A self‐preserving, partially biodegradable eDNA filter
A self‐preserving, partially biodegradable eDNA filter
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一种自我保护、部分可生物降解的 eDNA 过滤器
DOI：
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发表时间：
2019
影响因子：
6.6
通讯作者：
C. Goldberg
中科院分区：
文献类型：
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作者：
Austen C. Thomas;P. Nguyen;Jesse Howard;C. Goldberg
eDNA研究通常依赖于现场的水过滤和立即的样品保存，以防止样品运输期间的DNA降解。然而，用于保存的滤膜转移步骤可能会增加样品污染的风险，并且对典型的一次性过滤器外壳的依赖会产生大量的塑料废物。我们创造了一种新的eDNA过滤器外壳（与任何抽吸泵兼容），部分由可生物降解的亲水材料组成，其功能是通过干燥自动保存捕获的eDNA-无需滤膜转移步骤，无需化学或冷藏。我们通过在eDNA围隔生态系统研究中过滤重复样品来测试干燥过滤器外壳的自我保存能力，并与乙醇保存进行比较。将自保存过滤器放回原始包装中储存，并将两种保存方法的样品保存在室温下，直至过滤后规定时间点（11天、18天、25天、32天、60天、88天、172天）提取。还从六个池塘位置采集了成对的田间样品，以其他物种为目标，以证明田间性能。围隔生态系统研究的定量PCR结果表明，两种方法在6个月的储存期内有效地保存了eDNA，自我保存的过滤器平均产生的靶DNA（SQ = 329拷贝）略高于乙醇保存的样本（SQ = 288拷贝）（F1，38 = 4.050，p = 0.051）。两种方法在172天后均未显示降解迹象。现场采样的结果表明，保存方法之间存在较大差异，自我保存过滤器平均含有约2倍于乙醇保存样本的eDNA（配对t检验，p = 0.020）。这些数据表明，自我保存的eDNA过滤器外壳是标准乙醇保存方法的可行替代方案，并且在某些情况下可以提供更高的检测灵敏度。新的过滤器外壳还应有助于降低样品污染的风险，最大限度地减少方案步骤，并减少塑料废物。这些创新对于确保eDNA数据质量和帮助促进非专家样本收集者（例如公民科学家）参与研究计划非常重要。
eDNA studies often rely on water filtration in the field and immediate sample preservation to prevent DNA degradation during sample transport. However, filter membrane transfer steps for preservation can increase risk of sample contamination and the reliance on typical single‐use filter housings produces significant plastic waste. We created a new eDNA filter housing (compatible with any suction pump) partially comprised of a biodegradable, hydrophilic material that functions to automatically preserve captured eDNA via desiccation—no filter membrane transfer steps, no chemical or cold storage required. We tested the self‐preservation capabilities of the desiccating filter housings by filtering replicate samples in an eDNA mesocosm study and compared with ethanol preservation. Self‐preserving filters were placed back into original packaging for storage, and samples for both preservation methods were kept at room temperature until extraction at prescribed time points (11 days, 18 days, 25 days, 32 days, 60 days, 88 days, 172 days) post‐filtration. Paired field samples were also collected from six pond locations targeting an additional species to demonstrate field performance. Quantitative PCR results from the mesocosm study indicated that both methods effectively preserved eDNA over a 6‐month storage period, with the self‐preserving filters yielding slightly more target DNA on average (SQ = 329 copies) than ethanol‐preserved samples (SQ = 288 copies) (F1,38 = 4.050, p = 0.051). Neither method showed signs of degradation after 172 days. Results from field sampling indicated a larger difference between preservation methods, with the self‐preserving filters containing approximately 2X the eDNA of ethanol‐preserved samples on average (paired t test, p = 0.020). These data suggest that self‐preserving eDNA filter housings are a viable alternative to standard ethanol preservation methods and may provide higher detection sensitivity in some circumstances. The new filter housings should also help in reducing the risk of sample contamination, minimize protocol steps and result in less plastic waste. Such innovations are important to assure eDNA data quality and to help in facilitating the inclusion of non‐expert sample collectors (e.g. citizen scientists) in research programs.