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Volumn 107, Issue 4, 2009, Pages 1168-1177

An improved method to extract RNA from soil with efficient removal of humic acids

Author keywords

Bacteria; Humic acids; Real time polymerase chain reaction; RNA extraction; Soil

Indexed keywords

BIODEGRADATION; CHAINS; EXTRACTION; ORGANIC ACIDS; POLYMERASE CHAIN REACTION; RNA; SOILS; TRANSCRIPTION;

EID: 70349137950     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2009.04298.x     Document Type: Article
Times cited : (27)

References (42)
  • 1
    • 0033775613 scopus 로고    scopus 로고
    • The presence of humic substances and DNA in RNA extracts affects hybridization results
    • Alm, E.W., Zheng, D. Raskin, L. (2000) The presence of humic substances and DNA in RNA extracts affects hybridization results. Appl Environ Microbiol 66, 4547 4554.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 4547-4554
    • Alm, E.W.1    Zheng, D.2    Raskin, L.3
  • 2
    • 0034827343 scopus 로고    scopus 로고
    • Effects of humic substances on fluorometric DNA quantification and DNA hybridization
    • Bachoon, D.S., Otero, E. Hodson, R.E. (2001) Effects of humic substances on fluorometric DNA quantification and DNA hybridization. J Microbiol Methods 47, 73 82.
    • (2001) J Microbiol Methods , vol.47 , pp. 73-82
    • Bachoon, D.S.1    Otero, E.2    Hodson, R.E.3
  • 3
    • 0019805971 scopus 로고
    • Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas
    • Bagdasarian, M., Lurz, R., Rückert, B., Franklin, F.C., Bagdasarian, M.M., Frey, J. Timmis, K.N. (1981) Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16, 237 247.
    • (1981) Gene , vol.16 , pp. 237-247
    • Bagdasarian, M.1    Lurz, R.2    Rückert, B.3    Franklin, F.C.4    Bagdasarian, M.M.5    Frey, J.6    Timmis, K.N.7
  • 4
    • 0027730319 scopus 로고
    • Characterization by fluorescence of the dissolved organic matter in natural water. Application to fractions obtained by tangential ultrafiltration and XAD resin isolation
    • Belin, C., Quellec, C., Lamotte, M., Ewald, M. Simon, P. (1993) Characterization by fluorescence of the dissolved organic matter in natural water. Application to fractions obtained by tangential ultrafiltration and XAD resin isolation. Environ Technol 14, 1131 1144.
    • (1993) Environ Technol , vol.14 , pp. 1131-1144
    • Belin, C.1    Quellec, C.2    Lamotte, M.3    Ewald, M.4    Simon, P.5
  • 5
    • 0242668357 scopus 로고    scopus 로고
    • MRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil
    • Bürgmann, H., Widmer, F., Sigler, W.V. 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.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1928-1935
    • Bürgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 6
    • 34548548565 scopus 로고    scopus 로고
    • Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways
    • del Castillo, T. Ramos, J.L. (2007) Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 189, 6602 6610.
    • (2007) J Bacteriol , vol.189 , pp. 6602-6610
    • Del Castillo, T.1    Ramos, J.L.2
  • 7
    • 0033623422 scopus 로고    scopus 로고
    • BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida
    • Cowles, C.E., Nichols, N.N. Harwood, C.S. (2000) BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J Bacteriol 182, 6339 6346.
    • (2000) J Bacteriol , vol.182 , pp. 6339-6346
    • Cowles, C.E.1    Nichols, N.N.2    Harwood, C.S.3
  • 8
    • 0033772544 scopus 로고    scopus 로고
    • Fluorescence properties of well-characterized sedimentary estuarine humic compounds and surrounding pore waters
    • De Souza Sierra, M.M., Giovanela, M. Soriano-Sierra, E.J. (2000) Fluorescence properties of well-characterized sedimentary estuarine humic compounds and surrounding pore waters. Environ Technol 21, 979 988.
    • (2000) Environ Technol , vol.21 , pp. 979-988
    • De Souza Sierra, M.M.1    Giovanela, M.2    Soriano-Sierra, E.J.3
  • 9
    • 40549090963 scopus 로고    scopus 로고
    • Limited diffusive fluxes of substrate facilitate coexistence of two competing bacterial strains
    • Dechesne, A., Or, D. Smets, B.F. (2008) Limited diffusive fluxes of substrate facilitate coexistence of two competing bacterial strains. FEMS Microbiol Ecol 64, 1 8.
    • (2008) FEMS Microbiol Ecol , vol.64 , pp. 1-8
    • Dechesne, A.1    Or, D.2    Smets, B.F.3
  • 10
    • 0001059184 scopus 로고
    • Fluorescence excitation spectra of humic substances
    • Ghosh, K. Schnitzer, M. (1980) Fluorescence excitation spectra of humic substances. Can J Soil Sci 60, 373 379.
    • (1980) Can J Soil Sci , vol.60 , pp. 373-379
    • Ghosh, K.1    Schnitzer, M.2
  • 11
    • 0034468557 scopus 로고    scopus 로고
    • Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition
    • Griffiths, R.I., Whiteley, A.S., O'Donnell, A.G. Bailey, M.J. (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66, 5488 5491.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'Donnell, A.G.3    Bailey, M.J.4
  • 12
    • 1842614298 scopus 로고    scopus 로고
    • Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction
    • Han, J.I. Semrau, J.D. (2004) Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction. Environ Microbiol 6, 388 399.
    • (2004) Environ Microbiol , vol.6 , pp. 388-399
    • Han, J.I.1    Semrau, J.D.2
  • 14
    • 33645393449 scopus 로고    scopus 로고
    • Isolation and purification of hydrophilic fulvic acids by precipitation
    • Hiradate, S., Yonezawa, T. Takesako, H. (2006) Isolation and purification of hydrophilic fulvic acids by precipitation. Geoderma 132, 196 205.
    • (2006) Geoderma , vol.132 , pp. 196-205
    • Hiradate, S.1    Yonezawa, T.2    Takesako, H.3
  • 16
    • 0036933805 scopus 로고    scopus 로고
    • Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
    • Jiménez, J.I., Miñambres, B., García, J.L. Díaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4, 824 841.
    • (2002) Environ Microbiol , vol.4 , pp. 824-841
    • Jiménez, J.I.1    Miñambres, B.2    García, J.L.3    Díaz, E.4
  • 17
    • 0035795590 scopus 로고    scopus 로고
    • The chlorocatechol degradative genes, tfdT-CDEF, of Burkholderia sp. strain NK8 are involved in chlorobenzoate degradation and induced by chlorobenzoates and chlorocatechols
    • Liu, S., Ogawa, N. Miyashita, K. (2001) The chlorocatechol degradative genes, tfdT-CDEF, of Burkholderia sp. strain NK8 are involved in chlorobenzoate degradation and induced by chlorobenzoates and chlorocatechols. Gene 268, 207 214.
    • (2001) Gene , vol.268 , pp. 207-214
    • Liu, S.1    Ogawa, N.2    Miyashita, K.3
  • 18
    • 22144492300 scopus 로고    scopus 로고
    • A molecular method to evaluate basidiomycete laccase gene expression in forest soils
    • Luis, P., Kellner, H., Martin, F. Buscot, F. (2005) A molecular method to evaluate basidiomycete laccase gene expression in forest soils. Geoderma 128, 18 27.
    • (2005) Geoderma , vol.128 , pp. 18-27
    • Luis, P.1    Kellner, H.2    Martin, F.3    Buscot, F.4
  • 19
    • 0032528138 scopus 로고    scopus 로고
    • The detection of gram-negative bacterial mRNA from soil by RT-PCR
    • Mendum, T.A., Sockett, R.E. Hirsch, P.R. (1998) The detection of gram-negative bacterial mRNA from soil by RT-PCR. FEMS Microbiol Lett 164, 369 373.
    • (1998) FEMS Microbiol Lett , vol.164 , pp. 369-373
    • Mendum, T.A.1    Sockett, R.E.2    Hirsch, P.R.3
  • 20
    • 0035129246 scopus 로고    scopus 로고
    • Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments
    • Miller, D.N. (2001) Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments. J Microbiol Methods 44, 49 58.
    • (2001) J Microbiol Methods , vol.44 , pp. 49-58
    • Miller, D.N.1
  • 21
    • 0032846469 scopus 로고    scopus 로고
    • Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR
    • Miskin, I.P., Farrimond, P. Head, I.M. (1999) Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR. Microbiology 145, 1977 1987.
    • (1999) Microbiology , vol.145 , pp. 1977-1987
    • Miskin, I.P.1    Farrimond, P.2    Head, I.M.3
  • 22
    • 34948813038 scopus 로고    scopus 로고
    • Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1
    • Miyakoshi, M., Shintani, M., Terabayashi, T., Kai, S., Yamane, H. Nojiri, H. (2007) Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 189, 6849 6860.
    • (2007) J Bacteriol , vol.189 , pp. 6849-6860
    • Miyakoshi, M.1    Shintani, M.2    Terabayashi, T.3    Kai, S.4    Yamane, H.5    Nojiri, H.6
  • 23
    • 34547727714 scopus 로고    scopus 로고
    • Analysis of a bacterial community in 3-chlorobenzoate-contaminated soil by PCR-DGGE targeting the 16S rRNA gene and benzoate 1,2-dioxygenase gene (ben A)
    • Morimoto, S., Togami, K., Ogawa, N., Hasebe, A. Fujii, T. (2005) Analysis of a bacterial community in 3-chlorobenzoate-contaminated soil by PCR-DGGE targeting the 16S rRNA gene and benzoate 1,2-dioxygenase gene (ben A). Microbes Environ 20, 151 159.
    • (2005) Microbes Environ , vol.20 , pp. 151-159
    • Morimoto, S.1    Togami, K.2    Ogawa, N.3    Hasebe, A.4    Fujii, T.5
  • 25
    • 0141608699 scopus 로고    scopus 로고
    • Microbial genes and enzymes in the degradation of chlorinated compounds
    • Ogawa, N., Miyashita, K. Chakrabarty, A.M. (2003) Microbial genes and enzymes in the degradation of chlorinated compounds. Chem Rec 3, 158 171.
    • (2003) Chem Rec , vol.3 , pp. 158-171
    • Ogawa, N.1    Miyashita, K.2    Chakrabarty, A.M.3
  • 26
    • 0028851170 scopus 로고
    • Isolation and characterization of RNA from low-biomass deep-subsurface sediments
    • Ogram, A., Sun, W., Brockman, F.J. Fredrickson, J.K. (1995) Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl Environ Microbiol 61, 763 768.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 763-768
    • Ogram, A.1    Sun, W.2    Brockman, F.J.3    Fredrickson, J.K.4
  • 27
    • 0345310070 scopus 로고    scopus 로고
    • Engineering of quasi-natural Pseudomonas putida strains for toluene metabolism through an ortho-cleavage degradation pathway
    • Panke, S., Sánchez-Romero, J.M. de Lorenzo, V. (1998) Engineering of quasi-natural Pseudomonas putida strains for toluene metabolism through an ortho-cleavage degradation pathway. Appl Environ Microbiol 64, 748 751.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 748-751
    • Panke, S.1    Sánchez-Romero, J.M.2    De Lorenzo, V.3
  • 28
    • 0038351053 scopus 로고    scopus 로고
    • Molecular weight characteristics of humic substances from different environments as determined by size exclusion chromatography and their statistical evaluation
    • Perminova, I.V., Frimmel, F.H., Kudryavtsev, A.V., Kulikova, N.A., Abbt-Braun, G., Hesse, S. Petrosyant, V.S. (2003) Molecular weight characteristics of humic substances from different environments as determined by size exclusion chromatography and their statistical evaluation. Environ Sci Technol 37, 2477 2485.
    • (2003) Environ Sci Technol , vol.37 , pp. 2477-2485
    • Perminova, I.V.1    Frimmel, F.H.2    Kudryavtsev, A.V.3    Kulikova, N.A.4    Abbt-Braun, G.5    Hesse, S.6    Petrosyant, V.S.7
  • 29
    • 48749114482 scopus 로고    scopus 로고
    • Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil
    • Peršoh, D., Theuerl, S., Buscot, F. Rambold, G. (2008) Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J Microbiol Methods 75, 19 24.
    • (2008) J Microbiol Methods , vol.75 , pp. 19-24
    • Peršoh, D.1    Theuerl, S.2    Buscot, F.3    Rambold, G.4
  • 31
    • 33748349179 scopus 로고    scopus 로고
    • Fluorescence spectroscopy: A tool to characterize humic substances in soil colonized by microorganisms?
    • Rezácová, V. Gryndler, M. (2006) Fluorescence spectroscopy: a tool to characterize humic substances in soil colonized by microorganisms? Folia Microbiol (Praha) 51, 215 221.
    • (2006) Folia Microbiol (Praha) , vol.51 , pp. 215-221
    • Rezácová, V.1    Gryndler, M.2
  • 33
    • 0025100070 scopus 로고
    • Molecular and quantitative aspects of the chemistry of fulvic acid and its interactions with metal ions and organic chemicals: Part II. The fluorescence spectroscopy approach
    • DOI 10.1016/S0003-2670(00)81226-X
    • Senesi, N. (1990) Molecular and quantitative aspects of the chemistry of fulvic acid and its interactions with metal ions and organic chemicals. Part II. The fluorescence spectroscopy. Anal Chim Acta 232, 77 106. (Pubitemid 20275228)
    • (1990) Analytica Chimica Acta , vol.232 , Issue.1 , pp. 77-106
    • Senesi, N.1
  • 34
    • 0036069298 scopus 로고    scopus 로고
    • RNA isolation from soil for bacterial community and functional analysis: Evaluation of different extraction and soil conservation protocols
    • 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.
    • (2002) J Microbiol Methods , vol.51 , pp. 171-179
    • Sessitsch, A.1    Gyamfi, S.2    Stralis-Pavese, N.3    Weilharter, A.4    Pfeifer, U.5
  • 35
    • 36649000680 scopus 로고    scopus 로고
    • Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples
    • Shintani, M., Fukushima, N., Tezuka, M., Yamane, H. Nojiri, H. (2008) Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples. Biotechnol Lett 30, 117 122.
    • (2008) Biotechnol Lett , vol.30 , pp. 117-122
    • Shintani, M.1    Fukushima, N.2    Tezuka, M.3    Yamane, H.4    Nojiri, H.5
  • 36
    • 0027202733 scopus 로고
    • Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast
    • Tebbe, C.C. Vahjen, W. (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59, 2657 2665.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 2657-2665
    • Tebbe, C.C.1    Vahjen, W.2
  • 37
    • 0025893814 scopus 로고
    • Rapid method for direct extraction of mRNA from seeded soils
    • Tsai, Y.L., Park, M.J. Olson, B.H. (1991) Rapid method for direct extraction of mRNA from seeded soils. Appl Environ Microbiol 57, 765 768.
    • (1991) Appl Environ Microbiol , vol.57 , pp. 765-768
    • Tsai, Y.L.1    Park, M.J.2    Olson, B.H.3
  • 38
    • 33749405542 scopus 로고    scopus 로고
    • Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates
    • Ude, S., Arnold, D.L., Moon, C.D., Timms-Wilson, T. Spiers, A.J. (2006) Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates. Environ Microbiol 8, 1997 2011.
    • (2006) Environ Microbiol , vol.8 , pp. 1997-2011
    • Ude, S.1    Arnold, D.L.2    Moon, C.D.3    Timms-Wilson, T.4    Spiers, A.J.5
  • 39
    • 1842582678 scopus 로고    scopus 로고
    • Real-time PCR quantification of a green fluorescent protein-labeled, genetically engineered Pseudomonas putida strain during 2-chlorobenzoate degradation in soil
    • Wang, G., Gentry, T.J., Grass, G., Josephson, K., Rensing, C. Pepper, I.L. (2004) Real-time PCR quantification of a green fluorescent protein-labeled, genetically engineered Pseudomonas putida strain during 2-chlorobenzoate degradation in soil. FEMS Microbiol Lett 233, 307 314.
    • (2004) FEMS Microbiol Lett , vol.233 , pp. 307-314
    • Wang, G.1    Gentry, T.J.2    Grass, G.3    Josephson, K.4    Rensing, C.5    Pepper, I.L.6
  • 40
    • 41549145885 scopus 로고    scopus 로고
    • Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method of RNA preparation from soil
    • Wang, Y., Shimodaira, J., Miyasaka, T., Morimoto, S., Oomori, T., Ogawa, N., Fukuda, M. Fujii, T. (2008) Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method of RNA preparation from soil. Biosci Biotechnol Biochem 72, 694 701.
    • (2008) Biosci Biotechnol Biochem , vol.72 , pp. 694-701
    • Wang, Y.1    Shimodaira, J.2    Miyasaka, T.3    Morimoto, S.4    Oomori, T.5    Ogawa, N.6    Fukuda, M.7    Fujii, T.8
  • 41
    • 33644952730 scopus 로고    scopus 로고
    • Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray
    • Yuste, L., Hervás, A.B., Canosa, I., Tobes, R., Jiménez, J.I., Nogales, J., Pérez-Pérez, M.M., Santero, E. et al. (2006) Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol 8, 165 177.
    • (2006) Environ Microbiol , vol.8 , pp. 165-177
    • Yuste, L.1    Hervás, A.B.2    Canosa, I.3    Tobes, R.4    Jiménez, J.I.5    Nogales, J.6    Pérez-Pérez, M.M.7    Santero, E.8
  • 42
    • 0037394735 scopus 로고    scopus 로고
    • Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green i and consequences for the analysis of soils and aquatic sediments
    • Zipper, H., Buta, C., Lämmle, K., Brunner, H., Bernhagen, J. Vitzthum, F. (2003) Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acids Res 31, e39.
    • (2003) Nucleic Acids Res , vol.31 , pp. 39
    • Zipper, H.1    Buta, C.2    Lämmle, K.3    Brunner, H.4    Bernhagen, J.5    Vitzthum, F.6


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