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Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment

  • United Nations. Transforming our world: the 2030 Agenda for Sustainable Development. General Assembly https://doi.org/10.5040/9781782257790.part-008 (2015).

    Article 

    Google Scholar 

  • European Commission. Directive 2000/60/EC of the European Parliament and of the Council of 23 October 2000 establishing a framework for Community action in the field of water policy. Off. J. Eur. Communities L327, 1–72 (2000).

    Google Scholar 

  • Kelly, R. P. et al. Harnessing DNA to improve environmental management. Science (80-) 344, 1455–1456 (2014).

    ADS 
    CAS 

    Google Scholar 

  • Bálint, M. et al. Cryptic biodiversity loss linked to global climate change. Nat. Clim. Chang. 1, 313–318 (2011).

    ADS 

    Google Scholar 

  • Bohmann, K. et al. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol. Evol. 29, 358–367 (2014).

    PubMed 

    Google Scholar 

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

    PubMed 

    Google Scholar 

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

    PubMed 
    PubMed Central 

    Google Scholar 

  • Yang, J., Jeppe, K., Pettigrove, V. & Zhang, X. Environmental DNA metabarcoding supporting community assessment of environmental stressors in a field-based sediment microcosm study. Environ. Sci. Technol. https://doi.org/10.1021/acs.est.8b04903 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • DiBattista, J. D. et al. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci. Rep. 10, 1–15 (2020).

    Google Scholar 

  • Ministry of the Environment. Manual for Water Quality Assessment Method by Aquatic Organisms -Japanese version of average score method-. (2017).

  • Mayama, S. Taxonomic revisions to the differentiating diatom groups for water quality evaluation and some comments for taxa with new designations. Diatom 15, 1–9 (1994).

    Google Scholar 

  • Kobayashi, H. & Mayama, S. Evaluation of river water quality by diatoms. Korean J. Phycol. 4, 121–133 (1989).

    Google Scholar 

  • European Commission. Technical Guidance Document on Risk Assessment Part II. (2003).

  • Wang, P. et al. Environmental DNA: An emerging tool in ecological assessment. Bull. Environ. Contam. Toxicol. 103, 651–656 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Zhang, X. Environmental DNA shaping a new era of ecotoxicological research. Environ. Sci. Technol. 53, 5605–5612 (2019).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Cristescu, M. E. & Hebert, P. D. N. Uses and misuses of environmental DNA in biodiversity science and conservation. Annu. Rev. Ecol. Evol. Syst. 49, 209–230 (2018).

    Google Scholar 

  • Ficetola, G. F., Taberlet, P. & Coissac, E. How to limit false positives in environmental DNA and metabarcoding?. Mol. Ecol. Resour. 16, 604–607 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Yates, M. C., Derry, A. M. & Cristescu, M. E. Environmental RNA: A revolution in ecological resolution?. Trends Ecol. Evol. 36, 601–609 (2021).

    CAS 
    PubMed 

    Google Scholar 

  • Veilleux, H. D., Misutka, M. D. & Glover, C. N. Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring. Sci. Total Environ. 782, 146891 (2021).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Cristescu, M. E. Can Environmental RNA Revolutionize Biodiversity Science?. Trends Ecol. Evol. 34, 694–697 (2019).

    PubMed 

    Google Scholar 

  • Qian, T., Shan, X., Wang, W. & Jin, X. Effects of Temperature on the Timeliness of eDNA/eRNA: A Case Study of Fenneropenaeus chinensis. Water (Switzerland) 14, 1155 (2022).

    CAS 

    Google Scholar 

  • Jo, T., Tsuri, K., Hirohara, T., Yamanaka, H. & Toshiaki Jo, C. Warm temperature and alkaline conditions accelerate environmental RNA degradation. Environ. DNA 00, 1–13 (2022).

    Google Scholar 

  • Miyata, K. et al. Fish environmental RNA enables precise ecological surveys with high positive predictivity. Ecol. Indic. 128, 107796 (2021).

    Google Scholar 

  • Littlefair, J. E., Rennie, M. D. & Cristescu, M. E. Environmental nucleic acids: a field-based comparison for monitoring freshwater habitats using eDNA and eRNA. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13671 (2022).

    Article 
    PubMed 

    Google Scholar 

  • Broman, E., Bonaglia, S., Norkko, A., Creer, S. & Nascimento, F. J. A. High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient. Mol. Ecol. https://doi.org/10.1111/mec.15561 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Miya, M. et al. Use of a filter cartridge for filtration of water samples and extraction of environmental DNA. J. Vis. Exp. https://doi.org/10.3791/54741 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Oe, S., Sashika, M., Fujimoto, A., Shimozuru, M. & Tsubota, T. Predation impacts of invasive raccoons on rare native species. Sci. Rep. 10, 1–12 (2020).

    Google Scholar 

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • MLIT (Ministry of Land Infrastructure and Transport). IV Benthic invertebrate. Manual of National Census of the River Environment (River Edition) (in Japanese). http://www.nilim.go.jp/lab/fbg/ksnkankyo/mizukokuweb/system/DownLoad/H28KK_manual_river/H28KK_02.teisei.pdf (2016).

  • Hleap, J. S., Littlefair, J. E., Steinke, D., Hebert, P. D. N. & Cristescu, M. E. Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Mol. Ecol. Resour. 21, 2190–2203 (2021).

    PubMed 

    Google Scholar 

  • Jones, E. P. et al. Guidance for end users on DNA methods development and project assessment. JNCC Report (2020).

  • Littlefair, J. E., Rennie, M. D. & Cristescu, M. E. Environmental nucleic acids: A field-based comparison for monitoring freshwater habitats using eDNA and eRNA. Mol. Ecol. Resour. 22, 2928–2940. https://doi.org/10.1111/1755-0998.13671 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • MLIT (Ministry of Land Infrastructure and Transport). River Environmental Database (in Japanese). http://www.nilim.go.jp/lab/fbg/ksnkankyo/ (2018).

  • Kitahashi, T. et al. Meiofaunal diversity at a seamount in the Pacific Ocean: A comprehensive study using environmental DNA and RNA. Deep. Res. Part I Oceanogr. Res. Pap. 160, 103253. https://doi.org/10.1016/j.dsr.2020.103253 (2020).

    Article 

    Google Scholar 

  • Brandt, M. I. et al. An assessment of environmental metabarcoding protocols aiming at favoring contemporary biodiversity in inventories of deep-sea communities. Front. Mar. Sci. 7, 234 (2020).

    Google Scholar 

  • Laroche, O. et al. A cross-taxa study using environmental DNA / RNA metabarcoding to measure biological impacts of off shore oil and gas drilling and production operations. Mar. Pollut. Bull. 127, 97–107 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • Laroche, O. et al. Metabarcoding monitoring analysis: The pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5, e3347 (2017).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Pochon, X. et al. Wanted dead or alive ? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS ONE 12, 1–19 (2017).

    Google Scholar 

  • Foley, C. J., Bradley, D. L. & Höök, T. O. A review and assessment of the potential use of RNA: DNA ratios to assess the condition of entrained fish larvae. Ecol. Indic. 60, 346–357 (2016).

    CAS 

    Google Scholar 

  • Guardiola, M. et al. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 4, 1–31 (2016).

    Google Scholar 

  • Keeley, N., Wood, S. A. & Pochon, X. Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. Ecol. Indic. 85, 1044–1057 (2018).

    CAS 

    Google Scholar 

  • Whangbo, J. S. & Hunter, C. P. Environmental RNA interference. Trends Genet. 24, 297–305 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • Sidova, M., Tomankova, S., Abaffy, P., Kubista, M. & Sindelka, R. Effects of post-mortem and physical degradation on RNA integrity and quality. Biomol. Detect. Quantif. 5, 3–9 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wood, S. A. et al. Release and degradation of environmental DNA and RNA in a marine system. Sci. Total Environ. 704, 135314 (2020).

    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Watanabe, T. Picture Book and Ecology of the Freshwater Diatoms (UCHIDA ROKAKUHO PUBLISHING CO., LTD., 2005).

    Google Scholar 

  • Laroche, O. et al. First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site. Mar. Environ. Res. 120, 225–235 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Andruszkiewicz Allan, E. et al. Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes. Environ. DNA 3, 492–514 (2021).

    Google Scholar 

  • Hajibabaei, M. et al. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14, e0225409 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • the Orthopterological Society of Japan. Orthoptera of the Japanese archipelago in color (Hokkaido University Press, 2006).

  • Li, Z. H. et al. Enzymatic alterations and RNA/DNA ratio in intestine of rainbow trout, Oncorhynchus mykiss, induced by chronic exposure to carbamazepine. Ecotoxicology 19, 872–878 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • Chícharo, M. A. & Chícharo, L. RNA:DNA ratio and other nucleic acid derived indices in marine ecology. Int. J. Mol. Sci. 9, 1453–1471 (2008).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).

    CAS 
    PubMed 

    Google Scholar 

  • Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. Identification of birds through DNA barcodes. PLoS Biol. 2, e312 (2004).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Takenaka, M., Yano, K., Suzuki, T. & Tojo, K. Development of novel PCR primer sets for DNA metabarcoding of aquatic insects, and the discovery of some cryptic species. bioRxiv https://doi.org/10.1101/2021.11.05.467390 (2021).

    Article 

    Google Scholar 

  • Elbrecht, V. et al. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ 4, 1966 (2016).

    Google Scholar 

  • Leese, F. et al. Improved freshwater macroinvertebrate detection from environmental DNA through minimized nontarget amplification. Environ. DNA 3, 261–276 (2021).

    CAS 

    Google Scholar 

  • Hajibabaei, M., Porter, T. M., Wright, M. & Rudar, J. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14, e0220953 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Elbrecht, V. et al. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 7, 7745 (2019).

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Marquina, D., Andersson, A. F. & Ronquist, F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol. Ecol. Resour. 19, 90–104 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • Tochigi prefectural government. Results of continuous monitoring and measurement [Water quality] in Japanese. https://www.pref.tochigi.lg.jp/d03/eco/kankyou/hozen/joujikanshikekka-mizu.html (2020).

  • Emilson, C. E. et al. DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient. Sci. Rep. 7, 1–11 (2017).

    CAS 

    Google Scholar 

  • Uchida, N., Kubota, K., Aita, S. & Kazama, S. Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment. PeerJ 2020, e9176 (2020).

    Google Scholar 

  • Baird, D. J. & Hajibabaei, M. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol. Ecol. 21, 2039–2044 (2012).

    PubMed 

    Google Scholar 


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