Introduction to eDNA

Similar to remote sensing methods, eDNA monitoring has speed and cost advantages over traditional methods. Thus, it is rapidly becoming a preferred method to monitor biodiversity, including in agricultural systems [24-27]. eDNA refers to genetic material obtained directly from environmental samples, such as water, soil, or air, without capturing or observing the organisms themselves [28] and coupled with the metabarcoding approach allows for the simultaneous identification of multiple species from a single sample [29]. eDNA sampling approaches can monitor entire taxonomic groups at multiple spatial scales depending on whether eDNA is collected from leaves, soil, animal waste, water, or air [30-35]. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices.

Sampling Scheme

Species’ dispersal abilities and habitat selection, among other factors, drive the uneven distribution of organisms across the landscape (Shimada et al., 2020; Vinatier et al., 2010; Lovett et al., 2005). Thus, DNA shed by organisms is also heterogeneously distributed across the landscape (Hunter et al., 2015; Goldberg et al., 2018). Optimizing sampling design to maximize the probability of detection is therefore a critical issue in order to effectively use environmental DNA (eDNA) in conservation and management applications (Goldberg et al., 2018).

This is particularly true for soil sampling. Soil sampling for eDNA is a useful approach to assess ecological communities in specific locations, such as comparing community composition across different site treatments (Dyson et al., 2024). To accurately evaluate community composition using soil sampling, we need to the heterogeneity of eDNA distribution in a way that is both rigorous and easy to implement in the field. Many important research questions involving spatially discrete site treatments, including determining the efficacy of sustainable agricultural practices in contributing to biodiversity, would benefit from eDNA soil sampling approaches that account for heterogeneity (Dyson et al 2024).

scraps

edge-to-edge sampling strategy

volume testing approach: adapted from water based eDNA sampling approaches, to identify the amount of soil that needs to be collected in order to balance cost and species coverage.

We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest.

References

[24-27] F, Čiamporová-Zaťovičová Z, Costa FO, Duarte S. Why we need sustainable networks bridging countries, disciplines, cultures and generations for aquatic biomonitoring 2.0: a perspective derived from the DNAqua-Net COST action. In advances in ecological research 2018 Jan 1 (Vol. 58, pp. 63-99). Academic Press.

Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N. Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap. Molecular Ecology. 2021 Jul;30(13):2937-58.

Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, D’Amico V, Trammell TL, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Scientific Reports. 2021 Jan 15;11(1):1629.

Kestel, J.H., Field, D.L., Bateman, P.W., White, N.E., Allentoft, M.E., Hopkins, A.J., Gibberd, M. and Nevill, P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Science of the Total Environment, 847, 2022. p.157556.

[28] Taberlet P, PRUD’HOMME SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, CLÉMENT JC, Melodelima C. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular ecology. 2012 Apr;21(8):1816-20.

[29] Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière‐Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, De Vere N, Pfrender ME. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular ecology. 2017 Nov;26(21):5872-95.

[30-35] Thomsen, P. F. & Willerslev, E. Environmental DNA—An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 2015 183, 4–18.

Sales, N.G., McKenzie, M.B., Drake, J., Harper, L.R., Browett, S.S., Coscia, I., Wangensteen, O.S., Baillie, C., Bryce, E., Dawson, D.A. and Ochu, E. Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems. Journal of Applied Ecology. 2020 57(4), pp.707-716.

Nørgaard, L., Olesen, C.R., Trøjelsgaard, K., Pertoldi, C., Nielsen, J.L., Taberlet, P., Ruiz-González, A., De Barba, M. and Iacolina, L. eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Scientific reports, 2021 11(1), pp.1-12.

Banerjee, P., Stewart, K.A., Dey, G., Antognazza, C.M., Sharma, R.K., Maity, J.P., Saha, S., Doi, H., de Vere, N., Chan, M.W. and Lin, P.Y. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AoB Plants. 2022 14(4), p.plac031.

Altermatt F, Carraro L, Antonetti M, Albouy C, Zhang Y, Lyet A, Zhang X, Pellissier L. Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs. Environmental DNA. 2023 May 16..

Aucone E, Kirchgeorg S, Valentini A, Pellissier L, Deiner K, Mintchev S. Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring. Science Robotics. 2023 Jan 18;8(74):eadd5762.