Jun 25, 2026
Protocol for collecting eDNA sediment samples 2026
- Katrina Lohan1,
- Emma Palmer1,
- Calli Wise1,
- Ruth DiMaria1,
- Lael Collins1,
- Tara Sill1,
- Emma Palmer1
- 1Smithsonian Environmental Research Center, Coastal Disease Ecology Lab
- Coastal Disease Ecology Lab - SERC
Protocol Citation: Katrina Lohan, Emma Palmer, Calli Wise, Ruth DiMaria, Lael Collins, Tara Sill, Emma Palmer 2026. Protocol for collecting eDNA sediment samples 2026. protocols.io https://dx.doi.org/10.17504/protocols.io.81wgbmd6nvpk/v1
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
Created: May 27, 2026
Last Modified: June 25, 2026
Protocol Integer ID: 318057
Keywords: eDNA, sediment, sediment for edna, sediment samples 2026 this protocol, sediment sample, sediment, edna, modified syringe, sample
Abstract
This protocol describes how to collect sediment for eDNA using either a petite ponar or using a modified syringe.
Guidelines
This protocol was developed with the assumption that the end-user possesses baseline knowledge of appropriate aseptic/clean techniques and a comprehensive understanding of the potential risks of contamination inherent to the workflow.
Gloves need to be worn throughout the protocol and changed between sites, once the gloves become dirty, or IMMEDIATELY after any part of the sample has been touched. This minimizes cross contamination during sample collection.
Materials
- Modified BD Luer-Lok 10mL disposable syringe without needle (Fisher Scientific 14-823-2A; 1 per replicate)
- Sterile forceps, spatulas, or scraping tools (1 per replicate)
- Freezer Box 81-place storage (USA Scientific 2381-5048)
- 80-Place Tube Rack (USA Scientific 2380-1008)
- Cryo-Babies tube labels (USA Scientific 9188-2000; Available in roll or sheets)
- Tough-Spots cryo tube labels (USA Scientific 9185-4400)
- Fisherbrand Colored Labeling Tape (Fisher Scientific 15-901-20A; other colors and sizes available)
- Sharpies, ultra-fine and fine
- 3 Ziploc bags for: 1) clean syringes; 2) clean scraping tools; 3) and used syringes and scraping tools
- Cooler with ice
- Ponar grab device
Pre-Field Collection
Label sterile 1.5 mL tubes (total number of tubes = number of samples * number of sample replicates + number of field days) with the following information on the side:
a. Sample ID (should also be written on the top in permanent marker)
b. Collection date (mm/dd/yyyy)
c. Sediment (i.e., sample type)
Set aside an empty 1.5mL tube as a field control. The field control should be carried around in the cooler with ice during field collection and otherwise treated like a sample but remain empty.
Note: One field control is necessary per field day. This is the only kind of field control required for this kind of eDNA sampling.
Field Collection Option #1: Sampling with a Petite Ponar Grab
This is the preferred method when the water is too deep for an individual to readily collect the sediment.
This method can be used by one person or by two people, one with “dirty hands” and the other with “clean hands” handling the sample. “Clean hand” tasks should always be performed wearing a clean pair of nitrile gloves. Tasks designated as “dirty hands” can be performed with or without gloves, but gloves should be donned or changed before transitioning to “clean hand” tasks, such as touching the sample, to prevent contamination.
When collecting your sample, it is important to collect your sample(s) from areas of the sediment that did not contact the edge or bottom of the ponar grab which may be contaminated from past samples. There is currently no good way to sterilize the ponar device in the field completely before redeployment.
Dirty hands: Deploy a sediment ponar grab following gear-specific protocols.
Dirty hands: If your ponar has an open top and sediment can be reached without tilting or opening the device, proceed to step 3.4.
Or
If the top of your ponar is sealed and inaccessible, lift the ponar onto the working surface and lean it on its side so the sediment will not fall out when opened (see Figure below).
Dirty hands: open the ponar while it’s on its side so the sediment does not fall out of the device.
Clean hands: to collect your sample, start with the sterile syringe plunger pushed all the way down. Identify the area to be sampled.
Note: The edges of the ponar grab are contaminated, always sample from the middle of the sample (see figure below).
Clean hands: Place the sterile syringe into the sediment and push down while gently pulling up on the plunger so sediment fills the syringe.
Clean hands: Fill the syringe at least halfway with sediment, but do not remove the plunger.
Remove the syringe from the sediment.
Clean hands: Push the plunger a little to remove the first 1-2 mL of sediment.
Clean hands: If accessing the sediment to sample from the top of the ponar, fill the 1.5 mL tube with the surface sediment as depicted in the above figure using a sterile* tool (such as a scoop, spatula, pair of forceps, etc.).
Or
Clean hands: If accessing the sediment to sample from the bottom of the ponar, fill the appropriate 1.5 mL tube with the middle section of the sediment as shown in the above figure with a sterile* tool (such as a scoop, spatula, pair of forceps, etc.). Do not sample from the last ~2mL of sediment inside the syringe as it may have touched the edges of the ponar.
Note: A tube rack may be useful to stabilize the 1.5mL tubes while filling.
* See DNA Sterilization Techniques Protocol 2026 for appropriate sterilization methods.
Clean hands: Seal the lid of the 1.5 mL tube place the tube in a storage box (plastic ideal) in a cooler on ice.
Place the used syringe and forceps into a Ziplock bag labeled “dirty”.
Repeat steps 3.4-3.11 until all of the replicate sediment samples for the site have been collected from the middle section of the sediment, ensuring that the sampled area does not touch the edge of the ponar.
Note: every replicate sample needs to be collected using its own sterile syringe.
Rinse the ponar gear between samples by dipping repeatedly in surface water until it appears clean.
Repeat steps 3.1-3.13 until all the samples across every site have been collected.
Field Collection Option #2: Sampling with a Modified-Syringe
This is the preferred method when the water is shallow enough that an individual can readily reach into the water to collect the sediment, or when using SCUBA or snorkeling to reach the sediment.
While wearing gloves, stand downstream from where you plan to collect the sample.
Start with the sterile syringe plunger pushed all the way down.
Place the syringe into the sediment and push down while gently pulling up on the plunger of the syringe so the sediment core sample fills the syringe.
Fill the syringe at least halfway with sediment, but do not remove the plunger.
Remove the syringe from the sediment.
Push the syringe plunger until only ~2mL of sediment remains inside the syringe. Keep in mind that the bottom of the syringe has been cut for core sampling, so the measuring increments do not start at zero.
Using a sterile* tool (such as a scoop, spatula, pair of forceps, etc.), fill the appropriate 1.5 mL microcentrifuge tube with sediment.
Note: A tube rack may be useful to stabilize the 1.5mL tubes while filling.
* See DNA Sterilization Techniques Protocol 2026 for appropriate sterilization methods.
Seal the lid and place the tube in a storage box (plastic ideal) in a cooler on ice.
Place the used syringe and forceps into a Ziplock bag labeled “dirty”.
Repeat steps 4.1-4.9 until all the replicate sediment samples for the site have been collected.
Note: every replicate sample needs to be collected using its own sterile syringe.
Repeat steps 4.1-4.10 until all the samples across every site have been collected.
Back at the Lab
Upon returning to the lab, check that the sample tubes are properly labeled. Seal the tubes with parafilm and place the storage box in a -80°C freezer.
If using a -20°C freezer unit, make sure the freezer is manual defrost, especially if using the freezer for long-term storage. Repeated freeze/thaw cycle of automatic defrost freezers can lead to shearing and degradation of DNA.
The storage box should be labeled with:
a. Lab
b. Project and Year
c. Contact name
d. Contents: i.e. Sediment samples (include preservative if using)
e. Box X of Y (if multiple storage boxes are used for the project)
f. Label both the lid and the box base using lab tape and sharpie.
If needed, ship the samples overnight on dry ice to their final destination. Dry Ice shipping may require Dangerous Goods IATA/DOT shipping certification.
Syringe cores and forceps should be washed clean then sterilized in a bleach solution (see DNA Sterilization Techniques Protocol 2026 for appropriate sterilization methods) before being reused for additional sampling.