Extraction and purification of microbial DNA from soil and sediment samples

Applied Soil Ecology - Tập 18 - Trang 47-60 - 2001
C.L Roose-Amsaleg1, E Garnier-Sillam1, M Harry1
1Laboratoire de Biologie des Sols et des Eaux, UFR de Sciences, Université Paris XII-Val de Marne, Avenue du Général De Gaulle, Créteil 94010, France

Tài liệu tham khảo

Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143, 10.1128/MR.59.1.143-169.1995 Atlas, R.M., Bartha, R., 1993. Microbial Ecology, Fundamentals and Applications, 3rd Edition. Benjamin/Cummings, Menlo Park, CA, 563 pp. Bakken, 1985, Separation and purification of bacteria from soil, Appl. Environ. Microbiol., 49, 1482, 10.1128/AEM.49.6.1482-1487.1985 Bakken, L.R., Lindahl, V., 1995. Recovery of bacterial cells from soil. In: Trevors, J.T., Van Elsas, J.D. (Eds.), Nucleic Acids in the Environment. Springer, Berlin, pp. 9–27. Boivin-Jahns, 1996, Bacterial diversity in deep-subsurface clay environment, Appl. Environ. Microbiol., 62, 3405, 10.1128/AEM.62.9.3405-3412.1996 Borneman, 1997, Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation, Appl. Environ. Microbiol., 63, 2647, 10.1128/AEM.63.7.2647-2653.1997 Borneman, 1996, Molecular microbial diversity of agricultural soil in Wisconsin, Appl. Environ. Microbiol., 62, 1935, 10.1128/AEM.62.6.1935-1943.1996 Briglia, 1996, Rapid and sensitive method for the detection of mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR, Appl. Environ. Microbiol., 62, 1478, 10.1128/AEM.62.4.1478-1480.1996 Bruce, 1992, Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction, Appl. Environ. Microbiol., 58, 3413, 10.1128/AEM.58.10.3413-3416.1992 Chandler, 1997, Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries, Mol. Ecol., 6, 475, 10.1046/j.1365-294X.1997.00205.x Clegg, 1997, Direct extraction of microbial community DNA from humified upland soils, Lett. Appl. Microbiol., 25, 30, 10.1046/j.1472-765X.1997.00166.x Cullen, 1998, Simple and rapid method for direct extraction of microbial DNA from soil for PCR, Soil Biol. Biochem., 30, 983, 10.1016/S0038-0717(98)00001-7 Dijkmans, 1993, Rapid method for purification of soil DNA for hybridization and PCR analysis, Microb. Releases, 2, 29 Dunbar, 1999, Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning, Appl. Environ. Microbiol., 65, 1662, 10.1128/AEM.65.4.1662-1669.1999 El-Fantroussi, 1999, Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles, Appl. Environ. Microbiol., 65, 982, 10.1128/AEM.65.3.982-988.1999 Erb, 1993, Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction, Appl. Environ. Microbiol., 59, 4065, 10.1128/AEM.59.12.4065-4073.1993 Felske, 1999, Searching for predominant soil bacteria: 16S rDNA cloning versus strain cultivation, FEMS Microbiol. Ecol., 30, 137, 10.1111/j.1574-6941.1999.tb00642.x Frostegard, 1999, Quantification of bias related to the extraction of DNA directly from soils, Appl. Environ. Microbiol., 65, 5409, 10.1128/AEM.65.12.5409-5420.1999 Gray, 1996, Phylogenetic analysis of the bacterial communities in marine sediments, Appl. Environ. Microbiol., 62, 4049, 10.1128/AEM.62.11.4049-4059.1996 Harris, D., 1994. Analyses of DNA extracted from microbial communities. In: Ritz, K., Dighton, J., Giller, K.E. (Eds.), Beyond the Biomass. Chilchester, UK, pp. 111–118. Harry, 1999, Evaluation of purification procedures for DNA extracted from organic rich samples: interference with humic substances, Analusis, 27, 439, 10.1051/analusis:1999270439 Harry, 2001, Use of RAPD markers for the study of microbial community similarity from termite mounds and tropical soils, Soil Biol. Biochem., 31, 417, 10.1016/S0038-0717(00)00181-4 Herrick, 1993, Polymerase chain reaction amplification of naphtalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria, Appl. Environ. Microbiol., 59, 687, 10.1128/AEM.59.3.687-694.1993 Hilger, 1991, Method for extraction of Frankia DNA from soil, Agric. Ecosyst. Environ., 34, 107, 10.1016/0167-8809(91)90098-I Holben, 1988, DNA probe method for the detection of specific microorganisms in the soil bacterial community, Appl. Environ. Microbiol., 54, 703, 10.1128/AEM.54.3.703-711.1988 Jackson, 1997, A simple efficient method for the separation of humic substances and DNA from environmental samples, Appl. Environ. Microbiol., 63, 4993, 10.1128/AEM.63.12.4993-4995.1997 Jacobsen, 1995, Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay, Appl. Environ. Microbiol., 61, 3347, 10.1128/AEM.61.9.3347-3352.1995 Jacobsen, 1992, Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin, Appl. Environ. Microbiol., 58, 2458, 10.1128/AEM.58.8.2458-2462.1992 Kennedy, 1999, Bacterial diversity in agroecosystems, Agric. Ecosyst. Environ., 74, 65, 10.1016/S0167-8809(99)00030-4 Knaebel, 1995, Extraction and purification of microbial DNA from petroleum-contaminated soils and detection of low numbers of toluene, octane and pesticide degraders by multiplex polymerase chain reaction and southern analysis, Mol. Ecol., 4, 579, 10.1111/j.1365-294X.1995.tb00258.x Kuske, 1998, Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil, Appl. Environ. Microbiol., 64, 2463, 10.1128/AEM.64.7.2463-2472.1998 Lee, 1996, Estimation of the abundance of an uncultured soil bacterial strain by a comparative PCR method, Appl. Environ. Microbiol., 62, 3787, 10.1128/AEM.62.10.3787-3793.1996 Lessa, 1993, Screening techniques for detecting allelic variation in DNA sequences, Mol. Ecol., 2, 119, 10.1111/j.1365-294X.1993.tb00006.x Liesack, 1992, Occurrence of novel groups of the domain bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment, J. Bacteriol., 174, 5072, 10.1128/jb.174.15.5072-5078.1992 Liu, 1997, Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA, Appl. Environ. Microbiol., 63, 4516, 10.1128/AEM.63.11.4516-4522.1997 Lukow, 2000, Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants, FEMS Microbiol. Ecol., 32, 241, 10.1111/j.1574-6941.2000.tb00717.x Massol-Deya, A.A., Odelson, D.A., Hickey, R.F., Tiedje, J.M., 1995. Bacterial community fingerprinting of amplified 16S and 16S–23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA). In: Akkermans, A.D.L., Van Elsas, J.D., de Bruijn, F.J. (Eds.), Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, pp. 1–8. Miller, 1999, Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples, Appl. Environ. Microbiol., 65, 4715, 10.1128/AEM.65.11.4715-4724.1999 Moré, 1994, Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment, Appl. Environ. Microbiol., 60, 1572, 10.1128/AEM.60.5.1572-1580.1994 Muyzer, 1999, DGGE/TGGE a method for identifying genes from natural ecosystems, Curr. Microbiol., 2, 317, 10.1016/S1369-5274(99)80055-1 Muyzer, 1993, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl. Environ. Microbiol., 59, 695, 10.1128/AEM.59.3.695-700.1993 Muyzer, G., Hottenträger, S., Teske, A., Wawer, C., 1996. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA — a new molecular approach to analyze the genetic diversity of microbial communities. In: Akkermans, A.D.L., Van Elsas, J.D., de Bruijn, F.J. (Eds.), Molecular Microbial Ecology Manual 3.4.4. Kluwer Academic Publishers, Dordrecht, pp. 1–23. Nesme, X., Picard, C., Simonet, P., 1995. Specific DNA sequences for detection of soil bacteria. In: Trevors, J.T., Van Elsas, J.D. (Eds.), Nucleic Acids in the Environment. Springer, Berlin, pp. 111–139. Ogram, 1987, The extraction and purification of microbial DNA from sediments, J. Microbiol. Methods, 7, 57, 10.1016/0167-7012(87)90025-X Osborn, 1993, Polymerase chain reaction–restriction fragment length polymorphism analysis shows divergence among mer determinants from gram-negative bacteria indistinguishable by DNA/DNA hybridization, Appl. Environ. Microbiol., 59, 4024, 10.1128/AEM.59.12.4024-4030.1993 Øvreas, 1998, Microbial diversity and community structure in two different agricultural soil communities, Microb. Ecol., 36, 303, 10.1007/s002489900117 Øvreas, 1998, Microbial communities changes in a perturbed agricultural soil investigated by molecular and physiological approaches, Appl. Environ. Microbiol., 64, 2739, 10.1128/AEM.64.7.2739-2742.1998 Picard, 1992, Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction, Appl. Environ. Microbiol., 58, 2717, 10.1128/AEM.58.9.2717-2722.1992 Pillaı̈, 1991, Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences, Appl. Environ. Microbiol., 57, 2283, 10.1128/AEM.57.8.2283-2286.1991 Pitcher, 1989, Rapid extraction of bacterial genomic DNA guanidium thiocyanate, Lett. Appl. Microbiol., 8, 151, 10.1111/j.1472-765X.1989.tb00262.x Porteous, 1991, Recovery of bulk DNA from soil by a rapid, small-scale extraction method, Curr. Microbiol., 22, 345, 10.1007/BF02092152 Porteous, 1997, An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications, Mol. Ecol., 6, 787, 10.1046/j.1365-294X.1997.00241.x Purdy, 1996, Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method, Appl. Environ. Microbiol., 62, 3905, 10.1128/AEM.62.10.3905-3907.1996 Rheims, 1996, A molecular approach to search for diversity among bacteria in the environment, J. Ind. Microbiol., 17, 159, 10.1007/BF01574689 Robert, M., Chenu, C., 1991. Interactions between soil mineral and micro-organisms. In: Stotzky, G., Bollag, J.M. (Eds), Soil Biochemistry. New York, pp. 307–404. Rochelle, 1992, DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities, FEMS Microbiol. Lett., 100, 59, 10.1111/j.1574-6968.1992.tb14019.x Rochelle, P.A., Will, A.K., Fry, J.C., Jenkins, J.S., Parkes, R.J., Turley, C.M., Weightman, A.J., 1995. Extraction and amplification of 16S rRNA genes from deep marine sediments and seawater to assess bacterial community diversity. In: Trevors, J.T., Van Elsas, J.D. (Eds.), Nucleic Acids in the Environment. Springer, Berlin, pp. 219–239. Rölleke, 1996, Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA, Appl. Environ. Microbiol., 62, 2059, 10.1128/AEM.62.6.2059-2065.1996 Romanowski, 1992, Persistance of free plasmid DNA in soil monitored by various methods, including a transformation assay, Appl. Environ. Microbiol., 58, 3012, 10.1128/AEM.58.9.3012-3019.1992 Romanowski, 1993, Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils, Appl. Environ. Microbiol., 59, 3438, 10.1128/AEM.59.10.3438-3446.1993 Saano, A., Tas, E., Pippola, S., Lindström, K., Van Elsas, J.D., 1995. Extraction and analysis of microbial DNA from soil. In: Trevors, J.T., Van Elsas, J.D. (Eds.), Nucleic Acids in the Environment. Springer, Berlin, pp. 49–67. Schwieger, 1998, A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis, Appl. Environ. Microbiol., 64, 4870, 10.1128/AEM.64.12.4870-4876.1998 Selenska, 1991, Direct detection of nif-gene sequences of Enterobacter agglomerans in soil, FEMS Microbiol. Lett., 80, 243, 10.1111/j.1574-6968.1991.tb04669.x Smalla, K., Van Elsas, J.D., 1995. Application of the PCR for detection of antibiotic resistance genes in environmental samples. In: Trevors, J.T., Van Elsas, J.D. (Eds.), Nucleic Acids in the Environment. Springer, Berlin, pp. 241–256. Smalla, 1993, Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification, J. Appl. Bacteriol., 74, 78, 10.1111/j.1365-2672.1993.tb02999.x Smit, 1997, Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis, FEMS Microbiol. Ecol., 23, 249, 10.1111/j.1574-6941.1997.tb00407.x Stackebrandt, 1993, Bacterial diversity in soil sample from a subtropical Australian environment as determined by 16S rDNA analysis, FASEB J., 7, 232, 10.1096/fasebj.7.1.8422969 Steffan, 1988, DNA amplification to enhance detection of genetically engineered bacteria in environmental samples, Appl. Environ Microbiol., 54, 2185, 10.1128/AEM.54.9.2185-2191.1988 Steffan, 1988, Recovery of DNA from soils and sediments, Appl. Environ. Microbiol., 54, 2908, 10.1128/AEM.54.12.2908-2915.1988 Suzuki, 1996, Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR, Appl. Environ. Microbiol., 62, 625, 10.1128/AEM.62.2.625-630.1996 Tebbe, 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, 10.1128/AEM.59.8.2657-2665.1993 Thornhill, 1995, PCR for direct detection of indigenous uncultured magnetic cocci in sediment and phylogenetic analysis of amplified 16S ribosomal DNA, Appl. Environ. Microbiol., 61, 495, 10.1128/AEM.61.2.495-500.1995 Torsvik, 1980, Isolation of bacterial DNA from soil, Soil Biol. Biochem., 12, 15, 10.1016/0038-0717(80)90097-8 Torsvik, 1990, High diversity in DNA of soil bacteria, Appl. Environ. Microbiol., 56, 782, 10.1128/AEM.56.3.782-787.1990 Trevors, 1989, A review of selected methods in environmental microbial genetics, Can. J. Microbiol., 35, 895, 10.1139/m89-149 Tsai, 1991, Rapid method for direct extraction of mRNA from seeded soils, Appl. Environ. Microbiol., 57, 765, 10.1128/AEM.57.3.765-768.1991 Tsai, 1991, Rapid method for direct extraction of DNA from soils and sediments, Appl. Environ. Microbiol., 57, 1070, 10.1128/AEM.57.4.1070-1074.1991 Tsai, 1992, Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction, Appl. Environ. Microbiol., 58, 754, 10.1128/AEM.58.2.754-757.1992 Tsai, 1992, Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction, Appl. Environ. Microbiol., 58, 2292, 10.1128/AEM.58.7.2292-2295.1992 Tsai, 1993, Detection of Escherichia coli in sewage and sludge by polymerase chain reaction, Appl. Environ. Microbiol., 59, 353, 10.1128/AEM.59.2.353-357.1993 Turpin, 1993, An ion-exchange based extraction method for the detection of Salmonellas in soil, J. Appl. Bacteriol., 74, 181, 10.1111/j.1365-2672.1993.tb03013.x Ueda, 1995, Molecular phylogenetic analysis of a soil microbial community in a soybean field, Eur. J. Soil Sci., 46, 415, 10.1111/j.1365-2389.1995.tb01337.x Van Elsas, 1991, A specific marker, pat, for studying the fate of introduced bacteria and their DNA in soil using a combination of detection techniques, Plant and Soil, 138, 49, 10.1007/BF00011807 Van Elsas, 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, Biol. Fertil. Soils, 24, 188, 10.1007/s003740050230 Vettori, 1996, Amplification of bacterial DNA bound on clay minerals by random amplified polymorphic DNA (RAPD) technique, FEMS Microbiol. Ecol., 20, 251, 10.1111/j.1574-6941.1996.tb00323.x Volossiouk, 1995, Direct DNA extraction for PCR-mediated assays of soil organisms, Appl. Environ. Microbiol., 61, 3972, 10.1128/AEM.61.11.3972-3976.1995 Wilson, 1997, Minireview, inhibition and facilitation of nucleic acid amplification, Appl. Environ. Microbiol., 63, 3741, 10.1128/AEM.63.10.3741-3751.1997 Xia, 1995, Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D, Mol. Ecol., 4, 17, 10.1111/j.1365-294X.1995.tb00188.x Yeates, 1997, PCR amplification of crude microbial DNA extracted from soil, Lett. Appl. Microbiol., 25, 303, 10.1046/j.1472-765X.1997.00232.x Young, 1993, Polyvinylpyrrolidone–agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils, Appl. Environ. Microbiol., 59, 1972, 10.1128/AEM.59.6.1972-1974.1993 Zhou, 1996, DNA recovery from soils of diverse composition, Appl. Environ. Microbiol., 62, 316, 10.1128/AEM.62.2.316-322.1996 Zhou, 1997, Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA, Microbiology, 143, 3913, 10.1099/00221287-143-12-3913