Skip to main content

Mikrobielle Lebensgemeinschaften. Strukturelle und funktionelle Analysen mit molekularbiologischer Vorgehensweise

  • Chapter
  • First Online:
Umweltmikrobiologie

Zusammenfassung

Mittlerweile stützen sich Identifizierung und Klassifizierung weitgehend auf Sequenzanalysen von ribosomaler RNA (rRNA) beziehungsweise der diese kodierenden rDNA sowie von Genen universell verbreiteter Enzyme, da dies zu phylogenetisch korrekteren taxonomischen Gruppierungen führt als traditionelle Methoden und da auch sehr entfernte Verwandtschaften analysierbar sind. Im Folgenden sollen deshalb die Prinzipien hinter den wichtigsten molekulargenetischen Methoden zur Identifizierung und Klassifizierung von isolierten Bakterien und zur Charakterisierung mikrobieller Lebensgemeinschaften kurz dargestellt werden.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 44.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 59.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Literatur

  • Amann, R. I., Ludwig, W., Schleifer, K. H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143–169.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bench, S. R., Hanson, T. E., Williamson, K. E., Ghosh, D., Radosovich, M., Wang, K., Wommack, K. E. 2007. Metagenomic characterization of Chesapeake Bay virioplankton. Appl. Environ. Microbiol. 23: 629–7641.

    Google Scholar 

  • Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D. M., Saar, M. O., Alexander, S., Alexander, Jr E. C., Rohwer, F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57 https://doi.org/10.1186/1471-2164-7-57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R. A., Felts, B., Rayhawk, S., Knight, R., Rohwer, F., Jackson, R. B. 2007. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73:7059–7066.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., Nelson, K. E. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hugenholtz, P., Goebel, B. M., Pace, N. R. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity J. Bacteriol. 180:4765–4774.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nelson, D. L., Cox, M. M. 2005. Lehninger Principles of Biochemistry, 4th ed. W. H. Freeman & Company, New York.

    Google Scholar 

  • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. und 84 weitere Autoren. 2010. A human gutmicrobial gene catalogue established by metagenomic sequencing. Nature 464:59–65.

    Google Scholar 

  • Rajilić-Stojanović, M.,. de Vos, W. M. 2014. The First 1,000 Cultured Species of the Human Gastrointestinal Microbiota. FEMS Microbiol. Rev.https://doi.org/10.1111/1574-6976.12075.

    Article  PubMed  CAS  Google Scholar 

  • Riesenfeld, C. S., Goodman, R. M., Handelsman, J. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6:981–989.

    Article  CAS  PubMed  Google Scholar 

  • Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., Loiacono, K. A., Lynch, B. A., MacNeil, I. A., Minor, C., Tiong, C. L., Gilman, M., Osburne, M. S., Clardy, J., Handelsman, J. Goodman, R. M. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541–2547.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rusch, D. B., Halpern, A. L., Sutton, G., Heidelberg, K. B., Williamson, S., Yooseph, S., Wu, D., Eisen, J. A., Hoffman, J. M., Remington, K., Beeson, K., Tran, B., Smith, H., Baden-Tillson, H., Stewart, C., Thorpe, J., Freeman, J., Andrews-Pfannkoch, C., Venter, J. E., Li, K., Kravitz, S., Heidelberg, J. F., Utterback, T., Rogers, Y.-H., Falcón, L. I., Souza, V., Bonilla-Rosso, G., Eguiarte, L. E., Karl, D. M., Sathyendranath, S., Platt, T., Bermingham, E., Gallardo, V., Tamayo-Castillo, G., Ferrari, M. R., Strausberg, R. L., Nealson, K., Friedman, R., Frazier, M., Venter, J. C. 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3): e77. 0398–0431 https://doi.org/10.1371/journal.pbio.0050077.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Smith, C.R., Baco, A.R. 2003. Ecology of whale falls at the deep-sea floor. In: Oceanography and Marine Biology: an Annual Review. (Gibson, R. N., Atkinson, R. J. A., eds., Taylor & Francis 41:311–354.

    Google Scholar 

  • Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., Bork, P., Hugenholtz, P., Rubin, E. M. 2005. Comparative metagenomics of microbial communities. Science 308:554–557.

    Article  CAS  PubMed  Google Scholar 

  • Tringe, S. G., Zhang, T., Liu, X., Yu, Y., Lee, W. H., Yap, J., Yao, F., Suan, S. T., Ing, S., Haynes, M., Rohwer, F., Wei, C. L., Tan, P., Bristow, J., Rubin, E. M., Ruan, Y. 2008. The Airborne Metagenome in an Indoor Urban Environment. PLoS ONE 3(4): e1862. https://doi.org/10.1371/journal.pone.0001862.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turnbaugh, P. J., Ley, R. E., Hamady, M. Fraser-Liggett, C., Knight, R., Gordon, J. I. 2007. The human microbiome project. Nature 449:804–810.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., Banfield, J. F. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43.

    Article  CAS  PubMed  Google Scholar 

  • Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y. H., Smith, H. O. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74.

    Article  CAS  PubMed  Google Scholar 

  • Vieites, J. M., Guazzaroni, M.-E., Beloqui, A., Golyshin, P. N., Ferrer M. 2009. Metagenomics approaches in systems microbiology. FEMS Microbiol. Rev. 33:236–255.

    Article  CAS  PubMed  Google Scholar 

  • Walter, J., Ley, R. 2011. The Human Gut Microbiome: Ecology and recent evolutionary changes. Annu. Rev. Microbiol. 65:411–429.

    Article  CAS  PubMed  Google Scholar 

  • Warnecke, F., Luginbühl, P., Ivanova, N., Ghassemian, M., Richardson, T. H., Stege, J. T., Cayouette, M., McHardy, A. C., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S. G., Podar, M., Garcia Martin, H., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N. C., Matson, E. G., Ottesen, E. A., Zhang, X., Hernández, M., Murillo, C., Acosta, L. G., Rigoutsos, I., Tamayo, G., Green, B. D.,. Chang, C, Rubin, E. M., Mathur, E. J., Robertson, D. E., Hugenholtz, P., Leadbetter, J. R. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565.

    Article  CAS  PubMed  Google Scholar 

  • Woyke, T., Teeling, H., Ivanova, N.N., Huntemann, M., Richter, M., Gloeckner, F. O., Boffelli, D., Anderson, I. J., Barry, K. W., Shapiro, H. J., Szeto, E., Kyrpides, N. C., Mussmann, M., Amann, R., Bergin, C., Ruehland, C., Rubin, E. M., Dubilier, N. 2006. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950–955.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, T., Breitbart, M., Lee, W. H., Run, J. Q., Wei, C. L., Soh, S. W., Hibberd, M. L., Liu, E. T., Rohwer, F., Ruan, Y. 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 4: e3.

    Article  PubMed  CAS  Google Scholar 

  • Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., Wang, J., Imhann, F., Brandsma, E., Jankipersadsing, S. A., Joossens, M., Cenit, M. C., Deelen, P., Swertz, M. A, Weersma, R. K, Feskens, E. J., Netea, M. G., Gevers, D., Jonkers, D., Franke, L., Aulchenko, Y. S., Huttenhower, C., Raes, J., Hofker, M. H., Xavier, R. J., Wijmenga, C., Fu, J. 2016. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352:565–569.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Weiterführende Literatur

  • Akkermans, A. D. L., van Elsas, J. D., de Bruijn, F. J. 1995. Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, Boston, London.

    Book  Google Scholar 

  • Béjà, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, L. P., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., Spudich, E. N., DeLong, E. F. 2000. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289:1902–1906.

    Article  PubMed  Google Scholar 

  • Daniel, R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3:470–478.

    Article  CAS  PubMed  Google Scholar 

  • DeLong, E. F. 2005. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3:459–469.

    Article  CAS  PubMed  Google Scholar 

  • DeLong, E. F. 2005. Microbial community genomics in the ocean. Nature Reviews. Microbiology 3:459–469.

    Article  CAS  PubMed  Google Scholar 

  • DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N. U., Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W., Karl, D. M. 2006. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311:496–503.

    Article  CAS  PubMed  Google Scholar 

  • Deutschbauer, A. M., Chivian, D., Arkin, A. P. 2006. Genomics for environmental microbiology. Curr. Opin. Biotechnol. 17:229–235.

    Article  CAS  PubMed  Google Scholar 

  • Ehrenreich, A. 2006. DNA microarray technology for the microbiologist: an overview. Appl. Microbiol. Biotechnol. 73:255–273.

    Article  CAS  PubMed  Google Scholar 

  • Frigaard, N. U., Martinez, A. Mincer, T. J., DeLong, E. F. 2006. Proteorhodopsin lateral gene transfer between marine planktonic bacteria and archaea. Nature 439:847–850.

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Martinez, J., Rodriguez-Valera, F. 2000. Microdiversity of uncultured marine prokaryotes: The SAR11 cluster and the marine Archaea of Group I. Molec. Ecol. 9:935–948.

    Article  CAS  Google Scholar 

  • Gentry, T. J., Wickham, G. S., Schadt, C. W., He, Z., Zhou, J. 2006. Microarray applications in microbial ecology research. Microbial Ecol. 52:159–175.

    Article  CAS  Google Scholar 

  • Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., Field, K. G. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63.

    Article  CAS  PubMed  Google Scholar 

  • Gómez-Consarnau, L., González, J. M., Coll-Lladó, M., Gourdon, P., Pascher, T., Neutze, R. Pedrós-Alió, C., Pinhassi, J. 2007. Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445:210–213.

    Article  PubMed  CAS  Google Scholar 

  • Guazzaroni, M.-E., Golyshin, P. N., Ferrer, M. 2010. Analysis of Complex Microbial Communities through Metagenomic Survey. In: Metagenomics. Theory, Methods and Applications. (Diana Marco, ed.) Caister Academic Press, Norfolk, UK, p. 55–77.

    Google Scholar 

  • Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669–685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hoefs, J. 2004. Stable Isotope Geochemistry. 5. Aufl. Springer, Berlin.

    Book  Google Scholar 

  • Lesk, A. M. 2003. Bioinformatik. Eine Einführung. Spektrum, Heidelberg, Berlin.

    Google Scholar 

  • Liu, W.-T., Zhu, L. 2005. Environmental microbiology-on-a-chip and its future impacts. Trends Biotechnol. 23:174–179.

    Article  CAS  PubMed  Google Scholar 

  • Martiny, A.C., Coleman, M. L., Chisholm, S. W. 2006. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proc. Natl. Acad. Sci. USA 103:12552–12557.

    Article  CAS  Google Scholar 

  • Metzker, M. L. 2010. Sequencing technologies – the next generation. Nat. Rev. Genet. 11:31–46.

    Article  CAS  PubMed  Google Scholar 

  • Ram, R. J., VerBerkmoes, N. C., Thelen, M. P., Tyson, G. W., Baker, B. J., Blake, R. C. 2nd, Shah, M., Hettich, R. L., Banfield, J. F. 2005. Community proteomics of a natural microbial biofilm. Science 308:1915–1920.

    Article  CAS  PubMed  Google Scholar 

  • Rittmann, B. E., Hausner, M., Löffler, F., Love, N. G., Muyzer, G., Okabe, S., Oerther, D. B., Peccia, J., Raskin, L., Wagner, M. 2006. A vista for microbial ecology and environmental biotechnology. Environ. Sci. Technol. 40:1096–1103.

    Article  PubMed  Google Scholar 

  • Sessitsch, A., Hackl, E., Wenzl, P., Kilian, A., Kostic, T., Stralis-Pavese, N., Tankouo Sandjong, B., Bodrossy, L. 2006. Diagnostic microbial microarrays in soil ecology. New Phytologist 171:719–736.

    Article  CAS  Google Scholar 

  • Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., Herndl, G. J. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. USA 103:12115–12120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torsvik, V., Daae, F. L., Sandaa, R. A., Ovreas, L. 1998. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64:53–62.

    Article  CAS  PubMed  Google Scholar 

  • Torsvik, V., Ovreas, L., Thingstad, T. F. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:1064–1066.

    Article  CAS  PubMed  Google Scholar 

  • Torsvik, V., Ovreas, L. 2002. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 5:240–245.

    Article  CAS  PubMed  Google Scholar 

  • Wagner, M. 2004. Deciphering functions of uncultured microorganisms. ASM News 70:63–70.

    Google Scholar 

  • Wagner, M., Smidt, H., Loy, A., Zhou, J. 2007. Unravelling microbial communities with DNA-microarrays: Challenges and future directions. Microbial Ecol. 53:498–506.

    Article  CAS  Google Scholar 

  • Wilmes, P., Simmons, S. L., Denef, V. J., Banfield, J. F. 2009. The dynamic genetic repertoire of microbial communities. FEMS Microbiol. Rev. 33:109–132.

    Article  CAS  PubMed  Google Scholar 

  • Xu, J. 2006. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molec. Ecol. 15:1713–1731.

    Article  CAS  Google Scholar 

  • Zhou, J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288–294.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Walter Reineke .

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer-Verlag GmbH Deutschland, ein Teil von Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Reineke, W., Schlömann, M. (2020). Mikrobielle Lebensgemeinschaften. Strukturelle und funktionelle Analysen mit molekularbiologischer Vorgehensweise. In: Umweltmikrobiologie. Springer Spektrum, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-59655-5_12

Download citation

Publish with us

Policies and ethics