메뉴 건너뛰기




Volumn 6, Issue 4, 2012, Pages 814-826

The Hydrogenase Chip: A tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities

Author keywords

DNA microarray; hydrogenase; microbial mat; reductive dehalogenation

Indexed keywords

DNA; HYDROGENASE;

EID: 84858862650     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.136     Document Type: Article
Times cited : (34)

References (56)
  • 2
    • 77949272191 scopus 로고    scopus 로고
    • Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuousflow column
    • Azizian MF, Marshall IPG, Behrens S, Spormann AM, Semprini L. (2010). Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuousflow column. J Contam Hydrol 113: 77-92.
    • (2010) J Contam Hydrol , vol.113 , pp. 77-92
    • Azizian, M.F.1    Marshall, I.P.G.2    Behrens, S.3    Spormann, A.M.4    Semprini, L.5
  • 3
    • 0028973370 scopus 로고
    • UV B-induced vertical migrations of cyanobacteria in a microbial mat
    • Bebout BM, Garcia-Pichel F. (1995). UV B-induced vertical migrations of cyanobacteria in a microbial mat. Appl Environ Microbiol 61: 4215-4222. (Pubitemid 26476413)
    • (1995) Applied & Environmental Microbiology , vol.61 , Issue.12 , pp. 4215-4222
    • Bebout, B.M.1    Garcia-Pichel, F.2
  • 5
    • 0029798414 scopus 로고    scopus 로고
    • Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol
    • Bouchard B, Beaudet R, Villemur R, McSween G, Lepine F, Bisaillon JG. (1996). Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. Int J Syst Bacteriol 46: 1010-1015. (Pubitemid 26339227)
    • (1996) International Journal of Systematic Bacteriology , vol.46 , Issue.4 , pp. 1010-1015
    • Bouchard, B.1    Beaudet, R.2    Villemur, R.3    McSween, G.4    Lepine, F.5    Bisaillon, J.-G.6
  • 6
    • 67649621650 scopus 로고    scopus 로고
    • [FeFe]-hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community
    • Boyd E, Spear J, Peters J. (2009). [FeFe]-hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl Environ Microbiol 75: 4620-4623.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 4620-4623
    • Boyd, E.1    Spear, J.2    Peters, J.3
  • 8
    • 0014160647 scopus 로고
    • Methanobacillus omelianskii, a symbiotic association of two species of bacteria
    • Bryant MP, Wolin EA, Wolin MJ, Wolfe RS. (1967). Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Archiv für Mikrobiologie 59: 20-31.
    • (1967) Archiv für Mikrobiologie , vol.59 , pp. 20-31
    • Bryant, M.P.1    Wolin, E.A.2    Wolin, M.J.3    Wolfe, R.S.4
  • 9
    • 0029931803 scopus 로고    scopus 로고
    • Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium
    • Christiansen N, Ahring BK. (1996). Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium. Int J Syst Evol Microbiol 46: 442.
    • (1996) Int J Syst Evol Microbiol , vol.46 , pp. 442
    • Christiansen, N.1    Ahring, B.K.2
  • 10
    • 0031745322 scopus 로고    scopus 로고
    • Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners
    • Cord-Ruwisch R, Lovley D, Schink B. (1998). Growth of geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. Appl Environ Microbiol 64: 2232-2236. (Pubitemid 28252790)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.6 , pp. 2232-2236
    • Cord-Ruwisch, R.1    Lovley, D.R.2    Schink, B.3
  • 11
    • 34248159346 scopus 로고    scopus 로고
    • High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
    • DOI 10.1007/s00248-006-9134-9
    • DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. (2007). High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383. (Pubitemid 46716624)
    • (2007) Microbial Ecology , vol.53 , Issue.3 , pp. 371-383
    • DeSantis, T.Z.1    Brodie, E.L.2    Moberg, J.P.3    Zubieta, I.X.4    Piceno, Y.M.5    Andersen, G.L.6
  • 15
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar R. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 0036866545 scopus 로고    scopus 로고
    • Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds
    • DOI 10.1099/ijs.0.02121-0
    • Finneran KT, Forbush HM, VanPraagh CVG, Lovley DR. (2002). Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds. Int J Syst Evol Microbiol 52: 1929-1935. (Pubitemid 36004170)
    • (2002) International Journal of Systematic and Evolutionary Microbiology , vol.52 , Issue.6 , pp. 1929-1935
    • Finneran, K.T.1    Forbush, H.M.2    Gaw VanPraagh, C.V.3    Lovley, D.R.4
  • 17
    • 33746897713 scopus 로고    scopus 로고
    • Vertical migration of phototrophic bacterial populations in a hypersaline microbial mat from Salins-de-Giraud (Camargue, France)
    • DOI 10.1111/j.1574-6941.2006.00124.x
    • Fourc?ans A, Sole A, Diestra E, Ranchou-Peyruse A, Esteve I, Caumette P et al. (2006). Vertical migration of phototrophic bacterial populations in a hypersaline microbial mat from Salins-de-Giraud (Camargue, France). FEMS Microbiol Ecol 57: 367-377. (Pubitemid 44200461)
    • (2006) FEMS Microbiology Ecology , vol.57 , Issue.3 , pp. 367-377
    • Fourcans, A.1    Sole, A.2    Diestra, E.3    Ranchou-Peyruse, A.4    Esteve, I.5    Caumette, P.6    Duran, R.7
  • 18
    • 33846435742 scopus 로고    scopus 로고
    • Microarray-based analysis of microbial community RNAs by whole-community RNA amplification
    • DOI 10.1128/AEM.01771-06
    • Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, Zhou J. (2007). Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol 73: 563-571. (Pubitemid 46147587)
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.2 , pp. 563-571
    • Gao, H.1    Yang, Z.K.2    Gentry, T.J.3    Wu, L.4    Schadt, C.W.5    Zhou, J.6
  • 19
    • 0001244666 scopus 로고    scopus 로고
    • ScanProsite: A reference implementation of a PROSITE scanning tool
    • Gattiker A, Gasteiger E, Bairoch A. (2002). ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics 1: 107-108.
    • (2002) Appl Bioinformatics , vol.1 , pp. 107-108
    • Gattiker, A.1    Gasteiger, E.2    Bairoch, A.3
  • 20
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • DOI 10.1080/10635150390235520
    • Guindon S, Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704. (Pubitemid 37365050)
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 21
    • 77956094278 scopus 로고    scopus 로고
    • GeoChip 3.0 as a highthroughput tool for analyzing microbial community composition, structure and functional activity
    • He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL et al. (2010). GeoChip 3.0 as a highthroughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4: 1167-1179.
    • (2010) ISME J , vol.4 , pp. 1167-1179
    • He, Z.1    Deng, Y.2    Van Nostrand, J.D.3    Tu, Q.4    Xu, M.5    Hemme, C.L.6
  • 23
    • 33644824666 scopus 로고    scopus 로고
    • Biogeochemistry of dihydrogen (H2)
    • Hoehler TM. (2005). Biogeochemistry of dihydrogen (H2). Met Ions Biol Syst 43: 9-48.
    • (2005) Met Ions Biol Syst , vol.43 , pp. 9-48
    • Hoehler, T.M.1
  • 25
    • 0035913370 scopus 로고    scopus 로고
    • The role of microbial mats in the production of reduced gases on the early Earth
    • DOI 10.1038/35085554
    • Hoehler TM, Bebout BM, Des Marais DJ. (2001). The role of microbial mats in the production of reduced gases on the early Earth. Nature 412: 324-327. (Pubitemid 32691844)
    • (2001) Nature , vol.412 , Issue.6844 , pp. 324-327
    • Hoehler, T.M.1    Bebout, B.M.2    Des Marais, D.J.3
  • 27
    • 0028869891 scopus 로고
    • Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR
    • Karkhoff-Schweizer RR, Huber DP, Voordouw G. (1995). Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl Environ Microbiol 61: 290-296.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 290-296
    • Karkhoff-Schweizer, R.R.1    Huber, D.P.2    Voordouw, G.3
  • 28
    • 0036793318 scopus 로고    scopus 로고
    • Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses
    • Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. (2002). Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. Biotechniques 33: 924-930. (Pubitemid 35168078)
    • (2002) BioTechniques , vol.33 , Issue.4 , pp. 924-930
    • Kim, H.1    Zhao, B.2    Snesrud, E.C.3    Haas, B.J.4    Town, C.D.5    Quackenbush, J.6
  • 29
    • 65349096123 scopus 로고    scopus 로고
    • Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): Abundance and diversity related to geochemical zonation
    • Leloup J, Fossing H, Kohls K, Holmkvist L, Borowski C, J?rgensen BB. (2009). Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ Microbiol 11: 1278-1291.
    • (2009) Environ Microbiol , vol.11 , pp. 1278-1291
    • Leloup, J.1    Fossing, H.2    Kohls, K.3    Holmkvist, L.4    Borowski, C.5    Jrgensen, B.B.6
  • 31
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • DOI 10.1093/bioinformatics/btl158
    • Li W, Godzik A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659. (Pubitemid 43985301)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 35
    • 0028808217 scopus 로고
    • Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus
    • Ohkuma M, Noda S, Horikoshi K, Kudo T. (1995). Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus. FEMS Microbiol Lett 134: 45-50.
    • (1995) FEMS Microbiol Lett , vol.134 , pp. 45-50
    • Ohkuma, M.1    Noda, S.2    Horikoshi, K.3    Kudo, T.4
  • 37
    • 48749095973 scopus 로고    scopus 로고
    • Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information
    • Pozhitkov AE, Nies G, Kleinhenz B, Tautz D, Noble PA. (2008). Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information. J Microbiol Methods 75: 92-102.
    • (2008) J Microbiol Methods , vol.75 , pp. 92-102
    • Pozhitkov, A.E.1    Nies, G.2    Kleinhenz, B.3    Tautz, D.4    Noble, P.A.5
  • 39
    • 40949129223 scopus 로고    scopus 로고
    • Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes
    • DOI 10.1021/es071455s
    • Rahm BG, Richardson RE. (2008). Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. Environ Sci Technol 42: 416-421. (Pubitemid 351461887)
    • (2008) Environmental Science and Technology , vol.42 , Issue.2 , pp. 416-421
    • Rahm, B.G.1    Richardson, R.E.2
  • 40
    • 38049121331 scopus 로고    scopus 로고
    • Design and testing of 'genome-proxy' microarrays to profile marine microbial communities
    • Rich VI, Konstantinidis K, DeLong EF. (2008). Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. Environ Microbiol 10: 506-521.
    • (2008) Environ Microbiol , vol.10 , pp. 506-521
    • Rich, V.I.1    Konstantinidis, K.2    Delong, E.F.3
  • 41
    • 38849161370 scopus 로고    scopus 로고
    • Diversity and expression of cyanobacterial hupS genes in pure cultures and in a nitrogen-limited phototrophic biofilm
    • DOI 10.1111/j.1574-6941.2008.00435.x
    • Roeselers G, Huisjes EH, van Loosdrecht MCM, Muyzer G. (2008). Diversity and expression of cyanobacterial hupS genes in pure cultures and in a nitrogen-limited phototrophic biofilm. FEMS Microbiol Ecol 63: 292-300. (Pubitemid 351208040)
    • (2008) FEMS Microbiology Ecology , vol.63 , Issue.3 , pp. 292-300
    • Roeselers, G.1    Huisjes, E.H.2    Van Loosdrecht, M.C.M.3    Muyzer, G.4
  • 43
    • 9244251590 scopus 로고    scopus 로고
    • Anaerobic microbial dehalogenation
    • DOI 10.1146/annurev.micro.58.030603.123600
    • Smidt H, de Vos WM. (2004). Anaerobic microbial dehalogenation. Annu Rev Microbiol 58: 43-73. (Pubitemid 39551978)
    • (2004) Annual Review of Microbiology , vol.58 , pp. 43-73
    • Smidt, H.1    De Vos, W.M.2
  • 44
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • DOI 10.1016/S1046-2023(03)00155-5
    • Smyth GK, Speed T. (2003). Normalization of cDNA microarray data. Methods 31: 265-273. (Pubitemid 37338763)
    • (2003) Methods , vol.31 , Issue.4 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 45
    • 67651202726 scopus 로고    scopus 로고
    • Electron transfer in syntrophic communities of anaerobic bacteria and archaea
    • Stams AJM, Plugge CM. (2009). Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7: 568-577.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 568-577
    • Stams, A.J.M.1    Plugge, C.M.2
  • 46
    • 0037316061 scopus 로고    scopus 로고
    • Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment
    • DOI 10.1128/AEM.69.2.1159-1171.2003
    • 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. (Pubitemid 36204848)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.2 , pp. 1159-1171
    • Taroncher-Oldenburg, G.1    Griner, E.M.2    Francis, C.A.3    Ward, B.B.4
  • 48
    • 0028139018 scopus 로고
    • Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds
    • Utkin I, Woese C, Wiegel J. (1994). Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds. Int J Syst Bacteriol 44: 612-619. (Pubitemid 24315134)
    • (1994) International Journal of Systematic Bacteriology , vol.44 , Issue.4 , pp. 612-619
    • Utkin, I.1    Woese, C.2    Wiegel, J.3
  • 49
    • 44449159969 scopus 로고    scopus 로고
    • Hydrogenases and H(+)-reduction in primary energy conservation
    • Vignais PM. (2008). Hydrogenases and H(+)-reduction in primary energy conservation. Results Probl Cell Differ 45: 223-252.
    • (2008) Results Probl Cell Differ , vol.45 , pp. 223-252
    • Vignais, P.M.1
  • 50
    • 35748974830 scopus 로고    scopus 로고
    • Occurrence, classification, and biological function of hydrogenases: An overview
    • DOI 10.1021/cr050196r
    • Vignais PM, Billoud B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 107: 4206-4272. (Pubitemid 350041744)
    • (2007) Chemical Reviews , vol.107 , Issue.10 , pp. 4206-4272
    • Vignais, P.M.1    Billoud, B.2
  • 51
    • 0034886919 scopus 로고    scopus 로고
    • Classification and phylogeny of hydrogenases
    • DOI 10.1016/S0168-6445(01)00063-8, PII S0168644501000638
    • Vignais PM, Billoud B, Meyer J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25: 455-501. (Pubitemid 32778469)
    • (2001) FEMS Microbiology Reviews , vol.25 , Issue.4 , pp. 455-501
    • Vignais, P.M.1    Billoud, B.2    Meyer, J.3
  • 54
    • 39649083358 scopus 로고    scopus 로고
    • 2-coproducing system, analyzed using the [Fe]-hydrogenase gene
    • DOI 10.1128/AEM.01946-07
    • Xing D, Ren N, Rittmann BE. (2008). Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H2-coproducing system, analyzed using the [Fe]-hydrogenase gene. Appl Environ Microbiol 74: 1232-1239. (Pubitemid 351287095)
    • (2008) Applied and Environmental Microbiology , vol.74 , Issue.4 , pp. 1232-1239
    • Xing, D.1    Ren, N.2    Rittmann, B.E.3
  • 55
    • 0032533740 scopus 로고    scopus 로고
    • Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture
    • DOI 10.1021/es980363n
    • Yang Y, McCarty PL. (1998). Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture. Environ Sci Technol 32: 3591-3597. (Pubitemid 28527754)
    • (1998) Environmental Science and Technology , vol.32 , Issue.22 , pp. 3591-3597
    • Yang, Y.1    McCarty, P.L.2
  • 56
    • 11244253792 scopus 로고    scopus 로고
    • Kinetics and inhibition of reductive dechlorination of chlorinated ethylenes by two different mixed cultures
    • Yu S, Dolan M, Semprini L. (2005). Kinetics and inhibition of reductive dechlorination of chlorinated ethylenes by two different mixed cultures. Environ Sci Technol 39: 195-205.
    • (2005) Environ Sci Technol , vol.39 , pp. 195-205
    • Yu, S.1    Dolan, M.2    Semprini, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.