Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples

@article{Tsuji2016EffectsOW,
  title={Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples},
  author={Satsuki Tsuji and Hiroki Yamanaka and Toshifumi Minamoto},
  journal={Limnology},
  year={2016},
  volume={18},
  pages={1-7}
}
Environmental DNA (eDNA) analysis has recently been applied to the study of aquatic macroorganisms. In most studies, sample water was filtered and the extracted DNA from the residues on the filter used for the following molecular analysis to detect species of interest. This quick, new biomonitoring method has received broad attention, but some unknowns remain, such as the eDNA yield in relation to water quality. Previous studies suggest that eDNA is composed of various forms, such as the free… 

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References

SHOWING 1-10 OF 39 REFERENCES

Filtration recovery of extracellular DNA from environmental water samples.

TLDR
Potential differences in qPCR data from filtered waters characterized with low pH and high TSS and ionic strength should be considered in pollution assessments.

Concentration and susceptibility of dissolved DNA for enzyme degradation in lake watersome methodological remarks

TLDR
Concentrations of enzymatically hydrolysable DNA determined by the enzymatic method were 27 to 54 % lower than those measured by CTAB-DNA precipitation and DAPI staining and correlated positively with algal pigment concentrations and bacterial numbers.

Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction

TLDR
It is proposed that the appropriate selection method for eDNA analysis should be chosen based on context, when a high concentration of the target DNA is expected, such as in an aquarium experiment, ethanol precipitation is advantageous; however, when the targetDNA is rare, filtration followed by freezing or DNA fixation by ethanol and phenol treatment are recommended.

Use of environmental DNA to survey the distribution of an invasive submerged plant in ponds

TLDR
This work established an eDNA detection method for Egeria densa, an invasive aquatic plant species in Japan; used e DNA detection to survey the species in aquaria; and applied this method to water samples from 23 outdoor ponds, confirming that detection of aquatic plants by eDNA analysis is feasible.

Viral contribution to dissolved DNA in the marine environment as determined by differential centrifugation and kingdom probing

TLDR
Dissolved DNA concentrated by vortex flow filtration from offshore and coastal environments to differential centrifugation and probing with 16S rRNA-targeted kingdom oligonucleotide probes indicate that DNA in viral particles is a small component of the dissolved DNA, the majority being of eubacterial and eucaryotic origin.

Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds

TLDR
The eDNA method simply and rapidly detects the presence of the invasive bluegill sunfish with less disturbance to the environment during field surveys than traditional methods.

Persistence of Environmental DNA in Freshwater Ecosystems

TLDR
Improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems and to greatly influence planning of biodiversity inventories and biosecurity surveys.

Species detection using environmental DNA from water samples

TLDR
A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.

Estimation of Fish Biomass Using Environmental DNA

TLDR
An eDNA method to estimate the biomass of common carp using laboratory and field experiments and demonstrates that the distribution of carp eDNA concentration was explained by water temperature, suggesting that biomass data estimated from e DNA concentration reflects the potential distribution ofCommon carp in the natural environment.