Metabarcoding of ancient eukaryotic DNA from Chew Bahir, Ethiopia: Reconstruction of past biodiversity responses to drastic environmental change

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The Chew Bahir Drilling Project (CBDP) provides tropical sediment samples presumably spanning the last ~650 kyrs. DNA metabarcoding across these cores provides a record of a tropical lake environment, unique in resolution and time span. In a pilot study, we could analyze ancient eukaryotic DNA from the 280 m long Chew Bahir cores in sediment layers down to 70 m, corresponding to 150 kyrs BP by hybridization-capture-based metabarcoding. Sediment samples are subjected to taxon- and gene-specific DNA-enrichment with specific probes (“baits”) and analyzed by Next-Generation-Sequencing. We aim at further evaluating the possibility for DNA metabarcoding in the long CBDP cores. The principal research questions are: (1) How does the ecosystem react to short-term but significant disturbances, e.g., dramatic droughts or increased humidity in and around the lake? We will test the hypothesis that single disturbance events will perturbate affected ecosystems beyond resilience, i.e., alterate key components of the ecosystem. Thanks to our eukaryote-wide approach, we will be able to quantify effects on biodiversity and inferred impact on ecosystem function. (2) What are the consequences of global and regional climate shifts, for example at a tipping point? We will infer ecosystem shifts from one stable mode to another after a perturbation. Specifically, we will elucidate whether ecological niches are always reoccupied by the same species/evolutionary lineage or whether they will be replaced by other taxa/lineages, potentially changing ecosystem properties. (3) What are the long-term trends and shifts in the organismal communities in the Chew Bahir and other African core records? We will combine the results of all sampled sediment layers to elucidate the temporal trend in the occurrence of target eukaryotes, both regarding species identity, cryptic genetic variation, and (semiquantitative) relative abundance. This will include planktonic organisms previously used as environmental proxies (ostracods, cladocerans, rotifers, diatoms), but further encompass key taxa of the terrestrial environment as well (insects, rodents, ungulates, higher plants). (4) How far back in time can DNA remnants in the Chew Bahir and other HSPDP cores be extracted and analyzed? We aim at exploring the possibility for DNA-based detection of organisms in the deeper layers of the cores. Furthermore, we aim at further optimizing experimental conditions as to maximizing retrieval of DNA of our target taxa and to minimizing potential methodological biases. We will evaluate possibilities and limits of semiquantitative abundance estimation (via NGS read counts or qPCR) across strata of the core (corresponding to timepoints) and taxa.We use state-of-the-art DNA metagenomics, specifically targeting sediment layers before, at, and after drastic environmental perturbations (mostly wet-dry and dry-wet transitions), inferred by lithological analyses of project partners.