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Biodegradation - Are bacteria rendering your quarantine process useless?


Dr. Fish
Content Moderator
Feb 3, 2017
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Biodegradation is the term given to the breakdown of organic chemicals by the biological action of a living organism.

How is this relevant to our aquariums and in particular, a quarantine tank (QT)? Every single medication you dose (EXCEPT COPPER) is susceptible to biodegradation. (Liquid copper is a poison, not a true medication.) What happens in any aquarium is bacteria (especially biofilm and heterotrophic bacteria) decomposes any medication it comes into contact with. How rapidly this occurs is usually directly related to how mature an aquarium is. This is why it is often very difficult to successfully use medications in a display tank (DT) environment with rock & sand which harbors tons of bacteria.

Biodegradation in a QT: To be clear, it is always optimal to dose medications in as sterile an environment as possible (meaning, no biofilter). However, this is often not practical due to ammonia produced by fish waste, uneaten food, etc. So the next best thing is to setup your QT with as little nitrifying bacteria as possible. (I.E. Don't overdose the bacteria in a bottle product you are using when setting up a QT.) Also keep in mind the longer a QT is set up, the less effective the medications you dose will be. Therefore, you will eventually need to sterilize and reseed your QT. How long? I would do it no less than every 3-4 months.

QT and Biofilm: A biofilm is any group of microorganisms which stick to each other and then adhere to a surface. Think bacteria sticking to the glass of a QT. It will look hazy and you won't be able to just rub it off using an algae pad. The only way to remove it is drain the tank, and use detergent, Isopropyl Rubbing Alcohol or possibly H2O2. Ideally you would find a fish-safe detergent followed by 20 min alcohol application. H2O2 would be a second choice, but bleach is no good in this situation.

How to sterilize + reseed any tank: Ideally, you would take the QT outside, wipe everything down using vinegar and then allow to thoroughly air dry (which sterilizes). If you encounter any "rough patches" (like biofilm) on the tank or equipment use one of chemicals mentioned above to remove it. A faster method (assuming no biofilm is present) is outlined below:
  1. Dose 100ppm chlorine as per this guide: https://dec.vermont.gov/sites/dec/files/dwgwp/DW/chlorinedosageemergencydisinfection.pdf
  2. Stir the sand and use a powerhead to blow inside any large rock to ensure the chlorinated water reaches every part of your tank.
  3. Circulate well for 48 hours, and then use sodium thiosulfate to neutralize the chlorine in the water. Most pool places sell a product called Chlor Out which contains sodium thiosulfate and is safe to use. You can use this website to determine how much sodium thiosulfate to dose: https://www.edspumps.com/water-treatment/documents/Antichlorination.pdf
  4. After you are all finished, your alkalinity might need to be raised. If so, use baking soda as per this calculator: Reef Chemistry Calculator
  5. Dose nitrifying bacteria (products tested here and here) for at least 1 week in order to reseed.
P.S. I've also attached a spreadsheet you can use to determine all of the above.

Further reading:




Supporting Member
Apr 20, 2007
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it would explain why a 7 day prazi treatment in DT did not eliminate flukes. i suppose there really is no way of calculating breakdown rate and subsequent degradation in potency.. and another reason to set up a qt tank for incoming arrivals.