DNA recovery and direct detection of Tn5 sequences from soil

Selenska, Sonja; Klingmüller, Walter

doi:10.1111/j.1472-765x.1991.tb00559.x

Cited by 86 publications

(51 citation statements)

References 11 publications

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“…A corresponding loss of signal was found in total DNA isolated from the soil after amplification of an 800 bp fragment with plasmid-specific primers, indicating that the presence of the plasmid corresponded closely to host cell viability. Similarly, Selenska and Klingmüller (1991) introduced Enterobacter agglomerans into a loamy sand soil (10 7 CFU per gram soil) and obtained signal from the inoculum after 70 days by radioactive hybridization of extracted total DNA, while viable cells were only detected for up to 63 days. A later study by Recorbet et al (1993) provided evidence that, in some cases, chromosomal DNA persists longer in soil than detectable host cell viability suggests.…”

Section: Persistence Of Dna In Soilmentioning

confidence: 99%

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Release and persistence of extracellular DNA in the environment

Nielsen

Johnsen

Bensasson

et al. 2007

Environ. Biosafety Res.

484

382

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The introduction of genetically modified organisms (GMOs) has called for an improved understanding of the fate of DNA in various environments, because extracellular DNA may also be important for transferring genetic information between individuals and species. Accumulating nucleotide sequence data suggest that acquisition of foreign DNA by horizontal gene transfer (HGT) is of considerable importance in bacterial evolution. The uptake of extracellular DNA by natural transformation is one of several ways bacteria can acquire new genetic information given sufficient size, concentration and integrity of the DNA. We review studies on the release, breakdown and persistence of bacterial and plant DNA in soil, sediment and water, with a focus on the accessibility of the extracellular nucleic acids as substrate for competent bacteria. DNA fragments often persist over time in many environments, thereby facilitating their detection and characterization. Nevertheless, the long-term physical persistence of DNA fragments of limited size observed by PCR and Southern hybridization often contrasts with the short-term availability of extracellular DNA to competent bacteria studied in microcosms. The main factors leading to breakdown of extracellular DNA are presented. There is a need for improved methods for accurately determining the degradation routes and the persistence, integrity and potential for horizontal transfer of DNA released from various organisms throughout their lifecycles.

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Section: Persistence Of Dna In Soilmentioning

confidence: 99%

“…Using in situ transformation assays to determine the accessibility of chromosomal DNA in live bacterial Equal to (Henschke et al, 1991) or longer than (Recorbet et al, 1993;Selenska and Klingmüller, 1991) the period the introduced bacterial inoculum could be detected.…”

Section: Persistence Of Dna In Soilmentioning

confidence: 99%

Release and persistence of extracellular DNA in the environment

Nielsen

Johnsen

Bensasson

et al. 2007

Environ. Biosafety Res.

484

382

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“…In a comparative study, Miller et al [42] reported that the Chelex 100 treatment had detrimental effect by decreasing the DNA yield. A rapid protocol was reported by Selenska and Klingmüller [60] based only on gentle shaking of soil slurry in a SDSsodium phosphate buffer at 70°C. Nucleic acids recovered from this "gentle procedure" were on average approximately 25 kbp.…”

Section: Cell Lysismentioning

confidence: 99%

Extraction of DNA from soil

Robe¹,

Nalin²,

Capellano³

et al. 2003

European Journal of Soil Biology

253

164

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“…et Holben et al, 1988;Porteous et al, 1991;Selenska and Klingmüller, 1991;Bruce et al, 1992;Jacobsen and Rasmussen, 1992;Smalla et al, 1993;Holben, 1994;Lovell and Piceno, 1994;Courtois et al, 2001). These are rather labor intensive protocols that work best with relatively large quantities of DNA.…”

Section: Dna Purificationmentioning

confidence: 99%

“…The most popular detergent treatment includes SDS at 1% and salt concentrations of 1 M or more, often coupled with heating and shaking (Steffan et al, 1988;Bruce et al, 1992;Herrick et al, 1993;Smalla et al, 1993;Holben, 1994;Lovell and Piceno, 1994;Moré et al, 1994;Volossiouk et al, 1995;Porteous et al, 1997;Cullen and Hirsch, 1998;Edgcomb et al, 1999). A hot-SDS lysis method was first presented by Selenska and Klingmüller (1991). A persistent problem with soil extractions is that DNA tends to adsorb to soil Extraction of Soil DNA 3 particles giving lower yields (Greaves and Wilson, 1969;Lorenz and Wackernagel, 1987;Ogram et al, 1988).…”

Section: Cell Breakagementioning

confidence: 99%

Direct Extraction of DNA from Soils for Studies in Microbial Ecology

Schneegurt

Dore²,

Kulpa³

2003

Current Issues in Molecular Biology

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Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils. These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols. Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard. Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/ or enzymic digestion with lysozyme and proteases. After typical organic extraction and alcohol precipitation, further purification is usually needed to remove inhibitory substances from the extract. The purification steps include size-exclusion chromatography, ion-exchange chromatography, silica gel spin columns, and cesium chloride gradients, among others. A direct DNA extraction protocol is described that has been shown to be effective in a wide variety of soil types. This protocol is experimentally compared to several published protocols.

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DNA recovery and direct detection of Tn5 sequences from soil

Cited by 86 publications

References 11 publications

Release and persistence of extracellular DNA in the environment

Release and persistence of extracellular DNA in the environment

Extraction of DNA from soil

Direct Extraction of DNA from Soils for Studies in Microbial Ecology

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