Methods for DNA extraction from various soils: a comparison

Tien, Chih-Jen; Chao, C. C.; Chao, Wei-Liang

doi:10.1046/j.1365-2672.1999.00775.x

Cited by 49 publications

(30 citation statements)

References 19 publications

(24 reference statements)

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“…Compared to these two direct extraction methods, the indirect extraction method of Jacobsen and Rasmussen [28] based on centrifugation recovery of cell fraction before lysis and CsCl DNA purification, gave the lowest DNA yield but showed the highest DNA purity with a low degree of DNA shearing. Tien et al [65] reported that the direct lysis methods produced similarly DNA yield at least a 10-fold greater than the indirect extraction methods.…”

Section: Comparative Evaluation Of Direct and Indirect Methodsmentioning

confidence: 99%

“…3. Nucleic acid extraction should be performed as soon as possible after sample collection since storing samples at 4°C for several weeks can result in the degradation of the large molecular-weight DNA fraction [65].…”

Section: Toward a Universal Lysis Extraction Method?mentioning

confidence: 99%

“…Cesium chloride-Ethidium bromide equilibrium density centrifugation has been successfully used to recover pure DNA [28,65] of large size (at least 48 kb) [9,23].…”

Section: Nucleic Acid Separation and Purificationmentioning

confidence: 99%

See 2 more Smart Citations

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

253

164

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Section: Comparative Evaluation Of Direct and Indirect Methodsmentioning

confidence: 99%

Section: Toward a Universal Lysis Extraction Method?mentioning

confidence: 99%

See 1 more Smart Citation

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

253

164

View full text Add to dashboard Cite

“…Several environmental DNA isolation and purification strategies have previously been investigated with variable rates of success (Cullen and Hirsch 1998;Miller et al 1999;Tien et al 1999). In this study, extraction techniques that are compatible with sediments obtained from multiple depths were evaluated based on DNA yield, ability to detect microbial community members by PCR-DGGE, and ability to determine the relationships between the microbial community and environmental variables.…”

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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“…Fluorescent dyes have difficulty penetrating particular types of microorganisms in-situ (e.g., lichens (see Weinstein et al, submitted manuscript, 2007)); culturing has been known to underestimate microbial abundance by 1 to 2 orders of magnitude; a vast majority of microbial diversity has proven refractory to cultivation; and the efficiency of DNA extraction varies widely [Amman et al, 1995;Hartmann et al, 1997;Miller et al, 1999;Tien et al, 1999 Table 2). Geologic map units include m (mountain-forming materials), d (dissected materials, d1, d2 and d3), s (scalloped terrain) and f (fan materials).…”

Section: Habitats and Microbiologymentioning

confidence: 99%

Searching for microbial life remotely: Satellite‐to‐rover habitat mapping in the Atacama Desert, Chile

et al. 2007

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[1] The Atacama Desert, one of the most arid landscapes on Earth, serves as an analog for the dry conditions on Mars and as a test bed in the search for life on other planets. During the Life in the Atacama (LITA) 2004 field experiment, satellite imagery and ground-based rover data were used in concert with a 'follow-the-water' exploration strategy to target regions of biological interest in two (1 coastal, 1 inland) desert study sites. Within these regions, environments were located, studied and mapped with spectroscopic and fluorescence imaging (FI) for habitats and microbial life. Habitats included aqueous sedimentary deposits (e.g., evaporites), igneous materials (e.g., basalt, ash deposits), rock outcrops, drainage channels and basins, and alluvial fans. Positive biological signatures (chlorophyll, DNA, protein) were detected at 81% of the 21 locales surveyed with the FI during the long-range, autonomous traverses totaling 30 km. FI sensitivity in detecting microbial life in extreme deserts explains the high percentage of positives despite the low actual abundance of heterotrophic soil bacteria in coastal (<1-10 4 CFU/g-soil) and interior (<1-10 2 CFU/g-soil) desert soils. Remote habitat, microbial and climate observations agreed well with ground-truth, indicating a drier and less microbially rich interior compared to the relatively wetter and abundant biology of the coastal site where rover sensors detected the presence of fog and abundant surface lichens. LITA project results underscore the importance of an explicit focus by all engineering and science disciplines on microbially relevant scales (mm to nm), and highlight the success of satellite-based and 'follow-the-water' strategies for locating diverse habitats of biological promise and detecting the microbial hotspots within them.Citation: Warren-Rhodes, K., et al. (2007), Searching for microbial life remotely: Satellite-to-rover habitat mapping in the Atacama Desert, Chile,

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Methods for DNA extraction from various soils: a comparison

Cited by 49 publications

References 19 publications

Extraction of DNA from soil

Extraction of DNA from soil

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

Searching for microbial life remotely: Satellite‐to‐rover habitat mapping in the Atacama Desert, Chile

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