Skip to main content
SpringerLink
Log in

Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions

  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2

Similar content being viewed by others

References

  1. Adamczyk, J, Hesselsoe, M, Iversen, N, Horn, M, Lehner, A, Nielsen, PH, Schloter, M, Roslev, P, Wagner, M (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69: 6875–6887

    Article  PubMed  CAS  Google Scholar 

  2. Adey, NB, Lei, M, Howard, MT, Jensen, JD, Mayo, DA, Butel, DL, Coffin, SC, Moyer, TC, Slade, DE, Spute, MK, Hancock, AM, Eisenhoffer, GT, Dalley, BK, McNeely, MR (2002) Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-micron-thick chamber. Anal Chem 74: 6413–6417

    Article  PubMed  CAS  Google Scholar 

  3. Baner, J, Isaksson, A, Waldenstrom, E, Jarvius, J, Landegren, U, Nilsson, M (2003) Parallel gene analysis with allele-specific padlock probes and tag microarrays. Nucleic Acids Res 31: e103

    Article  PubMed  CAS  Google Scholar 

  4. Blom, H, Johansson, M, Hedman, AS, Lundberg, L, Hanning, A, Hard, S, Rigler, R (2002) Parallel fluorescence detection of single biomolecules in microarrays by a diffractive-optical-designed 2 × 2 fan-out element. Appl Opt 41: 3336–3342

    PubMed  CAS  Google Scholar 

  5. Bodrossy, L, Stralis-Pavese, N, Murrell, JC, Radajewski, S, Weilharter, A, Sessitsch, A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566–582

    Article  PubMed  CAS  Google Scholar 

  6. Bodrossy, L, Sessitsch, A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7: 245–254

    Article  PubMed  CAS  Google Scholar 

  7. Bodrossy, L, Stralis-Pavese, N, Konrad-Koszler, M, Weilharter, A, Reichenauer, TG, Schofer, D, Sessitsch, A (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72: 1672–1676

    Article  PubMed  CAS  Google Scholar 

  8. Brodie, EL, Desantis, TZ, Joyner, DC, Baek, SM, Larsen, JT, Andersen, GL, Hazen, TC, Richardson, PM, Herman, DJ, Tokunaga, TK, Wan, JM, Firestone, MK (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288–6298

    Article  PubMed  CAS  Google Scholar 

  9. Busti, E, Bordoni, R, Castiglioni, B, Monciardini, P, Sosio, M, Donadio, S, Consolandi, C, Rossi Bernardi, L, Battaglia, C, De Bellis, G (2002) Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). BMC Microbiol 2: 27

    Article  PubMed  Google Scholar 

  10. Castiglioni, B, Rizzi, E, Frosini, A, Sivonen, K, Rajaniemi, P, Rantala, A, Mugnai, MA, Ventura, S, Wilmotte, A, Boutte, C, Grubisic, S, Balthasart, P, Consolandi, C, Bordoni, R, Mezzelani, C, Battaglia, C, De Bellis, G (2004) Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70: 7161–7172

    Article  PubMed  CAS  Google Scholar 

  11. Cho, J-C, Tiedje, JM (2002) Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol 68: 1425–1430

    Article  PubMed  CAS  Google Scholar 

  12. Cole, JR, Chai, B, Farris, RJ, Wang, Q, Kulam, SA, McGarrell, DM, Garrity, GM, Tiedje, JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: 294–296

    Article  CAS  Google Scholar 

  13. Cox, WG, Beaudet, MP, Agnew, JY, Ruth, JL (2004) Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal Biochem 331: 243–254

    Article  PubMed  CAS  Google Scholar 

  14. Curtis, TP, Sloan, WT, Scannell, JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99: 10494–10499

    Article  PubMed  CAS  Google Scholar 

  15. DeLong, EF (2002) Microbial population genomics and ecology. Curr Opin Microbiol 5: 520–524

    Article  PubMed  Google Scholar 

  16. Denef, VJ, Park, J, Rodrigues, JL, Tsoi, TV, Hashsham, SA, Tiedje, JM (2003) Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5: 933–943

    Article  PubMed  CAS  Google Scholar 

  17. Dennis, P, Edwards, EA, Liss, SN, Fulthorpe, R (2003) Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol 69: 769–778

    Article  PubMed  CAS  Google Scholar 

  18. Desantis, TZ, Stone, CE, Murray, SR, Moberg, JP, Andersen, GL (2005) Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett 245: 271–278

    Article  PubMed  CAS  Google Scholar 

  19. DeSantis, TZ, Hugenholtz, P, Larsen, N, Rojas, M, Brodie, EL, Keller, T, Huber, T, Dalevi, D, Hu, P, Andersen, GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069–5072

    Article  PubMed  CAS  Google Scholar 

  20. El Fantroussi, S, Urakawa, H, Bernhard, AE, Kelly, JJ, Noble, PA, Smidt, H, Yershov, GM, Stahl, DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69: 2377–2382

    Article  PubMed  CAS  Google Scholar 

  21. Francois, P, Bento, M, Vaudaux, P, Schrenzel, J (2003) Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens. J Microbiol Methods 55: 755–762

    Article  PubMed  CAS  Google Scholar 

  22. Franke-Whittle, IH, Klammer, SH, Insam, H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Methods 62: 37–56

    Article  PubMed  CAS  Google Scholar 

  23. Gans, J, Wolinsky, M, Dunbar, J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387–1390

    Article  PubMed  CAS  Google Scholar 

  24. Gonzalez, JM, Portillo, MC, Saiz-Jimenez, C (2005) Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ Microbiol 7: 1024–1028

    Article  PubMed  CAS  Google Scholar 

  25. Guschin, DY, Mobarry, BK, Proudnikov, D, Stahl, DA, Rittmann, BE, Mirzabekov, AD (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63: 2397–2402

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  27. Hashsham, SA, Wick, LM, Rouillard, J-M, Gulari, E, Tiedje, JM (2004) Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens Bioelectron 20: 668–683

    Article  PubMed  CAS  Google Scholar 

  28. Hesse, J, Jacak, J, Kasper, M, Regl, G, Eichberger, T, Winklmayr, M, Aberger, F, Sonnleitner, M, Schlapak, R, Howorka, S, Muresan, L, Frischauf, AM, Schütz, GJ (2006) RNA expression profiling at the single molecule level. Genome Res 16: 1041–1045

    Article  PubMed  CAS  Google Scholar 

  29. Hong, BJ, Sunkara, V, Park, JW (2005) DNA microarrays on nanoscale-controlled surface. Nucleic Acids Res 33: e106

    Article  PubMed  CAS  Google Scholar 

  30. Jacobs, KA, Rudersdorf, R, Neill, SD, Dougherty, JP, Brown, EL, Fritsch, EF (1988) The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to identifying recombinant DNA clones. Nucleic Acids Res 16: 4637–4650

    Article  PubMed  CAS  Google Scholar 

  31. Kim, MG, Shin, YB, Jung, JM, Ro, HS, Chung, BH (2005) Enhanced sensitivity of surface plasmon resonance (SPR) immunoassays using a peroxidase-catalyzed precipitation reaction and its application to a protein microarray. J Immunol Methods 297: 125–132

    Article  PubMed  CAS  Google Scholar 

  32. Klappenbach, JA, Saxman, PR, Cole, JR, Schmidt, TM (2001) rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29: 181–184

    Article  PubMed  CAS  Google Scholar 

  33. Le Berre, V, Trevisiol, E, Dagkessamanskaia, A, Sokol, S, Caminade, AM, Majoral, JP, Meunier, B, Francois, J (2003) Dendrimeric coating of glass slides for sensitive DNA microarrays analysis. Nucleic Acids Res 31: e88

    Article  PubMed  CAS  Google Scholar 

  34. Lehner, A, Loy, A, Behr, T, Gaenge, H, Ludwig, W, Wagner, M, Schleifer, K-H (2005) Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol Lett 246: 133–142

    Article  PubMed  CAS  Google Scholar 

  35. Li, ES, Ng, JK, Wu, JH, Liu, WT (2004) Evaluating single-base-pair discriminating capability of planar oligonucleotide microchips using a non-equilibrium dissociation approach. Environ Microbiol 6: 1197–1202

    Article  PubMed  CAS  Google Scholar 

  36. Liang, RQ, Li, W, Li, Y, Tan, CY, Li, JX, Jin, YX, Ruan, KC (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res 33: e17

    Article  PubMed  CAS  Google Scholar 

  37. Liu, WT, Mirzabekov, AD, Stahl, DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3: 619–629

    Article  PubMed  CAS  Google Scholar 

  38. Loy, A, Lehner, A, Lee, N, Adamczyk, J, Meier, H, Ernst, J, Schleifer, K-H, Wagner, M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 5064–5081

    Article  PubMed  CAS  Google Scholar 

  39. Loy, A, Küsel, K, Lehner, A, Drake, HL, Wagner, M (2004) Microarray and functional gene analyses of sulfate-reducing prokaryotes in low sulfate, acidic fens reveal co-occurrence of recognized genera and novel lineages. Appl Environ Microbiol 70: 6998–7009

    Article  PubMed  CAS  Google Scholar 

  40. Loy, A, Schulz, C, Lücker, S, Schöpfer-Wendels, A, Stoecker, K, Baranyi, C, Lehner, A, Wagner, M (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order “Rhodocyclales”. Appl Environ Microbiol 71: 1373–1386

    Article  PubMed  CAS  Google Scholar 

  41. Loy, A, Bodrossy, L (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363: 106–119

    Article  PubMed  CAS  Google Scholar 

  42. Loy, A, Taylor, MW, Bodrossy, L, Wagner, M (2006) Applications of nucleic acid microarrays in soil microbial ecology. In: Cooper, JE, Rao, JR (Eds.) Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis, 1, CABI Publishing, Wallingford, Oxfordshire, UK, pp 18–41

    Google Scholar 

  43. Ludwig, W, Strunk, O, Klugbauer, S, Klugbauer, N, Weizenegger, M, Neumaier, J, Bachleitner, M, Schleifer, KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19: 554–568

    Article  PubMed  CAS  Google Scholar 

  44. Ludwig, W, Strunk, O, Westram, R, Richter, L, Meier, H, Yadhukumar, Buchner, A, Lai, T, Steppi, S, Jobb, G, Forster, W, Brettske, I, Gerber, S, Ginhart, AW, Gross, O, Grumann, S, Hermann, S, Jost, R, Konig, A, Liss, T, Lussmann, R, May, M, Nonhoff, B, Reichel, B, Strehlow, A, Stamatakis, A, Stuckmann, N, Vilbig, A, Lenke, M, Ludwig, T, Bode, A, Schleifer, KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363–1371

    Article  PubMed  CAS  Google Scholar 

  45. Manefield, M, Whiteley, AS, Griffiths, RI, Bailey, MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367–5373

    Article  PubMed  CAS  Google Scholar 

  46. Marcelino, LA, Backman, V, Donaldson, A, Steadman, C, Thompson, JR, Preheim, SP, Lien, C, Lim, E, Veneziano, D, Polz, MF (2006) Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A 103: 13629–13634

    Article  PubMed  CAS  Google Scholar 

  47. Maskos, U, Southern, EM (1992) Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Res 20: 1675–1678

    Article  PubMed  CAS  Google Scholar 

  48. Matveeva, OV, Shabalina, SA, Nemtsov, VA, Tsodikov, AD, Gesteland, RF, Atkins, JF (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 31: 4211–4217

    Article  PubMed  CAS  Google Scholar 

  49. McKendry, R, Zhang, J, Arntz, Y, Strunz, T, Hegner, M, Lang, HP, Baller, MK, Certa, U, Meyer, E, Guntherodt, HJ, Gerber, C (2002) Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array. Proc Natl Acad Sci U S A 99: 9783–9788

    Article  PubMed  CAS  Google Scholar 

  50. McQuain, MK, Seale, K, Peek, J, Fisher, TS, Levy, S, Stremler, MA, Haselton, FR (2004) Chaotic mixer improves microarray hybridization. Anal Biochem 325: 215–226

    Article  PubMed  CAS  Google Scholar 

  51. Neufeld, JD, Mohn, WW, de Lorenzo, V (2006) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ Microbiol 8: 126–140

    Article  PubMed  CAS  Google Scholar 

  52. Palmer, C, Bik, EM, Eisen, MB, Eckburg, PB, Sana, TR, Wolber, PK, Relman, DA, Brown, PO (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34: e5

    Article  PubMed  CAS  Google Scholar 

  53. Peplies, J, Lau, SC, Pernthaler, J, Amann, R, Glöckner, FO (2004) Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ Microbiol 6: 638–645

    Article  PubMed  CAS  Google Scholar 

  54. Polz, MF, Cavanaugh, CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724–3730

    PubMed  CAS  Google Scholar 

  55. Pozhitkov, A, Noble, PA, Domazet-Loso, T, Nolte, AW, Sonnenberg, R, Staehler, P, Beier, M, Tautz, D (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res 34: e66

    Article  PubMed  Google Scholar 

  56. Radajewski, S, Ineson, P, Parekh, NR, Murrell, JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649

    Article  PubMed  CAS  Google Scholar 

  57. Relogio, A, Schwager, C, Richter, A, Ansorge, W, Valcarcel, J (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 30: e51

    Article  PubMed  Google Scholar 

  58. Rhee, SK, Liu, X, Wu, L, Chong, SC, Wan, X, Zhou, J (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70: 4303–4317

    Article  PubMed  CAS  Google Scholar 

  59. Rudi, K, Rud, I, Holck, A (2003) A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feed. Nucleic Acids Res 31: e62

    Article  PubMed  CAS  Google Scholar 

  60. Schadt, CW, Liebich, J, Chong, SC, Gentry, TJ, He, Z, Pan, H, Zhou, J (2005) Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities. Methods Microbiol 34: 331–368

    Article  CAS  Google Scholar 

  61. Schena, M, Shalon, D, Davis, RW, Brown, PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470

    Article  PubMed  CAS  Google Scholar 

  62. Sekar, R, Fuchs, BM, Amann, R, Pernthaler, J (2004) Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl Environ Microbiol 70: 6210–6219

    Article  PubMed  CAS  Google Scholar 

  63. Shchepinov, MS, Case-Green, SC, Southern, EM (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res 25: 1155–1161

    Article  PubMed  CAS  Google Scholar 

  64. Southern, E, Mir, K, Shchepinov, M (1999) Molecular interactions on microarrays. Nat Genet 21: 5–9

    Article  PubMed  CAS  Google Scholar 

  65. Stoffels, M, Ludwig, W, Schleifer, KH (1999) rRNA probe-based cell fishing of bacteria. Environ Microbiol 1: 259–271

    Article  PubMed  CAS  Google Scholar 

  66. Stralis-Pavese, N, Sessitsch, A, Weilharter, A, Reichenauer, T, Riesing, J, Csontos, J, Murrell, JC, Bodrossy, L (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6: 347–363

    Article  PubMed  CAS  Google Scholar 

  67. Szemes, M, Bonants, P, de Weerdt, M, Baner, J, Landegren, U, Schoen, CD (2005) Diagnostic application of padlock probes-multiplex detection of plant pathogens using universal microarrays. Nucleic Acids Res 33: e70

    Article  PubMed  Google Scholar 

  68. Taroncher-Oldenburg, G, Griner, EM, Francis, CA, Ward, BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69: 1159–1171

    Article  PubMed  CAS  Google Scholar 

  69. Taylor, MW, Loy, A, Wagner, M (2007) Microarrays for studying the composition and function of microbial communities. In: Seviour, RJ, Blackall, LL (Eds.) The Microbiology of Activated Sludge, IWA Publishing, London, UK, (in press)

  70. Thompson, M, Cheran, LE, Zhang, M, Chacko, M, Huo, H, Sadeghi, S (2005) Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe. Biosens Bioelectron 20: 1471–1481

    Article  PubMed  CAS  Google Scholar 

  71. Tiquia, SM, Wu, L, Chong, SC, Passovets, S, Xu, D, Xu, Y, Zhou, J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36: 664–675

    PubMed  CAS  Google Scholar 

  72. Torsvik, V, Goksoyr, J, Daae, FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782–787

    PubMed  CAS  Google Scholar 

  73. Urakawa, H, Noble, PA, El Fantroussi, S, Kelly, JJ, Stahl, DA (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 68: 235–244

    Article  PubMed  CAS  Google Scholar 

  74. Urakawa, H, El Fantroussi, S, Smidt, H, Smoot, JC, Tribou, EH, Kelly, JJ, Noble, PA, Stahl, DA (2003) Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl Environ Microbiol 69: 2848–2856

    Article  PubMed  CAS  Google Scholar 

  75. Wagner, M, Horn, M, Daims, H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6: 302–309

    Article  PubMed  CAS  Google Scholar 

  76. Wagner, M (2004) Deciphering the function of uncultured microorganisms. ASM News 70: 63–70

    Google Scholar 

  77. Wagner, M (2005) The community level: physiology and interactions of prokaryotes in the wilderness. Environ Microbiol 7: 483–485

    Article  PubMed  Google Scholar 

  78. Wagner, M, Nielsen, PH, Loy, A, Nielsen, JL, Daims, H (2006) Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol 17: 1–9

    Article  CAS  Google Scholar 

  79. Wilson, KH, Wilson, WJ, Radosevich, JL, DeSantis, TZ, Viswanathan, VS, Kuczmarski, TA, Andersen, GL (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68: 2535–2541

    Article  PubMed  CAS  Google Scholar 

  80. Wu, L, Thompson, DK, Li, G, Hurt, RA, Tiedje, JM, Zhou, J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67: 5780–5790

    Article  PubMed  CAS  Google Scholar 

  81. Wu, L, Thompson, DK, Liu, X, Fields, MW, Bagwell, CE, Tiedje, JM, Zhou, J (2004) Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol 38: 6775–6782

    Article  PubMed  CAS  Google Scholar 

  82. Wu, L, Liu, X, Schadt, CW, Zhou, J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72: 4931–4941

    Article  PubMed  CAS  Google Scholar 

  83. Yu, F, Yao, D, Knoll, W (2004) Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS). Nucleic Acids Res 32: e75

    Article  PubMed  CAS  Google Scholar 

  84. Zhang, L, Hurek, T, Reinhold-Hurek, B (2005) Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations. Nucleic Acids Res 33: e166

    Article  PubMed  CAS  Google Scholar 

  85. Zhou, J, Thompson, DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13: 204–207

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  87. Zhou, X, Wu, L, Zhou, J (2004) Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir 20: 8877–8885

    Article  PubMed  CAS  Google Scholar 

  88. Zhou, X, Zhou, J (2004) Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal Chem 76: 5302–5312

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Research on DNA microarrays by MW and AL was financed by the German Bundesministerium für Bildung und Forschung in the framework of the BIOLOG I+II program, the Bayerische Forschungsstiftung, the Austrian Science Fund (FWF project P16580-B14), the European Community (Marie Curie Intra-European Fellowship to AL), and the University of Vienna. JZ’s effort was supported by The United States Department of Energy under the Natural and Accelerated Bioremediation Research Program, and the Genomics:GTL program of the Office of Biological and Environmental Research, Office of Science. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for DOE under contract #DE-AC05-96OR22464. Support to HS for array-related research was provided by the Ecogenomics programme of the Netherlands Genome Initiative, the Dutch Science Foundation (NWO-STW), the European Community (FP5:MicrobeDiagnostics, FP6:Aquaterra, FeedforPigHealth, Sedbarcah), The Wageningen Centre for Food Sciences, and the National Institutes of Health (NIH/NIDCR).

Author information

Authors and Affiliations

  1. Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A-1090, Wien, Austria

    Michael Wagner & Alexander Loy

  2. Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT, Wageningen, The Netherlands

    Hauke Smidt

  3. Institute for Environmental Genomics, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA

    Jizhong Zhou

Authors
  1. Michael Wagner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hauke Smidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alexander Loy
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jizhong Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael Wagner.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wagner, M., Smidt, H., Loy, A. et al. Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions. Microb Ecol 53, 498–506 (2007). https://doi.org/10.1007/s00248-006-9197-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-006-9197-7

Keywords

Search

Navigation