Which Members of the Microbial Communities Are Active? Microarrays

Conference paper

Abstract

Here, we introduce the concept of microarrays, discuss the advantages of several different types of arrays and present a case study that illustrates a targeted-profiling approach to bioremediation of a hydrocarbon-contaminated site in an Arctic environment. The majority of microorganisms in the terrestrial subsurface, particularly those involved in ‘heavy oil’ formation, reservoir souring or biofouling remain largely uncharacterised (Handelsman, 2004). There is evidence though that these processes are biologically catalysed, including stable isotopic composition of hydrocarbons in oil formations (Pallasser, 2000; Sun et al., 2005), the absence of biodegraded oil from reservoirs warmer than 80°C (Head et al., 2003) or negligible biofouling in the absence of biofilms (Dobretsov et al., 2009; Lewandowski and Beyenal, 2008), and all clearly suggest an important role for microorganisms in the deep biosphere in general and oilfield systems in particular. While the presence of sulphate-reducing bacteria in oilfields was first observed in the early twentieth century (Bastin, 1926), it was only through careful experiments with isolates from oil systems or contaminated environments that unequivocal evidence for hydrocarbon biodegradation under anaerobic conditions was provided (for a review, see Widdel et al., 2006). Work with pure cultures and microbial enrichments also led to the elucidation of the biochemistry of anaerobic aliphatic and aromatic hydrocarbon degradation and the identification of central metabolites and genes involved in the process, e.g. (Callaghan et al., 2008; Griebler et al., 2003; Kropp et al., 2000). This information could then be extrapolated to the environment to monitor degradation processes and determine if in situ microbial populations possessed the potential for contaminant bioremediation, e.g. Parisi et al. (2009). While other methods have also been developed to monitor natural attenuation of hydrocarbons (Meckenstock et al., 2004), we are only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

Keywords

Microbial Community Structure Hydrocarbon Degradation Microbiologically Influence Corrosion Hydrocarbon Biodegradation Nutrient Amendment 
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. Atlas RM (1995) Bioremediation of petroleum pollutants. Int Biodeterior Biodegrad 35:317–327CrossRefGoogle Scholar
  2. Bastin ES (1926) The presence of sulphate reducing bacteria in oil field waters. Science 63:21–24CrossRefGoogle Scholar
  3. Bragg JR, Prince RC et al (1994) Effectiveness of bioremediation for the Exxon Valdez oil spill. Nature 368:413–418CrossRefGoogle Scholar
  4. Brodie EL, DeSantis TZ et al (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288–6298CrossRefGoogle Scholar
  5. Caffrey SM, Park H-S et al (2008) Gene array analysis of sulfate-reducing bacteria grown on an iron-electrode under conditions of cathodic protection. Corrosion 64, New Orleans, LA, 16–20 Mar 2008Google Scholar
  6. Callaghan AV, Wawrik B et al (2008) Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes. Biochem Biophys Res Commun 366:142–148CrossRefGoogle Scholar
  7. Demeter J, Beauheim C et al (2007) The Stanford microarray database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35(suppl 1):D766–D770CrossRefGoogle Scholar
  8. Dobretsov S, Teplitski M et al (2009) Mini-review: quorum sensingin the marine environment and its relationship to biofouling. Biofouling 25:413–427CrossRefGoogle Scholar
  9. Duncan KE, Gieg LM et al (2009) Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ Sci Technol 43:7977–7984CrossRefGoogle Scholar
  10. Gentry TJ, He Z et al (2009) Detection and characterization of uncultivated microorganisms using microarrays. In: Steinbuechel A (ed) Microbiology monographs, vol. 13. Berlin, SpringerGoogle Scholar
  11. Griebler C, Safinowski M et al (2003) Combined application of stable carbon isotope analysis and specific metabolites determination for assessing in situ degradation of aromatic hydrocarbons in a tar oil-contaminated aquifer. Environ Sci Technol 38:617–631CrossRefGoogle Scholar
  12. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685CrossRefGoogle Scholar
  13. He Z, Gentry TJ et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J 1:67–77CrossRefGoogle Scholar
  14. Head IM, Jones DM et al (2003) Biological activity in the deep subsurface and the origin of heavy oils. Nature 426:344–352CrossRefGoogle Scholar
  15. Holden C (2009) Over the top. Science Magazine, AAAS 326:25Google Scholar
  16. Hong S, Bunge J et al (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J 3(12):1365–1373CrossRefGoogle Scholar
  17. Kropp KG, Davidova IA et al (2000) Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl Environ Microbiol 66:5393–5398CrossRefGoogle Scholar
  18. Kuntze K, Shinoda Y et al (2008) 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ Microbiol 10:1547–1556CrossRefGoogle Scholar
  19. Lewandowski Z, Beyenal H (2008) Mechanisms of microbially influenced corrosion. In: Flemming H-C, Murthy PS, Venkatesan R, Cooksey K (eds) Marine and industrial biofouling. Springer, Berlin, Heidelberg, p 4Google Scholar
  20. Liu W, Zhu L (2005) Environmental microbiology-on-a-chip and its future impacts. Trends Biotechnol 23:174–179CrossRefGoogle Scholar
  21. Meckenstock RU, Morasch B et al (2004) Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers. J Contaminant Hydrol 75:215–255CrossRefGoogle Scholar
  22. Orphan VJ, Taylor LT et al (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Micro 66:700–711CrossRefGoogle Scholar
  23. Pallasser RJ (2000) Recognising biodegradation in gas/oil accumulations through the d13C compositions of gas components. Organ Geochem 31:1363–1373CrossRefGoogle Scholar
  24. Parisi VA, Brubaker GR et al (2009) Field metabolomics and laboratory assessments of anaerobic intrinsic bioremediation of hydrocarbons at a petroleum-contaminated site. Microb Biotechnol 2:202–212CrossRefGoogle Scholar
  25. Pham VD, Hnatow LL et al (2009) Characterizing microbial diversity in petroleum wather from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol 11:176–187CrossRefGoogle Scholar
  26. Schena M, Shalon D et al (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470CrossRefGoogle Scholar
  27. Schulze A, Downward J (2001) Navigating gene expression using microarrays – a technology review. Nat Cell Biol 3:E190–E195CrossRefGoogle Scholar
  28. Shalon D, Smith SJ et al (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6:639–645CrossRefGoogle Scholar
  29. Stoevesandt O, Taussig MJ et al (2009) Protein microarrays: high-throughput tools for proteomics. Expert Rev 6:145–157CrossRefGoogle Scholar
  30. Sun Y, Chen Z et al (2005) Stable carbon and hydrogen isotopic fractionation of individual n-alkanes accompanying biodegradation: evidence from a group of progressively biodegraded oils. Organic Geochem 36:225–238CrossRefGoogle Scholar
  31. Widdel F, Boetius A et al (2006) Anaerobic biodegradation of hydrocarbons including methane. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Ecophysiology and biochemistry, vol 2. Springer, New York, pp 1028–1049Google Scholar
  32. Yergeau E, Arbour M et al (2009) Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments. Appl Environ Microbiol 75:6258–6267CrossRefGoogle Scholar
  33. Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotech 13:204–207CrossRefGoogle Scholar

Copyright information

© Springer Netherlands 2010

Authors and Affiliations

  1. 1.Department of Botany and MicrobiologyInstitute for Energy and the Environment, University of OklahomaNormanUSA

Personalised recommendations