Isolation of high molecular weight DNA from soil for cloning into BAC vectors

FEMS Microbiology Letters

Volumn 223, Issue 1, 2003, Pages 15-20

  Berry, Andrew E ^a   Chiocchini, Claudia ^b,c   Selby, Tina ^a   Sosio, Margherita ^b   Wellington, Elizabeth M H ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b Biosearch Italia   (Italy)

^c PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

Bacterial artificial chromosome cloning; DNA isolation; Escherichia coli streptomycete artificial chromosome; Nycodenz gradient; Soil environment

Indexed keywords

AGAROSE; DNA FRAGMENT; IOHEXOL;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; DNA ISOLATION; DNA PURIFICATION; ESCHERICHIA COLI; EXTRACTION; IMMOBILIZED BIOMASS; LYSIS; MOLECULAR CLONING; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; QUALITY CONTROL; SOIL;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0037870266     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(03)00248-9     Document Type: Article

References (28)

1. Beja O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L., Spudich E.N., DeLong E.F. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:2000;1902-1906.
2. Rondon M.R., August P.R., Bettermann P.D., Brady S.J., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., MacNeil I.A., Minor C., Clardy J., Handelsman J., Goodman R.M. Cloning of the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2000;2541-2547.
3. Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown microbes: a new frontier for natural products. Chem. Biol. 5:1998;R245-249.
4. Gillespie D.E., Brady S.F., Betterman A.D., Cianciotto N.P., Liles M.R., Rondon M.R., Clardy J., Goodman R.M., Handelsman J. Isolation of antibiotics Turbomycin A and B froma metagenomic library of Soil Microbial DNA. Appl. Environ. Microbiol. 69:2002;4301-4306.
5. Bull A.T., Ward A.C., Goodfellow M. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64:2000;573-606.
6. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thompson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collis M., Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.H., Keiser T., Larke L., Murphy L., Oliver K., O'Neil S., Rabbinowich E., Rajandream M.A., Rutherford K., Rutter S., Seeger K., Sauders D., Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A., Woodwardm J., Barrel B.G., Parkhill J., Hopwood D.A. Complete genoime sequence of the model actinomycete Streptomycetes coelicolor A3. Nature. 417:(2):2002;141-147.
7. Sosio M., Bossi E., Bianchi A., Donadio S. Multiple peptide synthetase gene clusters in actinomycetes. Mol. Gen. Genet. 264:2000a;213-221.
8. Omura S., Ikeda H., Ishikawa J., Hanamoto A., Takahashi C., Shinose M., Takahashi Y., Horikawa H., Nakazawa H., Osonoe T., Kikuchi H., Shiba T., Sakaki Y., Hattori M. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. USA. 98:2001;12215-12220.
9. Monciardini, P., Sosio, M., Cavaletti, L., Chiocchini, C. and Donadio, S. (2002) New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol. Ecol., in press.
10. Sosio M., Giusino F., Cappellano C., Bossi E., Puglia A.M., Donadio S. Artificial chromosomes for antibiotic-producing actinomycetes. Nat. Biotechnol. 8:2000;343-345.
11. Krsek M., Wellington E.M.W. Comparison of different methods for the isolation and purification of total community DNA. In process citation. J. Microbiol. Methods. 39:1999;1-16.
12. Zhou J., Bruns M.A., Tiedje J.M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:1996;316-322.
13. Stein J.L., Marsh T.L., Wu K.Y., Shizuya H., DeLong E.F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:1996;591-599.
14. Bakken, L.R. and Lindahl, V. (1995) Recovery of bacterial cells from soil. In: Nucleic Acids in the Environment: Methods and Applications (Van Elsas, J.D. and Trevors, J.T., Eds.), pp. 9-27. Springer, Heidelberg.
15. Wellington E.M.H., Cresswell N., Saunders V.A. Growth and survival of streptomycetes inoculants and the extent of plasmid transfer in sterile and non-sterile soil microcosms. Appl. Environ. Microbiol. 56:1990;3139-3145.
16. Forster, J. (1995) In: Methods in Applied Soil Microbiology and Biochemistry (Alef, K. and Nannipieri, P., Eds.), 55 pp. Academic Press, London.
17. Osoegawa K., Woon P.Y., Zhao B., Frengen E., Tateno M., Catanese J.J., de Jong P.J. An improved approach for construction of bacterial artificial chromosome libraries. Genomics. 52:1998;1-8.
18. Weinbauer M.G., Beckmann C., Hofle M.G. Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl. Environ. Microbiol. 64:1998;5000-5003.
19. Courtois S., Frostegard A., Pernilla G., Depret G., Jeannin P., Simonet P. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3:2001;431-439.
20. Lips, A. and Jessup, N.E. (1979) Colloidal aspects of bacterial adhesion. In: Adhesion of Microorganisms to Surfaces (Ellwood, D.C., Melling, J. and Rutter, P., Eds.), pp. 5-27. Academic, London.
21. Rutter, P.R. and Vincent, B. (1980) In: The Adhesion of Microorganisms to Surfaces: Physio-chemical Aspects (Berkeley, R.C.W., Lynch, J.M., Rutter, P.R.S. and Vincent, B., Eds.), pp. 79-92. Horwood, Chichester.
22. Marshall, K.C. (1985) Mechanisms of bacterial adhesion at solid state interfaces. In: Bacterial Adhesion (Savage, D.C. and Fletcher, M., Eds), pp. 133-161. Plenum Press, London.
23. Niepold F., Conrad R., Schlegel H.G. Evaluation of the efficiency of extraction for the quantitative estimation of hydrogen bacteria in soil. Antonie van Leeuwenhoek. 45:1979;485-497.
24. Stotzky, G. (1985) Mechanisms of adhesion to clays, with reference to soil systems. In: Bacterial Adhesion (Savage D.C. and Fletcher, M., Eds.), pp. 195-253. Plenum Press, London.
25. Fægri A., Torsvik V.L., Goksøyr J. Bacterial and Fungal activities in soil: separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol. Biochem. 9:1977;105-112.
26. Herron P.R., Wellington E.M.H. New method for extraction of streptomycete spores from soil and application to the study of lysogeny in sterile amended and non sterile soil. Appl. Environ. Microbiol. 56:1990;1406-1412.
27. Lindhal V., Bakken L.R. Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol. Ecol. 16:1995;135-142.
28. Quaiser A., Ochsenreiter H., Klenk H.-P., Kletzin A., Treusch A.H., Meurer G., Eck J., Sensen C.W., Schleper C. First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol. 10:2002;603-611.