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

周巴希尔钻探项目(CBDP)提供了热带沉积物样本，据推测，样本的时间跨度约为650年。这些岩心的DNA编码提供了热带湖泊环境的记录，在分辨率和时间跨度上都是独一无二的。在一项初步研究中，我们可以通过基于杂交捕获的后置编码来分析从沉积层到70米的280米长的Chew Burir岩芯中的古代真核DNA，相当于150 kyrBP。沉积物样本用特定的探针(“诱饵”)进行分类群和基因的DNA浓缩，并通过下一代测序进行分析。我们的目标是进一步评估在长CBDP核心中进行DNA元编码的可能性。主要的研究问题是：(1)生态系统如何应对短期但重大的干扰，例如，湖泊及其周围的剧烈干旱或湿度增加？我们将检验这样一种假设，即单一干扰事件将使受影响的生态系统受到超出弹性的扰动，即改变生态系统的关键组成部分。多亏了我们的真核生物范围的方法，我们将能够量化对生物多样性的影响和对生态系统功能的推断影响。(2)全球和区域气候变化的后果是什么，例如在一个临界点？我们将推断生态系统在一次扰动后从一种稳定模式转变到另一种模式。具体地说，我们将阐明生态位是否总是被相同的物种/进化谱系重新占据，或者它们是否会被其他分类群/谱系取代，从而潜在地改变生态系统的性质。(3)Chew bahir和其他非洲核心记录中的生物群落的长期趋势和变化是什么？我们将结合所有采样沉积物层的结果来阐明目标真核生物出现的时间趋势，包括物种鉴定、隐蔽的遗传变异和(半定量)相对丰度。这将包括以前用作环境替代品的浮游生物(介形虫、枝角类、轮虫、硅藻)，但还包括陆地环境的关键分类群(昆虫、啮齿动物、有蹄类、高等植物)。(4)可以在多长时间以前提取和分析Chew Babir和其他HSPDP核心中的DNA残留物？我们的目标是探索以DNA为基础对岩心更深层的生物体进行检测的可能性。此外，我们的目标是进一步优化实验条件，以最大限度地检索我们的目标分类群的DNA，并将潜在的方法偏差降至最低。我们将评估跨岩心地层(对应于时间点)和类群的半定量丰度估计(通过NGS读取计数或qPCR)的可能性和限度。我们使用最先进的DNA元基因组学，根据项目合作伙伴的岩性分析推断，专门针对剧烈环境扰动(主要是湿-干和干-湿转变)之前、那时和之后的沉积层。

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.