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.