Dec 11, 2025
Version 1
TorpeDNA sampling for Elkhorn Slough V.1
This protocol is a draft, published without a DOI.
- jbrant 1
- 1Stanford Center for Ocean Solutions
Protocol Citation: jbrant 2025. TorpeDNA sampling for Elkhorn Slough. protocols.io https://dx.doi.org/
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: Working
We use this protocol and it's working
Created: December 11, 2025
Last Modified: December 11, 2025
Protocol Integer ID: 234827
Keywords: environmental dna around elkhorn slough, torpedna sampling for elkhorn slough sample, elkhorn slough sample, environmental dna, ecological assessment after the fire, torpedna sampling, elkhorn slough into moss landing harbour, ecological assessment, elkhorn slough, sampling, rain event, measure throughout rain event, moss landing harbour, off of contaminant, baseline of diversity, contaminant
Abstract
Sample environmental DNA around Elkhorn Slough as an ecological assessment after the fire of a battery depot. The sampling aims to establish a baseline of diversity and measure throughout rain events for the run-off of contaminants (Cobalt, Nickel, and Manganese, not in this protocol) from the Elkhorn Slough into Moss Landing Harbour and MontereyBay.
Attachments
Guidelines
19. Use a pair of tweezers to remove the O-Ring. Either fold the filter (3x) on the surface of the sieve in the TORPeDNA cup or remove the filter from the surface and, while holding it with two tweezers, roll it like a small burrito to fit the Eppendorf tube.
20. Put the filter into the 2mL Eppendorf tube, try to avoid touching the filter surface with the tweezers to not scrape off any sedimented DNA.
21. Once the filter is in the tube, close the lid and add a label to the side of the tube. Put it into the tube box and put it on ice.
Materials
1. TORPeDNA device (a torpedo-shaped sampler to be towed)
2. Filters (20μM Nylon for our methods)
3. Gloves
4. RNAse away
5. Kimwipes
6. Eppendorf tubes (2 mL)
7. Tube racks
8. 2x Metal Tweezers
9. Wash station (50 mL Falcon tubes with 10% Bleach, RNAse away, MilliQ water, 70% EtOH)
10. Sharpie
11. Labels
Sampling of eDNA
Put on gloves.
As we are sampling replicates, take two TORPeDNA devices out of their bags to be used in parallel. Fix the two TORPeDNA Devices together with a cable tie and Ducttape so that they can be deployed pairwise.
Make sure the TorpeDNA have their mounts on or are properly attached to a rope.
If needed, take blanks first by rinsing the TORPeDNA with MilliQ or deionized water, set up filters, and filter 1L of MilliQ through a filter.
Open the cup at the bottom of the TorpeDNA and put it on a clean surface.
Before handling a filter, clean the tweezers. Submerge the tweezers in the four different wash solutions (bleach 3e EtOH) and dry them.
With one clean tweezer, take out the O-ring and either put it on a clean surface or push it to the site.
Open the filter box and remove the blue dish (spacer) with the pair of clean tweezers.
Get a hold of a white filter paper with your tweezers and place it directly onto the sieve, at the bottom of the cup, making sure it covers the entire area.
Add the O-ring on top of the filter and make sure to push it into the ring to make it fit tightly.
Screw back the bottom to the TorpeDNA device.
Once the boat is going at 2 knots, deploy the TorpeDNA device into the water and tow it for 3 mins behind the boat. Pull the device back on board and let the rest of the water drain through the filter.
With clean gloves, prepare a clean surface with two 2mL Eppendorf tubes, and slightly unscrew the top. Clean the tweezers through the wash station.
Unscrew the bottom of the TopeDNA device and put it onto a clean surface.
Use a pair of tweezers to remove the O-Ring. Either fold the filter (3x) on the surface of the sieve in the TORPeDNA cup or remove the filter from the surface and, while holding it with two tweezers, roll it like a small burrito to fit the Eppendorf tube.
Put the filter into the 2mL Eppendorf tube, try to avoid touching the filter surface with the tweezers to not scrape off any sedimented DNA.
Once the filter is in the tube, close the lid and add a label to the side of the tube. Put it into the tube box and put it on ice.
Acknowledgements
The TORPeDNA is a passive sampling device developed by Prof. Xavier Pochon et al. at the Calthrow Institute in New Zealand and deployed and tested for this project.