메뉴 건너뛰기




Volumn 105, Issue 3, 2008, Pages 813-821

Microbial DNA profiling by multiplex terminal restriction fragment length polymorphism for forensic comparison of soil and the influence of sample condition

Author keywords

Archaea; Bacteria; Forensic evidence; Fungi; Soil archive; Soil drying

Indexed keywords

DNA; DRYING; FORENSIC SCIENCE; FUNGI; SOIL SURVEYS;

EID: 49849101295     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2008.03819.x     Document Type: Article
Times cited : (31)

References (53)
  • 1
    • 30744473948 scopus 로고    scopus 로고
    • The limits and frontiers of desiccation-tolerant life
    • Alpert, P. (2005) The limits and frontiers of desiccation-tolerant life. Integr Comp Biol, 45, 685 695.
    • (2005) Integr Comp Biol , vol.45 , pp. 685-695
    • Alpert, P.1
  • 2
    • 3543138422 scopus 로고    scopus 로고
    • Diversity and ecology of soil fungal communities: Increased understanding through the application of molecular techniques
    • Anderson, I.C. Cairney, J.W.G. (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ Microbiol 6, 769 779.
    • (2004) Environ Microbiol , vol.6 , pp. 769-779
    • Anderson, I.C.1    Cairney, J.W.G.2
  • 3
    • 33644753759 scopus 로고    scopus 로고
    • A 'dirty' business: Testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi
    • Avis, P.G., Dickie, I.A. Mueller, G.M. (2006) A 'dirty' business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Molec Ecol 15, 873 882.
    • (2006) Molec Ecol , vol.15 , pp. 873-882
    • Avis, P.G.1    Dickie, I.A.2    Mueller, G.M.3
  • 4
    • 0036100201 scopus 로고    scopus 로고
    • The combined use of pollen and soil analyses in a search and subsequent murder investigation
    • Brown, A.G., Smith, A. Elmhurst, O. (2002) The combined use of pollen and soil analyses in a search and subsequent murder investigation. J Forensic Sci 47, 614 618.
    • (2002) J Forensic Sci , vol.47 , pp. 614-618
    • Brown, A.G.1    Smith, A.2    Elmhurst, O.3
  • 5
    • 0000398146 scopus 로고
    • Forensic palynology in the United States of America
    • Bryant, V.M., Jones, J.G. Mildenhall, D.C. (1990) Forensic palynology in the United States of America. Palynology 14, 193 208.
    • (1990) Palynology , vol.14 , pp. 193-208
    • Bryant, V.M.1    Jones, J.G.2    Mildenhall, D.C.3
  • 6
    • 0035065898 scopus 로고    scopus 로고
    • A strategy for optimizing quality and quantity of DNA extracted from soil
    • Burgmann, H., Pesaro, M., Widmer, F. Zeyer, J. (2001) A strategy for optimizing quality and quantity of DNA extracted from soil. J Microbiol Methods 45, 7 20.
    • (2001) J Microbiol Methods , vol.45 , pp. 7-20
    • Burgmann, H.1    Pesaro, M.2    Widmer, F.3    Zeyer, J.4
  • 7
    • 0035984122 scopus 로고    scopus 로고
    • Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern
    • Casamayor, E.O., Massana, R., Benlloch, S., Ovreas, L., Diez, B., Goddard, V.J., Gasol, J.M., Joint, I. et al. (2002) Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ Microbiol 4, 338 348.
    • (2002) Environ Microbiol , vol.4 , pp. 338-348
    • Casamayor, E.O.1    Massana, R.2    Benlloch, S.3    Ovreas, L.4    Diez, B.5    Goddard, V.J.6    Gasol, J.M.7    Joint, I.8
  • 8
    • 33744483524 scopus 로고    scopus 로고
    • Archaeal habitats - From the extreme to the ordinary
    • Chaban, B., Ng, S.Y.M. Jarrell, K.F. (2006) Archaeal habitats - from the extreme to the ordinary. Can J Microbiol 52, 73 116.
    • (2006) Can J Microbiol , vol.52 , pp. 73-116
    • Chaban, B.1    Ng, S.Y.M.2    Jarrell, K.F.3
  • 9
    • 0031149569 scopus 로고    scopus 로고
    • Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries
    • Chandler, D.P., Fredrickson, J.K. Brockman, F.J. (1997) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Molec Ecol 6, 475 482.
    • (1997) Molec Ecol , vol.6 , pp. 475-482
    • Chandler, D.P.1    Fredrickson, J.K.2    Brockman, F.J.3
  • 10
    • 0027804103 scopus 로고
    • Non-parametric multivariate analysis of changes in community structure
    • Clarke, K.R. (1993) Non-parametric multivariate analysis of changes in community structure. Aust J Ecol 18, 117 143.
    • (1993) Aust J Ecol , vol.18 , pp. 117-143
    • Clarke, K.R.1
  • 13
    • 9144269128 scopus 로고    scopus 로고
    • The effect of drying of soil samples on the number of bacteria and fungi
    • Evdokimova, G.A. Mozgova, N.P. (2003) The effect of drying of soil samples on the number of bacteria and fungi. Eurasian Soil Sci 36, 546 549.
    • (2003) Eurasian Soil Sci , vol.36 , pp. 546-549
    • Evdokimova, G.A.1    Mozgova, N.P.2
  • 14
    • 0037338334 scopus 로고    scopus 로고
    • Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils
    • Girvan, M.S., Bullimore, J., Pretty, J.N., Osborn, A.M. Ball, A.S. (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69, 1800 1809.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1800-1809
    • Girvan, M.S.1    Bullimore, J.2    Pretty, J.N.3    Osborn, A.M.4    Ball, A.S.5
  • 15
    • 33646548565 scopus 로고    scopus 로고
    • Towards a world soil survey archive and catalogue
    • Hallett, S.H., Bullock, P. Baillie, I. (2006) Towards a world soil survey archive and catalogue. Soil Use Manag 22, 227 228.
    • (2006) Soil Use Manag , vol.22 , pp. 227-228
    • Hallett, S.H.1    Bullock, P.2    Baillie, I.3
  • 16
    • 85101947152 scopus 로고
    • Effect of water potential on microbial growth and activity in soil
    • In. ed. Parr, J.F., Gardner, W.R. Elliott, L.F. pp. Madison, WI: Soil Science Society of America Journal.
    • Harris, R.F. (1981) Effect of water potential on microbial growth and activity in soil. In Water Potential Relationships in Soil Microbiology ed. Parr, J.F., Gardner, W.R. Elliott, L.F. pp. 23 96 Madison, WI : Soil Science Society of America Journal.
    • (1981) Water Potential Relationships in Soil Microbiology , pp. 23-96
    • Harris, R.F.1
  • 17
    • 33749024441 scopus 로고    scopus 로고
    • Assessing the potential of bacterial DNA profiling for forensic soil comparisons
    • Heath, L.E. Saunders, V.A. (2006) Assessing the potential of bacterial DNA profiling for forensic soil comparisons. J Forensic Sci 51, 1062 1068.
    • (2006) J Forensic Sci , vol.51 , pp. 1062-1068
    • Heath, L.E.1    Saunders, V.A.2
  • 18
    • 0032171129 scopus 로고    scopus 로고
    • Forensic palynology: Assessing the value of the evidence
    • Horrocks, M. Walsh, K.A.J. (1998) Forensic palynology: assessing the value of the evidence. Rev Palaeobotany Palynol 103, 69 74.
    • (1998) Rev Palaeobotany Palynol , vol.103 , pp. 69-74
    • Horrocks, M.1    Walsh, K.A.J.2
  • 19
    • 0032994831 scopus 로고    scopus 로고
    • Fine resolution of pollen patterns in limited space: Differentiating a crime scene and alibi scene seven meters apart
    • Horrocks, M. Walsh, K.A.J. (1999) Fine resolution of pollen patterns in limited space: differentiating a crime scene and alibi scene seven meters apart. J Forensic Sci 44, 417 420.
    • (1999) J Forensic Sci , vol.44 , pp. 417-420
    • Horrocks, M.1    Walsh, K.A.J.2
  • 20
    • 0031942957 scopus 로고    scopus 로고
    • Forensic palynology: Variation in the pollen content of soil surface samples
    • Horrocks, M., Coulson, S.A. Walsh, K.A.J. (1998) Forensic palynology: variation in the pollen content of soil surface samples. J Forensic Sci 43, 320 323.
    • (1998) J Forensic Sci , vol.43 , pp. 320-323
    • Horrocks, M.1    Coulson, S.A.2    Walsh, K.A.J.3
  • 22
    • 33746408754 scopus 로고    scopus 로고
    • The nature of forensic science opinion - A possible framework to guide thinking and practice in investigations and in court proceedings
    • Jackson, G., Jones, S., Booth, G., Champod, C. Evett, I.W. (2006) The nature of forensic science opinion - a possible framework to guide thinking and practice in investigations and in court proceedings. Sci Justice 46, 33 44.
    • (2006) Sci Justice , vol.46 , pp. 33-44
    • Jackson, G.1    Jones, S.2    Booth, G.3    Champod, C.4    Evett, I.W.5
  • 23
    • 0030033123 scopus 로고    scopus 로고
    • Assessing the unique characteristics of close-proximity soil samples: Just how useful is soil evidence?
    • Junger, E.P. (1996) Assessing the unique characteristics of close-proximity soil samples: just how useful is soil evidence? J Forensic Sci 41, 27 34.
    • (1996) J Forensic Sci , vol.41 , pp. 27-34
    • Junger, E.P.1
  • 24
    • 1942443842 scopus 로고    scopus 로고
    • Community analysis of methanogenic archaea within a riparian flooding gradient
    • Kemnitz, D., Chin, K.J., Bodelier, P. Conrad, R. (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol 6, 449 461.
    • (2004) Environ Microbiol , vol.6 , pp. 449-461
    • Kemnitz, D.1    Chin, K.J.2    Bodelier, P.3    Conrad, R.4
  • 25
    • 0031842281 scopus 로고    scopus 로고
    • Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil
    • Kuske, C.R., Banton, K.L., Adorada, D.L., Stark, P.C., Hill, K.K. Jackson, P.J. (1998) Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl Environ Microbiol 64, 2463 2472.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 2463-2472
    • Kuske, C.R.1    Banton, K.L.2    Adorada, D.L.3    Stark, P.C.4    Hill, K.K.5    Jackson, P.J.6
  • 26
    • 33646482082 scopus 로고    scopus 로고
    • Can denaturing gradient gel electrophoresis (DGGE) analysis of amplified 16s rDNA of soil bacterial populations be used in forensic investigations?
    • Lerner, A., Shor, Y., Vinokurov, A., Okon, Y. Jurkevitch, E. (2006) Can denaturing gradient gel electrophoresis (DGGE) analysis of amplified 16s rDNA of soil bacterial populations be used in forensic investigations? Soil Biol Biochem 38, 1188 1192.
    • (2006) Soil Biol Biochem , vol.38 , pp. 1188-1192
    • Lerner, A.1    Shor, Y.2    Vinokurov, A.3    Okon, Y.4    Jurkevitch, E.5
  • 27
    • 5344253948 scopus 로고    scopus 로고
    • Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis
    • de Lipthay, J.R., Enzinger, C., Johnsen, K., Aamand, J. Sorensen, S.J. (2004) Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol Biochem 36, 1607 1614.
    • (2004) Soil Biol Biochem , vol.36 , pp. 1607-1614
    • De Lipthay, J.R.1    Enzinger, C.2    Johnsen, K.3    Aamand, J.4    Sorensen, S.J.5
  • 28
    • 0035213531 scopus 로고    scopus 로고
    • Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils
    • Lloyd-Jones, G. Hunter, D.W.F. (2001) Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol Biochem 33, 2053 2059.
    • (2001) Soil Biol Biochem , vol.33 , pp. 2053-2059
    • Lloyd-Jones, G.1    Hunter, D.W.F.2
  • 29
    • 33644838781 scopus 로고    scopus 로고
    • Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity
    • Loisel, P., Harmand, J., Zemb, O., Latrille, E., Lobry, C., Delgenes, J.P. Godon, J.J. (2006) Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8, 720 731.
    • (2006) Environ Microbiol , vol.8 , pp. 720-731
    • Loisel, P.1    Harmand, J.2    Zemb, O.3    Latrille, E.4    Lobry, C.5    Delgenes, J.P.6    Godon, J.J.7
  • 30
    • 0033152351 scopus 로고    scopus 로고
    • Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of amplification products
    • Marsh, T.L. (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Current Opin Microbiol 2, 323 327.
    • (1999) Current Opin Microbiol , vol.2 , pp. 323-327
    • Marsh, T.L.1
  • 31
    • 0030616390 scopus 로고    scopus 로고
    • Application of fuzzy sets in soil science: Fuzzy logic, fuzzy measurements and fuzzy decisions
    • McBratney, A.B. Odeh, I.O.A. (1997) Application of fuzzy sets in soil science: fuzzy logic, fuzzy measurements and fuzzy decisions. Geoderma 77, 85 113.
    • (1997) Geoderma , vol.77 , pp. 85-113
    • McBratney, A.B.1    Odeh, I.O.A.2
  • 34
    • 34247169452 scopus 로고    scopus 로고
    • Physical constraints affecting bacterial habitats and activity in unsaturated porous media - A review
    • Or, D., Smets, B.F., Wraith, J.M., Dechesne, A. Friedman, S.P. (2007) Physical constraints affecting bacterial habitats and activity in unsaturated porous media - a review. Adv Water Res 30, 1505 1527.
    • (2007) Adv Water Res , vol.30 , pp. 1505-1527
    • Or, D.1    Smets, B.F.2    Wraith, J.M.3    Dechesne, A.4    Friedman, S.P.5
  • 36
    • 0030695483 scopus 로고    scopus 로고
    • Effects of air-drying and wetting cycles on the transforming ability of DNA bound on clay minerals
    • Pietramellara, G., Dalcanto, L., Vettori, C., Gallori, E. Nannipieri, P. (1997) Effects of air-drying and wetting cycles on the transforming ability of DNA bound on clay minerals. Soil Biol Biochem 29, 55 61.
    • (1997) Soil Biol Biochem , vol.29 , pp. 55-61
    • Pietramellara, G.1    Dalcanto, L.2    Vettori, C.3    Gallori, E.4    Nannipieri, P.5
  • 37
    • 0027948550 scopus 로고
    • Desiccation tolerance of prokaryotes
    • Potts, M. (1994) Desiccation tolerance of prokaryotes. Microbiol Rev 58, 755 805.
    • (1994) Microbiol Rev , vol.58 , pp. 755-805
    • Potts, M.1
  • 38
    • 0034803155 scopus 로고    scopus 로고
    • Quantitative and qualitative microscale distribution of bacteria in soil
    • Ranjard, L. Richaume, A.S. (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Res Microbiol 152, 707 716.
    • (2001) Res Microbiol , vol.152 , pp. 707-716
    • Ranjard, L.1    Richaume, A.S.2
  • 40
    • 0034882012 scopus 로고    scopus 로고
    • Extraction and purification of microbial DNA from soil and sediment samples
    • Roose-Amsaleg, C.L., Garnier-Sillam, E. Harry, M. (2001) Extraction and purification of microbial DNA from soil and sediment samples. Appl Soil Ecol 18, 47 60.
    • (2001) Appl Soil Ecol , vol.18 , pp. 47-60
    • Roose-Amsaleg, C.L.1    Garnier-Sillam, E.2    Harry, M.3
  • 41
    • 13444258109 scopus 로고    scopus 로고
    • Forensic geoscience: Applications of geology, geomorphology and geophysics to criminal investigations
    • Ruffell, A. Mckinley, J. (2005) Forensic geoscience: applications of geology, geomorphology and geophysics to criminal investigations. Earth Sci Rev 69, 235 247.
    • (2005) Earth Sci Rev , vol.69 , pp. 235-247
    • Ruffell, A.1    McKinley, J.2
  • 42
    • 4444277352 scopus 로고    scopus 로고
    • Conjunctive use of quantitative and qualitative X-ray diffraction analysis of soils and rocks for forensic analysis
    • Ruffell, A. Wiltshire, P. (2004) Conjunctive use of quantitative and qualitative X-ray diffraction analysis of soils and rocks for forensic analysis. Forensic Sci Int 145, 13 23.
    • (2004) Forensic Sci Int , vol.145 , pp. 13-23
    • Ruffell, A.1    Wiltshire, P.2
  • 43
    • 0037540844 scopus 로고
    • Changes in cytoplasmic carbon and nitrogen pools in a soil bacterium and a fungus in response to salt stress
    • Schimel, J.P., Scott, W.J. Killham, K. (1989) Changes in cytoplasmic carbon and nitrogen pools in a soil bacterium and a fungus in response to salt stress. Appl Environ Microbiol 55, 1635 1637.
    • (1989) Appl Environ Microbiol , vol.55 , pp. 1635-1637
    • Schimel, J.P.1    Scott, W.J.2    Killham, K.3
  • 44
    • 33744749620 scopus 로고    scopus 로고
    • Role of dipicolinic acid in resistance and stability of spores of Bacillus subtilis with or without DNA-protective alpha/beta-type small acid-soluble proteins
    • Setlow, B., Atluri, S., Kitchel, R., Koziol-Dube, K. Setlow, P. (2006) Role of dipicolinic acid in resistance and stability of spores of Bacillus subtilis with or without DNA-protective alpha/beta-type small acid-soluble proteins. J Bacteriol 188, 3740 3747.
    • (2006) J Bacteriol , vol.188 , pp. 3740-3747
    • Setlow, B.1    Atluri, S.2    Kitchel, R.3    Koziol-Dube, K.4    Setlow, P.5
  • 45
    • 34047275342 scopus 로고    scopus 로고
    • Multiplex-terminal restriction fragment length polymorphism (M-TRFLP)
    • Singh, B.K. Thomas, N. (2006) Multiplex-terminal restriction fragment length polymorphism (M-TRFLP). Nature Protoc 1, 2428 2433.
    • (2006) Nature Protoc , vol.1 , pp. 2428-2433
    • Singh, B.K.1    Thomas, N.2
  • 46
    • 33751006742 scopus 로고    scopus 로고
    • Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community
    • Singh, B.K., Nazaries, L., Munro, S., Anderson, I.C. Campbell, C.D. (2006) Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community. Appl Environ Microbiol 72, 7278 7285.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 7278-7285
    • Singh, B.K.1    Nazaries, L.2    Munro, S.3    Anderson, I.C.4    Campbell, C.D.5
  • 47
    • 42249083028 scopus 로고    scopus 로고
    • Water availability is a critical determinant of a population shift from Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting
    • Takebayashi, S., Narihiro, T., Fujii, Y. Hiraishi, A. (2007) Water availability is a critical determinant of a population shift from Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting. Microb Environ 22, 279 289.
    • (2007) Microb Environ , vol.22 , pp. 279-289
    • Takebayashi, S.1    Narihiro, T.2    Fujii, Y.3    Hiraishi, A.4
  • 48
    • 0032977102 scopus 로고    scopus 로고
    • Methods for DNA extraction from various soils: A comparison
    • Tien, C.C., Chao, C.C. Chao, W.L. (1999) Methods for DNA extraction from various soils: a comparison. J Appl Microbiol 86, 937 943.
    • (1999) J Appl Microbiol , vol.86 , pp. 937-943
    • Tien, C.C.1    Chao, C.C.2    Chao, W.L.3
  • 49
    • 0036270789 scopus 로고    scopus 로고
    • Microbial diversity and function in soil: From genes to ecosystems
    • Torsvik, V. Ovreas, L. (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5, 240 245.
    • (2002) Curr Opin Microbiol , vol.5 , pp. 240-245
    • Torsvik, V.1    Ovreas, L.2
  • 50
    • 8144221251 scopus 로고    scopus 로고
    • Development and application of a selective PCR-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil
    • Tzeneva, V.A., Li, Y.G., Felske, A.D.M., De Vos, W.M., Akkermans, A.D.L., Vaughan, E.E. Smidt, H. (2004) Development and application of a selective PCR-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil. Appl Environ Microbiol 70, 5801 5809.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 5801-5809
    • Tzeneva, V.A.1    Li, Y.G.2    Felske, A.D.M.3    De Vos, W.M.4    Akkermans, A.D.L.5    Vaughan, E.E.6    Smidt, H.7
  • 51
    • 22844451858 scopus 로고    scopus 로고
    • Physiology and microbial community structure in soil at extreme water content
    • Uhlirova, E., Elhottova, D., Triska, J. Santruckova, H. (2005) Physiology and microbial community structure in soil at extreme water content. Folia Microbiol 50, 161 166.
    • (2005) Folia Microbiol , vol.50 , pp. 161-166
    • Uhlirova, E.1    Elhottova, D.2    Triska, J.3    Santruckova, H.4
  • 52
    • 0033645455 scopus 로고    scopus 로고
    • Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use
    • Yao, H., He, Z., Wilson, M.J. Campbell, C.D. (2000) Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 40, 223 237.
    • (2000) Microb Ecol , vol.40 , pp. 223-237
    • Yao, H.1    He, Z.2    Wilson, M.J.3    Campbell, C.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.