eDNA监测方法标准化框架及未来图景  

A framework for standardizing the processes of eDNA monitoring and an accessible vision of the future

作　　者：杨海乐 张辉[1] 杜浩[1] Yang Haile;Zhang Hui;Du Hao(Key Laboratory of Freshwater Biodiversity Conservation,Ministry of Agriculture and Rural Affairs,Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences,Wuhan 430223,P.R.China)

机构地区：[1]中国水产科学研究院长江水产研究所,农业农村部淡水生物多样性保护重点实验室,武汉430223

出　　处：《湖泊科学》2023年第1期12-31,共20页Journal of Lake Sciences

基　　金：中央级公益性科研院所基本科研业务费专项(2021JC01,YFI202201)资助。

摘　　要：eDNA(environmental DNA)是指从环境样品(水体、土壤、沉积物、空气、混合物等)中提取的DNA,是各种生物的DNA混合物,区别于传统从单物种样品中提取的DNA。eDNA监测是指从环境样品中提取DNA,用物种特异性引物或特定DNA metabarcoding引物对其进行扩增测序、分类学分析、相对丰度分析、功能预测等,以监测环境中是否存在某特定物种,或者获得环境中物种组成、群落结构、生态功能等相关信息。eDNA监测主要应用在特定物种监测检出、生物多样性调查评估、群落结构和功能分析、生态系统过程分析评估等领域。eDNA监测可以应用在陆地、水体、空气、器物表面、生物(内)表面等任何有可能存在不确定DNA的场景。因为eDNA监测的非侵入性、灵敏检出、大类群检出、易标准化方法与结果、低人力物力时间成本、结果可核查等特点,未来很有希望发展成为一种常规的物种监测、群落功能预测、生态过程分析的方法,对象可涵盖所有生境条件下的所有生物类群。但要实现这个图景,需要从普遍性和特殊性层面完成eDNA监测技术链条中10个关键环节的技术标准化:样品重复数设计、采样时间设计、采样点设计、采样方法设计、样品前处理、样品保存、扩增引物选择、DNA提取扩增测序分析程序、序列比对注释、监测结果后评估。目前来看,10个环节的标准化基本不存在理论上的困难,并且一部分支撑标准化的研究已经启动,甚至一部分标准化的组织工作已在推进,在未来数年内有望完成关键知识、关键数据的积累,推动eDNA监测成为长期性周期性常规生态监测内容,支撑渐行渐近的数据驱动型科学研究和生态管理。Environmental DNA(eDNA)is DNA extracted from any type of environmental sample(e.g.water,soil,sediment,air,mixture,etc.),which is a DNA mixture originated from different species and individuals,distinguish from a pure DNA sample extracted from a particular organism.eDNA monitoring refers the processes that 1)extracting DNA sample from environmental sample,2)using definite species-specific primers or meta-barcoding primers to amplify and sequence eDNA sample,3)clustering the operational taxonomic units(OTUs)and identifying their taxa against reference databases,4)calculating the relative abundance of each OTUs/species and other biodiversity indexes,5)analyzing the corresponding ecosystem structure,processes or function.According to eDNA monitoring,a definite species(or other taxonomic units)in the sampling site could be identified,and the biological information about species composition,community structure,ecosystem processes,ecological function of the research area could be collected.eDNA monitoring has been applied in monitoring and early warning definite species,investigating and assessing biodiversity,detecting and analyzing community structure and function,studying and quantifying ecosystem processes and so on.eDNA monitoring could work in any type of environmental scene where there is unidentified DNA trace,such as in terrestrial environment,aquatic environment,air environment,body surface,organism(inner)surface and so on.As an emerging tool for documenting species presence without direct observation,allowing for sensitive and efficient detection,easy-to-standardize sampling and analyzing approach,comprehensive taxonomic groups coverage,less reliant on taxonomic expertise and auditable by third-party researchers,eDNA monitoring would be a prospective general method for species monitoring,community function predicting and ecosystem processes analyzing in future.Moreover,the objective scope of eDNA monitoring covers all environmental conditions and all biological taxonomies.However,to realize the prospective ap

关 键 词：环境DNA 生物信息 生物多样性监测 标准化 

分 类 号：X835[环境科学与工程—环境工程]