An improved method for purifying genomic DNA from forest leaf litters and soil suitable for PCR

Journal of Soils and Sediments

Volumn 9, Issue 3, 2009, Pages 261-266

  Zhang, Li ^a   Xu, Zhihong ^a   Patel, Bharat K C ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

DNA; DNA purification; Forest leaf litter; PCR amplification; PCR inhibitors

Indexed keywords

CONIFEROUS FOREST; DNA; ENZYME ACTIVITY; FOREST SOIL; HABITAT FRAGMENTATION; HUMIC ACID; INHIBITION; INHIBITOR; LEAF LITTER; MICROBIAL COMMUNITY; PHENOLIC COMPOUND; PLANTATION; POLYMERASE CHAIN REACTION; POLYSACCHARIDE;

BACTERIA (MICROORGANISMS); PINUS ELLIOTTII;

EID: 67650819221     PISSN: 14390108     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11368-009-0080-2     Document Type: Conference Paper

References (24)

1. B Calli N Tas B Mertoglu B Inanc I Ozturk 2003 Molecular analysis of microbial communities in nitrification and denitrification reactors treating high ammonia leachate J Environ Sci Health A Tox Hazard Subst Environ Eng 38 1997 2007 (Pubitemid 37187123)
2. CR Chen ZH Xu P Keay SL Zhang 2005 Total soluble nitrogen in forest soils as determined by persulfate oxidation and by high temperature catalytic oxidation Aust J Soil Res 43 515 523 (Pubitemid 41126463)
3. DW Cullen PR Hirsch 1998 Simple and rapid method for direct extraction of microbial DNA from soil for PCR Soil Biol Biochem 30 983 993 (Pubitemid 28329521)
4. S Donn BS Griffiths R Neilson T Daniell 2007 DNA extraction from soil fauna J Nematol 39 81 81
5. CA Flemming KT Leung H Lee JT Trevors CW Greer 1994 Survival of Lux-Lac-Marked Biosurfactant-Producing Pseudomonas-Aeruginosa Ug2L in Soil Monitored by Nonselective Plating and PCR Appl Environ Microbiol 60 1606 1613 (Pubitemid 24144821)
6. N Fortin D Beaumier K Lee CW Greer 2004 Soil washing improves the recovery of total community DNA from polluted and high organic content sediments J Microbiol Methods 56 181 191 (Pubitemid 38117177)
7. A Frostegard S Courtois V Ramisse S Clerc D Bernillon F Le Gall P Jeannin X Nesme P Simonet 1999 Quantification of bias related to the extraction of DNA directly from soils Appl Environ Microbiol 65 5409 5420 (Pubitemid 129520630)
8. M Harry B Gambier E Garnier-Sillam 2000 Soil conservation for DNA preservation for bacterial molecular studies Eur J Soil Biol 36 51 55 (Pubitemid 30674834)
9. JZ He ZH Xu J Hughes 2005 Pre-lysis washing improves DNA extraction from a forest soil Soil Biol Biochem 37 2337 2341 (Pubitemid 41757564)
10. RA Hurt XY Qiu LY Wu Y Roh AV Palumbo JM Tiedje JH Zhou 2001 Simultaneous recovery of RNA and DNA from soils and sediments Appl Environ Microbiol 67 4495 4503 (Pubitemid 33646077)
11. JS Kim G Sparovek RM Longo WJ De Melo D Crowley 2007 Bacterial diversity of terra preta and pristine forest soil from the Western Amazon Soil Biol Biochem 39 684 690 (Pubitemid 44820275)
12. M Labandeira-Rey F Couzon S Boisset EL Brown M Bes Y Benito EM Barbu V Vazquez M Hook J Etienne F Vandenesch MG Bowden 2007 Staphylococcus aureus Panton-Valentine leukocidin causes necrotizing pneumonia Science 315 1130 1133 (Pubitemid 46328024)
13. ZH Ma TJ Michailides 2007 Approaches for eliminating PCR inhibitors and designing PCR primers for the detection of phytopathogenic fungi Crop Protection 26 145 161 (Pubitemid 44881150)
14. DN Miller JE Bryant EL Madsen WC Ghiorse 1999 Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples Appl Environ Microbiol 65 4715 4724
15. Morgan JAW, Winstanley C (1997) Microbial biomarkers. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern Soil Microbiol. Marcel Dekker, New York, pp 331-352
16. S Poussier JJ Cheron A Couteau J Luisetti 2002 Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates J Microbiol Methods 51 349 359 (Pubitemid 35245855)
17. LA Proteous JL Armstrong 1991 Recovery of bulk DNA from soil by a rapid, small-scale extraction method Curr Microbiol 22 345 348
18. MR Rondon PR August AD Bettermann SF Brady TH Grossman MR Liles KA Loiacono BA Lynch IA MacNeil C Minor CL Tiong M Gilman MS Osburne J Clardy J Handelsman RM Goodman 2000 Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl Environ Microbiol 66 2541 2547 (Pubitemid 30353963)
19. E Tas A Saano P Leinonen K Lindstrom 1995 Identification of Rhizobium Spp in Peat-Based Inoculants by DNA Hybridization and PCR and Its Application in Inoculate Quality-Control Appl Environ Microbiol 61 1822 1827
20. YL Tsai BH Olson 1992 Detection of low numbers of bacterial cells in soil and sediments by polymerase chain reaction Appl Environ Microbiol 58 754 757
21. CA Whitehouse HE Hottel 2007 Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples Mol Cellular Probes 21 92 96 (Pubitemid 46074388)
22. ZH Yang Y Xiao GM Zeng ZY Xu YS Liu 2007 Comparison of methods for total community DNA extraction and purification from compost Appl Microbiol Biotechnol 74 918 925 (Pubitemid 46318657)
23. L Zhang ZH Xu BKC Patel 2007 Bacillus decisifrondis sp nov., isolated from soil underlying decaying leaf foliage Int J Syst Evol Microbiol 57 974 978 (Pubitemid 46796472)
24. J Zhou MA Bruin JM Tiedje 1995 DNA recovery from soils of diverse composition Appl Environ Microbiol 62 316 322