Thanks to visit codestin.com
Credit goes to link.springer.com

Skip to main content
Springer Nature Link
Log in

Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?

  • Original Article
  • Published:
The Science of Nature Aims and scope Submit manuscript

Abstract

Environmental DNA (eDNA) analysis is a promising tool for the sensitive and effective monitoring of species distribution and abundance. Traditional eDNA analysis has targeted mitochondrial DNA (mtDNA) fragments due to their abundance in cells; however, the quantification may vary depending on cell type and physiology. Conversely, some recent eDNA studies have targeted multi-copy nuclear DNA (nuDNA) fragments, such as ribosomal RNA genes, in water, and reported a higher detectability and more rapid degradation than mitochondrial eDNA (mt-eDNA). These properties suggest that nuclear eDNA (nu-eDNA) may be useful for the accurate estimation of species abundance relative to mt-eDNA, but which remains unclear. In this study, we compiled previous studies and re-analyzed the relationships between mt- and nu-eDNA concentration and species abundance by comparing the R2 values of the linear regression. We then performed an aquarium experiment using zebrafish (Danio rerio) to compare the relationships across genetic regions, including single-copy nuDNA. We found more accurate relationships between multi-copy nu-eDNA and species abundance than mt-eDNA in these datasets, although the difference was not significant upon weighted-averaging the R2 values. Moreover, we compared the decay rate constants of zebrafish eDNA across genetic regions and found that multi-copy nu-eDNA degraded faster than mt-eDNA under pH 7, implying a quick turnover of multi-copy nu-eDNA in the field. Although further empirical studies of nu-eDNA applications are necessary to support our findings, this study provides the groundwork for improving the estimation accuracy of species abundance via eDNA analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+
from £29.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Explore related subjects

Discover the latest articles, books and news in related subjects, suggested using machine learning.

Data availability

The raw data and corresponding R codes are to be uploaded to the Dryad Digital Repository upon acceptance.

References

  • Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Cook HT (2006) Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439(7078):851–855

    Article  CAS  PubMed  Google Scholar 

  • Amberg JJ, Merkes CM, Stott W, Rees CB, Erickson RA (2019) Environmental DNA as a tool to help inform zebra mussel, Dreissena polymorpha, management in inland lakes. Manag Biol Invasions 10(1):96

    Article  Google Scholar 

  • Balduzzi S, Rücker G, Schwarzer G (2019) How to perform a meta-analysis with R: a practical tutorial. Evid Based Ment Health 22(4):153–160

    Article  PubMed  Google Scholar 

  • Bylemans J, Furlan EM, Gleeson DM, Hardy CM, Duncan RP (2018) Does size matter? An experimental evaluation of the relative abundance and decay rates of aquatic environmental DNA. Environ Sci Technol 52(11):6408–6416

    Article  CAS  PubMed  Google Scholar 

  • Doi H, Uchii K, Takahara T, Matsuhashi S, Yamanaka H, Minamoto T (2015) Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS ONE 10(3):e0122763

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dugal L, Thomas L, Jensen MR, Sigsgaard EE, Simpson T, Jarman S, Meekan M (2021) Individual haplotyping of whale sharks from seawater environmental DNA. Mol Ecol Resour in press. https://doi.org/10.1111/1755-0998.13451

  • Dysthe JC, Franklin TW, McKelvey KS, Young MK, Schwartz MK (2018) An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I. PLoS ONE 13(11):e0206851

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eichmiller JJ, Miller LM, Sorensen PW (2016) Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Mol Ecol Resour 16(1):56–68

    Article  CAS  PubMed  Google Scholar 

  • Ellison SL, English CA, Burns MJ, Keer JT (2006) Routes to improving the reliability of low level DNA analysis using real-time PCR. BMC Biotechnol 6(1):1–11

    Article  CAS  Google Scholar 

  • Ernster L, Schatz G (1981) Mitochondria: a historical review. J Cell Biol 91(3):227s–255s

    Article  CAS  PubMed  Google Scholar 

  • Fediajevaite J, Priestley V, Arnold R, Savolainen V (2021) Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards. Ecol Evol 11(9):4803–4815

    Article  PubMed  PubMed Central  Google Scholar 

  • Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4(4):423–425

    Article  PubMed  PubMed Central  Google Scholar 

  • Fisher RA (1921) On the ‘probable error’ of a coefficient of correlation deduced from a small sample. Metron 1:1–32

    Google Scholar 

  • Guisan A, Thuiller W (2005) Predicting species distribution: offering more than simple habitat models. Ecol Lett 8(9):993–1009

    Article  PubMed  Google Scholar 

  • Harrison JB, Sunday JM, Rogers SM (2019) Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc R Soc B 286(1915):20191409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66(4):411–453

    Article  CAS  PubMed  Google Scholar 

  • Hirohara T, Tsuri K, Miyagawa K, Paine RT, Yamanaka H (2021) The application of PMA (Propidium Monoazide) to different target sequence lengths of zebrafish eDNA: a new approach aimed toward improving environmental DNA ecology and biological surveillance. Front Ecol Evol 9:277

    Article  Google Scholar 

  • James SA, O’Kelly MJ, Carter DM, Davey RP, Oudenaarden AV, Roberts IN (2009) Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res 19(4):626–635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jo T, Minamoto T (2021) Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses. Mol Ecol Resour 21(5):1490–1503

    Article  CAS  PubMed  Google Scholar 

  • Jo T, Yamanaka H (2022) Meta‐analyses of environmental DNA downstream transport and deposition in relation to hydrogeography in riverine environments. Freshw Biol in press. https://doi.org/10.1111/fwb.13920

  • Jo T, Arimoto M, Murakami H, Masuda R, Minamoto T (2020) Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass. Environ DNA 2(2):140–151

    Article  Google Scholar 

  • Jo T, Arimoto M, Murakami H, Masuda R, Minamoto T (2019) Particle size distribution of environmental DNA from the nuclei of marine fish. Environ Sci Technol 53(16):9947–9956

    Article  CAS  PubMed  Google Scholar 

  • Jo T, Takao K, Minamoto T (2022a) Linking the state of environmental DNA to its application for biomonitoring and stock assessment: targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes. Environ DNA 4(2):271–283

    Article  Google Scholar 

  • Jo T, Tsuri K, Hirohara T, Yamanaka H (2022b) Warm temperature and alkaline conditions accelerate environmental RNA degradation. Environ DNA in press. https://doi.org/10.1002/edn3.334

  • Kamoroff C, Goldberg CS (2018) An issue of life or death: using eDNA to detect viable individuals in wilderness restoration. Freshw Sci 37(3):685–696

    Article  Google Scholar 

  • Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Gladyshev VN (2011) Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479(7372):223–227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krulwich TA, Sachs G, Padan E (2011) Molecular aspects of bacterial pH sensing and homeostasis. Nat Rev Microbiol 9(5):330–343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuznetsova A, Brockhoff PB, Christensen RHB (2017) lmerTest Package: tests in linear mixed effects models. J Stat Softw 82(13):1–26

    Article  Google Scholar 

  • Ladell BA, Walleser LR, McCalla SG, Erickson RA, Amberg JJ (2019) Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA. Conserv Genet Resour 11(1):83–88

    Article  Google Scholar 

  • Lance RF, Klymus KE, Richter CA, Guan X, Farrington HL, Carr MR, …, Baerwaldt KL (2017). Experimental observations on the decay of environmental DNA from bighead and silver carps. Manag Biol Invasions 8(3):343-359

  • Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362(6422):709–715

    Article  CAS  PubMed  Google Scholar 

  • Magnuson MA, Andreone TL, Printz RL, Koch S, Granner DK (1989) Rat glucokinase gene: structure and regulation by insulin. Proc Natl Acad Sci 86(13):4838–4842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marshall NT, Vanderploeg HA, Chaganti SR (2021) Environmental (e) RNA advances the reliability of eDNA by predicting its age. Sci Rep 11:2769

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K (2022) The multiple states of environmental DNA and what is known about their persistence in aquatic environments. Environ Sci Technol 56(9):5322–5333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Merkes CM, McCalla SG, Jensen NR, Gaikowski MP, Amberg JJ (2014) Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS ONE 9(11):e113346

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Minamoto T, Hayami K, Sakata MK, Imamura A (2019) Real-time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: application to winter surveys. Ecol Res 34(1):237–242

    Article  CAS  Google Scholar 

  • Minamoto T, Uchii K, Takahara T, Kitayoshi T, Tsuji S, Yamanaka H, Doi H (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Mol Ecol Resour 17(2):324–333

    Article  CAS  PubMed  Google Scholar 

  • Nathans J (1999) The evolution and physiology of human color vision: insights from molecular genetic studies of visual pigments. Neuron 24(2):299–312

    Article  CAS  PubMed  Google Scholar 

  • Padan E, Bibi E, Ito M, Krulwich TA (2005) Alkaline pH homeostasis in bacteria: new insights. Biochim Biophys Acta Biomembr 1717(2):67–88

    Article  CAS  Google Scholar 

  • Panserat S, Blin C, Medale F, Plagnes-Juan E, Breque J, Krishnamoorthy J, Kaushik S (2000) Molecular cloning, tissue distribution and sequence analysis of complete glucokinase cDNAs from gilthead seabream (Sparus aurata), rainbow trout (Oncorhynchus mykiss) and common carp (Cyprinus carpio). Biochim Biophys Acta Gen Subj 1474(1):61–69

    Article  CAS  Google Scholar 

  • Piggott MP (2016) Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish. Ecol Evol 6(9):2739–2750

    Article  PubMed  PubMed Central  Google Scholar 

  • Pont D, Rocle M, Valentini A, Civade R, Jean P, Maire A, Roset N, Schabuss M, Zornig H, Dejean T (2018) Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Sci Rep 8:10361

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • R Core Team (2021) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/. Accessed 22 June 2022

  • Shogren AJ, Tank JL, Andruszkiewicz EA, Olds B, Jerde C, Bolster D (2016) Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments. J R Soc Interface 13(119):20160290

    Article  PubMed  PubMed Central  Google Scholar 

  • Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF (2020) Population-level inferences from environmental DNA—current status and future perspectives. Evol Appl 13(2):245–262

    Article  PubMed  Google Scholar 

  • Slade RW, Moritz C, Heideman A, Hale PT (1993) Rapid assessment of single-copy nuclear DNA variation in diverse species. Mol Ecol 2(6):359–373

    Article  CAS  PubMed  Google Scholar 

  • Song JW, Small MJ, Casman EA (2017) Making sense of the noise: he effect of hydrology on silver carp eDNA detection in the Chicago area waterway system. Sci Total Environ 605:713–720

    Article  PubMed  CAS  Google Scholar 

  • Stage DE, Eickbush TH (2007) Sequence variation within the rRNA gene loci of 12 Drosophila species. Genome Res 17(12):1888–1897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strickler KM, Fremier AK, Goldberg CS (2015) Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biol Conserv 183:85–92

    Article  Google Scholar 

  • Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE 8(2):e56584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z (2012) Estimation of fish biomass using environmental DNA. PLoS ONE 7(4):e35868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi S, Sakata MK, Minamoto T, Masuda R (2020) Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish. PLoS ONE 15(4):e0231718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi S, Takada S, Yamanaka H, Masuda R, Kasai A (2021) Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel. PLoS ONE 16(9):e0255576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7(8):e41732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torti A, Lever MA, Jørgensen BB (2015) Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 24:185–196

    Article  PubMed  Google Scholar 

  • Turner CR, Barnes MA, Xu CC, Jones SE, Jerde CL, Lodge DM (2014) Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol Evol 5(7):676–684

    Article  Google Scholar 

  • Vandal OH, Nathan CF, Ehrt S (2009) Acid resistance in Mycobacterium tuberculosis. J Bacteriol 191(15):4714–4721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei N, Nakajima F, Tobino T (2018) A microcosm study of surface sediment environmental DNA: decay observation, abundance estimation, and fragment length comparison. Environ Sci Technol 52(21):12428–12435

    Article  CAS  PubMed  Google Scholar 

  • Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE 8(3):e59520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamanaka H, Minamoto T (2016) The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecol Ind 62:147–153

    Article  CAS  Google Scholar 

  • Yamanaka H, Minamoto T, Matsuura J, Sakurai S, Tsuji S, Motozawa H, Kondo A (2017) A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 18(2):233–241

    Article  CAS  Google Scholar 

  • Yates MC, Fraser DJ, Derry AM (2019) Meta-analysis supports further refinement of eDNA for monitoring aquatic species-specific abundance in nature. Environ DNA 1(1):5–13

    Article  Google Scholar 

Download references

Acknowledgements

We thank Drs. Toshifumi Minamoto (Kobe University) and Teruhiko Takahara (Shimane University) for providing the raw data of eDNA quantification and species abundance in Minamoto et al. (2017). We also thank Crimson Interactive Japan Co., Ltd. (www.enago.jp) for English proofreading. We further thank the two anonymous reviewers and an editor who provided thoughtful advice to improve the manuscript.

Funding

This work was supported by the Grant-in-Aid for JSPS Research Fellows (Grant Numbers JP22J00439), the Environment Research and Technology Development Fund from the Ministry of the Environment, Japan (Grant Number JPMEERF20204004), the Grant-in-Aid for Scientific Research of JSPS KAKENHI (Grant Number JP20H03326), and partly by the Fund for the Promotion of Joint International Research of JSPS KAKENHI (Grant Number JP19KK0189).

Author information

Authors and Affiliations

  1. Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan

    Toshiaki S. Jo & Hiroki Yamanaka

  2. Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan

    Toshiaki S. Jo & Hiroki Yamanaka

  3. Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan

    Toshiaki S. Jo

  4. Graduate School of Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan

    Kenji Tsuri

Authors
  1. Toshiaki S. Jo
    View author publications

    Search author on:PubMed Google Scholar

  2. Kenji Tsuri
    View author publications

    Search author on:PubMed Google Scholar

  3. Hiroki Yamanaka
    View author publications

    Search author on:PubMed Google Scholar

Contributions

T.S.J. and H.Y. conceived the study. T.S.J. and K.T. performed aquarium experiments. T.S.J. compiled the datasets in previous studies, analyzed the data, and wrote the first draft of the manuscript. All authors edited and provided feedback on the manuscript.

Corresponding author

Correspondence to Toshiaki S. Jo.

Ethics declarations

Competing interest

The authors declare no competing interests.

Additional information

Communicated by: Matthias Waltert

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jo, T.S., Tsuri, K. & Yamanaka, H. Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?. Sci Nat 109, 38 (2022). https://doi.org/10.1007/s00114-022-01808-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00114-022-01808-7

Keywords