Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland.
NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK.
Sci Total Environ. 2022 Apr 20;818:151783. doi: 10.1016/j.scitotenv.2021.151783. Epub 2021 Nov 19.
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
环境 DNA(eDNA) 代谢组学(针对目标群体中的整个群落进行 DNA/RNA 的平行测序以进行鉴定)正在彻底改变水生生物监测领域。迄今为止，大多数旨在评估水生生态系统生态状况的代谢组学研究都集中在水 eDNA 和大型无脊椎动物的混合样本上。然而，eDNA 代谢组学也已应用于软底沉积物样本，主要用于评估微生物或小型后生动物群。与基于手动分类和底栖分类群形态鉴定的经典方法相比，eDNA 代谢组学为评估沉积物的环境质量提供了潜在的重要优势。用于沉积物 eDNA 代谢组学的方法和方案在研究之间可能有很大差异，需要进行标准化工作，以提高其稳健性、可比性，并在监管框架内使用。在这里，我们回顾了应用于沉积物样本的 eDNA 代谢组学的现有信息，重点是采样、保存和 DNA 提取步骤。我们讨论了特定于沉积物 eDNA 分析的挑战，包括不同来源和状态的 eDNA 的多样性及其在沉积物中的持久性。本文旨在确定良好的实践策略，并促进未来底栖监测中常规使用沉积物 eDNA 的方法协调。
