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Volumn 3, Issue SEP, 2012, Pages

Use of functional gene arrays for elucidating in situ biodegradation

Author keywords

Biodegradation; Bioremediation; Functional gene microarray; Geochip; Microbial communities

Indexed keywords


EID: 84875838108     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2012.00339     Document Type: Review
Times cited : (28)

References (126)
  • 3
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R. I., Ludwig, W., and Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 6
    • 29144459277 scopus 로고    scopus 로고
    • Microarray-based detection and typing of ht erhizo-bium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest
    • Bontemps, C, Goldier, G., Gris-Liebe, C, Carere, S., Talini, L, and Boivin-Masson, C. (2005). Microarray-based detection and typing of ht erhizo-bium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Appl. Environ. Microbiol. 71, 8042-8048.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 8042-8048
    • Bontemps, C.1    Goldier, G.2    Gris-Liebe, C.3    Carere, S.4    Talini, L.5    Boivin-Masson, C.6
  • 7
    • 33847221847 scopus 로고    scopus 로고
    • Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements
    • doi: 10.1186/1472-6750-7-8
    • Branham, W S., Melvin, C. D., Han, T., Gesai, V. G., Moland, C. L., Scully, A. T., and Fuscoe, J. C. (2007). Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol. 7, 8. doi: 10.1186/1472-6750-7-8
    • (2007) BMC Biotechnol , vol.7 , pp. 8
    • Branham, W.S.1    Melvin, C.D.2    Han, T.3    Gesai, V.G.4    Moland, C.L.5    Scully, A.T.6    Fuscoe, J.C.7
  • 9
    • 0242668357 scopus 로고    scopus 로고
    • mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil
    • Burgmann, H., Widmer, F., Sigler, W. V., and, Zeyer, J. (2003). mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ. Mkrobiol 69, 1928-1935.
    • (2003) Appl Environ. Mkrobiol , vol.69 , pp. 1928-1935
    • Burgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 11
    • 56949092761 scopus 로고    scopus 로고
    • Micro-array based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems
    • Chen, Q., Huaqun, Y., Luo, H., Xie, M., Qiu, G., and Liu, X. (2009). Micro-array based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems. Hydrometallurgy 95, 96-103.
    • (2009) Hydrometallurgy , vol.95 , pp. 96-103
    • Chen, Q.1    Huaqun, Y.2    Luo, H.3    Xie, M.4    Qiu, G.5    Liu, X.6
  • 12
    • 0036193078 scopus 로고    scopus 로고
    • Quantitative detection of microbial genes by using DNA microarrays
    • Cho, J. C, and Tiedje, J. M. (2002). Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Mkrobiol 58, 1425-1430.
    • (2002) Appl. Environ. Mkrobiol , vol.58 , pp. 1425-1430
    • Cho, J.C.1    Tiedje, J.M.2
  • 13
    • 33746216159 scopus 로고    scopus 로고
    • Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray
    • Cleven, B. E. E., Palka-Santini, M., Gielen, J., Meembor, S., Kronke, M., and Krut, O. (2006). Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J. Clin. Mkrobiol. 44, 2389-2397.
    • (2006) J Clin. Mkrobiol. , vol.44 , pp. 2389-2397
    • Cleven, B.E.E.1    Palka-Santini, M.2    Gielen, J.3    Meembor, S.4    Kronke, M.5    Krut, O.6
  • 14
    • 0141564886 scopus 로고    scopus 로고
    • Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities
    • Denef, V. J., Park, J., Rodrigues, J. L. M., Tsoi, T. V., Hashsham, S. A., and Tiedje, J. M. (2003). Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Mkrobiol 5, 933-943.
    • (2003) Environ. Mkrobiol , vol.5 , pp. 933-943
    • Denef, V.J.1    Park, J.2    Rodrigues, J.L.M.3    Tsoi, T.V.4    Hashsham, S.A.5    Tiedje, J.M.6
  • 15
    • 0037315779 scopus 로고    scopus 로고
    • Monitoring gene expression in mixed microbial communities by using DNA microarrays
    • Dennis, P., Edwards, E. A., Liss, S. N., and Fulthorpe, R. (2003). Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ. Mkrobiol. 69, 769-778.
    • (2003) Appl Environ. Mkrobiol. , vol.69 , pp. 769-778
    • Dennis, P.1    Edwards, E.A.2    Liss, S.N.3    Fulthorpe, R.4
  • 16
    • 84866011914 scopus 로고    scopus 로고
    • More functional genes and convergent overall functional patterns detected by GeoChip in phenanthrene spiked soils
    • doi: lO.llll/j.1574-6941.2012.01413.x [Epub ahead of print]
    • Ding, G. C, Heuer, H., He, Z., Xie, J., Zhou, J., and Smalla, K. (2012). More functional genes and convergent overall functional patterns detected by GeoChip in phenanthrene spiked soils. FEMS Mkrobiol. Ecol doi: lO.llll/j.1574-6941.2012.01413.x [Epub ahead of print].
    • (2012) FEMS Mkrobiol. Ecol
    • Ding, G.C.1    Heuer, H.2    He, Z.3    Xie, J.4    Zhou, J.5    Smalla, K.6
  • 17
    • 34547781320 scopus 로고    scopus 로고
    • DNA microarray technology for the microbiologist: an overview
    • Ehrenreich, A. (2006). DNA microarray technology for the microbiologist: an overview. Appl Mkrobiol Biotechnol 73,255-273.
    • (2006) Appl Mkrobiol Biotechnol , vol.73 , pp. 255-273
    • Ehrenreich, A.1
  • 19
    • 0032482354 scopus 로고    scopus 로고
    • Microbial Microdiversity. News and Views
    • Fuhrman, J. A., and Campbell, L. (1998). Microbial Microdiversity. News and Views. Nature 393, 410-411.
    • (1998) Nature , vol.393 , pp. 410-411
    • Fuhrman, J.A.1    Campbell, L.2
  • 20
    • 33846435742 scopus 로고    scopus 로고
    • Microarray-based analysis of microbial community RNAs by whole-community RNA amplification
    • Gao, H., Yang, Z. K., Gentry, T. J., Wu, L., Schadt, C. W., and Zhou, J. (2007). Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ. Microbiol 73, 563-571.
    • (2007) Appl Environ. Microbiol , vol.73 , pp. 563-571
    • Gao, H.1    Yang, Z.K.2    Gentry, T.J.3    Wu, L.4    Schadt, C.W.5    Zhou, J.6
  • 22
    • 40849097774 scopus 로고    scopus 로고
    • Comparing whole genomes using DNA microarrays
    • Gresham, D., Dunham, M. J., and Bot-stein, D. (2008). Comparing whole genomes using DNA microarrays. Nat. Rev. 9,291-302.
    • (2008) Nat. Rev. , vol.9 , pp. 291-302
    • Gresham, D.1    Dunham, M.J.2    Botstein, D.3
  • 23
    • 84946031884 scopus 로고
    • Procedures for detecting outlying observations in samples
    • Grubbs, F. (1969). Procedures for detecting outlying observations in samples. Technometrics 11, 469-479.
    • (1969) Technometrics , vol.11 , pp. 469-479
    • Grubbs, F.1
  • 24
    • 54349108833 scopus 로고    scopus 로고
    • An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes
    • Gudnason, H., Dufva, M., Bang, D. D., and Wolff, A. (2008). An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. Biotechniques 45, 261-271.
    • (2008) Biotechniques , vol.45 , pp. 261-271
    • Gudnason, H.1    Dufva, M.2    Bang, D.D.3    Wolff, A.4
  • 30
    • 25144487554 scopus 로고    scopus 로고
    • Use of microarrays with different probe sizes for monitoring gene expression
    • He, Z., Wu, L., Fields, M. W, and Zhou J. (2005a). Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ. Microbiol 71, 5154-5162.
    • (2005) Appl Environ. Microbiol , vol.71 , pp. 5154-5162
    • He, Z.1    Wu, L.2    Fields, M.W.3    Zhou, J.4
  • 31
    • 22144441403 scopus 로고    scopus 로고
    • Empirical establishment of oligonucleotide probe design criteria
    • He, Z., Wu, L. Y, Li, X. Y, Fields, M. W, and Zhou, J. Z. (2005b). Empirical establishment of oligonucleotide probe design criteria. Appl Environ. Microbiol 71, 3753-3760.
    • (2005) Appl Environ. Microbiol , vol.71 , pp. 3753-3760
    • He, Z.1    Wu, L.Y.2    Li, X.Y.3    Fields, M.W.4    Zhou, J.Z.5
  • 32
    • 44249085420 scopus 로고    scopus 로고
    • Empirical evaluation of a new method for calculating signal to noise ratio (SNR) for microarray data analysis
    • He, Z., and Zhou, J. (2008). Empirical evaluation of a new method for calculating signal to noise ratio (SNR) for microarray data analysis. Appl Environ. Microbiol 74,2957-2966.
    • (2008) Appl Environ. Microbiol , vol.74 , pp. 2957-2966
    • He, Z.1    Zhou, J.2
  • 36
    • 77649160808 scopus 로고    scopus 로고
    • The microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased (YBD) colonies
    • Kimes, N. E., Van Nostrand, J. D., Weil, E., Zhou, J., and Morris, P. J. (2009). The microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased (YBD) colonies. Environ. Microbiol 12, 541-556.
    • (2009) Environ. Microbiol , vol.12 , pp. 541-556
    • Kimes, N.E.1    Van Nostrand, J.D.2    Weil, E.3    Zhou, J.4    Morris, P.J.5
  • 37
    • 27644562321 scopus 로고    scopus 로고
    • High-sensitivity, polymerase chain reaction-free detection of microorganisms and their functional genes using 70-mer oligonucleotide diagnostic microarray
    • Kostic, T., Weilharter, A., Ses-sitsch, A., and Bodrossy, L. (2005). High-sensitivity, polymerase chain reaction-free detection of microorganisms and their functional genes using 70-mer oligonucleotide diagnostic microarray. Anal. Biochetn. 346,333-335.
    • (2005) Anal. Biochetn. , vol.346 , pp. 333-335
    • Kostic, T.1    Weilharter, A.2    Sessitsch, A.3    Bodrossy, L.4
  • 39
    • 0034660934 scopus 로고    scopus 로고
    • Silanized nucleic acids: a general platform for DNA immobilization
    • Kumar, A., Larsson, O., Parodi, D., and Liang, Z. (2000). Silanized nucleic acids: a general platform for DNA immobilization. Nucleic Acids Res. 28,e71.
    • (2000) Nucleic Acids Res , vol.28
    • Kumar, A.1    Larsson, O.2    Parodi, D.3    Liang, Z.4
  • 40
    • 0032967877 scopus 로고    scopus 로고
    • Distance-based redundancy analysis: testing multi-species responses in multi-factorial ecological experiments
    • Legendre, P., and Anderson, M. J. (1999). Distance-based redundancy analysis: testing multi-species responses in multi-factorial ecological experiments. Ecol Monogr. 69, 1-24.
    • (1999) Ecol Monogr , vol.69 , pp. 1-24
    • Legendre, P.1    Anderson, M.J.2
  • 41
    • 34249939326 scopus 로고    scopus 로고
    • Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with poly-chlorinated biphenyls (PCBs)
    • Leigh, M. B., Pellizari, V H., Uhlik, O., Sutka, R., Rodrigues, J., Ostrom, N. E., Zhou, J., and Tiedje, J. M. (2007). Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with poly-chlorinated biphenyls (PCBs). ISME J. 1,134-148.
    • (2007) ISME J , vol.1 , pp. 134-148
    • Leigh, M.B.1    Pellizari, V.H.2    Uhlik, O.3    Sutka, R.4    Rodrigues, J.5    Ostrom, N.E.6    Zhou, J.7    Tiedje, J.M.8
  • 42
    • 27244449595 scopus 로고    scopus 로고
    • Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
    • Li, X., He, Z., and Zhou, J. (2005). Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 33,6114-6123.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6114-6123
    • Li, X.1    He, Z.2    Zhou, J.3
  • 43
    • 76649114015 scopus 로고    scopus 로고
    • Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities
    • Liang, Y, He, Z., Wu, L., Deng, Y, Li, G., and Zhou, J. (2010). Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities. Appl Environ. Microbiol 76, 1088-1094.
    • (2010) Appl Environ. Microbiol , vol.76 , pp. 1088-1094
    • Liang, Y.1    He, Z.2    Wu, L.3    Deng, Y.4    Li, G.5    Zhou, J.6
  • 44
    • 70349860176 scopus 로고    scopus 로고
    • Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oilfield
    • Liang, Y., Li, G., Van Nostrand, J. D., He, Z., Wu, L., Deng, Y, Zhang, X., and Zhou, J. (2009a). Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oilfield. FEMS Microbiol Ecol 70, 324-333.
    • (2009) FEMS Microbiol Ecol , vol.70 , pp. 324-333
    • Liang, Y.1    Li, G.2    Van Nostrand, J.D.3    He, Z.4    Wu, L.5    Deng, Y.6    Zhang, X.7    Zhou, J.8
  • 45
    • 61849184404 scopus 로고    scopus 로고
    • Microarray-based functional gene analysis of soil microbial communities in ozonation and biodegradation of crude oil
    • Liang, Y, Wang, J., Van Nostrand, J. D., Zhou, J., Zhang, X., and Li, G. (2009b). Microarray-based functional gene analysis of soil microbial communities in ozonation and biodegradation of crude oil. Chetmosphere 75,193-199.
    • (2009) Chetmosphere , vol.75 , pp. 193-199
    • Liang, Y.1    Wang, J.2    Van Nostrand, J.D.3    Zhou, J.4    Zhang, X.5    Li, G.6
  • 46
    • 79951810368 scopus 로고    scopus 로고
    • Functional gene diversity of soil microbial communities from five oil-contaminated fields in China
    • Liang, Y T., Van Nostrand, J. D., Deng, Y, He, Z. H., Wu, L. Y, Zhang, X., Li, G., and Zhou, J. (2011). Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J. 5, 403-413.
    • (2011) ISME J , vol.5 , pp. 403-413
    • Liang, Y.T.1    Van Nostrand, J.D.2    Deng, Y.3    He, Z.H.4    Wu, L.Y.5    Zhang, X.6    Li, G.7    Zhou, J.8
  • 48
    • 33144457149 scopus 로고    scopus 로고
    • Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications
    • Liebich, J., Schadt, C. W., Chong, S. C, He, Z., Rhee, S. K., and Zhou, J. (2006). Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ. Microbiol. 72, 1688-1691.
    • (2006) Appl Environ. Microbiol. , vol.72 , pp. 1688-1691
    • Liebich, J.1    Schadt, C.W.2    Chong, S.C.3    He, Z.4    Rhee, S.K.5    Zhou, J.6
  • 49
    • 70349330561 scopus 로고    scopus 로고
    • Degradation of diffuse pesticide contaminants: screening for microbial potential using a functional gene microarray
    • Liebich, J., Wachtmeister, T., Zhou, J., and Burauel, P. (2009). Degradation of diffuse pesticide contaminants: screening for microbial potential using a functional gene microarray. Vadose Zone J. 8, 703-710.
    • (2009) Vadose Zone J , vol.8 , pp. 703-710
    • Liebich, J.1    Wachtmeister, T.2    Zhou, J.3    Burauel, P.4
  • 50
    • 0036795787 scopus 로고    scopus 로고
    • Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    • Loy, A., Lehner, A., Lee, N., Adamcsyk, J., Meier, H., Ernst, J., Schleifer, K. H., and 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, 5064-6081.
    • (2002) Appl Environ. Microbiol , vol.68 , pp. 5064-6081
    • Loy, A.1    Lehner, A.2    Lee, N.3    Adamcsyk, J.4    Meier, H.5    Ernst, J.6    Schleifer, K.H.7    Wagner, M.8
  • 53
    • 0037225001 scopus 로고    scopus 로고
    • Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism: analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts
    • Lueders, T., and Friedrich, M. W. (2003). Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism: analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Envrion. Microbiol 69, 320-326.
    • (2003) Appl Envrion. Microbiol , vol.69 , pp. 320-326
    • Lueders, T.1    Friedrich, M.W.2
  • 55
    • 58549119329 scopus 로고    scopus 로고
    • Prokaryotic diversity, distribution, and preliminary insights into their role in biogeochemical cycling in marine basalts
    • Mason, O. U., DiMeo-Savoie, C. A., Van Nostrand, J. D., Zhou, J., Fisk, M. R., and Giovannoni, S. J. (2009). Prokaryotic diversity, distribution, and preliminary insights into their role in biogeochemical cycling in marine basalts. ISME J. 3, 231-242.
    • (2009) ISME J , vol.3 , pp. 231-242
    • Mason, O.U.1    DiMeo-Savoie, C.A.2    Van Nostrand, J.D.3    Zhou, J.4    Fisk, M.R.5    Giovannoni, S.J.6
  • 57
    • 40349113425 scopus 로고    scopus 로고
    • The Macaque gut micro-biome in health, lentiviral infection, and chronic enterocolitis
    • doi: 10.1371/jour-nal.ppat.0040020
    • McKenna, P., Hoffmann, C, Minkah, N., Aye, P. P., Lackner, A., Liu, Z. (2008). The Macaque gut micro-biome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog. 4, e20. doi: 10.1371/journal.ppat.0040020
    • (2008) PLoS Pathog , vol.4
    • McKenna, P.1    Hoffmann, C.2    Minkah, N.3    Aye, P.P.4    Lackner, A.5    Liu, Z.6
  • 61
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler, T. C, and Ecker, J. R. (2005). Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15.
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1    Ecker, J.R.2
  • 62
    • 0035859896 scopus 로고    scopus 로고
    • DNA-DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes
    • Murray, A. E., Lies, D., Li, G., Neal-son, K., Zhou, J., and Tiedje, J. M. (2001). DNA-DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Acad. Sci. U.S.A. 98, 9853-9858.
    • (2001) Proc. Natl. Acad. Sci. U. S. A , vol.98 , pp. 9853-9858
    • Murray, A.E.1    Lies, D.2    Li, G.3    Nealson, K.4    Zhou, J.5    Tiedje, J.M.6
  • 63
    • 62949101230 scopus 로고    scopus 로고
    • Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study
    • Ning, J., Liebich, J., Kastner, M., Zhou, J.,Schaffer,A.,andBurauel,P. (2009). Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl Microbiol Biotechnol 82, 983-993.
    • (2009) Appl Microbiol Biotechnol , vol.82 , pp. 983-993
    • Ning, J.1    Liebich, J.2    Kastner, M.3    Zhou, J.4    Schaffer, A.5    Burauel, P.6
  • 64
    • 0034056315 scopus 로고    scopus 로고
    • Microarray fabrication with covalent attachment of DNA using Bubble Jet technology
    • Okamoto, T., Suzuki, T., and Yamamoto, N. (2000). Microarray fabrication with covalent attachment of DNA using Bubble Jet technology. Nat. Biotechnol 18,438-441.
    • (2000) Nat. Biotechnol , vol.18 , pp. 438-441
    • Okamoto, T.1    Suzuki, T.2    Yamamoto, N.3
  • 65
    • 0028176022 scopus 로고
    • Canonical correspondence analysis with variation partitioning: some comments and an application
    • Økland, R. H., and Eilertsen, O. (1994). Canonical correspondence analysis with variation partitioning: some comments and an application. J. Veg. Sci. 5,117-126.
    • (1994) J Veg. Sci. , vol.5 , pp. 117-126
    • Økland, R.H.1    Eilertsen, O.2
  • 67
    • 61449193503 scopus 로고    scopus 로고
    • Large scale multiplex PCR improves pathogen detection by DNA microarrays
    • doi: 10.1186/1471-2180-9-1
    • Palka-Santini, M., eleven, B. E., Eichinger, L., Kronke, M., and Krut, O. (2009). Large scale multiplex PCR improves pathogen detection by DNA microarrays. BMCMicrobiol 9, l.doi: 10.1186/1471-2180-9-1
    • (2009) BMC Microbiol , vol.9
    • Palka-Santini, M.1    Eleven, B.E.2    Eichinger, L.3    Kronke, M.4    Krut, O.5
  • 69
    • 80055120631 scopus 로고    scopus 로고
    • Analyzing gene expression from marine microbial communities using environmental transcriptomics
    • Poretsky, R. S., Gifford, S., Rinta-Kanto, J., Vila-Costa, M., and Moran, M. A. (2009a). Analyzing gene expression from marine microbial communities using environmental transcrip-tomics. J. Vis. Exp. 24, 1086.
    • (2009) J Vis. Exp. , vol.24 , pp. 1086
    • Poretsky, R.S.1    Gifford, S.2    Rinta-Kanto, J.3    Vila-Costa, M.4    Moran, M.A.5
  • 70
    • 66649089244 scopus 로고    scopus 로고
    • Compariative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
    • Poretsky, R. S., Hewson, I., Sun, S., Allan, A. E., Zehr, J. P., and Moran, M. A. (2009b). Com-pariative day/night metatranscrip-tomic analysis of microbial communities in the North Pacific subtropical gyre. Environ. Microbiol 11, 1358-1375.
    • (2009) Environ. Microbiol , vol.11 , pp. 1358-1375
    • Poretsky, R.S.1    Hewson, I.2    Sun, S.3    Allan, A.E.4    Zehr, J.P.5    Moran, M.A.6
  • 71
    • 33847318761 scopus 로고    scopus 로고
    • Multiscale responses of microbial life in spatial distance and environmental heterogeneity in a patchy ecosystem
    • Ramette, A., and Tiedje, J. M. (2007). Multiscale responses of microbial life in spatial distance and environmental heterogeneity in a patchy ecosystem. Proc. Natl Acad. Sci. U.S.A. 104, 2761-2766.
    • (2007) Proc. Natl. Acad. Sci. U. S. A , vol.104 , pp. 2761-2766
    • Ramette, A.1    Tiedje, J.M.2
  • 73
    • 3242773890 scopus 로고    scopus 로고
    • Detection of genes involved in biodegradation and biotransfor-mation in microbial communities by using 50-mer oligonucleotide microarrays
    • Rhee, S. K., Liu, X., Wu, L., Chong, S. C, Wan, X., and Zhou, J. (2004). Detection of genes involved in biodegradation and biotransfor-mation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ. Micro-biol 70,4303-4317.
    • (2004) Appl Environ. Microbiol , vol.70 , pp. 4303-4317
    • Rhee, S.K.1    Liu, X.2    Wu, L.3    Chong, S.C.4    Wan, X.5    Zhou, J.6
  • 76
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M., Shalon, D., Davis, R. W, and Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 77
    • 0029748326 scopus 로고    scopus 로고
    • Parallel human genome analysis: microarray-based expression monitoring of 1000 genes
    • Schena, M., Shalon, D., Heller, R., Chai, A., and Brown, P. O. (1996). Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. U.S.A. 93, 10614-10619.
    • (1996) Proc. Natl. Acad. Sci. U. S. A , vol.93 , pp. 10614-10619
    • Schena, M.1    Shalon, D.2    Heller, R.3    Chai, A.4    Brown, P.O.5
  • 78
    • 33746639717 scopus 로고    scopus 로고
    • Toward a census of bacteria in soil
    • doi: 10.1371/journal.pcbi.0020092
    • Schloss, P. D., and Handelsman, J. (2006). Toward a census of bacteria in soil. PLoS Comput. Biol 2, 786-793. doi: 10.1371/journal.pcbi.0020092
    • (2006) PLoS Comput. Biol , vol.2 , pp. 786-793
    • Schloss, P.D.1    Handelsman, J.2
  • 79
    • 0042530104 scopus 로고    scopus 로고
    • Metagenomic profiling: Microarray analysis of an environmental genomic library
    • Sebat, J. L., Colwell, F. S., and Crawford, R. L. (2003). Metagenomic profiling: Microarray analysis of an environmental genomic library. Appl. Environ. Microbiol 69, 4927-4934.
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 4927-4934
    • Sebat, J.L.1    Colwell, F.S.2    Crawford, R.L.3
  • 80
    • 4944263725 scopus 로고    scopus 로고
    • Preparation of functional DNA microarrays through laser-induced forward transfer
    • Serra, P., Colina, M., Fernandez, J. M., Sevilla, L., and Morenza, J. L. (2004). Preparation of functional DNA microarrays through laser-induced forward transfer. Appl Phys. Lett. 85, 1639-1641.
    • (2004) Appl Phys. Lett. , vol.85 , pp. 1639-1641
    • Serra, P.1    Colina, M.2    Fernandez, J.M.3    Sevilla, L.4    Morenza, J.L.5
  • 81
    • 0029812283 scopus 로고    scopus 로고
    • A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization
    • Shalon, D., Smith, S. J., and Brown, P. O. (1996). A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645.
    • (1996) Genome Res , vol.6 , pp. 639-645
    • Shalon, D.1    Smith, S.J.2    Brown, P.O.3
  • 82
    • 0035486807 scopus 로고    scopus 로고
    • Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays
    • Small, J., Call, D. R., Brockman, F. J., Straub, T. M., and Chandler, D. P. (2001). Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ. Microbiol 67,4708-4716.
    • (2001) Appl Environ. Microbiol , vol.67 , pp. 4708-4716
    • Small, J.1    Call, D.R.2    Brockman, F.J.3    Straub, T.M.4    Chandler, D.P.5
  • 83
    • 1642330746 scopus 로고    scopus 로고
    • Development and testing of a DNA macroar-ray to assess nitrogenase inijH) gene diversity
    • Steward, G. E, Jenkins, B. D., Ward, B. B., and Zehr, J. P. (2004). Development and testing of a DNA macroar-ray to assess nitrogenase inijH) gene diversity. Appl Environ. Microbiol 70,1455-1465.
    • (2004) Appl Environ. Microbiol , vol.70 , pp. 1455-1465
    • Steward, G.E.1    Jenkins, B.D.2    Ward, B.B.3    Zehr, J.P.4
  • 85
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki, M. T., and Giovannoni, S. J. (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Envrion. Microbiol 62, 625-630.
    • (1996) Appl Envrion. Microbiol , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 86
    • 0037316061 scopus 로고    scopus 로고
    • Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
    • Taroncher-Oldenburg, G., Griner, E. M., Francis, C. A., and Ward, B. B. (2003). Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Micro-biol. 69, 1159-1171.
    • (2003) Appl. Environ. Micro-biol. , vol.69 , pp. 1159-1171
    • Taroncher-Oldenburg, G.1    Griner, E.M.2    Francis, C.A.3    Ward, B.B.4
  • 87
    • 67650482588 scopus 로고    scopus 로고
    • Tracking functional guilds: Dehalococcoides spp. in European river basins contaminated with hexachlorobenzene
    • Tas, N., van Eekert, M. H. A., Schraa, G., Zhou, J., de Vos, W. M., and Smidt, H. (2009). Tracking functional guilds: Dehalococcoides spp. in European river basins contaminated with hexachlorobenzene. Appl Environ. Microbiol. 75, 4696-4704.
    • (2009) Appl Environ. Microbiol. , vol.75 , pp. 4696-4704
    • Tas, N.1    van Eekert, M.H.A.2    Schraa, G.3    Zhou, J.4    de Vos, W.M.5    Smidt, H.6
  • 88
    • 0022843649 scopus 로고
    • Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis
    • ter Braak, C. J. E (1986). Canonical correspondence analysis: a new eigenvector technique for multivari-ate direct gradient analysis. Ecology 67,1167-1179.
    • (1986) Ecology , vol.67 , pp. 1167-1179
    • ter Braak, C.J.E.1
  • 89
    • 1842579620 scopus 로고    scopus 로고
    • Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
    • 672, 674-675
    • Tiquia, S. M., Wu, L., Chong, S. C, Passovets, S., Xu, D., Xu, Y., and Zhou, J. (2004). Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotech-niques 36, 664-670, 672, 674-675.
    • (2004) Biotechniques , vol.36 , pp. 664-670
    • Tiquia, S.M.1    Wu, L.2    Chong, S.C.3    Passovets, S.4    Xu, D.5    Xu, Y.6    Zhou, J.7
  • 94
    • 70949102952 scopus 로고    scopus 로고
    • Next generation sequencing of microbial transcriptomics: challenges and opportunities
    • van Vliet, A. H. M. (2010). Next generation sequencing of microbial transcriptomics: challenges and opportunities. FEMS Microbiol Lett. 302,1-7.
    • (2010) FEMS Microbiol Lett , vol.302 , pp. 1-7
    • van Vliet, A.H.M.1
  • 98
    • 79960082882 scopus 로고    scopus 로고
    • Microarray-based evaluation of whole-community genome DNA amplification methods
    • Wang, J., Van Nostrand, J. D., Wu, L., He, Z., Li, G., and Zhou, J.-Z. (2011). Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ. Microbiol 77, 4241-4245.
    • (2011) Appl Environ. Microbiol , vol.77 , pp. 4241-4245
    • Wang, J.1    Van Nostrand, J.D.2    Wu, L.3    He, Z.4    Li, G.5    Zhou, J.-Z.6
  • 99
    • 0030697141 scopus 로고    scopus 로고
    • Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA
    • Warnecke, P. M., Stirzaker, C, Melki, J. R., Millar, D. S., Paul, C. L., and Clark, S. J. (1997). Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res. 25, 4422-4426.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4422-4426
    • Warnecke, P.M.1    Stirzaker, C.2    Melki, J.R.3    Millar, D.S.4    Paul, C.L.5    Clark, S.J.6
  • 100
    • 84855290788 scopus 로고    scopus 로고
    • Assimilatory nitrate utilization by bacteria on the West Florida shelf as determined by stable isotope probing and functional microarray analysis
    • Wawrik, B., Boling, W, Van Nostrand, J., Xie, J. P., Zhou, J.-Z., and Bronk, D. A. (2012a). Assimilatory nitrate utilization by bacteria on the West Florida shelf as determined by stable isotope probing and functional microarray analysis. FEMS Microbiol Ecol 79, 400-411.
    • (2012) FEMS Microbiol Ecol , vol.79 , pp. 400-411
    • Wawrik, B.1    Boling, W.2    Van Nostrand, J.3    Xie, J.P.4    Zhou, J.-Z.5    Bronk, D.A.6
  • 104
    • 0036018472 scopus 로고    scopus 로고
    • Sequence-specific identification of 18 pathogenic microorganisms using microarray technology
    • Wilson, W. J., Strout, C. L, DeSantis, T. Z., Stilwell, J. L., Carrano, A. V, and Andersen, G. L. (2002). Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes 16, 119-127.
    • (2002) Mol Cell Probes , vol.16 , pp. 119-127
    • Wilson, W.J.1    Strout, C.L.2    DeSantis, T.Z.3    Stilwell, J.L.4    Carrano, A.5    Andersen, G.L.6
  • 105
    • 47749143312 scopus 로고    scopus 로고
    • Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico
    • Wu, L., Kellogg, L, Devol, A. H., Tiedje, J. M., and Zhou, J. (2008). Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Appl Environ. Microbiol 74, 4516-4529.
    • (2008) Appl Environ. Microbiol , vol.74 , pp. 4516-4529
    • Wu, L.1    Kellogg, L.2    Devol, A.H.3    Tiedje, J.M.4    Zhou, J.5
  • 106
    • 33746095025 scopus 로고    scopus 로고
    • Microarray-based analysis of submicrogram quantities of microbial community DNAs by using whole-community genome amplification
    • Wu, L., Liu, X., Schadt, C. W, and Zhou, J. (2006a). Microarray-based analysis of submicrogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ. Microbiol.72, 4931-4941.
    • (2006) Appl Environ. Microbiol. , vol.72 , pp. 4931-4941
    • Wu, L.1    Liu, X.2    Schadt, C.W.3    Zhou, J.4
  • 109
    • 0035656126 scopus 로고    scopus 로고
    • Development and evaluation of functional gene arrays for detection of selected genes in the environment
    • Wu, L., Thompson, D. K., Li, G., Hurt, R. A., Tiedje, J. M., and Zhou, J. (2001). Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ. Microbiol 67, 5780-5790.
    • (2001) Appl Environ. Microbiol , vol.67 , pp. 5780-5790
    • Wu, L.1    Thompson, D.K.2    Li, G.3    Hurt, R.A.4    Tiedje, J.M.5    Zhou, J.6
  • 110
    • 10644242777 scopus 로고    scopus 로고
    • Development and evaluation of microarray-based whole genome hybridization for detection of microorganisms within the context of environmental applications
    • Wu, L., Thompson, D. K., Liu, X., Fields, M. W, Bagwell, C. E., Tiedje, J. M., and Zhou, J. (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.
    • (2004) Environ. Sci. Technol. , vol.38 , pp. 6775-6782
    • Wu, L.1    Thompson, D.K.2    Liu, X.3    Fields, M.W.4    Bagwell, C.E.5    Tiedje, J.M.6    Zhou, J.7
  • 111
    • 79551493063 scopus 로고    scopus 로고
    • GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage
    • Xie, J. P., He, Z. H., Liu, X. X., Liu, X. D., Van Nostrand, J. D., Deng, Y., Wu, L, Qiu, G., and Zhou, J. (2011). GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl Environ. Microbiol 77,991-999.
    • (2011) Appl Environ. Microbiol , vol.77 , pp. 991-999
    • Xie, J.P.1    He, Z.H.2    Liu, X.X.3    Liu, X.D.4    Van Nostrand, J.D.5    Deng, Y.6    Wu, L.7    Qiu, G.8    Zhou, J.9
  • 113
    • 78149458009 scopus 로고    scopus 로고
    • Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L
    • Xiong,J.B.,Wu,L.Y,Tu,S.X.,VanNos-trand, J. D., He, Z. H., Zhou, J.-Z., and Wang, G. J. (2010). Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant Pteris vittata L. Appl Environ. Microbiol 76, 7277-7284.
    • (2010) Appl Environ. Microbiol , vol.76 , pp. 7277-7284
    • Xiong, J.B.1    Wu, L.Y.2    Tu, S.X.3    Van Nostrand, J.D.4    He, Z.H.5    Zhou, J.-Z.6    Wang, G.J.7
  • 115
    • 34249932634 scopus 로고    scopus 로고
    • Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitude transect
    • Yergeau, E., Kang, S., He, Z., Zhou, J., and Kowalchuk, G. A. (2007). Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitude transect. ISME J. 1, 1-17.
    • (2007) ISME J , vol.1 , pp. 1-17
    • Yergeau, E.1    Kang, S.2    He, Z.3    Zhou, J.4    Kowalchuk, G.A.5
  • 116
    • 34250726464 scopus 로고    scopus 로고
    • Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleach-ing systems
    • Yin, H., Cao, L., Qiu, G., Wang, D., Kellogg, L., Zhou, J., Dai, Z., and Liu, X. (2007). Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleach-ing systems. J. Microbiol Methods 70, 165-178.
    • (2007) J Microbiol Methods , vol.70 , pp. 165-178
    • Yin, H.1    Cao, L.2    Qiu, G.3    Wang, D.4    Kellogg, L.5    Zhou, J.6    Dai, Z.7    Liu, X.8
  • 117
    • 34248172325 scopus 로고    scopus 로고
    • A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms
    • Zhang, L., Hurek, T., and Reihold-Hurek, B. (2007a). A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. Microbial Ecol 53, 456-70.
    • (2007) Microbial Ecol , vol.53 , pp. 456-470
    • Zhang, L.1    Hurek, T.2    Reihold-Hurek, B.3
  • 118
    • 33845630365 scopus 로고    scopus 로고
    • Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes
    • Zhang, Y, Zhang, X., Liu, X., Xiao, Y, Qu, L., Wu, L., and Zhou, J. (2007b). Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes. FEMS Lett. 266, 144-151.
    • (2007) FEMS Lett , vol.266 , pp. 144-151
    • Zhang, Y.1    Zhang, X.2    Liu, X.3    Xiao, Y.4    Qu, L.5    Wu, L.6    Zhou, J.7
  • 119
    • 2642536952 scopus 로고    scopus 로고
    • Library on a slide for bacterial comparative genomics
    • doi: 10.1186/1471-2180-4-12
    • Zhang, L., Srinivasan, U., Marrs, C. E, Ghosh, D., Gilsdorf, J. R., and Fox-man, B. (2004). Library on a slide for bacterial comparative genomics. BMC Microbiol. 4, 12-18. doi: 10.1186/1471-2180-4-12
    • (2004) BMC Microbiol , vol.4 , pp. 12-18
    • Zhang, L.1    Srinivasan, U.2    Marrs, C.E.3    Ghosh, D.4    Gilsdorf, J.R.5    Foxman, B.6
  • 120
    • 0037772204 scopus 로고    scopus 로고
    • Microarrays for bacterial detection and microbial community analysis
    • Zhou, J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol 6,288-294.
    • (2003) Curr. Opin. Microbiol , vol.6 , pp. 288-294
    • Zhou, J.1
  • 121
    • 0030070838 scopus 로고    scopus 로고
    • DNA recovery from soils of diverse composition
    • Zhou, J., Bruns, M. A., and Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Appl Environ. Microbiol 62,316-322.
    • (1996) Appl Environ. Microbiol , vol.62 , pp. 316-322
    • Zhou, J.1    Bruns, M.A.2    Tiedje, J.M.3
  • 123
    • 45549097485 scopus 로고    scopus 로고
    • Spatial scaling of functional gene diversity across various microbial taxa
    • Zhou, J., Kang, S., Schadt, C. W., and Garten, C. T. Jr. (2008). Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U.S.A. 105, 7768-7773.
    • (2008) Proc. Natl. Acad. Sci. U. S. A , vol.105 , pp. 7768-7773
    • Zhou, J.1    Kang, S.2    Schadt, C.W.3    Garten Jr, C.T.4
  • 124
    • 0036624982 scopus 로고    scopus 로고
    • Challenges in applying microarrays to environmental studies
    • Zhou, J., and Thompson, D. K. (2002). Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol 13,204-207.
    • (2002) Curr. Opin. Biotechnol , vol.13 , pp. 204-207
    • Zhou, J.1    Thompson, D.K.2
  • 126
    • 4544336805 scopus 로고    scopus 로고
    • Improving the signal sensitivity and pho-tostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles
    • Zhou, X., and Zhou, J. (2004). Improving the signal sensitivity and pho-tostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal. Chetn. 76,5302-5312.
    • (2004) Anal. Chetn. , vol.76 , pp. 5302-5312
    • Zhou, X.1    Zhou, J.2


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