Application of Molecular Microbiological Methods to the Oil Industry to Analyse DNA, RNA and Proteins

Conference paper

Abstract

Microorganisms have a tremendous impact on the deep biosphere. They are fundamental components of the global carbon, sulfur, nitrogen and energy cycles (Trudinger and Swaine, 1979). Microorganisms are also responsible for shaping our natural resources, for example the conversion of light to heavy petroleum reserves is a consequence of biodegredation (Head et al., 2003).

Keywords

Clone Library Phylogenetic Marker Deep Biosphere rRNA Gene Amplicon Sequencing Important Functional Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Aitken CM, Jones DM, Larter SR (2004) Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs. Nature 431:291–294CrossRefGoogle Scholar
  2. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers.J Microbiol Methods 55:541–555CrossRefGoogle Scholar
  3. Bayani J, Squire JA (2004) Fluorescence in situ Hybridisation (FISH). [Bonifacino JS, Dasso M, Harford JB, Lippincott-Schwartz J, Yamada KM (eds),] Current Protocols in Cell Biology ( Chapter 22). Bethesda, Maryland
  4. Dams E, Hendriks L, Van de Peer Y, Neefs JM, Smits G, Vandenbempt I, De Wachter R (1988) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 16(Suppl):r87–r173CrossRefGoogle Scholar
  5. Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68:3035–3045CrossRefGoogle Scholar
  6. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3:e3042CrossRefGoogle Scholar
  7. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63CrossRefGoogle Scholar
  8. Gray ND, Sherry A, Larter SR, Erdmann M, Leyris J, Liengen T, Beeder J, Head IM (2009) Biogenic methane production in formation waters from a large gas field in the North Sea. Extremophiles 13:511–519CrossRefGoogle Scholar
  9. Handelsman J, Liles MR, Mann DA, Riesenfeld CS, Goodman RM (2002) Cloning the metagenome: culture-independent access to the diversity and function of the uncultivated microbial world. In: Dorrell BWAN (ed) Functional microbial genomics. Academic Press Inc., New YorkGoogle Scholar
  10. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77CrossRefGoogle Scholar
  11. Head IM, Jones DM, Larter SR (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426:344–352CrossRefGoogle Scholar
  12. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100CrossRefGoogle Scholar
  13. Karr EA, Sattley WM, Rice MR, Jung DO, Madigan MT, Achenbach LA (2005) Diversity and distribution of sulfate-reducing bacteria in permanently frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 71:6353–6359CrossRefGoogle Scholar
  14. Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328–1333CrossRefGoogle Scholar
  15. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578, Table of ContentsCrossRefGoogle Scholar
  16. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959CrossRefGoogle Scholar
  17. Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326CrossRefGoogle Scholar
  18. Luna GM, Stumm K, Pusceddu A, Danovaro R (2009) Archaeal diversity in deep-sea sediments estimated by means of different terminal-restriction fragment length polymorphisms (T-RFLP) protocols. Curr Microbiol 59:356–361CrossRefGoogle Scholar
  19. Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493CrossRefGoogle Scholar
  20. Morales SE, Holben WE (2009) Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis. Appl Environ Microbiol 75:2677–2683CrossRefGoogle Scholar
  21. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek 73:127–141CrossRefGoogle Scholar
  22. Ollivier B, Magot M (2005) Petroleum microbiology. ASM Press, Washington, DCGoogle Scholar
  23. Parro V, Moreno-Paz M, Gonzalez-Toril E (2007) Analysis of environmental transcriptomes by DNA microarrays. Environ Microbiol 9:453–464CrossRefGoogle Scholar
  24. Radajewski S, McDonald IR, Murrell JC (2003) Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14:296–302CrossRefGoogle Scholar
  25. Schonmann S, Loy A, Wimmersberger C, Sobek J, Aquino C, Vandamme P, Frey B, Rehrauer H, Eberl L (2009) 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environ Microbiol 11:779–800CrossRefGoogle Scholar
  26. Smith CJ, Osborn AM (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67:6–20CrossRefGoogle Scholar
  27. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814CrossRefGoogle Scholar
  28. Trudinger PA, Swaine DJ (1979) Biogeochemical cycling of mineral-forming elements. Elsevier Scientific, AmsterdamGoogle Scholar
  29. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271Google Scholar
  30. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294CrossRefGoogle Scholar

Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  1. 1.Genome AlbertaCalgaryCanada

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