Rock absorbing nutrients?

[sixty_reefer]

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.

That’s the first factual ish thing you’ve said in a while, six members chasing me because their friend made an overly broad claim without providing evidence for it.

 

[A_Blind_Reefer]

Well, four pages in now and I still don’t know what nutrients can absorb rocks…..

 

[BeanAnimal]

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.

Are they fair questions in the context they were asked? The opening ignored context and moved it several times since, all riding on the gotcha question underpinned by the literal claim: some organisms prefer nitrate over ammonium. Does someone stuck with their own burden get to ignore context, ask questions to shift their way out of it, and call those questions fair?

EnterName, and everyone involved, has made their case. Sixty has yet to substantiate his.

 

[EnterName]

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.

Not sure why bacteria are the important part of the question when we are dosing ammonia for our corals and you answered yourself with cyanonacteria, but sure:

There are a lot of different bacteria that you may find in a reef tank, so I won't be able to give you a complete list, but if you are just looking for a few non-cyano examples, you can find them quite easily.
Candidatus Pelagibacter (SAR11 / Pelagibacteraceae) are an example
(https://journals.asm.org/doi/10.1128/mbio.00133-12)

Phaeobacter inhibens / roseobacters (Rhodobacteraceae) are another example (https://pubmed.ncbi.nlm.nih.gov/30124819/)

I think (not entirely sure) the entire SAR11 has no nitrate assimilation mechanism at all so most or all of them should be a fit.

For ammonia oxidizers, it depends on whether you are talking about energy source or nitrogen source. I don't want to accidentally confuse them, so I would ask you to look for yourself.

If you are looking for more general sources (for example: heterotrophic bacteria "in general"), you can find sources as well: "[...] in oligotrophic oceans where bacteria turn to ammonium and nitrate, although the latter only as a last resort." (https://link.springer.com/article/10.1007/BF00166816)

I think I have provided a decent collection of sources throughout my past responses that support the general consensus Dan mentioned.

 

[BeanAnimal]

That’s the first factual ish thing you’ve said in a while, six members chasing me because their friend made an overly broad claim without providing evidence for it.

That isn't a rebuttal, it's another reframe, now retreating to conspiracy. Every person who has challenged you on this site meets the same cycle of deflections. That is not a conspiracy, it is a matter of record with a single common denominator, your deflections.

It's only an "overly broad claim" if you ignore the context it was made in, for the purpose of turning it into a "claim" to hold him accountable to. What followed was a systematic pattern of reframing and narrowing to portray it as wrong, despite pages of evidence showing otherwise. That's not a conversation. He and others have refuted your deflections and supported the very thing he said to begin with.

Your engagement should have ended with Randy's response alone, but you ignored it and pivoted, making the exact kind of unsupported "overly broad claim," some organisms prefer nitrate over ammonium, you've spent two pages demanding everyone else be accountable to. This can't be overstated: he didn't make a broad claim, you did, while attacking his reasonable and supported position in this thread.

 

[Randy Holmes-Farley Verified Community Expert]

Unless I see an experiment suggesting some organism we want to keep prefers nitrate over ammonia, I am comfortable with and will use the generalization that …

“All experiments that I have seen suggest the organisms we keep prefer ammonia over nitrate. Other N sources may also be preferred, such as amino acids or urea since they confer other benefits that nitrate (and ammonia) do not”.

 

[sixty_reefer]

Unless I see an experiment suggesting some organism we want to keep prefers nitrate over ammonia, I am comfortable with and will use the generalization that …

“All experiments that I have seen suggest the organisms we keep prefer ammonia over nitrate. Other N sources may also be preferred, such as amino acids or urea since they confer other benefits that nitrate (and ammonia) do not”.

Does that generalisation include bacteria, algae and all corals, as stated by EnterName, or are we mainly talking about algae, including the zooxanthellae within photosynthetic corals?

We already know that macro algae don’t all follow a simple ammonium first, nitrate afterwards pattern. Some can assimilate both simultaneously and which source is favoured can depend on the species and conditions.

But this is where the generalisation gets interesting for me. If ammonium is the preferred nitrogen source for both zooxanthellae and the macro algae we deliberately grow in refugiums, they’re potentially competing for the same nitrogen pool.

Could an efficient refugium compete significantly with the coral holobiont for available ammonium? And could carbon dosing similarly reduce ammonium availability to the coral holobiont, as Dan’s earlier observation about carbon dosed bacteria preferentially consuming ammonium would suggest?

Sorry, I know that’s more questions than answers but with all the experts on this thread we should hopefully end up with some useful knowledge from the discussion.

 

[BeanAnimal]

Does that generalisation include bacteria, algae and all corals or are we mainly talking about algae and the zooxanthellae within photosynthetic corals?

We already know macro algae don’t all follow a simple ammonium first, nitrate afterwards pattern. Some can assimilate both simultaneously and which source is favoured can depend on the species and conditions.

But this is where the generalisation gets interesting for me. If ammonium is the preferred nitrogen source for both zooxanthellae and the macroalgae we deliberately grow in refugiums, they’re potentially competing for the same nitrogen pool.

Could an efficient refugium compete significantly with the coral holobiont for available ammonium? And could carbon dosing similarly reduce ammonium availability to the coral holobiont, as Dan’s earlier observation about carbon dosed bacteria preferentially consuming ammonium would suggest?

Sorry, I know that’s more questions than answers but with all the experts on this thread we should hopefully end up with some useful knowledge from the discussion.

A full sidestep to give the impression that this has been an evolving conversation and not 2 pages full of people shutting down a string of deflections. A raw pivot to three new topics: refugium competition, carbon dosing, ammonium pools, burying your unsupported claim in the process.

Framing it as "let's find some useful knowledge together" is either mocking the experts in this thread or pretending you've been conversing with them all along instead of being chased and corrected by them for two pages. Despite your deflections, this thread is full of useful knowledge, most of it refuting the position you took and the claim you made.

That wont work. We are still here:
You made the exact kind of unsupported "overly broad claim," some organisms prefer nitrate over ammonium, you've spent two pages demanding everyone else be accountable to. EnterName didn't make a broad claim, you did, while attacking his reasonable and supported position in this thread.

Word Soup:

"Could an efficient refugium compete significantly" and "could carbon dosing similarly reduce ammonium availability" aren't questions with any bearing on what this thread was actually about, rock and substrate binding nutrients. They ride on Randy's engagement, as if you and he were having a discussion, while offering "it depends" fog instead of supporting the claim you made.

 

[Dan_P]

Does that generalisation include bacteria, algae and all corals, as stated by EnterName, or are we mainly talking about algae and the zooxanthellae within photosynthetic corals?

I think Randy has clearly defined the bounds

“All experiments that I have seen suggest the organisms we keep prefer ammonia over nitrate”

Sorry, I know that’s more questions than answers but with all the experts on this thread we should hopefully end up with some useful knowledge from the discussion.

A smart alec remark like this makes your position clear.

 

[sixty_reefer]

I think Randy has clearly defined the bounds

“All experiments that I have seen suggest the organisms we keep prefer ammonia over nitrate”



A smart alec remark like this makes your position clear.

But that doesn’t really define the bounds. A fish is an organism we keep too. Does a fish prefer ammonium over nitrate? That’s exactly why I’m asking which organisms the generalisation is actually referring to.

 

[BeanAnimal]

But that doesn’t really define the bounds. A fish is an organism we keep too. Does a fish prefer ammonium over nitrate? That’s exactly why I’m asking which organisms the generalisation is actually referring to.

The deflections are reaching a level of absurdity that appear to be unbounded.

Nobody here is talking about fish nitrogen metabolism, it isn't even remotely in scope. That's not an undefined bound, it's another manufactured exception because you've run out of real ones.

This ceased being a serious thread the moment you entered it. You are derailing other people's threads now instead of your own. Two pages of this nonsense has followed Randy's first response, which already answered the gotcha question you opened with.

 

[sixty_reefer]

The deflections are reaching a level of absurdity that appear to be unbounded.

Nobody here is talking about fish nitrogen metabolism, it isn't even remotely in scope. That's not an undefined bound, it's another manufactured exception because you've run out of real ones.

This ceased being a serious thread the moment you entered it. You are derailing other people's threads now instead of your own. Two pages of this nonsense that should have ended after Randy's first post sunk your ridiculous gotcha stunt.

Bean, this running commentary on everything I post is becoming tiresome. If you think I’m derailing the thread, perhaps let the moderators deal with it rather than turning every reply into another discussion about me.

 

[BeanAnimal]

Bean, this running commentary on everything I post is becoming tiresome. If you think I’m derailing the thread, perhaps let the moderators deal with it rather than turning every reply into another discussion about me.

Every post above documents something you did, quote-anchored, in order. That's not commentary about you, it's the record, right here in real time. I'm responding to your posts, your mocking, your reframing, your deflections.

This time it isn't your thread. The damage is to somebody else's conversation and it started with your reframing of EnterName's point and pivoting away from Randy's, through numerous reframes before I ever entered. You even admit people are chasing you, but framed it as conspiracy.

You call this "tiresome," as if answering for two pages of your own claims and deflections is something being done to you. Ridiculous.

 

[Randy Holmes-Farley Verified Community Expert]

I’m generalizing to all creatures in our tanks that are taking up ammonia or nitrate as a source of N, unless I see any evidence otherwise. Not only do studies support it for some creatures, the idea that an organism would prefer nitrate seems almost implausible to me.

It would be like a person tasked with collecting a large number of apples. One could collect those within reach from the ground, or one could climb a different tree to get identical apples that are 20 feet up, each in a different tree.

I said nothing about how much of what they take up. No reefer has such info for their tanks and the creatures in it. It would be extremely complicated to get such info in an operating reef tank.

It is certainly true there is competition for ammonia, and it is exactly why I am against dosing nitrifying bacteria or adding media for purposes of housing them.

 

[EnterName]

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.

That’s the first factual ish thing you’ve said in a while, six members chasing me because their friend made an overly broad claim without providing evidence for it.

Every question you asked me was met with a respectful and detailed answer. I included scientific sources where they were necessary.
We have discussed the general tendency of ammonia preference and the bio-energetic reasoning behind it. We have discussed a few potential exceptions to this tendency and how they might make sense from an evolutionary standpoint. We differentiated between using nitrate as a nitrogen source vs. nitrate as an energy source, and I specifically took some time to ask you for clarification, to make sure your initial question got fully answered after you expressed dissatisfaction with my initial response.
You then received a very concrete list of bacteria that prefer ammonia over nitrate and can be found in reef tanks, to give you the answer you wanted.

We are currently at around 10 scientific papers and 1 article from Aquabiomics that I used over the course of this whole "argumentation". Saying I didn't provide any evidence seems a little odd, and also a bit late, considering how many times you had the chance to counter an actual argument and refute a source.

You have now made a second attempt (after the recent post in my microscopy thread) to make me look bad, because you didn't like that I pointed out how the interpretations in your last thread didn't follow from your observations. I still decided to take the time and join the discussion in good faith, but I have to express my disappointment about how arguments were ignored and how this turned into another attempt to frame someone in a certain way rather than debating the actual stated sources and facts.

 

[sixty_reefer]

I’m generalizing to all creatures in our tanks that are taking up ammonia or nitrate as a source of N, unless I see any evidence otherwise. Not only do studies support it for some creatures, the idea that an organism would prefer nitrate seems almost implausible to me.

It would be like a person tasked with collecting a large number of apples. One could collect those within reach from the ground, or one could climb a different tree to get identical apples that are 20 feet up, each in a different tree.

I said nothing about how much of what they take up. No reefer has such info for their tanks and the creatures in it. It would be extremely complicated to get such info in an operating reef tank.

It is certainly true there is competition for ammonia, and it is exactly why I am against dosing nitrifying bacteria or adding media for purposes of housing them.

I think this is exactly where the generalisation becomes problematic. The extra energetic cost of nitrate assimilation is real but apparently it doesn’t automatically determine preference.

Pseudo-nitzschia australis has been experimentally shown to have a “clear preference for nitrate at equivalent concentrations” over ammonium and other N sources. There’s also Phaeocystis globosa, where nitrate was the favoured nitrogen source for growth across three tested strains, despite ammonium being energetically cheaper to assimilate.

So perhaps the apple analogy is a little too simple for biology. Sometimes the organism apparently does climb the taller tree.

https://hero.epa.gov/reference/8778397/

https://www.tandfonline.com/doi/full/10.1080/09670262.2011.602430


Edit: There’s also a third possibility the generalisation overlooks, organisms that assimilate nitrate and ammonium simultaneously rather than simply using ammonium first and switching to nitrate once it’s depleted. There seem to be plenty of examples of this in the literature. Some apparently pick apples from both trees at the same time.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1976.tb00508.x

 

[sixty_reefer]

@EnterName I’m not trying to make you look bad. I’ve asked you difficult questions, just as I’ve asked Randy plenty of difficult questions. If questioning conclusions or asking for clarification is being interpreted as an attempt to make someone “look bad”, I’m not sure how we’re supposed to have a technical discussion. Bit sad really when difficult questions have to be reframed as personal attacks instead of just being answered as difficult questions.

 

[sixty_reefer]

Every post above documents something you did, quote-anchored, in order. That's not commentary about you, it's the record, right here in real time. I'm responding to your posts, your mocking, your reframing, your deflections.

This time it isn't your thread. The damage is to somebody else's conversation and it started with your reframing of EnterName's point and pivoting away from Randy's, through numerous reframes before I ever entered. You even admit people are chasing you, but framed it as conspiracy.

You call this "tiresome," as if answering for two pages of your own claims and deflections is something being done to you. Ridiculous.

And yet here we are again, another entire post analysing me instead of discussing the actual subject. You’ve made your opinion of me and how I participate in discussions abundantly clear, Bean. I’ve heard it repeatedly. At this point, continuing the running commentary is doing more to derail the thread than the questions you keep accusing me of derailing it with. Can we get back to the actual topic now?

 

[EnterName]

@EnterName I’m not trying to make you look bad. I’ve asked you difficult questions, just as I’ve asked Randy plenty of difficult questions. If questioning conclusions or asking for clarification is being interpreted as an attempt to make someone “look bad”, I’m not sure how we’re supposed to have a technical discussion. Bit sad really when difficult questions have to be reframed as personal attacks instead of just being answered as difficult questions.

And all your questions have been answered kindly, with appropriate sources and zero attempts to avoid them. I even double-checked that I got everything you asked about, as you'll remember.

Framing me as not accepting "difficult" questions, when all I've done so far is take my time to answer them and even double-check that I included everything you asked for, is unprofessional, dishonest, and an uncalled-for level of hostility. I will not participate in that level of hostility.

None of the other points I made in my previous response were addressed. Technical discussions require everyone involved to participate in good faith and address the counterarguments being made. I would very much welcome it if we could actually get to the technical and scientific part of the discussion. I have been awaiting actual counterarguments to the various points I made, or an acknowledgement that the discussion is resolved.

 

[SantaMonica Verified Sponsor]

Rock phosphate situations occur a lot with strong algae scrubbers; here is my description:

"Note that if you have rocks which are soaked with phosphate from having been in a nuisance algae problem aquarium, each 50 pounds (23 kg) of problem rock will add 1 cube a day to your feeding amounts because this phosphate starts coming out of the rocks, so be sure to account for this when choosing a scrubber size. For example if you feed 1 cube a day, but have 100 pounds of rock that came from an old tank with nuisance algae problems, this rock will add 2 cubes a day to your feeding, meaning that you would need a scrubber for 3 cubes a day. This applies even if the rock was dried out and bleached, because this does not remove nutrients from the rock."