology. ASM News 71, 262–263 (2005).
· Young, P. Major microbial diversity initiative recommended. ASM News 63, 417–421 (1997).
· Aoi, Y. et al. Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl. Environ. Microbiol. 75, 3826–3833 (2009).
· Bollmann, A., Lewis, K. & Epstein, S. S. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl. Environ. Microbiol. 73, 6386–6390 (2007). 31 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. 68, 3978–3987 (2002).
· 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. 68, 3878–3885 (2002). 33 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. 71, 826–834 (2005).
· 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. 71, 8714–8720 (2005).
· Kaeberlein, T., Lewis, K. & Epstein, S. S. Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).
· Gavrish, E., Bollmann, A., Epstein, S. & Lewis, K. A trap for in situ cultivation of filamentous actinobacteria. J. Microbiol. Methods. 72, 257–262 (2008).
· Nichols, D. et al. Short peptide induces an ‘uncultivable’ microorganism to grow in vitro. Appl. Environ. Microbiol. 74, 4889–4897 (2008).
· Rappe, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002).
· Stevenson, B. S., Eichorst, S. A., Wertz, J. T., Schmidt, T. M. & Breznak, J. A. New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70, 4748–4755 (2004).
· Zengler, K. et al. Cultivating the uncultured. Proc. Natl Acad. Sci. USA 99, 15681– 15686 (2002).
· Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69, 7210–7215 (2003).
· Nichols, D. et al. Use of ichip for high-throughput in situ cultivation of ‘uncultivable’ microbial species. Appl. Environ. Microbiol. 76, 2445–2450 (2010).
· McInerney, M. J. et al. Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann. NY Acad. Sci. 1125, 58–72 (2008).
· Williams, P., Winzer, K., Chan, W. C. & Camara, M. Look who’s talking: communication and quorum sensing in the bacterial world. Philos. Transact. R. Soc. London 362, 1119–1134 (2007).
· D’Onofrio, A. et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem. Biol. 17, 254–264 (2010).
· Challis, G. L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. Chembiochem 6, 601–611 (2005).
· Johnson, K. S., Gordon, R. M. & Coale, K. H. What controls dissolved iron concentrations in the world ocean?Mar. Chem. 57, 137–161 (1997).
· Wagner, M. & Horn, M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17, 241–249 (2006).
· Hedlund, B. P., Gosink, J. J. & Staley, J. T. Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the bacteria. Int. J. Syst. Bacteriol. 46, 960–966 (1996).
· Lee, K. B. et al. The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 55(Part 5), 1907–1919 (2005).
· Cho, J. C. & Giovannoni, S. J. Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the alpha-Proteobacteria. Int. J. Syst. Evol. Microbiol. 53(Part 4), 1031–1036 (2003).
· Luckey, M., Pollack, J. R., Wayne, R., Ames, B. N. & Neilands, J. B. Iron uptake in Salmonella typhimurium: utilization of exogenous siderochromes as iron carriers. J. Bacteriol. 111, 731–738 (1972).
· Schubert, S., Fischer, D. & Heesemann, J. Ferric enterochelin transport in Yersinia enterocolitica: molecular and evolutionary aspects. J. Bacteriol. 181, 6387–6395 (1999).
· Llamas, M. A. et al. The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J. Bacteriol. 188, 1882– 1891 (2006).
· Moon, C. D. et al. Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. BMC Microbiol. 8, 7 (2008).
· Winkelmann, G. Microbial siderophore-mediated transport. Biochem. Soc. Transact. 30, 691–696 (2002).
· Kraemer, S. Iron oxide dissolution and solubility in the presence of siderophores. Aquat. Sci. 66, 3–18 (2004).
· Challis, G. L. & Hopwood, D. A. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc. Natl Acad. Sci. USA 100 (Suppl 2), 14555–14561 (2003).
· Lewis, K. Persister cells, dormancy and infectious disease. Nat. Rev. Microbiol. 5, 48–56 (2007).
· 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 135, 486–496 (2008).
· Bollmann, A., Lewis, K. & Epstein, S. S. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl. Environ. Microbiol. 73, 6386–6390 (2007).
· Zengler, Karsten, et al. "Cultivating the uncultured." Proceedings of the National Academy of Sciences 99.24 (2002): 15681-15686.
· 김정명, 송새미, and 전체옥. "난배양성 미생물의 기능 분석 방법." 미생물학회지 45.1 (2009): 1-9.
· Jung, Dawoon, et al. "A new method for microbial cultivation and its application to bacterial community analysis in Buus Nuur, Mongolia." Fundamental and Applied Limnology/Archiv für Hydrobiologie 182.2 (2013): 171-181.
· Stewart, Eric J. "Growing unculturable bacteria." Journal of bacteriology 194.16 (2012): 4151-4160.
· Bollmann, Annette, Kim Lewis, and Slava S. Epstein. "Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates." Applied and Environmental Microbiology 73.20 (2007): 6386-6390.
· Lewis, Kim, et al. "Uncultured microorganisms as a source of secondary metabolites." The Journal of antibiotics 63.8 (2010): 468-476.