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Environmental DNA to assess biodiversity

Environmental DNA (eDNA) is the DNA released by organisms in the environmental matrix (e.g., water or soil) through mucus, feces, gametes, secretions, etc. Extraction of eDNA from environmental samples allow us to assess the presence of certain species, and even to assess the composition of entire communities in a non-invasive way, without the need to handle or catch the individuals. We use eDNA to study environmental successions in deglaciated forelands, diversity of soil communities, the effects of anthropic stressors related to urbanization on aquatic biodiversity, the spread of invasive species, and community composition in underground waters and remote areas, such as Antarctica. 

People

full professor

Francesco Gentile Ficetola

researcher

Mattia Falaschi

post-doc

Isabel Cantera

post-doc

Elia Lo Parrino

PhD student

Simone Giachello

PhD student

Andrea Simoncini

Project

Publications

  1. Cantera, I., Giachello, S., Münkemüller, T., Caccianiga, M., Gobbi, M., Losapio, G., Marta, S., Valle, B., Zawierucha, K., Thuiller, W., & Ficetola, F. G. (2025). Describing functional diversity of communities from environmental DNA. Trends in Ecology & Evolution, 40(2). https://doi.org/10.1016/j.tree.2024.10.007
  2. Bisaglia, B., Castelli, M., Soresinetti, L., Negri, A., Arnoldi, I., Montarsi, F., Gobbo, F., Defilippo, F., Callegari, E., Di Luca, M., Calzolari, M., Mastrantonio, V., Porretta, D., Ficetola, G. F., Sassera, D., Gabrieli, P., Bandi, C., & Epis, S. (2024). Barcoding of Italian mosquitoes (BITMO): Generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae. Parasites & Vectors, 17, 407. https://doi.org/10.1186/s13071-024-06478-0
  3. Ficetola, G. F., Guerrieri, A., Cantera, I., & Bonin, A. (2024). In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities. PLoS ONE, 19(4), e0298905. https://doi.org/10.1371/journal.pone.0298905
  4. Guerrieri, A., Cantera, I., Marta, S., Bonin, A., Carteron, A., Ambrosini, R., Caccianiga, M., Anthelme, F., Azzoni, R. S., Almond, P., Alvizgazitua, P., Cauvy-Fraunie, S., Ceballoslievano, J. L., Chand, P., Chandsharma, M., Clague, J., Cochachinrapre, J. A., Compostella, C., Cruzencarnacion, R., … Ficetola, G. F. (2024). Local climate modulates the development of soil nematode communities after glacier retreat. Global Change Biology, 30(1), e17057. https://doi.org/10.1111/gcb.17057
  5. Guerrieri, A., Cantera, I., Marta, S., Bonin, A., Carteron, A., Ambrosini, R., Caccianiga, M., Anthelme, F., Azzoni, R. S., Almond, P., Alvizgazitua, P., Cauvy-Fraunie, S., Ceballoslievano, J. L., Chand, P., Chandsharma, M., Clague, J., Cochachinrapre, J. A., Compostella, C., Cruzencarnacion, R., … Ficetola, G. F. (2024). Local climate modulates the development of soil nematode communities after glacier retreat. Global Change Biology, 30(1), 1–18. https://doi.org/10.1111/gcb.17057
  6. Bonin, A., Guerrieri, A., & Ficetola, G. F. (2023). Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Molecular Ecology Resources, 23(2), 368–381. https://doi.org/10.1111/1755-0998.13709
  7. Ficetola, G. F., & Taberlet, P. (2023). Towards exhaustive community ecology via DNA metabarcoding. Molecular Ecology, 32(23), 6320–6329. https://doi.org/10.1111/mec.16881
  8. Giachello, S., Cantera, I., Carteron, A., Marta, S., Cipriano, C., Guerrieri, A., Bonin, A., Thuiller, W., & Ficetola, G. F. (2023). Toward a common set of functional traits for soil protists. Soil Biology and Biochemistry, 187, 109207. https://doi.org/10.1016/j.soilbio.2023.109207
  9. Giguet-Covex, C., Bajard, M., Chen, W., Walsh, K. J., Rey, P.-., Messager, E., Etienne, D., Sabatier, P., Ficetola, G. F., Gielly, L., Blanchet, C., Guffond, C., Chiquet, P., Arnaud, F., & Poulenard, J. (2023). Long-term trajectories of mountain agro-ecosystems in the North-Western Alps. Regional Environmental Change, 23, 58. https://doi.org/10.1007/s10113-023-02030-5
  10. Huston, G. P., Lopez, M. L. D., Cheng, Y., King, L., Duxbury, L. C., Picard, M., Thomson-Laing, G., Myler, E., Helbing, C. C., Kinnison, M. T., Saros, J. E., Gregory-Eaves, I., Monchamp, M.-., Wood, S. A., Armbrecht, L., Ficetola, G. F., Kurte, L., Voneggers, J., Brahney, J., … Capo, E. (2023). Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities. Environmental DNA, 5(6), 1449–1472. https://doi.org/10.1002/edn3.467
  11. Guerrieri, A., Carteron, A., Bonin, A., Marta, S., Ambrosini, R., Caccianiga, M., Cantera, I., Compostella, C., Diolaiuti, G., Fontaneto, D., Gielly, L., Gili, F., Gobbi, M., Poulenard, J., Taberlet, P., Zerboni, A., Thuiller, W., & Ficetola, G. F. (2022). Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands. Molecular Ecology, 32(23), 6304–6319. https://doi.org/10.1111/mec.16669
  12. Lunghi, E., Valle, B., Guerrieri, A., Bonin, A., Cianferoni, F., Manenti, R., & Ficetola, G. F. (2022). Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. Science of The Total Environment, 826, 154022. https://doi.org/10.1016/j.scitotenv.2022.154022
  13. Arribas, P., Andujar, C., Bidartondo, M. I., Bohmann, K., Coissac, E., Creer, S., deWaard, J. R., Elbrecht, V., Ficetola, G. F., Goberna, M., Kennedy, S., Krehenwinkel, H., Leese, F., Novotny, V., Ronquist, F., Yu, D. W., Zinger, L., Creedy, T. J., Meramveliotakis, E., … Emerson, B. C. (2021). Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Molecular Ecology, 30(5), 1120–1135. https://doi.org/10.1111/mec.15797
  14. Brown, A. G., Van Hardenbroek, M., Fonville, T., Davies, K., Mackay, H., Murray, E., Head, K., Barratt, P., McCormick, F., Ficetola, G. F., Gielly, L., Henderson, A. C. G., Crone, A., Cavers, G., Langdon, P. G., Whitehouse, N. J., Pirrie, D., & Alsos, I. G. (2021). Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements. Scientific Reports, 11, 11807. https://doi.org/10.1038/s41598-021-91057-x
  15. Capo, E., Giguet-Covex, C., Rouillard, A., Nota, K., Heintzman, P. D., Vuillemin, A., Ariztegui, D., Arnaud, F., Belle, S., Bertilsson, S., Bigler, C., Bindler, R., Brown, A. G., Clarke, C. L., Crump, S. E., Debroas, D., Englund, G., Ficetola, G. F., Garner, R. E., … Parducci, L. (2021). Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations. Quaternary, 4(1), 6. https://doi.org/10.3390/quat4010006
  16. Ficetola, G. F., Marta, S., Guerrieri, A., Gobbi, M., Ambrosini, R., Fontaneto, D., Zerboni, A., Poulenard, J., Caccianiga, M., & Thuiller, W. (2021). Dynamics of ecological communities following current retreat of glaciers. Annual Review of Ecology, Evolution, and Systematics, 52(1), 405–426. https://doi.org/10.1146/annurev-ecolsys-010521-040017
  17. Meyer, A., Boyer, F., Valentini, A., Bonin, A., Ficetola, G. F., Beisel, J.-., Bouquerel, J., Wagner, P., Gaboriaud, C., Leese, F., Dejean, T., Taberlet, P., & Usseglio-Polatera, P. (2021). Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Molecular Ecology, 30(13), 3203–3220. https://doi.org/10.1111/mec.15723
  18. Ficetola, G. F., Boyer, F., Valentini, A., Bonin, A., Meyer, A., Dejean, T., Gaboriaud, C., Usseglio-Polatera, P., & Taberlet, P. (2020). Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Molecular Ecology, 30(13), 3189–3202. https://doi.org/10.1111/mec.15632
  19. Foucher, A., Evrard, O., Ficetola, G. F., Gielly, L., Poulain, J., Giguet-Covex, C., Laceby, J. P., Salvador-Blanes, S., Cerdan, O., & Poulenard, J. (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, 10502. https://doi.org/10.1038/s41598-020-67452-1
  20. Guerrieri, A., Bonin, A., Munkemuller, T., Gielly, L., Thuiller, W., & Ficetola, G. F. (2020). Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology, 30(13), 3313–3325. https://doi.org/10.1111/mec.15674
  21. Rota, N., Canedoli, C., Ferre, C., Ficetola, G. F., Guerrieri, A., & Padoa-Schioppa, E. (2020). Evaluation of soil biodiversity in alpine habitats through eDNA metabarcoding and relationships with environmental features. Forests, 11(7), 738. https://doi.org/10.3390/F11070738
  22. Vacher, J.-., Chave, J., Ficetola, G. F., Sommeria-Klein, G., Tao, S., Thebaud, C., Blanc, M., Camacho, A., Cassimiro, J., Colston, T. J., Dewynter, M., Ernst, R., Gaucher, P., Gomes, J. O., Jairam, R., Kok, P. J. R., Lima, J. D., Martinez, Q., Marty, C., … Fouquet, A. (2020). Large-scale DNA-based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism. Journal of Biogeography, 47(8), 1781–1791. https://doi.org/10.1111/jbi.13847