A molecular biologist perspective to the carbon dosing

[Tripod1404]

Hello Guys,
As a reefer and a molecular biologist I wanted to share with you my insights and a little biology behind the carbon dosing and how exactly it reduces nitrate/phosphate levels.
I must say that the stuff I say here are not based on a strict primary literature search but mostly what I know about microorganisms and biochemistry. In other words I am not claiming to be an expert on the issue (my real area of expertise as a scientist is on plant molecular biology). I just wanted to share with you what I think happens, when you are or I am am doing carbon :spin1:

Okay, the main idea behind denitrification and carbon dosing is that; we add carbon source to the water, in return some anaerobic bacteria takes up this carbon source and while metabolizing the carbon source these bacteria use nitrogen inside nitrate as terminal electron acceptor and release diatomic nitrogen (N2) gas. This process only happens in anaerobic conditions because, first, most bacteria capable of doing this reaction cannot survive in high oxygen concentrations and, second, even the species that can survive in high oxygen concentrations do not employ this reaction because oxygen is a far better terminal electron acceptor compared to nitrate. Therefore, as long as there is oxygen in the environment, there is no need for the bacteria to use less-ideal nitrate as a terminal electron acceptor.

Although the process I explained above is possible and is even being used in sewage treatment, I highly doubt it can be efficiently used in an aquarium system with oxygenated water. This does not mean it is not happening, I only think that it cannot happen in large quantities make a really big difference. The reason for this is the need for anaerobic conditions. For an environment to be anaerobic there need to be little oxygen diffusion to that area. In our aquariums this only happens in deep sand beds and deep crevices of live rock or other special media. Okay here comes the paradoxical part; denitrification also requires an carbon source. We add this source to the water but it also needs to diffuse to the anaerobic bacteria to be used for denitrification. All the carbon sources we add like ethanol, methanol, acetic acid or glucose are far larger molecules than diatomic oxygen. So any place these can diffuse, oxygen can diffuse far better. In addition to this, there are far more aerobic bacteria in an aquarium than there are anaerobic, so I would think almost all of the carbon source we add is being used up by these aerobic bacteria that have a much easier access to the carbon source.

But if this is the case, how does carbon dosing work. In my opinion, it all comes down to increasing the bacteria population in the aquarium. I looked up to the elemental composition of the human body as a reference. It is 65% oxygen, 18% carbon, 10% hydrogen, 3% nitrogen and 1.4% calcium and 1.1% phosphorus plus other elements in lower amounts. Bacteria would have different composition but not like wildly different than this. Since oxygen and hydrogen are practically limitless for these organism living in water, the limiting factor is carbon. So when we add carbon we increase the availability of this element and this allows more bacteria to be built. Look whats limiting after carbon, it is nitrogen. More bacteria means more need for nitrogen. In turn more nitrate is being sucked from the water for building more bacteria. It is the same thing as having lots of algae and no nitrate. In both cases nitrogen is the limiting factor for growth and it is being sucked up from the water. This explains why so many people claim their nitrate levels skyrocket if they stop dosing carbon. Without the carbon source, bacteria population collapse and all nitrogen is released back to the water. If it was denitrification, stopping carbon dosing could have not released nitrogen back to water. However, also consider that our skimmers can remove bacteria from the water, especially when wet skimming. So if you dose carbon for a long time, you would slowly export bacteria and therefore nitrogen and phosphorus out of the system, similar to growing then harvesting algae. As a result, in long run dosing carbon would reduce the nitrogen and phosphorus in the system.

 

[hotelbravo]

very interesting read, thanks for that!

 

[karimwassef]

agree. following.

any insights on comparing carbon dosing to algae scrubbers?

do you think carbon dosing has deeper impact on the food chain.. sponges, etc... vs. algae scrubbers where the food chain is in the biofauna it cultivates rather than as a food source up the chain?

Are they complementary or supplementary?

 

[Tripod1404]

In principle they are very similar. More bacteria requires more carbon. More carbon means more biomass and less nitrate in water. More algae requires more light (since algae can fix CO2 through photosynthesis, in a way more light also means more carbon ). Again more algae biomass and less nitrate in water.

For the biodiversity, it is hard to compare (at least for me). There are many organisms that feed on bacteria (most we cannot even see). Increasing the bacteria population would sure increase the number of all these organisms and in turn more food for filter feeders such as sponges. One of my friends was even claimed carbon dosing can reduce ich protist numbers due to increased number of predatory microorganism (such as amoebas) in a carbon dosed tanks, but this is hard to test Same can also be said for the algae as many organisms consume it and live in it. However you are right, when we harvest algae, the whole biofauna is harvested and cannot recover until the algae biomass reaches its former size.

 

[Subsea]

Tripod,
First, thank you for describing the carbon dosing protocal used by reef hobbiest and the science that drives it.

Does the following make sense to you?

"I would like to focus on the fact that everything alive and growing in our aquariums is carbon based. Meaning corals, macros and fish require carbon to grow. Therefore carbon assimilation determines life on earth. In the athmosphere, CO2 gas is dissolved in the water, then when combined with photosyntious produce sugars in the biomass of algae. In my mind, that would be natures way to carbon dose in the oceans."

 

[BlackTip]

Very informative. Thanks

 

[karimwassef]

except that that's carbon dioxide gas for photosynthesis, not carbon dosing in the form of complex organic molecules?

 

[C.Eymann]

Its going to take me a while to digest all this, all I can say is WOW! very informative and detailed, reefkeepers like myself would love to pick your brain a bit on other subjects too, the knowledge your career entails and you posses makes you a very important asset to the hobby.
Will be following your future posts for sure.

 

[Tripod1404]

Subsea, I do agree. But like karimwassef said the way carbon does in ocean is different. It enters to the food chain through the primary producers (photosynthetic autotrophs). In the end these either die or got eaten by other organisms so the carbon moves through the food chain. When we dose carbon, carbon does not enter through the primary producers. But in principle through carbon dosing we are somewhat making those bacteria the primary producers for organisms feeding on them.

karimwassef, I also edited my comment above, I realized I missed some part of your previous comment

 

[vhuang168]

A molecular biologist perspective to the carbon dosing

If I'm not wrong, we use carbon dosing not for denitrification but to increase the bacteria population so that it can be skimmed off as a form of nitrogen export.

Same principle used in bio pellets. Bio pellets fuel the growth of bacteria which are then skimmed off. That is why the recommendation is to have the effluent exit upstream of the skimmer.

Also why it is recommended to ramp up the use of carbon dosing or bio pellets because that can drive the O2 levels down too far too quickly.

Sent from my iPhone using Tapatalk

 

[Tripod1404]

vhuang168, yes you are right. This also explains why after carbon dosing skimmer output increase and oxygen levels can drop. All that carbon we add is being converted into bacteria. Rest of the components required like oxygen and nitrogen are being sucked up from the water.

 

[karimwassef]

when we harvest algae, the whole biofauna is harvested and cannot recover until the algae biomass reaches its former size.

So this makes the case for a refugia where the intent is not export, but rather cultivation of biofauna as a food source.

So there are three modes of carbon input -

carbon dosing = bacteria = food chain consuming bacteria + skimmer export
algae scrubbers = algae mass = manual export
algae refugium = algae mass = food chain consuming algae

 

[Subsea]

Subsea, I do agree. But like karimwassef said the way carbon does in ocean is different. It enters to the food chain through the primary producers (photosynthetic autotrophs). In the end these either die or got eaten by other organisms so the carbon moves through the food chain. When we dose carbon, carbon does not enter through the primary producers. But in principle through carbon dosing we are somewhat making those bacteria the primary producers for organisms feeding on them.

karimwassef, I also edited my comment above, I realized I missed some part of your previous comment

In our reef tanks, would not corals and macros costume bacteria? Would this not be considered moving carbon up the food chain.

 

[CStrickland]

Interesting read.
A weakness in your explanation is that you are treating an aquarium as if it has only 2 zones: aerobic, and anaerobic. This conception elides the possibility that colonies of bacteria exist in low flow areas, wherein bacteria form interdependent colonies. In such an area, the present oxygen would be utilized by the upper layers of bacteria, restricting the underneath guys to less efficient electron receptors. Those facultative heterotrophs would then denitrify at rates noticeable on our tests.

Additionally, you are correct that skimming is crucial during carbon dosing. However, I think it might have to do with the chosen form of carbon. For example, biopellets present themselves as a polysaccharide, but advise users to direct the effluent right into the skimmer. In this case, it sounds like they are attempting to remove the bacteria itself. Same, or more so, with zeolite based systems that advice fluffing or shaking the media to dislodge floc. On the other hand, a reefer cranking vodka into their tank may well be encouraging enhanced overall bacteria populations, in the hope that their waste product will be skimmer off as a stickier, hydrophobic or ampiphathic, compounds.

I doubt that all the carbon we dose is being used for any one thing in our complex ecosystem. Thank you for the careful write up. You have a knack for putting things into understandable terms. You may be interested to read up on the 'redfield ratio' as it pertains to reefing. The idea is similar to your investigation of the % used by the human body. I would caution that those threads tend to make subtle, unwarranted leaps of logic; but it's a good idea to think about, as far as it goes.

 

[CStrickland]

Also, I think the chemoautotrophs that use oxygen can also use the carbon from carbon dioxide in the water? And maybe alkalinity too. I'm a little rusty on that part though.

 

[Tripod1404]

So this makes the case for a refugia where the intent is not export, but rather cultivation of biofauna as a food source.

So there are three modes of carbon input -

carbon dosing = bacteria = food chain consuming bacteria + skimmer export
algae scrubbers = algae mass = manual export
algae refugium = algae mass = food chain consuming algae

karimwassef, yes you are right. However, if you do not harvest any algae like the refugium case, there is no nutrient export from the system. So the nitrogen is still in the system, but it would not show up in a nitrate test since it is bound to the algae .

 

[Tripod1404]

In our reef tanks, would not corals and macros costume bacteria? Would this not be considered moving carbon up the food chain.

I am not sure if corals or sponges or macros can directly consume bacteria. I dont know maybe they can . However, stuff that corals eat such as copepods or rotifers do can feed on bacteria. So carbon does indirectly move to the other larger members of our tanks. However, also consider the fact that most of the carbon probably moves outside of the system as carbon dioxide. So only a fraction of the added carbon would end up in something visible to naked eye.

 

[karimwassef]

I consider dosing phyto as carbon dosing

They have carbon and they consume N and P and are photosynthetic and add to the food chain. I know it's an oblique interpretation, but hey- why not?

 

[Tripod1404]

Interesting read.
A weakness in your explanation is that you are treating an aquarium as if it has only 2 zones: aerobic, and anaerobic. This conception elides the possibility that colonies of bacteria exist in low flow areas, wherein bacteria form interdependent colonies. In such an area, the present oxygen would be utilized by the upper layers of bacteria, restricting the underneath guys to less efficient electron receptors. Those facultative heterotrophs would then denitrify at rates noticeable on our tests.

Additionally, you are correct that skimming is crucial during carbon dosing. However, I think it might have to do with the chosen form of carbon. For example, biopellets present themselves as a polysaccharide, but advise users to direct the effluent right into the skimmer. In this case, it sounds like they are attempting to remove the bacteria itself. Same, or more so, with zeolite based systems that advice fluffing or shaking the media to dislodge floc. On the other hand, a reefer cranking vodka into their tank may well be encouraging enhanced overall bacteria populations, in the hope that their waste product will be skimmer off as a stickier, hydrophobic or ampiphathic, compounds.

I doubt that all the carbon we dose is being used for any one thing in our complex ecosystem. Thank you for the careful write up. You have a knack for putting things into understandable terms. You may be interested to read up on the 'redfield ratio' as it pertains to reefing. The idea is similar to your investigation of the % used by the human body. I would caution that those threads tend to make subtle, unwarranted leaps of logic; but it's a good idea to think about, as far as it goes.

CStrickland, I do agree that there should be colonies of anaerobic bacteria under the layers of aerobic bacteria. Since upper layers of aerobic bacteria consume oxygen, lower levels would effectively be anaerobic. However, what makes me think about the extend of denitrification is due to the penetrability of carbon to these lower levels and the metabolic rate of anaerobic bacteria. If the top aerobic bacterial colony is large enough to make the layers under it anaerobic, it would also take up large portions of the carbon available around it. Furthermore, organisms that can utilize oxygen have much higher metabolic rates compared to anaerobic ones. With oxygen, a cell can produce 38 ATP molecules per glucose, without oxygen it is just 2 ATP per glucose plus maybe some more from fermentation processes. Since ATP is the energy currency of the cell, an aerobic cell can potentially sustain a 14 times faster metabolism. Some carbon should reach to the under layers of anaerobic bacteria and perhaps waste from aerobic bacteria can be use to sustain denitrification. My concern is how large this denitrification would be.

 

[Tripod1404]

Also, I think the chemoautotrophs that use oxygen can also use the carbon from carbon dioxide in the water? And maybe alkalinity too. I'm a little rusty on that part though.

Yes they are, the only difference from photoautotrophs is the energy required to fix carbon dioxide into organic compounds comes from metabolizing other compounds rather than light energy. However this can be a dangerous pathway in aquarium. One such organisms produce hydrogen sulfide which can accumulate under sand bed and if released suddenly, can be very toxic to livestock.

Alkalinity, at least the bicarbonate portion, can even be used by most algae. There are a family of enzymes called carbonic anhydrases that can convert bicarbonate into carbon dioxide. This enzyme is super fast and it can convert a million bicarbonate ions into CO2 in a second, amazingly fast!