Water

Herein processes follow lab SOP for the ‘Detection of Non-Indigenous Marine Species from Port Water Samples’ (Chaves et al., 2025) within Biodiversity Genomics Europe project. This is mirror for the workflow hosted in WorkflowHub (which hosts the downloadable PDF).

Sylphium dual filters

The Biodiversity Genomics Europe project uses Sylphium dual filters to ensure efficient and clean filtration of water samples for metabarcoding. These filters are designed to capture a wide range of DNA fragments while minimizing contamination risks.

Note

Water samples are generally low DNA yeild samples, thus especially prone to contamination compared with other sample types. Thus, prepare the samples under laminar flow hood with UV lamps for UV sterilization.

Check filters

Clean the working space and material with disinfectant (e.g. 5-10% bleach) and ethanol (to vipe off bleach) and leave the UV light on for at least 15 mins.

Check if filters have leaked, have less than ~2 mL of ATL buffer inside. If yes, then:

Thaw and clean the outside of the capsules using a disinfectant. Refill them with 2.5 mL ATL buffer and seal each cap with parafilm.
Incubate in the oven at 37 ºC for 30 min.

Prepare filters for DNA extraction

Set the oven at 56ºC
Clean the working space and material with disinfectant and ethanol and leave the UV-light on for at least 15 minutes;
Use filtered pipette tips at all steps;
For each 23-sample batch, include a negative control (PNC) by preparing a 15-ml tube with 2 mL ATL + 50 μL Proteinase K (20mg/mL).

Thaw the capsules and clean the outside of each capsule using a disinfectant solution.
Fill each capsule with 60 μL of Proteinase K (20mg/mL) and shake it manually.
Seal each capsule cap with parafilm, and incubate at 56ºC overnight in the mechanical shaker.

Proceed with DNA extraction.

References

Chaves, C., Najera-Cortazar, L. A., Martins, F., Veríssimo, J., Dunshea, G., & Price, B. (2025). Detection of Non-Indigenous Marine Species from Port Water Samples. WorkflowHub. https://doi.org/10.48546/workflowhub.sop.11.2