A quantitative analysis of DNA extraction and purification from compost

Journal of Microbiological Methods

Volumn 54, Issue 1, 2003, Pages 37-45

  Howeler, Michael ^a   Ghiorse, William C ^a   Walker, Larry P ^a  

^a Cornell University ^*  (United States)

Author keywords

Compost; Direct microscopic observation; DNA; Extraction; Humic acids; Purification; Quantification

Indexed keywords

DNA; DNA FRAGMENT; DODECYL SULFATE SODIUM; HUMIC ACID; MACROGOL 8000; RESTRICTION ENDONUCLEASE; RIBOSOME DNA; SEPHADEX;

ARTICLE; CELL ASSAY; CHROMATOGRAPHY; COMPOST; CONCENTRATION (PARAMETERS); CYTOLYSIS; DNA DETERMINATION; DNA EXTRACTION; DNA PURIFICATION; ENZYMATIC ASSAY; GENE AMPLIFICATION; MICROSCOPY; NONHUMAN; POLYMERASE CHAIN REACTION; PRECIPITATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

EID: 0037728518     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00006-X     Document Type: Article

References (34)

1. Amann R.I., Ludwig W., Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169.
2. Bachoon D.S., Otero E., Hodson R.E. Effects of humic substances on fluorometric DNA quantification and DNA hybridization. J. Microbiol. Methods. 47:2001;73-82.
3. Beloin, R.M., 1987. The analysis of a direct counting method and the occurrence of 4-hydroxybenzoate degrading microorganisms in subsurface samples. Masters Thesis, Cornell University, Ithaca, NY.
4. Blanc M., Marilley L., Beffa T., Aragno M. Thermophilic bacterial communities in hot composts as revealed by most probably number counts and molecular (16S rDNA) methods. FEMS Microbiol. Ecol. 28:1999;141-149.
5. Clegg C.D., Ritz K., Griffiths B.S. Direct extraction of microbial community DNA from humified upland soils. Lett. Appl. Microbiol. 25:1997;30-33.
6. Cullen D.W., Hirsch P.R. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30:1998;983-993.
7. Dees P.M., Ghiorse W.C. Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol. Ecol. 35:2001;207-216.
8. Duarte G.F., Rosado A.S., Seldin L., Keijzer-Wolters A.C., van Elsas J.D. Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community. J. Microbiol. Methods. 32:1998;21-29.
9. Erb R.W., Wagner-Doebler I. Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 59:1993;4065-4073.
10. Hall, S.G., 1998. Temperature feedback and control via aeration rate regulation in biological composting systems. PhD Thesis, Cornell University, Ithaca, NY.
11. Head I.M., Saunders J.R., Pickup R.W. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1998;1-21.
12. Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M.H. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:1997;3233-3241.
13. Kuske C.R., Banton K.L., Adorada D.L., Stark P.C., Hill K.K., Jackson P.J. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol. 64:1998;2463-2472.
14. Leff L.G., Dana J.R., McArthur J.V., Shimkets L.J. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1995;1141-1143.
15. Miller D.N., Bryant J.E., Madsen E.L., Ghiorse W.C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:1999;4715-4724.
16. More M.I., Herrick J.B., Silva M.C., Ghiorse W.C., Madsen E.L. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1994;1572-1580.
17. Ogram A., Sayler G.S., Barkay T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods. 7:1987;57-66.
18. Pfaller S.L., Vesper S.J., Moreno H. The use of PCR to detect a pathogen in compost. Compost Sci. Util. 2:1994;48-54.
19. Picard C., Ponsonnet C., Paget E., Nesme X., Simonet P. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58:1992;2717-2722.
20. Sandaa R.A., Enger O., Torsvik V. Rapid method for fluorometric quantification of DNA in soil. Soil Biol. Biochem. 30:1998;265-268.
21. Schloss, P.D., 2002. Quantitative molecular analysis of microbial succession in compost and it's ramifications on process reproducibility. PhD, Cornell University, Ithaca, NY.
22. Shi Y., Zwolinski M.D., Schreiber M.E., Bahr J.M., Sewell G.W., Hickey W.J. Molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiments. Appl. Environ. Microbiol. 65:1999;2143-2150.
23. Singer V.L., Jones L.J., Yue S.T., Haugland R.P. Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation. Anal. Biochem. 249:1997;228-238.
24. Smalla K., Cresswell N., Mendonca-Hagler L.C., Wolters A., van Elsas J.D. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:1993;78-85.
25. Stark P.C., Mullen K.I., Banton K., Russotti R., Soran D., Kuske C.R. Pre-PCR DNA quantitation of soil and sediment samples: method development and instrument design. Soil Biol. Biochem. 32:2000;1101-1110.
26. Steffan R.J., Goksoyr J., Bej A.K., Atlas R.M. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:1988;2908-2915.
27. Tebbe C.C., Vahjen W. 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. 59:1993;2657-2665.
28. Torsvik V. Isolation of bacterial DNA from soil. Soil Biol. Biochem. 12:1980;15-21.
29. Torsvik V., Sorheim R., Goksoyr J. Total bacterial diversity in soil and sediment communities: a review. J. Ind. Microbiol. 17:1996;170-178.
30. Trevors J.T., Lee H., Cook S. Direct extraction of DNA from soil. Microb. Releases. 1:1992;111-115.
31. Tsai Y.L., Olson B.H. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1991;1070-1074.
32. Tsai Y.L., Olson B.H. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl. Environ. Microbiol. 58:1992;754-757.
33. Ward D.M., Bateson M.M., Weller R., Ruff-Roberts A.L. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12:1992;219-286.
34. Wilson K.H., Blitchington R.B., Greene R.C. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28:1990;1942-1946.