eDNA Sampling Protocol – Filtering Water to Capture DNA from Aquatic Organisms

Authors: M Laramie; David S Pilliod; Caren S Goldberg; K Strickler
Contribution Number: 509

https://pubs.usgs.gov/tm/02/a13/tm2a13.pdf

Abstract/Summary

This publication is meant to serve as a how-to guide for collection, concentration, and preservation of eDNA samples from lentic and lotic systems and provides three sampling protocols and a list of necessary supplies similar to those used by Goldberg and others (2011), Goldberg and others (2013), Pilliod and others (2013a), and Laramie and others (2015). These protocols have been used to reliably and consistently collect and concentrate eDNA from stream samples. However, adaptations to these protocols may be necessary, depending on target taxa or environmental conditions of the system being sampled. The protocols included in this document utilize cellulose nitrate filter membranes with a 0.45μm pore diameter (see Appendix A for supplies list) for water samples ideally ranging from 250ml to 1000ml. Samples collected from streams or ponds with an abundance of impurities such as tannins and organic materials will likely be limited to 500ml or less, using the described filter type. Alternative filter materials, with lower protein binding affinities, such as cellulose acetate have been successfully substituted to increase water sample volume and reduce clogging of the filter membrane (Takahara and others 2013). Additionally, filters with a greater pore diameter (0.45μm-3.0μm+) could also reduce clogging of the filter, increasing the sample volume, when desired. Turner and others (2013) provides an isocline equation to predict eDNA collection equivalents for various pore size and sample volumes using carp as a model organism. Essentially, with greater pore size, you risk eDNA molecules passing through the filter without being collected but are able to filter a greater volume of water. Examination of literature or empirical testing may be necessary to determine the most suitable materials for your desired application. Additionally, researchers must also consider the ecology of the target organism and the characteristics of the water body being sampled to determine the most suitable locations within a body of water to collect water samples (e.g. stream margins, thalweg). When possible, it is advised that samples be collected without entering a stream or pond, simply to reduce the probability of contaminating the site, boots and clothing, and/or sampling equipment.

Publication details
Published Date: 2015
Outlet/Publisher: US Geological Survey
Media Format:

ARMI Organizational Units:
Pacific Northwest - Biology
Topics:
Monitoring and Population Ecology
Keywords:
detection; DNA; eDNA; filter; genetics; methods; monitoring; PCR; primers; qPCR; water
Notice: PDF documents require Adobe Reader or Google Chrome Browser (recommended) for viewing.