Is anaerobic soil not as bad as we think? - The Planted Tank Forum
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post #1 of 7 (permalink) Old 09-10-2019, 06:22 PM Thread Starter
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Is anaerobic soil not as bad as we think?



Why is Anaerobic soil bad for my sealed ecosystem? It could be for two reasons. It will produce Methane and Hydrogen Sulfide. So That's what I looked into today. Here I will share what I learned about anaerobic respiration in soil. Here's my report.

Methane is the byproduct of bacteria using it's last choice (CO2) of electron acceptor for anaerobic respiration. Likewise Hydrogen Sulfide (H2S) is the product of anaerobic bacteria that is at it's second to least favorable electron acceptor (Suflate or SO4). Both gases produced by this anaerobic respiration would be harmful to organisms in the sealed container, as it would build up in the air space and then the water creating a toxic environment.

As the bacteria runs out of good options it has to choose electron acceptors aren't as efficient at supplying energy so their metabolism is much slower. By the time the bacteria are using Sulfate, they have exhausted (or don't have access to?) Oxygen, Nitrate, Manganese or Iron, in that order. The bacteria are consuming Sulfate and generating toxic Hydrogen Sulfide.

Energy yield difference shown in Y and also it's the order the anaerobic bacteria will utilize that compound and to the right, some metabolism equations for each electron acceptor.








When anaerobic bacteria are using CO2 as their electron acceptor they have exhausted their sources of N03, Manganese, Iron, and additionally Sulfate.

Bacteria using CO2 for respiration rely on anaerobic activity that utilized those better options for electron acceptors at some point (O2 -> NO3 -> Manganese -> Iron -> Sulfate). In order for the anaerobic bacteria to utilize CO2 it rely's on anaerobic bacteria that at one point did use the previous sources electron acceptors. Or for one reason or another, through lack of access or being unable to compete for better electron acceptors are using their byproducts now. Either way, The anaerobic bacteria utilizing CO2 need compounds created by previous anearobic bacteria that once fed on NO3, Manganese, Iron or Sulphate.

Better illustrated here:


The three reactions I know of so far to nuetralize the harmfulness of Methane:

Anaerobic: Using Nitrate and Nitrite:
CH4 + 4NO3- --> CO2 + 4NO2- + 2H2O
3CH4 + 8NO2- + 8H+ --> 3CO2 + 4N2 + 10H2O

Anaerobic Oxidation of Methane (AOM) isn't ideal because if methane is being produced the soil is already severely lacking in Nitrate. Using Nitrate for respiration is the second thing bacteria utilizes once it runs out of Oxygen. The first equation takes 4 Nitrates and returns 3 Nitrites, a loss. With the second reaction, the Sealed ecosystem loses 8 Nitrites. Or so it seems... But those 4N2's will go feed the Duckweed that will turn every one H2 into 2 NH3's, returning the Nitrogen to the system.

Anaerobic: Using Sulphate:
CH4 + (SO4^2-) --> (HCO^3-) + HS– + H2

This uses Sulphate (SO4) which is good because utilizing sulfate is slightly more favorable than utilizing CO2 and will produce Hydrogen Sulfide if not broken down at this point (or used by plants).

Aerobic:
CH4 + 2O2 --> CO2 + 2H20

This is better. It requires 2 Oxygen for every Methane molecule and yields one molecule of CO2. We "lost" one Oxygen. Think about it like this, normally in the cycle of Aerobic/plant respiration every one molecule of O2 an organism breathes produces one molecule of CO2. For every one molecule of CO2 a plant breathes it produces one O2. So, it technically is bad for aerobic organisms first, because 2 oxygens are not available and only slightly better for the plant which has 1 co2 instead of later having 2 after the aerobic organism respired.

These three reactions produce Carbon Dioxide, Nitrite, Inert N2 and Water. But the aerobic reaction is better as it wouldn't lead to further Nitrogen starvation of the soil, but results in a loss of one Oxygen for every Methane molecule reduced. The aerobic reaction is a net loss in sustainability between the O2 <---> CO2 respiration cycle.

While the anaerobic reaction would deplete my soil that's already close to depleted of Nitrite and Nitrate, leading to eventual plant decline and death due to nitrogen starvation. This result is the worse of them as plants are the a cornerstone to my sealed ecosystem.

Onto Hydrogen Sulfide...
Hydrogen Sulfide is produced by anaerobic organisms using Sulfate as their electron acceptor. I haven't found a reaction that breaks H2S down anaerobically but I did find this one that can do it aerobically if it can escape through the soil and into an aerobic layer or water. As you can see it produces 1 CO2 and 2 HSO. Very good indeed, though we do "lose" an oxygen again. Oh well. I'll take what I can get.
CH4 + 2 O2 = CO2 + 2 H2O.


"Losing" nutrients, O2 or CO2 etc is unavoidable in a closed system. For every change of energy from one organism to another or one chemical reaction to another energy is going to be lost and compounds are going to break down further and further until something runs out that "breaks the camels back" and largely collapses the system. This is just the way things are.

But the more I look into each part in depth the more I can tweak the system to make it last a little bit longer.

Name of the game is the same: Limit anaerobic activity, emulate the ecosystem as closely as possible, and include lots of diversity within the system.

Bump: Truth is, despite all I learned today. There's really no way to tell how all that will come together in my sealed 1 gallon glass ecosystem. And sadly, I after all that reading, I don't feel like it got me any closer to creating a more balanced system. I'm just going to keep doing what I have been doing. Emulate nature as best I can, all I can do. I'm no scientist, I can't say what effect all these minute things I just talked about would have.

I guess I do know more about what's going on within my system with the anaerobic soil. I'm just not any closer to being able to control it like I was hoping reading about it would allow me to. Bacteria gonna bacteria, sigh. Oh well, I'll stick with my method figuring out a creative way to keep the soil oxygenated. If you're interested I am keeping a Journal in that section.

Last edited by nothreat33; 09-10-2019 at 10:15 PM. Reason: i think too mcuh
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post #2 of 7 (permalink) Old 09-11-2019, 02:30 PM
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This is something I've wondered about a lot. Fine substrates become anaerobic/anoxic within a half inch of the surface, so it can't be that bad, or else you'd never see a healthy sand tank. These are my guesses:

1. Plant roots oxygenate the substrate, both preventing and removing the anaerobic spots.

2. Nitrate-containing wastes tend to sink, so the bacteria have more access to nitrate than we think. (But if nitrate can get through, why can't oxygen?)

3. Fungal or bacterial mats can move nutrients around the entire colony, so the nutrients are reaching areas that diffusion alone can't.

4. Something to do with the unique chemical properties of water, especially how lower pH means having free protons floating around, and how decomposition lowers the pH.

5. Snails, worms, and other substrate-dwellers mix nutrients into the substrate both through the movement of their bodies and by leaving waste behind.


I'm not sure how significant having a "closed" system is. If you're adding light, you're adding energy, so that shouldn't be a limiting factor. If everything that dies stays in the same place, then dead tissue will just be recycled. You might end up with algae and fungus instead of plants and snails, but I don't think the whole thing will just turn into dead sludge.

Maybe look up how deep sea substrates work. They don't even get light, but there's life (and the fish are able to breathe, so it can't be producing too much in the way of toxins).
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post #3 of 7 (permalink) Old 09-12-2019, 03:27 AM
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It just takes work to try and get it right. Before I had a foot of soil, and it didn't work. I removed most of the soil, and had a bag of 1/2" brown gravel which I added a LOT mixed all IN with the soil (which has clay hunks in it) (there's an additional top coating of pea gravel but I added those 1/2" gravel into the soil so it looked like a gravel bed just about. The rocks break up the soil allowing them to spread out but not being able to escape or spread out just vertically with a foot of soil and a scattering of pebbles, the soil can migrate in different directions with gravel all between them. And then I added 2" pond gravel for more aeration and sand to that clay soil, and a semi-light pea gravel coating and a light coating of regular sand on top. I can see big bubbles coming up from the soil that almost went bad and now it doesn't smell like vomit as there was a lot of soil before and hot compost in it saved it initially, but I don't think the compost is necessary. The total size of everything now is 3 1/2 inches.
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post #4 of 7 (permalink) Old 10-20-2019, 12:23 AM
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you might want to check out this sealed terrium

Hydrogen sulfate
H2S +H20 +O2<--> H2SO4 -> or H+ SO4
this isn't balanced reaction but it basically acidifies water and creates sulfate in the presence of water.
Sulfate is in turn uptaken by plants.
So pH down + sulfates.

water still flows through sand, much quicker than clay. Has to do with particle size thats why they use clay as a liner for large ponds, acts like a water barrier.
In nature water will travel underground above clay layers in viens of sand. If you have ever had a surface well dug, you know that hitting those viens of sand above the clay layer is key to getting enough water in the well.


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post #5 of 7 (permalink) Old 10-20-2019, 09:29 PM Thread Starter
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I wanted to include the most organic matter I could while keeping the soil balanced. I thought, a closed ecosystem of plants would require lots of organic matter in the substrate in order to last a long time, would it not? Seems self-explanatory. And in this thread, I am talking about anaerobic activity, the possible harm it can cause and how this activity relates to soil depth and it not getting oxygen.

However, I realize now that I missed something crucial. Anaerobic activity will occur anywhere where there is a lack of oxygen. I was so focused on soil depth and oxygenation I overlooked this simple fact. Bacteria will increase in population with food supply, not whether or not they happen to be using Oxygen or another electron acceptor like NO3, SO4, Fe, or Mn.So if there's food, they'll be there reproducing and consuming it using the electron acceptor that is the most energy efficient. If not O2 then NO3 and right down the line.
So if I include a very high amount of organic matter in the substrate of my Closed Aquatic System (CAS) then it will result in a large population of bacteria, if the plants in the system cannot supply the bacteria with enough Oxygen they will start to use the other compounds, no matter the soil depth or location in the system. This would result in the removal of Nitrogen from the system, and the production of toxic gases like Methane and Hydrogen Sulfide and even fermentation and acetate production.

We can set aside the harmful effects of all those compounds for now (as the focus of this article is on the Carbon Cycle in a CAS with high organic matter) no anaerobic respiration of the type I described above will create CO2 for the plants, which is a crucial role the bacteria *should* be providing. This creates a "break" in what should be a self-sustaining Carbon Cycle in the CAS (in a perfect system where O2/CO2 production/consumption is 1:1).

Now we have a system where there is a very large anaerobic bacterial population and much smaller aerobic bacterial population. Aerobic bacteria will still be present but in far fewer numbers. If the plants are alive they'll be producing some amount of O2 even if it is trivial. In the beginning stages of the CAS the plants are still capable of creating O2 from the depleting CO2. But the anaerobic activity is far greater and producing toxic compounds let's not forget.

This Hydrogen Sulfide gas and Methane will increase rapidly in the system, so will the population of bacteria that is able to feed on them. These reactions cost Oxygen to perform and the output of that reaction is not CO2, like you want to see in a normal CO2/O2 respiration cycle. In fact, it takes two O2's to process one molecule of Hydrogen Sulfide gas, and again, it returns no CO2 to the system. Similarly, methane requires more Oxygen to breakdown less methane and does not return CO2 to the system. Oxygen and CO2 respiration that takes place back and forth occur in a 1:1 ratio. So overall, a loss in one is a loss in another.

And while it's true that aerobic bacteria will try to use any O2 in the system, they are now competing with the Methane consuming bacteria and Hydrogen Sulfide consuming Bacteria for the Oxygen, and very quickly there will be a lot of both of those compounds. Competition will be tough, as the utilization of the free O2 is on a first come first serve basis and if there's more of those bacteria due to the greater amount of the compounds on which it feeds, the CO2 producing aerobic bacteria may be out competed.

What we would then see is an overall decrease in O2 and CO2 in the system. Continual loss of dwindling O2 to processes which produce no CO2 means less CO2 for plants which means less O2 created, which means the small population of CO2 producing aerobic bacteria that might have managed to compete with Methane and Hydrogen Sulfide consuming bacteria will find it increasingly difficult to find O2 for aerobic respiration, more of them will switch to anaerobic metabolism and use other electron acceptors available. The CAS will lose O2 and CO2 over time.

And it's frequently said in research papers that I've read that the overall metabolic activity of a closed system like this can be measured by measuring O2 and CO2 relationships. In essence, the system is powering down.

A system with too much organic matter like I described above creates a positive feedback loop where the O2 <--> CO2 connection seems irreversibly damaged. A system where, due to the quick growth/reproduction of bacteria compared to plants, bacteria can quickly switch to anaerobic respiration in a matter of a day or two if oxygen isn't present and stop producing CO2 for the plants which in turn, cannot provide O2, leaving the bacteria increasingly deprived and anaerobic. That anaerobic activity then (besides creating many harmful compounds that could by themselves crash the system) causes bacteria to breakdown the harmful compounds created causing the system to "lose" more CO2/O2 respiration potential (by costing more O2 molecules to process 1 molecule of the harmful compound).

If I'm correct, I was wrong to try to include a heavy amount of organic matter in my closed aquatic systems. It seems then that for a more balanced system that perhaps the Dead Organic Matter should be kept rather low and I should plant very heavily, ensuring the Oxygen needs of the bacteria are met. This would keep what looks like a self-destructing negative feedback loop of the break down of the Carbon cycle from occurring.

Another thing realized from this new understanding is it would be enormously beneficial to inject a high amount of CO2 into the water of my BioJars before sealing them ensuring that the water has enough CO2 in it for proper O2 production. Furthermore, studies have shown that oxygenating the water before CO2 injection allows for a higher concentration of CO2 to be in the water without it negatively effecting oxygen breathing organisms -simple with an airpump.

SIDE NOTE: Of course, I'd have to ensure the proper O2 being created in the first place. So proper light control is obviously very crucial. However, high light, while ensuring plentiful O2 production will cause plants to grow. Not ideal in the smaller closed systems I build. I don't want fast growing plants that take over the space. Plant amount, not plant size, is more important here. Lets say there's a CAS with two plants and a CAS with eight plants, both producing the same amount of O2. The CAS with two plants will be experiencing fast plant growth while the CAS with eight plants will be experiencing slow growth. "living within your means" is important here too.

Last edited by nothreat33; 10-21-2019 at 12:31 AM. Reason: i think too mcuh
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post #6 of 7 (permalink) Old 10-20-2019, 09:38 PM
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Originally Posted by nothreat33 View Post
Funny that someone should comment on this thread. I was just thinking about how I approached the problem of anaerobic activity in my closed aquatic system incorrectly. Recently, I was attempting to engineer the optimal substrate for long term use in my closed ecosystems that I build.

I wanted to include the most organic matter I could while keeping the soil balanced. I thought, an ecosystem of plants would require lots of organic matter in the substrate in order to last a long time, would it not? Seems self-explanatory. And in this thread, I am talking about anaerobic activity, the possible harm it can cause and how this activity relates to soil depth and it not getting oxygen.

However, I realize now that I missed something crucial. Anaerobic activity will occur anywhere where there is a lack of oxygen. This is connected to the amount of organic matter in the substrate. Bacteria will increase in population with food supply, not whether or not they happen to be using Oxygen or another electron acceptor like NO3, SO4, Fe, or Mn.

So if I include a very high amount of organic matter in the substrate of my Closed Aquatic System (CAS) then it will result in a large population of bacteria, if the plants in the system cannot supply the bacteria with enough Oxygen they will start to use the other compounds, no matter the soil depth or location in the system. This would result in the removal of an essential nutrient -Nitrogen from the system through denitrification, Methane gas production, fermentation, acetate production, and Hydrogen sulfide production.

None of these types of respiration will create CO2 for the plants, a crucial role the bacteria *should* be providing.

Bacteria exist to break Methane and Hydrogen Sulfide down but like I explained in the OP, H2S requires double the Oxygen and Methane requires more Oxygen per molecule as well.

So, in addition to not providing CO2 for the plants (because they don't have Oxygen themselves to perform O2 respiration) Oxygen is used and "lost" to breakdown Methane and Hyrdogen Sulfide by other bacteria.

Oxygen and CO2 respiration that takes place back and forth occur with a 1:1 ratio. So overall a loss in one is a loss in another in the CAS. And it's frequently said in research papers that I've read that the overall metabolic activity of a closed system like this can be measured by measuring O2 and CO2 relationships.

A system with too much organic matter like I described above creates a positive feedback loop where the O2 <--> CO2 connection seems irreversibly damaged. A system where, due to the quick reproduction of bacteria, they quickly switch to anaerobic respiration and stop producing CO2 for the plants which in turn, cannot provide O2, leaving the bacteria continually deprived and anaerobic. That anaerobic activity then (besides creating many harmful compounds that could by themselves damage the system) causes bacteria to breakdown the harmful compounds created causing the system to "lose" more CO2/O2 respiration potential (by costing more O2 molecules to process 1 molecule of the harmful compound).

If I'm correct, I was wrong to try to include a heavy amount of organic matter in my closed aquatic systems. It seems then that for a more balanced system that perhaps the Dead Organic Matter should be kept rather low and I should plant very heavily, ensuring the Oxygen needs of the bacteria are met. This would keep what looks like a self-destructing negative feedback loop of the break down of the Carbon cycle from occurring.
This is interesting conversation-- but, not coming from a scientific background-- much of it goes over my head because of my lack of base knowledge.
Im curious, however, why are you surprised others responded to your post? Wasn't the post provided to encourage conversation on the topic at hand? Or did I miss something... which is entirely possible...


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post #7 of 7 (permalink) Old 10-20-2019, 11:00 PM Thread Starter
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Originally Posted by Discusluv View Post
This is interesting conversation-- but, not coming from a scientific background-- much of it goes over my head because of my lack of base knowledge.
Im curious, however, why are you surprised others responded to your post? Wasn't the post provided to encourage conversation on the topic at hand? Or did I miss something... which is entirely possible...
Sorry I should have included "after all this time" the post is kind of old that's all.
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