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

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Randy Holmes-Farley

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Maybe it’s Alga that are the bigger consumers of ammonia than bacteria in some tanks.

Algae, corals, anemones, etc. all may be bigger users. Anything that photosynthesizes might be a user. :)
 
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taricha

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So I went to the LFS to shop for some nitrifying sand :p
I picked a tank that had like a dozen small clowns in a 20 gallon, good flow across the sand, minimal visible algae. The water was recirculating in the tank itself, not pumped through a central filtration system. There was a tiny dusting of brown diatoms on one side of the sandbed. I got some sand from the other side. No other algae, corals, etc in the tank. only two small rocks in the tank.
Ought to be the best case scenario for sandbed nitrification right??

Nitrification RateLFS.png


(LFS sand data in gray triangles).
It's more of the same. Very much like the results I get from my own sandbed.
Is this really close agreement just (another) coincidence? Did I catch the sandbed at a bad time? Maybe it was very new. Or maybe this is just what sand does.

The hunt for high nitrification sand continues. But I wonder if there is something fundamental here, that makes it harder for larger nitrifier capability to persist in a sandbed long term.
 

flampton

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So I went to the LFS to shop for some nitrifying sand :p
I picked a tank that had like a dozen small clowns in a 20 gallon, good flow across the sand, minimal visible algae. The water was recirculating in the tank itself, not pumped through a central filtration system. There was a tiny dusting of brown diatoms on one side of the sandbed. I got some sand from the other side. No other algae, corals, etc in the tank. only two small rocks in the tank.
Ought to be the best case scenario for sandbed nitrification right??

Nitrification RateLFS.png


(LFS sand data in gray triangles).
It's more of the same. Very much like the results I get from my own sandbed.
Is this really close agreement just (another) coincidence? Did I catch the sandbed at a bad time? Maybe it was very new. Or maybe this is just what sand does.

The hunt for high nitrification sand continues. But I wonder if there is something fundamental here, that makes it harder for larger nitrifier capability to persist in a sandbed long term.
This is one of those times where the data doesn't seem to support the realities. Basically something seems off. A small 20 gallon low light, minimal algae system with 12 sloppy heterotrophs suggests highly efficient nitrification. I'm not sure two small rocks would cut it so did it have a filter? e.g. a cascading HOB? If so that may be where the nitrifiers are at. If not...

I want to make sure I have the experiment straight.

100ml of new saltwater at ?ppm
1, 2, or 5 ml of sand
add ammonium chloride to 0.5ppm TAN
rock at 70rpm for 24 hours
retest sample for TAN.

Is all the above correct?

If so one issue is that 70rpm is really slow rocking. For proper aeration you'll want to use baffled flasks at at least 200 rpm preferably 250rpm. You can also increase water surface area, try an air pump etc. This might not change anything as you're not trying to grow a dense culture of bacteria. However I think it is worth a shot to try to understand this anomaly.
 

brandon429

why did you put a reef in that
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I have a question regarding ammonia fixation in plants

was unaware of a mechanism whereby plants continually uptake ammonia and it doesn’t go to mass / new growth / shoots


meaning to fulfill a resting metabolic demand— seems like such a low demand rate I struggle to locate what machinery in plant cells burns through daily / per minute ammonia from fish without turning into actual visible plant material we can see as obvious mass. Not all reefs trend towards obvious plant growths, mine certainly aren’t allowed to, the surfaces are high flow coralline areas but not plants other than microscopic ones I can’t readily see.



if I’m not misreading, algae we cannot see is attributed to uptake that outpaces nitrifiers...consider how funky ats crews must grow the screen beard to get true measured uptake

before the algal scrubber grows in, param control is low

how are my invisible algae doing the workhorse loading here in that context

should we be able to see algae and see it’s mass forming on rocks before we can be sure plant uptake factors heavily against bac command for free ammonia or total ammonia in reefs?
 
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taricha

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A small 20 gallon low light, minimal algae system with 12 sloppy heterotrophs suggests highly efficient nitrification. I'm not sure two small rocks would cut it so did it have a filter? e.g. a cascading HOB? If so that may be where the nitrifiers are at.
yeah, I think there are a couple of likely options.
1 - there was a HOB with a filter pad, which could be doing the bulk of the nitrification
2 - maybe the sand was new, and that's why it was so white. Other tanks had brown film or red cyano. I'll peek back in on the tank in a week.
3 - (along the lines of 2) maybe it's not keeping up with the bioload (kicking myself for not testing the water in the bag from the LFS to look for NH3+4, NO2, NO3.) and the shop is using water changes, prime etc to deal with it.
4 - Or like you say, maybe the sand can nitrify way more than what my protocol is showing.

I want to make sure I have the experiment straight.

100ml of new saltwater at ?ppm
1, 2, or 5 ml of sand
add ammonium chloride to 0.5ppm TAN
rock at 70rpm for 24 hours
retest sample for TAN.

Is all the above correct?
yea, the rest is correct, but 100mL of my tank water (new I.O. tests at a few tenths ppm ammonia, so I avoid it for this) - it tests 0.0 ammonia, NO3.

here's more detail...
LFS_sand rates.png


The right graph is just confirmation that it's in fact nitrification.
The left graph shows that the rates are dependent on nitrifying sand amount, which I had interpreted as demonstrating it's not the rate of water motion limiting it.
That assumption needs revisiting.
 
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taricha

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I have a question regarding ammonia fixation in plants

was unaware of a mechanism whereby plants continually uptake ammonia and it doesn’t go to mass / new growth / shoots


meaning to fulfill a resting metabolic demand— seems like such a low demand rate I struggle to locate what machinery in plant cells burns through daily / per minute ammonia from fish without turning into actual visible plant material we can see as obvious mass. Not all reefs trend towards obvious plant growths, mine certainly aren’t allowed to, the surfaces are high flow coralline areas but not plants other than microscopic ones I can’t readily see.



if I’m not misreading, algae we cannot see is attributed to uptake that outpaces nitrifiers...consider how funky ats crews must grow the screen beard to get true measured uptake

before the algal scrubber grows in, param control is low

how are my invisible algae doing the workhorse loading here in that context

should we be able to see algae and see it’s mass forming on rocks before we can be sure plant uptake factors heavily against bac command for free ammonia or total ammonia in reefs?

This is a good point - worth making distinction, I don't think invisible algae can be doing the bulk work here.
(but I would point out Brandon, you frequently tell people that as soon as they see a flush of green or brown on the rock they are "cycled" - and you're right...ish. The arrival of visible photosynthetic film on the rock means that ammonia accumulation won't happen in that tank going forward. I'd just be pedantic and point out it's got nothing to do with nitrifiers.)

This article (shimek - down the drain) ballparks the total nitrogen in caulerpa at ~1000mg / kg of tissue (wet weight).
He puts xenia coral at ~9000 mg N / kg tissue.

This means a 3g cube of average frozen fish food at 6% protein (I've seen 3-10%) is bringing in 3000mg x 6% x (16% N per protein) = 30 mg N

If it went to caulerpa at the above cited rate, that would be 30 grams of Caulerpa from 30 mg of N. This seems ridiculously high, to get 30 grams of algae growth per cube of food.

But if it's soft coral instead, then it's only 3.3g of coral tissue per cube of food. More believable.

Add in the coralline algae and it gets more believable still.

None of this counts the ~10% that may be nitrified, the ~20% that gets assimilated into fish, shrimp, crabs, worms etc, nor does it count the ???% that gets into heterotroph bacteria (skimmed out of water) fed by the organic carbon in the food + the DOC thrown out by coral and algae.
 

brandon429

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yes that helps it’s not the algae and the bacteria alone it’s the shared uptake from those two groups and all other organisms that makes sense, Randy said it as well I see the collective now.

The algae can play a larger or smaller uptake roll based on presentation, makes good sense. Truly I have just been thinking pure bacteria this whole time and we knew plants uptake ammonia as well, but the guess was 1% overall for plants and bac 99%, not so can see. nice discovery for the hobby for sure.

even though we certainly hadn’t differentiated nitrifiers vs algae in creating the safe ammonia start date for visual cycling, it really has been neat seeing those patterns of visual benthic cues reveal safe start dates for new reef cyclers, the claim is about fourteen years old now and tested in feedback posts.

I think it’s the single oldest and most tested web pattern I’ve seen from them all...for any cycling tank when we can see new growths on any surface it means adding fish will not drive ammonia to dangerous levels, an inherent control is there, signified by growths we can see and didn’t have to stumble with test kits to discern.

if I’m understanding those actual growths themselves contribute to the ammonia uptake, its not always bacteria and in some cases may not be at all.
 

TCoach

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@brandon429 - If I understand what I'm reading here, this also helps to confirm your 100% RIP tank move/clean procedure. If only a small part of ammonia in my tank is being processed by the sand bed, then removing it and rinsing out the detritus before returning it to my tank will have very little to no negative effect on the tank due to ammonia process being done else where.

Also validated by the multiple tanks that have gone through the full RIP process. :)
 

brandon429

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agreed. I truly thought we were pulling off the greatest heist of surface area in the presence of thousands in coral ever documented.

its more like we challenged the nitrification by 1-2% ha well at least this group hasn't been risking too much on that surface area shortage

the real risk was the messy mixed-states of decay we call detritus/Lasse calls particulate organic matter. mixing all that around frivolously would have a drastically different outcome in a work thread for sure :)

but kept clean like we do, it turns out we had not been losing much by ditching or rinsing or swapping out totally a sandbed. if T had not made this thread and Dan his detailed findings on zonation we'd have never known it, these are the details and ratios and attributions chemists will discover.

lots of sandbed work critics were too hyperfocused it isn't all that bad of a risk apparently. blasting them clean will clear out worms and pods and foodstores but not at the expense of ammonia control at least.
 
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lots of sandbed work critics were too hyperfocused it isn't all that bad of a risk apparently. blasting them clean will clear out worms and pods and foodstores but not at the expense of ammonia control at least.

This *may* turn out to be a truism for reef aquaria, but I think we need a much larger sampling of sand beds from different systems to say this is actually so for all.
 

Garf

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I have a question regarding ammonia fixation in plants

was unaware of a mechanism whereby plants continually uptake ammonia and it doesn’t go to mass / new growth / shoots


meaning to fulfill a resting metabolic demand— seems like such a low demand rate I struggle to locate what machinery in plant cells burns through daily / per minute ammonia from fish without turning into actual visible plant material we can see as obvious mass. Not all reefs trend towards obvious plant growths, mine certainly aren’t allowed to, the surfaces are high flow coralline areas but not plants other than microscopic ones I can’t readily see.



if I’m not misreading, algae we cannot see is attributed to uptake that outpaces nitrifiers...consider how funky ats crews must grow the screen beard to get true measured uptake

before the algal scrubber grows in, param control is low

how are my invisible algae doing the workhorse loading here in that context

should we be able to see algae and see it’s mass forming on rocks before we can be sure plant uptake factors heavily against bac command for free ammonia or total ammonia in reefs?
The theory was that ammonia could defuse across the cell membranes without an actual mechanism, just using the gradient of ammonia. Nitrate it seems needed a transport mechanism to get it into the cells via a nitrite ammonia reduction system. But if I told you I totally understand that I would be lying. Perhaps one of the chemistry folks could help.

Edit - I would add that when a biologist, chemist sais “may” or “might” or “could”, they really don’t know. I came across a lot of that researching algae.
 
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Randy Holmes-Farley

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The theory was that ammonia could defuse across the cell membranes without an actual mechanism, just using the gradient of ammonia. Nitrate it seems needed a transport mechanism to get it into the cells via a nitrite ammonia reduction system. But if I told you I totally understand that I would be lying. Perhaps one of the chemistry folks could help.

I do not know if this is actually how organisms take up ammonia, but it does readily diffuse across cell membranes in the uncharged NH3 form.

Neither nitrate nor nitrite can diffuse across cell membranes since both are charged (charges cannot readily get across the very hydrophobic part of a cell membrane), so organisms taking it up will need a specific transporter of some sort to do so.
 

Garf

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I do not know if this is actually how organisms take up ammonia, but it does readily diffuse across cell membranes in the uncharged NH3 form.

Neither nitrate nor nitrite can diffuse across cell membranes since both are charged (charges cannot readily get across the very hydrophobic part of a cell membrane), so organisms taking it up will need a specific transporter of some sort to do so.
Mission - learn one thing every day, accomplished :)
 
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taricha

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@brandon429 - If I understand what I'm reading here, this also helps to confirm your 100% RIP tank move/clean procedure. If only a small part of ammonia in my tank is being processed by the sand bed, then removing it and rinsing out the detritus before returning it to my tank will have very little to no negative effect on the tank due to ammonia process being done else where.
Yeah, that's another thought I had. I'd no longer discourage anyone from ripping out a sandbed, temporarily or longer.

The pro/con list for a sandbed that was in my head when I first put it in
vs
The pro/con list for a sandbed based on things I know now is very different.

The Pro list has gotten much much shorter. It now basically is:

I like the look
shrimp/goby pairs, or jawfish, or wrasse that bury
aragonite PO4 stabilizer
 

Garf

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Yeah, that's another thought I had. I'd no longer discourage anyone from ripping out a sandbed, temporarily or longer.

The pro/con list for a sandbed that was in my head when I first put it in
vs
The pro/con list for a sandbed based on things I know now is very different.

The Pro list has gotten much much shorter. It now basically is:

I like the look
shrimp/goby pairs, or jawfish, or wrasse that bury
aragonite PO4 stabilizer
So the general consensus is that sand beds are purely aesthetic in reef tanks?
 
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taricha

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Nitrate it seems needed a transport mechanism to get it into the cells via a nitrite ammonia reduction system.
For kicks, check out Nitrate Reductase - what's generally responsible for getting through the slowest step in the NO3 reduction to usable N for algae etc.

and there's a fun rabbit-hole in the connection to Iron here as well.
The reduction of nitrate to ammonium requires large quantities of reducing power (8 mol e- / mole N), as well as the enzymes nitrate and nitrite reductase, both of which need iron. Therefore, effects of iron on nitrogen metabolism in (marine) phytoplankton have received much attention
-Iron-mediated effects on nitrate reductase in marine phytoplankton


Chem is an acquired taste for me, but the picture generally is that ammonia (in the right doses) is by far preferable to NO3 / NO2 for just about anything that needs N.

That can be good and bad.
 

Garf

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For kicks, check out Nitrate Reductase - what's generally responsible for getting through the slowest step in the NO3 reduction to usable N for algae etc.

and there's a fun rabbit-hole in the connection to Iron here as well.

-Iron-mediated effects on nitrate reductase in marine phytoplankton


Chem is an acquired taste for me, but the picture generally is that ammonia (in the right doses) is by far preferable to NO3 / NO2 for just about anything that needs N.

That can be good and bad.
When things get this confusing I generally sit back and drink :)
 
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taricha

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So the general consensus is that sand beds are purely aesthetic in reef tanks?
Certainly not "general consensus". I'm not even sure I've convinced myself. :)

But if you pressed me right now to come up with something chemically biologically necessary to a reef tank that happens in my sandbed... I'd have to think a long time.

(If I had high NO3, I would want anaerobic space where denitrification might be accelerated)
 

Garf

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Certainly not "general consensus". I'm not even sure I've convinced myself. :)

But if you pressed me right now to come up with something chemically biologically necessary to a reef tank that happens in my sandbed... I'd have to think a long time.

(If I had high NO3, I would want anaerobic space where denitrification might be accelerated)
It seems ridiculous that crushed up rock can’t do the job of rock. It should do it better. I would say that I recently dismantled some live rock to make rubble for frags and it oozed liquid.
 
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