In a context of widespread degradation of freshwater ecosystems and erosion of biodiversity, increased monitoring of the ecological status of these environments is essential. The assessment of the ecological status of freshwaters is generally carried out by means of inventories of the biological communities that reside there, which are indicators of the quality of the ecosystem (e.g. ichthyofauna, benthic macroinvertebrates, diatoms, macrophytes). Whatever the bioindicator group targeted, the inventory methods are based on the capture of living organisms, their identification on the basis of their morphological traits and the calculation of environmental quality indices in relation to a reference ecosystem. In addition to being extremely invasive, these methods prove to be inoperative or even impossible to implement in certain complex environments, due to their dynamism, their inaccessibility and the lack of knowledge of the species that inhabit them (i.e. intermittent rivers, groundwater). The emergence of molecular approaches to the study of biodiversity offers new perspectives for integrating these complex ecosystems into bioindication. In particular, the sampling of DNA released by living organisms into their environment, known as environmental DNA (eDNA), makes it possible to detect the presence of species from samples taken from the environment (e.g. water, sediments). eDNA offers the possibility of inventorying biodiversity in a non-invasive way, even in the most dynamic and difficult-to-access environments. Nevertheless, the lack of fundamental knowledge on eDNA dynamics and methodological barriers limit the application of eDNA for the bioindication of complex environments. The objectives of this thesis are i) to better understand the characteristics and dynamics of eDNA released by living organisms, ii) to develop a standardised sampling tool applicable to a wide variety of habitats and iii) to explore the potential of eDNA-based approaches for bioindication, in comparison with conventional inventories.

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Cite the thesis

Héloïse Verdier. L'ADN environnemental pour la bioindication du futur : aspects fondamentaux, méthodologiques et applicabilité en rivière intermittente. Ecologie, Environnement. Université Claude Bernard - Lyon I, 2022. Français. ⟨NNT : 2022LYO10178⟩. ⟨tel-04341638v2⟩

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