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Advances in Microarray-Based Technologies for Soil Microbial Community Analyses

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Nucleic Acids and Proteins in Soil

Part of the book series: Soil Biology ((SOILBIOL,volume 8))

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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

    Article  PubMed  CAS  Google Scholar 

  • Asai T, Zaporojets D, Squires C, Squires CL (1999a) An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci 96:1971–1976

    Article  PubMed  CAS  Google Scholar 

  • Asai T, Condon C, Voulgaris J, Zaporojets D, Shen B, Al-Omar M, Squires C, Squires CL (1999b) Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons. J Bacteriol 181:3803–3809

    PubMed  CAS  Google Scholar 

  • Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of archaea from soil. Proc Natl Acad Sci USA 94:277–282

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDPII): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  PubMed  CAS  Google Scholar 

  • Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380

    Article  PubMed  Google Scholar 

  • Dawson SC, Pace NR (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99:8324–8329

    Article  PubMed  CAS  Google Scholar 

  • DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686

    Article  PubMed  CAS  Google Scholar 

  • DeSantis TZ, Dubosarskiy I, Murray SR, Andersen GL (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19:1461–1468

    Article  PubMed  CAS  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

    Article  PubMed  Google Scholar 

  • Fukushima M, Kakinuma K, Hayashi H, Nagai H, Ito K, Kawaguchi R (2003) Detection and identification of Mycobacterium species isolates by DNA microarray. J Clin Microbiol 41:2605–2615

    Article  PubMed  CAS  Google Scholar 

  • Greene EA, Voordouw G (2003) Analysis of environmental microbial communities by reverse sample genome probing. J Microbiol Methods 53:211–219

    Article  PubMed  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Kakinuma K, Fukushima M, Kawaguchi R (2003) Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol Bioeng 20:721–728

    Article  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 57:369–278

    Article  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

    Article  PubMed  CAS  Google Scholar 

  • Liu Y, Zhou J-Z, Omelchenko M, Beliaev A, 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 100:4191–4196

    Article  PubMed  CAS  Google Scholar 

  • Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Loy A, Horn M, Wagner M (2003) probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31:514–516

    Article  PubMed  CAS  Google Scholar 

  • 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 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 Res 32:1363–1371

    Article  PubMed  CAS  Google Scholar 

  • Rhee SK, Liu X, Wu L-Y, 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 

  • Schadt CW, Martin AP, Lipson DA, Schmidt SK (2003) Seasonal dynamics of novel fungal lineages in tundra soils. Science 301:1359–1361

    Article  PubMed  CAS  Google Scholar 

  • Schadt CW, Liebich J, Chong SC, Gentry TJ, He Z, Pan H, Zhou J-Z (2005) Design and use of functional gene microarrays (FGAs) for the characterization of microbial communities. In: Savidge T, Charalabos P (eds) Methods in microbiology, vol 34: Microbial imaging. Elsevier, Amsterdam, pp 331–368

    Google Scholar 

  • Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93:10614–10619

    Article  PubMed  CAS  Google Scholar 

  • Steward GF, Jenkins BD, Ward BB, Zehr JP (2004) Development and testing of a DNA macroarray to assess nitrogenase (nif H) gene diversity. Appl Environ Microbiol 70:1455–1465

    Article  PubMed  CAS  Google Scholar 

  • Taniguchi M, Miura K, Iwao H, Yamanaka S (2001) Quantitative assessment of DNA microarrays — comparison with northern blot analyses. Genomics 71:34–39

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Thompson DK, Beliaev AS, Giometti CS, Tollaksen SL, Khare T, Lies DP, Nealson KH, Lim H, Yates J III, Brandt CC, Tiedje JM, Zhou J-Z (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

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Torsvik V, Sorheim R, Goksoyr J (1996) Total bacterial diversity in soil and sediment communities — a review. J Ind Microbiol 17:170–178

    Article  CAS  Google Scholar 

  • Valinsky L, Della-Vedova G, Jiang T, Borneman J (2002a) Oligonucleotide fingerprinting of ribosomal RNA genes for analysis of fungal community composition. Appl Environ Microbiol 68:5999–6004

    Article  PubMed  CAS  Google Scholar 

  • Valinsky L, Della-Vedova G, Scupham AJ, Alvey S, Figueroa A, Yin B, Hartin J, Chrobak M, Crowley DE, Jiang T, Borneman J (2002b) Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 68:3243–3250

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Wu L, Thompson DK, Liu X, Fields MW, Bagwell CE, Tiedje JM, Zhou J-Z (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 

  • Ye RW, Tao W, Beddzyk L, Young T, Chen M, Li L (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182:4458–4465

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z, Wilson RC, Fox GE (2002) Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset. Bioinformatics 18:244–250

    Article  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zhou J-Z, Thompson D (2002) Microarrays: applications in environmental microbiology. In: Bitton G (ed) Encyclopedia of environmental microbiology, vol. 4. John Wiley & Sons, New York, pp 1968–1979

    Google Scholar 

  • Zhou J-Z, Xia B, Treves DS, Wu L, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2003) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334

    Article  Google Scholar 

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Authors and Affiliations

  1. Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee, 37831-6038, USA

    Christopher W. Schadt & Jizhong Zhou

Authors
  1. Christopher W. Schadt
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  2. Jizhong Zhou
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Editor information

Editors and Affiliations

  1. Dipartimento della Scienza del Suolo e Nutrizione della Pianta, P.le delle Cascine 28, 50144, Firenze, Italy

    Paolo Nannipieri

  2. Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Biologische Bundesanstalt für Land- und Forstwirtschaft (BBA), Messeweg 11/12, 38104, Braunschweig, Germany

    Kornelia Smalla

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Schadt, C.W., Zhou, J. (2006). Advances in Microarray-Based Technologies for Soil Microbial Community Analyses. In: Nannipieri, P., Smalla, K. (eds) Nucleic Acids and Proteins in Soil. Soil Biology, vol 8. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-29449-X_9

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