Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0–2 and 3–5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite >1,000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (<2%), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13% ASVs, 86% reads), derived both from the high-biomass upper ocean as well as deep pelagic residents. While most pelagic metazoan eDNA found in sediments and on nodules could be sourced from the epipelagic, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0–2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3–5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40 to 74%, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities.

中文翻译：

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从海面到海底：深海海底异地 eDNA 调查

环境 DNA (eDNA) 元条形码可以促进深海中快速和全面的生物调查，但深海中 eDNA 的来源和分布的许多方面仍然知之甚少。为了检查水体对深海多金属结核开采目标区域的底栖 eDNA 调查的影响，我们调查了远洋 eDNA 的发生情况：(1) 两种不同的深海栖息地类型，深海平原和海山， (2) 底栖样本类型，包括底栖边界层 (BBL) 内的结核、沉积物和海水，以及 (3) 沉积物深度层（0-2 和 3-5 厘米）。尽管这些栖息地的深度差异超过 1,000 米，但在海底山和邻近的深海平原中，在海底采集的遗留远洋 eDNA 的比例方面几乎没有观察到差异。就读数和扩增子序列变体 (ASV) 而言，沉积物和结核样本中的远洋 eDNA 极少（<2%），并且不太可能影响监测深海底常驻生物的底栖调查。然而，BBL 中的远洋 eDNA 含量很高（高达 13% 的 ASV，86% 的读数），来自高生物量的上层海洋和深海居民。虽然在沉积物和结核中发现的大多数远洋后生动物 eDNA 可能来自上层，但在这些基质上采样的原生生物遗产 eDNA 似乎起源于水体中的一系列深度。在原生生物中观察到了垂直沉积物剖面上 eDNA 降解的一些证据，0-2 厘米层的多样性更高，而更深的沉积物（3-5 厘米）中遗留的远洋 eDNA 比例显着降低。全学习，尽管样本量相对较大，但我们估计的后生动物采样覆盖率在 40% 到 74% 之间。未来的深海 eDNA 调查应检查海洋学对 eDNA 运输和停留时间的影响，考虑深渊中一系列空间尺度的栖息地异质性，并旨在处理每个样本的大量材料（通过复制）以增加采样覆盖这些不同的深海社区。