Oligonucleotide microarray methodology for taxonomic and functional monitoring of microbial community composition

Plant, Soil and Environment

Volumn 55, Issue 9, 2009, Pages 379-388

  Kyselkova M ^a,b,c   Kopecky J ^d   Sagova Mareckova M ^d   Grundmann, G L ^a,b,c   Moenne Loccoz Y ^a,b,c  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

^c University of Lyon   (France)

^d CROP RESEARCH INSTITUTE   (Czech Republic)

Author keywords

Functional microarray; Microbial community; Oligonucleotide microarray; Taxonomic microarray

Indexed keywords

EID: 70350151245     PISSN: 12141178     EISSN: None     Source Type: Journal    
DOI: 10.17221/140/2009-pse     Document Type: Article

References (74)

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.
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.
3. Bodrossy L., Sessitsch A. (2004): Oligonucleotide micro- arrays in microbial diagnostics. Current Opinion in Microbiology, 7: 245-254.
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.
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.
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.
7. Cho J.-C, Tiedje J.M. (2002): Quantitative detection of microbial genes by using DNA microarrays. Applied and Environmental Microbiology, 68: 1425-1430.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 pa- rahaemolyticus. FEMS Microbiology Letters, 246: 213-219.
22. Günther S., Groth I., Grabley S., Munder T. (2006): Design and evaluation of an oligonucleotide-microar- ray for the detection of different species of the genus Kitasatospora. Journal of Microbiological Methods, 65: 226-236.
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.
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.
25. Hope A.C.A. (1968): A simplified Monte Carlo test procedure. Journal of the Royal Statistical Society Series B, 30: 582-598.
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.
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.
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.
29. Kyselková M., Kopecký J., Felföldi T., Čermák L., Omel- ka M., Grundmann G., Moënne-Loccoz Y., Ságová- Marečková M. (2008): Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera. Antonie van Leeuwen- hoek, 94: 439-453.
30. Kyselková M., Kopecký J., Frapolli M., Défago G., Ságová-Marečková M., Grundmann G.L., Mönne-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
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.
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.
33. Lindroos K., Liljedahl U., Raitio M., Syvanen A.-C. (2001): Minisequencing on oligonucleotide micro- arrays: comparison of immobilisation chemistries. Nucleic Acids Research, 29: 69.
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.
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.
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.
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 prokaryo- tes in the environment. Applied and Environmental Microbiology, 68: 5064-5081.
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 betaproteobacte- rial order Rhodocydales. Applied and Environmental Microbiology, 71: 1373-1386.
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.
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.
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.
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.
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.
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.
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.
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.
47. Peplies J., Lau S.C.K., Pernthaler J., Amann R., Glock- ner F.O. (2004): Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environmental Microbiology, 6: 638-645.
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.
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.
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.
51. Ramette A. (2007): Multivariate analyses in microbial ecology. FEMS Microbiology Ecology, 62: 142-160.
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.
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.
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.
55. Sanguin H., Herrera A., Oger-Desfeux C, Dechesne A., Simonet P., Navarro E., Vogel T.M., Moenne-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.
56. Sanguin H., Kroneisen L., Gazengel K., Kyselkova 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.
57. Sanguin H., Remenant B., Dechesne A., Thioulouse J., Vogel T.M., Nesme X., Moenne-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.
58. SantaLucia J., Allawi H.T., Seneviratne A. (1996): Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35: 3555-3562.
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.
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.
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.
62. Southern E., Mir K., Shchepinov M. (1999): Molecular interactions on microarrays. Nature Genetics Supplement, 21: 5-9.
63. Stralis-Pavese N., Sessitsch A., Weilharter A., Reichen- auer 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.
64. Taylor A.F.S. (2002): Fungal diversity in ectomycorrhizal communities: sampling effort and species detection. Plant and Soil, 244: 19-28.
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.
66. van Doom R., Szemes M., Bonants P., Kowalchuk G.A., Salles J.F., Ortenberg E., Schoen CD. (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.
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.
68. Wu L., Liu X., Schadt C.W, Zhou J. (2006): Microar- ray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Applied and Environmental Microbiology, 72: 4931-4941.
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.
70. Zammatteo N., Jeanmart L., Hamels S., Courtois S., Louette P., Hevesi L., Remacle ). (2000): Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Analytical Biochemistry, 280: 143-150.
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.
72. Zhou J. (2003): Microarrays for bacterial detection and microbial community analysis. Current Opinion in Microbiology, 6: 288-294.
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.
74. Zhou J., Thompson D.K. (2002): Challenges in applying microarrays to environmental studies. Current Opinion in Biotechnology, 13: 204-207.