Améliorer la compréhension de la structure des têtes de bassins versants (1) en développant un outil d'identification moléculaire adapté à l'étude des communautés, (2) en étudiant la structure spatiale des communautés de différentes têtes de bassins versants avec une approche morphologique classique et une approche moléculaire et (3) en étudiant la structure spatio-temporelle des communautés d'une tête de bassin versant.

The metacommunity concept allowed to explicitly incorporate the role of dispersal in the structure of local communities at multiple spatial and temporal scales in ecological studies. In river systems, which are highly structured spatially and where hydrological and environmental conditions vary in time and space, taking dispersal into account improved substantially our knowledge of aquatic biodiversity organisation. However, our knowledge of the metacommunity dynamics in the headwaters, the upstream parts of river networks, remains sparse. Yet, headwaters constitute the majority of river networks and play a key role in the functioning of river ecosystems thanks to their high biodiversity. Due to their upstream position, which isolates their communities within river networks, and the high fragmentation they undergo, by both natural drying and man-made structures, the metacommunity framework seems the most relevant to understand the spatio-temporal structure of their biodiversity. The objective of this thesis is to improve our understanding of metacommunity dynamics in headwaters (i) by revealing the processes at work in ten headwaters undergoing different degrees of fragmentation, (ii) by describing the temporal dynamics of these processes in a headwater fragmented by man-made structures and drying, and (iii) by developing a novel molecular identification method to refine invertebrate community differentiation within the network and better characterize the dynamics of their metacommunities. First, our results showed that alpha diversity was lower in intermittent reaches than perennial ones and that intermittent communities constituted subsets of those of perennial reaches. At the network scale, metacommunities were structured primarily by spatial distances, particularly those associated with fragmentation. All these results suggest that dispersal process is a major process in dynamic and fragmented headwaters, through extinction and recolonization events of intermittent reaches by perennial refuge zones and by dispersal limitation induced by fragmentation and network dendritism. Second, we showed that the processes structuring metacommunity in dynamic and fragmented headwater varied considerably through time, echoing recent studies which emphases the importance of integrating the temporal component in metacommunity studies of dynamic ecosystems. This result, coupled with the fact that dispersal is the dominant process, reflects the response of communities to the hydrological cycles characterizing these ecosystems, which involves frequent events of extinction and recolonization from refuges. In the headwater context of high fragmentation by man-made structures, responses to fragmentation by drying were undetectable, suggesting that the role of fragmentation in metacommunity structure depends on the nature and context of the fragmentation. Finally, we developed an efficient and reliable molecular identification method to obtain qualitative, and even quantitative, information for metacommunity studies in comparison with molecular identification methods traditionally used. The use of the developed method on in situ collected samples demonstrated its potential to study spatial distribution patterns in invertebrate groups for which morphological identification analyses are not possible due to coarse taxonomic level. This thesis offers many areas for further research and improvement in the assessment of metacommunity structure with a need to better describe and quantify dispersal and fragmentation and in the development of molecular methods. Nevertheless, our findings can already be used to guide headwater management and conservation programs by highlighting some priorities, particularly related to the dispersal, temporal variability and fragmentation context encountered in these ecosystems. In addition, this thesis proposes many avenues for optimisations of the molecular identification method .

References

• Campbell Grant, E. H., Lowe, W. H., & Fagan, W. F. (2007). Living in the branches: Population dynamics and ecological processes in dendritic networks. Ecology Letters, 10(2), 165–175.
• Datry, T., Bonada, N., & Heino, J. (2016). Towards understanding the organisation of metacommunities in highly dynamic ecological systems. Oikos, 125(2), 149–159.
• Leibold, M. A., Holyoak, M., Mouquet, N., Amarasekare, P., Chase, J. M., Hoopes, M. F., … Gonzalez, A. (2004). The metacommunity concept: A framework for multi-scale community ecology. Ecology Letters, 7(7), 601–613.
• Martin, G. K., Adamowicz, S. J., & Cottenie, K. (2016). Taxonomic resolution based on DNA 736 barcoding a ff ects environmental signal in metacommunity structure. Freshwater Science, 35, 737 701-711. doi:10.1086/686260.
• Meyer, J. L., Strayer, D. L., Wallace, J. B., Eggert, S. L., Helfman, G. S., & Leonard, N. E. (2007). The contribution of headwater streams to biodiversity in river networks. Journal of the American Water Resources Association, 43(1), 86–103.
• Wallace, J. B., & Webster, J. R. (1996). The Role of Macroinvertebrates in Stream Ecosystem Function. Annual Review of Entomology, 41(1), 115–139.

Publications

• M. Gauthier, L. Konecny-Dupré, A. Nguyen, V. Elbrecht, T. Datry, C.J. Douady, T. Lefébure. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. (In review). Preprint disponible: https://doi.org/10.1101/580464

Communications

• Metacommunity organization in spatially constrained, dynamic systems: a molecular perspective. Présentation orale. Congrès SEFS10 Symposium for european freshwater sciences (Juillet 2017).
• Development of bait capture for DNA enrichment for metabarcoding purposes: a robust alternative to PCR-based methods. Présentation orale. Congrès Limnologia2018 (Juin 2018).
• Structure of benthic macroinvertebrate metacommunities in IRES: comparison of DNA metabarcoding and morphological approaches. Congrès SEFS11 Symposium for european freshwater sciences (Juillet 2019).

Cite the thesis

Maïlys Gauthier. Dynamique des métacommunautés dans les têtes de bassin versant fragmentées : une perspective moléculaire. Sciences de la Terre. Université de Lyon, 2020. Français. ⟨NNT : 2020LYSE1171⟩. ⟨tel-03352894⟩

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