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Try 50mg/L of salt and do a water change a week later. That should hurt the organism. The dirt is leaching food for the organism. With enough water change, the food should reduce.
 

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Too much salt can be bad for plants but 2.5g in 50L is fine.

Another option is 3% hydrogen peroxide. Dose no more than 1.5ml/Gallon.

Another option is biological. Small fish should eat those protozoans. Filter-feeding crustaceans should work too like daphnia.
 

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Correction on the peroxide dose. It’s 1.5ml/ gallon. Or 1.5ml/ 3.7L

Oh, on the peroxide, do a water change after an hour of dosing. Peroxide is relatively safe in appropriate dose. It breaks down to water and oxygen.
 
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