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Volumn 35, Issue 10, 2008, Pages 1139-1147

A comparison of methods for total community DNA preservation and extraction from various thermal environments

Author keywords

DGGE; DNA extraction; Environmental microbiology; Thermophile

Indexed keywords

BUFFER; SUCROSE;

EID: 51649098690     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-008-0393-y     Document Type: Article
Times cited : (70)

References (46)
  • 2
    • 0028343555 scopus 로고
    • Remarkable archaeal diversity in a Yellowstone National Park hot spring environment
    • doi: 10.1073/pnas.91.5.1609
    • Barns SM, et al. (1994) Remarkable archaeal diversity in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91(March):1609-1613 doi: 10.1073/pnas.91.5.1609
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.MARCH , pp. 1609-1613
    • Barns, S.M.1
  • 3
    • 51649108208 scopus 로고    scopus 로고
    • Testing the UltraClean soil DNA purification kit on a diverse range of soils by PCR amplification of 16S rDNA
    • Braid MD, et al. Testing the UltraClean soil DNA purification kit on a diverse range of soils by PCR amplification of 16S rDNA. In: ASM General Meeting. 1999
    • (1999) ASM General Meeting
    • Braid, M.D.1
  • 5
    • 34547568706 scopus 로고    scopus 로고
    • Candidatus Chloracidobacterium thermophilum: An aerobic phototrophic acidobacterium
    • 10.1126/science.1143236
    • DA Bryant 2007 Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium Science 317 523 526 10.1126/science.1143236
    • (2007) Science , vol.317 , pp. 523-526
    • Bryant, D.A.1
  • 6
    • 0027551748 scopus 로고
    • Identification and localization of bacterial endosymbionts in hydrothermal vent taxa with symbiont-specific polymerase chain reaction amplification and in situ hybridization techniques
    • 1
    • SC Cary 1993 Identification and localization of bacterial endosymbionts in hydrothermal vent taxa with symbiont-specific polymerase chain reaction amplification and in situ hybridization techniques Mol Mar Biol Biotechnol 2 1 51 62
    • (1993) Mol Mar Biol Biotechnol , vol.2 , pp. 51-62
    • Cary, S.C.1
  • 7
    • 0030613348 scopus 로고    scopus 로고
    • Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis
    • 4
    • MJ Ferris DM Ward 1997 Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis Appl Environ Microbiol 63 4 1375 1381
    • (1997) Appl Environ Microbiol , vol.63 , pp. 1375-1381
    • Ferris, M.J.1    Ward, D.M.2
  • 8
    • 0032188995 scopus 로고    scopus 로고
    • Empirical evaluation of preservation methods for faecal DNA
    • 10.1046/j.1365-294x.1998.00449.x
    • MAJ Frantzen 1998 Empirical evaluation of preservation methods for faecal DNA Mol Ecol 7 1423 1428 10.1046/j.1365-294x.1998.00449.x
    • (1998) Mol Ecol , vol.7 , pp. 1423-1428
    • Frantzen, M.A.J.1
  • 9
    • 18744374590 scopus 로고    scopus 로고
    • Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns
    • 11. 10.1046/j.1462-2920.2002.00358.x
    • N Fromin 2002 Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns Environ Microbiol 4 11 634 643 10.1046/j.1462-2920.2002.00358.x
    • (2002) Environ Microbiol , vol.4 , pp. 634-643
    • Fromin, N.1
  • 10
    • 0032710940 scopus 로고    scopus 로고
    • Quantification of bias related to the extraction of DNA directly from soils
    • 12
    • A Frostegard 1999 Quantification of bias related to the extraction of DNA directly from soils Appl Environ Microbiol 65 12 5409 5420
    • (1999) Appl Environ Microbiol , vol.65 , pp. 5409-5420
    • Frostegard, A.1
  • 11
    • 0037447816 scopus 로고    scopus 로고
    • Effecient recovery of environmental DNA for expression cloning by indirect extraction methods
    • 10.1016/S0168-6496(02)00462-2
    • EM Gabor EJ de Vries DB Janssen 2003 Effecient recovery of environmental DNA for expression cloning by indirect extraction methods FEMS Microbiol Ecol 44 153 163 10.1016/S0168-6496(02)00462-2
    • (2003) FEMS Microbiol Ecol , vol.44 , pp. 153-163
    • Gabor, E.M.1    De Vries, E.J.2    Janssen, D.B.3
  • 12
    • 0004122931 scopus 로고
    • Field C (ed) Saunders College Publishing, Philadelphia
    • Garrett RH, Grisham CM (1995) In: Field C (ed) Biochemistry, Saunders College Publishing, Philadelphia
    • (1995) Biochemistry
    • Garrett, R.H.1    Grisham, C.M.2
  • 13
    • 0037816286 scopus 로고    scopus 로고
    • Molecular phylogenetic exploration of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles
    • 7. 10.1128/AEM.69.7.4332-4336.2003
    • D Ghosh 2003 Molecular phylogenetic exploration of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles Appl Environ Microbiol 69 7 4332 4336 10.1128/AEM.69.7.4332-4336.2003
    • (2003) Appl Environ Microbiol , vol.69 , pp. 4332-4336
    • Ghosh, D.1
  • 14
    • 0025322547 scopus 로고
    • Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton
    • SJ Giovannoni 1990 Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton Appl Environ Microbiol 56 2572 2575
    • (1990) Appl Environ Microbiol , vol.56 , pp. 2572-2575
    • Giovannoni, S.J.1
  • 15
    • 0027963464 scopus 로고
    • Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C
    • 8. 10.1128/AEM.70.2.845-849.2004
    • DL Haldeman 1994 Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C Appl Environ Microbiol 60 8 2697 2703 10.1128/AEM.70.2.845-849.2004
    • (1994) Appl Environ Microbiol , vol.60 , pp. 2697-2703
    • Haldeman, D.L.1
  • 16
    • 2342531664 scopus 로고    scopus 로고
    • New perspective on uncultured bacterial phylogenetic division OP11
    • 2. 10.1128/AEM.70.2.845-849.2004
    • KJ Harris ST Kelley NR Pace 2004 New perspective on uncultured bacterial phylogenetic division OP11 Appl Environ Microbiol 70 2 845 849 10.1128/AEM.70.2.845-849.2004
    • (2004) Appl Environ Microbiol , vol.70 , pp. 845-849
    • Harris, K.J.1    Kelley, S.T.2    Pace, N.R.3
  • 17
    • 0033857077 scopus 로고    scopus 로고
    • Soil conservation for DNA preservation for bacterial molecular studies
    • M Harry B Gambier E Garnier-Sillam 2000 Soil conservation for DNA preservation for bacterial molecular studies Eur J Soil Sci 36 51 55
    • (2000) Eur J Soil Sci , vol.36 , pp. 51-55
    • Harry, M.1    Gambier, B.2    Garnier-Sillam, E.3
  • 18
    • 34250730303 scopus 로고    scopus 로고
    • Exploring microbial diversity in volcanic environments: A review of methods in DNA extraction
    • 10.1016/j.mimet.2007.04.005
    • A Herrera CS Cockell 2007 Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction J Microbiol Methods 70 1 12 10.1016/j.mimet.2007.04.005
    • (2007) J Microbiol Methods , vol.70 , pp. 1-12
    • Herrera, A.1    Cockell, C.S.2
  • 19
    • 11944273392 scopus 로고    scopus 로고
    • Use of low nutrient enrichments to access novel amylase genes in silent diversity of thermophiles
    • 10.1007/s11274-004-2623-4
    • CFV Hobel 2004 Use of low nutrient enrichments to access novel amylase genes in silent diversity of thermophiles World J Microbiol Biotechnol 20 801 809 10.1007/s11274-004-2623-4
    • (2004) World J Microbiol Biotechnol , vol.20 , pp. 801-809
    • Hobel, C.F.V.1
  • 20
    • 0031662188 scopus 로고    scopus 로고
    • Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
    • 18
    • P Hugenholtz BM Goebel NR Pace 1998 Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity J Bacteriol 180 18 4765 4774
    • (1998) J Bacteriol , vol.180 , pp. 4765-4774
    • Hugenholtz, P.1    Goebel, B.M.2    Pace, N.R.3
  • 21
    • 0026638675 scopus 로고
    • Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA
    • 6
    • M Khanna G Stotzky 1992 Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA Appl Environ Microbiol 58 6 1930 1939
    • (1992) Appl Environ Microbiol , vol.58 , pp. 1930-1939
    • Khanna, M.1    Stotzky, G.2
  • 22
    • 34248211629 scopus 로고    scopus 로고
    • Finding the needles in the metagenome haystack
    • 10.1007/s00248-006-9201-2
    • GA Kowalchuk 2007 Finding the needles in the metagenome haystack Microb Ecol 53 475 485 10.1007/s00248-006-9201-2
    • (2007) Microb Ecol , vol.53 , pp. 475-485
    • Kowalchuk, G.A.1
  • 23
    • 0036008790 scopus 로고    scopus 로고
    • Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis
    • 10.1016/S0167-7012(01)00377-3
    • MG LaMontagne 2002 Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis J Microbiol Methods 49 255 264 10.1016/S0167-7012(01)00377-3
    • (2002) J Microbiol Methods , vol.49 , pp. 255-264
    • Lamontagne, M.G.1
  • 24
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • Stackebrandt E, Goodfellow M, (eds) Wiley, Chichester
    • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115-175
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 115-175
    • Lane, D.J.1
  • 25
    • 40349103383 scopus 로고    scopus 로고
    • Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment
    • 10.1007/s00792-007-0124-8
    • S Leuko 2008 Lysis efficiency of standard DNA extraction methods for Halococcus spp. in an organic rich environment Extremophiles 12 301 308 10.1007/s00792-007-0124-8
    • (2008) Extremophiles , vol.12 , pp. 301-308
    • Leuko, S.1
  • 26
    • 19144366814 scopus 로고    scopus 로고
    • Metagenomics and industrial applications
    • 10.1038/nrmicro1161
    • P Lorenz J Eck 2005 Metagenomics and industrial applications Nat Rev Microbiol 3 510 516 10.1038/nrmicro1161
    • (2005) Nat Rev Microbiol , vol.3 , pp. 510-516
    • Lorenz, P.1    Eck, J.2
  • 27
    • 33644871362 scopus 로고    scopus 로고
    • DNA extraction procedure: A critical issue for bacterial diversity assessment in marine sediments
    • 2. 10.1111/j.1462-2920.2005.00896.x
    • GM Luna A Dell'Anno R Danovaro 2006 DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments Environ Microbiol 8 2 308 320 10.1111/j.1462-2920.2005.00896.x
    • (2006) Environ Microbiol , vol.8 , pp. 308-320
    • Luna, G.M.1    Dell'Anno, A.2    Danovaro, R.3
  • 28
    • 33747134982 scopus 로고    scopus 로고
    • Factors affecting DNA preservation from museum-collected lepidopteran specimens
    • 3. 10.1111/j.1570-7458.2006.00451.x
    • M Mandrioli F Borsatti L Mola 2006 Factors affecting DNA preservation from museum-collected lepidopteran specimens Entomol Exp Appl 120 3 239 244 10.1111/j.1570-7458.2006.00451.x
    • (2006) Entomol Exp Appl , vol.120 , pp. 239-244
    • Mandrioli, M.1    Borsatti, F.2    Mola, L.3
  • 29
    • 33644829921 scopus 로고    scopus 로고
    • Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA
    • 10.1111/j.1472-4669.2005.00052.x
    • DR Meyer-Dombard EL Shock JP Amend 2005 Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA Geobiology 3 211 227 10.1111/j.1472-4669.2005.00052.x
    • (2005) Geobiology , vol.3 , pp. 211-227
    • Meyer-Dombard, D.R.1    Shock, E.L.2    Amend, J.P.3
  • 30
    • 0032703237 scopus 로고    scopus 로고
    • Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples
    • 11
    • DN Miller 1999 Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples Appl Environ Microbiol 65 11 4715 4724
    • (1999) Appl Environ Microbiol , vol.65 , pp. 4715-4724
    • Miller, D.N.1
  • 31
    • 0032812081 scopus 로고    scopus 로고
    • Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis
    • 8
    • MM Moeseneder 1999 Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis Appl Environ Microbiol 65 8 3518 3525
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3518-3525
    • Moeseneder, M.M.1
  • 32
    • 0028269319 scopus 로고
    • Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment
    • 5
    • MI More 1994 Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment Appl Environ Microbiol 60 5 1572 1580
    • (1994) Appl Environ Microbiol , vol.60 , pp. 1572-1580
    • More, M.I.1
  • 33
    • 27844502481 scopus 로고    scopus 로고
    • Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense
    • 10.1099/ijs.0.63708-0
    • S Nakagawa 2005 Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense Int J Syst Evol Microbiol 55 2263 2268 10.1099/ijs.0.63708-0
    • (2005) Int J Syst Evol Microbiol , vol.55 , pp. 2263-2268
    • Nakagawa, S.1
  • 34
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • 10.1126/science.276.5313.734
    • NR Pace 1997 A molecular view of microbial diversity and the biosphere Science 276 734 740 10.1126/science.276.5313.734
    • (1997) Science , vol.276 , pp. 734-740
    • Pace, N.R.1
  • 35
    • 34250337335 scopus 로고    scopus 로고
    • Molecular approaches: Advantages and artifacts in assessing bacterial diversity
    • 10.1007/s10295-007-0219-3
    • DS Pontes 2007 Molecular approaches: advantages and artifacts in assessing bacterial diversity J Ind Microbiol Biotechnol 34 463 473 10.1007/s10295-007-0219-3
    • (2007) J Ind Microbiol Biotechnol , vol.34 , pp. 463-473
    • Pontes, D.S.1
  • 36
    • 0034013150 scopus 로고    scopus 로고
    • Microbial diversity at 83 degrees C in Calcite Springs, Yellowstone National Park: Another environment where the Aquificales and "korarchaeota" coexist
    • 1
    • AL Reysenbach M Ehringer K Hershberger 2000 Microbial diversity at 83 degrees C in Calcite Springs, Yellowstone National Park: another environment where the Aquificales and "Korarchaeota" coexist Extremophiles 4 1 61 67
    • (2000) Extremophiles , vol.4 , pp. 61-67
    • Reysenbach, A.L.1    Ehringer, M.2    Hershberger, K.3
  • 38
    • 3242782680 scopus 로고    scopus 로고
    • Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria
    • 7. 10.1128/AEM.70.7.4363-4366.2004
    • L Schoenborn 2004 Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria Appl Environ Microbiol 70 7 4363 4366 10.1128/AEM.70.7.4363-4366.2004
    • (2004) Appl Environ Microbiol , vol.70 , pp. 4363-4366
    • Schoenborn, L.1
  • 39
    • 51649096510 scopus 로고    scopus 로고
    • Viral diversity and improved DNA polymerases
    • Mammoth Hot Springs, WY, USA
    • Schoenfeld T, et al. (2008) Viral diversity and improved DNA polymerases, In: YNP RCN/TBI workshop, Mammoth Hot Springs, WY, USA
    • (2008) YNP RCN/TBI Workshop
    • Schoenfeld, T.1
  • 40
    • 0035163597 scopus 로고    scopus 로고
    • Microvariation artifacts introduced by pcr and cloning of closely related 16S rRNA gene sequences
    • 1. 10.1128/AEM.67.1.469-472.2001
    • AGCL Speksnijder 2001 Microvariation artifacts introduced by pcr and cloning of closely related 16S rRNA gene sequences Appl Environ Microbiol 67 1 469 472 10.1128/AEM.67.1.469-472.2001
    • (2001) Appl Environ Microbiol , vol.67 , pp. 469-472
    • Agcl, S.1
  • 41
    • 0024077490 scopus 로고    scopus 로고
    • DNA amplification to enhance detection of genetically engineered bacteria in environmental samples
    • 9
    • RJ Steffan RM Atlas 1998 DNA amplification to enhance detection of genetically engineered bacteria in environmental samples Appl Environ Microbiol 54 9 2185 2191
    • (1998) Appl Environ Microbiol , vol.54 , pp. 2185-2191
    • Steffan, R.J.1    Atlas, R.M.2
  • 42
    • 0030023659 scopus 로고    scopus 로고
    • Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
    • 3
    • JL Stein 1996 Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon J Bacteriol 178 3 591 599
    • (1996) J Bacteriol , vol.178 , pp. 591-599
    • Stein, J.L.1
  • 43
    • 44849108291 scopus 로고    scopus 로고
    • Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles
    • 7. 10.1111/j.1462-2920.2008.01584.x
    • CD Takacs-Vesbach 2008 Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles Environ Microbiol 10 7 1681 1689 10.1111/j.1462-2920.2008.01584.x
    • (2008) Environ Microbiol , vol.10 , pp. 1681-1689
    • Takacs-Vesbach, C.D.1
  • 44
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • 3. 10.1111/j.1574-6976.1997.tb00351.x
    • F von Wintzingerode UB Gobel E Stackebrandt 1997 Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol Rev 21 3 213 229 10.1111/j.1574-6976.1997.tb00351.x
    • (1997) FEMS Microbiol Rev , vol.21 , pp. 213-229
    • Von Wintzingerode, F.1    Gobel, U.B.2    Stackebrandt, E.3
  • 45
    • 33847289745 scopus 로고    scopus 로고
    • Comparison of methods for total community DNA extraction and purification from compost
    • 10.1007/s00253-006-0704-z
    • ZH Yang 2007 Comparison of methods for total community DNA extraction and purification from compost Appl Microbiol Biotechnol 74 918 925 10.1007/s00253-006-0704-z
    • (2007) Appl Microbiol Biotechnol , vol.74 , pp. 918-925
    • Yang, Z.H.1


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