Extraction and purification of microbial DNA from soil and sediment samples

Roose‐Amsaleg, Céline; Garnier-Sillam, É.; Harry, Myriam

doi:10.1016/s0929-1393(01)00149-4

Cited by 197 publications

(113 citation statements)

References 88 publications

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“…This optimised DNA extraction technique is absolutely essential for molecular biology, since a modification of the extraction method is required for each different sample and each tissue (Roose-Amsaleg et al 2001). Two previous studies on the extraction of DNA from copepod-associated bacteria for PCR-DGGE analysis have been published so far (Tang et al 2006b;Møller et al 2007).…”

Section: Discussionmentioning

confidence: 99%

Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods

et al. 2010

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Marine zooplanktic organisms, such as copepods, are usually associated with large numbers of bacteria. Some of these bacteria live attached to copepods' exoskeleton, while others prevail in their intestine and faecal pellets. Until now, general conclusions concerning the identity of these bacteria are problematic since the majority of previous studies focused on cultivable bacteria only. Hence, to date little is known on whether copepod genera or species harbour distinct bacterial populations and about the nature of this association. To shed more light on these copepod/bacteria consortia, the focus of this study was the development and evaluation of a suitable approach to extract bacterial DNA from different North Sea copepod genera. Furthermore, the bacterial DNA was analysed by PCR-DGGE and subsequent sequencing of excised bands. The result of this work was an appropriate extraction method for batches of ten to one copepod specimens and offered first insights as to which bacteria are attached to the copepods Acartia sp. and Temora sp. from Helgoland Roads (German Bight) and a laboratory-grown Acartia tonsa culture. It revealed the prevalence of Alphaproteobacteria.

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Section: Discussionmentioning

confidence: 99%

Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods

et al. 2010

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“…Then, this bacterial fraction is lysed and the nucleic acids purified [10,23,67]. Both approaches have advantages and disadvantages related to DNA yields, DNA purity for molecular purposes, and the unbiased representation of the entire microbial diversity [10,58].…”

Section: Introductionmentioning

confidence: 99%

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

254

164

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“…These results agree with a previous report that showed a significant correlation between crude DNA yield and soil organic carbon content (r ¼ 0.73, p ¼ 0.01, Zhou et al 1996). It has been documented that the efficiency of soil microbial DNA extraction depends on soil quality, particularly on its clay and organic matter contents, because microorganisms can interact with soil colloids, such as clayÀorganic aggregates (Roose-Amsaleg et al 2001). Higher cell counts are directly proportional to high levels of organic carbon and nitrogen, clay, and humic acid; high levels of organic carbon and nitrogen also indicate greater microbial activity (Lakay et al 2007).…”

Section: Discussionmentioning

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 and purification of microbial DNA from soil and sediment samples

Cited by 197 publications

References 88 publications

Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods

Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods

Extraction of DNA from soil

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

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