Department of Genetics and Evolution, University of Geneva, Boulevard d'Yvoy 4, 1205, Geneva, Switzerland.
Department of Earth Sciences, University of Geneva, Rue des Maraîchers 13, 1205, Geneva, Switzerland.
Sci Rep. 2020 Nov 23;10(1):20351. doi: 10.1038/s41598-020-77179-8.
Environmental DNA (eDNA) metabarcoding of marine sediments has revealed large amounts of sequences assigned to planktonic taxa. How this planktonic eDNA is delivered on the seafloor and preserved in the sediment is not well understood. We address these questions by comparing metabarcoding and microfossil foraminifera assemblages in sediment cores taken off Newfoundland across a strong ecological gradient. We detected planktonic foraminifera eDNA down to 30 cm and observed that the planktonic/benthic amplicon ratio changed with depth. The relative proportion of planktonic foraminiferal amplicons remained low from the surface down to 10 cm, likely due to the presence of DNA from living benthic foraminifera. Below 10 cm, the relative proportion of planktonic foraminifera amplicons rocketed, likely reflecting the higher proportion of planktonic eDNA in the DNA burial flux. In addition, the microfossil and metabarcoding assemblages showed a congruent pattern indicating that planktonic foraminifera eDNA is deposited without substantial lateral advection and preserves regional biogeographical patterns, indicating deposition by a similar mechanism as the foraminiferal shells. Our study shows that the planktonic eDNA preserved in marine sediments has the potential to record climatic and biotic changes in the pelagic community with the same spatial and temporal resolution as microfossils.
海洋沉积物的环境 DNA（eDNA）宏条形码技术揭示了大量属于浮游生物类群的序列。然而，这些浮游 eDNA 是如何被输送到海底并在沉积物中保存的，目前还不是很清楚。为了解决这些问题，我们在纽芬兰沿岸的一系列具有强烈生态梯度的沉积物岩芯中，比较了宏条形码和微体有孔虫的组合。我们在 30 厘米深的沉积物中检测到了浮游有孔虫的 eDNA，并观察到浮游/底栖扩增子的比例随深度而变化。从表面到 10 厘米深，浮游有孔虫的相对丰度仍然较低，这可能是由于生活在底栖有孔虫中的 DNA 的存在。在 10 厘米以下，浮游有孔虫的相对丰度急剧增加，这可能反映了 DNA 埋藏通量中浮游 eDNA 的比例更高。此外，微体化石和宏条形码组合也呈现出一致的模式，表明浮游有孔虫 eDNA 在没有大量侧向平流的情况下被沉积下来，并保存了区域生物地理模式，表明其沉积机制与有孔虫壳类似。我们的研究表明，保存在海洋沉积物中的浮游 eDNA 有可能以与微体化石相同的空间和时间分辨率，记录浮游生物群落中的气候和生物变化。
