Can bacteria nitrify ammonia if it is bonded to a base?

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nst.john
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If an ammonium ion is bonded to let's say chlorine for simplicity sake, and NH4Cl is created, can nitrifying bacteria come in and still create nitrites and nitrates from the ammonia if it is bonded to the chlorine? I am asking this because I am planning to make a schematic for an aquaponics set-up and I want to balance the amount of ammonia in the water as possible, in my case with a base not chlorine, in order to be able to add more ammonia at once to the system without the water reaching toxic levels. Thank You!
 
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Can you rephrase your question? It appears you wish to use a different anion than chloride, but the way you've written it, it also appears you think that ammonium salts are undissociated in aqueous solution.
 
Thats true. So the dissociated salts will have no effect since the ammonia is In ion form. Thank you
 
NH4+ is very soluble in combination with most common anions, but not all ions bacteria want to use are nicely soluble. For example, Fe3+ often sediments and concentrations naturally become very low. So siderophores are released to chelate Fe3+ ions away from their salts to make them bioavailable.
 
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