See post for details on extracting DNA from the mussel shell swabs part 2.
Background info on the project
Post: FHL 2026 Experiment Details
Swabbing the Mussel Shells
At the experiment take-down, I saved the mussels in the treatment bags they were already in by putting them immediately into the -80C.
Dissecting out the mussel tissue for DNA extraction happened in the Roberts’ Lab, and at the same time I swabbed the shells and saved the swabs at -80C.
Protocol here.
Essentially, I pulled the whirlpak bags out of the -80C and let them thaw at room temp for 1.5hours.
Then for each bag, I opened it wide, laid it flat on the table, and pushed the mussel up towards the opening of the bag, making sure the upward-facing shell half was not rubbing along the inside of the bag on the way up. I then took a sterile flocked-tipped cotton swab and swabbed the mussel shell for 10 s, put it into a labeled 1.5mL tube, and into the -80C.
Extracting the DNA
I followed the same protocol as for the eelgrass tissue swabs. I used the modified protocol from Becca Maher (she extracted DNA from cotton swabs that had swabbed eelgrass tissue). I used the DNeasy PowerSoil Pro Kit (50) (QIAGEN® catalogue: 47014). Protocol notes: here.
Samples Processed:
| sample_id | treatment_id | treatment | sample_type |
|---|---|---|---|
| SM_EM_02 | EM | eelgrass + mussel + sw | shell swab |
| SM_EM_06 | EM | eelgrass + mussel + sw | shell swab |
| SM_EMVP_04 | EMVP | eelgrass + mussel + vp | shell swab |
| SM_EMVP_05 | EMVP | eelgrass + mussel + vp | shell swab |
| SM_EMVP_07 | EMVP | eelgrass + mussel + vp | shell swab |
| SM_MSW_05 | MSW | mussel + sw | shell swab |
| SM_MSW_06 | MSW | mussel + sw | shell swab |
| SM_MVP_03 | MVP | mussel + vp | shell swab |
| SM_MVP_05 | MVP | mussel + vp | shell swab |
| SM_MVP_06 | MVP | mussel + vp | shell swab |
| SM_ShSW_02 | ShSW | mussel shell + sw | shell swab |
| SM_ShSW_03 | ShSW | mussel shell + sw | shell swab |
| SwabBLANK3 | BLANK | NA | shell swab BLANK |
| SwabBLANK4 | BLANK | NA | shell swab BLANK |
Becuase in yesterday’s extraction I initially was going to process n=16 samples + 2 Blanks, today’s DNA extraction Blanks are 3 and 4. I forgot to adjust the numbering from yesterday’s sample loss which resulted in my extracting DNA from n=15 samples and 1 blank.
Next Steps
Run 2ul of the DNA in triplicate on qPCR targetted for Vibrio pectenicida.
The extracted DNA lives in the right -80C in FTR.