Apr 06, 2026
eDNA Leaf Swabbing Protocol
- Christina Lynngaard1,
- Benitho Konan Goli2,
- Olivia Dimov2,
- Lorenzo Lagostina2,
- Cato Vangenechten3,
- Pauline Van Leeuwen3,
- Lucinda Kirkpatrick4,
- Jan F. Gogarten2
- 1Section for Molecular Ecology & Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;
- 2Helmholtz Institute for One Health Helmholtz-Centre for Infection Research (HZI) Department of Applied Zoology and Nature Conservation, University of Greifswald, Greifswald, Germany;
- 3The Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium;
- 4School of Environmental and Natural Sciences, Bangor University, Bangor LL57 2DG, United Kingdom
Protocol Citation: Christina Lynngaard, Benitho Konan Goli, Olivia Dimov, Lorenzo Lagostina, Cato Vangenechten, Pauline Van Leeuwen, Lucinda Kirkpatrick, Jan F. Gogarten 2026. eDNA Leaf Swabbing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly5eqrvx9/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 28, 2026
Last Modified: April 06, 2026
Protocol Integer ID: 241723
Keywords: Environmental DNA (eDNA), Surface swabbing, Biodiversity monitoring, Non-invasive sampling, compatible method for leaf edna sampling, leaf edna sampling, leaf swabbing protocol, leaf swabbing protocol this protocol, dna capture, environmental dna, diversity of leaf surface, plant species, biodiversity study, leaf surface, dna, plant leaf, edna, swab, species
Funders Acknowledgements:
Horizon europe
Grant ID: 101134969
Abstract
This protocol outlines a standardized method for non-invasive collection of environmental DNA (eDNA) from plant leaves. Swabbing is conducted on a diversity of leaf surfaces, heights, and plant species, with swabs moistened in NAP buffer or RNAlater to maximize DNA capture. This approach provides a reproducible and field-compatible method for leaf eDNA sampling, suitable for ecological and biodiversity studies.
Guidelines
- Apply consistent sampling startegies across all sites to ensure comparability of data.
- Record metadata for each sampling session, including date, time, GPS coordinates, habitat type, and prevailing weather conditions.
- Avoid sampling during rainfall or immediately following rain events.
Materials
Materials:
- Watch/Timer
- 1mL tubes, suitable for freezing samples down to -20°C, filled with 0.5mL NAP buffer.
- NAP buffer (link for how to make NAP buffer: https://www.consevol.org/resources/buffer_miguel.pdf) or RNAlater.
- FLOQSwabs or sterile cotton swabs
- Gloves (not necessary)
Safety warnings
When sampling, wear appropriate field gear (e.g., gloves, boots, long sleeves) to prevent injury from terrain, insects, or sharp vegetation.
Ethics statement
The protocol involves non-invasive environmental sampling and does not involve the handling, disturbance, or harm of animals or protected plant species. Necessary permits and permissions for site access and sample collection should be obtained where required.
Before start
- Ensure all permissions (e.g., landowner consent, protected area access) are obtained ahead of time.
- Ensure all required materials, reagents, and equipment are prepared and available.
- Confirm that NAP buffer or RNAlater is at room temperature and fully dissolved (no visible crystals).
Preparing material for sampling
Add 0.5 mL of NAP buffer or RNAlater to each cryotube.
If crystallization is observed in the NAP buffer prior to sample collection, dissolve the crystals by warming the buffer to 37 °C, or if required to 65 °C for up to 30 min. The presence of small crystals at the tube opening is common and does not affect buffer performance.
Label crytotubes with a sample ID.
When using acoustic monitoring devices: Select swabbing locations based on the placement of the acoustic detectors. Swabbing should be conducted within a 50 m radius of each acoustic detector location.
Sampling protocol
3m
Personnel must wear clean disposable gloves at all times during sample collection and handling to minimize contamination risk. At the beginning and end of each swabbing session, collect a negative control by opening a sterile swab and transferring it directly into the storage buffer without contacting any surfaces.
For approximately 3 minutes, swab leaf surfaces, targeting a diversity of plant species and heights within the sampling area and moving between plants as needed.
3m
Open a cryotube containing NAP buffer and briefly dip a sterile swab into the buffer to moisten it. Close the cryotube immediately to prevent spillage during swabbing. Swab the entire leaf surface, including grooves or rills where dust and particulate matter may accumulate. Apply moderate pressure during swabbing, avoiding excessive force that could damage or crush leaves. Avoid collecting excessive plant material (e.g. visibly green swabs), as plant compounds may interfere with downstream laboratory analyses.
Place the swab into the labeled cryotube according to the established labeling protocol.
Store the cryotube at room temperature for a minimum of 24 h to allow thorough interaction between the swab and the buffer. Transfer the cryotube to a −20 °C freezer as soon as feasible. Maintain an optimal cold chain throughout handling and storage, and minimize freeze–thaw cycles.