Does my decade old sand bed actually nitrify? Who eats Ammonia in our tanks?

taricha

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Key points:
  • My system is capable of removing ammonia quickly: ~4ppm/day total ammonia-Nitrogen (TAN)
  • The sand processes ammonia slowly: ~0.1-0.2ppm/day TAN meaning the other 95+% happens somewhere else
  • The tank water itself also has detectable ammonia processing: ~0.05ppm/day TAN [Tank water itself not doing anything: see update in post 48]
  • In the sand and the water, the processing is provably Nitrification
  • A Recommended Minimum Dose of Biospira consumes ammonia faster straight out of the bottle than my 10 year old sand
  • I don't know if this is good or bad


The classic idea of nitrification is that ammonia is oxidized to nitrite and nitrate by bacteria in surfaces like sand, rock, and filters. But ammonia is also the preferred N source for photosynthetic organisms. Everything from coral to single cell algae. Additionally, heterotrophic bacteria can use whatever organic carbon sources are available to consume ammonia as well. So Just because ammonia disappears doesn't mean that it went through the ammonia -> NO2 -> NO3 "cycle", it might've just been consumed and become biomass instead.

There's a somewhat contrarian theory that in some tanks, ammonia mostly goes to algae and coral and very little gets nitrified at all.
See this article for that idea: #1 WHAT IF I TOLD YOU... Ammonia is causing your algae problems?
Also AquaBiomics finds some systems that have lots of nitrifiers and some that have barely any Ammonia Oxidizing Bacteria (AOB) and undetectably low Nitrite Oxidizing Bacteria (NOB). Article: The Microbial Community in a Professional Coral Aquaculture System
As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae.


Anyway: Some things made me think I have a system that would fit this - processing ammonia in non "cycling" ways, so I went looking for data to measure my ammonia eaters. This answered a lot of Q's for me and raised a few more.

As a baseline comparison, here's the tank response to a one-time dose of ammonia during the day period, just a few measurement to get the general size and scale of the rates my system processes ammonia. (pH was 8.0 - this level of ammonia is well below EPA 1-hr level of 2.9 TAN @ pH 8)

Ammonia Tank Rate.png


The tank consumed ammonia at 0.161ppm/hr Total Ammonia Nitrogen (TAN). This works out to 3.9ppm/day.

So how much of this actually happens in the sand?

I dosed tank water to just under 0.5ppm TAN and split it into 100mL samples. Four samples got a series of different amounts of sand 0%,1%, 2% or 5% (a.k.a. 1, 2, or 5mL in 100mL sample) of white sand from the top of the sandbed where water flows across it pretty well.
Two other samples got1% sand + newly opened bottled starter products:
1% sand + BioSpira (recommended minimum dose)
1% sand + One and Only (5x recommended minimum dose)
They were placed in the dark on an orbital shaker at 70 rpm to keep the water moving and tested over 2.5 days.

Ammonia Rates .png


The series of samples with varying amounts of sand are in shades of blue, the 1% sand + biospira (red) acted more like the 5% sand. The 1% sand + One and Only (green) acted basically like just 1% sand. The trendlines were used to estimate the consumption rates.
Surprisingly, even no sand at all - just 100mL of water clearly consumed ammonia. [not repeatable: see post 48 update]

Here's visualizing the rate of ammonia consumption (slopes from previous graph) vs the amount of sand there was.
Amm Rate vs Sand.png


There is probably diminishing returns for higher levels of sand since at 5% the sand is piling up and a smaller portion is in contact with the moving water. BioSpira +1% sand clearly effective above what the 1% sand in the sample could do, while One and Only had no detectable effect. What proportion of sand is most applicable to my tank? My tank water is 40cm deep, and likely only the top 1cm of sand (or less) is reasonably in contact with moving water above, so 2% or less seems a good ballpark approximation to how my sandbed behaves.
I therefore estimate my tank sand can eat somewhere in the range of 0.10 to 0.15ppm/day TAN, or only <4% of my overall system consumption of 3.9ppm/day, meaning only 4% of that maximum daily ammonia consumption could be done in the sand+water.
Speaking of water, this graph makes it really clear that my tank water processes ammonia. In the 1% sand samples, the water may be doing half the work. Crazy! (Ammonia Oxidizing Archaea??)
[edit: Not repeatable. See post 48 for better data]

Okay one last thing. I haven't actually shown this ammonia was oxidized to nitrite/nitrate. It might have just been consumed by heterotrophs or algae in the sand. So let's look for NO2 / NO3.
Nitrite is not worth plotting a graph: Biospira produced 0.35ppm NO2, all other samples produced zero NO2. So maybe it was oxidized to NO3.

So lets take a look at NO3.

NO3 produced.png


Wow that looks a lot like the Ammonia consumption data in the previous graph (except there's more NO3 than expected in the One and Only). So let's see how tightly they match up. (The NO3 measurement in Biospira sample was corrected for the Nitrite interference using @Dan_P work here)

Ammonia to NO2_3.png


This plot compares the amount of Total Ammonia - Nitrogen consumed over the 2.5 days (on the left) to the NO2 + NO3 - nitrogen accumulated at the end (on the right)
First, the sand-only samples (in blue) match up very well. Secondly, the bottle products (solid red and green lines) showed way too much NO3 for the amount of Ammonia they consumed, so I checked for NO3 in the bottles - they are nitrifiers after all. Indeed, recommended min dose of Biospira adds 2.8ppm NO3, and 5x Rec'd min dose of O&O adds 2.3ppm NO3. After correcting for the NO3 that came in the bottles, the ammonia consumption and NO2 & NO3 production line up very well (red and green dashed lines). So clearly the ammonia consumption that happens in the sand and water really is nitrification, oh, and the bottle of O&O really was dead - guess it got frozen at some point. (BTW the slight increase from ammonia-N consumption to NO3-N production in these samples is probably from some organics in the sand being remineralized during the 2.5 day experiment. Note the effect increases with increasing sand level.)

So here's the takeaway.
I can measure the consumption of ammonia by my sand (and water!) and show that it's nitrification. And it's really small - maybe only 4% of the rate of the ammonia consumption in my system overall. The bulk of ammonia in my system is probably eaten by algae and coral.
I think my tank may be an extreme case. My 70 gal system has probably a kg of mixed coral and several hundred grams of algae, algae grows and exports quickly. It's had a history of sometimes large carbon dosing, but nothing in the past few months. Either my tank or my sump is always lighted. The rates of ammonia consumption capable by coral and algae when lighted is huge. So it makes sense that nitrification looks like a bit player in my system, my tank always runs zero detectable NO3, and any that is dosed disappears quickly. I plan to send a sample to Aquabiomics tomorrow to see if the genetic approach tells the same story.
But I don't think I have the only tank like this! I think the hobby might have quite a few systems where the traditional nitrogen cycle is essentially a non-factor. Is this good? Bad? I don't know. But it's clear from the effect of biospira, that this would be easy to change if someone wanted to.
 
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Randy Holmes-Farley

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Thanks for the data. :)

I think it would be really interesting if we actually knew in a given reef tank how much ammonia was consumed and used for tissues, and how much was converted into nitrate before consumption.

I agree that a lot of ammonia may be consumed directly in a packed reef tank. Maybe nearly all of it.
 

flampton

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@taricha This is nice work, and your results are not shocking at all!! The reefing world has been very slow to accept that nitrification is a bit player in a properly working aquarium.

This should have been the mantra for the last thirty years, but instead excuses were made for filtration methodologies. If someone had just sat down and thought about it for a second they would have concluded that wet/dry filters produce more nitrates because they 'steal' ammonia, NOT because they are detritus traps. However there was no money to be made with that conclusion.

Yet to this day people want to make their aquarium the GOAT for nitrification/dentrification. And all of this starts from being taught incorrectly that ammonia is BAD, and that the nitrogen cycle is where all the ammonia is 'detoxified'.
 

brandon429

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seneye shows bottle bac skip cycle *dry rock (removes algae uptake variable, biomass incorporation) setups to run just like full reefs...thousandths ppm active conversion rate. that’s if we believe seneye is correct or can be made correct.

but if it’s a true tell of nitrification, a tuned seneye, we can narrow performance down to the expression of activated surface area as the driver for nh3 in new tanks by simply doing a full water change before the test, exporting suspended bac if any, and using seneye or other accurate meters to test the new system. if the job of handling nh3 shifts into collective environmental uptake from a rather barren initial start handled solely by bacteria, that makes sense.
 

Dan_P

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Key points:
  • My system is capable of removing ammonia quickly: ~4ppm/day total ammonia-Nitrogen (TAN)
  • The sand processes ammonia slowly: ~0.1-0.2ppm/day TAN meaning the other 95+% happens somewhere else
  • The tank water itself also has detectable ammonia processing: ~0.05ppm/day TAN
  • In the sand and the water, the processing is provably Nitrification
  • A Recommended Minimum Dose of Biospira consumes ammonia faster straight out of the bottle than my 10 year old sand
  • I don't know if this is good or bad


The classic idea of nitrification is that ammonia is oxidized to nitrite and nitrate by bacteria in surfaces like sand, rock, and filters. But ammonia is also the preferred N source for photosynthetic organisms. Everything from coral to single cell algae. Additionally, heterotrophic bacteria can use whatever organic carbon sources are available to consume ammonia as well. So Just because ammonia disappears doesn't mean that it went through the ammonia -> NO2 -> NO3 "cycle", it might've just been consumed and become biomass instead.

There's a somewhat contrarian theory that in some tanks, ammonia mostly goes to algae and coral and very little gets nitrified at all.
See this article for that idea: #1 WHAT IF I TOLD YOU... Ammonia is causing your algae problems?
Also AquaBiomics finds some systems that have lots of nitrifiers and some that have barely any Ammonia Oxidizing Bacteria (AOB) and undetectably low Nitrite Oxidizing Bacteria (NOB). Article: The Microbial Community in a Professional Coral Aquaculture System



Anyway: Some things made me think I have a system that would fit this - processing ammonia in non "cycling" ways, so I went looking for data to measure my ammonia eaters. This answered a lot of Q's for me and raised a few more.

As a baseline comparison, here's the tank response to a one-time dose of ammonia during the day period, just a few measurement to get the general size and scale of the rates my system processes ammonia. (pH was 8.0 - this level of ammonia is well below EPA 1-hr level of 2.9 TAN @ pH 8)

Ammonia Tank Rate.png


The tank consumed ammonia at 0.161ppm/hr Total Ammonia Nitrogen (TAN). This works out to 3.9ppm/day.

So how much of this actually happens in the sand?

I dosed tank water to just under 0.5ppm TAN and split it into 100mL samples. Four samples got a series of different amounts of sand 0%,1%, 2% or 5% (a.k.a. 1, 2, or 5mL in 100mL sample) of white sand from the top of the sandbed where water flows across it pretty well.
Two other samples got1% sand + newly opened bottled starter products:
1% sand + BioSpira (recommended minimum dose)
1% sand + One and Only (5x recommended minimum dose)
They were placed in the dark on an orbital shaker at 70 rpm to keep the water moving and tested over 2.5 days.

Ammonia Rates .png


The series of samples with varying amounts of sand are in shades of blue, the 1% sand + biospira (red) acted more like the 5% sand. The 1% sand + One and Only (green) acted basically like just 1% sand. The trendlines were used to estimate the consumption rates.
Surprisingly, even no sand at all - just 100mL of water clearly consumed ammonia.

Here's visualizing the rate of ammonia consumption (slopes from previous graph) vs the amount of sand there was.
Amm Rate vs Sand.png


There is probably diminishing returns for higher levels of sand since at 5% the sand is piling up and a smaller portion is in contact with the moving water. BioSpira +1% sand clearly effective above what the 1% sand in the sample could do, while One and Only had no detectable effect. What proportion of sand is most applicable to my tank? My tank water is 40cm deep, and likely only the top 1cm of sand (or less) is reasonably in contact with moving water above, so 2% or less seems a good ballpark approximation to how my sandbed behaves.
I therefore estimate my tank sand can eat somewhere in the range of 0.10 to 0.15ppm/day TAN, or only <4% of my overall system consumption of 3.9ppm/day, meaning only 4% of that maximum daily ammonia consumption could be done in the sand+water.
Speaking of water, this graph makes it really clear that my tank water processes ammonia. In the 1% sand samples, the water may be doing half the work. Crazy! (Ammonia Oxidizing Archaea??)

Okay one last thing. I haven't actually shown this ammonia was oxidized to nitrite/nitrate. It might have just been consumed by heterotrophs or algae in the sand. So let's look for NO2 / NO3.
Nitrite is not worth plotting a graph: Biospira produced 0.35ppm NO2, all other samples produced zero NO2. So maybe it was oxidized to NO3.

So lets take a look at NO3.

NO3 produced.png


Wow that looks a lot like the Ammonia consumption data in the previous graph (except there's more NO3 than expected in the One and Only). So let's see how tightly they match up. (The NO3 measurement in Biospira sample was corrected for the Nitrite interference using @Dan_P work here)

Ammonia to NO2_3.png


This plot compares the amount of Total Ammonia - Nitrogen consumed over the 2.5 days (on the left) to the NO2 + NO3 - nitrogen accumulated at the end (on the right)
First, the sand-only samples (in blue) match up very well. Secondly, the bottle products (solid red and green lines) showed way too much NO3 for the amount of Ammonia they consumed, so I checked for NO3 in the bottles - they are nitrifiers after all. Indeed, recommended min dose of Biospira adds 2.8ppm NO3, and 5x Rec'd min dose of O&O adds 2.3ppm NO3. After correcting for the NO3 that came in the bottles, the ammonia consumption and NO2 & NO3 production line up very well (red and green dashed lines). So clearly the ammonia consumption that happens in the sand and water really is nitrification, oh, and the bottle of O&O really was dead - guess it got frozen at some point. (BTW the slight increase from ammonia-N consumption to NO3-N production in these samples is probably from some organics in the sand being remineralized during the 2.5 day experiment. Note the effect increases with increasing sand level.)

So here's the takeaway.
I can measure the consumption of ammonia by my sand (and water!) and show that it's nitrification. And it's really small - maybe only 4% of the rate of the ammonia consumption in my system overall. The bulk of ammonia in my system is probably eaten by algae and coral.
I think my tank may be an extreme case. My 70 gal system has probably a kg of mixed coral and several hundred grams of algae, algae grows and exports quickly. It's had a history of sometimes large carbon dosing, but nothing in the past few months. Either my tank or my sump is always lighted. The rates of ammonia consumption capable by coral and algae when lighted is huge. So it makes sense that nitrification looks like a bit player in my system, my tank always runs zero detectable NO3, and any that is dosed disappears quickly. I plan to send a sample to Aquabiomics tomorrow to see if the genetic approach tells the same story.
But I don't think I have the only tank like this! I think the hobby might have quite a few systems where the traditional nitrogen cycle is essentially a non-factor. Is this good? Bad? I don't know. But it's clear from the effect of biospira, that this would be easy to change if someone wanted to.
Nothing like data to raise questions :) Nice effort Jonathan. I really appreciate the amount of wok you put into this. Just to be a pain though, I have to wonder what the variation is in these experimental results :)

I will repeat your experiment in my system And post the results here In a couple weeks. I have already observed that my tank water does not consume ammonia, my sand does consume ammonia and washing the sand in tap water kills ammonia consumption. Maybe we can get a few more reefers doing the same.
 

flampton

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Nothing like data to raise questions :) Nice effort Jonathan. I really appreciate the amount of wok you put into this. Just to be a pain though, I have to wonder what the variation is in these experimental results :)

I will repeat your experiment in my system And post the results here In a couple weeks. I have already observed that my tank water does not consume ammonia, my sand does consume ammonia and washing the sand in tap water kills ammonia consumption. Maybe we can get a few more reefers doing the same.
Hey Dan was wondering what you mean by consume ammonia?
 

Nano sapiens

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@taricha This is nice work, and your results are not shocking at all!! The reefing world has been very slow to accept that nitrification is a bit player in a properly working aquarium.

This should have been the mantra for the last thirty years, but instead excuses were made for filtration methodologies. If someone had just sat down and thought about it for a second they would have concluded that wet/dry filters produce more nitrates because they 'steal' ammonia, NOT because they are detritus traps. However there was no money to be made with that conclusion.

Yet to this day people want to make their aquarium the GOAT for nitrification/dentrification. And all of this starts from being taught incorrectly that ammonia is BAD, and that the nitrogen cycle is where all the ammonia is 'detoxified'.

So true! Many reef aquarium related books, magazines and online articles have reinforced the view that ammonia processing is facilitated primarily by bacteria and anything else, if mentioned at all, are just bit players. While this can be true for a system with few corals, once a full compliment of healthy actively growing corals ('packed', as Randy puts it) is present it would seem quite likely that a majority of the available ammonia would be utilized directly by these animals.
 

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So true! Many reef aquarium related books, magazines and online articles have reinforced the view that ammonia processing is facilitated primarily by bacteria and anything else, if mentioned at all, are just bit players. While this can be true for a system with few corals, once a full compliment of healthy actively growing corals is present it would seem quite likely that a majority of the available ammonia would be utilized directly by these animals.
I heard of folks that use algae scrubbers in QT purely for ammonia removal. Its been thought for a long time that at least some types of algae prefer ammonia, probably most/ all.
 

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Really funny how the hobby has changed with increased knowledge. Was not that long ago dosing nitrates or phosphates was unheard of. Maybe it wont be long dosing ammonia wont be unheard of (I know some people already do, but I would say it is still a concept that would make 99% of SW enthusiasts gasp).
 
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Nano sapiens

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I heard of folks that use algae scrubbers in QT purely for ammonia removal. Its been thought for a long time that at least some types of algae prefer ammonia, probably most/ all.

I remember seeing a packed 'Xenia Refugium' in one of the reef books a while back and that it was able to keep phosphates and nitrates at low levels. Specifically looking at the nitrate part, the Xenia were actually removing ammonia (mostly or completely?) since it's the preferred source (metabolically less demanding to use than nitrate) and so there was little excess nitrate in the system. Just like in an algae refugium, the Xenia needed to be regularly harvested. While great in concept, and shows the capability of fast growing corals to assimilate PO4 and NO3, the potential crashing of the Xenia population undoubtedly favored the use of certain fast growing algae like Chaetomorpha instead.

However, as the old saying goes, 'More than one way to skin a ca...'onion' ;)
 
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flampton

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I heard of folks that use algae scrubbers in QT purely for ammonia removal. Its been thought for a long time that at least some types of algae prefer ammonia, probably most/ all.

I remember seeing a packed 'Xenia Refugium' in one of the reef books a while back and that it was able to keep phosphates and nitrates at low levels. Specifically looking at the nitrate part, the Xenia were actually removing ammonia since it's the preferred source (metabolically less demanding to use than nitrate).

As the saying goes, 'More than one way to skin a ca...'onion' ;)

This is the thing that a lot of reefers don't understand. When nitrates go down they believe it is because the nitrates are consumed. However what is happening in a lot of these schemes is that the ammonia is being consumed before it has a chance to be converted. :D

Another thing is that the coral animal itself cannot use nitrate. The nitrate usage falls to the Symbiodinium. And the overall nitrogen flux that has been reported in the literature is mainly from the animal to the symbiont. Thus extra nitrate added to a nitrogen limited system is probably detrimental. One reason I'm not a fan of nitrate dosing.
 
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taricha

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I think it would be really interesting if we actually knew in a given reef tank how much ammonia was consumed and used for tissues, and how much was converted into nitrate before consumption.

For those interested, a very rough way to think about the proportion of nitrification vs assimilation is the Nitrate production. If your tank is one of the extremes that generates endless NO3, or like mine that tests zero NO3 and consumes 2+ppm NO3 per day if dosed (a production of negative 2ppm NO3 per day) then you are likely on nitrification or assimilation extreme.
For all the cases in between it's harder to draw any conclusions.

Yet to this day people want to make their aquarium the GOAT for nitrification/dentrification.

How deep is the sandbed? Most theories i hear require atleast 4in for anaerobic bacteria that process nitrates to survive.
See Flampton, I thought my tank with my 2" sandbed was a denitrifying machine because my NO3 is always flat zero.
Little did I know, there's almost no NO3 produced to denitrify in the first place. You can't denitrify what was never nitrified!

And all of this starts from being taught incorrectly that ammonia is BAD
I'll poke some more at your opinion that ammonia is a net positive later. I'm on the fence but slight lean against that. My tank has had nuisance algae of every kind over the years - I'm tempted to round up the pitchforks and scapegoat these nitrifiers that weren't showing up for work. :)
 
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taricha

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Just to be a pain though, I have to wonder what the variation is in these experimental results
me too. which part bugs you the most?
The clearly measurable nitrification in blank tank water still feels unlikely to me, even though we are learning that Ammonia Oxidizing Archaea is a thing in every environment.
 

Randy Holmes-Farley

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I heard of folks that use algae scrubbers in QT purely for ammonia removal. Its been thought for a long time that at least some types of algae prefer ammonia, probably most/ all.

I always put a bunch of macroalgae in my QT tanks with new fish for that reason.
 

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Hey Dan was wondering what you mean by consume ammonia?
Eric, short hand for depletion of measured total ammonia. The experiment was 2.5 mL aquarium sand in 50 mL Instant Ocean spiked with ammonium chloride (0.25 ppm NH3). Overnight total ammonia went to 0 ppm (I did not measure NO2- %&[email protected]!!). I will try to repeat Jonathan’s observations.
 

flampton

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For those interested, a very rough way to think about the proportion of nitrification vs assimilation is the Nitrate production. If your tank is one of the extremes that generates endless NO3, or like mine that tests zero NO3 and consumes 2+ppm NO3 per day if dosed (a production of negative 2ppm NO3 per day) then you are likely on nitrification or assimilation extreme.
For all the cases in between it's harder to draw any conclusions.




See Flampton, I thought my tank with my 2" sandbed was a denitrifying machine because my NO3 is always flat zero.
Little did I know, there's almost no NO3 produced to denitrify in the first place. You can't denitrify what was never nitrified!


I'll poke some more at your opinion that ammonia is a net positive later. I'm on the fence but slight lean against that. My tank has had nuisance algae of every kind over the years - I'm tempted to round up the pitchforks and scapegoat these nitrifiers that weren't showing up for work. :)

Haha looking forward to that discussion. I'm going to come at it from the aspect of overall anabolism vs. catabolism and what it means in relation to keeping our likeable creatures happy while limiting pests. Thus I wouldn't state that ammonia is 'positive' because that ignores all other variables we would need to consider.
 

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This is the thing that a lot of reefers don't understand. When nitrates go down they believe it is because the nitrates are consumed. However what is happening in a lot of these schemes is that the ammonia is being consumed before it has a chance to be converted. :D

Another thing is that the coral animal itself cannot use nitrate. The nitrate usage falls to the Symbiodinium. And the overall nitrogen flux that has been reported in the literature is mainly from the animal to the symbiont. Thus extra nitrate added to a nitrogen limited system is probably detrimental. One reason I'm not a fan of nitrate dosing.

Noted that the Symbiodinium are responsible for nitrate usage and it has been demonstrated that an excess of nitrogen can cause a severe imbalance in the holobiont (the coral animal typically controls/limits nitrogen to the Zooxanthellae so they don't overpopulate and thus maintains a high rate of photosynthesis, which in turn provides the coral carbohydrate waste products...'Junk Food' as it has been called).

One scenario that really highlights the uber-important role of ammonia is when a healthy packed system with growing corals and low sustained NO3 & PO4 levels experiences a major issue that drastically reduces coral growth and consequent ammonia uptake. Typically, the system continues to be fed to sustain the fish (ammonia released by the fish's gills and feces and nitrate from the food itself), but now it's up to the bacteria to take up the slack. However, since numbers are limited (due to the corals previously using most of the available ammonia), nitrates rise due to the relatively slow reproductive capacity of denitrifying bacteria. At the same time, algae can now do a little happy dance and multiply contently with the abundant and regularly replenished source of ammonia and nitrate. Once the corals start growing again and they assimilate the available ammonia and some nitrate, the algae and bacteria once again become nutrient limited and their numbers decline to reef 'normal' levels.
 
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Dan_P

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me too. which part bugs you the most?
The clearly measurable nitrification in blank tank water still feels unlikely to me, even though we are learning that Ammonia Oxidizing Archaea is a thing in every environment.

If I hadn’t just recently watched 2 L of aerated tank water spiked with ammonia do nothing for several weeks, your results would have interested me not disturbed me :)

I am washing out flasks now to repeat your experiments.
 
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taricha

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For the moment, I'm going to sidestep the big question: whether having robust true Nitrification is actually important/beneficial in a system.
And say that if what you want is to establish a system with strong nitrification, it seems clear that for best results you've gotta be pretty intentional about it.

Nitrifiers can be outcompeted for ammonia by coral, algae, and heterotrophs.
so...
No Light, no coral, no algae.
Start with ammonia dosing, not ghost feeding or a shrimp. Organics in the food will get the heterotrophs going, and the nitrifiers would only get ammonia as leftovers.
If you use a bottle starter, be sure it's true chemoautotroph nitrifiers. Some are actually "heterotrophic nitrifiers" that require Organic carbon. Adding ammonia-only, not a shrimp or fish food in the beginning will help distinguish.
 
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