Journal sudiorca's non-CO2 supplemented softwater tanks

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Isn't it amazing how nature can take care of itself without us humans stabilising pH and CO2?

A lot to think about, including which assumptions we have in our mental models that are merely fabricated, not really reflecting what's going on with our plants. One of those classic assumptions is CO2 stability, which we usually track hourly within one day in the pH profile. But perhaps, if indeed stability is important and we do have a point here, it should be more on a moving average day-to day basis, or even longer periods, for the plant's Rubisco's machinery to stay well tuned and at minimum cost of adjustments? I am actually suspecting this is the case, but am no biologist and do not have data to prove or disprove the point.
I would expect some amount of daily CO2 fluctuations would be found in the natural systems where these plants evolved, so there's probably some sort of adaptive mechanism to handle it.

Iirc, in Tom Barr's ancient non-CO2 post he uses this concern about concern about plants wasting resources changing their carbon fixing enzymes as an argument against too frequent water changes because, and I understand what he's saying theoretically, but as a practical matter I've only seen good things from frequent water changes. Is that your experience, @sudiorca? It may be that this CO2 injection is just too small and brief to matter like you were getting at, especially considering the daily ups and downs.

It's worth noting that co2-injected tanks also have some endogenous CO2 production, though I'm sure just how much varies between tanks and of course it's dwarfed by what gets added. @GreggZ, didn't you measure an appreciable nightly pH drop in your tank when not running CO2 for a brief period? I could be remembering wrong.
 
It's worth noting that co2-injected tanks also have some endogenous CO2 production, though I'm sure just how much varies between tanks and of course it's dwarfed by what gets added. @GreggZ, didn't you measure an appreciable nightly pH drop in your tank when not running CO2 for a brief period? I could be remembering wrong.
Yes one time I ran my tank for almost a week with no CO2.

I tracked the pH very closely as I was curious what it would do. My fully degassed reading is 6.25. First thing in the morning the pH in the tank was consistently about 5.85. That’s a 0.4 pH drop overnight. Then it would rise as the day went on back to 6.25.

Is it because plants use O2 and expel CO2 at night. That's my educated guess. Was there other factors affecting pH? Maybe?

All I can say for sure is that the pH was about 5.85 at 7:00 in the morning and back to 6.25 at 7:00 at night. Every single day.
 
Rubisco's machinery to stay well tuned and at minimum cost of adjustments?
Rubisco is a remarkable enzyme. Almost all of the fixed carbon on earth exist because of Rubisco. I got fascinated by it when I did some readings on it for my AGA talk. It is the most abundant enzyme present in plant leaves and accounts for approximately 50% of soluble leaf protein in most plants. Plants spend enormous amounts of energy and resources to produce this enzyme and it is highly regulated inside cells to maximize the benefits. I had no idea the plants turn this enzyme Inactive every day after sunset and they
turn this enzyme active when the sun rises in the morning and the cycle continues. Plants use another enzyme called Rubisco activase which plays a crucial role activating Rubisco. The proportion of active Rubisco increases with light intensity upto a certain level. I did discuss about this during my AGA talk. I need to do further readings to get a better idea about the regulation of this enzyme.
 
Rubisco is a remarkable enzyme. Almost all of the fixed carbon on earth exist because of Rubisco. I got fascinated by it when I did some readings on it for my AGA talk. It is the most abundant enzyme present in plant leaves and accounts for approximately 50% of soluble leaf protein in most plants. Plants spend enormous amounts of energy and resources to produce this enzyme and it is highly regulated inside cells to maximize the benefits. I had no idea the plants turn this enzyme Inactive every day after sunset and they
turn this enzyme active when the sun rises in the morning and the cycle continues. Plants use another enzyme called Rubisco activase which plays a crucial role activating Rubisco. The proportion of active Rubisco increases with light intensity upto a certain level. I did discuss about this during my AGA talk. I need to do further readings to get a better idea about the regulation of this enzyme.
It is absolutely amazing to read about Rubisco complexity, the mechanisms that control its activity during the day, its inefficiency and cost, and how it continues to improve in the evolutionary process (a recent interesting article):

I have tried to find scientific sources to validate some of the assumptions that we use in our hobby. Are assumptions based in science, are they based in experiments in the hobby, or are they perhaps myths that are echoed from generation to generation in our hobby? One "tradition" I find interesting to understand better is why CO2 stability is important in our (supplemented) tank, and if it is what would be the timescales to be more specific about a recommendation for the hobby. A lot of research has been published on Rubisco, but not so much specifically on CO2 in aquatic plants as that has probably little economic relevance for farming and does not get as much funding as research terrestrial plants and agriculture (where CO2 is constant on relevant timescales).

One of the best write ups about Rubisco is from Clive, for example in this post
But Clive makes an interesting statement here, 10 years ago, which he probably would not repeat now:
"In a low tech, non-CO2 enriched environment, because the CO2 levels are low and constant, and because the metabolic rates are also very low, the plant has time to slowly increase the RuBisCO content of the leaves."

From what I've found it seems that Clive @ceg4048 and Tom @plantbrain have most knowledge on the topic, and when delving deeper in the articles some of Tom's former colleagues/mentors (like Madsen, Maberly etc). But most of the help they have given explaining Rubisco is at least 10 years ago, and insights may have been evolved.

So what interests me is if we can correctly connect the scientific knowledge regarding Rubisco and CO2 concentrating mechanisms in plants (terrestrial and aquatic) to practical and specific recommendations for our tank. Are our current recommendations for CO2 stability correct, and if so why, and can we be a bit more specific about it (like relevant timescales). A general explanation about Rubisco is not fully satisfactory imo, I would hope for some more evidence that the recommendations for our tank are based in science and have these a bit more specific and concrete than we have now. Where is the science, where is the tradition, where is the myth?

I do not intend to derail your non-CO2 supplemented thread @sudiorca , but I hope you agree that your measurements could quite rightly be interpreted as a challenge to traditions for CO2 supplemented tanks. We're talking the same plants, the same CO2 concentrating mechanisms and the same enzymes after all.
 
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Rubisco is a remarkable enzyme. Almost all of the fixed carbon on earth exist because of Rubisco. I got fascinated by it when I did some readings on it for my AGA talk. It is the most abundant enzyme present in plant leaves and accounts for approximately 50% of soluble leaf protein in most plants. Plants spend enormous amounts of energy and resources to produce this enzyme and it is highly regulated inside cells to maximize the benefits. I had no idea the plants turn this enzyme Inactive every day after sunset and they
turn this enzyme active when the sun rises in the morning and the cycle continues. Plants use another enzyme called Rubisco activase which plays a crucial role activating Rubisco. The proportion of active Rubisco increases with light intensity upto a certain level. I did discuss about this during my AGA talk. I need to do further readings to get a better idea about the regulation of this enzyme.

I went to your AGA talk!

Rubisco is a funny enzyme because it's slow, costly, and has competing carboxylase and oxygenase activity. These obvious shortcomings has generated interest in engineering a better enzyme, but it's been a fruitless search thus far AFAIK.

If you haven't dug into this already you would probably be interested in the different pathways for carbon fixation in photosynthesis, because although rubisco is conserved among plant lineages, there are different adaptive tricks that manipulate CO2 concentrations within the plant.

Schematic-diagram-of-C3-CAM-and-C4-photosynthesis-Rubisco-ribulose-1-5-bisphosphate.png
The C3 pathways covers 85% of plant species, but there are environments that give the others the upper hand. Most of the information you'll find about this will be about terrestrial plants obviously, but I understand that there are aquatic c4 and CAM plants as well and there are probably some really interesting adaptations that facilitate plant growth under low CO2 aquatic conditions. (If you have already dug into this, my apologies - maybe someone else will benefit.) Also, if there's a Barr Report on this already, send me a link. :ROFLMAO: I haven't seen it talked about much.
 
there are different adaptive tricks that manipulate CO2 concentrations within the plant
This is a really good point. I have been reading a bit about Carbon Concentration Mechanisms recently, and there is a large variety how aquatic plants have adapted to low CO2 availability. One of them is use bicarbonates, but this is less efficient than CO2, costly, and these plants usually perform less on CO2 capture than plants who don't have the bicarbonate capability. Then I found it also interesting that there are hints that higher light may be beneficial, as light energy will help to pay the price for building Rubisco and CCM's. What I didn't know is that some plants (CAM) can also capture CO2 during the night.

Based on my limited knowledge, I would make some guesses but could be totally wrong
  • The plants that perform best are soft water plants that do not have the mechanism for bicarbonates and are totally focussed to optimise their efficiency for CO2 capture from sediment and water column (rather than have bicarbonates as back up).
  • High(ish) light may be a trick to cover the cost of building the machinery for most efficient carbon capture.
  • There is a correlation between a plant species carbon capture mechanism and its success in @sudiorca 's tank.
@sudiorca , would you have some idea which plant species work well, and which would struggle or simply don't make it in your tanks?
 
Most plants actually prefer lower KH (low pH) because lower KH means most of the available CO2 in the water will be present in the form of dissolved CO2 gas rather than bicarbonates in planted tanks based on the pH range ...
I don't want to be a nitpicker, but I would beg to differ here. I simulated aquarium water with pH 5.5, 6.5 and 7.5 in PhreeqcI (which is a program used by hydrogeologists) and the following came out:

co2-hco3-co3.png

As you can see, the CO2 concentration (at equilibrium) will be very low and almost identical in all cases (0.31-0.47 ppm). Maybe I'm missing something, but if those calculations are correct, the absolute concentration of free CO2 (from the atmosphere) will be virtually the same in the water, regardless of its pH. This is because at lower pH there will be less TIC (total inorganic carbon) in the water than in water with higher pH, so even though it may look like there is more CO2 in the water at lower pH (e.g. at pH 5.5 = 92.77%, while at pH 7.5 it is only 4.56%), in fact there will be the same 0.47 ppm CO2 in both cases.

PS: Maybe I did some mistake in the simulation for pH 6.5, because I think the absolute CO2 concentration should be the same as in the other cases (= 0.47 ppm).

CO2 from organic sediment is another matter, of course.
 
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I don't want to be a nitpicker, but I would beg to differ here. I simulated aquarium water with pH 5.5, 6.5 and 7.5 in PhreeqcI (which is a program used by hydrogeologists) and the following came out:

View attachment 5967

As you can see, the CO2 concentration (at equilibrium) will be very low and almost identical in all cases (0.31-0.47 ppm). Maybe I'm missing something, but if those calculations are correct, the absolute concentration of free CO2 (from the atmosphere) will be virtually the same in the water, regardless of its pH. This is because at lower pH there will be less TIC (total inorganic carbon) in the water than in water with higher pH, so even though it may look like there is more CO2 in the water at lower pH (e.g. at pH 5.5 = 92.77%, while at pH 7.5 it is only 4.56%), in fact there will be the same 0.47 ppm CO2 in both cases.

PS: Maybe I did some mistake in the simulation for pH 6.5, because I think the absolute CO2 concentration should be the same as in the other cases (= 0.47 ppm).

CO2 from organic sediment is another matter, of course.
Although I don’t have a lot of knowledge on CO2 chemistry, I have some issues with this simulation.

  • I still see mistakes in some numbers. I checked the math and the numbers for pH 5.5 looks good but the math is not correct for pH 6.5 and 7.5, particularly for bicarbonate and carbonate numbers. How do you explain different outputs for the exact same inputs for those two pH values (red boxes)?
  • Why would at pH 6.5, the ppm value for CO2 be lower than pH 7.5? It does not make sense based on the equilibrium properties of CO2 at various pH.
Picture1.png


However, the final numbers (blue boxes) might still be correct (at least the logic). As the pH increases, the dissolved CO2 gets converted to bicarbonate and carbonate which allows more CO2 to dissolve from the atmosphere to maintain the equilibrium. This should explain the overall increase in TIC at higher pH.

CO2 generated from sediment gets dissolved in water for the most part (depending on the rate of production) as it doesn’t have to breach the diffusion barrier from atmosphere to the surface of water. Higher solubility of CO2 allows helps in this regard.
 
Yes, it is quite fascinating to read about these different strategies that some plants use for capturing and concentrating CO2 for optimum utilization.
The plants that perform best are soft water plants that do not have the mechanism for bicarbonates and are totally focussed to optimise their efficiency for CO2 capture from sediment and water column (rather than have bicarbonates as back up).
The fact is every single plant would prefer dissolved CO2 over bicarbonate as it requires more energy and machinery to import and convert it back to CO2 because CO2 is the actual substrate for RuBisCO. The so called bicarbonate users will always first use the dissolved CO2 before trying to utilize bicarbonate as it is mentioned in this fascinating study.
https://www.science.org/doi/epdf/10.1126/science.aay5945
It makes a lot of sense when you try to think about any aquatic plant available in the hobby which doesn't prefer CO2 injected tank (I can't think of any such plant from my experience).

High(ish) light may be a trick to cover the cost of building the machinery for most efficient carbon capture.
I did briefly discuss about the role of high light in RuBisCO activation during my AGA talk. I would highly recommend you to watch that talk if you haven't watched it yet. I can promise you that you won't be disappointed.

would you have some idea which plant species work well, and which would struggle or simply don't make it in your tanks?
I have tried many species in the last 5 years or so and I have been able to grow most of them in my tanks. Two of the prominent genus in hobby are Rotala and Ludwigia, I can grow most of available species from those two genus in my tanks, except Rotala Ramosoir Florida and Sunset. However, I don't think that lack of bicarbonate is the actual reason as I am successfully growing Florida in 0 dKH water in my pressurized CO2 injected tank. I have also not been able to grow Eriocaulon quinquangulare in my setups so far but I can grow Eriocaulon sulawesi. I can also grow Hygrophila sp. Chai in my non-CO2 setups (at much slower rate) which I showed during my AGA talk.
 
I did briefly discuss about the role of high light in RuBisCO activation during my AGA talk. I would highly recommend you to watch that talk if you haven't watched it yet.
I believe I can't as I have no subscription. Your replies here and this thread are very helpful though.

I am fascinated by your tanks, if not a little obsessed, as you demonstrate incredible results in non CO2 injected tanks. Unfortunately very few can, or try to replicate what you do, but looking at the results it is worth trying to use your techniques as a starting point and perhaps apply some minor modifications so that is easier to replicate without necessarily having all expertise that you have, or the special conditions like low temperatures.

I have probably too high temperatures, and also I am less excited to experiment with organic substrates as I find them less durable and less predictable. But what I try to understand is how your low CO2 tanks work, and if that could be replicated with just a little CO2 injection rather than relying on the soil and low temperatures. I feel we miss a lot in the hobby when we forget that no plant told us they need 30 ppm to look great.

Thanks again for setting such a great example @sudiorca , I expect that your work will prove to have much more broader application than we appreciate today.
 
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Although I don’t have a lot of knowledge on CO2 chemistry, I have some issues with this simulation.

  • I still see mistakes in some numbers. I checked the math and the numbers for pH 5.5 looks good but the math is not correct for pH 6.5 and 7.5, particularly for bicarbonate and carbonate numbers. How do you explain different outputs for the exact same inputs for those two pH values (red boxes)?
  • Why would at pH 6.5, the ppm value for CO2 be lower than pH 7.5? It does not make sense based on the equilibrium properties of CO2 at various pH.
View attachment 5977


However, the final numbers (blue boxes) might still be correct (at least the logic). As the pH increases, the dissolved CO2 gets converted to bicarbonate and carbonate which allows more CO2 to dissolve from the atmosphere to maintain the equilibrium. This should explain the overall increase in TIC at higher pH.

CO2 generated from sediment gets dissolved in water for the most part (depending on the rate of production) as it doesn’t have to breach the diffusion barrier from atmosphere to the surface of water. Higher solubility of CO2 allows helps in this regard.
My mistake! I copied the data for pH 5.5 to the following blocks (6.5 and 7.5), but then I forgot to adjust it to the current values.
So here's the corrected version:
co2-hco3-co3.png
But it doesn't change the result.
PS: You may be overlooking the fact that a higher pH cannot be achieved without adding (bi)carbonates (given normal conditions).
 
My mistake! I copied the data for pH 5.5 to the following blocks (6.5 and 7.5), but then I forgot to adjust it to the current values.
So here's the corrected version:
View attachment 5982
But it doesn't change the result.
PS: You may be overlooking the fact that a higher pH cannot be achieved without adding (bi)carbonates (given normal conditions).
My concern with this calculation is that physics laws give that partial pressure of CO2 in water and ambient air will equilibrate, and this is independent of other sources of inorganic carbon in the water. 0.47 ppm for pH 5.5 and 7.5 look right, but the 0.3 ppm for pH 6.5 is probably incorrect.
 
My concern with this calculation is that physics laws give that partial pressure of CO2 in water and ambient air will equilibrate, and this is independent of other sources of inorganic carbon in the water. 0.47 ppm for pH 5.5 and 7.5 look right, but the 0.3 ppm for pH 6.5 is probably incorrect.
In his video presentation, Sudipta says that the reason he prefers low pH to high is because he believes that a lower pH means more free CO2 in the water. I tried to explain to him that physically this is nonsense. Now I was just trying to support this explanation with a simulation from that hydrogeology program (the program is free, so anyone can check it out). Yes, I acknowledge that the data for pH 6.5 is a bit odd there (i.e. the CO2 concentration of 0.31 ppm is too low). Why that is, I don't know, but it doesn't seem to me (given the point) significant. So forget about the data for pH 6.5 and just focus on the data for pH 5.5 vs. 7.5. The data clearly show (and you confirm it yourself) that at equilibrium there cannot be different concentrations of free CO2 in the water at different pHs. In both cases (i.e. at low and high pH), the free CO2 in the water will be dissolved equally (= 0.47 ppm)! So justifying the preference for a lower pH by saying that there will be more free CO2 in the water is not correct IMO. That is the only point I was trying to make with my post. Lower pH may benefit plants for other reasons, but it certainly cannot be due to higher CO2 concentration (in non-CO2 supplemented tanks). In other words, if I have two tanks with organic substrate, and I have a pH of 5.5 in the first and 7.5 in the second, then there will be the same amount of free CO2 (which gets in from the air) in both, and probably the same amount of it from the organic sediment. Well, maybe I'll get a little more CO2 from the sediment uder higher pH because many bacteria prefer neutral or even alkaline rather than acidic pH (as far as I know). But let's just drop it. I didn't mean to cause any heated reactions. I just wanted to point it out. I already know it was a bad idea. I'll keep it to myself next time.
 
So justifying the preference for a lower pH by saying that there will be more free CO2 in the water is not correct IMO.
I think you are getting confused with the term "FREE". It is referred to the form of CO2 that is present in water and freely available as dissolved CO2 rather than bicarbonate. Let's take the example from your pH 7.5 simulation result. In this case 0.47 ppm CO2 is free CO2 and the rest 9.92 ppm is not freely available (bicarbonate and carbonate). However, for pH 5.5, same amount of free CO2 is coming from just 0.51 ppm total TIC. This means that a tank with lower KH (read 0 dKH) and organic substrate, there will be more "free" CO2 compared to the tank with high KH if the rate of CO2 production is same. So, even with lower CO2 production, most or the produced CO2 will be available for plants as '"free"' CO2 (preferred substrate for any plant) in 0 dKH tank compared to the tank with detectable KH.
Same thing happens with CO2 injected tanks. It would require more CO2 to drop same unit of pH (say from pH 7 to 6) for a tank with high KH (say 4 dH and 0 dKH). This means, you have to inject more CO2 for higher dKH tank to achieve the same amount of "free" CO2.
 
Rubisco is a funny enzyme because it's slow, costly, and has competing carboxylase and oxygenase activity.
I did some kindergarten level search on RuBisCo before my AGA talk and I found some very interesting articles about RuBisCo. I wanted to show this graph regarding kinetic parameters of RuBisCo for CO2 during my talk but I decided to exclude this due to lack of time. It seems like it is not that slow for CO2 carboxylation when compared to 2000 other enzymes from the database.
Rubisco catalytic parameters - KM and kcat over KM.jpg

However, it is also true that RuBP is another substrate for RuBisCo apart from CO2 and then there is the competing oxygenase activity (oxygenation of O2). These factors make the overall process quite complex and slower like you correctly pointed out.

This paragraph from the supporting information of an article precisely summarizes all the challenges regarding RuBisCo.
RuBisCo - folding, activation and catalytic limitations.jpg


We can then add the four isoforms of RuBisCo to make things even more complicated. :p Here is another omitted slide from my talk about those forms.
Screenshot (76).png


These obvious shortcomings has generated interest in engineering a better enzyme, but it's been a fruitless search thus far AFAIK.
yeah, there are many labs trying to improve the catalytic properties of RuBisCo but the progress has been quite slow. This is not surprising considering the fact it is an ancient enzyme (it is estimated to be >2.5 billion years old). It is not easy to change a system that has been optimized for so many years. However, I have found few papers which show some decent advancement in this area. The article below discusses the use of directed evolution to create a variant of Rhodobacter sphaeroides (bacteria) with an enhanced form of RuBisCo.
Picture4.jpg
 
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