Environmental DNA metabarcoding: an approach for biodiversity monitoring

Authors

  • Padilla-García Padilla-García Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Conservation Medicine Laboratory, boulevard del maestro s/n esquina Elías Piña, col. Narciso Mendoza, Reynosa, Tamaulipas México. C. P. 88710.
  • Fátima Yedith Camacho-Sánchez Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Conservation Medicine Laboratory, boulevard del maestro s/n esquina Elías Piña, col. Narciso Mendoza, Reynosa, Tamaulipas México. C. P. 88710. https://orcid.org/0000-0001-5557-2565
  • Miguel Ángel Reyes-López Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Conservation Medicine Laboratory, boulevard del maestro s/n esquina Elías Piña, col. Narciso Mendoza, Reynosa, Tamaulipas México. C. P. 88710. https://orcid.org/0000-0001-9939-3032

DOI:

https://doi.org/10.29059/cienciauat.v16i1.1509

Keywords:

eDNA, biodiversity, PCR, sequencing

Abstract

Environmental deoxyribonucleic acid or environmental DNA (eDNA) is a term coined to define the deoxyribonucleic acid (DNA) that can be recovered or detected in an environment (for example: soil, air, or water) sample, but not specimen physically present (metagenome). The objective of this review was to understand, analyze, and define the uses, applications, and potential of eDNA. eDNA brings together several fields ranging from ecological assessment for historical community reconstruction, ecosystem restoration to human health, making it extremely versatile and important for the future in research, such as studies of conservation, taxonomic, or phylogenetic reconstruction. To achieve this, the metabarcoding procedure is used, which is based on obtaining DNA of any origin (in this case eDNA), in the physical absence or not of organisms, with the polymerase chain reaction (PCR), to finally sequence them and develop barcodes. The application of eDNA in biological research seems almost limitless, but it requires collaboration and coordination of scientific teams. eDNA studies will probably become an essential tool for different scientific tasks not only in monitoring biodiversity, but also in human health analysis or in the development of DNA barcodes.

References

Adams, C. I., Knapp, M., Gemmell, N. J., Jeunen, G. J., Bunce, M., Lamare, M. D., and Taylor, H. R. (2019). Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes. 10(3): 192. DOI: https://doi.org/10.3390/genes10030192

Andruszkiewicz, E. A., Sassoubre, L. M., and Boehm, A. B. (2017a). Persistence of marine fish environmental DNA and the influence of sunlight. PLoS One. 12(9). DOI: https://doi.org/10.1371/journal.pone.0185043

Andruszkiewicz, E. A., Starks, H. A., Chavez, F. P., Sassoubre, L. M., Block, B. A., and Boehm, A. B. (2017b). Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS One. 12(4): e0176343. DOI: https://doi.org/10.1371/journal.pone.0176343

Austin, B. (2017). The value of cultures to modern microbiology. Antonie Van Leeuwenhoek. 110(10): 1247-1256. Banchi, E., Ametrano, C. G., Stanković, D., Verardo, P., Moretti, O., Gabrielli, F., …, and Muggia, L. (2018). DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy. PLoS One. 13: e0194489. DOI: https://doi.org/10.1371/journal.pone.0194489

Baker, C. S., Steel, D., Nieukirk, S., and Klinck, H. (2018). Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science. 5: 1-11. DOI: https://doi.org/10.3389/fmars.2018.00133

Barnes, M. A. and Turner, C. R. (2016). The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics. 17(1): 1-17. DOI: https://doi.org/10.1007/s10592-015-0775-4

Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2013). GenBank. Nucleic Acids Research. 41(D1): D36-D42. DOI: https://doi.org/10.1093/nar/gks1195

Bortolus, A. (2008). Error cascades in the biological sciences: The unwanted consequences of using bad taxonomy in ecology. AMBIO: A Journal of the Human Environment. 37(2): 114-118. DOI: https://doi.org/10.1579/0044-7447(2008)37[114:ECITBS]2.0.CO;2

Boyer, F., Mercier, C., Bonin, A., Le-Bras, Y., Taberlet, P., and Coissac, E. (2016). Obitools: a unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources. 16(1): 176-182. DOI: https://doi.org/10.1111/1755-0998.12428

Buxton, A. S., Groombridge, J. J., and Griffiths, R. A. (2018). Seasonal variation in environmental DNA detection in sediment and water samples. PLoS One. 13(1): 1-14. DOI: https://doi.org/10.1371/journal.pone.0191737

Bylemans, J., Gleeson, D. M., Hardy, C. M., and Furlan, E. (2018). Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). Ecology and Evolution. 8(17): 8697-8712. DOI: https://doi.org/10.1002/ece3.4387

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J., and Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods. 13(7): 581-583. DOI: https://doi.org/10.1038/nmeth.3869

Cao, C., Jiang, W., Wang, B., Fang, J., Lang, J., Tian, G., …, and Zhu, T. F. (2014). Inhalable microorganisms in Beijing’s PM2.5 and PM10 pollutants during a severe smog event. Environmental Science & Technology. 48(3): 1499-1507. DOI: https://doi.org/10.1021/es4048472

Cowart, D. A., Murphy, K. R., and Cheng, C. H. C. (2018). Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. Marine Genomics. 37: 148-160. DOI: https://doi.org/10.1016/j.margen.2017.11.003

Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W., …, and Bik, H. (2016). The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution. 7(9): 1008-1018. DOI: https://doi.org/10.1111/2041-210X.12574

Deiner, K., Bik, H. M., Mächler, E., Seymour, M., Lacoursière-Roussel, A., Altermatt, F., …, and Bernatchez, L. (2017). Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology. 26(21): 5872-5895. DOI: https://doi.org/10.1111/mec.14350

Deiner, K., Fronhofer, E. A., Mächler, E., Walser, J. C., and Altermatt, F. (2016). Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nature Communications. 7(1): 1-9. DOI: https://doi.org/10.1038/ncomms12544

Díaz-Ferguson, E. E. and Moyer, G. R. (2014). History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. Revista de Biología Tropical. 62(4): 1273-1284. DOI: https://doi.org/10.15517/rbt.v62i4.13231

DOF, Diario Oficial de la Federación (2020). Ley de Aguas Nacionales. [En línea]. Disponible en: http://www.diputados.gob.mx/LeyesBiblio/pdf/16_060120.pdf. Fecha de consulta: 10 de junio de 2021.

Doi, H., Uchii, K., Takahara, T., Matsuhashi, S., Yamanaka, H., and Minamoto, T. (2015). Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS One. 10(3): e0122763. DOI: https://doi.org/10.1371/journal.pone.0122763

Dougherty, M. M., Larson, E. R., Renshaw, M. A., Gantz, C. A., Egan, S. P., Erickson, D. M., and Lodge, D. M. (2016). Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances. Journal of Applied Ecology. 53(3): 722-732. DOI: https://doi.org/10.1111/1365-2664.12621

Epp, L. S., Boessenkool, S., Bellemain, E. P., Haile, J., Esposito, A., Riaz, T., …, and Brochmann, C. (2012). New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology. 21: 1821-1833. DOI: https://doi.org/10.1111/j.1365-294X.2012.05537.x

Evans, N. T., Olds, B. P., Renshaw, M. A., Turner, C. R., Li, Y., Jerde, C. L., ..., and Lodge, D. M. (2016). Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources. 16(1): 29-41. DOI: https://doi.org/10.1111/1755-0998.12433

Ficetola, G. F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessière, J., ..., and Pompanon, F. (2010). An in silico approach for the evaluation of DNA barcodes. BMC Genomics: 11(1): 434. DOI: https://doi.org/10.1186/1471-2164-11-434

Ficetola, G. F., Miaud, C., Pompanon, F., and Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters. 4(4): 423-425. DOI: https://doi.org/10.1098/rsbl.2008.0118

Gibson, J. F., Shokralla, S, Curry, C., Baird, D. J., Monk, W. A., King, I., and Hajibabaei, M. (2015). Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing. PLoS One. 10(10): e0138432. DOI: https://doi.org/10.1371/journal.pone.0138432

Green, M. R. and Sambrook, J. (2017). Isolation of High-Molecular-Weight DNA Using Organic Solvents. Cold Spring Harb Protoc. (4): pdb.prot093450. DOI: https://doi.org/10.1101/pdb.prot093450

Hänfling, B., Handley, L. L., Read, D. S., Hahn, C., Li, J., Nichols, P., …, and Winfield, I. J. (2016). Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular Ecology. 25(13): 3101-3119. DOI: https://doi.org/10.1111/mec.13660

Hering, D., Borja, A., Jones, J. I., Pont, D., Boets, P., Bouchez, A., …, and Kelly, M. (2018). Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research. 138: 192-205. DOI: https://doi.org/10.1016/j.watres.2018.03.003

Hernández-González, J., Inza, I., and Lozano, J. A. (2016). Weak supervision and other non-standard classification problems: A taxonomy. Pattern Recognition Letters. 69: 49-55. DOI: https://doi.org/10.1016/j.patrec.2015.10.008

Ivanova, N., Valdez-Moreno, M., and Elias-Gutierrez, M. (2019). Resident or Invasive Species? Environmental DNA Can Provide Reliable Answers. IBOL Barcode Bulletin. 9(1): 9-11. DOI: https://doi.org/10.21083/ibol.v9i1.5474

Kraaijeveld, K., de-Weger, L. A., Ventayol-García, M., Buermans, H., Frank, J., Hiemstra, P. S., and den-Dunnen, J. T. (2015). Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing. Molecular Ecology Resources. 15(1): 8-16. DOI: https://doi.org/10.1111/1755-0998.12288

Koch, J., Gantenbein, S., Masania, K. Stark, W. J., Erlich, Y., and Grass, R. N. (2020). A DNA-of-things storage architecture to create materials with embedded memory. Nature Biotechnology. 38(1): 39-43. DOI: https://doi.org/10.1038/s41587-019-0356-z

Koslowski, M., Moran, D., Tisserant, A., Verones, F., and Wood, R. (2020). Quantifying Europe’s biodiversity foot-prints and the role of urbanization and income. Global Sustainability. 3: E1. DOI: https://doi.org/10.1017/sus.2019.23

Lacoursière-Roussel, A., Dubois, Y., Normandeau, E., and Bernatchez, L. (2016). Improving herpetological surveys in eastern North America using the environmental DNA method1. Genome. 59(11): 991-1007. DOI: https://doi.org/10.1139/gen-2015-0218

Liu, Q., Zhang, Y., Wu, H., Liu, F., Peng, W., Zhang, X., ..., and Zhang, H. (2020). A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Fresh-water and Marine Ecosystems. Microorganisms. 8(3): 417. DOI: https://doi.org/10.3390/microorganisms8030417

Macher, T. H., Beermann, A. J., and Leese, F. (2021). Taxon TableTools: A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data. Molecular Ecology Resources. 21(5):1705-1714. DOI: https://doi.org/10.1111/1755-0998.13358

Mani, I. (2020). Current Status and Challenges of DNA Sequencing. In V. Singh (Ed.), Advances in Synthetic Biology (pp. 71-80). Alemania: Springer, Singapore. DOI: https://doi.org/10.1007/978-981-15-0081-7_5

McHugo, G. P., Dover, M. J., and MacHugh, D. E. (2019). Un locking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biology. 17(1): 1-20. DOI: https://doi.org/10.1186/s12915-019-0724-7

Muha, T. P., Robinson, C. V., Garcia-de-Leaniz, C., and Consuegra, S. (2019). An optimised eDNA protocol for detecting fish in lentic and lotic freshwaters using a small water volume. PLoS One. 14(7): e0219218. DOI: https://doi.org/10.1371/journal.pone.0219218

Olds, B. P., Jerde, C. L., Renshaw, M. A., Li, Y., Evans, N. T., Turner, C. R., …, and Lamberti, G. A. (2016). Estimating species richness using environmental DNA. Ecology and Evolution. 6(12): 4214-4226. DOI: https://doi.org/10.1002/ece3.2186

Pedersen, M. W., Overballe-Petersen, S., Ermini, L., DerSarkissian, C., Haile, J., Hellstrom, M., ..., and Willerslev, E. (2015). Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society B: Biological Sciences. 370(1660): 20130383. DOI: https://doi.org/10.1098/rstb.2013.0383

Pizarro, O. R. (2003). Proyecto de ley para un registro de ADN de utilización Criminalística. Revista Conamed. 8(2): 21-34.

Pont, D., Rocle, M., Valentini, A., Civade, R., Jean, P., Maire, A., …, and Dejean, T. (2018). Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Scientific Reports. 8(1): 1-13. DOI: https://doi.org/10.1038/s41598-018-28424-8

Ratnasingham, S. (2019). mBRAVE: The Multiplex Barcode Research And Visualization Environment. Biodiversity Information Science and Standards. 3. DOI: https://doi.org/10.3897/biss.3.37986

Raven, P. H. (2020) Biodiversity: A Global Perspective. In G.Dar and A. Khuroo (Eds.), Biodiversity of the Himalaya: Jammu and Kashmir State. Topics in Biodiversity and Conservation (pp. 156-180). Alemania: Springer, Singapore. DOI: https://doi.org/10.1007/978-981-32-9174-4_2

Rimieri, P. (2017). Genetic Diversity and Genetic Variability: Two Different Concepts Associated To Plant Germplasm and Breeding. Journal of Basic and Applied Genetics. 28(2): 7-13.

Ruppert, K. M., Kline, R. J., and Rahman, M. S. (2019). Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation. 17: e00547. DOI: https://doi.org/10.1016/j.gecco.2019.e00547

Salipante, S. J. and Jerome, K. R. (2020). Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clinical Chemistry. 66(1): 117-123. DOI: https://doi.org/10.1373/clinchem.2019.304048

Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 74(12): 5463-7. DOI: https://doi.org/10.1073/pnas.74.12.5463

Scheffers, B., Joppa, L., Pimm, S., and Laurance, W. (2012). What we know and don’t know about Earth’s missing biodiversity. Trends in Ecology & Evolution. 27(9): 501-10. DOI: https://doi.org/10.1016/j.tree.2012.05.008

Shaw, J. L. A., Clarke, L. J., Wedderburn, S. D., Barnes, T. C., Weyrich, L. S., and Cooper, A. (2016). Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biological Conservation. 197: 131-138. DOI: https://doi.org/10.1016/j.biocon.2016.03.010

Soliman, T., Yang, S. Y., Yamazaki, T., and Jenke-Kodama, H. (2017). Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise.PeerJ. 5: e4178. DOI: https://doi.org/10.7717/peerj.4178

Taberlet, P., Coissac, E., Hajibabaei, M., and Rieseberg, L. H. (2012). Environmental DNA. Molecular Ecology. 21(8): 1789-1793. DOI: https://doi.org/10.1111/j.1365-294X.2012.05542.x

Thomsen, P. F., Møller, P. R., Sigsgaard, E. E., Knudsen, S. W., Jørgensen, O. A., and Willerslev, E. (2016). Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes. PLoS One. 11(11): e0165252. DOI: https://doi.org/10.1371/journal.pone.0165252

Thomsen, P. F. and Willerslev, E. (2015). Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation. 183: 4-18. DOI: https://doi.org/10.1016/j.biocon.2014.11.019

Turner, C. R., Uy, K. L., and Everhart, R. C. (2015). Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biological Conservation. 183: 93-102. DOI: https://doi.org/10.1016/j.biocon.2014.11.017

UNEP, United Nations Environment Programme (2011). Convention of Biological Diversity: Strategic Plan for Biodiveristy 2011-2020. [En línea]. Disponible en: https://www.cbd.int/doc/strategic-plan/2011-2020/Aichi-Targets-EN.pdf. Fecha de consulta: 21 de enero de 2021.

Ushio, M., Fukuda, H., Inoue, T., Makoto, K., Kishida, O., Sato, K., ..., and Miya, M. (2017). Environmental DNA enables detection of terrestrial mammals from forest pond water. Molecular Ecology Resources. 17(6): e63-e75. DOI: https://doi.org/10.1111/1755-0998.12690

Valdez-Moreno, M., Ivanova, N. V., Elías-Gutiérrez, M., Pedersen, S. L., Bessonov, K., and Hebert, P. D. (2019). Using Edna to biomonitor the fish community in a tropical oligotrophic lake. PLoS One. 14(4): 1-22. DOI: https://doi.org/10.1371/journal.pone.0215505

Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., …, and Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology. 25(4): 929-942. DOI: https://doi.org/10.1111/mec.13428

van-Dijk, E. L, Jaszczyszyn, Y., Naquin, D., and Thermes, C. (2018). The Third Revolution in Sequencing Technology. Trends in Genetics. 34(9): 666-681. DOI: https://doi.org/10.1016/j.tig.2018.05.008

Vázquez-Ramos, J. (2016). Reparación del ADN: un asunto de vida... y de Premios Nobel. Educación Química. 27(2): 93-96. DOI: https://doi.org/10.1016/j.eq.2016.02.002

Wang, M. Y., Zhao, R., Gao, L. J., Gao, X. F., Wang, D. P., and Cao, J. M. (2020). SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development. Frontiers in Cellular and Infection Microbiology. 10: 587269. DOI: https://doi.org/10.3389/fcimb.2020.587269

Wang, S., Yan, Z., Hänfling, B., Zheng, X., Wang, P., Fan, J., and Li, J. (2021). Methodology of fish eDNA and its applications in ecology and environment. Science of the Total Environment. 755: 142622. DOI: https://doi.org/10.1016/j.scitotenv.2020.142622

Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., ..., and Miya, M. (2017). Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports. 7(1): 1-12. DOI: https://doi.org/10.1038/srep40368

Yildiz, I., Açıkkalp, E., Caliskan, H., and Mori, K. (2019). Environmental pollution cost analyses of biodiesel and diesel fuels for a diesel engine. Journal of Environmental Management. 243: 218-226. DOI: https://doi.org/10.1016/j.jenvman.2019.05.002

Yooseph, S., Andrews-Pfannkoch, C., Tenney, A., McQuaid, J., Williamson, S., Thiagarajan, M., …, and Venter, J. C. (2013). A metagenomic framework for the study of airborne microbial communities. PLoS One. 8(12): e81862. DOI: https://doi.org/10.1371/journal.pone.0081862

Zhu, H., Zhang, H., Xu, Y., Laššáková, S., Korabečná, M., and Neužil, P. (2020). PCR past, present and future. Biotechniques. 69(4): 317-325. DOI: https://doi.org/10.2144/btn-2020-0057

Published

2021-07-30

How to Cite

Padilla-García, P.-G., Camacho-Sánchez, F. Y., & Reyes-López, M. Ángel. (2021). Environmental DNA metabarcoding: an approach for biodiversity monitoring. CienciaUAT, 16(1), 136–149. https://doi.org/10.29059/cienciauat.v16i1.1509

Issue

Section

Biotechnology and Agricultural Sciences

Most read articles by the same author(s)

Similar Articles

1 2 3 4 > >> 

You may also start an advanced similarity search for this article.