An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil

Dineen, Shauna M.; Aranda, Roman; Anders, Douglas L.; Robertson, James

doi:10.1111/j.1365-2672.2010.04816.x

Cited by 113 publications

(94 citation statements)

References 56 publications

(108 reference statements)

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“…The results showed that both the quantity (yield of extraction) and the quality (purity, degree of degradation, easiness of amplification) of the extracted DNA depended on the extraction method and the type of environmental sample (Table 3), which was in agreement with earlier observations reported in the literature [9,10,14,32,33]. Moreover, Table 6.…”

Section: Discussionsupporting

confidence: 82%

“…However, the E.Z.N.A. conventional method provided much lower yields of extraction in comparison to its alternative method, as was also observed in other investigations [32,33]. Because of the demonstrated conflicts among different extraction methods and criteria, the selection of the optimum method for different types of soil was not straightforward (Table 4).…”

Section: Discussionmentioning

confidence: 73%

“…The literature indicates lower yields of extraction (0.80 to 9.12 µg of DNA/g of soil), A 260/280 ratios (1.53 to 1.64) and A 260/230 ratios (0.24 to 0.28) [10,[29][30][31]33].…”

Section: Discussionmentioning

confidence: 99%

“…For the PowerSoil kit, which ranked first in the present work, the yields of extraction ranged between 3.78 and 11.97 µg of DNA/g of soil, while the A 260/280 and A 260/230 ratios varied from 1.55 to 1.96 and 0.86 to 2.07, respectively. Previous studies reported yields of extraction of 0.12 to 23.0 µg of DNA/g of soil, as well as A 260/280 and A 260/230 ratios of 1.34 -1.65 and 0.55 -0.61, respectively [10,14,32,33].…”

Section: Discussionmentioning

confidence: 99%

“…In spite of many advantages of direct methods, they generally show lower DNA purity with a high degree of DNA shearing that can negatively affect PCR efficiency or specificity [1,20,27]. Due to the fact that some of the steps of DNA extraction using these direct methods might make DNA isolation expensive or impractical for processing the large number of samples usually required in ecological studies, commercial kits have been increasingly utilized for DNA extraction and purification from soil and sediments [9,10,14,[29][30][31][32][33][34].…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

DNA extraction method selection for agricultural soil using TOPSIS multiple criteria decision-making model

Pakpour¹,

Olishevska²,

Prasher³

et al. 2013

AJMB

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There is an increased interest in the extraction of nucleic acids from various environmental samples since culture-independent molecular techniques contribute to deepen and broaden the understanding of a greater portion of uncultivable microorganisms. Due to difficulties to select the optimum DNA extraction method in view of downstream molecular analyses, this article presents a straightforward mathematical framework for comparing some of the most commonly used methods. Four commercial DNA extraction kits and two physical-chemical methods (bead-beating and freeze-thaw) were compared for the extraction of DNA under several quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A 260/280 and A 260/230 ratios), degradation degree of DNA, easiness of PCR amplification, duration of extraction, and cost per extraction. From a practical point of view, it is unlikely that a single DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) was employed to compare the methods. The PowerSoil ® DNA Isolation Kit was systematically defined as the best performing method for extracting DNA from soil samples. More specifically, for soil:manure and soil:manure:biochar mixtures, the PowerSoil ® DNA Isolation Kit method performed best, while for neat soil samples its alternative version gained the first rank.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 73%

“…The literature indicates lower yields of extraction (0.80 to 9.12 µg of DNA/g of soil), A 260/280 ratios (1.53 to 1.64) and A 260/230 ratios (0.24 to 0.28) [10,[29][30][31]33].…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

DNA extraction method selection for agricultural soil using TOPSIS multiple criteria decision-making model

Pakpour¹,

Olishevska²,

Prasher³

et al. 2013

AJMB

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Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment

Ramírez

Graham

Dhondt

2018

Limnology & Ocean Methods

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Commercial DNA extraction kits are widely used for cultivation-free surveys of marine sediment. However, the consequences of popular extraction-kit choices for sequence-based biological inferences about marine sedimentary communities have not previously been exhaustively assessed. To address this issue, we extracted DNA from multiple paired subsamples of marine sediment using two popular commercial extraction kits (MO BIO Laboratories PowerSoil V R DNA isolation kit and MP Biomedicals FastDNA TM Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene-targeted quantification, and (4) postsequencing ecological inferences in near-seafloor (< 1 meter below seafloor [mbsf]) and subsurface (> 1 mbsf) marine sediment. In near-seafloor sediment, the MP Biomedicals FastDNA TM Spin Kit for Soil exhibits higher extraction yields, higher 16S rRNA gene loads, higher taxonomic diversity, and lower contaminant loads. In subseafloor sediment, both kits yield similar values for all of these parameters. The MO BIO Laboratories PowerSoil V R DNA isolation kit generally co-extracts less protein with the DNA in both near-seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth-dependent community richness patterns, taxonomic composition, and ordination-based similarity trends. We conclude that, despite kitspecific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next-generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.

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Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real‐time PCR

Desneux

Pourcher

2014

MicrobiologyOpen

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Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log10 the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

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An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil

Abstract: The results of this study aid in the selection of an appropriate DNA extraction kit for a given soil sample. Its application could expedite sample processing for real-time PCR detection of a pathogen in soil.

Cited by 113 publications

References 56 publications

DNA extraction method selection for agricultural soil using TOPSIS multiple criteria decision-making model

DNA extraction method selection for agricultural soil using TOPSIS multiple criteria decision-making model

Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real‐time PCR

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