Rock absorbing nutrients?

[keagan]

I’m not sure denitrifying bacteria would count as an exception here. They use nitrate mainly as an electron acceptor for respiration, which is a different process from preferring nitrate as a nitrogen source for assimilation. Maybe cyanobacteria would actually be a better example here.

I must be missing something. Why would cyanobacteria be a better example?

"Ammonia is the inorganic nitrogen source preferentially used by most cyanobacteria. Moreover,
even in nitrate utilizers or N2-fixers, ammonia is an obligate intracellular intermediate in nitrogen
assimilation."

 

[sixty_reefer]

I must be missing something. Why would cyanobacteria be a better example?

"Ammonia is the inorganic nitrogen source preferentially used by most cyanobacteria. Moreover,
even in nitrate utilizers or N2-fixers, ammonia is an obligate intracellular intermediate in nitrogen
assimilation."

I think you misunderstood me. I meant cyanobacteria as a better example of bacteria that preferentially assimilate ammonium over nitrate, not as an exception. The quote you posted is actually exactly what I meant. The original comment from EnterName that I quoted suggested that bacteria in our tanks generally prefer ammonium over nitrate. I’m just struggling to identify which bacteria in a reef tank, besides cyanobacteria, that generalisation actually applies to and by extension, which corals? With corals it’s even more complicated because much of the inorganic nitrogen assimilation we’re talking about involves their symbiotic algae rather than simply “the coral” itself.

 

[keagan]

I think you misunderstood me. I meant cyanobacteria as a better example of bacteria that preferentially assimilate ammonium over nitrate, not as an exception. The quote you posted is actually exactly what I meant. The original comment from EnterName that I quoted suggested that bacteria in our tanks generally prefer ammonium over nitrate. I’m just struggling to identify which bacteria in a reef tank, besides cyanobacteria, that generalisation actually applies to and by extension, which corals? With corals it’s even more complicated because much of the inorganic nitrogen assimilation we’re talking about involves their symbiotic algae rather than simply “the coral” itself.

The distinction you made didn't seem to undermine the point enter name made. That's where my confusion came from.

But challenging the scope of the generalization is different from how I interpreted it (challenging Ammonium being energetically cheaper to assimilate than nitrate). That makes more sense thanks for the clarification.

 

[Pod_01]

Fascinating discussion and most of it is above my pay grade but out of curiosity

some organisms have been shown to prefer nitrate over ammonium

What organisms in a reef tank do this?

My understanding of “prefer” means if provided the option of nitrate and ammonium the organisms will take nitrate and ignore ammonium.

 

[sixty_reefer]

Fascinating discussion and most of it is above my pay grade but out of curiosity

What organisms in a reef tank do this?

My understanding of “prefer” means if provided the option of nitrate and ammonium the organisms will take nitrate and ignore ammonium.

I wouldn’t take “prefer” to mean completely ignoring ammonium. It just means preferential uptake when both are available. Some marine diatoms can prefer nitrate and some organisms can even prefer urea. My only objection to the statement I quoted earlier, was that the comment seemed too broad.

 

[EnterName]

[...] and by extension, which corals? With corals it’s even more complicated because much of the inorganic nitrogen assimilation we’re talking about involves their symbiotic algae rather than simply “the coral” itself.

For coral symbionts there are some quite good resources so it's easier than going through thousand of bacteria species:

• Domotor et al. 1984 - Note Gymnodinium microadriaticum is an old classification, today it's considered Symbiodinium microadriaticum afaik
• Grover et al. (2002, 2003, Limnology and Oceanography) - Stylophora pistillata specific
• Li et al. 2021 - A non Symbiodinium sp. for a change
• Gordon et al. 2010 - This one quite clearly mentions that nitrate uptake is possible, but considered secondary to ammonia (that's all that was claimed so far).

Some marine diatoms can prefer nitrate and some organisms can even prefer urea.

We specifically compared nitrate and ammonia. In my initial response I wasn't talking about Urea, amino acids, and other potential nitrogen sources.

I could imagine due to the high nitrate levels in reef tanks compared to natural coral reefs the more common bacteria have good nitrate uptake mechanisms. High nitrate environments will obviously benefit those that are adapted to deal with nitrate "efficiently", but we have no reason to believe that these bacteria or diatoms are better or more beneficial to our tanks than others, so why prefer nitrate over ammonia dosing? Dosing ammonia will obviously also increase nitrate so it benefits both worlds.

But maybe we can settle this a bit simpler:
I would still say ammonia uptake is preferred by corals, their symbionts, algae, and bacteria in general. If we are arguing about that, I would like to see sources that show that the opposite applies in general, because ever source I shared so far (and as I understood Randy, but I don't want to put words in his mouth) is pointing towards this general tendency.

But I can agree with you, that bacteria are diverse and exceptions from this general tendency will probably be more common than for the other mentioned organisms. However, there is no reason to believe those bacteria are more beneficial than ammonia-preferring ones, so I don't think recommending ammonia dosing over nitrate dosing is the wrong choice, especially considering we don't care too much about the bacteria in this case, but want to feed our corals (and/or their symbionts).

 

[BeanAnimal]

I think you misunderstood me. I meant cyanobacteria as a better example of bacteria that preferentially assimilate ammonium over nitrate, not as an exception. The quote you posted is actually exactly what I meant. The original comment from EnterName that I quoted suggested that bacteria in our tanks generally prefer ammonium over nitrate. I’m just struggling to identify which bacteria in a reef tank, besides cyanobacteria, that generalisation actually applies to and by extension, which corals? With corals it’s even more complicated because much of the inorganic nitrogen assimilation we’re talking about involves their symbiotic algae rather than simply “the coral” itself.

Nobody has misunderstood you. You tried a gotcha question, and it was answered. You reframed, and that was answered too. Calling it a misunderstanding now is just retreat wearing clarification clothes. One reframe after the next follows.

Step by step since you entered this thread:

1. You asked EnterName "preferred under what conditions and by which organisms," implying his claim was too broad.
2. Randy shot that down with a simple statement.
3. In response, you claimed some organisms have been shown to prefer nitrate over ammonium.
4. EnterName answered that point by point, denitrifiers, dinoflagellates, diatoms, bioenergetics, with citations.
5. You didn't concede. You picked one item off that list, called it not an exception, and swapped in cyanobacteria as a "better example."
6. When that backfired, you called it a misunderstanding and asked which bacteria besides cyanobacteria the generalization applies to, and by extension which corals.
7. Pod1 asked the question directly: what organisms in a reef tank actually do this?
8. You didn't name any. Instead you redefined "prefer" to mean preferential uptake rather than exclusive uptake, and introduced diatoms and urea, neither of which were part of the original comparison.
9. EnterName supplied sourced literature on coral symbionts addressing exactly that.
10. You then narrowed the scope back down to "we specifically compared nitrate and ammonia," the same scope you had just expanded past one post earlier.

This isn't an evolving conversation, it is a group of 4 people chasing you through a series of deflections and reframes from your original statement posed as a gotcha question to EnterName, pedantically hedging on edge cases already excluded by context alone. Your own attempt at gotcha amounts to a claim itself, and you are now running from it.

You demanded proof across an entire taxonomy of bacteria and corals, then broadened it further with diatoms and urea nobody asked about. When EnterName supplied sourced answers anyway, you narrowed straight back down to "nitrate and ammonia." Broad when it protects the claim, narrow when it dodges the evidence.

What is the goal here? You attempted to hold EnterName accountable to a ridiculous standard and that hasn't panned out. In the process you had to claim some exception proves him wrong. It doesn't, even if you find one, and you still haven't. You're just playing word games at this point.

 

[sixty_reefer]

Nobody has misunderstood you. You tried a gotcha question, and it was answered. You reframed, and that was answered too. Calling it a misunderstanding now is just retreat wearing clarification clothes. One reframe after the next follows.

Step by step since you entered this thread:

1. You asked EnterName "preferred under what conditions and by which organisms," implying his claim was too broad.
2. Randy shot that down with a simple statement.
3. In response, you claimed some organisms have been shown to prefer nitrate over ammonium.
4. EnterName answered that point by point, denitrifiers, dinoflagellates, diatoms, bioenergetics, with citations.
5. You didn't concede. You picked one item off that list, called it not an exception, and swapped in cyanobacteria as a "better example."
6. When that backfired, you called it a misunderstanding and asked which bacteria besides cyanobacteria the generalization applies to, and by extension which corals.
7. Pod1 asked the question directly: what organisms in a reef tank actually do this?
8. You didn't name any. Instead you redefined "prefer" to mean preferential uptake rather than exclusive uptake, and introduced diatoms and urea, neither of which were part of the original comparison.
9. EnterName supplied sourced literature on coral symbionts addressing exactly that.
10. You then narrowed the scope back down to "we specifically compared nitrate and ammonia," the same scope you had just expanded past one post earlier.

This isn't an evolving conversation, it is a group of 4 people chasing you through a series of deflections and reframes from your original statement posed as a gotcha question to EnterName, pedantically hedging on edge cases already excluded by context alone. Your own attempt at gotcha amounts to a claim itself, and you are now running from it.

You demanded proof across an entire taxonomy of bacteria and corals, then broadened it further with diatoms and urea nobody asked about. When EnterName supplied sourced answers anyway, you narrowed straight back down to "nitrate and ammonia." Broad when it protects the claim, narrow when it dodges the evidence.

What is the goal here? You attempted to hold EnterName accountable to a ridiculous standard and that hasn't panned out. In the process you had to claim some exception proves him wrong. It doesn't, even if you find one, and you still haven't. You're just playing word games at this point.

FYI, I haven’t even read most of what you just wrote, but out of curiosity, how long did it take you to get all of that so wrong? By the way, I still haven’t actually got an answer to my original question.

 

[BeanAnimal]

FYI, I haven’t even read most of what you just wrote, but out of curiosity, how long did it take you to get all of that so wrong? By the way, I still haven’t actually got an answer to my original question.

Every post here is a clear deflection of one form or another, not conversation. This one is raw deflection and contradiction, not a meaningful response.

You mockingly said you didn't read it, then said it was wrong. That is a direct contradiction. You said you're still waiting on an answer to a question that has been answered, no matter how many times you've moved the goalposts to pretend otherwise. Every one of your deflections has been refuted, only to spawn a new one. That is precisely the record, clearly outlined in the 10 points you didn't read, but still claimed I "got wrong".

You took on burden here. Please clearly address the claim you built on pedantic semantics hinging on edge cases you claim but can't actually cite, first in the question you posed to EnterName, then stated outright: some organisms prefer nitrate over ammonium. You still haven't named one. And even if you finally do, it doesn't refute EnterName's original point or anything he, Randy, Pod1, or Keagan actually said chasing your deflections. It just confirms this was never about the science and all about a backfired gotcha you refuse to let go.

 

[EnterName]

Nobody has misunderstood you. You tried a gotcha question, and it was answered. You reframed, and that was answered too. Calling it a misunderstanding now is just retreat wearing clarification clothes. One reframe after the next follows.

Step by step since you entered this thread:

1. You asked EnterName "preferred under what conditions and by which organisms," implying his claim was too broad.
2. Randy shot that down with a simple statement.
3. In response, you claimed some organisms have been shown to prefer nitrate over ammonium.
4. EnterName answered that point by point, denitrifiers, dinoflagellates, diatoms, bioenergetics, with citations.
5. You didn't concede. You picked one item off that list, called it not an exception, and swapped in cyanobacteria as a "better example."
6. When that backfired, you called it a misunderstanding and asked which bacteria besides cyanobacteria the generalization applies to, and by extension which corals.
7. Pod1 asked the question directly: what organisms in a reef tank actually do this?
8. You didn't name any. Instead you redefined "prefer" to mean preferential uptake rather than exclusive uptake, and introduced diatoms and urea, neither of which were part of the original comparison.
9. EnterName supplied sourced literature on coral symbionts addressing exactly that.
10. You then narrowed the scope back down to "we specifically compared nitrate and ammonia," the same scope you had just expanded past one post earlier.

This isn't an evolving conversation, it is a group of 4 people chasing you through a series of deflections and reframes from your original statement posed as a gotcha question to EnterName, pedantically hedging on edge cases already excluded by context alone. Your own attempt at gotcha amounts to a claim itself, and you are now running from it.

You demanded proof across an entire taxonomy of bacteria and corals, then broadened it further with diatoms and urea nobody asked about. When EnterName supplied sourced answers anyway, you narrowed straight back down to "nitrate and ammonia." Broad when it protects the claim, narrow when it dodges the evidence.

What is the goal here? You attempted to hold EnterName accountable to a ridiculous standard and that hasn't panned out. In the process you had to claim some exception proves him wrong. It doesn't, even if you find one, and you still haven't. You're just playing word games at this point.

FYI, I haven’t even read most of what you just wrote, but out of curiosity, how long did it take you to get all of that so wrong? By the way, I still haven’t actually got an answer to my original question.

Can you elaborate what is missing?

I answered your intial question (post #35) in my first response (post #38) and split it into multiple sections to get both parts of your question right:
1. under what conditions ammonia would be preferred
2. and which organisms would prefer ammonia

Even if you disagree with denitrifiers being one of the exceptions, you yourself mentioned diatoms in a later post which was one of the other organisms I listed. So maybe you can read the rest of the response and find your answer? Otherwise, you will need to help me what is missing.

 

[Dan_P]

Here is a demonstration of bacteria preferring ammonia over nitrate that you can do yourself.

We are all familiar with carbon dosing aquarium water to lower nitrate concentration. What may not be as obvious is that if ammonia is present nitrate consumption stops and ammonia consumption takes over. Not until the ammonia is depleted as judged by hobby tests, will nitrate consumption begin. I do not know how many species are involved but it seems frasonable to put this observation in the category of at least one aquarium bacteria species prefers ammonia over nitrate.

 

[sixty_reefer]

Every post here is a clear deflection of one form or another, not conversation. This one is raw deflection and contradiction, not a meaningful response.

You mockingly said you didn't read it, then said it was wrong. That is a direct contradiction. You said you're still waiting on an answer to a question that has been answered, no matter how many times you've moved the goalposts to pretend otherwise. Every one of your deflections has been refuted, only to spawn a new one. That is precisely the record, clearly outlined in the 10 points you didn't read, but still claimed I "got wrong".

You took on burden here. Please clearly address the claim you built on pedantic semantics hinging on edge cases you claim but can't actually cite, first in the question you posed to EnterName, then stated outright: some organisms prefer nitrate over ammonium. You still haven't named one. And even if you finally do, it doesn't refute EnterName's original point or anything he, Randy, Pod1, or Keagan actually said chasing your deflections. It just confirms this was never about the science and all about a backfired gotcha you refuse to let go.

Lol, are you sure that’s what he said? For someone who just read the whole thread, you seem to have missed a rather important part of it.

 

[sixty_reefer]

Can you elaborate what is missing?

I answered your intial question (post #35) in my first response (post #38) and split it into multiple sections to get both parts of your question right:
1. under what conditions ammonia would be preferred
2. and which organisms would prefer ammonia

Even if you disagree with denitrifiers being one of the exceptions, you yourself mentioned diatoms in a later post which was one of the other organisms I listed. So maybe you can read the rest of the response and find your answer? Otherwise, you will need to help me what is missing.

Post #38 still didn’t answer the specific part I’m asking about. Which bacteria in our reef tanks, besides cyanobacteria, have been shown to preferentially assimilate ammonium over nitrate? And which corals themselves, rather than their symbionts, have been shown to do the same? I’m looking for several examples if this is a general preference across bacteria and corals. We already know many algae have that preference, it’s the other two groups I’m not aware of.

 

[keagan]

Lol, are you sure that’s what he said? For someone who just read the whole thread, you seem to have missed a rather important part of it.

How would you quantify a species having a preference for nitrate over ammonium? Halophytes can take up massive amounts of nitrate, but they don’t necessarily use it much for metabolism; they can use nitrate for osmoregulation. Would you consider that a preference for nitrate simply because they’re taking up more nitrate than ammonium? They aren’t using it preferentially for nitrogen assimilation, which is the energetically less efficient process compared with directly assimilating ammonium.

 

[Dan_P]

Preferred under what conditions and by which organisms? “Corals, algae and bacteria” covers an enormous range of metabolisms. Surely the nitrogen source preference depends on the organism.

A couple thoughts.

First the generalization of nitrogen preferences was not created by @EnterName and is often stated on R2R by many forum members. I suspect if we look through your posts, you have said the same thing.

Your generalization that “corals, algae and bacteria covers an enormous range in metabolism” seems misleading. While it is a true statement, @EnterName was talking about a fairly narrow range of metabolism which only covers inorganic nitrogen utilization. Just how different are bacteria metabolisms for nitrate and ammonia utilization?

The comment “surely the nitrogen source preference depends on the organism” is true but again misleading. It is fine to point out potential shortcomings of the stated generalization but I think it is up to you to provide some information or a sense of what percent of bacteria prefer nitrate or diatoms preferentially utilizing nitrate.

Recently, EnterName did a thorough job pointing out the misinformation you have been posting. I wonder if your post to his comment is another revenge post rather than engaging in a good faith technical discussion.

 

[Dan_P]

Post #38 still didn’t answer the specific part I’m asking about. Which bacteria in our reef tanks, besides cyanobacteria, have been shown to preferentially assimilate ammonium over nitrate? And which corals themselves, rather than their symbionts, have been shown to do the same? I’m looking for several examples if this is a general preference across bacteria and corals. We already know many algae have that preference, it’s the other two groups I’m not aware of.

So, fair questions, but I don’t think the onus is on @EnterName to fill gaps in your knowledge. Why don’t you just perform a quick search of the internet, it won’t take long, and report back here on what you find. If the internet search supports your skepticism, great let’s trash the generalization, Remember, EnterName is repeating a popular, and generally accepted generalization. It is not some nutty idea he imagined.

 

[Dan_P]

Preferred under what conditions and by which organisms? “Corals, algae and bacteria” covers an enormous range of metabolisms. Surely the nitrogen source preference depends on the organism

I think you’ve already conceded being wrong about algae, so here is evidence you are wrong about bacteria.

https://pmc.ncbi.nlm.nih.gov/articles/PMC123768/

I will look for similar information on coral.

 

[BeanAnimal]

Lol, are you sure that’s what he said? For someone who just read the whole thread, you seem to have missed a rather important part of it.

That is now two mocking deflections that avoid factual substantive points.

This tactic is not lost on anybody here.

Now 6 people are chasing you through deflections. This isn't about "me" or my comprehension, its about your deflections of at least 4 other responders' points, before I ever entered the thread. Every one of your posts has been a deflection away from accountability to your own words and claims, not furtherance of a conversation.

 

[BeanAnimal]

Recently, EnterName did a thorough job pointing out the misinformation you have been posting. I wonder if your post to his comment is another revenge post rather than engaging in a good faith technical discussion.

This can't be overstated here, it's hard to read it any other way, 2 threads in a row. The deflections that follow remove reasonable doubt in both cases. Here, running from a claim he made himself when he tried to gotcha EnterName. Two pages later he still hasn't named an organism, and every post since has been another deflection away from doing it. One narrowing after the next to move the goalposts from the original post he made that was refuted -- now even slicing the coral animal away from its zooxanthellae just to throw out valid symbiont literature. Every deflection since has been refuted as well. None of it matters, his original "gotcha" missed context anyway. There is no recovery here from the targeted entrance into this thread.

 

[Dan_P]

FYI, I haven’t even read most of what you just wrote, but out of curiosity, how long did it take you to get all of that so wrong? By the way, I still haven’t actually got an answer to my original question.

HaHa, still playing the butt.

I doubted your initial comment was an attempt to start a good faith technical discussion. Your later replies just made it more obvious that this was another revenge post. Now you are following your usual pattern of suggesting you were.misunderstood just as the posts are gaining momentum demonstrating your bad faith behavior and the depth of your ignorance.