POSSIBILITIES FOR USING eDNA TO DETECT WEEDS AND OTHER PLANTS FROM THE SOIL SEED BANK
POSSIBILITIES OF USING eDNA TECHNIQUES FOR DETECTING WEEDS AND OTHER PLANTS FROM THE SOIL SEED BANK Ahmet Uludağ, Muhamad Shakirin Mispan, Sze-Looi Song
Abstracts
Environmental DNA (eDNA) is short DNA fragments left behind by organisms into the nonliving elements of environment and have become a foremost tool of life and environmental sciences to develop models for future, detect current level of ecosystems, get info from past situations since 1980’s. The early use of eDNA to detect microorganisms in water, sediment and soil followed by macroorganisms detection in seas and freshwater in the beginning of the 21 st centuary. Today it is possible to detect non-living pollutants in various environments. eDNA barcoding and metabarcoding has opened new horizons. Combining traditional methods or newest ones such as environmental RNA and using apps on site, modelling approach, and new generation sequencing and bioenformatics enabled getting more preciese results. eDNA has been used in plant sciences and agriculture but its use in weed science is not common. Introducing eDNA with other related innovations into weed science and invasive alien plants strategies to detect alien introductions and current soil seed bank can make ecological approach more applicable.
Keywords
Weeds, eDNA, Soil seed bank
References
- 1. Abdelfattah, A., Malacrinò, A., Wisniewski, M., Cacciola, S.O., Schena, L. (2018). Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies. Biological Control, 120, 1-10.
- 2. Ahi, E.P., Schenekar, T. (2025). The promise of environmental RNA research beyond mRNA. Molecular Ecology, 34(12), e17787. Asav, Ü., Serim, A.T., Kaya, Y., Başaran, B. (2025). Herbicide Strategies for Weed Control and Soil Seed Bank Dynamics in Winter Wheat. Journal of Crop Health, 77(4), 129.
- 3. Banerjee, P., Stewart, K.A., Dey, G., Antognazza, C.M., Sharma, R.K., Maity, J.P. et al. (2022). Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AoB Plants, 14(4), plac031.
- 4. Catlin, B.W. (1956). Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor. Science, 124(3219), 441-442.
- 5. Clement, R.A., Lee, H., Manoukis, N.C., Pacheco, Y.M., Ross, F., Sisterson, M.S., Owen, C.L. (2025). Addressing Biological Invasions in Agriculture with Big Data in an Informatics Age. Agriculture, 15(11), 1157.
- 6. Collins, C., Price, T., Dugdale, T. (2022). Cabomba caroliniana eradication-integrated weed control success in the NT.
- 7. Deiner, K., Yamanaka, H., Bernatchez, L. (2021). The future of biodiversity monitoring and conservation utilizing environmental DNA. Environmental DNA, 3(1), 3-7.
- 8. Díaz-Ferguson, E.E., Moyer, G.R. (2014). History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. Revista de biologia tropical, 62(4), 1273-1284.
- 9. Doi, H., Watanabe, T., Nishizawa, N., Saito, T., Nagata, H., Kameda, Y. et al. (2021). On‐site environmental DNA detection of species using ultrarapid mobile PCR. Molecular Ecology Resources, 21(7), 2364-2368.
- 10. Echeverria, P., Seriwatana, J., Chityothin, O., Chaicumpa, W., Tirapat, C. (1982). Detection of enterotoxigenic Escherichia coli in water by filter hybridization with three enterotoxin gene probes. Journal of Clinical Microbiology, 16(6), 1086-1090. Espinosa Prieto, A.E., Hardion, L., Debortoli, N., Bournonville, T., Marescaux, J., van der Zon, K.A.E., Beisel, J.N. (2025). Environmental DNA metabarcoding for catchment-scale detection of aquatic plants, invasive species, and land-use indicators in a large river. Ecological Indicators, 178, 113943. Espinosa Prieto, A., Beisel, J.N., Verschuren, P., Hardion, L. (2023). Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding. Environmental DNA, 5(4), 648- 670. Espinosa Prieto, A., Hardion, L., Debortoli, N., Beisel, J. N. (2024). Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding. Molecular ecology resources, 24(4), e13937.
- 11. Fabšičová, M., Vymyslický, T., Frei, I., Zdražílková, M., Smetanová, S., Winkler, J., Jiroušek, M. (2024). The importance of soil seed banks for biodiversity restoration in degraded grasslands. Folia Geobotanica, 59(1), 17-37.
- 12. Forcella, F., Eradat-Oskoui, K., Wagner, S.W. (1993). Application of weed seedbank ecology to low‐input crop management. Ecological Applications, 3(1), 74-83.
- 13. Foucher, A., Evrard, O., Ficetola, G.F., Gielly, L., Poulain, J., Giguet-Covex, C. et al. (2020). Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes. Scientific Reports, 10(1), 10502.
- 14. Giroux, M.S., Reichman, J.R., Langknecht, T., Burgess, R.M., Ho, K.T. (2023). Using eRNA/eDNA metabarcoding to detect community-level impacts of nanoplastic exposure to benthic estuarine ecosystems. Environmental Pollution, 338, 122650.
- 15. Greco, M., Lejzerowicz, F., Reo, E., Caruso, A., Maccotta, A., Coccioni, R. et al. (2022). Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test. Chemosphere, 298, 134239. Hernández Martínez de la Riva, A., Rytwinski, T., Spetka, M., Bennett, J.R. (2025). An evidence map and guide for using community science, remote sensing, and environmental DNA for rare plant detection. Conservation Science and Practice, 7(10), e70156. Janik‐Superson, K., Krawczyk, D., Baranowska, M., Królikowska, K., Seweryn, M., Lach, J. et al. (2025). Comparing eDNA and eRNA Sampling Methodologies From Pond Environments. Aquatic Conservation: Marine and Freshwater Ecosystems, 35(2), e70083.
- 16. Javed, Q., Bouhadi, M., Ban, S.G., Ban, D., Heath, D., Iqbal, B. et al. (2025). Smart Chip Technology for the Control and Management of Invasive Plant Species: A Review. Plants, 14(10), 1510.
- 17. Johnson, M.D., Fokar, M., Cox, R.D., Barnes, M.A. (2021). Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey. BMC Ecology and Evolution, 21(1), 218.
- 18. Jones, R.E., Medd, R.W. (2000). Economic thresholds and the case for longer term approaches to population management of weeds. Weed Technology, 14(2), 337-350.
- 19. Kagzi, K., Millette, K.L., Littlefair, J.E., Pochon, X., Wood, S.A., Fussmann, G.F., Cristescu, M.E. (2023). Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context. Environmental DNA, 5(5), 1016-1031.
- 20. Kestel, J.H., Field, D.L., Bateman, P.W., White, N.E., Allentoft, M.E., Hopkins, A.J. et al. (2022). Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Science of the Total Environment, 847, 157556.
- 21. Kushbokov, A., Deák, B., Valkó, O. (2025). Characteristics of soil seed bank in global drylands - A review. Arid Land Research and Management, 1-22.
- 22. Lakay, F.M., Botha, A., Prior, B.A. (2007). Comparative analysis of environmental DNA extraction and purification methods from different humic acid‐rich soils. Journal of applied microbiology, 102(1), 265-273.
- 23. Longhi, S., Cristofori, A., Gatto, P., Cristofolini, F., Grando, M.S. et al. (2009). Biomolecular identification of allergenic pollen: a new perspective for aerobiological monitoring? Annals of allergy, asthma and immunology, 103(6), 508-514.
- 24. Macher, T.H., Arle, J., Beermann, A.J., Frank, L., Hupało, K., Koschorreck, J. et al. (2024). Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream. PeerJ, 12, e18016.
- 25. Mahé, I., Cordeau, S., Bohan, D.A., Derrouch, D., Dessaint, F., Millot, D., Chauvel, B. (2021). Soil seedbank: Old methods for new challenges in agroecology?. Annals of Applied Biology, 178(1), 23-38.
- 26. Martins, V.C., Nunes, G.L., Oliveira, R.R., Gastauer, M., Oliveira, G., Vasconcelos, S. (2025). DNA Metabarcoding as a Complementary Approach to Traditional Surveys for Monitoring the Plant Diversity in the Amazon canga. Environmental DNA, 7(4), e70155.
- 27. Matsuhashi, S., Doi, H., Fujiwara, A., Watanabe, S., Minamoto, T. (2016). Evaluation of the environmental DNA method for estimating distribution and biomass of submerged aquatic plants. PLoS One, 11(6), e0156217.
- 28. Miyata, K., Inoue, Y., Amano, Y., Nishioka, T., Nagaike, T., Kawaguchi, T. et al. (2022). Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment. Scientific reports, 12(1), 19828.
- 29. Nannipieri, P., Ciardi, C., Badalucco, L., Casella, S. (1986). A method to determine soil DNA and RNA. Soil Biology and Biochemistry, 18(3), 275-281.
- 30. Ogram, A., Sayler, G.S., Barkay, T. (1987). The extraction and purification of microbial DNA from sediments. Journal of microbiological methods, 7(2-3), 57-66.
- 31. Ogram, A.V. (1988). The extraction and purification of microbial DNA from sediments. PhD diss., University of Tennessee.
- 32. Olsen, G.J., Lane, D.J., Giovanoni, S.J., Pace, N.R., Stahl, D.A. (1986). Molecular ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol., 40, 337-355.
- 33. Paul, J.H., DeFlaun, M.F., Jeffrey, W.H. (1988). Mechanisms of DNA utilization by estuarine microbial populations. Applied and environmental microbiology, 54(7), 1682-1688.
- 34. Pedersen, M.W., Overballe-Petersen, S., Ermini, L., Sarkissian, C.D., Haile, J., Hellstrom, M. et al. (2015). Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660), 20130383.
- 35. Pont, D., Meulenbroek, P., Bammer, V., Dejean, T., Erős, T., Jean, P. et al. (2023). Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR. Molecular Ecology Resources, 23(2), 396-409.
- 36. Rishan, S.T., Kline, R.J., Rahman, M.S. (2023). Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: a critical review on the challenges and limitations of eDNA metabarcoding. Environmental Advances, 12, 100370.
- 37. Rishan, S.T., Kline, R.J., Rahman, M.S. (2024). Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. Chemosphere, 141238.
- 38. Sayler, G. S., Shields, M. S., Tedford, E. T., Breen, A., Hooper, S. W., Sirotkin, K., & Davis, J. W. (1985). Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Applied and Environmental Microbiology, 49(5), 1295-1303.
- 39. Schwartz-Lazaro, L.M., Copes, J.T. (2019). A review of the soil seedbank from a weed scientists perspective. Agronomy, 9(7), 369.
- 40. Šikuljak, D., Uludag, A., Anđelković, A., Trkulja, N., Božić, D., Vrbničanin, S. (2024). Evaluation of the viability of old seeds of several important agricultural weeds. Pesticides and Phytomedicine, 39(1), 13-26.
- 41. Torsvik, V.L. (1980). Isolation of bacterial DNA from soil. Soil Biology and Biochemistry, 12(1), 15-21.
- 42. Uremıs, I., Uludag, A., Aksoy, E.O., Gonen, O., Kadıoglu, I. (2003). Relations between seedbank and weed flora in cotton areas. Aspects of Applied Biology, 69, 113-118.
- 43. Vasar, M., Davison, J., Moora, M., Sepp, S.K., Anslan, S., Al-Quraishy, S. et al. (2023). Metabarcoding of soil environmental DNA to estimate plant diversity globally. Frontiers in Plant Science, 14, 1106617.
- 44. Warrier, R.R., Kunhikannan, C. (2022). Significance of soil seed bank in forest vegetation - a review. Seeds, 1(3), 181-197.
- 45. Wei, Z., Zhang, X., Chen, Y., Liu, H., Wang, S., Zhang, M. et al. (2024). A new strategy based on a cascade amplification strategy biosensor for on-site eDNA detection and outbreak warning of crown-of-thorns starfish. Science of The Total Environment, 927, 172258.
- 46. Willerslev, E., Hansen, A.J., Binladen, J., Brand, T.B., Gilbert, M.T.P., Shapiro, B. et al. (2003). Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300(5620), 791-795.
- 47. Yoccoz, N.G., Bråthen, K.A., Gielly, L., Haile, J., Edwards, M.E., Goslar, T. et al. (2012). DNA from soil mirrors plant taxonomic and growth form diversity. Molecular ecology, 21(15), 3647- 3655.
- 48. Zhu, X., Bell, K.L., Wu, H., Gopurenko, D. (2024). Development of an Environmental DNA Assay for Prohibited Matter Weed Amazon Frogbit (Limnobium laevigatum). Environments, 11(4), 66.