Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1007/s13205-016-0383-0 |
An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer | |
Narayan, Avinash; Jain, Kunal; Shah, Amita R.; Madamwar, Datta | |
通讯作者 | Madamwar, Datta |
来源期刊 | 3 BIOTECH |
ISSN | 2190-5738 |
EISSN | 2190-572X |
出版年 | 2016 |
卷号 | 6 |
英文摘要 | The present study describes the rapid and efficient indirect lysis method for environmental DNA extraction from athalassohaline soil by newly formulated cell extraction buffer. The available methods are mostly based on direct lysis which leads to DNA shearing and co-extraction of extra cellular DNA that influences the community and functional analysis. Moreover, during extraction of DNA by direct lysis from athalassohaline soil, it was observed that, upon addition of poly ethylene glycol (PEG), isopropanol or absolute ethanol for precipitation of DNA, salt precipitates out and affecting DNA yield significantly. Therefore, indirect lysis method was optimized for extraction of environmental DNA from such soil containing high salts and low microbial biomass (CFU 4.3 x 10(4) per gram soil) using newly formulated cell extraction buffer in combination with low and high speed centrifugation. The cell extraction buffer composition and its concentration were optimized and PEG 8000 (1 %; w/v) and 1 M NaCl gave maximum cell mass for DNA extraction. The cell extraction efficiency was assessed with acridine orange staining of soil samples before and after cell extraction. The efficiency, reproducibility and purity of extracted DNA by newly developed procedure were compared with previously recognized methods and kits having different protocols including indirect lysis. The extracted environmental DNA showed better yield (5.6 +/- 0.7 mu g g(-1)) along with high purity ratios. The purity of DNA was validated by assessing its usability in various molecular techniques like restriction enzyme digestion, amplification of 16S rRNA gene using PCR and UV-Visible spectroscopy analysis. |
英文关键词 | Environmental DNA Saline desert soil DNA extraction Athalassohaline Microbial cell extraction |
类型 | Article |
语种 | 英语 |
国家 | India |
收录类别 | SCI-E |
WOS记录号 | WOS:000370363400011 |
WOS关键词 | POLYMERASE-CHAIN-REACTION ; REACTION AMPLIFICATION ; COMMUNITIES ; BACTERIAL ; METAGENOMICS ; LIMITATIONS ; SEDIMENTS ; SAMPLES ; SIZE |
WOS类目 | Biotechnology & Applied Microbiology |
WOS研究方向 | Biotechnology & Applied Microbiology |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/190896 |
作者单位 | Sardar Patel Univ, BRD Sch Biosci, Vadtal Rd,Satellite Campus, Anand 388315, Gujarat, India |
推荐引用方式 GB/T 7714 | Narayan, Avinash,Jain, Kunal,Shah, Amita R.,et al. An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer[J],2016,6. |
APA | Narayan, Avinash,Jain, Kunal,Shah, Amita R.,&Madamwar, Datta.(2016).An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer.3 BIOTECH,6. |
MLA | Narayan, Avinash,et al."An efficient and cost-effective method for DNA extraction from athalassohaline soil using a newly formulated cell extraction buffer".3 BIOTECH 6(2016). |
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