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I am completely perplexed right now and am hoping someone who is more knowledgeable in waste water treatment can help me out. I recently moved a media flood and drain system from an old setup into an ibc system that I built. The old system had been running for a year or so with a fairly heavy stocking density and had developed quite a bit of organic matter accumulation. I decided to extend the amount of time I could go before I would have to clean out the new system's grow bed by not transfering the bottom inch or two of Hydroton. (commonly reffered to as the sludge zone) Every study I have read about nitrifying bacteria has said that 80 % of the bacteria reside in the top 20 % of the grow bed. If this were true, and I transfered the top 80% of the old media to the new grow bed, I expected not to see much of an ammonia spike. However, I did this about 2 weeks ago and initially my ammonia spiked to almost 2 ppm and is still sitting at about .5 ppm. I didn't feed the fish until the ammonia dropped to .25 ppm (about a week later) and after feeding them a very minimal amount it jumped back up to .5 ppm. It has been at .5 ppm for about 1 week now. I have salted the system to 2 ppt and have been doing 50% water exchanges every two days. (huge pain in the ass)

I did a system transfer around December last year and moved ALL the media and water from the old system into the new and saw a slight ammonia spike for a couple days and then it dropped back down to zero. This transfer was almost the exact amount of fish ans system size. The only difference between the two moves was leaving behind the sludge zone in the recent move.

I did a water analysis of the new system yesterday and got the following readings: ammonia - .5 ppm, nitrite - 0 ppm, nitrate - 100 ppm. These reading are quite peculiar. It would appear that there are some Nitrosomonas  and Nitrobacter bacteria because I am registering nitrates, quite a bit of them.

So this is my theory; a lot of the nitrifying bacteria do in fact reside in the "sludge zone". When I transferred the system I left behind a large amount of the nitrifying bacteria. The bacteria that was successfully transferred was to little to effectively convert all the ammonia the fish are producing to nitrites. Because of this, There is an ammonia spike. Once the nitrosomonas bacteria establish a population to cope with the ammonia load, I'm guessing I'll get a nitrite spike until the nitrobacter builds up it's population. But since it has been two weeks and the ammonia has begun to drop I expected to see at least a slight nitrite spike, but nothing. So perhaps the nitrobacter bacteria can establish themselves quicker than the nitrosomonas bacteria? I guess only time will tell for sure but in the mean time..........If anyone has any other theories or would like to add to this please  do so. Thanks.

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you said the last transfer (with little NH3 spike) was in December. Was the temperature also the same? If the water temp was substantially cooler, then the fish would be providing much less ammonia than they are during warmer times (like now).  Just a thought.

Yes it was. Sorry for not being very specific, I am limited on aquaponics related typing time at work ;) My pH and temperature were the same for each move. I have a 1,000 watt titanium heater in the system and run it at a constant 77 F.  If anything, I was running my pH higher back in December than I am now. I used to keep it around 6.8-7.0. I am wiser now   and keep it between 6.2-6.4

From what I have learned from those with Dr. in front of their names is that a good portion of of the nitrification occurs in the water column itself. So the media is only a portion of the colony.

It makes sense that Benjamin's numbers suggest that the Nitrosomonas didn't make the transfer--though evidently the Nitrobacter/Nitrospira did given the absence of a nitrite spike. the thing that bothers me about Benjamin's model that nitrification is an aerobic process, and the sludge zone sounds like the part of the growbed with the poorest oxygen access. Of the nitrifying bacteria, Nitrosomonas are the ones with supposedly the fastest cycle--they should bounce back quickly.

My next thought is in regard to the pH difference. The bacteria prefer higher pH and would recover faster at the higher pH that you had in December. Maybe you could try goosing the pH upwards for a spell to see if that doesn't let your Nitrosomonas come charging back to life.

@ Jeffery - You said that my numbers suggest that the Nitrosomonas didn't make the transfer, though evidently the nitrobacter did given the the absence of a nitrite spike. I have to partially disagree with that.

I had also mentioned that nitrates were registering close to 100 ppm. Nitrates present in the water means that there is in fact Nitrosomonas converting NH4 to NO2 and the Nitrobacter are doing the NO2 to NO3. If there was no nitrosomonas bacteria present in the water there would be no NO2 and there also would be no NO3. I can only assume that a small portion of my bacterial colony survived the trip, both Nitrosomonas and Nitrobacter. I think it's safe to say the NH4 generated by the fish post transfer is close to the same as it was pre transfer. So if you have the same amount of NH4 entering your system and your bacterial colony has taken a substantial loss, it's only going to be able to convert a portion of that NH4 and you are going to be left with an NH4 surplus. If the Nitrosomonas and nitrobacter sustained equal losses it would make sense that there is no NO2 registering because there was none prior to the transfer. It won't be until the Nitrosomonas bacteria have reestablished that they will be producing enough NO2 to see a spike. But by the time that happens the nitrobacter will have been slowly reestablishing themselves as well and then you wouldn't see a NO2 spike.

I agree with you 100% about the sludge zone and the nitrification process being an aerobic process and it wouldn't make sense for there to be a large population of aerobic bacteria in that part of the grow bed. I have even read in one of Dr. Wilson Lennards papers on aquaponics that 80% of the bacteria reside in the top 20% of the media. If this is 100% true then I don't have the slightest clue what the hell is going on. That theory described above is based off of that ratio being slightly skewed. and the only reason I went down that avenue is for lack of a better theory.

In regards to the pH don't you think that the bacteria would have been acclimated to a lower pH being that they were doing quite well in that environment prior to the move. But, if there is any truth to my above theory, then a part of the bacterial colony is having to reestablish itself, meaning that this new part of the colony has not yet adjusted to the lower than ideal pH for bacteria and thus, is having a hard time establishing itself. Even if all that is true though, trying to bump up the pH to mitigate a .5 ppm ammonia spike might cause more stress to the fish....

@ Jonathan - I have no Dr. in front of my name but that is a very interesting topic and all those guys with Dr. in front of their name could argue whether or not the bacteria prefer free swimming or attachment to a surface. Either way I transferred all the water to the new system too.

I just meant that the Nitrobacter/Nitrospira were evidently abundant enough to at least keep pace with the Nitrosomonas, however the Nitrosomonas that made the transfer were not adequate to keep up with the processing of ammonia from your fish.

BTW, I do have the Dr. tag but it's not like we all become well-versed in everything in "Dr. school," right?

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