APPLICATIONS OF ENVIRONMENTAL DNA IN LAKE BIODIVERSITY
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摘要: 环境DNA(Environmental DNA, eDNA)可用于监测湖泊生物多样性, 该技术对湖泊生态环境破坏性小, 对于开展湖泊生态保护具有重要意义。湖泊流速较为缓慢, 相对于河流更容易富集DNA, 更适合于应用eDNA方法开展生物多样性研究。文章对eDNA在湖泊生物多样性上的应用进行了回顾, 综述了其实验设计, 分析了该技术存在的问题和未来发展前景。eDNA方法具有研究对象广, 从细菌、真核微生物到高等动植物, 样品类型为水和沉积物, 可针对单一物种或对多个物种进行同时检测等特点。eDNA实验技术包括样品采集和保存、DNA提取和检测。eDNA应用在湖泊生物多样性研究中仍面临着最佳实验方案不确定、污染、抑制反应、误差和错误及DNA分类数据库不完善等问题, 在未来还需要通过改进相关实验技术和发展DNA数据平台去解决相应困境。Abstract: Lake is indispensable part of inland water ecosystem, and China harbors numerous lakes with rich biodiversity. In recent years, the degradation of lakes severely lead to the decreasing of level of biodiversity. Therefore, lake biodiversity has always been a research hot-spot in limnology. All efforts to research on lake biodiversity essentially depend on monitoring species composition, population size and distribution. Such studies traditionally rely on morphological identification through biological specimen surveys, until to Environmental DNA (eDNA) arose. eDNA exists in the environmental samples such as water, soil and sediments. This feature makes eDNA to be a good indicator to monitor past and current biodiversity. Using molecular biology methods to monitor lake biodiversity is conducive to understanding the dynamic changes of lake ecosystems and is of great significance to the development of lake ecological protection. Compared to traditional investigation methods, eDNA is an non-invasive, efficient and easy to be standardized research approach. It especially doesn’t rely on experts’ experience and professional level of morphological classification. With the development of high-throughput sequencing (HTS) technology and emergence of eDNA metabarcoding, eDNA can be used as a supplement or alternative to traditional investigations. It is currently the most economical and effective method for lake biodiversity research. Lakes are easier to be enriched DNA owing to static water environment, therefore more suitable for applying eDNA methods to carry out their biodiversity researches. This article reviewed the application of eDNA in studies of the lake biodiversity. We also summarized the related experimental design, and analyzed challenges and prospects of this method. The application of eDNA in the lake biodiversity indicated characters of research objects from low-level organisms to high-level organisms. The samples are mainly water and sediments. By extracting ancient DNA from lake sediments, the lake history and the evolution of biodiversity have been studied; eDNA extracted from water samples can be used to understand the current aquatic biodiversity in the lake. The experimental technology of eDNA includes sampling and preservation, DNA extraction and detection. The three main aspects to determine quality of eDNA samples include suitable amount of samples, sampling methods and storage ways. eDNA can be used to detect specific taxa or multi-taxa based on PCR/qPCR with specific primer or meta-barcoding technology. The application of eDNA in lake biodiversity faces challenges such as lack of optimal experimental protocols, contamination, errors and imperfect taxa DNA database. In the future, the application of eDNA method needs to improve relevant experimental techniques and develop DNA database to solve the corresponding dilemmas. We recommend that human contamination and cross-contamination between samples should be avoided as much as possible during sampling. For the lack of database, we suggest establishing a regional eDNA database, conducting targeted data management and strengthening data sharing among various laboratories.
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图 1 利用eDNA研究湖泊生物多样性的关键实验步骤
Figure 1. Key experimental steps for detecting lake biodiversity based on eDNA
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图 2 eDNA高通量测序序列主要分析步骤
Figure 2. Major analysis steps of eDNA high-throughput sequences
表 1 湖泊样品中eDNA提取的常用方法
Table 1 Common methods for extracting eDNA from lake samples
eDNA提取方法Methods of eDNA extraction 样品量Sample Size eDNA浓度eDNA concentration 实验花费Experiment cost 抑制作用Inhibition 安全性Security 适用样品类型Applicable sample type 涉及研究案例
Relevant researchesPCI法 少 低 低 高 低 水样品沉积物 eDNA发展初期用于高盐湖泊古细菌及湖泊中微生物、真核生物多样性监测, 近年用于监测淡水湖泊鱼类动态分布[16, 30, 49] 试剂盒Reagent
kitsDNeasy
试剂盒多 中 中 高 高 水样品 用于监测脊椎动物及浮游动植物种和生物量估算, 监测入侵物种的分布[50－52] PowerWater试剂盒 多 高 高 中 高 水样品 用于监测真核生物、水生动植物多样性及分布, 及入侵物种监测[31, 53, 54] PowerSoil
试剂盒多 中 中 低 高 水样品沉积物 用于研究细菌群落结构及多样性、重建古生态系统等; 监测鱼类物种组成及其分布[27, 55] PowerMax试剂盒 多 中 中 低 高 沉积物 用于监测水生生物多样性, 重建陆生植被等[56] Biomedicals试剂盒 多 高 中 低 高 水样品沉积物 近年来用于水样品提取, 研究鱼类物种组成及其分布等[27] 
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