title: Comparisons of direct extraction methods of microbial DNA from different paddy soils.
abstract: Molecular analyses for the study of soil microbial communities often depend on the direct extraction of DNA from soils. The present work compares the effectiveness of three different methods of extracting microbial DNA from seven different paddy soils. Comparison among different DNA extraction methods against different paddy soil samples revealed a marked variation in DNA yields from 3.18-20.17 μg DNA/g of dry soil. However, irrespective of the soil samples and extraction methods the DNA fragment size was >10 kb. Among the methods evaluated, method-C (chemical-enzymatic-mechanical) had better cell lysis efficiency and DNA yield. After purification of crude DNA by Purification Kit, A260/A230 and A260/A280 ratios of the DNA obtained by method-C reached up to 2.27 and 1.89, respectively, sustaining the efficacy of this technique in removing humic acid, protein and other contaminants. Results of the comprehensive evaluation of DNA extraction methods suggest that method-C is superior to other two methods (chemical-enzymatic and chemical-mechanical), and was the best choice for extraction of total DNA from soil samples. Since soil type and microbial community characteristics influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods according to experimental goals.
authors: Department of Agricultural Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea ; Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea.
authors: Md Rashedul
authors: MR
authors: Islam
authors: Tahera
authors: T
authors: Sultana
authors: M
authors: M
authors: Melvin Joe
authors: Jang-Cheon
authors: JC
authors: Cho
authors: Tongmin
authors: T
authors: Sa
keywords: Extraction method; Microbial DNA; Paddy soil; Purification
references: Biol Proced Online. 1998 May 14;1:40-47
references: 12734590
references: J Mol Microbiol Biotechnol. 2003;5(1):46-56
references: 12673061
references: J Microbiol Methods. 2003 Jul;54(1):37-45
references: 12732420
references: J Microbiol Methods. 2001 May;45(1):7-20
references: 11295193
references: Appl Environ Microbiol. 1997 Sep;63(9):3614-21
references: 9293013
references: Appl Environ Microbiol. 2001 May;67(5):2354-9
references: 11319122
references: Microb Ecol. 1991 Dec;21(1):191-8
references: 24194210
references: J Appl Microbiol. 2007 Jan;102(1):265-73
references: 17184343
references: Curr Opin Microbiol. 2002 Jun;5(3):240-5
references: 12057676
references: Biotechnol Lett. 2007 Dec;29(12):1845-55
references: 17680211
references: Appl Environ Microbiol. 1996 Feb;62(2):316-22
references: 8593035
references: Appl Environ Microbiol. 1991 Apr;57(4):1070-4
references: 1647749
references: Appl Biochem Biotechnol. 2006 Aug;134(2):97-112
references: 16943632
references: Environ Microbiol. 2001 Jul;3(7):431-9
references: 11553233
references: Environ Microbiol. 2006 Feb;8(2):308-20
references: 16423017