Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste

Genetics and Molecular Research

Volumn 8, Issue 1, 2009, Pages 375-388

  Maciel, B M ^a   Santos, A C F ^a   Dias, J C T ^a   Vidal, R O ^a   Dias, R J C ^a   Gross, E ^a   Cascardo, J C M ^a   Rezende, R P ^a  

^a DEPARTAMENTO DE CIÊNCIAS BIOLÓGICAS   (Brazil)

Author keywords

Bacterial diversity; Cloning assay; DGGE; Direct lysis; Microbial dna; Petroleum degradation

Indexed keywords

BACTERIAL DNA; CHLOROFORM; DNA 16S; ISOPENTYL ALCOHOL; LIQUID NITROGEN; ORGANIC SOLVENT; PETROLEUM; PHENOL; RIBOSOME RNA; RNA 16S; TAQ POLYMERASE;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTEROIDETES; BIOREMEDIATION; CHEMICAL WASTE; CHLOROFLEXI; CYTOLYSIS; DELTAPROTEOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; SOIL; SOIL ANALYSIS; SOIL POLLUTION; TROPICS;

BIODEGRADATION, ENVIRONMENTAL; BIODIVERSITY; DNA, BACTERIAL; DNA, RIBOSOMAL; ENVIRONMENTAL MICROBIOLOGY; PETROLEUM; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SOIL POLLUTANTS; TROPICAL CLIMATE;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); FIRMICUTES; PLANCTOMYCETES;

EID: 66749097256     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: 10.4238/vol8-1gmr559     Document Type: Article

References (30)

1. Amann RI, Ludwig W and Schleifer KH (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
2. Ausma S, Edwards GC and Gillespie TJ (2003). Laboratory-scale measurement of trace gas fluxes from landfarm soils. J. Environ. Qual. 32: 8-22.
3. Berthelet M, Whyte LG and Greer CW (1996). Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMSMicrobiol. Lett. 138: 17-22.
4. Cole JR, Chai B, Farris RJ, Wang Q, et al. (2005). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33: D294-D296.
5. Doyle JJ and Doyle JL (1991). Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
6. Felsenstein J (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
7. Fernandez A, Huang S, Seston S, Xing J, et al. (1999). How stable is stable? Function versus community composition. Appl. Environ. Microbiol. 65: 3697-3704.
8. Harry M, Gambier B, Bourezgui Y and Garnier-Sillam E (1999). Evaluation of purification procedures for DNA extracted from rich organic samples: interference with humic substances. Analusis 27: 439-441.
9. Heuer H, Krsek M, Baker P, Smalla K, et al. (1997). Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63: 3233-3241.
10. Juck D, Charles T, Whyte LG and Greer CW (2000). Polyphasic microbial community analysis of petroleum hydrocarboncontaminated soils from two northern Canadian communities. FEMS Microbiol. Ecol. 33: 241-249.
11. Krsek M and Wellington EM (1999). Comparison of different methods for the isolation and purification of total community DNA from soil. J. Microbiol. Methods 39: 1-16.
12. Lane DJ (1991). 16S/23S rRNA sequencing. In: Nucleic acid techniques in bacterial systematics (Stackbrandt E and Goodfellow M, eds.). Wiley, Chichester, 115-176.
13. G, Huang W, Lerner DN and Zhang X (2000). Enrichment of degrading microbes and bioremediation of petrochemical contaminants in polluted soil. Water Res. 34: 3845-3853.
14. Muyzer G and Smalla K (1998). Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73: 127-141.
15. Ogram A, Sayler GS and Barkay T (1987). The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7: 57-66.
16. Olsen GJ, Woese CR and Overbeek R (1994). The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176: 1-6.
17. Picard C, Ponsonnet C, Paget E, Nesme X, et al. (1992). Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58: 2717-2722.
18. Roose-Amsaleg CL, Garnier-Sillman E and Harry M (2001). Extraction and purification of microbial DNA from soil and sediment samples. Appl. SoilEcol. 18: 47-60.
19. Sheffield VC, Cox DR, Lerman LS and Myers RM (1989). Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. U. S. A. 86: 232-236.
20. Simmon KE, Steadman DD, Durkin S, Baldwin A, et al. (2004). Autoclave method for rapid preparation of bacterial PCRtemplate DNA. J. Microbiol. Methods 56: 143-149.
21. Smalla K, Cresswell N, Mendoca-Hagler LC, Wolters A, et al. (1993). Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74: 78-85.
22. Steffan RJ, Goksoyr J, Bej AK and Atlas RM (1988). Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54: 2908-2915.
23. Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
24. Tsai YL and Olson BH (1991). Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57: 1070-1074.
25. Tsai YL and Olson BH (1992). Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58: 2292-2295.
26. Volossiouk T, Robb EJ and Nazar RN (1995). Direct DNA extraction for PCR-mediated assays of soil organisms. Appl. Environ. Microbiol. 61: 3972-3976.
27. Wang Q, Garrity GM, Tiedje JM and Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267.
28. Wechter P, Williamson J, Robertson A and Kluepfel D (2003). A rapid, cost-effective procedure for the extraction of microbial DNA from soil. World J. Microbiol. Biotechnol. 19: 85-91.
29. Woese CR (1987). Bacterial evolution. Microbiol. Rev. 51: 221-271.
30. Zhou J, Bruns MA and Tiedje JM (1996). DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-332.