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

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taricha

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The narrative seems to be that dosing organic carbon shifts the microbiome to being more heterotrophic and less chemoautotrophic. This in turn renders two risks. One is altered coral associated bacteria (coral can become sick) and the other is a diminished chemoautotrophic bacteria population (the risk is having nitrification shift from a system that works by itself versus one that is actively managed by carbon dosing, i.e., passive control is inherently safer than active control).

From what I have read from Rohwer and others, when excess DOC is rapidly delivered to the coral the current prevailing theory is that the coral's own resident bacterial population overpopulate and this starves the coral of oxygen.

To me it's a bit ironic that the studies on some DOC having detrimental effects on coral are used to target Carbon Dosing as a bad idea, when algae is the actual study design emphasis.
The studies are meant to explain why algae-derived DOC are harmful to coral. I.e. how algae in close contact causes coral health decline. The research is pretty clear, the DOC from the algae affects the O2 levels but more importantly the microbiome of the corals (antibiotics can save corals from detrimental effects of growing too close to algae).
But those studies use either algae itself, or DOC sources that approximate algal sources.
These studies aren't using acetate or ethanol.
Maybe @Belgian Anthias could point to studies on detrimental effect of acetate addition on coral microbiome?

If you were going to use a big algae scrubber, these papers could be a reason to think hard about it (though it seems to work for many).
If you were going to pour glucose or galactose or mannose in your tank, these papers would be a reason to reconsider.
If your carbon dosing routine is 2 teaspoons of sugar in your coffee and one in your tank, then yeah....don't.

But these papers don't show that acetate (or ethanol) has these effects, it doesn't take much experimenting to realize different carbon sources are used wildly differently in a tank by organisms. (Try it! bottle up tank samples and add equal C of different DOC sources - differences are naked-eye apparent. It's wild.)
So simply stating that carbon dosing, as practiced in the hobby, has been proven detrimental by these studies is incorrect. It could be, but that requires assuming acetate and ethanol act like glucose, mannose etc, when my eyeballs tell me they don't.

By the way, if I use the elevated C/N ratio of input fish flake to keep NO3 low, the excess carbon input is stuff like "wheat gluten, wheat flour, wheat starch..." not sure those are better Carbons than acetate either.
 
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To me it's a bit ironic that the studies on some DOC having detrimental effects on coral are used to target Carbon Dosing as a bad idea, when algae is the actual study design emphasis.
The studies are meant to explain why algae-derived DOC are harmful to coral. I.e. how algae in close contact causes coral health decline. The research is pretty clear, the DOC from the algae affects the O2 levels but more importantly the microbiome of the corals (antibiotics can save corals from detrimental effects of growing too close to algae).
But those studies use either algae itself, or DOC sources that approximate algal sources.
These studies aren't using acetate or ethanol.
Maybe @Belgian Anthias could point to studies on detrimental effect of acetate addition on coral microbiome?

If you were going to use a big algae scrubber, these papers could be a reason to think hard about it (though it seems to work for many).
If you were going to pour glucose or galactose or mannose in your tank, these papers would be a reason to reconsider.
If your carbon dosing routine is 2 teaspoons of sugar in your coffee and one in your tank, then yeah....don't.

But these papers don't show that acetate (or ethanol) has these effects, it doesn't take much experimenting to realize different carbon sources are used wildly differently in a tank by organisms. (Try it! bottle up tank samples and add equal C of different DOC sources - differences are naked-eye apparent. It's wild.)
So simply stating that carbon dosing, as practiced in the hobby, has been proven detrimental by these studies is incorrect. It could be, but that requires assuming acetate and ethanol act like glucose, mannose etc, when my eyeballs tell me they don't.

By the way, if I use the elevated C/N ratio of input fish flake to keep NO3 low, the excess carbon input is stuff like "wheat gluten, wheat flour, wheat starch..." not sure those are better Carbons than acetate either.

The main reason I selected acetate is because it is so widely taken up and used by a very wide range of organisms, including bacteria, algae, and sponges.
 

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To me it's a bit ironic that the studies on some DOC having detrimental effects on coral are used to target Carbon Dosing as a bad idea, when algae is the actual study design emphasis.
The studies are meant to explain why algae-derived DOC are harmful to coral. I.e. how algae in close contact causes coral health decline. The research is pretty clear, the DOC from the algae affects the O2 levels but more importantly the microbiome of the corals (antibiotics can save corals from detrimental effects of growing too close to algae).
But those studies use either algae itself, or DOC sources that approximate algal sources.
These studies aren't using acetate or ethanol.
Maybe @Belgian Anthias could point to studies on detrimental effect of acetate addition on coral microbiome?

If you were going to use a big algae scrubber, these papers could be a reason to think hard about it (though it seems to work for many).
If you were going to pour glucose or galactose or mannose in your tank, these papers would be a reason to reconsider.
If your carbon dosing routine is 2 teaspoons of sugar in your coffee and one in your tank, then yeah....don't.

But these papers don't show that acetate (or ethanol) has these effects, it doesn't take much experimenting to realize different carbon sources are used wildly differently in a tank by organisms. (Try it! bottle up tank samples and add equal C of different DOC sources - differences are naked-eye apparent. It's wild.)
So simply stating that carbon dosing, as practiced in the hobby, has been proven detrimental by these studies is incorrect. It could be, but that requires assuming acetate and ethanol act like glucose, mannose etc, when my eyeballs tell me they don't.

By the way, if I use the elevated C/N ratio of input fish flake to keep NO3 low, the excess carbon input is stuff like "wheat gluten, wheat flour, wheat starch..." not sure those are better Carbons than acetate either.

Good point that one should differentiate algae specific DOC from other types of DOC since the different types can have different effects on a system.

What I do find interesting is that so many reef keepers have used algae successfully in various ways to control nutrients. The demonstrated deleterious effects of algae derived DOC on the coral holobiont seem to be mitigated in a typical reef aquarium setting. Considering water volume vs. algal mass, is this a case of 'dilution is the cure for pollution', skimmers and especially GAC usage removing DOC or is it simply that the coral holobiont adapts to the algal DOC load? My best guess is that it's a combination of all these.

What I infer from these algal DOC studies is that when antibiotics are administered the coral holobiont bacteria numbers drop substantially and O2 levels return back to a more normal level...which then saves the coral. Due to the short exposure to the algae DOC in the experiments, I don't see this as a change in the holobiont's bacterial species causing an issue, but rather an explosion in the resident bacterial numbers resulting in O2 depravation.

Great point noting that the carbon source added via flake food or pellets typically is wheat. Looks like we need a study: 'Effects of wheat byproducts when used as a source of carbon dosing' :)
 
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Dan_P

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To me it's a bit ironic that the studies on some DOC having detrimental effects on coral are used to target Carbon Dosing as a bad idea, when algae is the actual study design emphasis.
The studies are meant to explain why algae-derived DOC are harmful to coral. I.e. how algae in close contact causes coral health decline. The research is pretty clear, the DOC from the algae affects the O2 levels but more importantly the microbiome of the corals (antibiotics can save corals from detrimental effects of growing too close to algae).
But those studies use either algae itself, or DOC sources that approximate algal sources.
These studies aren't using acetate or ethanol.
Maybe @Belgian Anthias could point to studies on detrimental effect of acetate addition on coral microbiome?

If you were going to use a big algae scrubber, these papers could be a reason to think hard about it (though it seems to work for many).
If you were going to pour glucose or galactose or mannose in your tank, these papers would be a reason to reconsider.
If your carbon dosing routine is 2 teaspoons of sugar in your coffee and one in your tank, then yeah....don't.

But these papers don't show that acetate (or ethanol) has these effects, it doesn't take much experimenting to realize different carbon sources are used wildly differently in a tank by organisms. (Try it! bottle up tank samples and add equal C of different DOC sources - differences are naked-eye apparent. It's wild.)
So simply stating that carbon dosing, as practiced in the hobby, has been proven detrimental by these studies is incorrect. It could be, but that requires assuming acetate and ethanol act like glucose, mannose etc, when my eyeballs tell me they don't.

By the way, if I use the elevated C/N ratio of input fish flake to keep NO3 low, the excess carbon input is stuff like "wheat gluten, wheat flour, wheat starch..." not sure those are better Carbons than acetate either.
Good recap on the literature.

I think starch has been used in fish or shrimp culture ponds as way to increase C to N. Of course, we don’t know if coral would mind.
 

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Very interesting read so far. I must admit that a lot of it is a little over my head, but generally I get the point.
Going back point of Carbon dosing & that being detrimental to coral due to its zooxanthellae exploding in numbers & as a result can potentially kill the coral.
We have already established from previous posts that not all carbon is the same. So that leads me to TMC tropic marin products of carbon dosing to my knowledge they are the only company that has spent a considerable amount of effort & research in to effects of carbon dosing & which type of polymers target specific type of bacteria.
Lou Ekus from tropic marin did a presentation on in at reef dudes youtube channel here is a link To summarise from what I took away is that there NP Bacto pellets which are essentially made of seaweed polymers just like reef actif specifically target phosphate consuming bacteria and in turn the bacteria consumes that polymer & in turns lowers phosphate anyway that's kind of the process. Then according to hans-werner balling because coral has a very poor mechanism to uptake phosphate the coral can capture this bacteria which is full of po4 from water column & in turn get there required phosphate needs. I would be interested in comments on this presentation from Lou other people's thoughts ect.
 
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Very interesting read so far. I must admit that a lot of it is a little over my head, but generally I get the point.
Going back point of Carbon dosing & that being detrimental to coral due to its zooxanthellae exploding in numbers & as a result can potentially kill the coral.
We have already established from previous posts that not all carbon is the same. So that leads me to TMC tropic marin products of carbon dosing to my knowledge they are the only company that has spent a considerable amount of effort & research in to effects of carbon dosing & which type of polymers target specific type of bacteria.
Lou Ekus from tropic marin did a presentation on in at reef dudes youtube channel here is a link To summarise from what I took away is that there NP Bacto pellets which are essentially made of seaweed polymers just like reef actif specifically target phosphate consuming bacteria and in turn the bacteria consumes that polymer & in turns lowers phosphate anyway that's kind of the process. Then according to hans-werner balling because coral has a very poor mechanism to uptake phosphate the coral can capture this bacteria which is full of po4 from water column & in turn get there required phosphate needs. I would be interested in comments on this presentation from Lou other people's thoughts ect.

To clarify a bit, all biopellets are some form of poly(hydroxybutyrate). That material may be natural or synthetic, but is the polymer that some species of bacteria use as a form of energy storage, like a human storing fat.

While those species of bacteria obviously have the correct enzymes to break it down, they are not the only ones. Many species can break down poly(hydroxybutyrate) and use it for their own purposes, presumably because they have evolved to naturally find it in their environment after other bacteria that made it have died.

I've never seen it reported that corals can use PHB, and I'd be surprised if they could since it is insoluble and is generally degraded by biofilms of bacteria that coat the surface and release enzymes to break it down.

Certainly many corals can consume the bacteria that are driven by all types of organic carbon dosing methods, and may well benefit from that consumption. Some types of organic carbon, such as acetate, are also known to be directly used by corals, and they may benefit from that direct uptake as well.
 

ineption

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To clarify a bit, all biopellets are some form of poly(hydroxybutyrate). That material may be natural or synthetic, but is the polymer that some species of bacteria use as a form of energy storage, like a human storing fat.

While those species of bacteria obviously have the correct enzymes to break it down, they are not the only ones. Many species can break down poly(hydroxybutyrate) and use it for their own purposes, presumably because they have evolved to naturally find it in their environment after other bacteria that made it have died.

I've never seen it reported that corals can use PHB, and I'd be surprised if they could since it is insoluble and is generally degraded by biofilms of bacteria that coat the surface and release enzymes to break it down.

Certainly many corals can consume the bacteria that are driven by all types of organic carbon dosing methods, and may well benefit from that consumption. Some types of organic carbon, such as acetate, are also known to be directly used by corals, and they may benefit from that direct uptake as well.
Mr Randy don't shoot the messenger sort of speak. Apparently from what Lou said there pellets are totally different from all others on the market because they extract the contents from some kind of seaweed so called polymers & that is what the pellets made of. They also have the same product in power form which is called "reef actif" . I don't know if that true or not or exact procedure or process all I am saying is this is what was stressed over and over again. Probably poly(hydroxybutyrate) is that so called seaweed polymer that Mr Ekus was referring to.
To me I am trying to extract any information that I could implement to improve health growth colouration of my corals.



It would be great if Mr Lou or Mr Balling or some one from TMC could join this conversation & really expand on there carbon dosing products & why they are different. Does any one know if anyone could tag any of them gents?
 

ineption

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Good point that one should differentiate algae specific DOC from other types of DOC since the different types can have different effects on a system.

What I do find interesting is that so many reef keepers have used algae successfully in various ways to control nutrients. The demonstrated deleterious effects of algae derived DOC on the coral holobiont seem to be mitigated in a typical reef aquarium setting. Considering water volume vs. algal mass, is this a case of 'dilution is the cure for pollution', skimmers and especially GAC usage removing DOC or is it simply that the coral holobiont adapts to the algal DOC load? My best guess is that it's a combination of all these.

What I infer from these algal DOC studies is that when antibiotics are administered the coral holobiont bacteria numbers drop substantially and O2 levels return back to a more normal level...which then saves the coral. Due to the short exposure to the algae DOC in the experiments, I don't see this as a change in the holobiont's bacterial species causing an issue, but rather an explosion in the resident bacterial numbers resulting in O2 depravation.

Great point noting that the carbon source added via flake food or pellets typically is wheat. Looks like we need a study: 'Effects of wheat byproducts when used as a source of carbon dosing' :)
Sorry for stupid questions however I am not entirely sure what is algae doc I am guessing that DOC stands for desolved organic content? Are you saying that algae can produce such staff as byproduct which has the potential to harm the coral? Also what does GAC stand for?
 

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Sorry for stupid questions however I am not entirely sure what is algae doc I am guessing that DOC stands for desolved organic content? Are you saying that algae can produce such staff as byproduct which has the potential to harm the coral? Also what does GAC stand for?
Yes, i think so. Algal exudates can cause bacterial populations to explode in high enough concentration, which may prevent the corals normal function, boundary layer, from working properly (gas exchange ). I think small amounts of exudate may be beneficial though. There’s probably a similar problem with overdosing any organic carbon source. However, with algae, you don’t have to dose the DOC, you merely have to grow too much algae, as upto 40% of algal growth can be released as DOC.
 
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Sorry for stupid questions however I am not entirely sure what is algae doc I am guessing that DOC stands for desolved organic content? Are you saying that algae can produce such staff as byproduct which has the potential to harm the coral? Also what does GAC stand for?

Looks like you have your answers in the previous posts :)

I would only add that each company naturally has a vested interest in promoting their particular product(s). While many claims are legitimate, others can be misleading and occasionally downright false. The trick for the reef keeper is in recognizing 'the wheat from the chaff'.

While often challenging for the layman, reading and comprehending non-commercial scientific articles on a particular subject can help one discern fact from hyperbole.
 
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Mr Randy don't shoot the messenger sort of speak. Apparently from what Lou said there pellets are totally different from all others on the market because they extract the contents from some kind of seaweed so called polymers & that is what the pellets made of. They also have the same product in power form which is called "reef actif" . I don't know if that true or not or exact procedure or process all I am saying is this is what was stressed over and over again. Probably poly(hydroxybutyrate) is that so called seaweed polymer that Mr Ekus was referring to.
To me I am trying to extract any information that I could implement to improve health growth colouration of my corals.



It would be great if Mr Lou or Mr Balling or some one from TMC could join this conversation & really expand on there carbon dosing products & why they are different. Does any one know if anyone could tag any of them gents?

The main seaweed polymer that folks use (like as a food thickener in milk shakes) is the protein alginate. It's already in many fish foods. I've not heard of folks making biopellets from it, but they might.

If that is what they use, since it is a protein, any organism eating it is likely getting a lot of its N that way, so will be a net user of more P than N. Perhaps that is what they mean.
 
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taricha

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I just realized that we are veering off track here a bit from this Ammonia titled thread ;)
yeah. Carbon dosing is the shiny trinket that pops up in so many discussions :)

I'm looking at ways of extending the data.

1) I'm pulling as much algae from my system as possible, see if I can cut the algae consumption way way down and see what the ammonia consumption difference is.

2) I'm aiming to compare to data from the "bottled bacteria myth or fact" thread. See what nitrification is typical in a newly cycled system. I think much higher than mine.

3) would be cool if we had data from someone on the opposite end of the nitrification spectrum: one with purported high nitrifiers, a NO3 factory. What is the rate of sand nitrification in that system?
 
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taricha

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Does a bag of "Live Sand" nitrify?
Another adjacent question that I was wondering about is whether bags of "live sand" could possibly be alive with nitrification capability. The hobby almost universally regards this stuff as "wet sand" and almost nobody thinks it nitrifies.
But on the other hand if the product was ever cultured by the manufacturer in a system with nitrifiers and an ammonia source, those bacteria can stay dormant for a really long time so it's not impossible the bags could have some nitrification ability.

I was sure somebody had tested it, and I found a few people have posted data on this, so... here you go, saves me an experiment :)
(click through the quotes to see the original threads)

Seems I may have missed the test yesterday. I'm Reading about 1.5 again much more orange. So I would says live sand does little to ammonia.
IMG_20200505_200310.jpg

For those who may protest about the accuracy of the above kit, it's true it wouldn't catch a 0.1-0.2 ppm/day rate.

but this would...
From my limited testing I've done, the answer is no. I have no idea how much bacteria is still present in the samples or their activity (and the heterogeneity of "live sand" is probably too great to draw meaningful conclusions), but the samples I tested were unable to process any meaningful amounts of ammonia in 24 hours.
Testing was performed with a Hach Colorimeter.
(using the sensitive salicylate - blue/green - method not the nessler yellow).

That ammonia kit read with a colorimeter would indeed catch an ammonia consumption as little as a tenth or two ppm of ammonia. So, probably accurate for the hobby to carry on derisively calling these products "dead wet sand" as far as nitrification goes.
 
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wonderful studies we will link this right now to sand rinse thread because we have asked that question before and I did assume 100% it would be active, but why spend more $ to add bottle bac makes sense for the companies. Still amazed they get a wet product to remain sterile, that’s amazing in fact, maybe they can run food production alongside their sand bagging machinery lol but in the end we know corps save money vs expend it where applic

also the unison findings: aquabiomics hinted about this wet dead status. We know Eli has access to relatively decent testing lol and due to business restricts I don’t think he could go into great detail posting under his business moniker but he let us know on another post the sand was ‘ looked at ‘ and found wanting.


I think Dan has done some initial testing and found the same but that may be on known-active sand and he was testing rinse losses. Yours and Eli’s findings on the sand also matches a few forum posts we’ve collected on the matter. Nice patterning I’m sold.

my lfs honestly used to keep twenty or so baby clowns in a 20 high with sand only in the tank and a power head. That is what made it seem like it was active but there’s also the phenomena of catch up cycling ( made up term just now ) where adding in small bioloads to a new tank, and likely some nitrifying clades from the transfer water they rode in on and stuck to the actual fish, are enough to begin catch up cycling for the inert sand. A few timed water changes, no bottle bac, and pretty much any system seeded like this will still cycle with bioload in place. We have done this on a small scale years ago at nano-reef.com where the keeper moved his old coral into a new white dry start reef, no bottle bac, and we used the corals to seed the bac themselves and all he did was feed lightly and change water a couple times then the system became normal such that feeding didn’t require water changes thereafter.


nice work as always
b
 
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taricha

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also the unison findings: aquabiomics hinted about this wet dead status. ...but he let us know on another post the sand was ‘ looked at ‘ and found wanting.


I think Dan has done some initial testing and found the same but that may be on known-active sand and he was testing rinse losses.
Thanks for sharing the confirmation "hint" on that.
Yeah, @Dan_P found that a vigorous tapwater rinse killed dead the nitrification capability he had previously measured in a sample of his aquarium sand.

my lfs honestly used to keep twenty or so baby clowns in a 20 high with sand only in the tank and a power head. That is what made it seem like it was active but there’s also the phenomena of catch up cycling ( made up term just now )
Seems like a LFS sand would be a best-possible case for big nitrification capabilities in the sand, right? (plan to test this)

No need for make-up terms. AOB can double in as fast as 8-24 hours. Sure it's not the 20 minutes of heterotrophs, but if a capability is already present, it doesn't take that long to scale up ... if the conditions are right.
 
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Check out this data for some comparisons of nitrification rates from a few different sources.

NitrificationComparisons4-7.png


Black points are my sand, blue and red circles are my sand plus One & Only and Biospira respectively. Purple is from a measurement @Dan_P made on a sample of his sand. The next 9 points (squares) are rates calculated from reported values in the Bottle Bacteria, Myth or Fact thread. The rates are initial nitrification rates for Fritz TurboStart, One and Only, and Biospira (the numbers in each label are the post number in the thread). The tank conditions in that thread are comparable in that Dr Reef used about 2% sand and in those posts selected, the initial ammonia amount was 1ppm. In mine it's about 0.5ppm starting ammonia.

What's interesting here to me is how close all these rates are to each other - all in the ballpark of 0.1-0.3 ppm / day Total Ammonia - Nitrogen.
That clustering is interesting because the total ammonia processing rate (not nitrification) for my tank was an order of magnitude bigger - 3.9ppm TAN/day, repeated measurement 3.3ppm/day. And Dan measured a bucket with an algae film taking in 2ppm/day.

Will this general trend hold? Established systems having an order of magnitude more ammonia consumption capability than nitrification ability? I'm still hunting high nitrification systems, if they exist! Data from sand at the LFS coming soon :)
 

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Check out this data for some comparisons of nitrification rates from a few different sources.

NitrificationComparisons4-7.png


Black points are my sand, blue and red circles are my sand plus One & Only and Biospira respectively. Purple is from a measurement @Dan_P made on a sample of his sand. The next 9 points (squares) are rates calculated from reported values in the Bottle Bacteria, Myth or Fact thread. The rates are initial nitrification rates for Fritz TurboStart, One and Only, and Biospira (the numbers in each label are the post number in the thread). The tank conditions in that thread are comparable in that Dr Reef used about 2% sand and in those posts selected, the initial ammonia amount was 1ppm. In mine it's about 0.5ppm starting ammonia.

What's interesting here to me is how close all these rates are to each other - all in the ballpark of 0.1-0.3 ppm / day Total Ammonia - Nitrogen.
That clustering is interesting because the total ammonia processing rate (not nitrification) for my tank was an order of magnitude bigger - 3.9ppm TAN/day, repeated measurement 3.3ppm/day. And Dan measured a bucket with an algae film taking in 2ppm/day.

Will this general trend hold? Established systems having an order of magnitude more ammonia consumption capability than nitrification ability? I'm still hunting high nitrification systems, if they exist! Data from sand at the LFS coming soon :)
Go Jonathan!

One storyline is that every system has approximately the same ammonia oxidation rate but a different ammonia consumption rate. The byline is ammonia oxidation might be a minor component of ammonia removal. And nuisance microorganisms blooms happen when the ammonia oxidation and ammonia consumption leave too much leftover ammonia. Whether or not that last sentence is 100% baloney, I will look at how biofilms develop with ammonia hanging around.
 
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