Filtering techniques affect recovered biodiversity in environmental DNA analysis. eDNA filtering techniques affect biodiversity

DNA metabarcoding of freshwater metazoan communities through analysis of environmental DNA (eDNA) captured on filters offers new opportunities for biodiversity assessment. Filtering of water in the field usually is an advantage compared to transport of water to the nearest lab, for both logistical reasons and to avoid DNA degradation. Thus, appropriate filter preservation becomes crucial for maximum DNA recovery and sample replicability. Here, the effect of two filter types, pre-filtration and four different filter preservation strategies were evaluated by measuring DNA yield, metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. At the river site, sterile, individually packed 0.2-µm polyethersulfone (PES) and 0.45-µm mixed cellulose ester (CN) filters were used. At the lake site, 0.45-µm CN filters and pre-filtration using 12-µm CN filters were tested. To test different preservation strategies, the filters were preserved in ethanol, in lysis buffer, dry in silica gel and cold on ice. Our results show that 0.45-µm CN filters yield higher DNA concentration, higher number of taxa and more consistent community composition than 0.20-µm PES filters; pre-filtration yields lower DNA concentration, lower number of taxa, but more consistent community composition than direct filtration; and filters preserved either dry or in lysis buffer give the most consistent community composition. Ethanol may be a poor filter preservative as the number of taxa is lower and community composition is more variable than using other preservation strategies. Our study sets the stage for developing guidelines for aquatic community-level eDNA biomonitoring applications.

通过分析滤膜捕获的环境DNA（environmental DNA, eDNA）开展淡水后生动物群落的DNA元条形码研究，为生物多样性评估提供了全新路径。相较于将水样运送至就近实验室，野外原位滤水在后勤保障层面更具优势，同时还可避免DNA发生降解。因此，合理的滤膜保存方案对实现最大化DNA回收率与样本可重复性至关重要。本研究针对两种滤膜类型、预过滤处理以及四种不同的滤膜保存策略的效果展开评估，通过测定DNA得率、后生动物多样性与群落组成，分析对象为采自河流与湖泊生态系统的环境DNA。在河流采样点，实验采用了无菌独立包装的0.2 μm聚醚砜（polyethersulfone, PES）滤膜与0.45 μm混合纤维素酯（mixed cellulose ester, CN）滤膜；在湖泊采样点，实验测试了0.45 μm CN滤膜，以及采用12 μm CN滤膜进行的预过滤处理。为评估不同保存策略的效果，研究中将滤膜分别置于乙醇、裂解缓冲液中保存，或是采用硅胶干燥法、冰上冷藏法进行保存。研究结果表明，相较于0.20 μm PES滤膜，0.45 μm CN滤膜可获得更高的DNA浓度、更多的分类单元数以及更一致的群落组成；预过滤处理的DNA得率与分类单元数均低于直接过滤法，但群落组成一致性更佳；而采用硅胶干燥法或裂解缓冲液保存的滤膜，其群落组成一致性最优。乙醇作为滤膜保存剂效果欠佳，相较于其他保存策略，其获得的分类单元数更少，且群落组成变异度更高。本研究为制定水生群落水平环境DNA生物监测应用指南奠定了坚实基础。