Abstract
Soil is made up of mineral particles of varying sizes, organic matter, humus, water, and air. The chemical composition is dependent on the geology of the underlying rock, climate, and vegetation. Minerals in the rock will erode, forming grains of varying size, sand, silt, and eventually clay. When inhabited by plants of varying types, litter is formed and decomposed to make humus, which is a complex group of compounds, characterized by its content of aromatic ring systems, and which is more or less water soluble, depending on the molecular (aggregate) size. Important is the porous structure of soil, creating large surface areas of clay and humus with different physicochemical characteristics. Water and air in the pores are required for plant roots and the organisms that inhabit soil. From this it follows there are many soil types, differing in biological, chemical, and physical characteristics. It is necessary to consider this point when using methods for isolation of DNA from soil. The procedures described here are therefore not necessarily optimal for all soil types and purposes.
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References
Aardema BW, Lorenz MG, Krumbein WE (1983) Protection of sediment-adsorbed transforming DNA against enzymatic inactivation. Appl Environ Microbiol 46: 417–420
Bak AL, Christiansen C, Stenderup A (1970) Bacterial genome sizes determined by DNA renaturation studies. J Gen Microbiol 64: 377–380
Bakken LR, Olsen RA (1989) DNA-content of soil bacteria of different cell size. Soil Biol Biochem 21: 789–793
Balkwill DL, Labeda DP, Casida LEJ (1975) Simplified procedures for releasing and concentrating microorganisms from soil for transmission electron microscopy viewing as thin- sectioned and frozen-etched preparations. Can J Microbiol 21: 252–262
Bergh Ø, Børsheim KY, Bratbak G, Heldal M (1988) High abundance of viruses found in aquatic environments. Nature 340: 467–468
Britten RJ, Kohne DE (1968) Repeated sequences in DNA. Science 161: 529–540
Crombach WHJ (1972) DNA base composition of soil arthrobacters and other coryneforms from cheese and sea fish. Antonie van Leuwenhoek 38: 105–120
De Ley J, Muylem JV (1963) Some applications of deoxyribonucleic base composition in bacterial taxonomy. Antonie van Leeuwenhoek 29: 344–358
Dons JJM, De Vries OHM, Wessels JGH (1979) Characterization of the genome of the basidiomycete Schizophyllum commune. Bioch Biophys Acta 378: 363–377
Faegri A, Torsvik VL, Goksoyr J (1977) Bacterial and fungal activities in soil: Separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol Biochem 9: 105–112
Geck P, Nasz I (1983) Concentrated, digestible DNA after hydroxyapatite chromatography with cetylpyridinium bromide precipitation. Anal Biochem 135:1426–1429
Gillis M, De Ley J, Cleene D (1970) The determination of molecular weight of bacterial genome DNA from denaturation rates. Eur J Biochem 12: 143–153
Hill BT, Whatley S (1975) A simple, rapid microassay for DNA. FEBS Letters 56: 20–23
Hobbie JE, Daley RJ, Jasper S (1977) Use of Nucleopore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33: 1225–1228
Holben WE, Jansson JK, B.K. Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54: 703–711
Hopkins DW, Maenaughton SJ, O’Donnell AG (1991) A dispersion and differential centrifugation technique for representative sampling of microorganisms from soil. Soil Biol Biochem 23: 217–225
Jacobsen CS, Rasmussen OF (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: 2458–2462
Lien T, Knutsen G (1976) Fluorometric determination of DNA in Chlamydomonas. Anal Biochem 74: 560–566
Lorenz MG, Wackernagel W (1987) Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl Environ Microbiol 64: 225–230
Lorenz MG, Aardema BW, Krumbein WE (1981) Interaction of marine sediment with DNA and DNA availability to nucleases. Marine Biol 64: 225–230
Macdonald RM (1986) Sampling soil microfloras: dispersion of soil by ion exhange and extraction of specific microorganisms from suspension by elutriation. Soil Biol Biochem 18: 399–406
Mandel M, Igambi L, Bergendahl J, Dodson ML Jr., Scheltgen E (1970) Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 101: 333–338
Marmur J (1963) A procedure for the isolation of deoxyribonucleic acid from microorganisms. Methods Enzym VL 726–738
Marmur J, Rownd R, Schildkraut CL (1963) Denaturation and renaturation of deoxyribonucleic acid. Prog Nucleic Acid Res 1: 231–300
Ogram A, Sayler GS, Barkay T (1987) DNA extraction and purification from sediments. J Microbiol Meth 7: 57–66
Olsen RA, Bakken LR (1987) Viability of soil bacteria: optimization of plate-counting technique and comparison between total counts and plate counts within different size groups. Microbial Ecol 13: 59–74
Paul JH, Myers B (1982) Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258. Appl Environ Microbiol 43: 1393–1399
Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 58: 2717–2722
Pochon J (1954) Manuel technique d’ analyse microbiologique du Sol. Masson et Cie, Paris
Porter KG, Feig YS (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25: 943–948
Rake A (1972) Isopropanol preservation of biological samples for subsequent DNA extraction and reassociation studies. Anal Biochem 48: 365–368
Richards BN (1974) Introduction to the soil ecosystem. Longman, London
Roszak DH, Grimes DJ, Colwell RR (1984) Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems. Can J Microbiol 30: 1393–1399
Selenska S, Klingmueller W (1991a) Direct detection of nif-gene sequences of Enterobacter agglomerans in soil. FEMS Microbiol Lett 80: 243–246
Selenska S, Klingmueller W (1991 b) DNA recovery and direct detection of Tn5 sequences in soil. Lett Appl Microbiol 13: 21–24
Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A, van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction mediated amplification. J Appl Bacteriol 74: 78–85
Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appi Environ Microbiol 54: 2908–2915
Torsvik V, Gokseyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782–787
Torsvik VL (1980) Isolation of bacterial DNA from soil. Soil Biol Biocheml2: 15–21
Torsvik VL, Goksoyr J (1978) Determination of bacterial DNA in soil. Soil Biol Biochem 10: 7–12
Trevors JT, Cook S (1992) Direct extraction of DNA from soil. Microbial Rel 1: 111–115
Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 63–65
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Torsvik, V., Daae, F.L., Goksøyr, J. (1995). Extraction, Purification, and Analysis of DNA from Soil Bacteria. In: Trevors, J.T., van Elsas, J.D. (eds) Nucleic Acids in the Environment. Springer Lab Manuals. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79050-8_3
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DOI: https://doi.org/10.1007/978-3-642-79050-8_3
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