Ammonia is our Friend: thoughts needed

[Lasse]

And my preference is to use preferential

Excuse me but could not stop myself

Nothing more to discuss about this but the article is good and gives a good description of the problem at least with one species of stone corals

Sincerely Lasse

 

[Hans-Werner]

It has been speculated that the same channels (chloride cells) in the gills of fish that in freshwater fish is responsible for the input of NO2 into the fish blood stream is responsible for the output. If so - it must be an active process - from low to high. This cost energy and could probably end up with stress. I do not know if this is true or not but IMO - it is better to not introduce fish in high nitrite environment than risk that these speculations is false.

I think the few ppm at max are so small compared to the chloride present in saltwater and going into the blood of the fish you just can neglect it. The additional energy expenditure for pumping of nitrite will be close to nil. You have to keep in mind, the fish are pumping chloride and nitrite is just pumped "by accident"

That was new from me - I have learned that chlorophyll A and C in zooxanthella is responsible for the photosynthesis and the carotenoids are responsible for protection and harvest and transform wavelengths that chlorophyll can´t harvest by them selves - the need a pre prepared wavelength.

Yes, but it is fact. The antenna pigments of zooxanthellae (antennae of cyanobacteria, plants and algae compared) and other brown or golden algae are mainly carotenoids with some chlorophyll. This is what really gives them the brown or golden color, not the protective carotenoids which do not contribute much to the color. Trees have protective carotenoids and some antenna carotenoids also but they only get visible in autumn when the trees degrade and recycle the useful chlorophylls leaving the N-free carotenoids in the dropping leaves. It is the yellow and orange color of dropping leaves.

IMO the graphs does not show any precedence for either of the N species because it done with one N species at a time. Not with both together. The graph show only the rate of uptake in single species experiment

This doesn't really matter since nitrate and ammonium don't compete for uptake sites. It must be different ion pumps since one is a cation and the other is an anion. The competition for uptake was only for energy, not for uptake sites. The curves show the affinity of the uptake sites, the rates in which uptake sites can pump the ions.

This 4:th conclusion is interesting - in both 0.5 an 3 µmol/L PO4 - uptake of NH3/NH4 was significantly increased but only the lowest tested PO4 concentration - NO3 uptake show the same.

Yes, very interesting. I think it is because nitrate is not supporting coral growth in the same way and extend ammonium does. So it is not necessary to take up more phosphate since the available nitrogen compound, nitrate, is limiting growth.

This article is much more than the earlier shown graphs and its well worth to read and to think about

Yes, it is.

 

[Hans-Werner]

That was new from me - I have learned that chlorophyll A and C in zooxanthella is responsible for the photosynthesis and the carotenoids are responsible for protection and harvest and transform wavelengths that chlorophyll can´t harvest by them selves - the need a pre prepared wavelength.

After I have read this excellent book on the ecological physiology of algae maybe 30 (+) years ago and came to the conviction that corals behave much like algal cultures and that so much more was known about ecological physiology of algae than about ecological physiology of corals, of course I tried to learn as much as I could about dinoflagellates. Nutrients and lighting are of central importance to coral husbandry.

 

[Lasse]

I think the few ppm at max are so small compared to the chloride present in saltwater and going into the blood of the fish you just can neglect it. The additional energy expenditure for pumping of nitrite will be close to nil. You have to keep in mind, the fish are pumping chloride and nitrite is just pumped "by accident"

I was not talking about pumping chloride - I was talking about chloride cells pumping NO2 backwards - chloride cells in fish gills have more tasks than regulate chlorides.

Yes, very interesting. I think it is because nitrate is not supporting coral growth in the same way and extend ammonium does. So it is not necessary to take up more phosphate since the available nitrogen compound, nitrate, is limiting growth.

I see it the other way - it is the PO4 that is limited for the growth - not uptake rate of NH3/NH4 or NO3

Yes, but it is fact. The antenna pigments of zooxanthellae (antennae of cyanobacteria, plants and algae compared) and other brown or golden algae are mainly carotenoids with some chlorophyll. This is what really gives them the brown or golden color, not the protective carotenoids which do not contribute much to the color. Trees have protective carotenoids and some antenna carotenoids also but they only get visible in autumn when the trees degrade and recycle the useful chlorophylls leaving the N-free carotenoids in the dropping leaves. It is the yellow and orange color of dropping leaves.

Its a little more complicated than that - neither PSI or PS II (as I know it) can use the energy quanta that the wavelengths that carotenoids capture directly. They need to be transferred to around 680 resp around 700 nm. As I know it it happens in or near chlorophyll centra

During photosynthesis carotenoids normally serve as antenna pigments, transferring singlet excitation energy to chlorophyll

This doesn't really matter since nitrate and ammonium don't compete for uptake sites. It must be different ion pumps since one is a cation and the other is an anion. The competition for uptake was only for energy, not for uptake sites. The curves show the affinity of the uptake sites, the rates in which uptake sites can pump the ions.

I do not agree with this - neither do the authors of the article - my bold

On the contrary, it is well-known, for example, that nitrate uptake is generally inhibited in the presence of ammonium , either through a repression of the nitrate reductase or a competition of ammonium and nitrate uptake mechanisms for energy resources, leading to the preferential uptake of ammonium

Sincerely Lasse

 

[Randy Holmes-Farley]

I do not see any disagreement between what Hans-Werner wrote and what the authors wrote. They do not use the same transporters, and can compete for energy usage.

This doesn't really matter since nitrate and ammonium don't compete for uptake sites. It must be different ion pumps since one is a cation and the other is an anion. The competition for uptake was only for energy, not for uptake sites. The curves show the affinity of the uptake sites, the rates in which uptake sites can pump the ions.

I do not agree with this - neither do the authors of the article - my bold

On the contrary, it is well-known, for example, that nitrate uptake is generally inhibited in the presence of ammonium , either through a repression of the nitrate reductase or a competition of ammonium and nitrate uptake mechanisms for energy resources, leading to the preferential uptake of ammonium

 

[Hans-Werner]

Lasse, I am sorry, I have to say you just don't want to understand what I say. I don't know why, or whether it is a language problem.

I was not talking about pumping chloride - I was talking about chloride cells pumping NO2 backwards - chloride cells in fish gills have more tasks than regulate chlorides.

You mean, excretion of chloride and nitrite ions goes different ways? Any proof for this?

I see it the other way - it is the PO4 that is limited for the growth - not uptake rate of NH3/NH4 or NO3

The uptake rate of ammonium was significantly increased in the presence of 0.5 and 3.0 µmol l–1 phosphate (r20.76, F57.04,P<0.0001; Fisher’s PLSD, both P<0.05; Fig.5A). Linear regression followed by Fisher’s PLSD revealed that, overall, nitrate uptake rate was not impacted by phosphate availability (P0.93; Fig.5B),although an unpaired t-test revealed that nitrate uptake was significantly enhanced by a low phosphate enrichment (0.5 µ mol l–1;unpaired t-test, t–2.45, P0.049).

What does the citation mean in your opinion? Of course phosphate is limiting initially, but the phosphate concentration was increased. Increase of phosphate concentration increased ammonium uptake but in nitrate it had a limited effect. Why?

Its a little more complicated than that - neither PSI or PS II (as I know it) can use the energy quanta that the wavelengths that carotenoids capture directly. They need to be transferred to around 680 resp around 700 nm. As I know it it happens in or near chlorophyll centra

This was not the question. The question was, are carotenoids involved in photosynthesis or are they just protective pigments. They are involved in photoysynthesis, nothing else had to be clarified.

I do not agree with this - neither do the authors of the article - my bold

I just see, this was already commented by RHF. Yes, I am talking about uptake systems. Since nitrate uptake is switched off when ammonium is present, as you cite yourself, uptake of both N-compounds had to be tested separately.

I have to say, I don't want to discuss with someone who is just blocking.

 

[Hans-Werner]

Its a little more complicated than that - neither PSI or PS II (as I know it) can use the energy quanta that the wavelengths that carotenoids capture directly. They need to be transferred to around 680 resp around 700 nm. As I know it it happens in or near chlorophyll centra

I am sorry, Lasse, here I have to say I initially did not understand your original post completely. Yes, carotenoids are antenna pigments which transfer energy to the reaction centers which are chlorophylls. But I mean, the antenna pigments are mainly carotenoids which saves the dinoflagellates some N compared to antennae that are mainly chlorophylls. You can tell the differences in the proportions from the color.

The carotenoids absorb mainly blue-green light and since the energy of blue-green light is higher than the red light that is absorbed by chlorophylls, the energy transfer is no problem. I don't see the point. Why does it matter how the carotenoids are involved in photosynthesis? The efficiency of the energy transfer from antennae to reaction centers is high. Why does it matter where the carotenoids are?

 

[danimal1211]

A couple of questions in reading this article. First I want to make sure I converted to ppm correctly
Molecular weight of trisodoum phosphate= 163.94, so .05 x 163.94/1000= .08 ppm?
Second the article seems to say ammonia uptake will be limited below this amount so at least according to the article a target range of .08 to .49 ppm PO4 is desirable?

 

[Randy Holmes-Farley]

A couple of questions in reading this article. First I want to make sure I converted to ppm correctly
Molecular weight of trisodoum phosphate= 163.94, so .05 x 163.94/1000= .08 ppm?
Second the article seems to say ammonia uptake will be limited below this amount so at least according to the article a target range of .08 to .49 ppm PO4 is desirable?

"The uptake rate of ammonium was significantly increased in the presence of 0.5 and 3.0 μmol l–1 phosphate (r2=0.76, F=57.04, P<0.0001; Fisher's PLSD, both P<0.05; Fig. 5A). "

Not sure where exactly you are looking to convert the weight to ppm, but 0.5 umolar phosphate (molecular weight 96 g/mole) would be 48 ug/L, or 0.05 ppm.

 

[Randy Holmes-Farley]

Second the article seems to say ammonia uptake will be limited below this amount so at least according to the article a target range of .08 to .49 ppm PO4 is desirable?

I would not draw that conclusion, since the only level they tested below 0.5 uM (0.05 ppm) was 0.

So 0.05 M is better than zero. No info whether it is better than, say, 0.03 ppm.

Uptake rates were measured with six different concentrations of phosphate (0, 0.5, 1.0, 2.0, 3.0 and 4.0 μmol l–1), ammonium (0, 0.5, 1.0, 2.0, 4.0 and 6.5 μmol l–1) or nitrate (0, 0.5, 1.5, 3.5, 5.0 and 9.0 μmol l–1).

 

[danimal1211]

Thank you

 

[Lasse]

Zooxanthella have only Chlorophyll A and C - not B The Absorption spectra of Chl A, B C and some carotenoids below

As you can see Chlorophyll C have two very high absorption peaks and carotenoids is most effective between 420 and 540 nm - but not very high peaks. I would say that chlorophyll is more effective below 470 nm and above 620 nm.

Now the million dollar question is - are corals brown colour a prove that carotenoids is the main contributor to photosynthesis below high light intensity or is it something else - like sunscreen. If we go back and try to define what a colour is - the answer is that is the sum of the wavelengths that are reflected (if we for the moment exclude fluorescence and talk about full spectra lighting and only reflecting colours) Corals have one problem with photosynthesis - where should I be rid of the dangerous active oxygen radicals that is produced. - mostly by diffusion of O2. This means that they must have mechanisms to regulate the amount of incoming light in the absorptions peaks.

If you see a reflection of brown colour - its just a mix of blue, yellow and red wavelengths - it means that carotenoids can function as an inbuild sunscreen for the whole zooxanthella - IMO

There is also a lot of both montipora, Porites, acropora and other stony corals that mainly reflect green wavelengths - do they not have the same type of zooxanthella? IMO - the brown corals I have seen in nature is mostly in the upper layer of a reef - and sometimes above the surface (ebb and tide)

I have to mention the strong fluorescence many corals have. If your light is mainly below 500 nm - you are able to see this florescence but they are not reflecting colours - they are small light emitters of different wavelengths.

I do not see any disagreement between what Hans-Werner wrote and what the authors wrote. They do not use the same transporters, and can compete for energy usage.


I do not agree with this - neither do the authors of the article - my bold

Hans - Werner replied to my statement

IMO the graphs does not show any precedence for either of the N species because it done with one N species at a time. Not with both together. The graph show only the rate of uptake in single species experiment

with

This doesn't really matter since nitrate and ammonium don't compete for uptake sites. It must be different ion pumps since one is a cation and the other is an anion. The competition for uptake was only for energy, not for uptake sites. The curves show the affinity of the uptake sites, the rates in which uptake sites can pump the ions.

The authors did not argue that way - with different uptake sites - they just state that NO3 uptake was either a repression of the nitrate reductase or a competition of ammonium and nitrate uptake mechanisms for energy resources. This - as I understand this not coupled to different uptake sites - it is a general mechanism.

You mean, excretion of chloride and nitrite ions goes different ways? Any proof for this?

The opposite - and that is my concern

Chloride cells in gills is responsible for much of the osmosis regulation in fish

IMO it use the same mechanism - it has been shown that in low chloride concentrations - nitrite compete with the CL uptake in freshwater and inhibit the Cl uptake. It is an active process (against a concentration). If the concentration of Cl in the water rise - the opposite happens - the chloride block the uptake of NO2. In freshwater fish chloride cells is responsible for transport in chloride into the fish body in order to compensate for the loss of chloride caused by osmosis.

In saltwater - they are responsible for the outward transport of chlorides that has enter the fish through osmosis and that the drink saltwater. The findings of active NO2 uptake int the gastrointestinal tract and that in spite of this - the body fluids content lesser NO2 than the ambient water indicate that NO2 compete with CL even in this mechanism and therefore inhibit some of the Cl outwards transport - creating osmotic stress.

For me - its enough to consider a low concentration of NO2 in my water. I´m sorry - I could not find that article again - but I´m looking



Sincerely Lasse

 

[Randy Holmes-Farley]

The authors did not argue that way - with different uptake sites - they just state that NO3 uptake was either a repression of the nitrate reductase or a competition of ammonium and nitrate uptake mechanisms for energy resources. This - as I understand this not coupled to different uptake sites - it is a general mechanism.

But it clearly is different uptake transporters, whether they explicitly say so or not. Protein transporters take only a single species, or closely similar species. Ammonium and nitrate are very different chemically and would not use the same transporter.

 

[Randy Holmes-Farley]

The opposite - and that is my concern

Chloride cells in gills is responsible for much of the osmosis regulation in fish

IMO it use the same mechanism - it has been shown that in low chloride concentrations - nitrite compete with the CL uptake in freshwater and inhibit the Cl uptake. It is an active process (against a concentration). If the concentration of Cl in the water rise - the opposite happens - the chloride block the uptake of NO2. In freshwater fish chloride cells is responsible for transport in chloride into the fish body in order to compensate for the loss of chloride caused by osmosis.

In saltwater - they are responsible for the outward transport of chlorides that has enter the fish through osmosis and that the drink saltwater. The findings of active NO2 uptake int the gastrointestinal tract and that in spite of this - the body fluids content lesser NO2 than the ambient water indicate that NO2 compete with CL even in this mechanism and therefore inhibit some of the Cl outwards transport - creating osmotic stress.

For me - its enough to consider a low concentration of NO2 in my water. I´m sorry - I could not find that article again - but I´m looking



Sincerely Lasse

I do not see any reason to think nitrite is going to cause issues in chloride balance. It just doesn't make sense to me that, say, 1-10 ppm nitrite will so occupy the transporter for chloride that 19,000 ppm chloride is going to be made appreciably harder to keep in balance. I cannot imagine it is worse than 19,010 ppm of chloride being present. That extra 10 ppm chloride load is not a problem, so why would 10 ppm of a nitrite load on that transporter be bad?

 

[BeanAnimal]

My simple questions would be -

If there are two different transporters, then how is the decision made that makes one or the other "active" if both sources are available?

Or

Do both transporters work at their optimal rate at all times in the presence of food, but one is simply more efficient than the other and therefore processes faster, giving the appearance of "favorability".

Or

Is simply a matter of the ratio at any given time of available transporters, maybe based on recently available sources? I.E. does the type expand and contract based on food available?

Apologies to all if these are dumb questions. I am comfortable with physics and logic, but I paid far less attention in chemistry and bology.

 

[Randy Holmes-Farley]

My simple questions would be -

If there are two different transporters, then how is the decision made that makes one or the other "active" if both sources are available?

Or

Do both transporters work at their optimal rate at all times in the presence of food, but one is simply more efficient than the other and therefore processes faster, giving the appearance of "favorability".

Most likely, both work all the time they are present, but the numbers of each get regulated.

All organisms are constantly changing the number and types of transporters expressed at their surfaces to take advantage of what is present without wasting energy and resources making things that are not needed or may even become detrimental.

It's also why, for example, stable conditions can be better for corals and such. Take alkalinity. They express a certain number of transporters on their membrane surfaces to get what they need. If alk is suddenly raised, those same transporters are still there and suddenly they take in too much alk internally. It takes time to readjust protein transporter numbers, and in the meantime, the coral may have too much or too little bicarbonate/carbonate to calcify as it wants.

Same applies to nitrate, ammonium, phosphate, iron, manganese, etc., etc.

For example:

https://www.sciencedirect.com/science/article/pii/S1674205215004657

 

[Lasse]

What does the citation mean in your opinion? Of course phosphate is limiting initially, but the phosphate concentration was increased. Increase of phosphate concentration increased ammonium uptake but in nitrate it had a limited effect. Why?

It may shed some light on these findings

But it clearly is different uptake transporters, whether they explicitly say so or not. Protein transporters take only a single species, or closely similar species. Ammonium and nitrate are very different chemically and would not use the same transporter.

I did not claim otherwise - I just say that the authors suggest that ammonium may inhibit the actual enzyme for NO3 conversion into NH3/NH4. That means that if both NH3/NH4 and NO3 exist - the NO3 uptake should not happen regardless. There was no discussion about competition about the same transporter either from me or from the authors.

I do not see any reason to think nitrite is going to cause issues in chloride balance. It just doesn't make sense to me that, say, 1-10 ppm nitrite will so occupy the transporter for chloride that 19,000 ppm chloride is going to be made appreciably harder to keep in balance. I cannot imagine it is worse than 19,010 ppm of chloride being present. That extra 10 ppm chloride load is not a problem, so why would 10 ppm of a nitrite load on that transporter be bad?

I´m not sure if you understand what I try to say. The chloride cells work in both directions depending on ambient waters content of chlorides. The transport out of a saltwater fish of Cl ions is against a gradient of 19 000 mg/L and the Cl content is rather low in the fish. The article I saw indicate that i spite of an active uptake in gastrointestinal tract of NO2 - the very low levels of NO2 (lower than in ambient water) indicate that the chloride cells actively transported out NO2 from the fish body fluids into the water. The article I linked to show that when the situation was the opposite (in freshwater) the active transport of NO2 by chloride cells into the fish inhibit the active transport of Cl by the chloride cells until the ambient waters concentration was high enough to block the NO2 transport. The chloride cells of a saltwater fish works all the time in order to maintain a body salinity of around 0.9 %. If outward NO2 (that have enter the body by the gastrointestinal tract) transport by the chloride cells inhibit the Cl transport in the same way (but the direction is opposite) it may create an osmotic stress.

Edit:
I do not know if this is a real problem or only a theoretical but it make me to see enough of red signals in order to not introduce gill breathing animals in water with elevated NO2 concentrations. My own measurements in my aquarium and 15 + analysis of my water by OCEAMO indicate that my NO2 concentrations is in the 0 - 0.1 mg/L NO2 range. I think that my measurements can serve as an base line how it looks like in many mature aquariums. It is not zero (as many believe) but low.

Sincerely Lasse

 

[Randy Holmes-Farley]

It may shed some light on these findings


I did not claim otherwise - I just say that the authors suggest that ammonium may inhibit the actual enzyme for NO3 conversion into NH3/NH4. That means that if both NH3/NH4 and NO3 exist - the NO3 uptake should not happen regardless. There was no discussion about competition about the same transporter either from me or from the authors.

I’m not sure I understand the point, but show me where they suggest direct inhibition of the transporter for nitrate by ammonia rather than reducing the uptake by regulating transporter numbers.

 

[Lasse]

but show me where they suggest direct inhibition of the transporter for nitrate by ammonia rather than reducing the uptake by regulating transporter numbers.

I have not claim that there is direct inhibition of the transporter. I have not ment it at all before Hans Werner answered that it did not matter if they did the test separately for each inorganic N species or if they did it with both of them present because it was different transporter. I refer the whole time to this below. And the actual enzyme I refer to is nitrate reductase

Sincerely Lasse

 

[Randy Holmes-Farley]

I have not claim that there is direct inhibition of the transporter. I have not ment it at all before Hans Werner answered that i did not matter if they did the test separately for each inorganic N species or if the did it with both of them present because it was different transporter. I refer the whole time to this below. And the actual enzyme I refer to is nitrate reductase

Sincerely Lasse

Ok, I understand. To me, that just says bacteria prefer ammonium to nitrate, and will do what it takes to get what they prefer. Lol