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Volumn 165, Issue 2, 2011, Pages 454-464

An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries

Author keywords

Humic substances; Metagenomic DNA; Polyethylene glycol 8000; Polyvinylpolypyrrolidone; Powdered activated charcoal

Indexed keywords

ALKALINE SOILS; CELL LYSIS; DNA EXTRACTION; HUMIC SUBSTANCES; ISO-PROPANOLS; ISOLATION AND PURIFICATION; METAGENOMIC DNA; METAGENOMIC LIBRARIES; PCR AMPLIFICATION; POLYVINYLPOLYPYRROLIDONE; PURITY LEVEL; RESTRICTION DIGESTION; SINGLE-STEP;

EID: 81455141559     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-011-9264-5     Document Type: Article
Times cited : (55)

References (47)
  • 1
    • 0021779934 scopus 로고
    • Measurement of in situ activities of non photosynthetic microorganisms in aquatic and terrestrial habitats
    • Staley, J. T., & Kanopka, A. (1985). Measurement of in situ activities of non photosynthetic microorganisms in aquatic and terrestrial habitats. Annual Review of Microbiology, 39, 321-346.
    • (1985) Annual Review of Microbiology , vol.39 , pp. 321-346
    • Staley, J.T.1    Kanopka, A.2
  • 2
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R. I., Ludwig, W., & Schleifer, K. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59, 143-169.
    • (1995) Microbiological Reviews , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.3
  • 4
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • DOI 10.1126/science.276.5313.734
    • Pace, N. R. (1997). A molecular view of microbial biodiversity and the biosphere. Science, 276, 734-740. (Pubitemid 27199842)
    • (1997) Science , vol.276 , Issue.5313 , pp. 734-740
    • Pace, N.R.1
  • 5
    • 0036270789 scopus 로고    scopus 로고
    • Microbial diversity and function in soil: From genes to ecosystems
    • DOI 10.1016/S1369-5274(02)00324-7
    • Torsvik, V., & Ovreas, L. (2002). Microbial diversity and function in soil: from genes to Ecosystems. Current Opinion in Microbiology, 5, 240-245. (Pubitemid 34614934)
    • (2002) Current Opinion in Microbiology , vol.5 , Issue.3 , pp. 240-245
    • Torsvik, V.1    Ovreas, L.2
  • 6
    • 2942576144 scopus 로고    scopus 로고
    • The soil metagenome - A rich resource for the discovery of novel natural products
    • DOI 10.1016/j.copbio.2004.04.005, PII S0958166904000576
    • Daniel, R. (2004). The soil metagenome-a rich resource for the discovery of novel natural products. Current Opinion in Biotechnology, 15, 199-204. (Pubitemid 38749041)
    • (2004) Current Opinion in Biotechnology , vol.15 , Issue.3 , pp. 199-204
    • Daniel, R.1
  • 9
    • 81455148659 scopus 로고    scopus 로고
    • Developments in metagenomics for accessing novel genes for useful microbial products
    • P. C. Trivedi (Ed.), Jaipur: Aavishkar Publishers
    • Verma, D., Kawarabayasi, Y., & Satyanarayana, T. (2010). Developments in metagenomics for accessing novel genes for useful microbial products. In P. C. Trivedi (Ed.), Applications of microbiology (pp. 27-57). Jaipur: Aavishkar Publishers.
    • (2010) Applications of Microbiology , pp. 27-57
    • Verma, D.1    Kawarabayasi, Y.2    Satyanarayana, T.3
  • 10
    • 25444515486 scopus 로고    scopus 로고
    • Isolation of novel lipolytic genes from uncultured bacteria of pond water
    • DOI 10.1016/j.bbrc.2005.07.046, PII S0006291X0501524X
    • Ranjan, R., Grover, A., Kapardar, R. K., & Sharma, R. (2005). Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochemical and Biophysical Research Communications, 335, 57-65. (Pubitemid 41357462)
    • (2005) Biochemical and Biophysical Research Communications , vol.335 , Issue.1 , pp. 57-65
    • Ranjan, R.1    Grover, A.2    Kapardar, R.K.3    Sharma, R.4
  • 11
    • 0038725668 scopus 로고    scopus 로고
    • A gene encoding a novel extremely thermostable 1,4-β-xylanase isolated directly from an environmental DNA sample
    • DOI 10.1007/s00792-002-0296-1
    • Sunna, A., & Bergquist, P. L. (2003). A gene encoding a novel extremely thermostable 1, 4 β xylanase isolated directly from an environmental DNA sample. Extremophiles, 7, 63-70. (Pubitemid 40856328)
    • (2003) Extremophiles , vol.7 , Issue.1 , pp. 63-70
    • Sunna, A.1    Bergquist, P.L.2
  • 12
    • 0029808356 scopus 로고    scopus 로고
    • Simultaneous detection of microorganisms in soil suspension based on PCR amplification of bacterial 16S rRNA fragments
    • McGregor, D. P., Forster, S., Steven, J., Adair, J., Leary, S. E. C., Leslie, D. L., et al. (1996). Simultaneous detection of microorganisms in soil suspension based on PCR amplification of bacterial 16S rRNA fragments. BioTechniques, 21, 463-471. (Pubitemid 26304354)
    • (1996) BioTechniques , vol.21 , Issue.3 , pp. 463-471
    • McGregor, D.P.1    Forster, S.2    Steven, J.3    Adair, J.4    Leary, S.E.C.5    Leslie, D.L.6    Harris, W.J.7    Titball, R.W.8
  • 13
    • 0026708461 scopus 로고
    • Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction
    • Tsai, Y., & Olson, B. H. (1992). Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Applied and Environmental Microbiology, 58, 2292-2295.
    • (1992) Applied and Environmental Microbiology , vol.58 , pp. 2292-2295
    • Tsai, Y.1    Olson, B.H.2
  • 14
    • 0025740131 scopus 로고
    • Recovery of bulk DNA from soil by a rapid, small-scale extraction method
    • Porteous, L. A., & Armstrong, J. L. (1991). Recovery of bulk DNA from soil by a rapid, small-scale extraction method. Current Microbiology, 22, 345-348.
    • (1991) Current Microbiology , vol.22 , pp. 345-348
    • Porteous, L.A.1    Armstrong, J.L.2
  • 15
    • 0037447816 scopus 로고    scopus 로고
    • Efficient recovery of environmental DNA for expression cloning by indirect extraction methods
    • DOI 10.1016/S0168-6496(02)00462-2
    • Gabor, E. M., de Vries, E. J., & Janssen, D. B. (2003). Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiology Ecology, 44, 153-163. (Pubitemid 36423411)
    • (2003) FEMS Microbiology Ecology , vol.44 , Issue.2 , pp. 153-163
    • Gabor, E.M.1    De Vries, E.J.2    Janssen, D.B.3
  • 16
    • 0032145986 scopus 로고    scopus 로고
    • Simple and rapid method for direct extraction of microbial DNA from soil for PCR
    • DOI 10.1016/S0038-0717(98)00001-7, PII S0038071798000017
    • Cullen, D. W., & Hirsch, P. R. (1998). Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biology and Biochemistry, 30, 983-993. (Pubitemid 28329521)
    • (1998) Soil Biology and Biochemistry , vol.30 , Issue.8-9 , pp. 983-993
    • Cullen, D.W.1    Hirsch, P.R.2
  • 17
    • 34848861111 scopus 로고    scopus 로고
    • An improved method for single step purification of metagenomic DNA
    • DOI 10.1007/s12033-007-0015-3
    • Sharma, P. K., Capalash, N., & Kaur, J. (2007). An improved method for single step purification of metagenomic DNA. Molecular Biotechnology, 36, 61-63. (Pubitemid 350133601)
    • (2007) Molecular Biotechnology , vol.36 , Issue.1 , pp. 61-63
    • Sharma, P.K.1    Capalash, N.2    Kaur, J.3
  • 18
    • 0035129246 scopus 로고    scopus 로고
    • Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments
    • DOI 10.1016/S0167-7012(00)00228-1, PII S0167701200002281
    • Miller, D. N. (2001). Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments. Journal of Microbiological Methods, 44, 49-58. (Pubitemid 32144677)
    • (2001) Journal of Microbiological Methods , vol.44 , Issue.1 , pp. 49-58
    • Miller, D.N.1
  • 19
    • 3042607971 scopus 로고    scopus 로고
    • DNA isolation from soil samples for cloning in different hosts
    • DOI 10.1007/s00253-003-1528-8
    • Kauffmann, I. M., Schmitt, J., & Schmidt, R. D. (2004). DNA isolation from soil samples for cloning in different hosts. Applied Microbiology and Biotechnology, 64, 665-670. (Pubitemid 38822630)
    • (2004) Applied Microbiology and Biotechnology , vol.64 , Issue.5 , pp. 665-670
    • Kauffmann, I.M.1    Schmitt, J.2    Schmid, R.D.3
  • 20
    • 0029759760 scopus 로고    scopus 로고
    • Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method
    • Purdy, K. J., Embley, T. M., Takii, S., & Nedwell, D. B. (1996). Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method. Applied and Environmental Microbiology, 62, 3905-3907. (Pubitemid 26329636)
    • (1996) Applied and Environmental Microbiology , vol.62 , Issue.10 , pp. 3905-3907
    • Purdy, K.J.1    Embley, T.M.2    Takii, S.3    Nedwell, D.B.4
  • 22
    • 0037224331 scopus 로고    scopus 로고
    • Direct extraction of DNA from soils for studies in microbial ecology
    • Schneegurt, M. A., Dore, S., & Kulpa, C. F., Jr. (2003). Direct extraction of DNA from soils for studies in microbial ecology. Current Issues in Molecular Biology, 5, 1-8. (Pubitemid 36335929)
    • (2003) Current Issues in Molecular Biology , vol.5 , Issue.1 , pp. 1-8
    • Schneegurt, M.A.1    Dore, S.Y.2    Kulpa Jr., C.F.3
  • 23
    • 33748543962 scopus 로고    scopus 로고
    • Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments
    • DOI 10.1016/j.biortech.2006.04.004, PII S0960852406001556
    • Desai, C., & Madamwar, D. (2006). Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion exchange treatments. Bioresource Technology, 98, 761-768. (Pubitemid 44375144)
    • (2007) Bioresource Technology , vol.98 , Issue.4 , pp. 761-768
    • Desai, C.1    Madamwar, D.2
  • 25
    • 0031854206 scopus 로고    scopus 로고
    • Rapid purification of DNA from soil for molecular biodiversity analysis
    • DOI 10.1046/j.1472-765X.1998.00383.x
    • Yeates, C., & Gillings, M. R. (1998). Rapid purification of DNA from soil for molecular biodiversity analysis. Letters in Applied Microbiology, 27, 49-53. (Pubitemid 28369921)
    • (1998) Letters in Applied Microbiology , vol.27 , Issue.1 , pp. 49-53
    • Yeates, C.1    Gillings, M.R.2
  • 26
  • 27
    • 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
    • DOI 10.1128/AEM.66.12.5488-5491.2000
    • 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 rRNAbased microbial community composition. Applied and Environmental Microbiology, 66, 5488-5491. (Pubitemid 32217162)
    • (2000) Applied and Environmental Microbiology , vol.66 , Issue.12 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'Donnell, A.G.3    Bailey, M.J.4
  • 28
    • 0033830857 scopus 로고    scopus 로고
    • Soil molecular microbial ecology at age 20: Methodological challenges for the future
    • Ogram, A. (2000). Soil molecular microbial ecology at age 20: methodological challenges for the future. Soil Biology and Biochemistry, 32, 1499-1505.
    • (2000) Soil Biology and Biochemistry , vol.32 , pp. 1499-1505
    • Ogram, A.1
  • 29
    • 0029660135 scopus 로고    scopus 로고
    • Phylogenetic analysis of the bacterial communities in marine sediments
    • Gray, J. P., & Herwig, R. P. (1996). Phylogenetic analysis of the bacterial communities in marine sediments. Applied and Environmental Microbiology, 62, 4049-4059.
    • (1996) Applied and Environmental Microbiology , vol.62 , pp. 4049-4059
    • Gray, J.P.1    Herwig, R.P.2
  • 30
    • 0023420963 scopus 로고
    • The adsorption of heavy metals onto hydrous activated carbon
    • DOI 10.1016/0043-1354(87)90024-8
    • Corapcioglu, M. O., & Huang, C. P. (1987). The adsorption of heavy metals onto hydrous activated carbon. Water Research, 21, 1031-1044. (Pubitemid 18052796)
    • (1987) Water Research , vol.21 , Issue.9 , pp. 1031-1044
    • Corapcioglu, M.O.1    Huang, C.P.2
  • 32
    • 0030617408 scopus 로고    scopus 로고
    • Adsorption of heavy metals from aqueous solutions onto activated carbon in single Cu and Ni systems and in binary Cu-Ni, Cu-Cd and Cu-Zn systems
    • Seco, A., Marzal, P., Gabaldo'n, C., & Ferrer, J. (1997). Adsorption of heavy metals from aqueous solutions onto activated carbon in single Cu and Ni systems and in binary Cu-Ni, Cu-Cd and Cu-Zn systems. Journal of Chemical Technology and Biotechnology, 68, 123-130.
    • (1997) Journal of Chemical Technology and Biotechnology , vol.68 , pp. 123-130
    • Seco, A.1    Marzal, P.2    Gabaldo'n, C.3    Ferrer, J.4
  • 34
    • 0034747878 scopus 로고    scopus 로고
    • Evaluation of refractory organic removal in combined biological powdered activated carbon - Microfiltration for advanced wastewater treatment
    • Seo, G. T., & Ohgaki, S. (2001). Evaluation of refractory organic removal in combined biological powdered activated carbon-microfiltration for advanced waste water treatment. Water Science and Technology, 43, 67-74. (Pubitemid 33026217)
    • (2001) Water Science and Technology , vol.43 , Issue.11 , pp. 67-74
    • Seo, G.T.1    Ohgaki, S.2
  • 38
    • 0036008790 scopus 로고    scopus 로고
    • Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis
    • DOI 10.1016/S0167-7012(01)00377-3, PII S0167701201003773
    • La Montagne, M. G., Michel, F. C., Jr., Holden, P. A., & Reddy, C. A. (2002). Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. Journal of Microbiological Methods, 49, 255-264. (Pubitemid 34183472)
    • (2002) Journal of Microbiological Methods , vol.49 , Issue.3 , pp. 255-264
    • LaMontagne, M.G.1    Michel Jr., F.C.2    Holden, P.A.3    Reddy, C.A.4
  • 39
  • 41
    • 0034837255 scopus 로고    scopus 로고
    • Rapid extraction of DNA from diverse soils by guanidine thiocyanate method
    • Agarwal, A., Kumar, C., & Goel, R. (2001). Rapid extraction of DNA from diverse soils by guanidine thiocyanate method. Indian Journal of Experimental Biology, 39, 906-910. (Pubitemid 32824520)
    • (2001) Indian Journal of Experimental Biology , vol.39 , Issue.9 , pp. 906-910
    • Agarwal, A.1    Kumar, C.2    Goel, R.3
  • 42
    • 0031833974 scopus 로고    scopus 로고
    • Phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in Japan
    • Yamamoto, H., Hiraishi, A., Kato, K., Chiura, H. X., Maki, Y., & Shimizu, A. (1998). Phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in Japan. Applied and Environmental Microbiology, 64, 1680-1687. (Pubitemid 28234769)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.5 , pp. 1680-1687
    • Yamamoto, H.1    Hiraishi, A.2    Kato, K.3    Chiura, H.X.4    Maki, Y.5    Shimizu, A.6
  • 43
    • 0030613148 scopus 로고    scopus 로고
    • Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunofluorescence
    • Van Elsas, J. D., Mäntynen, V., & Wolters, A. C. (1997). Soil DNA extraction and assessment of the fate of Mycobacterium chlorophenolicum strain PCP-1 in different soils by 16S ribosomal RNA gene sequence based most-probable-number PCR and immunofluorescence. Biology and Fertility of Soils, 24, 188-195.
    • (1997) Biology and Fertility of Soils , Issue.24 , pp. 188-195
    • Van Elsas, J.D.1    Mäntynen, V.2    Wolters, A.C.3
  • 44
    • 0037345089 scopus 로고    scopus 로고
    • Removal of PCR inhibitors from soil DNA by chemical flocculation
    • DOI 10.1016/S0167-7012(02)00210-5, PII S0167701202002105
    • Braid, M. D., Daniels, L. M., & Kitts, C. L. (2003). Removal of PCR inhibitors from soil DNA by chemical flocculation. Journal of Microbiological Methods, 52, 389-393. (Pubitemid 36078424)
    • (2003) Journal of Microbiological Methods , vol.52 , Issue.3 , pp. 389-393
    • Braid, M.D.1    Daniels, L.M.2    Kitts, C.L.3
  • 45
    • 0031194474 scopus 로고    scopus 로고
    • Xylanase production by thermophilic Bacillus licheniformis A99 in solid-state fermentation
    • DOI 10.1016/S0141-0229(96)00207-4, PII S0141022996002074
    • Archana, A., & Satyanarayana, T. (1997). Xylanase production by thermophilic Bacillus licheniformis A99 in solid state fermentation. Enzyme and Microbial Technology, 21, 12-17. (Pubitemid 27334185)
    • (1997) Enzyme and Microbial Technology , vol.21 , Issue.1 , pp. 12-17
    • Archana, A.1    Satyanarayana, T.2
  • 47
    • 0000432452 scopus 로고
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
    • M. A. Innis D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), San Diego: Academic Press
    • White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols. A guide to methods and applications (pp. 315-322). San Diego: Academic Press.
    • (1990) PCR Protocols. A Guide to Methods and Applications , pp. 315-322
    • White, T.J.1    Bruns, T.2    Lee, S.3    Taylor, J.4


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