Marine biomonitoring with eDNA: can metabarcoding of water samples cut it as a tool for surveying benthic communities?

In the marine realm, biomonitoring using eDNA of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at distances from a few centimetres to 20 m from the benthic habitat. Using as marker a fragment of the Cytochrome c oxidase subunit I gene with universal primers, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs) from the samples. The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida Rhodophyta and Stramenopiles being the most diverse group in benthic samples, and HacrobiaAlveolata, Metaz...

在海洋环境中，利用底栖群落（benthic communities）的环境DNA（eDNA）开展生物监测（biomonitoring），需采用破坏性直接采样或搭建沉降结构。相较而言，水体采样所需工作量大幅降低，且可通过远程方式开展。本研究旨在评估通过采集毗邻底栖生境的水层样本，获取真核底栖群落相关信息的可行性。本研究采用基于样方采样（quadrat sampling）的技术，对两类不同岩质基质底栖群落开展研究。同时，我们在距底栖生境数厘米至20米的范围内采集了重复水体样本。本研究以携带通用引物（universal primers）的细胞色素c氧化酶亚基I基因（Cytochrome c oxidase subunit I）片段作为分子标记，共从样本中获得3543个分子操作分类单元（molecular operational taxonomic units, MOTUs）。两类生境中获得的群落结构存在显著差异：底栖样本中物种多样性最高的类群为后生动物（Metazoa）、古质体类（Archaeplastida）、红藻门（Rhodophyta）以及不等鞭毛类（Stramenopiles），而HacrobiaAlveolata、后生动物等……