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Comparison of commercial kits for the extraction of DNA from paddy soils
Author(s) -
Knauth S.,
Schmidt H.,
Tippkötter R.
Publication year - 2013
Publication title -
letters in applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.698
H-Index - 110
eISSN - 1472-765X
pISSN - 0266-8254
DOI - 10.1111/lam.12038
Subject(s) - lysis , dna extraction , lysis buffer , agarose gel electrophoresis , soil water , polymerase chain reaction , dna , extraction (chemistry) , chromatography , temperature gradient gel electrophoresis , gel electrophoresis , bacteria , biology , soil test , agarose , chemistry , microbiology and biotechnology , 16s ribosomal rna , biochemistry , gene , genetics , ecology
The objective of this study was to compare the extraction efficiency of commercial DNA kits by evaluating the quantity and purity of DNA extracts obtained from paddy soils. DNA was extracted from three paddy soils using the F ast DNA ® SPIN kit for soil ( FD ), the innu SPEED soil DNA kit ( INS ) and the N ucleo S pin ® soil kit ( NSP ). DNA extracts were analysed by agarose gel electrophoresis and UV spectroscopy. Polymerase chain reaction–denaturing gradient gel electrophoresis ( PCR ‐ DGGE ) analyses were conducted to evaluate the potential bias of the DNA extractions on fingerprinting techniques. Regarding the quantity and the purity of the extracted DNA , the NSP kit was detected superior to the FD kit, while the INS kit failed to extract detectable amounts of DNA . DGGE fingerprints generated from PCR products ( FD , NSP ) showed high levels of similarity for the amplified 16 S rRNA genes of methanogenic archaea (>95%) and bacteria (up to 100%) in each soil. This study suggested that the recently introduced NSP kit allowed for the adjustment of the lysis buffer composition to the soil of interest and is at least equivalent to the well‐established FD kit for the extraction of DNA from paddy soils. Significance and Impact of the Study The choice of commercial kits ( FD , INS , NSP ) has been of great importance regarding the quantity and purity of DNA extracted from paddy soils in this study. The composition of the cell lysis buffer represented a key component for successful extractions of DNA from different soils. The possibility of adjusting the lysis buffer to the soil of interest as well as the reproducibility of DGGE banding patterns makes the recently introduced NSP kit a strong competitor to the well‐established FD kit for the extraction of DNA from paddy soils.