To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments
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.
KeywordseDNA Paleogenetics Sediment Metabarcoding Plankton
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”.
- Coolen MJL, Gibson JAE (2009) Ancient DNA in lake sediment records. PAGES News 17:104–106Google Scholar
- Dell’Anno A, Corinaldesi C (2004) Degradation and turnover of extracellular DNA in marine sediments: ecological and methodological considerations degradation and turnover of extracellular dna in marine sediments—ecological and methodological considerations. Appl Environ Microbiol 70:4384–4386CrossRefGoogle Scholar
- Epp LS, Gussarova G, Boessenkool S, Olsen J, Haile J, Schrøder-Nielsen A, Ludikova A, Hassel K, Stenøien HK, Funder S, Willerslev E, Kjær K, Brochmann C (2015) Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes. Quat Sci Rev 117:152–163CrossRefGoogle Scholar
- Hagelberg E, Hofreiter M, Keyser C (2015) Ancient DNA: the first three decades. Philos Trans R Soc Biol Sci 4:9Google Scholar
- Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9Google Scholar
- Jones EBG, Hyde KD, Pang KL (2014) Freshwater fungi and fungal-like organisms. Walter de Gruyter, Berlin, p 496Google Scholar
- Kirkpatrick JB, Walsh EA, D’Hondt S (2016) Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales. Geology G37933:1Google Scholar
- Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d’Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J (2015) Determinants of community structure in the global plankton interactome. Science 348:1262073CrossRefGoogle Scholar
- Oksanen AJ, Blanchet FG, Kindt R, Legendre P, Minchin PR, Hara RBO, Simpson GL, Solymos P, Stevens MHH, Wagner H (2015) Package “vegan.” http://CRANR-project.org/package=vegan
- Sparrow F (2013) Ecology of freshwater fungi. In: Ainsworth G, Sussman A (eds) The fungi, an advanced treatise. Academic Press, New York, pp 41–93Google Scholar