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I clean when I do an uprooting.
1. Shut the filter off,
2. Run a system one diatom filter
3. Uproot the section I will be working on
4. Let the whole thing settle for a half hour
5. Vacuum the section (surface only)
6. Replant
7. Run the system one for several hours.
8. Turn on the main filter.
I find it's important to get all of the biomass out of the substrate, so I am careful about getting all of the root ball out when I uproot.
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