# Deep Substrates, evil or good?



## Hank Junior (Oct 1, 2020)

Am presently experimenting with deep-anaerobic substrates as a plant medium and so far am having positive results and have noticed alot of O2 gas being released from the substrate when the plants are heavily photosynthesising (intense LED lighting + CO2 injection system).

This article link seems to confirm it and is probably the most important aquarium article I have ever read. Highly recommended reading - explains the importance of both aerobic and anearobic bacteria in natural systems and aquaria.

http://www.aquaworldaquarium.com/Articles/TonyGriffitts/AnaerobicBacteria.html

The other day I removed some planted pots from my aquarium and removed the Amazonia substrate and was surprised how organic and horrible it smelled. My aquarium doesn't smell. Except for the little organisms swimming around (lots of things I don't know the names of) - the water looks like you could drink it. I keep plants in small pots in ADA Amazonia soil. I must have a good amount of anaerobic bacteria going on in my tank. Even in a small 5-6 cm deep pot there seems to be enough depth for this beneficial bacteria.

By the way I want to thank "mistergreen" for his comment about CO2 and natural systems - he was 100% correct of course. You never stop learning. The CO2 problem was the opposite to what I thought - natural systems have CO2 in abundance. I see that now.

The other 2 articles help explain the importance of removing nitrates - the point of deep substrates and water changes, though the Walstad method may be an effective nitrate reducer already using plants? Interesting read all round. Now I know what to look for with water changes.

Article 2

http://www.aquaworldaquarium.com/Articles/TonyGriffitts/Water_Changes.htm

Article 3

http://www.aquaworldaquarium.com/Articles/TonyGriffitts/AdverseAffectofNitrateontheAquarium.htm

From reading this forum I understand some people have had bad experiences with too deep substrates - I haven't enough experience to have that yet, and I don't really keep fish - plants only so far in my tanks. Will give it a go and maybe learn the hard way.


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## Daz (Aug 15, 2020)

Hobbyist' articles can be eye-catching and easy to understand, but without proper references to properly planned, executed and published experiments (i.e. papers), they aren't reliable. Most hobbyist' articles you will find around are a bunch of untested hypothesis with weak biological fundaments and based on a bunch of other untested hypothesis formulated by other hobbyists.
There has been some degree of experimentation with deep substrates in marine aquariums and there are a few very very old articles. The method is called "monaco system" or "Jaubert's method" and consists of a thick 10cm layer of >2 mm gravel on top of a 1cm water pocket; basically an undergravel filter without the lift tubes. That system seems to work just fine for salt water, without plants (obviously), without added soil, and with animals that dig and stir the top 5cm of the substrate. 
But, will that work on our tanks?, don't know. First, fresh water tanks with plants, dirt and very little substrate-stirring are obviously very different to reef tanks. Second, Jaubert's method main measure of success was the reduction of nitrates in the water, and that is not something we normally need in a planted tank.


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## Hank Junior (Oct 1, 2020)

Yes fair point Daz. I should explain that my interest in anaerobic (rotten-egg smelling) bacteria is because I am looking for an alternative supply of natural CO2 for plant photosynthesis, both aerobic and anaerobic bacteria.

And my amateur research (experiments) are just as dodgy and possibly unprovable. I find it interesting though that both kinds of bacteria are present in natural systems and are to some extent in all aquariums.

Personally I think that anaerobic bacteria is more important to a healthy aquarium than we probably realise and the lack of this kind of bacteria could explain many problems. My understanding is that the anaerobic bacteria are the ones that do the "heavy-lifting" in dealing with decomposing matter and are widely used in septic tank outflows along with aerobic bacteria - they use both. Tends to suggest that something that smells bad or looks bad isn't necessarily so.


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## Daz (Aug 15, 2020)

Hank Junior said:


> the lack of this kind of bacteria could explain many problems.


A few mm into the substrate and you already got a nice anaerobic environment, according to Ms. Walstad research. Unless you are using an undergravel filter, "lack of anaerobic bacteria" is highly unlikely in a dirted tank.



Hank Junior said:


> My understanding is that the anaerobic bacteria are the ones that do the "heavy-lifting" in dealing with decomposing matter


Actually, no, aerobic decomposition of organic matter is a lot faster and reaches higher levels of decomposition than anaerobic decomposition.


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## mistergreen (Mar 3, 2007)

Sadly, anaerobic bacteria will consume CO2 for energy as well as NO3. They wouldnt supply CO2 to plants. Only aerobic bacteria will. It’s not to say deep substrate can’t work But it might limit the type of plants Like stem plant. Root plants seem to work.

You have to make sure the deep substrate tank is well oxygenated too to oxidize the toxic H2S.


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## Daz (Aug 15, 2020)

mistergreen said:


> Sadly, anaerobic bacteria will consume CO2 for energy as well as NO3.


Bacteria that use NO3, MnO2, Fe(OH)3 and SO4 as electron acceptors actually produce CO2. Once all those other electron acceptors have been depleted, some bacteria use CO2 as electron acceptor and produce methane [doi.org/10.1016/B0-12-348530-4/00178-8, table 2], but then aerobic bacteria in the upper layers can oxidize some of that methane down to CO2.


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## mistergreen (Mar 3, 2007)

Daz said:


> Bacteria that use NO3, MnO2, Fe(OH)3 and SO4 as electron acceptors actually produce CO2. Once all those other electron acceptors have been depleted, some bacteria use CO2 as electron acceptor and produce methane [doi.org/10.1016/B0-12-348530-4/00178-8, table 2], but then aerobic bacteria in the upper layers can oxidize some of that methane down to CO2.


Interesting, so they use CO2 when they have to.

****Update****
Looks like certain species (heterotrophic bacteria) do require CO2.
https://jb.asm.org/content/jb/68/6/749.full.pdf


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## Hank Junior (Oct 1, 2020)

Yes my reading of literature suggests there are different kinds of anaerobic bacteria and some produce CO2 (not sure I am right here?, its a complicated subject it seems).

As part of my quest to find a natural source of CO2 I set up an indoor pond as an experiment. I have taken pond mud from a natural pond near my house with hornwort and fish in it, and put it in a 50L plastic aquarium which gets direct sunlight for 2 hours a day. I have noticed an enormous amount of degassing going on every morning when the water heats from 20 to 25 degrees (its almost our summer here). Originally the temperature swing was 15 degrees C to 25, but I put in a heater to maintain a lower temperature of 20 degrees at the base, there is no water movement. There is no artificial CO2 supply to this planted tank. The rise in tank water temperature is because the tank is an outdoor shed with very little insulationand no heatingor cooling - its effectively an outdoor tank covered from the sun and weather.

The various plants in pots are doing differently. The hornwort, taken from the pond, is photosynthesising intensely as would be expected as it came from the pond. But there are as many bubbles coming from the mud as from the plants (maybe more). The tank everymorning resembles a new tank when you fill it and heat it for the first time - bubbles everywhere on everything. I can only assume that some of the gases are CO2. If they are bad gases the hornwort must be protecting the fish in the pond. 

Sitting at the pond I have noticed that the pond mud there is degassing as well, quite a lot, not just in my tank. The bubbles in my tank continue during the day a bit, but not as much, there is no artificial lighting.I assume this is the result of organic decomposition within the smelly mud.

The Ambulia is struggling and going brown - not sure if it was temperature or the hornwort chemically attacking it? Its the reason I put a heater in. The Cryptocoryne developed black spots but now seems to be recovering with new leaves coming up. The tank water is river water (GH 10, KH 7, PH 8. Actually the water in the tank looks better than parts of the river as in places the river does not look good, even though its the same water. The tank water after 2 months has not turned green - I can only assume that is because of the plants in it.

I know hornwort is a tough plant and the other plants are not pearling, but the hornwort is pearling almost constantly under sunlight. It looks just like ambulia does in my other tank when it was having CO2 injection. The hornwort is rooted and in pots and only just reaching the surface - I don't want any floating plants in the tank nor floating hornwort. In the wild it tends to float but is rooted at one end. The smaller hornwort pots (not reaching the surface) are pearling as much as the taller ones so it is not CO2 in the air they are accessing (the fully submerged ones). All plants in the tank are fully submerged except one particular hornwort pot which has grown now to the surface. Probably about 10 different species of plants, some carpet varieties which so far are not dying but don't seem to be prospering - they are surviving I would say but its early days, too early to say. They also tend to have light grey dusting of mud on their leaves which makes them appear paler than they might actually be.

The plant pots with mud vary from 5cm to 10 cm, but the tiny bubbles of gas that appear on the mud surface seem much more in the wider 5 cm deep pots as they are a wider surface area. Mud depth doesn't seem to matter.

As an experiment I may create a kind of 'Winogradsky Column' in a deep clear pot, but in another tank as that may be too aggressive for my main planted pond-tank which I intend to put fish in.

The water is very clear both in the natural pond and in my set up. The fine mud particles settle after a few days after initial set up. The mud is a grey colour which I assume has a very high clay content. I can't feel any sand in it at all.

I have measured the original natural pond water temperature variation (measured close to the surface which means it will be cooler down lower, pond depth is I estimate about 2-3m at its deepest point in the center), of 16 degrees C (early am) to 25-26 degrees (late afternoon). This pond gets constant sunlight no shade at all. The temperature swing is about the same as my pond-tank setup (15-25 deg C without heating) which suggests to me that outdoor fish can handle temperature swings quite well. I have heard that fish in the wild can handle temperatures of 10-30 deg C, but what I didn't realise is that I suspect they can handle this in one day! We routinely get summer air temperatures of lower 40s so it will be interesting to observe this pond this summer. Summer hasn't started yet and we are already in the lower 30s most days.


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## Daz (Aug 15, 2020)

mistergreen said:


> Interesting, so they use CO2 when they have to.
> 
> ****Update****
> Looks like certain species (heterotrophic bacteria) do require CO2.
> https://jb.asm.org/content/jb/68/6/749.full.pdf


Yes, there is a good variety of bacteria that fixate CO2, some heterotrophic and anaerobic [10.1093/femsec/fiy163]. I still doubt that having a deeper substrate would result in less total CO2 produced by the soil with anaerobic CO2 fixation as the culprit.

Yes Hank, soil is a natural source of CO2, as Diana explained in her book and as we talked about in a previous thread. The main source of CO2 in water bodies in nature is CO2 produced in the soils that are in and surrounding the stream.


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## Hank Junior (Oct 1, 2020)

By the way to illustrate the high 'organic load' in the pond mud I am using, it is not uncommon for wild animals inc. pigs and birds and whole cows to die in our farm dams, which gives you an idea of the amount of organics. I used to think that a dead cow was polluting our dams, now I am starting to see it differently. Its a bonanza for the bacteria! and other micro-organisms. However it must be said that after a cow or large pig has died in a dam I won't be drinking the water! Nature has an amazing ability to recycle.


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## dwalstad (Apr 14, 2006)

Daz said:


> Yes, there is a good variety of bacteria that fixate CO2, some heterotrophic and anaerobic [10.1093/femsec/fiy163]. I still doubt that having a deeper substrate would result in less total CO2 produced by the soil with anaerobic CO2 fixation as the culprit.
> 
> The main source of CO2 in water bodies in nature is CO2 produced in the soils that are in and surrounding the stream.


In natural water bodies, tree leaves, algae, and plant debris also contribute CO2 as they decompose.

Bacterial fixation of CO2 is done by chemoautotrophic bacteria, which includes nitrifying bacteria. The vast majority of bacteria, though, are heterotrophic, the ordinary decomposers that generate CO2. CO2 fixation by chemoautotrophic bacteria is not a major force in reducing CO2 levels.

A deep substrate generates no CO2, because it is severely anaerobic, not because bacteria are fixing CO2. Nitrifying bacteria do fix CO2, but at the same time they require oxygen to generate energy (via oxidation of ammonia and/or nitrites). Thus, there is not much CO2 fixation in a severely anaerobic substrate. The _efficient_ generation of CO2 requires oxygen.

Deep soil layers, especially if they are organic, mainly generate toxins--H2S, aluminum, fermentative acids, etc. The basic problem is that there is not enough oxygen and other efficient electron acceptors (e.g., nitrates).


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## Hank Junior (Oct 1, 2020)

Great reply thanks Diana, still only on chapter 2 of your book, chemical warfare by plants.

I should say that animals using (and dying sometimes) in farm dams and 'livestock', especially cattle, can damage dams greatly. On our place the only two dams in good condition are the ones with only wild animals using them. A dead cow or sheep is probably too big a bioload for most dams. I have noticed a great deterioration in water quality from our dams used by cattle especially if an a large animal dies in the water - only algae seems to grow in the water and the turbidity is major - the water is clay brown basically. Where we have water plants, duckweed, rushes, swamp lillies etc...the water is clear though sometimes a bit brown, tea-like, not mud like. Our livestock dams in contrast are bare clay brown dirt with green-brown water. Its the main reason we tend to use water troughs for the animals rather than ground tanks (dams) - better water quality.

Will keep your thoughts on deep substrates to mind. The gas bubbles I get from pond mud does puzzle me - its gas, probably methane-like. The degassing of the mud in the pond did surprise me and now I have it in an aquarium I can see it close up.


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## mistergreen (Mar 3, 2007)

Rotten egg smell is H2S, Hydrogen sulfide. CO2 has no smell.


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## Hank Junior (Oct 1, 2020)

Yes thanks that is the hardest. Trying to work out what gases they are.


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## tiger15 (Apr 9, 2017)

Degassing from substrate is fairly common if it is disturbed, specially in deep substrate, under rock or drift wood where oxygenation cannot reach.

Off gas is most likely nitrogen, which has no smell, nearly insoluble, and is produced by denitrification of nitrate in anaerobic conditions. In farming, loss of nitrogen to denitrification in poor drained soil is a concern.

A second possibility is methane, which is also odorless, nearly insoluble, and is produced by anaerobic decay of organic matter such as plant debris. But more often than not, you may detect slight rotten egg odor as H2S and methane are often co generated.


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## nickandjess2008 (Sep 16, 2020)

While I will not pretend to know anything about the science of why it works, I have a 20 gallon that has 5-6 inches of substrate and it works just fine. When I do disturb the substrate, it releases bubbles, they don't smell like eggs or anything like that and they don't seem to bother anyone, so, it works for me! I do have a heavy load of fish in it and a pretty high plant count in there, too. Good luck with it, OP!
Also, sometimes the bubbles just pop out on their own, there ends up being a lot of gas in the substrate, which I always thought was terrible for everyone in that tank, but, no one seems to care, or notice for that matter!
I am an older fish keeper. 30+ years! When I was first introduced into the hobby, it was "common knowledge" that you needed both anaerobic and aerobic bacteria and others in the substrate. When I recently looked into it, it seems that the "common knowledge" of today is that you shouldn't have deep substrates. Idk when it changed, but, it was news to me. It seems these things go in cycles, first popular, then not, then back to popular. At least, that is what I have noticed in this hobby. Just like in fashion, things go in and out of style. 
There is a lot of "mulm", I think that is what people call it, but, the mulm seems to reach a point where it stays in a perpetual state. No more comes in and none disappears. I vacuum the top of it, but, I don't go down too far, I don't want to disturb the bottom layer, I just want it to do it's thing and it seems to work for me. I can give you an idea of what my layers are and here it is, from bottom to top:
3 inches of regular aquarium gravel, nothing special
1 inch of sand on that
1 inch of laterite on that
1 inch of shrimp stratum on top of that
There is about 5.5 inches total, roughly, some spots are higher than others. Left to right, though, it is 5" on the left and 5.5" on the right. Hope that helps!
What I can say is that the regular gravel was first, then I added the sand for the cory's. Then the laterite, then the stratum, that Fluval shrimp stratum. I have a huge cryptocoryne wendtii in there from the beginning and she loves it in there! Yes, it is a girl, j/k. The crypts love it in there for whatever reason, they do well. Idk if the substrate has anything to do with it, the point being that they were added slowly over many years, not just throw in at the beginning. This tank is easily 10-15 years old. The crypt that I just mentioned was the first and only for a long time! Like 10-14 years and earlier this year I started to add new plants and fertilize and add Co2 and it just took off! I prune a LOT!
I guess that the main take-away is that I have a lot of substrate compared to the average tank that I see and it works for me and I hope it works for the OP and I hope everyone does really well with their individual tanks! Good luck everyone! 
Here is a pic, but, I am SO sorry, I don't know why it won't show it correct side up, I will work on it......I am sorry, again, it just won't work right. I had this problem on another forum site, too and I just can't figure it out, hopefully, it is enough to illustrate my point that it is a lot of substrate.
Edit: To answer the original question by the OP, I think deep substrates are good and NOT evil.


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## jatcar95 (Oct 30, 2019)

I wonder if part of the reason it has worked for you is the lack of organic soil under the substrate. I think the reason dirt tends to go severely anaerobic (to the point of killing plants) is largely due to it being very rich and decomposing more than an inert substrate like gravel. Since your nutrient substrate is on top, it's still getting more oxygen than someone who buries their soil under inches of gravel.


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## tiger15 (Apr 9, 2017)

There have been many discussions in fish forums on adopting deep sand system as used in saltwater, but it has not gotten traction in freshwater. Saltwater has more diverse fauna in live deep sand to carry out denitrification more efficiently than in freshwater. Making artificial saltwater is expensive and tedious, so saltwater folks employ every biochemical filtration option available to minimize WC. Freshwater is cheap and the easiest way to achieve nitrate reduction is do water change or to grow plants. 

Having deep sand in freshwater has minimal benefit as denitrification is too low to worth the effort. Nevertheless, denitrification kits are sold by a few vendors as snake oil.

I am a long time cichlid keeper and recent aquascaper. I have always maintained very thin substrate barely to cover the bottom as the aerobic zone is no deeper than 1/2 inch, so more depth is not needed. My cichlid will dig and having deep sand risk getting stirred up to release toxic gases. I keep mostly epiphytes attached to rock and potted plants, so I don't need thick substrate to root plants. Moreover, having deep substrate reduces the volume available for my fish and plants.


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## mistergreen (Mar 3, 2007)

tiger15 said:


> There have been many discussions in fish forums on adopting deep sand system as used in saltwater, but it has not gotten traction in freshwater. Saltwater has more diverse fauna in live deep sand to carry out denitrification more efficiently than in freshwater. Making artificial saltwater is expensive and tedious, so saltwater folks employ every biochemical filtration option available to minimize WC. Freshwater is cheap and the easiest way to achieve nitrate reduction is do water change or to grow plants.


I've always wanted to make a small low maintenance sw tank. They have their version of plants in macro algae.


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