DNA extraction method affects microbial community profiles from soils and sediment

Carrigg, Cora; Rice, Olivia; Kavanagh, Siobhán; Collins, Gavin; O’Flaherty, Vincent

doi:10.1007/s00253-007-1219-y

Cited by 152 publications

(123 citation statements)

References 56 publications

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“…These factors may have resulted in artificially high estimates of initial DNA yields based on PicoGreen analysis and exaggerated DNA losses upon purification (Carrigg et al 2007). Although humic acids are known to interfere with PicoGreen at high concentrations (Bachoon et al 2001), PicoGreen can be used on dilute samples in which small amounts of DNA are still present and humic acid interference is negligible (Sandaa et al 1998;Stark et al 2000).…”

Section: Discussionmentioning

confidence: 99%

“…This depth-related gradient of biogeochemical properties provides niches for metabolically diverse microorganisms (Koizumi et al 2003). Although there have been many published studies describing methods for the extraction of DNA from environmental samples, such as soil, marine sediment, and compost (Tsai and Olson 1991;Carrigg et al 2007;Kallmeyer and Smith 2009), few studies have focused on the combined effects of depth and DNA extraction method on microbial community profiles from lake sediments.…”

Section: Introductionmentioning

confidence: 99%

“…It is therefore possible to discriminate between different organisms or ribotypes within a DGGE profile of the whole community. Although this technique has several drawbacks and is only semi-quantitative at best, it remains the most efficient technique for the measurement of relative differences or temporal changes in microbial community structure in environmental samples (Carrigg et al 2007). Additionally, the bacterial community structure can be revealed by the mobility of DGGE bands; that is, from the DGGE banding patterns, the identities of individual PCR amplicons (bands in the gel) can be resolved by sequencing and phylogenetic analysis (Koizumi et al 2003).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…In the context, however, of quantifying DNA or RNA targets from complex microbial communities, and to develop reliable diagnostic tools to support optimized bioreactor operation, including, for example, TM dosing strategies, several additional considerations may apply. Nucleic acids extractions techniques may require optimisation [46] and PCR assays with environmental and bioengineered samples are often particularly challenging [47]. The sensitivity and specificity of qPCR assays, and of the Nucleic Acids diagnostic Tests (NATs) developed thereof, are critical considerations [48].…”

Section: Trace Metal Microbiology and Microbial Ecologymentioning

confidence: 99%

Fate of Trace Metals in Anaerobic Digestion

Fermoso

Hullebusch²,

Guibaud

et al. 2015

Biogas Science and Technology

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A challenging, and largely uncharted, area of research in the field of anaerobic digestion science and technology is in understanding the roles of trace metals in enabling biogas production. This is a major knowledge gap and a multifaceted problem involving metal chemistry; physical interactions of metal and solids; microbiology; and technology optimization. Moreover, the fate of trace metals, and the chemical speciation and transport of trace metals in environmentsoften agricultural lands receiving discharge waters from anaerobic digestion processes -is completely unknown but simultaneously represents challenges for environmental protection and opportunities to close process loops in anaerobic biotechnologies. Affiliation 1.

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“…Since less than 1% of soil microorganisms can be grown in laboratory conditions using culture media [3,4] and the vast majority are not cultivable [5,6], a significant number of studies dealing with microbial diversity utilize molecular tools such as competitive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing based on the extraction of environmental nucleic acids [7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

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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DNA extraction method affects microbial community profiles from soils and sediment

Cited by 152 publications

References 56 publications

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

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

Fate of Trace Metals in Anaerobic Digestion

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

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