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To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments

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Abstract

Paleogenetics provides a powerful framework to reconstruct the long-term temporal dynamics of various biological groups from aquatic sediments. However, validations are still required to ensure the authenticity of the molecular signal obtained from sedimentary DNA. Here, we investigated the effects of early diagenesis on the DNA signal from micro-eukaryotes preserved in sediments by comparing metabarcoding inventories obtained for two sediment cores sampled in 2007 and 2013 respectively. High-throughput sequencing (Illumina MiSeq) of sedimentary DNA was utilized to reconstruct the composition of microbial eukaryotic communities by targeting the V7 region of the 18S rDNA gene. No significant difference was detected between the molecular inventories obtained for the two cores both for total richness and diversity indices. Moreover, community structures obtained for the two cores were congruent as revealed by procrustean analysis. Though most of the eukaryotic groups showed no significant difference in terms of richness and relative proportion according to the core, the group of fungi was found to differ both in terms of richness and relative proportion (possibly due to their spatial heterogeneity and potential activity in sediments). Considering the OTUs level (i.e. Operational Taxonomic Units as a proxy of ecological species), our results showed that, for the older analyzed strata (age: 15–40 years), the composition and structure of communities were very similar for the two cores (except for fungi) and the DNA signal was considered stable. However, for the uppermost strata (age < 15 years), changes of moderate magnitude were detected in the relative abundance of few OTUs. Overall, this study points out that, in Nylandssjön sediments, early diagenesis did not induce marked modifications in the micro-eukaryotic DNA signal, thus opening new perspectives based on the analysis of eukaryotic sedimentary DNA to address scientific issues both in the domains of paleolimnology and microbial ecology. Because this study site is ideal for DNA preservation in sediment (quick sedimentation processes, no sediment resuspension, anoxic conditions at sediment–water interface), the generalization of our conclusions, in particular for less favorable sites, must be considered cautiously.

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Acknowledgements

Funding for this project was provided by a grant from la Région Rhône-Alpes. We thank the Région Rhône-Alpes for the financial support of the Ph.D. thesis of E Capo through the “ARC Environnement” scheme. We thank the EC2CO INSU program (France) who supported the program “REPLAY”.

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  1. Eric Capo and Isabelle Domaizon have contributed equally to this work.

Authors and Affiliations

  1. CARRTEL, INRA, Université de Savoie Mont Blanc, 74200, Thonon-Les-Bains, France

    Isabelle Domaizon

  2. CARRTEL, INRA, Université de Savoie Mont Blanc, 74000, Thonon-Les-Bains, France

    Eric Capo & Isabelle Domaizon

  3. Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden

    Eric Capo, Dominique Maier & Christian Bigler

  4. Université Clermont Auvergne, Université Blaise Pascal, LMGE, 63000, Clermont-Ferrand, France

    Didier Debroas

  5. CNRS, UMR 6023, LMGE, 63171, Aubière, France

    Didier Debroas

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  1. Eric Capo
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Correspondence to Isabelle Domaizon.

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Capo, E., Domaizon, I., Maier, D. et al. To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments. J Paleolimnol 58, 479–495 (2017). https://doi.org/10.1007/s10933-017-0005-9

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