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

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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 pretty clear to that for best results you've gotta be 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.

So are you saying that if you started your tank as described above, you would have a system with initially strong nitrifiers?

What do you postulate will happen as the tank gets light, algae, CUC, pods, fish, corals, and generally matures? Would the nitrifiers lose out?
 

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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.
Yeah I wouldn't go to that extent, just need to create the proper niche, so...
Why not just add a wet/dry filter? Doesn't have to be huge. You can add one to your current tank.
 

brandon429

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what is the benefit of adding that in addition to the live rock surface area

my thinking is the nh3 control is already permanently controlled even wo extra surface area
 

flampton

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Oh and more simply since you're running lights in both sections is decrease photoperiod and/or intensity.

what is the benefit of adding that in addition to the live rock surface area

my thinking is the nh3 control is already permanently controlled even wo extra surface area

He doesn't want ammonia controlled per se, he wants more nitrification. For nitrifiers to compete in this setup with all the algae, coral and 24 hour light they need some help, I.e. the air/water interface and extensive surface area of a wet/dry filter.
 
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taricha

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So are you saying that if you started your tank as described above, you would have a system with initially strong nitrifiers?
I don't see why not.
With straight ammonia and no light and no organic carbon source, the only thing that could thrive would be the true chemoautotroph nitrifiers. You can reliably get them from a few products and they come out of a bottle already at near the levels you would want for consuming whatever ammonia would be introduced to the system.
(quick summary of Results from bottle bacteria, myth or fact thread)
Out of 8 products tested i have found FRITZ TURBOSTART 900 ...normally in a 5 gal tank about 2 days with ammonia as high as 8-10ppm. Followed by Bio Spira and Dr Tim that took a day to two extra days to reduce/cycle tank fully
So it wouldn't take many days at all (or many bottles) to scale up the nitrifiers as high as you could want.


What do you postulate will happen as the tank gets light, algae, CUC, pods, fish, corals, and generally matures? Would the nitrifiers lose out?
This is a really good question. I don't know. It would be cool if the answer was that the nitrifiers are pretty stable and aren't easily displaced from the sand. There are some reasons to think so, other reasons weigh against.
 
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taricha

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my thinking is the nh3 control is already permanently controlled even wo extra surface area
NH3 as a risk for livestock is of course permanently controlled in a mature system.
I'm interested in ammonia from a nuisance growth perspective. The low level of sandbed nitrifiers is an opening that benthic nuisance algae seems to exploit.
 
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taricha

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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.


To your point, I'm replicating this (mostly the "water-only" nitrification) as well. It's weird enough to look at harder. I'll see in a couple of days.

The other part of the data that bugs me is that I was surprised I didn't detect significant assimilation of ammonia (at the scale of a few tenths ppm) in the dark. I expected to see most of the ammonia consumed to just be gone into biomass - not a very close agreement of ammonia-N consumed and NO3-N produced.
The reason I thought I'd see ammonia just vanish (even from tank-water-rinsed white sand) is that there are still cells of diatoms, algae etc on the substrate that shouldn't totally quit uptake in the dark. And there are heterotrophs too. If there were any appreciable amount of digestible organic carbon, then growth by heterotrophs could consume ammonia.
 
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taricha

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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.

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.
My half-thought out argument is pretty simple. It revolves around location.
Ammonia generated in the water is fine - in fact it's my friend. It feeds my coral, and the tighter in proximity to the coral, the better. But ammonia in the sand may well be an enemy.
[BTW, MVP award to the gobies that grab food from the water and spend all day sitting on my corals. Transforming my 1 or 2 a-day feedings into slow release coral nutrition.]

But what about ammonia generated in the sand? Sure, breakdown of organic material in the sand is not as much as some bottle heterotroph bacteria makers would suggest - most all my fish food gets grabbed pretty fast by fish, crabs or shrimp. I think all these excrete ammonia primarily through gills into the water. Fecal Nitrogen in fish seems a small fraction from what I can gather.
So "uneaten food and waste" in a sandbed is small - but it still exists. Algae as well as pods, worms and various other sandbed microfauna eat and are eaten and die in the sandbed.
So if my sandbed is largely absent of nitrifiers, then the ammonia generated there would just hang around until some "algae" (cyano, diatoms, dinos, gha etc) fills the niche. It's not like my corals can come down and get it, or would start new colonies in the sand.

So maybe a weak sandbed nitrifier population is a boon to nuisances on the substrate. And it's pretty clear that this weak nitrification in the sand would be very easy to fix.
 

brandon429

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Is it absent of nitrifiers or low in surface area and contact on only one presentation plane compared to live rock- can't move as much ammonia but still can move some into nitrate?

the water shear over just the top zone of sand, in eddy currents, seems like it would be less engaging than live rocks jutting mid water and all sides contact


Was thinking most surfaces keep bacteria but some ultra present the available bacteria to wastewater better than others

Surely something so in contact with the general tank has some nitrification ability, stuck to the sand grains?
 
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@taricha here are the total ammonia concentrations for a sample of my aquarium water spiked with ammonium chloride over 48 hours. 30 mL samples were placed in glass stoppered 50 mL flasks which were placed on an orbital shaker in the dark. Triplicate measurements. My aquarium water was bashful about taking up NH3.

This week, I will run the same experiment with sand samples in Instant Ocean spiked with ammonium chloride and PO4.

Edit: More Data

I isolated my algae scrubber, a repurposed kitty litter bucket, from the aquarium along with 11 liters of water which I spiked with ammonium chloride (0.15 ppm total ammonia). 1.5 hours after turning on the light the total ammonia was at 0 ppm.

I pipetted surface sand with the aid of a 20 mL syringe and length of rigid tubing. Each 5 mL sample collected from different location was gently rinsed in 20 mL tank water 3-5 times with slow rocking in the syringe. After transferring each sand sample to a stoppered 50 mL flask, 30 mL freshly prepared Instant Ocean dosed with PO4 and ammonium chloride (0.24 ppm total ammonia) was added. The flasks were placed on an orbital shaker in the dark. Ambient temperature was 22 C. After 1-2 a 10 mL sample from each flask was removed to check the total ammonia level. Very little was consumed. The bulk of the experiment time was done with 20 mL of medium and 5 mL of sand. After 16 hours (or less?), no ammonia remained, no nitrite detected and 1.5 ppm nitrate detected. From the amount of ammonium chloride dosed I expected to find 0.9 ppm nitrate. I am pretty sure the difference is a result of analytical variation.

00E12ED5-169E-4AD4-B301-92BF2F3F4BDC.png
 
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taricha

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@taricha here are the total ammonia concentrations for a sample of my aquarium water spiked with ammonium chloride over 48 hours. 30 mL samples were placed in glass stoppered 50 mL flasks which were placed on an orbital shaker in the dark. Triplicate measurements.

00E12ED5-169E-4AD4-B301-92BF2F3F4BDC.png

Dan, Thanks so much for the legwork to attempt to replicate an unlikely result.
I have to suspect most people's water doesn't have a measurable appetite for ammonia. I won't really believe mine does either unless I see it again in a day or two, and even then - I'd feel a lot better if aquabiomics can find sufficient nitrifying microbes in the water to account for the result.

Big picture, what I found in the water was well smaller than what was in the sand - which itself was negligible compared to my overall system consumption of ammonia
 
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taricha

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Is it absent of nitrifiers or low in surface area and contact on only one presentation plane compared to live rock- can't move as much ammonia but still can move some into nitrate?

the water shear over just the top zone of sand, in eddy currents, seems like it would be less engaging than live rocks jutting mid water and all sides contact
Since I put variable amounts of sand (0, 1, 2, or 5mL) in the same volume (100mL) of water moving the same way (orbital shaker), and I found that the amount of sand increased the ammonia consumed & NO3 produced, I have to conclude that it's mostly the amount of nitrifiers there controlling the rate in this test.
Here's visualizing the rate of ammonia consumption (slopes from previous graph) vs the amount of sand there was.
Amm Rate vs Sand.png



Why are these rates low compared to the ammonia consumption of the tank in general? Your point about flow is likely true, laminar vs turbulent, boundary layers etc all matter in terms of what surfaces actually contact the ammonia in the water. Algae and coral enjoy flow for a reason. Polyps of coral and filaments of algae high in the tank likely see many more ammonia molecules than a biofilm on my sand grains.

Surely something so in contact with the general tank has some nitrification ability, stuck to the sand grains?
Well yes. Some. I'm definitely measuring some ammonia nitrification in the sand. It's just like 0.1 or 0.2ppm Total Ammonia-N per day compared to 20x-40x higher for my system overall.
 

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Dan, Thanks so much for the legwork to attempt to replicate an unlikely result.
I have to suspect most people's water doesn't have a measurable appetite for ammonia. I won't really believe mine does either unless I see it again in a day or two, and even then - I'd feel a lot better if aquabiomics can find sufficient nitrifying microbes in the water to account for the result.

Big picture, what I found in the water was well smaller than what was in the sand - which itself was negligible compared to my overall system consumption of ammonia

FWIW: I don't want to make this about 'my tank', but here is an apparent example of the opposite of what you found sampling your sand and water. I thought this might be of interest as AquaBiomics produced an analysis of my 12g nano a while back:

"Your tank has nice high levels of nitrifying microbes. My view here is that a tank can process N through three different pathways (nitrification, heterotrophic assimilation, or photoautotrophic assimilation). In this context your tank appears to rely primarily on nitrification (rather than algal or heterotrophic uptake) to remove ammonia."

"Most tanks that have low scores have low Pelagibacteraceae, almost universally. Yours differs in the opposite direction -- your tank is dominated by this group. Pelagibacteracea are dominant in low-nutrient waters of the open ocean and is a major component of the typical reef tank. By having high levels, your tank is less like many reef tanks and more like natural reef waters."


From Wiki: Pelagibacteraceae ubique and related species are oligotrophs (scavengers) and feed on dissolved organic carbon and nitrogen.

Since I have very little visible algae, it seems that having a large percentage of nitrogen scavenging bacteria in the water column can contribute meaningfully to nitrogen processing. I just don't know the percentage breakdown for all the different pathways in the system.
 

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FWIW: I don't want to make this about 'my tank', but here is an apparent example of the opposite of what you found sampling your sand and water. I thought this might be of interest as AquaBiomics produced an analysis of my 12g nano a while back:

"Your tank has nice high levels of nitrifying microbes. My view here is that a tank can process N through three different pathways (nitrification, heterotrophic assimilation, or photoautotrophic assimilation). In this context your tank appears to rely primarily on nitrification (rather than algal or heterotrophic uptake) to remove ammonia."

"Most tanks that have low scores have low Pelagibacteraceae, almost universally. Yours differs in the opposite direction -- your tank is dominated by this group. Pelagibacteracea are dominant in low-nutrient waters of the open ocean and is a major component of the typical reef tank. By having high levels, your tank is less like many reef tanks and more like natural reef waters."


From Wiki: Pelagibacteraceae ubique and related species are oligotrophs (scavengers) and feed on dissolved organic carbon and nitrogen.

Since I have very little visible algae, it seems that having a large percentage of nitrogen scavenging bacteria in the water column can contribute meaningfully to nitrogen processing. I just don't know the percentage breakdown for all the different pathways in the system.
Would you think that your aquarium water would show ammonia uptake? Or are the Pelagibacteraceae living in the sand doing their thing?

Interesting point about the potential interplay between Pelagibacteraceae and algae. I am studying biofilm formation in my system and looking for connections such as these.
 
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Dan_P

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Dan, Thanks so much for the legwork to attempt to replicate an unlikely result.
I have to suspect most people's water doesn't have a measurable appetite for ammonia. I won't really believe mine does either unless I see it again in a day or two, and even then - I'd feel a lot better if aquabiomics can find sufficient nitrifying microbes in the water to account for the result.

Big picture, what I found in the water was well smaller than what was in the sand - which itself was negligible compared to my overall system consumption of ammonia
No problem, though I admit the “Tom Sawyer painting the fence“ force is strong with you!

The sand samples get started this week and I will isolate my bucket algae scrubber and measure the NH3 uptake of that piece of the system. The other data I will get for you is the aquarium NH3 uptake with the scrubber disconnected. Then we can compare and contrast.

Should I get AquaBiomics to test my system to round out the data collection?
 

Nano sapiens

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Would you think that your aquarium water would show ammonia uptake? Or are the Pelagibacteraceae living in the sand doing their thing?

Interesting point about the potential interplay between Pelagibacteraceae and algae. I am studying biofilm formation in my system and looking for connections such as these.

Based on the high proportion of Pelagibacteraceae (looks like ~75% of all in-tank microorganisms in my sample), I would suspect that they should play a role and possibly a significant one.

"The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living marine bacteria that make up roughly one in three cells at the ocean's surface.[1][2][3] Overall, members of the Pelagibacterales are estimated to make up between a quarter and a half of all prokaryotic cells in the ocean.

So, not a substrate oriented nitrifying organism.
 

flampton

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So maybe a weak sandbed nitrifier population is a boon to nuisances on the substrate. And it's pretty clear that this weak nitrification in the sand would be very easy to fix.

Not so sure this would be easy to fix. Maintaining an aquarium with carbon dosing will necessarily favor heterotrophs. This includes utilizing algae for carbon dosing as they also increase overall DOC and POC levels.

If you want to maintain a larger nitrifying population (especially in areas with lower O2 percentage) you will need to decrease carbon input some how.
 

flampton

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FWIW: I don't want to make this about 'my tank', but here is an apparent example of the opposite of what you found sampling your sand and water. I thought this might be of interest as AquaBiomics produced an analysis of my 12g nano a while back:

"Your tank has nice high levels of nitrifying microbes. My view here is that a tank can process N through three different pathways (nitrification, heterotrophic assimilation, or photoautotrophic assimilation). In this context your tank appears to rely primarily on nitrification (rather than algal or heterotrophic uptake) to remove ammonia."

"Most tanks that have low scores have low Pelagibacteraceae, almost universally. Yours differs in the opposite direction -- your tank is dominated by this group. Pelagibacteracea are dominant in low-nutrient waters of the open ocean and is a major component of the typical reef tank. By having high levels, your tank is less like many reef tanks and more like natural reef waters."


From Wiki: Pelagibacteraceae ubique and related species are oligotrophs (scavengers) and feed on dissolved organic carbon and nitrogen.

Since I have very little visible algae, it seems that having a large percentage of nitrogen scavenging bacteria in the water column can contribute meaningfully to nitrogen processing. I just don't know the percentage breakdown for all the different pathways in the system.

Would you think that your aquarium water would show ammonia uptake? Or are the Pelagibacteraceae living in the sand doing their thing?

Interesting point about the potential interplay between Pelagibacteraceae and algae. I am studying biofilm formation in my system and looking for connections such as these.

Pelagibacterales are heterotrophs so cannot incorporate ammonia without having access to organic carbon. (They're also auxotrophic for glycine and reduced sulfur) This suggests to me you have decent nutrition in your tank and started with some amount of ocean substrate.
 

Dan_P

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Not so sure this would be easy to fix. Maintaining an aquarium with carbon dosing will necessarily favor heterotrophs. This includes utilizing algae for carbon dosing as they also increase overall DOC and POC levels.

If you want to maintain a larger nitrifying population (especially in areas with lower O2 percentage) you will need to decrease carbon input some how.

Interesting notion: deliberately shifting from heterotrophic dominated nitrogen consumption to chemoautotrophic. What sort of “crowbar” would you need to perform the shift?
 
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