Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing
By Masayuki Ushio, Hiroaki Murakami, R. Masuda, T. Sado, M. Miya, S. Sakurai, H. Yamanaka, Toshifumi Minamoto, Michio Kondoh. bioRxiv, 2017
190 citations recorded by the source corpus.
Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs, and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, our method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced > 70 quantitative fish eDNA time series in our study, showing that our method could contribute to more efficient and quantitative monitoring of biodiversity.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/35c99a896ffcf1549cdae1600369e558ce21620d
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In Ecology
In Molecular Biology
- P. Møller
- E. E. Sigsgaard
- P. F. Thomsen
- Toshifumi Minamoto
- Satoshi Yamamoto
- Einar E. Nielsen
- Masayuki K. Sakata
Citations in the corpus
- Dispersion and degradation of environmental DNA from caged fish in a marine environment (2019, methodology): “Quantification in eDNA metabarcoding has recently been established by simultaneously using artificial DNA internal standards with known concentration (Ushio et al. 2018).”
- Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, background): “Nevertheless, there are studies where quantitative levels of eDNA in water samples have correlated with catch size of fish caught with traditional fishing methods in marine environments (e.g. Yamamoto et al., 2016; Thomsen et al., 2016; Ushio et al., 2017).”
- Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, unknown): “, 2012b), but more recent studies have used the 12S ribosomal rRNA locus (Hänfling et al., 2016; Kelly et al., 2014a; Port et al., 2016; Stoeckle, Soboleva, & Charlop‐Powers, 2017; Ushio et al., 2018; Yamamoto et al., 2017), and also 16S rRNA (Berry et al.”