Aug 31, 2025
Version 1
eDNA Collection from Freshwaters using Filter Capsules V.1
This protocol is a draft, published without a DOI.
- Vid Švara1
- 1FH Kärnten gGmbH
Protocol Citation: Vid Švara 2025. eDNA Collection from Freshwaters using Filter Capsules. protocols.io https://protocols.io/view/edna-collection-from-freshwaters-using-filter-caps-g8r5bzv87
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: August 29, 2025
Last Modified: August 31, 2025
Protocol Integer ID: 225821
Keywords: filter capsules edna collection protocol, using filter capsules edna collection protocol, collection from freshwater, biological material from freshwater, freshwater, collecting biological material, collection
Funders Acknowledgements:
ÖAW
Grant ID: DI-2023-035
Abstract
eDNA collection protocol for collecting biological material from freshwaters.
Materials
Waders
DNA-free Gloves
Tellescope pole with a bottle holder
DNA-free Bottles/Cup for water collection
Distilled water
5 mL tubes filled with preservative (e.g. lysis buffer, Longmire solution, absolute
EtOH)
ATL buffer per tube
50 mL Syringes water pump
eDNA filters (Glas fiber, 2,5 and 5 cm GFF 0,7 µm) with a housing inclding a Luer connector
DNA-free Forceps
Negative controls (e.g., distilled water and a bottle for testing)
A box for storing sample tubes
Paper towels
Storage box with ice packs
Troubleshooting
Sampling Preparation
Wear new disposable gloves for each sample and while handling DNA-free material to avoid cross-contamination.
Prepare and 5 ml Eppendorf tubes containing 600 µl of ATL buffer for each sample. are labeled.
In you notebook or smartphone, note (describe) exact location where the sample was taken.
Select up to 5 sampling sites along the stretch of the water body that shall be sampled.
Rinse the collecting pole with some distiled water before the start of the sampling and dip the in the water body at least 5 m away from sampling points to clean it.
Attach the collecting bottle.
Water Collection
From the shore, collect water using a telescope pole with a bottle attached to it by dipping the pole with the bottle up to 50 cm deep in the water.
In a river, this step may be substituted by entering the river and collecting the water into the bottle against the current or by filtering the water directly to the filter by a pump.
Collect the bottle and detach it from the pole and put it on a flat clean surface.
Sample Filtering
Grab a syringe and pull the water into the syringe.
Grab a filter capsule with a filtering sheet from a sterile bag.
Screw a filter capsule on the syringe and press the water through the filter.
Repeat these two steps until you filtered a minimum 200 mL of water from each of the five sampling points you selected.
In case you are using a pump, you can attach the filter on a a pump tube and proceed filtering the water from the bottle.
Sample Storage
When the sampling is finished, remove the filter capsule from the syringe, pull air in the syringe, attach the filter capsule again and push air through the filter to dry it. Repeat 3-5 times.
Prepare DNA-free forceps and the 5 mL tubes.
Open the filter capsule and, using sterile, forceps take the filter from the capsule and place it in a tube with buffer or in a in a sterile, DNA-free tube.
Place the tubes in the sample box and keep it at 4 °C or lower until further processing.