Nucleic Acid Extraction from Soil

Bakken, Lars R.; Frostegård, Åsa

doi:10.1007/3-540-29449-x_3

Cited by 31 publications

(11 citation statements)

References 117 publications

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“…Although direct extraction seems to be widely in use now, both DNA extraction methods present contrasting advantages and drawbacks in terms of DNA quantity and quality. The intricacies of current soil DNA extraction methods have been examined elsewhere (Robe et al , 2003; Schneegurt et al , 2003; Purdy, 2005; Bakken & Frostegård, 2006; Herrera & Cockell, 2007). In this review, a summary of the currently used methods is provided, as well as complementary information on the physicochemical interactions of DNA and bacterial cells with the soil matrix in the respective indirect and direct methods.…”

Section: Microbial Dna Extractionmentioning

confidence: 99%

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Lombard¹,

Prestat²,

Elsas³

et al. 2011

FEMS Microbiology Ecology

210

157

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Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

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Section: Microbial Dna Extractionmentioning

confidence: 99%

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Lombard¹,

Prestat²,

Elsas³

et al. 2011

FEMS Microbiology Ecology

210

157

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“…Compared to LSC, NDGC is preferable for two reasons: one is that the yield is similar to or even slightly higher than that obtained with LSC, and the other is that the purity is dramatically improved . For different soil types, the cell yields vary from 3% to 36% of total soil bacteria with the NDGC method Lindahl, 1996;Mayr et al, 1999;Berry et al, 2003;Bertrand et al, 2005;Bakken and Frostegård, 2006). Usually, the extraction procedure involves either directly extracting bacterial cells from soil particles with NDGC after soil dispersion, or separating the released bacteria from soil with repeated LSC first, and then concentrating them, and finally using NDGC for purification of these cells (Bertrand et al, 2005;Maron et al, 2006).…”

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confidence: 99%

An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction

Liu

et al. 2010

J Microbiol.

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Separation of bacterial cells from soil is a key step in the construction of metagenomic BAC libraries with large DNA inserts. Our results showed that when combined with sodium pyro-phosphate and homogenization for soil dispersion, sucrose density gradient centrifugation (SDGC) was more effective at separating bacteria from soil than was low speed centrifugation (LSC). More than 70% of the cells, along with some soil colloids, were recovered with one round of centrifugation. A solution of 0.8% NaCl was used to resuspend these cell and soil pellets for purification with nycodenz density gradient centrifugation (NDGC). After purification, more than 30% of the bacterial cells in the primary soil were extracted. This procedure effectively removed soil contamination and yielded sufficient cells for high molecular weight (HMW) DNA isolation. Ribosomal intergenic spacer analysis (RISA) showed that the microbial community structure of the extracted cells was similar to that of the primary soil, suggesting that this extraction procedure did not significantly change the the soil bacteria community structure. HMW DNA was isolated from bacterial cells extracted from red soil for metagenomic BAC library construction. This library contained DNA inserts of more than 200 Mb with an average size of 75 kb.

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“…It has been suggested that the lower the DNA yield, the higher the possibility that the sample represents unique phyla (36). Additionally, metabolically active and/or large cells have the potential to be severely over-represented in the community structures of soil DNA extracts, due to cell wall structures that are less resistant to lysis (11). It is not clear whether PCT lysis is sensitive to cell size and/or metabolic activity; however, future studies on extraction bias may elucidate the mechanisms behind the increased diversity.…”

Section: Resultsmentioning

confidence: 99%

“…Studies comparing direct lysis procedures (e.g., mechanical, chemical, or enzymatic) among soils of varying characteristics indicate that the choice of lysis technique strongly impacts the purity, fragmentation, community representation, and recovery of targeted bacterial DNA from soil samples (610). Lysis treatment effects are less understood for fungi than bacteria (11), and previous investigations have generated mixed results. For example, a study of three forest soils of contrasting sand, clay, and organic matter content indicated that the extraction step had no effect on eukaryote community composition (12); while the extraction step appeared to exert a greater influence than soil type on fungal community structure recovered from forest, grassland, and arable soils (13).…”

mentioning

confidence: 99%

Use of Pressure Cycling Technology for Cell Lysis and Recovery of Bacterial and Fungal Communities from Soil

Bruner

Okubara²,

Abi-Ghanem

et al. 2015

BioTechniques

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Selection of cell lysis methodology is critical to microbial community analyses due to the inability of any single extraction technology to recover the absolute genetic structure from environmental samples. Numerous methodologies are currently applied to interrogate soil communities, each with its own inherent bias. Here we compared the efficacy and bias of three physical cell lysis methods in conjunction with the PowerLyzer PowerSoil DNA Isolation Kit (MO BIO) for direct DNA extraction from soil: bead-beating, vortex disruption, and hydrostatic pressure cycling technology (PCT). PCT lysis, which is relatively new to soil DNA extraction, was optimized for soils of two different textures prior to comparison with traditional bead-beating and vortex disruption lysis. All cell lysis methods successfully recovered DNA. Although the two traditional mechanical lysis methods yielded greater genomic, bacterial, and fungal DNA per gram soil than the PCT method, the latter resulted in a greater number of unique terminal restriction fragments by terminal RFLP (T-RFLP) analysis. These findings indicate the importance of diversity and quantity measures when assessing DNA extraction bias, as soil DNA retrieved by PCT lysis represented populations not found using traditional mechanical lysis methods.

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Nucleic Acid Extraction from Soil

Cited by 31 publications

References 117 publications

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction

Use of Pressure Cycling Technology for Cell Lysis and Recovery of Bacterial and Fungal Communities from Soil

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