Data from: Ancient DNA complements microfossil record in deep-sea subsurface sediments

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on foraminifera and radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropaleontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian SSU rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the Last Glacial Maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.深海次表层沉积物是海洋生物多样性最为重要的沉积档案。迄今为止，相关研究主要依托微化石记录展开，却忽视了堆积于深海海底的海量DNA物质。获取保存在岩芯剖面中的古代DNA（ancient DNA, aDNA）分子，将为解析海洋生物多样性演化历史提供独特视角，覆盖已化石化与未化石化的所有生物类群。本研究从南大西洋深海带采集的4根岩芯中，成功获取源自真核生物的古代DNA，其保存于距今可达3.25万年的沉积物层内。本研究聚焦于有孔虫（Foraminifera）与放射虫（Radiolaria）这两类核心海洋微化石类群，二者均包含丰富的未化石化生物类群。我们同时采用微古生物学与环境DNA测序两种技术手段，对岩芯剖面沉积物中的生物类群组合开展描述与分析。从沉积物DNA提取物中获取的有孔虫与放射虫小亚基核糖体RNA基因（SSU rRNA gene）短片段，证实深海沉积物中保存有真核生物古代DNA，其保存时限可覆盖末次冰盛期（Last Glacial Maximum）。绝大多数古代DNA被归类为未化石化生物类群，这类类群在现代环境的分子研究中同样占据主导地位。本研究揭示了古代DNA在更精准记录过去海洋生态系统演化方面的应用潜力，同时为深海古基因组学（palaeogenomics）的发展开辟了全新研究视野。