Microarray Applications in Microbial Ecology Research (original) (raw)
References
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 PubMedCAS Google Scholar
Barnett, MJ, Toman, CJ, Fisher, RF, Long, SR (2004) A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote–host interaction. Proc Natl Acad Sci USA 101: 16636–16641 PubMedCAS Google Scholar
Behr, MA, Wilson, MA, Gill, WP, Salamon, H, Schoolnik, GK, Rane, S, Small, PM (1999) Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284: 1520–1523 PubMedCAS Google Scholar
Berry, AE, Chiocchini, C, Selby, T, Sosio, M, Wellington, EM (2003) Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett 223: 15–20 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Bodrossy, L, Sessitsch, A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7: 245–254 PubMedCAS Google Scholar
Botero, LM, D'Imperio, S, Burr, M, McDermott, TR, Young, M, Hassett, DJ (2005) Poly(A) polymerase modification and reverse transcriptase PCR amplification of environmental RNA. Appl Environ Microbiol 71: 1267–1275 PubMedCAS Google Scholar
Bozdech, Z, Zhu, J, Joachimiak, MP, Cohen, FE, Pulliam, B, DeRisi, JL (2003) Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 4: R9 PubMed Google Scholar
Burgmann, H, Widmer, F, Sigler, WV, Zeyer, J (2003) mRNA extraction and reverse transcription–PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69: 1928–1935 PubMedCAS Google Scholar
Cannone, JJ, Subramanian, S, Schnare, MN, Collett, JR, D'Souza, LM, Du, Y, Feng, B, Lin, N, Madabusi, LV, Muller, KM, Pande, N, Shang, Z, Yu, N, Gutell, RR (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2 PubMed Google Scholar
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, A, 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 PubMedCAS Google Scholar
Chandler, DP, Newton, GJ, Small, JA, Daly, DS (2003) Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Appl Environ Microbiol 69: 2950–2958 PubMedCAS Google Scholar
Chandler, DP, Jarrell, AE (2004) Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles. Appl Environ Microbiol 70: 2621–2631 PubMedCAS Google Scholar
Cho, JC, Tiedje, JM (2001) Bacterial species determination from DNA–DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67: 3677–3682 PubMedCAS Google Scholar
Cho, JC, Tiedje, JM (2002) Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol 68: 1425–1430 PubMedCAS Google Scholar
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: D294–D296 PubMedCAS Google Scholar
Cook, KL, Sayler, GS (2003) Environmental application of array technology: promise, problems and practicalities. Curr Opin Biotechnol 14: 311–318 PubMedCAS Google Scholar
Crosby, LD, Criddle, CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790–798 PubMedCAS Google Scholar
de los Reyes, FL, 3rd, Raskin, L (2002) Role of filamentous microorganisms in activated sludge foaming: relationship of mycolata levels to foaming initiation and stability. Water Res 36: 445–459 PubMed Google Scholar
Denef, VJ, Park, J, Rodrigues, JLM, 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 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Dong, Y, Glasner, JD, Blattner, FR, Triplett, EW (2001) Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl Environ Microbiol 67: 1911–1921 PubMedCAS Google Scholar
Duburcq, X, Olivier, C, Malingue, F, Desmet, R, Bouzidi, A, Zhou, F, Auriault, C, Gras-Masse, H, Melnyk, O (2004) Peptide–protein microarrays for the simultaneous detection of pathogen infections. Bioconjug Chem 15: 307–316 PubMedCAS Google Scholar
Dudley, AM, Aach, J, Steffen, MA, Church, GM (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci USA 99: 7554–7559 PubMedCAS Google Scholar
Dziejman, M, Balon, E, Boyd, D, Fraser, CM, Heidelberg, JF, Mekalanos, JJ (2002) Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci USA 99: 1556–1561 PubMedCAS Google Scholar
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 PubMed Google Scholar
Emrich, SJ, Lowe, M, Delcher, AL (2003) PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res 31: 3746–3750 PubMedCAS Google Scholar
Farrelly, V, Rainey, FA, Stackebrandt, E (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: 2798–2801 PubMedCAS Google Scholar
Gans, J, Wolinsky, M, Dunbar, J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387–1390 PubMedCAS Google Scholar
Greene, EA, Voordouw, G (2003) Analysis of environmental microbial communities by reverse sample genome probing. J Microbiol Methods 53: 211–219 PubMedCAS Google Scholar
Guschin, D, Yershov, G, Zaslavsky, A, Gemmell, A, Shick, V, Proudnikov, D, Arenkov, P, Mirzabekov, A (1997) Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem 250: 203–211 PubMedCAS Google Scholar
Gutell, RR, Lee, JC, Cannone, JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12: 301–310 PubMedCAS Google Scholar
Handelsman, J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669–685 PubMedCAS Google Scholar
He, Z, Wu, L, Fields, MW, Zhou, J (2005) Comparison of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 71: 5154–5162 PubMedCAS Google Scholar
Held, GA, Grinstein, G, Tu, Y (2003) Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci USA 100: 7575–7580 PubMedCAS Google Scholar
Hughes, TR, Mao, M, Jones, AR, Burchard, J, Marton, MJ, Shannon, KW, Lefkowitz, SM, Ziman, M, Schelter, JM, Meyer, MR, Kobayashi, S, Davis, C, Dai, H, He, YD, Stephaniants, SB, Cavet, G, Walker, WL, West, A, Coffey, E, Shoemaker, DD, Stoughton, R, Blanchard, AP, Friend, SH, Linsley, PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342–347 PubMedCAS Google Scholar
Hurt, RA, Qiu, X, Wu, L, Roh, Y, Palumbo, AV, Tiedje, JM, Zhou, J (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67: 4495–4503 PubMedCAS Google Scholar
Jenkins, BD, Steward, GF, Short, SM, Ward, BB, Zehr, JP (2004) Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl Environ Microbiol 70: 1767–1776 PubMedCAS Google Scholar
Kane, MD, Jatkoe, TA, Stumpf, CR, Lu, J, Thomas, JD, Madore, SJ (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28: 4552–4557 PubMedCAS Google Scholar
Kim, BC, Park, JH, Gu, MB (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: 6767–6774 PubMedCAS Google Scholar
Kingsley, MT, Straub, TA, Call, DR, Daly, DS, Wunschel, SC, Chandler, DP (2002) Fingerprinting closely related Xanthomonas pathovars with random nonamer oligonucleotide microarrays. Appl Environ Microbiol 68: 6361–6370 PubMedCAS Google Scholar
Koizumi, Y, Kelly, JJ, Nakagawa, T, Urakawa, H, El-Fantroussi, S, Al-Muzaini, S, Fukui, M, Urushigawa, Y, Stahl, DA (2002) Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA–DNA membrane hybridization, and DNA microarray technology. Appl Environ Microbiol 68: 3215–3225 PubMedCAS Google Scholar
Larsen, N, Olsen, GJ, Maidak, BL, McCaughey, MJ, Overbeek, R, Macke, TJ, Marsh, TL, Woese, CR (1993) The ribosomal database project. Nucleic Acids Res 21: 3021–3023 PubMedCAS Google Scholar
Letowski, J, Brousseau, R, Masson, L (2004) Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods 57: 269–278 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Li, F, Stormo, GD (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17: 1067–1076 PubMedCAS Google Scholar
Li, X, He, Z, Zhou, J (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 33: 6114–6123 PubMedCAS Google Scholar
Liebich, J, Schadt, CW, Chong, SC, He, Z, Rhee, SK, Zhou, J (2006) Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol 72: 1688–1691 PubMedCAS Google Scholar
Liu, RH, Yang, J, Lenigk, R, Bonanno, J, Grodzinski, P (2004) Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal Chem 76: 1824–1831 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Liu, WT, Zhu, L (2005) Environmental microbiology-on-a-chip and its future impacts. Trends Biotechnol 23: 174–179 PubMedCAS Google Scholar
Liu, Y, Zhou, J, Omelchenko, MV, Beliaev, AS, Venkateswaran, A, Stair, J, Wu, L, Thompson, DK, Xu, D, Rogozin, IB, Gaidamakova, EK, Zhai, M, Makarova, KS, Koonin, EV, Daly, MJ (2003) Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci USA 100: 4191–4196 PubMedCAS Google Scholar
Loy, A, Lehner, A, Lee, N, Adamczyk, J, Meier, H, Ernst, J, Schleifer, KH, 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 PubMedCAS Google Scholar
Loy, A, Horn, M, Wagner, M (2003) probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31: 514–516 PubMedCAS Google Scholar
Loy, A, Kusel, K, Lehner, A, Drake, HL, Wagner, M (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: 6998–7009 PubMedCAS Google Scholar
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.” Appl Environ Microbiol 71: 1373–1386 PubMedCAS Google Scholar
Mitra, RM, Shaw, SL, Long, SR (2004) Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume–rhizobia symbiosis. Proc Natl Acad Sci USA 101: 10217–10222 PubMedCAS Google Scholar
Murray, AE, Lies, D, Li, G, Nealson, K, Zhou, J, Tiedje, JM (2001) DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci USA 98: 9853–9858 PubMedCAS Google Scholar
Nielsen, HB, Wernersson, R, Knudsen, S (2003) Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31: 3491–3496 PubMedCAS Google Scholar
Noller, HF, Kop, J, Wheaton, V, Brosius, J, Gutell, RR, Kopylov, AM, Dohme, F, Herr, W, Stahl, DA, Gupta, R, Waese, CR (1981) Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res 9: 6167–6189 PubMedCAS Google Scholar
Noller, HF (1984) Structure of ribosomal RNA. Annu Rev Biochem 53: 119–162 PubMedCAS Google Scholar
Ochman, H, Lerat, E, Daubin, V (2005) Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci USA 102(Suppl 1): 6595–6599 PubMedCAS Google Scholar
Ochman, H, Santos, SR (2005) Exploring microbial microevolution with microarrays. Infect Genet Evol 5: 103–108 PubMedCAS Google Scholar
Olsen, GJ, Lane, DJ, Giovannoni, SJ, Pace, NR, Stahl, DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40: 337–365 PubMedCAS Google Scholar
Olsen, GJ, Overbeek, R, Larsen, N, Marsh, TL, McCaughey, MJ, Maciukenas, MA, Kuan, WM, Macke, TJ, Xing, Y, Woese, CR (1992) The Ribosomal Database Project. Nucleic Acids Res 20(Suppl): 2199–2200 PubMedCAS Google Scholar
Peplies, J, Glockner, FO, Amann, R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69: 1397–1407 PubMedCAS Google Scholar
Polz, MF, Bertilsson, S, Acinas, SG, Hunt, D (2003) A(r)Ray of hope in analysis of the function and diversity of microbial communities. Biol Bull 204: 196–199 PubMedCAS Google Scholar
Radajewski, S, Ineson, P, Parekh, NR, Murrell, JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649 PubMedCAS Google Scholar
Ratushna, VG, Weller, JW, Gibas, CJ (2005) Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 6: 31 PubMed Google Scholar
Reymond, N, Charles, H, Duret, L, Calevro, F, Beslon, G, Fayard, JM (2004) ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics 20: 271–273 PubMedCAS Google Scholar
Reysenbach, AL, Giver, LJ, Wickham, GS, Pace, NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58: 3417–3418 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Ro, HS, Jung, SO, Kho, BH, Hong, HP, Lee, JS, Shin, YB, Kim, MG, Chung, BH (2005) Surface plasmon resonance imaging-based protein array chip system for monitoring a hexahistidine-tagged protein during expression and purification. Appl Environ Microbiol 71: 1089–1092 PubMedCAS Google Scholar
Rouillard, JM, Herbert, CJ, Zuker, M (2002) OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics 18: 486–487 PubMedCAS Google Scholar
Rouillard, JM, Zuker, M, Gulari, E (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31: 3057–3062 PubMedCAS Google Scholar
Rudi, K, Skulberg, OM, Skulberg, R, Jakobsen, KS (2000) Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl Environ Microbiol 66: 4004–4011 PubMedCAS Google Scholar
Salama, N, Guillemin, K, McDaniel, TK, Sherlock, G, Tompkins, L, Falkow, S (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA 97: 14668–14673 PubMedCAS Google Scholar
Saleh-Lakha, S, Miller, M, Campbell, RG, Schneider, K, Elahimanesh, P, Hart, MM, Trevors, JT (2005) Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 63: 1–19 PubMedCAS Google Scholar
Schadt, CW, Liebich, J, Chong, SC, Gentry, TJ, He, Z, Pan, H, Zhou, J (2005) Chapter 11, Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities. In: Savidge, T, Pothulakis, H (Eds.) Microbial Imaging, Methods in Microbiology, vol. 34. Academic Press, Inc., London, UK, pp 331–368 Google Scholar
Schadt, CW, Zhou, J (2005) Advances in microarrays for soil microbial community analyses. In: Nannipieri, P, Smalla, K (Eds.) Soil Biology: Nucleic Acids and Proteins in Soil. Springer-Verlag, Berlin Google Scholar
Sebat, JL, Colwell, FS, Crawford, RL (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 69: 4927–4934 PubMedCAS Google Scholar
Sessitsch, A, Gyamfi, S, Stralis-Pavese, N, Weilharter, A, Pfeifer, U (2002) RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. J Microbiol Methods 51: 171–179 PubMedCAS Google Scholar
Small, J, Call, DR, Brockman, FJ, Straub, TM, Chandler, DP (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67: 4708–4716 PubMedCAS Google Scholar
Stahl, DA, Lane, DJ, Olsen, GJ, Pace, NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S ribosomal-RNA sequences. Appl Environ Microbiol 49: 1379–1384 PubMedCAS Google Scholar
Steward, GF, Jenkins, BD, Ward, BB, Zehr, JP (2004) Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl Environ Microbiol 70: 1455–1465 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Suzuki, MT, Giovannoni, SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625–630 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Thompson, DK, Beliaev, AS, Giometti, CS, Tollaksen, SL, Khare, T, Lies, DP, Nealson, KH, Lim, H, Yates, J, 3rd, Brandt, CC, Tiedje, JM, Zhou, J (2002) Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol 68: 881–892 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Torsvik, V, Goksoyr, J, Daae, FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782–787 PubMedCAS Google Scholar
Torsvik, V, Daae, FL, Sandaa, RA, Ovreas, L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64: 53–62 PubMedCAS Google Scholar
Torsvik, V, Ovreas, L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240–245 PubMedCAS Google Scholar
Torsvik, V, Ovreas, L, Thingstad, TF (2002) Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296: 1064–1066 PubMedCAS Google Scholar
Tringe, SG, von Mering, C, Kobayashi, A, Salamov, AA, Chen, K, Chang, HW, Podar, M, Short, JM, Mathur, EJ, Detter, JC, Bork, P, Hugenholtz, P, Rubin, EM (2005) Comparative metagenomics of microbial communities. Science 308: 554–557 PubMedCAS Google Scholar
Tsai, YL, Le, JY, Olson, BH (2003) Magnetic bead hybridization to detect enterotoxigenic Escherichia coli strains associated with cattle in environmental water sources. Can J Microbiol 49: 391–398 PubMedCAS Google Scholar
Tyson, GW, Chapman, J, Hugenholtz, P, Allen, EE, Ram, RJ, Richardson, PM, Solovyev, VV, Rubin, EM, Rokhsar, DS, Banfield, JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Van Dyk, TK, DeRose, EJ, Gonye, GE (2001) LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J Bacteriol 183: 5496–5505 PubMed Google Scholar
Venter, JC, Remington, K, Heidelberg, JF, Halpern, AL, Rusch, D, Eisen, JA, Wu, D, Paulsen, I, Nelson, KE, Nelson, W, Fouts, DE, Levy, S, Knap, AH, Lomas, MW, Nealson, K, White, O, Peterson, J, Hoffman, J, Parsons, R, Baden-Tillson, H, Pfannkoch, C, Rogers, YH, Smith, HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74 PubMedCAS Google Scholar
von Wintzingerode, F, Gobel, UB, Stackebrandt, E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213–229 Google Scholar
Wang, X, Seed, B (2003) Selection of oligonucleotide probes for protein coding sequences. Bioinformatics 19: 796–802 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Woese, CR, Magrum, LJ, Gupta, R, Siegel, RB, Stahl, DA, Kop, J, Crawford, N, Brosius, J, Gutell, R, Hogan, JJ, Noller, HF (1980) Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8: 2275–2293 PubMedCAS Google Scholar
Woese, CR, Gutell, R, Gupta, R, Noller, HF (1983) Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev 47: 621–669 PubMedCAS Google Scholar
Wu, LY, Thompson, DK, Li, GS, Hurt, RA, Tiedje, JM, Zhou, JZ (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67: 5780–5790 PubMedCAS Google Scholar
Wu, LY, Thompson, DK, Liu, XD, Fields, MW, Bagwell, CE, Tiedje, JM, Zhou, JZ (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 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Yilmaz, LS, Noguera, DR (2004) Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Appl Environ Microbiol 70: 7126–7139 PubMedCAS Google Scholar
Yilmaz, LS, Okten, HE, Noguera, DR (2006) Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl Environ Microbiol 72: 733–744 PubMedCAS Google Scholar
Zhou, J, Xia, B, Treves, DS, Wu, LY, Marsh, TL, O'Neill, RV, Palumbo, AV, Tiedje, JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68: 326–334 PubMedCAS Google Scholar
Zhou, J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288–294 PubMedCAS Google Scholar
Zhou, JZ, Thompson, DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13: 204–207 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
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 PubMedCAS Google Scholar
Zuker, M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415 PubMedCAS Google Scholar
Zverlov, V, Klein, M, Lucker, S, Friedrich, MW, Kellermann, J, Stahl, DA, Loy, A, Wagner, M (2005) Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. J Bacteriol 187: 2203–2208 PubMedCAS Google Scholar