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Dynamique temporelle des communautés microbiennes eucaryotes en lien avec les forçages climatiques et anthropiques : approche paléolimnologique basée sur le séquençage massif d'ADN sédimentaire

Abstract : Eutrophication and climate warming are key factors governing lake functioning. However, there is a lack of knowledge about the response of microbial eukaryotic communities to these forcing factors even though microbial eukaryotes represent a huge taxonomic and functional diversity within lacustrine trophic networks. Paleolimnology has a well-established reputation for providing valuable insights into the drivers of biological assemblages over long time scales. The emergence of DNA analyses of lake sediments opens up many new opportunities for the reconstruction of past lacustrine biodiversity, including taxa that do not leave distinct morphological fossils. The present work aimed (i) to gain knowledge about the preservation of microbial eukaryotes DNA in lacustrine sediments (ii) to apply DNA-based methods to dated sediments in order to reveal the long-term dynamics (centennial to millennial) of microbial eukaryotes related to climatic and anthropogenic changes. The results obtained for Lake Bourget demonstrated the good efficiency of planktonic DNA archiving in recent sediments for most of microbial groups (chrysophyceae, chytrids, chlorophytes, cercozoa, ciliates, dinophyceae …). In complement, the use of a unique collection of freeze cores of varved sediment (Lake Nylandssjön, Sweden) allowed to assess the effects of diagenetic processes on microbial eukaryotes DNA occurring during the first years of burying. While the richness of the microbial eukaryotic community was not impacted, modifications were detected on the community structure during the first 15 years after deposition, then the DNA signal became stable. The paleoecological approach was applied to quantify centennial to millennial-scale dynamics on two deep peri-alpine lakes selected for their contrasted trophic history (lakes Bourget and Annecy, France) and two lakes with contrasted typologies (Lake Bourget, France and Lake Igaliku, Greenland). The results showed that some community rearrangements were concomitant with climate events (i.e. medieval warming, little ice age, recent warming) and that the recent climatic warming (over the last 30 years) favored more particularly some microbial groups including the dinophyceae (in terms of richness and relative abundance, in lakes Annecy and Bourget). However, the eutrophication seemed to prevail as a driver of these biological assemblages, in particular for Lake Bourget submitted to a marked eutrophication (up to 120 µg P. L-1 in the 1970s). The strong impact of the eutrophication was detected both at the whole community level and for specific groups such as chlorophytes and ciliates. Major rearrangements within eukaryotes community were also marked by the mobilization of rare taxa suggesting an important role of the rare biosphere as a reservoir of diversity to buffer the impacts of environmental stress. This multidisciplinary work thus provide new insights into the long-term dynamics of microbial eukaryotes communities. Our results confirm the potential of the application of high-throughput sequencing to sedimentary DNA for the lacustrine biodiversity reconstruction. Although these approaches are promising for further revolutionizing our understanding of long-term ecological dynamics, careful calibration studies are still to be conducted, as with any paleolimnological proxy. The generalization of our results is also to be tested using a sufficient number of lakes selected for their specific typologies and ecological histories (multi-lakes approach).
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https://tel.archives-ouvertes.fr/tel-01517017
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Éric Capo. Dynamique temporelle des communautés microbiennes eucaryotes en lien avec les forçages climatiques et anthropiques : approche paléolimnologique basée sur le séquençage massif d'ADN sédimentaire. Biodiversité et Ecologie. Université Grenoble Alpes, 2016. Français. ⟨NNT : 2016GREAA032⟩. ⟨tel-01517017⟩

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