Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance

Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water te...

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Vydáno v:PloS one Ročník 12; číslo 4; s. e0176608
Hlavní autoři: Tsuji, Satsuki, Ushio, Masayuki, Sakurai, Sho, Minamoto, Toshifumi, Yamanaka, Hiroki
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Public Library of Science 27.04.2017
Public Library of Science (PLoS)
Témata:
Abundance
Animals
Aquariums
Bacteria
Biodegradation
Biology and Life Sciences
Biomass
Carp
Carps - genetics
Cyprinus carpio
Degradation
Deoxyribonucleic acid
DNA
Earth Sciences
Ecology and Environmental Sciences
Endangered & extinct species
Environmental conditions
Environmental degradation
Environmental DNA
Environmental Monitoring - methods
Experiments
Fish
Incubation
Lakes
Linear Models
Nucleic Acid Denaturation
Osmeriformes - genetics
Reliability analysis
Research and analysis methods
Rivers
Science
Soil water
Species
Statistical models
Temperature
Temperature dependence
Temperature effects
Water - chemistry
Water Microbiology
Water quality
Water temperature
Denmark
Japan
ISSN:1932-6203, 1932-6203
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Shrnutí:Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water temperature, and the relationship between eDNA degradation and bacterial abundance. This subject has not been well clarified, even though it is essential for improving the reliability of eDNA analysis. To determine the time- and water temperature-dependent degradation of eDNA, river water was sampled and eDNA concentrations were determined for ayu sweetfish (Plecoglossus altivelis altivelis) and common carp (Cyprinus carpio) at seven time points, over a 48-h period, and at three different water temperatures. The degradation of eDNA was modeled for each species using an existing exponential decay model with an extension to include water temperature effects. The degradation models were constructed for ayu sweetfish as Nt = 229,901.2 × exp [- (0.01062 × k - 0.07081) × t] and for common carp as Nt = 2,558.0 × exp [- (0.01075 × k - 0.07372) × t]. Nt is the DNA concentration at time t (elapsed time in hours) and k is the water temperature (°C). We also measured the concentration of eDNA derived from purified genomic DNA of the common carp, which was spiked into aquarium water without the target species, and we measured the bacterial abundance in the sample water after 12 and 24 h of incubation. Environmental DNA degradation was accelerated at higher water temperatures (generalized linear model, GLM; p < 0.001), but bacterial abundance did not have a significant effect on eDNA degradation (GLM, p = 0.097). These results suggest that the proper treatment of this temperature effect in data interpretations and adjustments would increase the reliability of eDNA analysis in future studies.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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Conceptualization: ST TM HY.Formal analysis: ST MU SS.Investigation: ST.Writing – original draft: ST MU TM HY.
Competing Interests: The authors have declared that no competing interests exist.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0176608