Apr 09, 2026

WildinSync - eDNA sampling of surfaces

DOI
https://dx.doi.org/10.17504/protocols.io.3byl489kjvo5/v1
  • David Racine1,2,
  • Martina Lüthi1,2,
  • Kerstin Glaus1,2,
  • Monika Goralczyk1,2,
  • Meret Jucker1,2,
  • Camille Albouy1,2,
  • Arnaud Lyet3,
  • Loïc Pellissier1,2
  • 1Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürch, Zürich, Switzerland;
  • 2Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland;
  • 3World Wildlife Fund, Wildlife Conservation Team, Washington, DC, USA
  • WildinSync
Loïc Pellissier
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DOI: https://dx.doi.org/10.17504/protocols.io.3byl489kjvo5/v1
Protocol Citation: David Racine, Martina Lüthi, Kerstin Glaus, Monika Goralczyk, Meret Jucker, Camille Albouy, Arnaud Lyet, Loïc Pellissier 2026. WildinSync - eDNA sampling of surfaces. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl489kjvo5/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
We use this protocol and it's working
Created: January 22, 2026
Last Modified: April 09, 2026
Protocol  Integer ID: 239117
Keywords: environmental DNA, eDNA, surface, swabbing, sampling, term global biodiversity monitoring under the wildinsync initiative, global biodiversity monitoring, swabbing edna sampling, manual swabbing sampling, detection of species presence, environmental dna, distribution across diverse global habitat, swabbing sampling, diverse global habitat, edna sampling of surface, edna sampling, dna trace, standardized animal inventories for different site, dna extraction, species presence, wildinsync initiative, generating standardized animal inventory, habitat type, vegetation, ecosystem, species, wildinsync, animal, land use, dna
Abstract
This protocol was developed to support long-term global biodiversity monitoring under the WildinSync initiative, which uses environmental DNA (eDNA) to assess the effects of nature-positive actions on ecosystems. Swabbing sampling is performed to capture DNA traces left by animals, enabling detection of species presence and distribution across diverse global habitats. The method consists of standardized swabbing eDNA sampling to capture DNA traces left by animals that interact with vegetation to identify their presence and activity, generating standardized animal inventories for different sites across land uses. It provides guidance on required materials, field sampling steps, and preparation of samples for later molecular analyses (e.g., DNA extraction and sequencing). The protocol is applicable across a wide range of habitat types and environmental conditions worldwide. It does not involve primary sensors or remote-sensing devices; instead, it focuses on manual swabbing sampling as the observing platform.
Materials
Durable equipment
  • Field Sticks flags
  • Extensible Meter (1)
  • Watch (1)
  • Plastic tray to prepare the material (1)

Consumable equipment
  • Swab sampling kit (water tube, 1 swab, 1 pair gloves) (2)
  • Buffer sampling kit (1 buffer tube, 1 pair gloves) (2)
  • Disposable rubber gloves (2 pair / Site)
  • Plastic resealable bags (1000 g) (4 per site)
  • Sample ID label stickers (1 per sample)
  • Pencil (2)
  • Permanent marker (2)
  • Paper tissues (1 package)

Chemicals
  • Ethanol 70% (500 ml)
  • Commercial Bleach (500 ml)
Safety warnings
Sterile technique, chemical handling (Bleach, ethanol)

- Always wear Personal Protective Equipment (PPE): disposable nitrile gloves during sampling, subsampling, and equipment handling.
- Replace gloves between sampling sites and whenever they become contaminated.
- Wear long sleeves and closed footwear suitable for fieldwork conditions.
- Do not leave ethanol, bleach, or used consumables in the field and pack out all waste.
Before start
1 technician or 1 scientist required.

Training Requirements
Available protocol description

Time Needed to Execute the Procedure
150 minutes per site
Safety
  • Always wear Personal Protective Equipment (PPE): disposable nitrile gloves during sampling, subsampling, and equipment handling.
  • Replace gloves between sampling transects and whenever they become contaminated.
  • Wear long sleeves and closed footwear suitable for fieldwork conditions.
  • Do not leave ethanol, bleach, or used consumables in the field and pack out all waste.
  • When ethanol and bleach come into contact, they can generate toxic chloroform vapors.
  • Proper PPE use is essential to reduce the risk of chemical burns caused by bleach and other hazardous reagents.
Material

ABCDE
DESCRIPTIONPRODUCT NAME AND MODELMANUFACTURERQUANTITYREMARK
Durable equipment
Field Sticks flags4To mark the start of transects
Extensible Meter1To measure distances
Watch1To measure sampling time
Tray1To use as a DNA free clean surface for sampling preparation
Consumable equipment
Swab sampling kit (1 water tube, 1 swab, 1 pair gloves)4To collect eDNA
Buffer sampling kit (1 buffer tube)4To preserve eDNA after swabbing
Disposable rubber gloves2 pairs per siteTo clean material before sampling
Plastic resealable bags (1000 g)as many as necessary depending on how many buffer tubes you wish to store per ziplock bagTo store buffer tubes.
Sample ID label stickers1 per sampleTo label buffer tubes
Pencil / pen2To fill metadata, take notes
Permanent marker2To label samples if label stickers are not available
Paper tissues1 package
Chemicals
Ethanol 80%500 mLTo rinse material if no DNA free water is available.
Commercial Bleach 500 mLTo remove DNA from material
Material required for the eDNA sampling of surfaces and taking of plant pictures.

Preparation
  • Before collecting the samples, prepare a space to organise the equipment to ensure the good planification of the sampling process.
  • Put on gloves from the additional glove box.
  • Clean the plastic tray with bleach and paper towels.

CAUTION: To avoid bleach contamination of the environment, wipe the plastic tray with DNA free water and paper towels. If you do not have access to DNA free water, you can use 80% ethanol instead. However, use extreme caution with bleach and ethanol as they can lead to the generation of toxic chloroform vapors. Make sure all bleach residue on the tray has dried before wiping with ethanol.

  • Lay the plastic tray on the defined preparation ground space. It will serve as a clean preparation space for the sampling procedure.
  • Clean the outside of the swabbing and buffer kits with bleach.
  • Set the clean kits on the plastic tray.
  • Clean the scissors and if it is required for labelling the permanent marker, with bleach. Wipe the scissors and the permanent marker with DNA free water. If you do not have access to DNA free water, you can use 80% ethanol instead.

CAUTION: However, use extreme caution with bleach and ethanol as, when mixed, they can generate toxic chloroform vapors. Make sure the cap of the marker is closed to prevent bleach or ethanol from entering into contact with the marker fluid. Make sure all bleach residue on the scissors and permanent marker has dried before wiping with ethanol. Set the cleaned scissors and cleaned permanent marker on the tray.

CAUTION: Swabbing and buffer kits were previously prepared in a sterile clean lab and should be handled carefully.


Sampling kit containing nitrile gloves, DNA-free water and a swab.

  • The sampling takes place within a 1 ha plot. If a specific plot is smaller than 1 ha, it is extended by the surrounding area of the exact same land use type to reach 1 ha.
  • Identify features of the site, such as vegetation, rocks, dead wood, bare soil, buildings, concrete and asphalt and map the site, take overview pictures of the plot.

CAUTION: To prevent eDNA contamination from your shoes, do not walk within the sampling site yet.

  • Place 4 non-overlapping 100 m transects in the sampling area (T1, T2, T3, T4), maximizing vegetation coverage but also representing the overall site ground cover composition to prevent bias. The transects do not need to be parallel but should not overlap.

CAUTION: For better consistency, define the position of the four transects before initiating the sampling.

CAUTION: If the plot is for long term monitoring, preferably use permanent markers and/or precisely note their coordinates.

  • Using field sticks to mark the start and end of transects may be useful.


Illustration of the placement of 4 transects

Sampling
  • Start by putting a marker (e.g. a flag) at the start of the first transect.

Example of marker to mark the position of the start of the transect.
  • Open the swabbing kit with scissors while still wearing the first pair of gloves. Do the same for the buffer kit. Leave both kits in the tray.
  • Remove the first pair of gloves from the swabbing kit and put them on.
  • Do not remove anything from the buffer kit at this point.

CAUTION: Do not touch the exterior of the gloves or anything else inside the sampling kit with your hands to prevent DNA contamination.
Sampling kit containing nitrile gloves, DNA-free water and the swab.

  • While wearing the new gloves, take out the swab and tube containing DNA free water from the swabbing kit.

CAUTION: Make sure not to touch the outside of the swabbing kit to prevent DNA contamination.

  • Moisten the swab with half of the water.
  • For a given transect, at each of 10 points every ten meters, in a 2 meter radius (except behind you, where you have already walked), swab equally for 45 seconds: soil litter (avoid collecting dirt), stems, leaves, and flowers and any surface you deem relevant.

Illustration of vegetation swabbing.

  • If the swab is dried out at the fifth point of the transect, re-wet the swab with the remaining water to prevent it from drying out. Otherwise, continue without re-wetting the swab for the rest of the transect.
  • After having completed one transect, walk back to the clean tray. Follow instructions of the sample preservation section.
  • Repeat the same procedure for the other 3 transects for a total of 4 buffer tubes with swabs per site.



Illustration of the transect method where surface is swabbed every 10m.

Sample Preservation
  • Having returned back to the clean tray, take out the buffer tube from the buffer kit. Make sure to not touch the outside of the buffer kit while doing so.
  • Put the swab in the buffer tube, close the tube tightly and shake vigorously for ten seconds to ensure the buffer is well incorporated into the swab.
  • Label the buffer tube.
  • Put the buffer tube containing the swab into a ziplock plastic bag. Label the ziplock plastic bag.
  • Close the ziplock plastic bag.
  • Remove and dispose of the gloves.
  • Add the label to the metadata. Complete the metadata sheet.
Storage
Store the samples (labeled buffer tubes) in a dry room temperature away from light until extraction.

The use of a refrigerator or freezer for storage is strictly prohibited.
Acknowledgements
The development of this protocol benefited from collaborations with Hoflabor and ETH sustainability as well as the support of the Swiss National Science Foundation and donation via the ETH Foundation.