in

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community

  • Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67 (2012).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Dornelas, M. et al. Assemblage time series reveal biodiversity change but not systematic loss. Science 344, 296–299 (2014).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Magurran, A. E. et al. Divergent biodiversity change within ecosystems. Proc. Natl. Acad. Sci. 115, 1843–1847 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Blowes, S. A. et al. Local biodiversity change reflects interactions among changing abundance, evenness, and richness. Ecology online, e3820 (2022).

  • Crowder, D. W., Northfield, T. D., Gomulkiewicz, R. & Snyder, W. E. Conserving and promoting evenness: Organic farming and fire-based wildland management as case studies. Ecology 93, 2001–2007 (2012).

    Article 

    Google Scholar 

  • Hillebrand, H., Bennett, D. M. & Cadotte, M. W. Consequences of dominance: A review of evenness effects on local and regional ecosystem processes. Ecology 89, 1510–1520 (2008).

    Article 

    Google Scholar 

  • Masuda, R. et al. Fish assemblages associated with three types of artificial reefs: density of assemblages and possible impacts on adjacent fish abundance. Fishery Bulletin, National Oceanic and Atmospheric Administration. 108, 162–173 (2010).

    Google Scholar 

  • Miyazono, S., Patiño, R. & Taylor, C. M. Desertification, salinization, and biotic homogenization in a dryland river ecosystem. Sci. Total Environ. 511, 444–453 (2015).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Yonekura, R., Kita, M. & Yuma, M. Species diversity in native fish community in Japan: Comparison between non-invaded and invaded ponds by exotic fish. Ichthyol. Res. 51, 176–179 (2004).

    Article 

    Google Scholar 

  • Evans, N. T., Shirey, P. D., Wieringa, J. G., Mahon, A. R. & Lamberti, G. A. Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing. Fisheries 42, 90–99 (2017).

    Article 

    Google Scholar 

  • Miya, M., Gotoh, R. O. & Sado, T. MiFish metabarcoding: A high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples. Fish. Sci. 86, 939–970 (2020).

    Article 
    CAS 

    Google Scholar 

  • Oka, S. et al. Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation. Environ. DNA 3, 55–69 (2021).

    Article 
    CAS 

    Google Scholar 

  • Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012).

    Article 
    CAS 

    Google Scholar 

  • Pimm, S. L. et al. Emerging technologies to conserve biodiversity. Trends Ecol. Evol. 30, 685–696 (2015).

    Article 

    Google Scholar 

  • Rourke, M. L. et al. Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys. Environ. DNA 4, 9–33 (2022).

    Article 
    CAS 

    Google Scholar 

  • Tsuji, S. et al. Real-time multiplex PCR for simultaneous detection of multiple species from environmental DNA: An application on two Japanese medaka species. Sci. Rep. 8, 1–8 (2018).

    Article 
    CAS 

    Google Scholar 

  • Kissling, W. D. et al. Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale. Biol. Rev. 93, 600–625 (2018).

    Article 

    Google Scholar 

  • Rodríguez-Ezpeleta, N. et al. Biodiversity monitoring using environmental DNA. Mol. Ecol. Resour. 21, 1405–1409 (2021).

    Article 

    Google Scholar 

  • Boivin-Delisle, D. et al. Using environmental DNA for biomonitoring of freshwater fish communities: Comparison with established gillnet surveys in a boreal hydroelectric impoundment. Environ. DNA 3, 105–120 (2021).

    Article 
    CAS 

    Google Scholar 

  • Deiner, K. et al. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol. Ecol. 26, 5872–5895 (2017).

    Article 

    Google Scholar 

  • Doi, H. et al. Compilation of real-time PCR conditions toward the standardization of environmental DNA methods. Ecol. Res. 36, 379–388 (2021).

    Article 
    CAS 

    Google Scholar 

  • Kelly, R. P. Making environmental DNA count. Mol. Ecol. Resour. 16, 10–12 (2016).

    Article 
    CAS 

    Google Scholar 

  • Kumar, G., Eble, J. E. & Gaither, M. R. A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA. Mol. Ecol. Resour. 20, 29–39 (2020).

    Article 

    Google Scholar 

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

    Article 

    Google Scholar 

  • Kuwae, M. et al. Sedimentary DNA tracks decadal-centennial changes in fish abundance. Commun. Biol. 3, 1–12 (2020).

    Article 

    Google Scholar 

  • Lynggaard, C. et al. Airborne environmental DNA for terrestrial vertebrate community monitoring. Curr. Biol. 32, 701–707.e5 (2022).

    Article 
    CAS 

    Google Scholar 

  • Tsuji, S., Takahara, T., Doi, H., Shibata, N. & Yamanaka, H. The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection. Environ. DNA 1, 99–108 (2019).

    Article 

    Google Scholar 

  • Bylemans, J., Gleeson, D. M., Duncan, R. P., Hardy, C. M. & Furlan, E. M. A performance evaluation of targeted eDNA and eDNA metabarcoding analyses for freshwater fishes. Environ. DNA 1, 402–414 (2019).

    Article 

    Google Scholar 

  • Wozney, K. M. & Wilson, C. C. Quantitative PCR multiplexes for simultaneous multispecies detection of Asian carp eDNA. J. Great Lakes Res. 43, 771–776 (2017).

    Article 
    CAS 

    Google Scholar 

  • Evans, N. T. et al. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol. Ecol. Resour. 16, 29–41 (2016).

    Article 
    CAS 

    Google Scholar 

  • Fraija-Fernández, N. et al. Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area. Ecol. Evol. 10, 7560–7584 (2020).

    Article 

    Google Scholar 

  • Kelly, R. P., Port, J. A., Yamahara, K. M. & Crowder, L. B. Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE 9, e86175 (2014).

    Article 
    ADS 

    Google Scholar 

  • Thomsen, P. F. et al. Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS ONE 11, e0165252 (2016).

    Article 

    Google Scholar 

  • Lamb, P. D. et al. How quantitative is metabarcoding: A meta-analytical approach. Mol. Ecol. 28, 420–430 (2019).

    Article 

    Google Scholar 

  • Lim, N. K. M. et al. Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities. R. Soc. Open Sci. 3, 160635 (2016).

    Article 
    ADS 

    Google Scholar 

  • Hoshino, T., Nakao, R., Doi, H. & Minamoto, T. Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Sci. Rep. 11, 4372 (2021).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Smets, W. et al. A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing. Soil Biol. Biochem. 96, 145–151 (2016).

    Article 
    CAS 

    Google Scholar 

  • Ushio, M. et al. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcod. Metagenom. 2, e23297 (2018).

    Google Scholar 

  • Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2, 150088 (2015).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Sato, M. et al. Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey. Sci. Rep. 11, 1–14 (2021).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Ushio, M. Interaction capacity as a potential driver of community diversity. Proc. R. Soc. B Biol. Sci. 289, 20212690 (2022).

    Article 

    Google Scholar 

  • Andruszkiewicz, E. A., Sassoubre, L. M. & Boehm, A. B. Persistence of marine fish environmental DNA and the influence of sunlight. PLoS ONE 12, e0185043 (2017).

    Article 

    Google Scholar 

  • Bylemans, J., Gleeson, D. M., Hardy, C. M. & Furlan, E. Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). Ecol. Evol. 8, 8697–8712 (2018).

    Article 

    Google Scholar 

  • Civade, R. et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11, e0157366 (2016).

    Article 

    Google Scholar 

  • Deiner, K., Fronhofer, E. A., Mächler, E., Walser, J.-C. & Altermatt, F. Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nat. Commun. 7, 12544 (2016).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Hänfling, B. et al. Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol. Ecol. 25, 3101–3119 (2016).

    Article 

    Google Scholar 

  • Nakagawa, H. et al. Comparing local-and regional-scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods. Freshw. Biol. 63, 569–580 (2018).

    Article 
    CAS 

    Google Scholar 

  • Sato, H., Sogo, Y., Doi, H. & Yamanaka, H. Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Sci. Rep. 7, 14860 (2017).

    Article 
    ADS 

    Google Scholar 

  • Shaw, J. L. A. et al. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol. Cons. 197, 131–138 (2016).

    Article 

    Google Scholar 

  • Valentini, A. et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol. Ecol. 25, 929–942 (2016).

    Article 
    CAS 

    Google Scholar 

  • Yamamoto, S. et al. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep. 7, 40368 (2017).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Jane, S. F. et al. Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams. Mol. Ecol. Resour. 15, 216–227 (2015).

    Article 
    CAS 

    Google Scholar 

  • Harper, L. R. et al. Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecol. Evol. 8, 6330–6341 (2018).

    Article 

    Google Scholar 

  • Nichols, R. V. et al. Minimizing polymerase biases in metabarcoding. Mol. Ecol. Resour. 18, 927–939 (2018).

    Article 
    CAS 

    Google Scholar 

  • Hosoya, K. Yamakei Handy Illustrated Book 15: Freshwater fishes of Japan (Yama-Kei Publishers, 2019).

    Google Scholar 

  • Nakabo, T. Fishes of Japan with Pictorial Keys to the Species (3-Volume Set). (Tokai University Press, 2013).

  • Goutte, A., Molbert, N., Guérin, S., Richoux, R. & Rocher, V. Monitoring freshwater fish communities in large rivers using environmental DNA metabarcoding and a long-term electrofishing survey. J. Fish Biol. 97, 444–452 (2020).

    Article 
    CAS 

    Google Scholar 

  • Barnes, M. A. & Turner, C. R. The ecology of environmental DNA and implications for conservation genetics. Conserv. Genet. 17, 1–17 (2016).

    Article 
    CAS 

    Google Scholar 

  • Collins, R. A. et al. Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol. Evol. 10, 1985–2001 (2019).

    Article 

    Google Scholar 

  • Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T. & Yamanaka, H. Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS ONE 12, e0176608 (2017).

    Article 

    Google Scholar 

  • Elbrecht, V. & Leese, F. Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass—sequence relationships with an innovative metabarcoding protocol. PLoS ONE 10, e0130324 (2015).

    Article 

    Google Scholar 

  • Nester, G. M. et al. Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environ. DNA 2, 614–626 (2020).

    Article 

    Google Scholar 

  • Piñol, J., Mir, G., Gomez-Polo, P. & Agustí, N. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol. Ecol. Resour. 15, 819–830 (2015).

    Article 

    Google Scholar 

  • Zhang, S., Zhao, J. & Yao, M. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods Ecol. Evol. 11, 1609–1625 (2020).

    Article 
    ADS 

    Google Scholar 

  • Yamanaka, H. et al. A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 18, 233–241 (2017).

    Article 
    CAS 

    Google Scholar 

  • Minamoto, T. et al. An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environ. DNA 3, 8–13 (2021).

    Article 
    CAS 

    Google Scholar 

  • Tsuji, S., Nakao, R., Saito, M., Minamoto, T. & Akamatsu, Y. Pre-centrifugation before DNA extraction mitigates extraction efficiency reduction of environmental DNA caused by the preservative solution (benzalkonium chloride) remaining in the filters. Limnology 23, 9–16 (2022).

    Article 
    CAS 

    Google Scholar 

  • R Core Team. R. A Language and Environment for Statistical Computing. (2021).

  • Venables, W. N. & Ripley, B. D. Modern Applied Statistics with S. (Springer, 2002).

  • Coulter, D. P. et al. Nonlinear relationship between Silver Carp density and their eDNA concentration in a large river. PLoS ONE 14, e0218823 (2019).

    Article 
    CAS 

    Google Scholar 

  • Doi, H. et al. Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshw. Biol. 62, 30–39 (2017).

    Article 
    CAS 

    Google Scholar 

  • Kanno, K., Onikura, N., Kurita, Y., Koyama, A. & Nakajima, J. Morphological, distributional, and genetic characteristics of Cottus pollux in the Kyushu Island, Japan: indication of fluvial and amphidromous life histories within a single lineage. Ichthyol. Res. 65, 462–470 (2018).

    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    Microparticles could help prevent vitamin A deficiency

    Energy, war, and the crisis in Ukraine