Chapter 83 : Functional Gene Arrays for Microbial Community Analysis

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The major advantage of microarrays is that attachment to the solid surface confers the ability to print an enormous number of different probes (thousands to hundreds of thousands per square centimeter) on an individual array. The authors proposed that microarrays of potential use for environmental samples can be divided into three or more major groups based on the type of nucleic acid probes arrayed including (i) phylogenetic oligonucleotide arrays (POAs), (ii) community genome arrays (CGAs), and (iii) functional gene arrays (FGAs). Due to the analytical versatility of FGAs, this chapter focuses on their development, application, and use in characterizing functional genes involved in biogeochemical processes and bioremediation. Along with the size and sequence of the FGA probes, the temperature and composition of the hybridization solution control the stringency of hybridization. It is preferable to use highly specific hybridization conditions for FGAs because of the potential for many similar sequences to be present. Researchers have successfully used FGAs to examine microbial involvement in several environmental processes including nitrogen fixation, nitrification, denitrification, and sulfate reduction in freshwater and marine systems; degradation of organic contaminants including polychlorinated biphenyls and polycyclic aromatic hydrocarbons in soils and sediments; and methane-oxidizing capacity and diversity in landfill-simulating soil. Development of prokaryotic mRNA amplification methods will likely broaden the range of samples for which FGA analysis of microbial activity is possible.

Citation: Gentry T, Schadt C, He Z, Zhou J. 2007. Functional Gene Arrays for Microbial Community Analysis, p 1052-1062. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch83
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Citation: Gentry T, Schadt C, He Z, Zhou J. 2007. Functional Gene Arrays for Microbial Community Analysis, p 1052-1062. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch83
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Citation: Gentry T, Schadt C, He Z, Zhou J. 2007. Functional Gene Arrays for Microbial Community Analysis, p 1052-1062. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch83
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1. Beißbarth, T.,, K. Fellenberg,, B. Brors,, R. Arribas-Prat,, J. Boer,, N. C. Hauser,, M. Scheideler,, J. D. Hoheisel,, G. Schütz,, A. Poustka, and, M. Vingron. 2000. Processing and quality control of DNA array hybridization data. Bioinformatics 16:10141022.
2. Bodrossy, L.,, and A. Sessitsch. 2004. Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Micro-biol. 7:245254.
3. Bodrossy, L.,, N. Stralis-Pavese,, J. C. Murrell,, S. Radajewski,, A. Weilharter, and, A. Sessitsch. 2003. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5:566582.
4. Botero, L. M.,, S. D’Imperio,, M. Burr,, T. R. McDermott,, M. Young, and, D. J. Hassett. 2005. Poly(A) polymerase modification and reverse transcriptase PCR amplification of environmental RNA. Appl. Environ. Microbiol. 71:12671275.
5. Bozdech, Z.,, J. Zhu,, M. P. Joachimiak,, F. E. Cohen,, B. Pulliam, and, J. L. DeRisi. 2003. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 4:R9.
6. Burgmann, H.,, F. Widmer,, W. V. Sigler, and, J. Zeyer. 2003. mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl. Environ. Microbiol. 69:19281935.
7. Cho, J. C.,, and J. M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67:36773682.
8. Cho, J. C.,, and J. M. Tiedje. 2002. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68:14251430.
9. Chou, H. H.,, A. P. Hsia,, D. L. Mooney, and, P. S. Schnable. 2004. Picky: oligo microarray design for large genomes. Bioinformatics 20:28932902.
10. Cook, K. L.,, and G. S. Sayler. 2003. Environmental application of array technology: promise, problems and practicalities. Curr. Opin. Biotechnol. 14:311318.
11. Crosby, L. D.,, and C. S. Criddle. 2003. Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. BioTechniques 34:790798.
12. Denef, V. J.,, J. Park,, J. L. M. Rodrigues,, T. V. Tsoi,, S. A. Hashsham, and, J. M. Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5:933943.
13. Dennis, P.,, E. A. Edwards,, S. N. Liss, and, R. Fulthorpe. 2003. Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl. Environ. Microbiol. 69:769778.
14. Dudley, A. M.,, J. Aach,, M. A. Steffen, and, G. M. Church. 2002. Measuring absolute expression with micro-arrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99:75547559.
15. Eisen, M. B.,, P. T. Spellman,, P. O. Brown, and, D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:1486314868.
16. El Fantroussi, S.,, H. Urakawa,, A. E. Bernhard,, J. J. Kelly,, P. A. Noble,, H. Smidt,, G. M. Yershov, and, D. A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl. Environ. Microbiol. 69:23772382.
17. Emrich, S. J.,, M. Lowe, and, A. L. Delcher. 2003. PROBEmer: a web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res. 31:37463750.
18. Farrelly, V.,, F. A. Rainey, and, E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:27982801.
19. Gans, J.,, M. Wolinsky, and, J. Dunbar. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:13871390.
20. Gilbert, D. R.,, M. Schroeder, and, J. van Helden. 2000. Interactive visualization and exploration of relationships between biological objects. Trends Biotechnol. 18:487494.
21. Gordon, P. M.,, and C. W. Sensen. 2004. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res. 32:e133.
22. Guschin, D.,, G. Yershov,, A. Zaslavsky,, A. Gemmell,, V. Shick,, D. Proudnikov,, P. Arenkov, and, A. Mirzabekov. 1997. Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal. Biochem. 250:203211.
23. He, Z.,, L. Wu,, M. W. Fields, and, J. Zhou. 2005. Use of microarrays with different probe sizes for monitoring gene expression. Appl. Environ. Microbiol. 71:51545162.
24. He, Z.,, L. Wu,, X. Li,, M. W. Fields, and, J. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl. Environ. Microbiol. 71:37533760.
25. Hughes, T. R.,, M. Mao,, A. R. Jones,, J. Burchard,, M. J. Marton,, K. W. Shannon,, S. M. Lefkowitz,, M. Ziman,, J. M. Schelter,, M. R. Meyer,, S. Kobayashi,, C. Davis,, H. Dai,, Y. D. He,, S. B. Stephaniants,, G. Cavet,, W. L. Walker,, A. West,, E. Coffey,, D. D. Shoemaker,, R. Stoughton,, A. P. Blanchard,, S. H. Friend, and, P. S. Linsley. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19:342347.
26. Hurt, R. A.,, X. Qiu,, L. Wu,, Y. Roh,, A. V. Palumbo,, J. M. Tiedje, and, J. Zhou. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67:44954503.
27. Jenkins, B. D.,, G. F. Steward,, S. M. Short,, B. B. Ward, and, J. P. Zehr. 2004. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl. Environ. Microbiol. 70:17671776.
28. Kane, M. D.,, T. A. Jatkoe,, C. R. Stumpf,, J. Lu,, J. D. Thomas, and, S. J. Madore. 2000. Assessment of the sensitivity and specificity of oligonucleotide (50mer) micro-arrays. Nucleic Acids Res. 28:45524557.
29. Kim, B. C.,, J. H. Park, and, M. B. Gu. 2004. Development of a DNA microarray chip for the identification of sludge bacteria using an unsequenced random genomic DNA hybridization method. Environ. Sci. Technol. 38:67676774.
30. Letowski, J.,, R. Brousseau, and, L. Masson. 2004. Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J. Microbiol. Methods 57:269278.
31. Li, X.,, Z. He, and, J. Zhou. 2005. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33:61146123.
32. Liebich, J.,, C. W. Schadt,, S. C. Chong,, Z. He,, S.-K. Rhee, and, J. Zhou. 2006. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl. Environ. Microbiol. 72:16881691.
33. Li, F.,, and G. D. Stormo. 2001. Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17:10671076.
34. Loy, A.,, K. Kusel,, A. Lehner,, H. L. Drake, and, M. Wagner. 2004. Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages. Appl. Environ. Microbiol. 70:69987009.
35. Loy, A.,, A. Lehner,, N. Lee,, J. Adamczyk,, H. Meier,, J. Ernst,, K. H. Schleifer, and, M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:50645081.
36. Magurran, A. E. 2004. Measuring Biological Diversity. Blackwell Publishing, Malden, Mass.
37. Murray, C. J. 2002. Sampling and data analysis for environmental microbiology, p. 166–177. In C. J. Hurst,, R. L. Crawford,, G. R. Knudsen,, M. J. McInerney, and, L. D. Stetzenbach (ed.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington, D.C.
38. Nielsen, H. B.,, R. Wernersson, and, S. Knudsen. 2003. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res. 31:34913496.
39. Nordberg, E. K. 2005. YODA: selecting signature oligonucleotides. Bioinformatics 21:13651370.
40. Reymond, N.,, H. Charles,, L. Duret,, F. Calevro,, G. Beslon, and, J. M. Fayard. 2004. ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics 20:271273.
41. Reysenbach, A. L.,, L. J. Giver,, G. S. Wickham, and, N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Micro-biol. 58:34173418.
42. Rhee, S. K.,, X. Liu,, L. Wu,, S. C. Chong,, X. Wan, and, J. Zhou. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:43034317.
43. Rimour, S.,, D. Hill,, C. Militon, and, P. Peyret. 2005. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics 21:10941103.
44. Rouillard, J. M.,, C. J. Herbert, and, M. Zuker. 2002. OligoArray: genome-scale oligonucleotide design for micro-arrays. Bioinformatics 18:486487.
45. Rouillard, J. M.,, M. Zuker, and, E. Gulari. 2003. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 31:30573062.
46. Saleh-Lakha, S.,, M. Miller,, R. G. Campbell,, K. Schneider,, P. Elahimanesh,, M. M. Hart, and, J. T. Trevors. 2005. Microbial gene expression in soil: methods, applications and challenges. J. Microbiol. Methods 63:119.
47. Schadt, C. W.,, J. Liebich,, S. C. Chong,, T. J. Gentry,, Z. He,, H. Pan, and, J. Zhou. 2005. Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities, p. 331–368. In T. Savidge and, H. Pothulakis (ed.), Microbial Imaging, vol. 34. Academic Press, Inc., London, United Kingdom.
48. Schadt, C. W.,, and J. Zhou. 2005. Advances in microar-rays for soil microbial community analyses. In P. Nannipieri and, K. Smalla (ed.), Soil Biology: Nucleic Acids and Proteins in Soil. Springer-Verlag, Berlin, Germany.
49. Schena, M.,, D. Shalon,, R. W. Davis, and, P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467470.
50. Sebat, J. L.,, F. S. Colwell, and, R. L. Crawford. 2003. Metagenomic profiling: microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 69:49274934.
51. Sessitsch, A.,, S. Gyamfi,, N. Stralis-Pavese,, A. Weilharter, and, U. Pfeifer. 2002. RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. J. Microbiol. Methods 51:171179.
52. Small, J.,, D. R. Call,, F. J. Brockman,, T. M. Straub, and, D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67:47084716.
53. Steward, G. F.,, B. D. Jenkins,, B. B. Ward, and, J. P. Zehr. 2004. Development and testing of a DNA macro-array to assess nitrogenase (nifH) gene diversity. Appl. Environ. Microbiol. 70:14551465.
54. Stralis-Pavese, N.,, A. Sessitsch,, A. Weilharter,, T. Reichenauer,, J. Riesing,, J. Csontos,, J. C. Murrell, and, L. Bodrossy. 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6:347363.
55. Suzuki, M. T.,, and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625630.
56. Tamayo, P.,, D. Slonim,, J. Mesirov,, Q. Zhu,, S. Kitareewan,, E. Dmitrovsky,, E. S. Lander, and, T. R. Golub. 1999. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96:29072912.
57. Taroncher-Oldenburg, G.,, E. M. Griner,, C. A. Francis, and, B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69:11591171.
58. Tiquia, S. M.,, L. Wu,, S. C. Chong,, S. Passovets,, D. Xu,, Y. Xu, and, J. Zhou. 2004. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 36:664675.
59. Torsvik, V.,, J. Goksøyr, and, F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782787.
60. Torsvik, V.,, L. Ovreas, and, T. F. Thingstad. 2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:10641066.
61. Tsai, Y. L.,, J. Y. Le, and, B. H. Olson. 2003. Magnetic bead hybridization to detect enterotoxigenic Escherichia coli strains associated with cattle in environmental water sources. Can. J. Microbiol. 49:391398.
62. Urakawa, H.,, S. El Fantroussi,, H. Smidt,, J. C. Smoot,, E. H. Tribou,, J. J. Kelly,, P. A. Noble, and, D. A. Stahl. 2003. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Environ. Microbiol. 69:28482856.
63. von Wintzingerode, F.,, U. B. Gobel, and, E. Stacke-brandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213229.
64. Wang, X.,, and B. Seed. 2003. Selection of oligonucleotide probes for protein coding sequences. Bioinformatics 19:796802.
65. Wilson, K. H.,, W. J. Wilson,, J. L. Radosevich,, T. Z. DeSantis,, V. S. Viswanathan,, T. A. Kuczmarski, and, G. L. Andersen. 2002. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68:25352541.
66. Wu, L.,, X. Liu,, C. W. Schadt, and, J. Zhou. Microarray-based analysis of sub-nanogram quantities of microbial community DNA using whole community genome amplification (WCGA). Proc. Natl. Acad. Sci. USA, in press.
67. Wu, L. Y.,, D. K. Thompson,, G. S. Li,, R. A. Hurt,, J. M. Tiedje, and, J. Z. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67:57805790.
68. Wu, L. Y.,, D. K. Thompson,, X. D. Liu,, M. W. Fields,, C. E. Bagwell,, J. M. Tiedje, and, J. Z. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38:67756782.
69. Xu, D.,, G. Li,, L. Wu,, J. Zhou, and, Y. Xu. 2002. PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18:14321437.
70. Xu, Y. 2004. Microarray gene expression data analysis, p. 177–206. In J. Zhou,, D. K. Thompson,, Y. Xu, and, J. M. Tiedje (ed.), Microbial Functional Genomics. John Wiley & Sons, Inc., Hoboken, N.J.
71. Zhou, J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288294.
72. Zhou, J.,, and D. K. Thompson. 2004. DNA microarray technology, p. 141–176. In J. Zhou,, D. K. Thompson,, Y. Xu, and, J. M. Tiedje (ed.), Microbial Functional Genomics. John Wiley & Sons, Inc., Hoboken, N.J.
73. Zhou, J.,, M. A. Bruns, and, J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316322.
74. Zhou, J.,, and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13:204207.
75. Zhou, X.,, L. Wu, and, J. Zhou. 2004. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir 20:88778885.
76. Zhou, X.,, and J. Zhou. 2004. Improving the signal sensitivity and photostability of DNA hybridizations on micro-arrays by using dye-doped core-shell silica nanoparticles. Anal. Chem. 76:53025312.
77. Zhou, Y.-X.,, P. Kalocsai,, J.-Y. Chen, and, S. Shams. 2000. Information processing issues and solutions associated with microarray technology, p. 167–200. In M. Schena (ed.), Microarray Biochip Technology. Eaton Publishing, Natick, Mass.


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Freely available programs for oligonucleotide probe design

Citation: Gentry T, Schadt C, He Z, Zhou J. 2007. Functional Gene Arrays for Microbial Community Analysis, p 1052-1062. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch83

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