Open Access
Issue |
BIO Web Conf.
Volume 147, 2024
11th International Symposium of East Asia Fisheries and Technologist Association (EAFTA 2024)
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Article Number | 01013 | |
Number of page(s) | 19 | |
DOI | https://doi.org/10.1051/bioconf/202414701013 | |
Published online | 10 January 2025 |
- K. Bohmann, A. Evans, M. T. P. Gilbert, G. R. Carvalho, S. Creer, M. Knapp, D. W. Yu, and M. de Bruyn, Environmental DNA for wildlife biology and biodiversity monitoring, Trends Ecol Evol (2014). https://doi.org/10.1016/j.tree.2014.04.003 [Google Scholar]
- H. Ma, K. Stewart, S. Lougheed, J. Zheng, Y. Wang, and J. Zhao, Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal, Conserv Genet Resour 8, 561 (2016). https://doi.org/10.1007/s12686-016-0597-9 [CrossRef] [Google Scholar]
- L. E. Ogden, The Emergence of eDNA, Bioscience 72, 5 (2022). https://doi.org/10.1093/biosci/biab120 [CrossRef] [PubMed] [Google Scholar]
- D. M. Grant, O. B. Brodnicke, A. M. Evankow, A. O. Ferreira, J. T. Fontes, A. K. Hansen, M. R. Jensen, T. E. Kalaycı, A. Leeper, S. K. Patil, S. Prati, A. Reunamo, A. J. Roberts, R. Shigdel, V. Tyukosova, M. Bendiksby, R. Blaalid, F. O. Costa, P. M. Hollingsworth, E. Stur, and T. Ekrem, The future of dna barcoding: Reflections from early career researchers, Diversity (Basel) 13 (2021) [Google Scholar]
- C. Varela, DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters, J. Crust. Biol 41 (2021). https://doi.org/10.1093/jcbiol/ruab005 [CrossRef] [Google Scholar]
- S. Antil, J. S. Abraham, S. Sripoorna, S. Maurya, J. Dagar, S. Makhija, P. Bhagat, R. Gupta, U. Sood, R. Lal, and R. Toteja, DNA barcoding, an effective tool for species identification: a review, Mol Biol Rep 50, 761 (2023). https://doi.org/10.1007/s11033-022-08015-7 [CrossRef] [PubMed] [Google Scholar]
- T. J. R. Fernandes, J. S. Amaral, and I. Mafra, DNA barcode markers applied to seafood authentication: an updated review, Crit Rev Food Sci Nutr 61, 3904 (2021). https://doi.org/10.1080/10408398.2020.1811200 [CrossRef] [PubMed] [Google Scholar]
- G. E. Forrester, M. T. Mccaffrey, K. X. Terpis, and C. E. Lane, Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida), Zootaxa 5048, 99 (2021). https://doi.org/10.11646/zootaxa.5048.1.5 [CrossRef] [PubMed] [Google Scholar]
- M. R. Gostel and W. J. Kress, The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation, Diversity (Basel) 14, 213 (2022). https://doi.org/10.3390/d14030213 [CrossRef] [Google Scholar]
- K. C. Beng and R. T. Corlett, Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects, Biodivers Conserv 29, 2089 (2020). https://doi.org/10.1007/s10531-020-01980-0 [CrossRef] [Google Scholar]
- E. Capo, G. Spong, H. Königsson, and P. Byström, Effects of filtration methods and water volume on the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) eDNA concentrations via droplet digital PCR, Environmental DNA 2, 152 (2020). https://doi.org/10.1002/edn3.52 [CrossRef] [Google Scholar]
- T. M. Sanches and A. D. Schreier, Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time, PLoS One 15, e0233522 (2020). https://doi.org/10.1371/journal.pone.0233522 [CrossRef] [PubMed] [Google Scholar]
- H. C. Rees, B. C. Maddison, D. J. Middleditch, J. R. M. Patmore, and K. C. Gough, The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology, (2014). https://doi.org/10.1111/1365-2664.12306 [Google Scholar]
- U. von Ammon, X. Pochon, P. Casanovas, B. Trochel, M. Zirngibl, A. Thomas, J. Witting, P. Joyce, and A. Zaiko, Net overboard: Comparing marine <scp>eDNA</scp> sampling methodologies at sea to unravel marine biodiversity, Mol Ecol Resour 23, 440 (2023). https://doi.org/10.1111/1755-0998.13722 [CrossRef] [PubMed] [Google Scholar]
- K. M. Ruppert, R. J. Kline, and M. S. Rahman, Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA, Glob Ecol Conserv 17, e00547 (2019). https://doi.org/10.1016/j.gecco.2019.e00547 [Google Scholar]
- G.-J. Jeunen, S. Mills, S. Mariani, J. Treece, S. Ferreira, J.-A. L. Stanton, B. Durán- Vinet, Duffy G. A., Gemmell N. J., and M. Lamare, Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel’s continuous pump underway seawater systems, Science of The Total Environment 946, 174354 (2024). https://doi.org/10.1016/j.scitotenv.2024.174354 [CrossRef] [Google Scholar]
- V. G. Fonseca, P. I. Davison, V. Creach, D. Stone, D. Bass, and H. J. Tidbury, The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations, Diversity (Basel) 15, 631 (2023). https://doi.org/10.3390/d15050631 [CrossRef] [Google Scholar]
- L. E. Holman, Y. Chng, and M. Rius, How does eDNA decay affect metabarcoding experiments?, Environmental DNA 4, 108 (2022). https://doi.org/10.1002/edn3.201 [CrossRef] [Google Scholar]
- A. M. Danziger, Z. H. Olson, and M. Frederich, Limitations of eDNA analysis for Carcinus maenas abundance estimations, BMC Ecol Evol 22, 14 (2022). https://doi.org/10.1186/s12862-022-01969-z [CrossRef] [PubMed] [Google Scholar]
- M. S. Rappé, P. F. Kemp, and S. J. Giovannoni, Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina, Limnol Oceanogr 42, 811 (1997). https://doi.org/10.4319/lo.1997.42.5.0811 [CrossRef] [Google Scholar]
- A. Sahu, N. Kumar, C. Pal Singh, and M. Singh, Environmental DNA (eDNA): Powerful technique for biodiversity conservation, J Nat Conserv 71, 126325 (2023). https://doi.org/10.1016/j.jnc.2022.126325 [CrossRef] [Google Scholar]
- P. Bhadury, M. Austen, D. Bilton, P. Lambshead, A. Rogers, and G. Smerdon, Molecular detection of marine nematodes from environmental samples: overcoming eukaryotic interference, Aquatic Microbial Ecology 44, 97 (2006). https://doi.org/10.3354/ame044097 [CrossRef] [Google Scholar]
- T. Nagahama, E. Takahashi, Y. Nagano, M. A. Abdel‐Wahab, and M. Miyazaki, Molecular evidence that deep‐branching fungi are major fungal components in deep‐ sea methane cold‐seep sediments, Environ Microbiol 13, 2359 (2011). https://doi.org/10.1111/j.1462-2920.2011.02507.x [CrossRef] [PubMed] [Google Scholar]
- P. F. Thomsen, J. Kielgast, L. L. Iversen, P. R. Møller, M. Rasmussen, and E. Willerslev, Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples, PLoS One 7, e41732 (2012). https://doi.org/10.1371/journal.pone.0041732 [CrossRef] [PubMed] [Google Scholar]
- A. D. Foote, P. F. Thomsen, S. Sveegaard, M. Wahlberg, J. Kielgast, L. A. Kyhn, A. B. Salling, A. Galatius, L. Orlando, and M. T. P. Gilbert, Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals, PLoS One 7, e41781 (2012). https://doi.org/10.1371/journal.pone.0041781 [CrossRef] [PubMed] [Google Scholar]
- F. Lejzerowicz, P. Esling, L. Pillet, T. A. Wilding, K. D. Black, and J. Pawlowski, High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems, Sci Rep 5, 13932 (2015). https://doi.org/10.1038/srep13932 [CrossRef] [PubMed] [Google Scholar]
- P. K. Nichols and P. B. Marko, Rapid assessment of coral cover from environmental DNA in Hawai’i, Environmental DNA 1, 40 (2019). https://doi.org/10.1002/edn3.8 [CrossRef] [Google Scholar]
- E. Andruszkiewicz Allan, W. G. Zhang, A. C. Lavery, and A. F. Govindarajan, Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes, Environmental DNA 3, 492 (2021). https://doi.org/10.1002/edn3.141 [CrossRef] [Google Scholar]
- L. M. Gargan, T. Morato, C. K. Pham, J. A. Finarelli, J. E. L. Carlsson, and J. Carlsson, Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts, Mar Biol 164, 112 (2017). https://doi.org/10.1007/s00227-017-3141-x [CrossRef] [Google Scholar]
- K. Deiner, H. M. Bik, E. Mächler, M. Seymour, A. Lacoursière‐Roussel, F. Altermatt, S. Creer, I. Bista, D. M. Lodge, N. de Vere, M. E. Pfrender, and L. Bernatchez, Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Mol Ecol 26, 5872 (2017). https://doi.org/10.1111/mec.14350 [CrossRef] [PubMed] [Google Scholar]
- J. Bakker, O. S. Wangensteen, D. D. Chapman, G. Boussarie, D. Buddo, T. L. Guttridge, H. Hertler, D. Mouillot, L. Vigliola, and S. Mariani, Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact, Sci Rep 7, 16886 (2017). https://doi.org/10.1038/s41598-017-17150-2 [CrossRef] [PubMed] [Google Scholar]
- R. A. Collins, O. S. Wangensteen, E. J. O’Gorman, S. Mariani, D. W. Sims, and M. J. Genner, Persistence of environmental DNA in marine systems, Commun Biol 1, 185 (2018). https://doi.org/10.1038/s42003-018-0192-6 [CrossRef] [PubMed] [Google Scholar]
- M. Miya, Y. Sato, T. Fukunaga, T. Sado, J. Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh, and W. Iwasaki, 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). https://doi.org/10.1098/rsos.150088 [CrossRef] [PubMed] [Google Scholar]
- K. W. A. Masengi, I. F. Mandagi, L. Manu, F. Silooy, I. L. Labaro, A. W. R. Masengi, N. Sebua, E. I. K. G. Masengi, B. Pinontoan, Y. Hutabarat, F. Hukom, M. Iwata, Y. Abe, Y. Sato, R. Kimura, and K. Yamahira, Study on existence of the fisheries resources abundance by using environmental deoxyribonucleic acid (e-DNA) approach at fishing grounds in the Sulawesi Sea, Indonesia, IOP Conf Ser Mater Sci Eng 567, 012026 (2019). https://doi.org/10.1088/1757-899X/567/1/012026 [CrossRef] [Google Scholar]
- S. Andriyono, J. Alam, and H.-W. Kim, Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia, Biodiversitas 20 (2019). https://doi.org/10.13057/biodiv/d201241 [Google Scholar]
- E. R. E. Gelis, M. M. Kamal, B. Subhan, I. Bachtiar, L. M. I. Sani, and H. Madduppa, Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle, Environ Biol Fishes 104, 887 (2021). https://doi.org/10.1007/s10641-021-01118-3 [CrossRef] [Google Scholar]
- H. Madduppa, N. K. D. Cahyani, A. W. Anggoro, B. Subhan, E. Jefri, L. M. I. Sani, D. Arafat, N. Akbar, and D. G. Bengen, eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs, Biodivers Conserv 30, 3087 (2021). https://doi.org/10.1007/s10531-021-02237-0 [CrossRef] [Google Scholar]
- L. Mathon, V. Marques, D. Mouillot, C. Albouy, M. Andrello, F. Baletaud, G. H. Borrero-Pérez, T. Dejean, G. J. Edgar, J. Grondin, P.-E. Guerin, R. Hocdé, J.-B. Juhel, Kadarusman, E., G. Mariani, M. McLean, A.F. Polanco, L. Pouyaud, R. D. Stuart-Smith, H. Y. Sugeha, A. Valentini, L. Vigliola, I. B. Vimono, L. Pellissier, and S. Manel, Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding, Proceedings of the Royal Society B: Biological Sciences 289 (2022). https://doi.org/10.1098/rspb.2022.0162 [CrossRef] [Google Scholar]
- J. Juhel, V. Marques, R. S. Utama, I. B. Vimono, H. Y. Sugeha, K. Kadarusman, C. Cochet, T. Dejean, A. Hoey, D. Mouillot, R. Hocdé, and L. Pouyaud, Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions, Ecography 2022 (2022). https://doi.org/10.1111/ecog.06299 [CrossRef] [PubMed] [Google Scholar]
- J.-B. Juhel, R. S. Utama, V. Marques, I. B. Vimono, H. Y. Sugeha, Kadarusman L., T. Dejean, D. Mouillot, and R. Hocdé, Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle, Proceedings of the Royal Society B: Biological Sciences 287, 20200248 (2020). https://doi.org/10.1098/rspb.2020.0248 [CrossRef] [PubMed] [Google Scholar]
- A. M. Moore, J. Jompa, A. Citra, M. A. R. Tassakka, I. Yasir, S. Ndobe, W. Umar, Z. Gold, and P. H. Barber, Sharks and rays (Chondrichthyes) around Banggai Island, Banggai MPA, Indonesia: biodiversity data from an environmental DNA pilot study, (2021).at http://www.bioflux.com.ro/aacl [Google Scholar]
- M. Sato, N. Inoue, R. Nambu, N. Furuichi, T. Imaizumi, and M. Ushio, Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey, Sci Rep 11, 19477 (2021). https://doi.org/10.1038/s41598-021-98926-5 [CrossRef] [PubMed] [Google Scholar]
- N. Levy, N. Simon-Blecher, S. Ben-Ezra, M. Yuval, T. Doniger, M. Leray, S. Karako-Lampert, E. Tarazi, and O. Levy, Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding, Science of The Total Environment 856, 159051 (2023). https://doi.org/10.1016/j.scitotenv.2022.159051 [CrossRef] [Google Scholar]
- A. Djurhuus, C. J. Closek, R. P. Kelly, K. J. Pitz, R. P. Michisaki, H. A. Starks, K. R. Walz, E. A. Andruszkiewicz, E. Olesin, K. Hubbard, E. Montes, D. Otis, F. E. Muller-Karger, F. P. Chavez, A. B. Boehm, and M. Breitbart, Environmental DNA reveals seasonal shifts and potential interactions in a marine community, Nat Commun 11, 254 (2020). https://doi.org/10.1038/s41467-019-14105-1 [CrossRef] [PubMed] [Google Scholar]
- M. Y. Stoeckle, J. Adolf, Z. Charlop-Powers, K. J. Dunton, G. Hinks, and S. M. VanMorter, Trawl and eDNA assessment of marine fish diversity, seasonality, and relative abundance in coastal New Jersey, USA, ICES Journal of Marine Science 78, 293 (2021). https://doi.org/10.1093/icesjms/fsaa225 [Google Scholar]
- I. Salter, Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation, PLoS One 13, e0192409 (2018). https://doi.org/10.1371/journal.pone.0192409 [CrossRef] [PubMed] [Google Scholar]
- M. Greco, F. Lejzerowicz, E. Reo, A. Caruso, A. Maccotta, R. Coccioni, J. Pawlowski, and F. Frontalini, Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test, Chemosphere 298, 134239 (2022). https://doi.org/10.1016/j.chemosphere.2022.134239 [CrossRef] [PubMed] [Google Scholar]
- S. Jarman, F. Ackermann, M. Marnane, O. Berry, M. Bunce, K. Dawkins, E. Furlan, S. Lukehurst, J. McDonald, X. Pochon, S. Wilkinson, A. Zaiko, and E. Harvey, Research horizons for invasive marine species detection with eDNA/eRNA, Biol Invasions 26, 3715 (2024). https://doi.org/10.1007/s10530-024-03406-2 [CrossRef] [Google Scholar]
- H. Bowers, X. Pochon, U. von Ammon, N. Gemmell, J.-A. Stanton, G.-J. Jeunen, C. Sherman, and A. Zaiko, Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance, Water (Basel) 13, 1113 (2021). https://doi.org/10.3390/w13081113 [Google Scholar]
- E. Valsecchi, J. Bylemans, S. J. Goodman, R. Lombardi, I. Carr, L. Castellano, A. Galimberti, and P. Galli, Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates, Environmental DNA 2, 460 (2020). https://doi.org/10.1002/edn3.72 [CrossRef] [Google Scholar]
- C. Yang, Y. Du, X. Zeng, and G. Ni, Development and Testing of Species-Specific Primers for Detecting the Presence of the Northern Pacific Sea Star (Asterias amurensis) from Environmental DNA, Marine Biotechnology 26, 215 (2024). https://doi.org/10.1007/s10126-024-10292-1 [CrossRef] [PubMed] [Google Scholar]
- J. R. Freeland, The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA, Genome 60, 358 (2017). https://doi.org/10.1139/gen-2016-0100 [CrossRef] [PubMed] [Google Scholar]
- S. L. T. Kwong, C. Villacorta-Rath, J. Doyle, and S. Uthicke, Quantifying shedding and degradation rates of environmental DNA (eDNA) from Pacific crown-of-thorns seastar (Acanthaster cf. solaris), Mar Biol 168, 85 (2021). https://doi.org/10.1007/s00227-021-03896-x [CrossRef] [Google Scholar]
- K. C. Morey, T. J. Bartley, and R. H. Hanner, Validating environmental DNA metabarcoding for marine fishes in diverse ecosystems using a public aquarium, Environmental DNA 2, 330 (2020). https://doi.org/10.1002/edn3.76 [CrossRef] [Google Scholar]
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