Extraction of DNA from soil

Robe, Patrick; Nalin, Renaud; Capellano, Carmela; Vogel, Timothy M.; Simonet, Pascal

doi:10.1016/s1164-5563(03)00033-5

Cited by 253 publications

(170 citation statements)

References 77 publications

(73 reference statements)

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“…DNA adsorption is observed in some clay minerals (Ivarson et al 1982;Demanèche et al 2001;Takada-Hoshino and Matsumoto 2005), and DNA extraction efficiency is low in Andosols containing a high concentration of the clay mineral allophane, which strongly adsorbs many substances (Yoshida et al 1992;Zhou et al 1996;Takada-Hoshino and Matsumoto 2005;Miura et al 2009). In contrast, PCR is inhibited by humic acid, which is mainly present in decomposing organic matter (Tsai and Olson 1992;Jacobsen 1995;Robe et al 2003). Thus, we made a distinction between DNA adsorption and PCR inhibition, and our study addressed the former problem.…”

Section: Introductionmentioning

confidence: 98%

“…The influence of soil components on DNA quantification is thought to involve two processes: DNA adsorption to soil particles during DNA extraction (Trevors 1996;Frostegå rd et al 1999;Demanèche et al 2001) and polymerase chain reaction (PCR) inhibition by humic substances during DNA amplification (Tsai and Olson 1992;Jacobsen 1995;Robe et al 2003). DNA adsorption and PCR inhibition are mainly caused by different substrates.…”

Section: Introductionmentioning

confidence: 99%

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A method for obtaining the relationship between the amount of DNA and the fine root weight from mixtures of fine roots and soil particles

Ugawa

Yamaguchi

Miura

et al. 2012

Soil Science and Plant Nutrition

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Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

A method for obtaining the relationship between the amount of DNA and the fine root weight from mixtures of fine roots and soil particles

Ugawa

Yamaguchi

Miura

et al. 2012

Soil Science and Plant Nutrition

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“…They have a key role in the biogeochemical cycles of the biosphere and represent an enormous reservoir of novel valuable molecules for health or industry [1].…”

Section: Introductionmentioning

confidence: 99%

“…Though various methods of direct DNA extraction have been devised, it remains difficult to extract DNA from some soils [6]. Microorganisms through different mechanisms to bind soil particles of clay that reduce access to the bacteria [1].…”

Section: Introductionmentioning

confidence: 99%

An Improved Procedure of the Metagenomic DNA Extraction from Saline Soil, Sediment and Salt

Kashi

2016

ILNS

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Abstract.A new modified protocol has been developed for extracting pure community inhibitorsfree DNA from saline soils, sediments and salts. Amplification of DNA from soil and sediment is often inhibited by copurified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to saline samples. Using a widely used a newly modified direct DNA extraction method proposed in this report, DNA was extracted from samples of Urmia Lake in diverse geological location in Iran and quantity of the DNA were examined. We developed an improved method to extract DNA include the combination of physical, chemical and mechanical lysis methods from saline samples. In the earlier reports, skim milk as an adsorption competitor was added to buffer DNA extract. In current study, we added skim milk to buffer DNA extraction. The results showed that skim milk was useful as an additive for extract DNA from saline samples. This method is applicable to molecular community analysis of saline samples which strongly adsorb DNA. The methods appear to have wide applicability in investigating molecular diversity and exploring functional genes from the total DNA. The extracted DNA was used to successfully amplify 16SrRNA region and functional genes. The amplicons were suitable for further applications such as diversity based analysis by denaturing gradient gel electrophoresis (DGGE) and cloning library.

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“…Indeed, many previous studies have relied on similar techniques to evaluate DNA extraction protocols for use with environmental samples (e.g. Krsek and Wellington 1999;Griffiths et al 2000;Robe et al 2003). DGGE can be used to separate small variable regions of the 16S rRNA gene based on nucleotide differences (Muyzer et al 1993).…”

Section: Introductionmentioning

confidence: 99%

The effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods

Xiong

Xie

Wang

et al. 2014

Journal of Freshwater Ecology

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We evaluated the effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods. DNA yields and the number of ribotypes differed significantly by depth. The mean yields at the depth interval of 0À8 cm from the two extraction methods were both higher than those within the depth range of 10À44 cm. Significant differences were also observed between the two methods in DNA yields from the deeper (10À44 cm) samples. An analysis of denaturing gradient gel electrophoresis (DGGE) profiles demonstrated that the choice of the DNA extraction method has a profound effect on the bacterial community profiles generated, which was reflected in the number of bands or ribotypes detected from samples from all depths. Higher DNA yield did not lead to a higher diversity of phylotypes. In almost all cases, extraction method 2 (M2, soil DNA test kit) resulted in a greater diversity of phylotypes compared to method 1 (M1, liquid nitrogen/cetyl trimethylammonium bromide extraction). Moreover, notable changes in bacterial diversity were detected in the uppermost layers (0À5 cm). The results of canonical correspondence analysis illustrated that the DNA extraction method did not affect the evaluation of the relationship between bacterial community structure and environmental variables in lake sediments at multiple depths, and the differences in community structure in the two extraction methods were both related to the same environmental variables (pH, total phosphorus concentration) and depth. Vertically, the community structure of sediment layers formed several separate clusters along the depth gradient. This study expands our understanding of the depth-related microbial community structure in lake sediments.

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Extraction of DNA from soil

Cited by 253 publications

References 77 publications

A method for obtaining the relationship between the amount of DNA and the fine root weight from mixtures of fine roots and soil particles

A method for obtaining the relationship between the amount of DNA and the fine root weight from mixtures of fine roots and soil particles

An Improved Procedure of the Metagenomic DNA Extraction from Saline Soil, Sediment and Salt

The effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods

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