Plant Soil Environ., 2009, 55(9):379-388 | DOI: 10.17221/140/2009-PSE

Oligonucleotide microarray methodology for taxonomic and functional monitoringof microbial community composition

M. Kyselková1,2,3, J. Kopecký4, M. Ságová-Marečková4, G.L. Grundmann1,2,3, Y. Moënne-Loccoz1,2,3
1 Universitéde Lyon, F-69622, Lyon, France
2 UniversitéLyon 1, Villeurbanne, France
3 CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
4 Crop Research Institute, Prague, Czech Republic

Microarray analysis is a cultivation-independent, high-throughput technology that can be used for direct and simultaneous identification of microorganisms in complex environmental samples. This review summarizes current methodologies for oligonucleotide microarrays used in microbial ecology. It deals with probe design, microarray manufacturing, sample preparation and labeling, and data handling, as well as with the key features of microarray analysis such as specificity, sensitivity and quantification potential. Microarray analysis has been validated as an effective approach to describe the composition and dynamics of taxonomic and functional microbial communities, in environments including soil, compost, sediment, air or humans. It is now part of the technical arsenal available to address key issues in microbial community ecology, ranging from biogeography to ecosystem functioning.

Keywords: Keywords: oligonucleotide microarray; taxonomic microarray; functional microarray; microbial community

Published: September 30, 2009  Show citation

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Kyselková M, Kopecký J, Ságová-Marečková M, Grundmann GL, Moënne-Loccoz Y. Oligonucleotide microarray methodology for taxonomic and functional monitoringof microbial community composition. Plant Soil Environ. 2009;55(9):379-388. doi: 10.17221/140/2009-PSE.
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    References

    1. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. (1990): Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, 56: 1919-1925. Go to original source... Go to PubMed...
    2. Belosludtsev Y., Iverson B., Lemeshko S., Eggers R., Wiese R., Lee S., Powdrill T., Hogan M. (2001): DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Analytical Biochemistry, 292: 250-256. Go to original source... Go to PubMed...
    3. Bodrossy L., Sessitsch A. (2004): Oligonucleotide microarrays in microbial diagnostics. Current Opinion in Microbiology, 7: 245-254. Go to original source... Go to PubMed...
    4. Bodrossy L., Stralis-Pavese N., Murrell J.C., Radajewski S., Weilharter A., Sessitsch A. (2003): Development and validation of a diagnostic microbial microarray for methanotrophs. Environmental Microbiology, 5: 566-582. Go to original source... Go to PubMed...
    5. Brodie E.L., DeSantis T.Z., Joyner D.C., Baek S.M., Larsen J.T., Andersen G.L., Hazen T.C., Richardson P.M., Herman D.J., Tokunaga T.K., Wan J.M.M., Firestone M.K. (2006): Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Applied and Environmental Microbiology, 72: 6288-6298. Go to original source... Go to PubMed...
    6. Cébron A., Bodrossy L., Chen Y., Singer A.C., Thompson I.P., Prosser J.I., Murrell J.C. (2007): Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiology Ecology, 62: 12-23. Go to original source... Go to PubMed...
    7. Cho J.-C., Tiedje J.M. (2002): Quantitative detection of microbial genes by using DNA microarrays. Applied and Environmental Microbiology, 68: 1425-1430. Go to original source... Go to PubMed...
    8. DeAngelis K.M., Brodie E.L., DeSantis T.Z., Andersen G.L., Lindow S.E., Firestone M.K. (2009): Selective progressive response of soil microbial community to wild oat roots. ISME Journal, 3: 168-178. Go to original source... Go to PubMed...
    9. DeSantis T.Z., Brodie E.L., Moberg J.P., Zubieta I.X., Piceno Y.M., Andersen G.L. (2007): High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology, 53: 371-383. Go to original source... Go to PubMed...
    10. DeSantis T.Z., Dubosarskiy I., Murray S.R., Andersen G.L. (2003): Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics, 19: 1461-1468. Go to original source... Go to PubMed...
    11. DeSantis T.Z., Stone C.E., Murray S.R., Moberg J.P., Andersen G.L. (2005): Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiology Letters, 245: 271-278. Go to original source... Go to PubMed...
    12. Dolan P.L., Wu Y., Ista L.K., Metzenberg R.L., Nelson M.A., Lopez G.P. (2001): Robust and efficient synthetic method for forming DNA microarrays. Nucleic Acids Research, 29: 107. Go to original source... Go to PubMed...
    13. Fisher W., Zhang M.J. (2007): A biochip microarray fabrication system using inkjet technology. IEEE Transactions on Automation Science and Engineering, 4: 488-500. Go to original source...
    14. Flanagan J.L., Brodie E.L., Weng L., Lynch S.V., Garcia O., Brown R., Hugenholtz P., DeSantis T.Z., Andersen G.L., Wiener-Kronish J.P., Bristow J. (2007): Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology, 45: 1954-1962. Go to original source... Go to PubMed...
    15. Fotin A.V., Drobyshev A.L., Proudnikov D.Y., Perov A.N., Mirzabekov A.D. (1998): Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Research, 26: 1515-1521. Go to original source... Go to PubMed...
    16. Franke-Whittle I.H., Klammer S.H., Insam H. (2005): Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. Journal of Microbiological Methods, 62: 37-56. Go to original source... Go to PubMed...
    17. Franke-Whittle I.H., Knapp B.A., Fuchs J., Kaufmann R., Insam H. (2009): Application of COMPOCHIP microarray to investigate the bacterial communities of different composts. Microbial Ecology, 57: 510-521. Go to original source... Go to PubMed...
    18. Franssen-val Hal N.L.W., Vorst O., Kramer E., Hall R.D., Keijer J. (2002): Factors influencing cDNA microarray hybridization on silylated glass slides. Analytical Biochemistry, 308: 5-17. Go to original source... Go to PubMed...
    19. Gao H., Yang Z.K., Gentry T.J., Wu L., Schadt C.W., Zhou J. (2007): Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Applied and Environmental Microbiology, 73: 563-571. Go to original source... Go to PubMed...
    20. Gebert J., Stralis-Pavese N., Alawi M., Bodrossy L. (2008): Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray. Environmental Microbiology, 10: 1175-1188. Go to original source... Go to PubMed...
    21. González-Escalona N., Romero J., Espejo R.T. (2005): Polymorphism and gene conversion of the 16S rRNA genes in the multiple rRNA operons of Vibrio parahaemolyticus. FEMS Microbiology Letters, 246: 213-219. Go to original source... Go to PubMed...
    22. Günther S., Groth I., Grabley S., Munder T. (2006): Design and evaluation of an oligonucleotide-microarray for the detection of different species of the genus Kitasatospora. Journal of Microbiological Methods, 65: 226-236. Go to original source... Go to PubMed...
    23. He Z.L., Gentry T.J., Schadt C.W., Wu L.Y., Liebich J., Chong S.C., Huang Z.J., Wu W.M., Gu B.H., Jardine P., Criddle C., Zhou J. (2007): GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME Journal, 1: 67-77. Go to original source... Go to PubMed...
    24. Hessner M., Meyer L., Tacke, J., Muheisen S., Wang X. (2004): Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics, 5: 53. Go to original source... Go to PubMed...
    25. Hope A.C.A. (1968): A simplified Monte Carlo test procedure. Journal of the Royal Statistical Society Series B, 30: 582-598. Go to original source...
    26. Kane M.D., Jatkoe T.A., Stumpf C.R., Lu J., Thomas J.D., Madore S.J. (2000): Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays. Nucleic Acids Research, 28: 4552-4557. Go to original source... Go to PubMed...
    27. Kelly J.J., Siripong S., McCormack J., Janus L.R., Urakawa H., El Fantroussi S., Noble P.A., Sappelsa L., Rittmann B.E., Stahl D.A. (2005): DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research, 39: 3229-3238. Go to original source... Go to PubMed...
    28. Klappenbach J.A., Saxman P.R., Cole J.R., Schmidt T.M. (2001): Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Research, 29: 181-184. Go to original source... Go to PubMed...
    29. Kyselková M., Kopecký J., Felföldi T., Čermák L., Omelka M., Grundmann G., Moënne-Loccoz Y., SágováMarečková M. (2008): Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera. Antonie van Leeuwenhoek, 94: 439-453. Go to original source... Go to PubMed...
    30. Kyselková M., Kopecký J., Frapolli M., Défago G., Ságová-Marečková M., Grundmann G.L., Moënne-Loccoz Y. (2009): Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME Journal, doi:10.1038/ismej.2009.61 Go to original source... Go to PubMed...
    31. Lee M.-L.T., Kuo F.C., Whitmore G.A., Sklar J. (2000): Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proceedings of the National Academy of Sciences of the United States of America, 97: 9834-9839. Go to original source... Go to PubMed...
    32. Li X.Y., He Z.L., Zhou J.Z. (2005): Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Research, 33: 6114-6123. Go to original source... Go to PubMed...
    33. Lindroos K., Liljedahl U., Raitio M., Syvanen A.-C. (2001): Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. Nucleic Acids Research, 29: 69. Go to original source... Go to PubMed...
    34. Lipshutz R.J., Fodor S.P.A., Gingeras T.R., Lockhart D.J. (1999): High density synthetic oligonucleotide arrays. Nature Genetics, 21: 20-24. Go to original source... Go to PubMed...
    35. Liu W.T., Guo H.L., Wu J.H. (2007): Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays. Applied and Environmental Microbiology, 73: 73-82. Go to original source... Go to PubMed...
    36. Liu W.T., Mirzabekov A.D., Stahl D.A. (2001): Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environmental Microbiology, 3: 619-629. Go to original source... Go to PubMed...
    37. 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. Applied and Environmental Microbiology, 68: 5064-5081. Go to original source... Go to PubMed...
    38. Loy A., Schulz C., Lucker S., Schopfer-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. Applied and Environmental Microbiology, 71: 1373-1386. Go to original source... Go to PubMed...
    39. 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 A.W., Gross O., Grumann S., Hermann S., Jost R., Konig A., Liss T., Lussmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.H. (2004): ARB: a software environment for sequence data. Nucleic Acids Research, 32: 1363-1371. Go to original source... Go to PubMed...
    40. Marchandin H., Teyssier C., Siméon de Buochberg M., Jean-Pierre H., Carriere C., Jumas-Bilak E. (2003): Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiology, 149: 1493-1501. Go to original source... Go to PubMed...
    41. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. (2008): Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). International Journal of Systematic and Evolutionary Microbiology, 58: 200-214. Go to original source... Go to PubMed...
    42. Maskos U., Souther E.M. (1992): Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Research, 20: 1675-1678. Go to original source... Go to PubMed...
    43. McGall G., Labadie J., Brock P., Wallraff G., Nguyen T., Hinsberg W. (1996): Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proceedings of the National Academy of Sciences of the United States of America, 93: 13555-13560. Go to original source... Go to PubMed...
    44. Naum M., Brown E.W., Mason-Gamer R.J. (2008): Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the Enterobacteriaceae? Journal of Molecular Evolution, 66: 630-642. Go to original source... Go to PubMed...
    45. Palmer C., Bik E.M., Eisen M.B., Eckburg P.B., Sana T.R., Wolber P.K., Relman D.A., Brown P.O. (2006): Rapid quantitative profiling of complex microbial populations. Nucleic Acids Research, 34: 5. Go to original source... Go to PubMed...
    46. Oh S.J., Cho S.J., Kim C.O., Park J.W. (2002): Characteristics of DNA microarrays fabricated on the various aminosilane layers. Langmuir, 18: 1764-1769. Go to original source...
    47. Peplies J., Lau S.C.K., Pernthaler J., Amann R., Glockner F.O. (2004): Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environmental Microbiology, 6: 638-645. Go to original source... Go to PubMed...
    48. Pozhitkov A., Noble P.A., Domazet-Loso T., Nolte A.W., 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 Research, 34: 66. Go to original source... Go to PubMed...
    49. Pozhitkov A.E., Bailey K.D., Noble P.A. (2007): Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays. Journal of Microbiological Methods, 70: 292-300. Go to original source... Go to PubMed...
    50. Prosser J.I., Bohannan B.J.M., Curtis T.P., Ellis R.J., Firestone M.K., Freckleton R.P., Green J.L., Green L.E., Killham K., Lennon J.J., Osborn A.M., Solan M., van der Gast C.J., Young J.P.W. (2007): The role of ecological theory in microbial ecology. Nature Reviews Microbiology, 5: 384-392. Go to original source... Go to PubMed...
    51. Ramette A. (2007): Multivariate analyses in microbial ecology. FEMS Microbiology Ecology, 62: 142-160. Go to original source... Go to PubMed...
    52. Rees W., Yager T., Korte J., Von Hippel P. (1993): Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry, 32: 137-144. Go to original source... Go to PubMed...
    53. Rhee S.-K., Liu X., Wu L., Chong S.C., Wan X., Zhou J. (2004): Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Applied and Environmental Microbiology, 70: 4303-4317. Go to original source... Go to PubMed...
    54. Roesch L.F.W., Fulthorpe R.R., Riva A., Casella G., Hadwin A.K.M., Kent A.D., Daroub S.H., Camargo F.A.O., Farmerie W.G., Triplett E.W. (2007): Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1: 283-290. Go to original source... Go to PubMed...
    55. Sanguin H., Herrera A., Oger-Desfeux C., Dechesne A., Simonet P., Navarro E., Vogel T.M., Moënne-Loccoz Y., Nesme X., Grundmann G.L. (2006b): Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environmental Microbiology, 8: 289-307. Go to original source... Go to PubMed...
    56. Sanguin H., Kroneisen L., Gazengel K., Kyselková M., Remenant B., Prigent-Combaret C., Grundmann G.L., Sarniguet A., Moënne-Loccoz Y. (2008): Development of a 16S rRNA microarray approach for the monitoring of rhizosphere Pseudomonas populations associated with the decline of take-all disease of wheat. Soil Biology and Biochemistry, 40: 1028-1039. Go to original source...
    57. Sanguin H., Remenant B., Dechesne A., Thioulouse J., Vogel T.M., Nesme X., Moënne-Loccoz Y., Grundmann G.L. (2006a): Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Applied and Environmental Microbiology, 72: 4302-4312. Go to original source... Go to PubMed...
    58. SantaLucia J., Allawi H.T., Seneviratne A. (1996): Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35: 3555-3562. Go to original source... Go to PubMed...
    59. Schena M., Shalon D., Davis R.W., Brown P.O. (1995): Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science, 270: 467-470. Go to original source... Go to PubMed...
    60. Schouls L.M., Schot C.S., Jacobs J.A. (2003): Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. Journal of Bacteriology, 185: 7241-7246. Go to original source... Go to PubMed...
    61. Shchepinov M.S., Case-Green S.C., Southern E.M. (1997): Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Research, 25: 1155-1161. Go to original source... Go to PubMed...
    62. Southern E., Mir K., Shchepinov M. (1999): Molecular interactions on microarrays. Nature Genetics Supplement, 21: 5-9. Go to original source... Go to PubMed...
    63. Stralis-Pavese N., Sessitsch A., Weilharter A., Reichenauer T., Riesing J., Csontos J., Murrell, J.C., Bodrossy L. (2004): Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environmental Microbiology, 6: 347-363. Go to original source... Go to PubMed...
    64. Taylor A.F.S. (2002): Fungal diversity in ectomycorrhizal communities: sampling effort and species detection. Plant and Soil, 244: 19-28. Go to original source...
    65. Urakawa H., Noble P.A., El Fantroussi S., Kelly J.J., Stahl D.A. (2002): Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Applied and Environmental Microbiology, 68: 235-244. Go to original source... Go to PubMed...
    66. van Doorn R., Szemes M., Bonants P., Kowalchuk G.A., Salles J.F., Ortenberg E., Schoen C.D. (2007): Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArrays™. BMC Genomics, 8: 276. Go to original source... Go to PubMed...
    67. Wagner M., Smidt H., Loy A., Zhou J.Z. (2007): Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microbial Ecology, 53: 498-506. Go to original source... Go to PubMed...
    68. Wu L., Liu X., Schadt C.W., Zhou J. (2006): Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Applied and Environmental Microbiology, 72: 4931-4941. Go to original source... Go to PubMed...
    69. Xu D., Li G., Wu L., Zhou J., Xu Y. (2002): PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18: 1432-1437. Go to original source... Go to PubMed...
    70. Zammatteo N., Jeanmart L., Hamels S., Courtois S., Louette P., Hevesi L., Remacle J. (2000): Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Analytical Biochemistry, 280: 143-150. Go to original source... Go to PubMed...
    71. Zhang L., Chunlei W., Carta R., Zhao H. (2006): Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Research, 35: 18. Go to original source... Go to PubMed...
    72. Zhou J. (2003): Microarrays for bacterial detection and microbial community analysis. Current Opinion in Microbiology, 6: 288-294. Go to original source... Go to PubMed...
    73. Zhou J., Kang S., Schadt C.W., Garten C.T. (2008): Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences of the United States of America, 105: 7768-7773. Go to original source... Go to PubMed...
    74. Zhou J., Thompson D.K. (2002): Challenges in applying microarrays to environmental studies. Current Opinion in Biotechnology, 13: 204-207. Go to original source... Go to PubMed...

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