The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems
The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems
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DOI：
10.5670/oceanog.2020.211
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发表时间：
2020-06-01
期刊：
影响因子：
2.8
通讯作者：
Armbrecht, Linda H.
中科院分区：
文献类型：
--
作者：
Armbrecht, Linda H.
沉积古DNA（sedaDNA）提供了一种新的方法来调查过去的海洋生态系统，从最小的细菌浮游植物和他们的捕食者在地质时间尺度。关于这种古食物网的知识可以为古海洋学和环境重建提供广泛的生物背景。然而，海洋sedaDNA研究领域仍处于起步阶段;群落重建因沉积物中保存的微量古代DNA而变得复杂。因此，在sedaDNA中识别大多数原核生物和真核生物是困难的，并且sedaDNA采样、提取和分析需要优化的程序和严格的污染控制，以确保sedaDNA信号是真实的并且不被现代环境DNA覆盖。本文介绍了海洋sedaDNA研究的一些最新进展，包括使用宏基因组学研究过去的海洋食物网，和新的实验和计算技术，以最大限度地提高分类分辨率，特别是真核生物。生物信息学技术的一个例子，旨在提高分类的洞察力，展示了从海洋沉积物中提取的古生物信号的广度。随着遗传参考数据库、sedaDNA提取技术、物种特异性富集方法和计算工具的不断改进，海洋sedaDNA将继续提高我们对海洋生态系统如何随着环境条件的变化而演变的理解。
Sedimentary ancient DNA (sedaDNA) offers a novel approach to investigating past marine ecosystems-from the smallest bacteria to phytoplankton and their predators-over geological timescales. Knowledge about such paleo-food webs can provide broad-scale biological context to paleoceanographic and environmental reconstructions. However, the field of marine sedaDNA research is still in its infancy; community reconstructions are complicated by the minuscule amounts of ancient DNA preserved in the sediments. Consequently, the identification of most prokaryotes and eukaryotes in sedaDNA is difficult, and sedaDNA sampling, extraction, and analysis require optimized procedures and rigorous contamination control to ensure that the sedaDNA signal is authentic and not overridden by modern environmental DNA. This article describes some of the latest developments in marine sedaDNA research, including the use of metagenomics to study past marine food webs, and new experimental and computational techniques to maximize taxonomic resolution, particularly that of eukaryotes. An example of bioinformatic techniques designed to increase taxonomic insight is presented, demonstrating the breadth of paleogenetic signals that could be extracted from marine sediments. With ongoing improvements in genetic reference databases, sedaDNA extraction techniques, species-specific enrichment approaches, and computational tools, marine sedaDNA will continue to improve our understanding of how marine ecosystems evolved in concert with changing environmental conditions.