Ammonia is our Friend 2: Article Outline

Lasse

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I do not think that you can compare a long time more or less in vivo studie with short time studies that more or less are done in vitro.

What really stands out from that article is how little N is required
An euphyllia coral, as an example - has not very much body tissue - it is just only the elastic casing of a balloon.

It was interesting to read the following part in this article - linked by Hans-Werner. Have not seen that mentioned before in any of the arguments about ammonia contra nitrate - (my bold)

Most experimental work on the effect of nitrogen enrichment on zooxanthellae and corals has centred on nitrogen in its ammonium form. Ammonium enrichment often resulted in an increase in algal density, a decrease in the rate of photosynthesis per algal cell Hoegh Guldberg and Smith, 1989, Dubinsky et al., 1990, Stimson and Kinzie, 1991 and a decrease in the rate of skeletogenesis Stambler et al., 1991, Ferrier-Pagès et al., 2000. Very little information, however, exists on the effects of nitrate on coral physiology Bythell, 1990, Marubini and Davies, 1996, Marubini and Atkinson, 1999. Bythell (1990) showed that corals are able to use nitrate at natural environmental concentrations (up to 2 μM) for their nitrogen requirements for tissue growth and production of gametes. However, under certain conditions, nitrate enrichment can also induce an increase in the algal density and a decrease in the rates of calcification Marubini and Davies, 1996, Marubini and Atkinson, 1999.

Sincerely Lasse
 

Hans-Werner

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It was interesting to read the following part in this article - linked by Hans-Werner. Have not seen that mentioned before in any of the arguments about ammonia contra nitrate - (my bold)
I think this is more of theoretical interest to us. Like I have already mentioned, in many reef tanks you just cannot control what corals take up. This is a big difference to the scientific research. They use water with really low N concentrations. After adding some phosphate, corals will take up whatever N form you give them.

In reef tanks corals have "free choice", "what do I prefer today, some highly processed nitrate or rather some freshly excreted ammonium?" :grinning-face-with-smiling-eyes:
 

Reefahholic

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I do not think that you can compare a long time more or less in vivo studie with short time studies that more or less are done in vitro.


An euphyllia coral, as an example - has not very much body tissue - it is just only the elastic casing of a balloon.

It was interesting to read the following part in this article - linked by Hans-Werner. Have not seen that mentioned before in any of the arguments about ammonia contra nitrate - (my bold)



Sincerely Lasse

So are you for or against ammonia dosing Lassee. What are your thoughts?
 

Lasse

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So are you for or against ammonia dosing Lassee. What are your thoughts?
I am not in generally against it - I´ll think its a good way in some aquariums where the organics and fish bioloads are low and there it is a N limitation - but I am also sure that NO3 dosing works as well.

However - in my aquarium, never rinsed for organics, no WC the last 3-4 years, high fish biolad (high feeding rate), sand beds, cryptic zones and so on - my bacterial mineralisation of organic matter give me the NH3/NH4 the system needs.

I have done a rough mass-balance of inorganic N in my aquarium. It shows that my load of NH4-N every day is around 2.6 mg/L NH4-N (1.1 mg/L NH4-N from feeding and 1.5 mg/L NH-N from bacterial minrealisation)
I also know that my nitrification rate each day is at least 5 mg/L NO3 => 1.1 mg/L NO3-N. Återstår då ca 1.5 mg/L NH4-N that I have only weak ideas around- some provably ands up as uptake but either is my nitrification/denitrification rate larger than I´m able to prove or I have an active anammox process in my reversed flow sand bed.

In the end of the day - knowing all this - I think I would be reckless if I did not offer a dedicated nitrification step in my system

Sincerely Lasse
 
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Randy Holmes-Farley

Randy Holmes-Farley

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What about amino acids as an optional additive instead of ammonia . that covers “too low” nitrates and at the same time directly feeds corals with protein constituents. This is in light of the fact that corals have effective uptake mechanisms. Only issue is the cost and the lack of knowledge which AAs are essential in the sense that corals cannot synthesize (maybe there aren’t any as their symbionts produce all of them).

I have nothing against amino acids except they may promote cyano.
 

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Since this article and what exactly gets incorporated into it is still evolving, I thought I'd open it up for discussion of things I should include that are not mentioned or things that I mention that should not be included.

There will be lots of standard ammonia science stuff as well, such as ammonia in the ocean, free vs total ammonia, testing methods and complexities, etc.

Here's the start of the article:

Ammonia is Our Friend

By Randy Holmes-Farley

Yes, I know the title is provocative, and likely goes against much of what you read and hear in the reef aquarium hobby. I believe, however, that the hobby may have been harmed by the continual vilification of ammonia as something that one wants to reduce as much as possible. Products and procedures to keep driving it down may well be detrimental in many reef tanks.

This bulleted summary contains the points that I make in detail in the subsequent sections of this article along with some basic science about ammonia. They are presented in a logical order of progression, but if you already know you agree with certain points, it may not be needed to read those sections to get a complete story.

1. While ammonia is toxic at very high levels, the levels needed to be lethal to a marine fish are higher than many people think. I’ve not seen any study in the literature that shows an LC50 (half of fish die) in less than 15 ppm total ammonia in seawater over 4 days or more of exposure at normal pH.

2. Sublethal toxic effects of ammonia, such as gill lesions observed by histopathology, do not seem to become significant until levels reach 5-10 ppm total ammonia at pH 8.1.

3. The toxicity of ammonia is a function of pH. At pH 8.5, toxic effects kick in at ammonia levels 2.5x lower than at pH 8.1. Likewise, at pH 7.8, it takes twice as much ammonia to be toxic as at pH 8.1. In a situation where ammonia might well reach toxic levels, such as a shipping bag, raising pH in the bag should not be a goal.

4. Toxic levels of ammonia are just not reached in typical operating reef aquaria. Seeing a measured value of 0.25 ppm, whether real or test error, is not a concern. It may be a benefit.

5. Chemical methods to control or detoxify ammonia in marine systems at doses recommended are generally ineffective at impacting ammonia, despite folks thinking they were effective. If you believe that 2 ppm ammonia will kill a fish, and you add an ammonia detoxifier and it survives, you may falsely conclude it worked, as opposed to you misunderstood how toxic ammonia was.

6. Corals demonstrate a preference for obtaining the N (nitrogen) they need from ammonia over nitrate when both are available. Organisms using nitrate as an N source need to spend extra energy to convert the nitrate to ammonia before use.

7. Continually driving ammonia down in a reef tank may be making it unnecessarily difficult for corals to easily obtain the nitrogen they need. Actions such as providing media designed for nitrifiers or adding nitrifying bacteria on a regular basis may thus be doing more harm than good.

8. Reef aquaria where N is in short supply may benefit from dosing ammonia, and that benefit may be greater than dosing nitrate. Ammonium bicarbonate is a good source of ammonia as it is inexpensive and readily available in food grade purity.

9. While measuring a detectable level of nitrate in a reef aquarium can be very useful to ensure there is some source of N available for corals, one should not assume that corals are primarily using that source since there are other sources that they may prefer to use.

10. “Cycling” a new reef tank with nitrifying bacteria is just one way to start a tank, and reefers should not simply accept the idea that it is the only way. It may be a fast way to add fish, but perhaps reefers should at least be aware of other options. There will be no stopping nitrifying bacteria from naturally growing in any reef system, but a system where consumption of N is the focus (corals, macroalgae, anemones etc.) as opposed to producers (fish and anything else fed outside food) may not require the addition of bacteria or the time spent waiting for them to develop.

So it seems that everything is old farts were told in the past is false. Can I just tick in my tank.
 

Koty

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I have nothing against amino acids except they may promote cyano.
Yes, AAs may promote cyano but not specifically. In my case I actually have a lot of algae that I manually remove in the display and let live in the sump with Aiptasia and macro algae. For me it has a dual purpose: to act as an N source as my NO3 drops to 0, and to replace coral feeding in a way that will maintain stability.
 
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SDchris

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What is the evidence it does?
In respect to ammonia vs nitrate.
Just going back to this:
Were you asking for evidence that nitrate reduces growth or whether ammonia promotes faster growth over nitrate
There are at least a few people that imply when switching from nitrate to ammonium dosing say they saw an increase in growth and colouration.
Dose Ammonia Instead of Nitrate? Dr. Sanjay Joshi & Mike Paletta
Was the swap equivalent? Would need to ask them!
Maybe semantics on whether to describe growth as a reduction with nitrate or increase using ammonia as there is no real baseline measurement.
 

Reefahholic

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If you believe that 2 ppm ammonia will kill a fish, and you add an ammonia detoxifier and it survives, you may falsely conclude it worked, as opposed to you misunderstood how toxic ammonia was.

So true! :)

While measuring a detectable level of nitrate in a reef aquarium can be very useful to ensure there is some source of N available for corals, one should not assume that corals are primarily using that source since there are other sources that they may prefer to use.

Makes me wonder about systems that have a large fish population. They always seem to be very successful. Maybe this is due to the constant ammonia excretion, or the consistent natural fertilizer (N&P). With heavy fish bioloads, I wonder if ammonia dosing is necessary or doing more harm than good.

Yes, AAs may promote cyano but not specifically.
I don’t know. In most cases it certainly seems to promote cyano specifically. I’m pretty confident I can create a big cyano bloom on command if you hand me a bottle of AA’s, and give me a few weeks. :)
 

Lasse

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With heavy fish bioloads, I wonder if ammonia dosing is necessary or doing more harm than good.
That's exactly where I land with my thoughts! But will not end up with 0 in NO3 of other reasons than nutrition demand.

Sincerely Lasse
 

Hans-Werner

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Makes me wonder about systems that have a large fish population. They always seem to be very successful. Maybe this is due to the constant ammonia excretion, or the consistent natural fertilizer (N&P). With heavy fish bioloads, I wonder if ammonia dosing is necessary or doing more harm than good.
What are your thoughts behind the last sentence?

If the ammonia excretion is already high and would totally fulfill the needs of the corals, it is not necessary to dose additional ammonium, this may be true.

What is the difference between dosing nitrate and dosing ammonium in this situation?

If dosing ammonium in an already ammonium saturated situation I would expect that nitrifiers and nitrification will catch up and you will end up with nitrate.

From a practitioners perspective, what is the disadvantage of dosing ammonium and would dosing nitrate being more advantageous?

At the moment I can't see the point.
 

Dan_P

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Since this article and what exactly gets incorporated into it is still evolving, I thought I'd open it up for discussion of things I should include that are not mentioned or things that I mention that should not be included.

There will be lots of standard ammonia science stuff as well, such as ammonia in the ocean, free vs total ammonia, testing methods and complexities, etc.

Here's the start of the article:

Ammonia is Our Friend

By Randy Holmes-Farley

Yes, I know the title is provocative, and likely goes against much of what you read and hear in the reef aquarium hobby. I believe, however, that the hobby may have been harmed by the continual vilification of ammonia as something that one wants to reduce as much as possible. Products and procedures to keep driving it down may well be detrimental in many reef tanks.

This bulleted summary contains the points that I make in detail in the subsequent sections of this article along with some basic science about ammonia. They are presented in a logical order of progression, but if you already know you agree with certain points, it may not be needed to read those sections to get a complete story.

1. While ammonia is toxic at very high levels, the levels needed to be lethal to a marine fish are higher than many people think. I’ve not seen any study in the literature that shows an LC50 (half of fish die) in less than 15 ppm total ammonia in seawater over 4 days or more of exposure at normal pH.

2. Sublethal toxic effects of ammonia, such as gill lesions observed by histopathology, do not seem to become significant until levels reach 5-10 ppm total ammonia at pH 8.1.

3. The toxicity of ammonia is a function of pH. At pH 8.5, toxic effects kick in at ammonia levels 2.5x lower than at pH 8.1. Likewise, at pH 7.8, it takes twice as much ammonia to be toxic as at pH 8.1. In a situation where ammonia might well reach toxic levels, such as a shipping bag, raising pH in the bag should not be a goal.

4. Toxic levels of ammonia are just not reached in typical operating reef aquaria. Seeing a measured value of 0.25 ppm, whether real or test error, is not a concern. It may be a benefit.

5. Chemical methods to control or detoxify ammonia in marine systems at doses recommended are generally ineffective at impacting ammonia, despite folks thinking they were effective. If you believe that 2 ppm ammonia will kill a fish, and you add an ammonia detoxifier and it survives, you may falsely conclude it worked, as opposed to you misunderstood how toxic ammonia was.

6. Corals demonstrate a preference for obtaining the N (nitrogen) they need from ammonia over nitrate when both are available. Organisms using nitrate as an N source need to spend extra energy to convert the nitrate to ammonia before use.

7. Continually driving ammonia down in a reef tank may be making it unnecessarily difficult for corals to easily obtain the nitrogen they need. Actions such as providing media designed for nitrifiers or adding nitrifying bacteria on a regular basis may thus be doing more harm than good.

8. Reef aquaria where N is in short supply may benefit from dosing ammonia, and that benefit may be greater than dosing nitrate. Ammonium bicarbonate is a good source of ammonia as it is inexpensive and readily available in food grade purity.

9. While measuring a detectable level of nitrate in a reef aquarium can be very useful to ensure there is some source of N available for corals, one should not assume that corals are primarily using that source since there are other sources that they may prefer to use.

10. “Cycling” a new reef tank with nitrifying bacteria is just one way to start a tank, and reefers should not simply accept the idea that it is the only way. It may be a fast way to add fish, but perhaps reefers should at least be aware of other options. There will be no stopping nitrifying bacteria from naturally growing in any reef system, but a system where consumption of N is the focus (corals, macroalgae, anemones etc.) as opposed to producers (fish and anything else fed outside food) may not require the addition of bacteria or the time spent waiting for them to develop.

Some thoughts about other things to mention,..

A typical new aquarium starts out with two types of bacteria. One that oxidizes ammonia and the other that oxidizes nitrite (nitrogen cycling). This is to say that the aquarium surfaces have a limited function. Over time (I don’t have number in mind), the functional complexity of the sand/rocks/surfaces increases, for example, addition of the digestion odpf organic matter, particulate and dissolved (carbon cycling), and removal of nitrate through the reduction of nitrate to molecular nitrogen and consumption of nitrate for biomass (nitrogen cycling). Phosphate and maybe sulfur cycling are also added. Behind the scenes of this functionality build up is a very complex process of microorganism population growth in number and species. There is a tremendous amount of change that occurs until things settle down, though the species and each species size is unlikely to ever stop fluctuating. Amid all this change, the bacteria that once dominated the new aquarium biome providing nitrogen cycling, have become minor players in the cycling nitrogen. Etc.
 

Lasse

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In my system with high microbiological activity and a high "standing Stock" of organic matter - I am afraid of one thing - hydrogen sulphide - especially if I risk to run low in oxygen during night hours. Around 2- 4 mg/L NO3 will effectively lower hydrogen sulphide production to a minimum. That´s the reason why I would dos external NO3 if my NO3 goes near zero and I can´t tweak it with lovering my denitrification rate.

Sincerely Lasse
 

Lasse

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Some thoughts about other things to mention,..

A typical new aquarium starts out with two types of bacteria. One that oxidizes ammonia and the other that oxidizes nitrite (nitrogen cycling). This is to say that the aquarium surfaces have a limited function. Over time (I don’t have number in mind), the functional complexity of the sand/rocks/surfaces increases, for example, addition of the digestion odpf organic matter, particulate and dissolved (carbon cycling), and removal of nitrate through the reduction of nitrate to molecular nitrogen and consumption of nitrate for biomass (nitrogen cycling). Phosphate and maybe sulfur cycling are also added. Behind the scenes of this functionality build up is a very complex process of microorganism population growth in number and species. There is a tremendous amount of change that occurs until things settle down, though the species and each species size is unlikely to ever stop fluctuating. Amid all this change, the bacteria that once dominated the new aquarium biome providing nitrogen cycling, have become minor players in the cycling nitrogen. Etc.
Exactly - and all of this was one of the reasons why I put together my 15 steps to start a saltwater aquarium a couple of years ago.

Sincerely Lasse
 

Hans-Werner

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In my system with high microbiological activity and a high "standing Stock" of organic matter - I am afraid of one thing - hydrogen sulphide - especially if I risk to run low in oxygen during night hours.
Maybe I am wrong but I think usually the risk of hydrogen sulphide is overestimated.

After introducing fresh live rock with dead sponges "out of the box" you may notice white mold-like patches. These are Beggiatoa https://en.wikipedia.org/wiki/Beggiatoa suphur bacteria. I have checked this with a microscope. They are oxidating sulphide to elemental sulfur grains they store and which give them the white color.
 

Dom

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Since this article and what exactly gets incorporated into it is still evolving, I thought I'd open it up for discussion of things I should include that are not mentioned or things that I mention that should not be included.

There will be lots of standard ammonia science stuff as well, such as ammonia in the ocean, free vs total ammonia, testing methods and complexities, etc.

Here's the start of the article:

Ammonia is Our Friend

By Randy Holmes-Farley

Yes, I know the title is provocative, and likely goes against much of what you read and hear in the reef aquarium hobby. I believe, however, that the hobby may have been harmed by the continual vilification of ammonia as something that one wants to reduce as much as possible. Products and procedures to keep driving it down may well be detrimental in many reef tanks.

This bulleted summary contains the points that I make in detail in the subsequent sections of this article along with some basic science about ammonia. They are presented in a logical order of progression, but if you already know you agree with certain points, it may not be needed to read those sections to get a complete story.

1. While ammonia is toxic at very high levels, the levels needed to be lethal to a marine fish are higher than many people think. I’ve not seen any study in the literature that shows an LC50 (half of fish die) in less than 15 ppm total ammonia in seawater over 4 days or more of exposure at normal pH.

2. Sublethal toxic effects of ammonia, such as gill lesions observed by histopathology, do not seem to become significant until levels reach 5-10 ppm total ammonia at pH 8.1.

3. The toxicity of ammonia is a function of pH. At pH 8.5, toxic effects kick in at ammonia levels 2.5x lower than at pH 8.1. Likewise, at pH 7.8, it takes twice as much ammonia to be toxic as at pH 8.1. In a situation where ammonia might well reach toxic levels, such as a shipping bag, raising pH in the bag should not be a goal.

4. Toxic levels of ammonia are just not reached in typical operating reef aquaria. Seeing a measured value of 0.25 ppm, whether real or test error, is not a concern. It may be a benefit.

5. Chemical methods to control or detoxify ammonia in marine systems at doses recommended are generally ineffective at impacting ammonia, despite folks thinking they were effective. If you believe that 2 ppm ammonia will kill a fish, and you add an ammonia detoxifier and it survives, you may falsely conclude it worked, as opposed to you misunderstood how toxic ammonia was.

6. Corals demonstrate a preference for obtaining the N (nitrogen) they need from ammonia over nitrate when both are available. Organisms using nitrate as an N source need to spend extra energy to convert the nitrate to ammonia before use.

7. Continually driving ammonia down in a reef tank may be making it unnecessarily difficult for corals to easily obtain the nitrogen they need. Actions such as providing media designed for nitrifiers or adding nitrifying bacteria on a regular basis may thus be doing more harm than good.

8. Reef aquaria where N is in short supply may benefit from dosing ammonia, and that benefit may be greater than dosing nitrate. Ammonium bicarbonate is a good source of ammonia as it is inexpensive and readily available in food grade purity.

9. While measuring a detectable level of nitrate in a reef aquarium can be very useful to ensure there is some source of N available for corals, one should not assume that corals are primarily using that source since there are other sources that they may prefer to use.

10. “Cycling” a new reef tank with nitrifying bacteria is just one way to start a tank, and reefers should not simply accept the idea that it is the only way. It may be a fast way to add fish, but perhaps reefers should at least be aware of other options. There will be no stopping nitrifying bacteria from naturally growing in any reef system, but a system where consumption of N is the focus (corals, macroalgae, anemones etc.) as opposed to producers (fish and anything else fed outside food) may not require the addition of bacteria or the time spent waiting for them to develop.


I am still working to understand this concept.

I am on board with the idea that ammonia is more beneficial to corals. The reason; corals are more efficient in the uptake of ammonia as opposed to nitrates.

Am I correct to think that while ammonia may be beneficial in reef tanks, it is still detrimental to fresh water?

With the absence of corals in fresh water, there is nothing to take up ammonia. Wouldn't ammonia be an issue?

Maybe this is a point to make?
 

Hans-Werner

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Am I correct to think that while ammonia may be beneficial in reef tanks, it is still detrimental to fresh water?

With the absence of corals in fresh water, there is nothing to take up ammonia. Wouldn't ammonia be an issue?
In freshwater the situation is a bit different. Most freshwater tanks have oxidizing filter, i. e. canister filters, which rapidly oxidize ammonia to nitrate.

The proportions of total ammonia which are ammonium and ammonia depend on pH. In low pH feshwater the ammonium is quite harmless. At higher pH the proportion of free ammonia rises and it gets more toxic in this way.

While Echinodorus in my experience prefers nitrate as nitrogen source, Cryptocoryne are said to prefer ammonium. Cryptocoryne are Araceae and some species grow in soft and acidic peat bog waters. The preference of land plants and feshwater plants for nitrate on one side or for ammonium on the other side may be family related.
 

Lasse

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Maybe I am wrong but I think usually the risk of hydrogen sulphide is overestimated
Oh no - IMO is underestimated. If you have deep sand and a high loaded aquarium like mine you sometimes can see that the sand is grey to black deeper down in the sand bed. Its iron reduced by H2S. Black and grey patches in sand is a sign of H2S production. Normally - it will be oxidized directly in contact with oxygen in the water column and will not do any harm. However if you have no or low in oxygen H2S will be still formed and not oxidised into non toxic form . If NO3 is present - it will favour the anaerobic bacteria that quickly can change from aerobic respiration into anaerobic respiration with NO3 as electron acceptor. If NO3 not present or totally consumed - the bacteria strains that use sulfate as the final electron acceptor will take over and its waste is H2S. Its a different bacteria process from the one you describe.

There has been fatal episodes in some public aquariums when personnel were sent down into large tanks that had been emptied of water after a long time to retrieve or clean the sand left behind. Since my time as an employee in a sewage treatment plant I know the processes of H2S forming and have a huge respect for it. And believe me - it will be formed in many aquaria but because it is easily oxidised - its normally no problems and you will not notice it.

Sincerely Lasse
 

brandon429

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here are some simple tank kills that happened only after sandbed disturbance. nothing other than stirring up the sand caused the losses, and it wasn't ammonia. nobody knows what the lethal compound within tank detritus is, it doesn't express in every system it expresses rarely but effectively when it does...h2s needs to be inspected/the killing agent found one day. ***we see losses that happen in shallow, non gray/black spot beds sometimes as well***the color of the sandbed is absolutely not an indicator of safety status.

https://www.reef2reef.com/threads/re-aquascaping-nightmare-nearly-killed-all-my-fish.665829/






the reason I'm 100% sure the death is found within the detritus cloud, and it's varying states of oxygen/bacterial decay within sand grains, is because on the flipside we have prevented 100% of sandbed losses for ten straight years running in one thread, where we simply rinsed all the sand out with tap water.

by removing the detritus cloud and never exposing it to reef animals, we are able to handle any reef tank on this site without loss in the sand rinse thread currently underway with perfect outcomes for 10 years running.

it's not up for debate that sandbeds can and routinely do kill reefs, what's up for debate is the chemical causative. cool mysteries are still underway in reefing, that's fun business. nobody here today knows the cause of those losses. no article exists to cover the losses with certainty, other than the certainty that doom resides for many tank owners within the cloud of waste we have all been told was mineralized/harmless/inert.
 
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