Ammonia as route cause to all nuisance in the hobby.

damsels are not mean

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this is what most of us still believe, @MnFish1 has a nice mature tank, I believe last year me and a few fellow reefer including Mnfish1 done a lot of work on nitrifying bacteria. One of the test was to remove a piece of mature live rock and transfer it to a new tank to analyse the ammonia performance of live rock. In that test we adde 2 ppm of ammonia to the live rock and to my surprise it took 4 days I believe for the live rock to transform that ammonia into nitrates. @MNFish could you share the results of the test you done?
His test illustrate that our system can’t deal straight away with increasing ammonia levels. I’m here to show my side of the debate I will expect many to disagree with me although all the evidence is in front of us.
Was not the macro algae tank new wend you had the macro algaes and Cyanobacteria issue? I had a similar event in the past although I was already in the suspicion that my tank wasn’t fully ready to deal with increased ammonia.
The tank was new technically yes but it was seeded with several pieces of established rock.
 

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this is what most of us still believe, @MnFish1 has a nice mature tank, I believe last year me and a few fellow reefer including Mnfish1 done a lot of work on nitrifying bacteria. One of the test was to remove a piece of mature live rock and transfer it to a new tank to analyse the ammonia performance of live rock. In that test we adde 2 ppm of ammonia to the live rock and to my surprise it took 4 days I believe for the live rock to transform that ammonia into nitrates. @MNFish could you share the results of the test you done?
His test illustrate that our system can’t deal straight away with increasing ammonia levels. I’m here to show my side of the debate I will expect many to disagree with me although all the evidence is in front of us.
Was not the macro algae tank new wend you had the macro algaes and Cyanobacteria issue? I had a similar event in the past although I was already in the suspicion that my tank wasn’t fully ready to deal with increased ammonia.
The results are all posted in the 'Research section' of R2R
 

MnFish1

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The results are all posted in the 'Research section' of R2R
 
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sixty_reefer

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The tank was new technically yes but it was seeded with several pieces of established rock.
It doesn’t makes no difference unfortunately look at this results from @MnFish1 experiment on day one.
He uses rock from his display, containing some photosynthetic organisms and lit for 12 hours and rock from his mature dark sump.


Post in thread 'New Nitrifying Bacteria Experiment.'
https://www.reef2reef.com/threads/new-nitrifying-bacteria-experiment.872593/post-9592653

None was able to deal with the increased ammonia although the rock containing photosynthetic organisms done slightly better at processing ammonia, nevertheless all the tests done from myself, @MnFish1 and @Coxey81 demonstrate that even mature live rock struggled to deal with increased ammonia, if I remember correctly @Coxey81 rock coming from a younger system took almost a week to be able to process the increased ammonia for reference demonstrating that ammonia is the culprit for the ‘ugly stage’ in new systems. In one of the tests carry out by myself the result was actually a Cyanobacteria bloom I never really understood what was feeding the bloom until recently. We were adding constantly ammonium chloride to the system we never added food or livestock to the testing and scrubbed the rocks for organics prior to testing.

those tests carry strong information in support of my claims and would be interesting to see @Lasse thoughts on the debate.
 
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Seeing from the live rock test mentioned above demonstrating that live rock can’t deal with increasing ammonia levels effectively even in mature systems and much less effective in new systems as coxey test demonstrates I believe we have enough evidence to support ammonia being the culprit to all known nuisances during the ugly stage and during the systems maturing process. The tests mentioned above were verified by many knowledge members on R2R as they were happening and the way they were performed by several members brought consist results. In addition to those tests @Beuchat made several testing on how to eradicate dinoflagellates, from his article he mentioned that natural sources of carbohydrates make the eradication process more efficient, for those who know carbohydrates are used elsewhere in the hobby to stimulate the growth and division of nitrifying and denitrifying autotrophic bacteria, a very effective bacteria at processing ammonia into nitrates and nitrogen gas. My intention soon is to carry out a new test hopefully with enough information to demonstrate that all nuisances can be avoided during the ugly stage using natural sources of carbohydrates to keep ammonia levels under control in new systems making the ugly stage normality a thing from the past, so that many others don’t have to deal with a stage and nuisances that can be avoided by implementing good nutrition for beneficial bacteria from day one.

the testing thread can be find here for those curious on the results

 
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Lasse

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those tests carry strong information in support of my claims and would be interesting to see @Lasse thoughts on the debate.
I have no prove for this claims but I´m glad to see that others have thoughts in the same direction. We know that plants and algae prefer (of energy reasons) NH4/NH3 complex. To use other nitrogen sources (excluding some amino acids) always means a need of extra energy. Why I exclude amino acids is because a guy here in Sweden that is an expert of nitrogen transports through cellmembrans always has stressed that amino acids can move themselves through single human cell walls as god as the NH4/NH3 complex does. He means that´s also the case for at least unicellular algae and bacteria. There is reports of cyanobacteria outbreaks when using amino acids as a nitrogen source - this can be one of the explanation for these observations. - Back to the known fact that the NH3/NH4 is the preferred nitrogen sources for plants (including freshwater plants) - it is interesting to know tha few or any nutrient solutions for freshwater plants conten NH3/NH4 - instead they use the less energy effective NO3 as N source (PMDD as an example). The reasons for this are exactly the same as @sixty_reefer reasons why not use NH3/NH4 complex in saltwater - it will feed nuisance organisms.

To the NH3/NH4 contra H2O2 question. - I have never seen any prove for that H2O2 is a strong enough oxidizer too chemical oxidise NH3/NH4 into NO2 (or not even NO2 into NO3)- I have tested. However - H2O2 will support the normal bacterial nitrification process through rise the oxygen concentration in the water - especially important in saltwater with is lower content of oxygen. Does it really rise the oxygen content - this curves can be interesting. First an overview

Edit: In the first graph - ytan=surface; pumpgrop = sump

1670583797438.png

The more interesting part - how did it turns

H2O2 och syre.jpg


Even the NH3/NH4 was stalled during period before H2O2 addition - after that and the defeat/decrease of the organic load - that process started and it took 4 - 5 days to go down to 0 from ridiculous levels. However the NO2-NO3 stall too but now it is closer to zero.

To the discussion about nitrification and live rocks. At high loads - its not a chance that live rocks can process enough of N from NH4-N to NO3-N in a short time. In optimal conditions (and freshwater) the most effective nitrification process ( the Kaldnes process) can process 1 gram N per m2 surface and day totally from NH4-N to NO3-N. In newly started aquaria - the bacteria population is low but even in established aquaria - high loads can be difficult to process because of more or less different oxygen levels around living rocks - the effective surface is much, much lower compared with K1, K3 and K5 media

for those who know carbohydrates are used elsewhere in the hobby to stimulate the growth and division of nitrifying and denitrifying autotrophic bacteria,
I do not agree with this - carbohydrates are organic carbon - its sugar. The nitrifying bacteria is autotrophic - they can´t use carbohydrates at all - they use inorganic carbon in the HCO3/CO3/CO2 complex. The classic denitrifying bacteria is heterotrophic - they can use organic carbon. There is autotrophic denitrification bacteria too - but mostly - they are different sulphur bacteria

Sincerely Lasse
 
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sixty_reefer

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I have no prove for this claims but I´m glad to see that others have thoughts in the same direction. We know that plants and algae prefer (of energy reasons) NH4/NH3 complex. To use other nitrogen sources (excluding some amino acids) always means a need of extra energy. Why I exclude amino acids is because a guy here in Sweden that is an expert of nitrogen transports through cellmembrans always has stressed that amino acids can move themselves through single human cell walls as god as the NH4/NH3 complex does. He means that´s also the case for at least unicellular algae and bacteria. There is reports of cyanobacteria outbreaks when using amino acids as a nitrogen source - this can be one of the explanation for these observations. - Back to the known fact that the NH3/NH4 is the preferred nitrogen sources for plants (including freshwater plants) - it is interesting to know tha few or any nutrient solutions for freshwater plants conten NH3/NH4 - instead they use the less energy effective NO3 as N source (PMDD as an example). The reasons for this are exactly the same as @sixty_reefer reasons why not use NH3/NH4 complex in saltwater - it will feed nuisance organisms.

To the NH3/NH4 contra H2O2 question. - I have never seen any prove for that H2O2 is a strong enough oxidizer too chemical oxidise NH3/NH4 into NO2 (or not even NO2 into NO3)- I have tested. However - H2O2 will support the normal bacterial nitrification process through rise the oxygen concentration in the water - especially important in saltwater with is lower content of oxygen. Does it really rise the oxygen content - this curves can be interesting. First an overview

The more interesting part

1670583797438.png

The more interesting part - how did it turns

H2O2 och syre.jpg


Even the NH3/NH4 was stalled during period before H2O2 addition - after that and the defeat/decrease of the organic load - that process started and it took 4 - 5 days to go down to 0 from ridiculous levels. However the NO2-NO3 stall too but now it is closer to zero.

To the discussion about nitrification and live rocks. At high loads - its not a chance that live rocks can process enough of N from NH4-N to NO3-N in a short time. In optimal conditions (and freshwater) the most effective nitrification process ( the Kaldnes process) can process 1 gram N per m2 surface and day totally from NH4-N to NO3-N. In newly started aquaria - the bacteria population is low but even in established aquaria - high loads can be difficult to process because of more or less different oxygen levels around living rocks - the effective surface is much, much lower compared with K1, K3 and K5 media


I do not agree with this - carbohydrates are organic carbon - its sugar. The nitrifying bacteria is autotrophic - they can´t use carbohydrates at all - they use inorganic carbon in the HCO3/CO3/CO2 complex. The classic denitrifying bacteria is heterotrophic - they can use organic carbon. There is autotrophic denitrification bacteria too - but mostly - they are different sulphur bacteria

Sincerely Lasse
Thanks @Lasse yout knowledge always fascinates me. And thanks for bringing up the amino acids as a source of nitrogen there is a hole thread on here in support of folks having outbreaks of Cyanobacteria after dosing them into their system.
and apologies for messing up with the carbohydrates and nitrifying bacteria, I’ve tried to ask @Hans-Werner if they knew what specie of bacteria was being stimulated by one of they’re products (reef actif) as it’s the only source of ready available source of natural seaweed carbohydrates, I’ve been experiencing with the product a lot lately and it seems much more safe to use than others the claims that not many nuisances can use this long chain polymers seems to be real in my system it seems also a safer way to use in comparison to acetic acid and ethanol for some reason as even in higher dosing so far I wasn’t able to induce a bacteria bloom.
Would in your view carbohydrates stimulate the same heterotrophic bacteria as acetic acid and ethanol?

@atoll mentioning earlier that hydrogen peroxide could be helpful with ammonia, is the increase in oxygen that aids the nitrifying bacterial growth would that be the same with ozone?
 

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One comment about rocks. Today’s dry rock or dry rock seeded isn’t the same porous live rock from the 80s. I’d place zero confidence in todays dry rock as a form of filtration.

The Berlin Method was founded on porous rock to replace not only the function of the wet dry but also due to it’s internal structure to provide some level of denitrification yet bulk of the filtration via the use of a skimmer to export organics before having a chance to break down. Somewhat similar to the clinical method previously used.

Based on today’s rock options, I’d use some other media to replace the biological function and if denitrification is required then contact time needs to be enhanced by adding more media along the path of water travel at a slower speed although carbon dosing has solved that and now I just focus on ensuring proper amount to handle nitrification.
 
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One comment about rocks. Today’s dry rock or dry rock seeded isn’t the same porous live rock from the 80s. I’d place zero confidence in todays dry rock as a form of filtration.

The Berlin Method was founded on porous rock to replace not only the function of the wet dry but also due to it’s internal structure to provide some level of denitrification yet bulk of the filtration via the use of a skimmer to export organics before having a chance to break down. Somewhat similar to the clinical method previously used.

Based on today’s rock options, I’d use some other media to replace the biological function and if denitrification is required then contact time needs to be enhanced by adding more media along the path of water travel at a slower speed although carbon dosing has solved that and now I just focus on ensuring proper amount to handle nitrification.
Very true I believe we had that in one of the nitrifying test, if I remember correctly it was a piece of dense marco rock that performed very poorly
 

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Very true I believe we had that in one of the nitrifying test, if I remember correctly it was a piece of dense marco rock that performed very poorly
Finding Fiji or Pukani on the used market might be in my plans
 

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is the increase in oxygen that aids the nitrifying bacterial growth would that be the same with ozone?
May be that way but I suspect that O3 is more "fast" in its breakdown compared with H2O2. hence produce more active oxygen radicals in shorter time - be careful if you chose that path

Sincerely Lasse
 
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It has long been my opinion that Obligate autotrophs grow/multiply until there is a steady state between the number of bacteria and the ammonia source. Then the numbers of bacteria stay the same. I think this is why as @sixty_reefer mentioned that the experiments that the threes of us did would not immediately process 2 ppm ammonia/24 hours. But - the interesting thing is - that in a couple days - they could process that much ammonia - with the same surface area present. Which suggests either some kind ability of the bacteria in the tanks to process more ammonia/minute - or the numbers of bacteria increased. Thereafter - the ability to rapidly process ammonia was much better than when taken out of a multi year 'mature' tank.

One thing I noticed - is that when using Dr. Tim's - when following the instructions - using drops per gallon - the ammonia was perhaps up to 5-6 ppm instead of 2 ppm. Which is why I went to using a TB syringe to measure out the amount of ammonia used.
 

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Finding Fiji or Pukani on the used market might be in my plans
I'm curious - where do you get the idea that rocks before were more porous? I tend to agree with you - especially with 'man-made' live rock. However, It has always escaped my abilities to understand how enough water was getting into these micro areas to remain oxygenated (which as @Lasse stated - autotrophic bacteria of this type require). I know many feel the porosity of rock is not very significant - since - in a mature tank - those pores may be filled with corralline covered by coral, etc
 
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May be that way but I suspect that O3 is more "fast" in its breakdown compared with H2O2. hence produce more active oxygen radicals in shorter time - be careful if you chose that path

Sincerely Lasse
thank you, it’s not a path that I like although I got curious on how could ammonia be affected as both methods were proposed earlier in the thread.
 
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I'm curious - where do you get the idea that rocks before were more porous? I tend to agree with you - especially with 'man-made' live rock. However, It has always escaped my abilities to understand how enough water was getting into these micro areas to remain oxygenated (which as @Lasse stated - autotrophic bacteria of this type require). I know many feel the porosity of rock is not very significant - since - in a mature tank - those pores may be filled with corralline covered by coral, etc
What I was told in the 80s was that much of that rock was just old coral skeletons and not actual rock. I believe Fiji and Pukani are just that. Old coral skeletons or coralline. BRS did a comparison against Marine Pure and it appeared based on the findings that Fiji and Pukani were able to retain water and likely confirmed the theory they are porous.

One easy test is placing an item in a puddle and seeing if it draws water. There's also the fact that by outside volume these supposed rocks are lighter. That tends to suggest the internal structure not being as dense. Another test is pouring water over it to see if it drains over the edges or through the structure as it does with the Marine Pure blocks. Been a while since I've seen that BRS video so going off memory. Been a very long while (mid 90s) since I handled Fiji or Pukani but do recall that by volume they were considerably lighter than say Florida Rock. Don't recall Tonga but for some reason don't recall that being light.
 
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It has long been my opinion that Obligate autotrophs grow/multiply until there is a steady state between the number of bacteria and the ammonia source. Then the numbers of bacteria stay the same. I think this is why as @sixty_reefer mentioned that the experiments that the threes of us did would not immediately process 2 ppm ammonia/24 hours. But - the interesting thing is - that in a couple days - they could process that much ammonia - with the same surface area present. Which suggests either some kind ability of the bacteria in the tanks to process more ammonia/minute - or the numbers of bacteria increased. Thereafter - the ability to rapidly process ammonia was much better than when taken out of a multi year 'mature' tank.

One thing I noticed - is that when using Dr. Tim's - when following the instructions - using drops per gallon - the ammonia was perhaps up to 5-6 ppm instead of 2 ppm. Which is why I went to using a TB syringe to measure out the amount of ammonia used.
What I take from this is that nitrifying autotrophic bacteria doesn’t have the ability to deal with raises in ammonia levels, this shouldn’t be a problem under normal circumstances as we have also heterotrophic nitrifying bacteria in our systems oxidising ammonia although this bacteria has 3 limitations and if heterotrophic bacteria becomes limited by any of the 3 a raise in ammonia happens this is we’re we normally see some of this nuisances appear as heterotrophic bacteria becomes limited by nitrates or phosphateswhat some folks don’t realize is that they can also become limited by carbon allowing ammonia to also become available, carbon limitation can only be identified with the raise in residual nitrates or phosphates, I wrote of this method of identification limitation in a few threads.
Carbon limitation will go in line with this nuisance also blooming under high nutrients.
raising levels of ammonia due to limitations in heterotrophic bacteria is the reason to all nuisances blooming, the blooms are just our system trying to handle the extra ammonia.
 

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I know many feel the porosity of rock is not very significant - since - in a mature tank - those pores may be filled with corralline covered by coral, etc
I´ll try to explain how area, effective area, porous and other things will be affected of a nitrifying biofilm. First - its only the a tiny layer (maybe thinner than 1 µ) that get enough of oxygen for attaching nitrifying organisms - the rest of the film just act as organic load, carrier etc. The pores of porous rocks will not only be filled by coraline algae (@MnFish1) - the biofilm itself will grove over small pores and form a biofilm like ice on a ice hockey rink - the effective area will be like a homogeneous wall not a porous wall. The best media for nitrifying bacteria I have worked with is Kaldnes K5 media. In a Kaldnes reactor this media is mixed together with water with help of heavy aeration, The film will be very thin and active. The second picture show a K% taken up from a good working Kaldnes tank. all of the area is effective.

1670604273347.png
1670604784849.png


Sincerely Lasse
 
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I´ll try to explain how area, effective area, porous and other things will be affected of a nitrifying biofilm. First - its only the a tiny layer (maybe thinner than 1 µ) that get enough of oxygen for attaching nitrifying organisms - the rest of the film just act as organic load, carrier etc. The pores of porous rocks will not only be filled by coraline algae (@MnFish1) - the biofilm itself will grove over small pores and form a biofilm like ice on a ice hockey rink - the effective area will be like a homogeneous wall not a porous wall. The best media for nitrifying bacteria I have worked with is Kaldnes K5 media. In a Kaldnes reactor this media is mixed together with water with help of heavy aeration, The film will be very thin and active. The second picture show a K% taken up from a good working Kaldnes tank. all of the area is effective.

1670604273347.png
1670604784849.png


Sincerely Lasse
Does this then imply that not only is porosity in rocks poor conduit for nitrification/denitrification but also claims of using porpous materials such as Matrix (pumice) and bricks by Brightwell and Marine Pure nothing more than marketing without function?
 

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