Data from: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.

海洋沉积物是地球上物种库最为丰富的生境之一，但采样后勤保障不足以及分类学研究人力匮乏，制约了人类对其生物多样性的认知。本研究依托环境DNA宏条形码技术（environmental DNA metabarcoding），对西地中海海底峡谷的深海群落的α多样性（α-diversity）与β多样性（β-diversity）进行了表征分析。本研究设计了一套靶向真核生物18S短序列（约110碱基对）的全新引物组，并采用了一套针对重复采集的沉积物岩芯样本、旨在富集胞外DNA的提取流程。通过该策略，我们成功获取了吸附于无机颗粒上、可缓冲短期空间与时间异质性的DNA信息——这些DNA既可能源自原位环境，也可由水体沉降而来。本研究分析了来自20个采样点的重复样本，涵盖2处深海峡谷、1处浅海水道以及2处开阔斜坡，采样深度范围为100至2250米。本研究共鉴定出1629个分子操作分类单元（MOTUs），其中优势类群包括后生动物（涵盖19个门的代表类群）、囊泡虫总门、不等鞭毛总门以及根足虫总门。岩芯内部以及采样点内部的重复样本间存在显著差异，这表明研究区域存在明显的小型空间异质性。不同峡谷之间的空间变异极为显著，在所测试的其中一处峡谷中，深度梯度带来的群落差异同样显著。类似地，沉积物表层1厘米的群落组成与深层沉积物存在显著差异。研究发现，定性（物种有无）数据与定量（读段相对数量）数据均呈现出样本间及地理区域间群落分化的一致趋势。仅包含底栖生物的MOTUs子集，其β多样性与群落结构模式与全数据集的结果高度一致。针对主要后生动物门（按MOTUs数量统计）的单独分析显示，不同生活型类群的分布模式存在一定差异。本研究结果凸显了即便地理距离相近的群落之间也存在的群落分化现象，同时为后续针对这些兼具生态与经济价值的海底生境的监测与保护工作奠定了基础。