Environmental DNA (eDNA) Collection Protocol

NAMC eDNA sampling methods are derived from the methods published by the Carim et al 2015 publication.

General procedures

  • Prior to sampling in the field, the detailed published protocol should be thoroughly reviewed (Carim et al. 2015 – A Protocol for Collecting Environmental DNA Samples From Streams). This protocol details how to collect the eDNA sample in a sterile way to minimize the risk of cross contamination. It also describes the necessary equipment.
  • Collect the eDNA sample at the most downstream location of each reach.  Note that the beginning of each reach is considered meter 0. If the reach being sampled is partially dry, or very low flow, it may be necessary to move upstream until a suitably wet location is found. 
  • Use a measuring tape to measure as accurately as possible where the sample is taken and record the meter number. Again, the meter number will generally be 0 for each reach.
  • Applying the protocol by Carim et al. (2015), filter 5 liters of stream water or use a maximum of two filters per reach (however many liters of water that turns out to be, up to 5 liters maximum). Note that using multiple filters becomes necessary when turbidity is high or flows are very low and sediment gets stirred up and clogs the filter.
    • In certain circumstances, when flow is very low in late summer, it may be necessary to use a plastic cup (included in the eDNA test kit) to fill the filter apparatus. This is required because the low flow does not permit adequately submerging the filter apparatus.
  • After placing the filter(s) in the vial with desiccant, label the vial with a Sharpie or other permanent marker. Then place the vial inside a Ziploc sandwich bag which is also labeled with the Sharpie. Finally, add a labeled rite-in-the-rain tag inside the Ziploc bag.
  • All labels should consist of: date collected (mm-dd-yyyy)
    • stream name
    • reach #
    • meter #
    • # of filters used
    • # of liters of water filtered total
  • At the end of each day, take a blank sample with distilled water when you get back to the field vehicle. The blank sample entails using a new eDNA test kit to filter 1 L of distilled water. These blanks are used to assess potential cross contamination.
  • Store the eDNA samples in a refrigerator before transport to lab. When transporting the eDNA samples back to the lab, place them in a cooler with ice. Care should be taken at all stages of transport to keep the eDNA samples out of the heat and direct sunlight. On return from field sampling, eDNA samples should be stored in a -80C freezer.

Sterilize equipment

  • At the end of each day, use bleach solution to sterilize all equipment that was used in sampled streams. These items include the dip-net, ruler, and pump tubing used for eDNA collection, as well as waders if used.