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Let diatoms do their work. After a week or so I would do check with microscope again to se how it goes. If mos diatoms I would vacuum the top up the silicates and wait again. Once you see more than 90 % diatoms only I would stop dosing and vacuum after an another week. The rest would be work for CUC. You will see fish will start to pick if it is mainly diatoms.For how long should I do that? It has been months and not much progress.
Also, should I siphon the sand bed or just leave it and let diatoms kill it?
On which stain did it work? On the Amphidinium tread people had mixed results.Have you looked into elegant corals dino treatment? I'm a big fan of that. It worked on 2 of my tanks. Just watch your nutrients as it'll bottom them out rapidly. I had to do it 3 weeks in a row and I've been dino free in one tank since. The other was dino free for about 8 months until I decided to do a series of 30% water changes every day for a week straight to drop my nitrates from over 100 to 10.