Thesis project: Urban footprint on marine biodiversity: an environmental DNA-based approach in the French Mediterranean
Coastal ecosystems, true mosaics of habitats, are major biodiversity hotspots. However, they are under strong anthropogenic pressures, particularly due to the concentration of human populations along coastlines. Urbanization does not spare the marine environment either, and manifests itself through intense artificialization of coastlines, accompanied by multiple forms of pollution and disturbance. The replacement of natural substrates by artificial structures profoundly alters habitat heterogeneity, with potential consequences for community composition and the ecological processes shaping them. In terrestrial environments, urban ecology has extensively documented the effects of urbanization on biodiversity, which generally result in a reorganization of communities favoring generalist species over specialists, sometimes leading to biotic homogenization at the regional scale. At the intraspecific level, the isolation of urbanized patches is also associated with increased genetic differentiation and reduced genetic diversity within populations. By contrast, the consequences of urbanization on marine biodiversity remain poorly documented: the biodiversity of artificialized coastal areas, such as seaports, remains largely unknown, and the associated ecological processes have received little attention.
This thesis aims to characterize the footprint of urbanization on marine biodiversity across different levels of biological organization, using environmental DNA (eDNA) metabarcoding. It draws on data collected in the French Mediterranean and targets a wide diversity of organisms. The first chapter develops occupancy models adapted to eDNA data in order to account for false negatives. Synthesized into an R package, these models make it possible to estimate species occurrence and detection probabilities, and to determine the minimum sampling effort required to reliably detect species. The second chapter examines the local effects of urbanization by comparing the community structure of fish, metazoans, eukaryotes, and prokaryotes between seaports and marine reserves. While the number of species observed is comparable between the two habitat types, marked differences in composition emerge across all groups studied, revealing a profound reorganization of communities in urbanized contexts. The third chapter extends the analysis to the regional scale of the French Mediterranean to investigate biotic homogenization. While seaports locally host more fish species, their communities are markedly more similar to one another at the regional scale, both taxonomically and phylogenetically. Finally, the fourth chapter explores the consequences of urbanization at the intraspecific level, using a metaphylogeographic approach applied to eukaryotic communities. By exploiting a marker with sufficient intraspecific variability, the analyses show marked genetic differentiation between populations from seaports and those from outer habitats, as well as among different seaports, suggesting limited connectivity between seaport and external populations.
This thesis provides an original framework for studying the effects of urbanization on marine biodiversity, combining eDNA metabarcoding, community ecology, and metaphylogeography. It shows that conceptual frameworks derived from urban ecology can be meaningfully applied to the marine environment.
Keywords: urbanization – marine communities – biotic homogenization – environmental DNA – metabarcoding
Publications
Macé, B., Delrieu-Trottin, E., Mouillot, D., Valentini, A., Bruno, M., Velez, L., Avouac, A., Deter, J., Bockel, T., Orblin, M., Boissery, P., Le Roux, G., & Manel, S. (2026). Cities at Sea: Coastal Urbanization Generates Local Biodiversity Hotspots but Homogenizes Marine Fish Communities Regionally. Global Change Biology, 32(6), e70965. https://doi.org/10.1111/gcb.70965
Macé, B., Manel, S., Valentini, A., Rocle, M., Roset, N., & Delrieu-Trottin, E. (2026). NeMO: A Flexible R Package for Nested Multi-Species Occupancy Modeling and eDNA Study Optimization. Environmental DNA, 8(3), e70326. https://doi.org/10.1002/edn3.70326
Manel, S., Gauthier, J., Benestan, L., Dubois, M.-P., Romant, L., Macé, B., Bruno, M., Arnal, V., Testud, G., Garcia, M., Carrasquer Puyal, I., Bilat, J., Miaud, C., & Alvarez, N. (2025). An enrichment-based capture method from nuclear environmental DNA presents new opportunities for population genomics: A case study on the common frog. Methods in Ecology and Evolution, 16, 1106-1115. https://doi.org/10.1111/2041-210X.70039
Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, 33(12), e17373. https://doi.org/10.1111/mec.17373
Faure, N., Manel, S., Macé, B., Arnal, V., Guellati, N., Holon, F., Barroil, A., Pichot, F., Riutort, J.-J., Insacco, G., Zava, B., Mouillot, D., & Deter, J. (2023). An environmental DNA assay for the detection of Critically Endangered angel sharks (Squatina spp.). Aquatic Conservation: Marine and Freshwater Ecosystems, 33(10), 1088–1097. https://doi.org/10.1002/aqc.3954
Macé, B., Hocdé, R., Marques, V., Guerin, P.-E., Valentini, A., Arnal, V., Pellissier, L., & Manel, S. (2022). Evaluating bioinformatics pipelines for population-level inference using environmental DNA. Environmental DNA, 4(3), 674–686. https://doi.org/10.1002/edn3.269
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