# Smelly Substrates



## dwalstad (Apr 14, 2006)

I just received this question from a hobbyist:

_I am fascinated with your book! I have my own aquarium set up now with soil and plants are thriving. I do have one thing that's kept me up at night though regarding your method. Amongst the people and research I have done I notice a lot of people mentioning the substrate getting smelly in about 6 months, on the other hand you mention in your book a tank you had for 5 years with a soil substrate. My question is this, why do some experience this and others not, and what is your experience this issue? Thanks for your time and response!
_

I have had soil tanks set up for many years and have never had this problem. Usually, new substrates may be challenging the first 6-8 weeks, but your question opens up a whole new avenue.

Substrates that smell mean they've gone anaerobic. Not good. It can become a downward spiral, because severely anaerobic conditions can kill plant roots. Then, decomposing roots make the substrate even more anaerobic, kill more plant roots, etc.

I'm going to envision one scenario where this could happen. After tank setup, the soil is giving off plentiful CO2 and the plants are growing great. Over time and often right around 6-12 months, the soil settles down and gives off less CO2. If the plants are poor growers (e.g., many popular aquascaping plants and stem plants) that need lots of CO2, they'll stop growing such that they cannot keep their root area oxygenated. They die and substrate becomes more and more anaerobic.

Solution: Plant good growing plants with vigorous root systems-Sagittaria, Swordplants, Cryptocoryne, Tiger Lotus, Vallisneria, etc

Another scenario: Substrate is covered with driftwood, too much gravel/mulm/sand, etc creating dead zones that gradually become severely anaerobic.

Solution: Remove some of the gravel. Poke the substrate with a pencil. Don't place driftwood on top of a soil layer.

The problem is all about keeping the substrate from going anaerobic. The good news is that it is something that can be either prevented or fixed. Hobbyists that don't appreciate or understand submerged soil chemistry and its interplay with aquatic plants, may indeed, have the problems you describe.

Please reread my book's chapter on Substrates. Thank you for sending such a challenging question.


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## mistergreen (Mar 3, 2007)

The smelly gas produced is hydrogen sulfide which can be toxic to fish as well.

Removing large bits of organics like twigs and bark from the soil may help. Having burrowing snails like Malaysian trumpet snails may help as well. They can move the soil above the capping substrate over time though.


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## mysiak (Jan 17, 2018)

I'm wondering - how do you notice smelly substrate? I do not uproot plants and don't dig into the substrate. The most disruptive action is adding root fertilizer sticks every couple of months and very occasional rooting of new plants, both done with thin tweezers. I do not see any black residue on tweezers nor smell anything unusual. 

Should we be actively looking for and try preventing anaerobic conditions? I'm usually sticking to the rule "if it ain't broke, don't fix it", but "better be safe than sorry" makes sense too


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## zolteeC (Dec 26, 2017)

mysiak said:


> I'm wondering - how do you notice smelly substrate? I do not uproot plants and don't dig into the substrate. The most disruptive action is adding root fertilizer sticks every couple of months and very occasional rooting of new plants, both done with thin tweezers. I do not see any black residue on tweezers nor smell anything unusual.
> 
> Should we be actively looking for and try preventing anaerobic conditions? I'm usually sticking to the rule "if it ain't broke, don't fix it", but "better be safe than sorry" makes sense too


Once I had an NPT where I used several larger rocks for the 'scape. I put soil everywhere (approx 2-3 cm) even under the stones. The tank did fine, and never did have a smell.

However, when I took the tank apart and I was removing the larger rocks I could definitely smell H2S. It really does stink. So probably avoiding dirt under larger rocks is a good idea.

Maybe some of the H2S gets also oxidized already in the substrate before it could reach the water column / air...


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## Michael (Jul 20, 2010)

When I use large stones or drift wood in my tanks, I "bed" them in pure gravel, or make a base from tile or flagstone for them to sit on. The base is covered by a thin layer of cap when the tank is finished.


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## dwalstad (Apr 14, 2006)

Excellent advice!

There are "good bacteria" that oxidize H2S (my book pp. 67, 153). However, if you've got numerous dead zones in the substrate that are pouring out H2S, these H2S-oxidizing bacteria may not be able to counteract the problem.


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## Gerald (Mar 24, 2008)

Could the hobbyist's fish load also be a factor? They don't mention fish, but maybe there's more biochemical oxygen demand (BOD loading) from fish poop and decaying food than the plants can offset (pumping O2 to their roots). I agree that vigorous-rooting plants are best for preventing anaerobic soil and H2s production.


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## dwalstad (Apr 14, 2006)

Gerald said:


> Could the hobbyist's fish load also be a factor?


Yes. A substrate covered with an inch of fish mulm is tempting fate--and it is not a good one!

Back to new setup with gassy substrate... Another reason to poke the substrate and release gas is to compress the substrate. Barko and Smart* explain that organic substrates have a low density that increases the distance between substrate nutrients and plant roots. When the investigators compressed an organic substrate (using a centrifuge), Hydrilla plants grew significantly better than in the same substrate that wasn't compressed.

So if you've got an "fluffy" organic substrate loaded with gas, roots will have trouble getting nutrients. By poking the substrate, you will compress the substrate and make it a bit easier for plants to get substrate nutrients.

Thus, you get two benefits from poking a gassy substrate.

For poking, I would advise using a very thin object so that you don't injure plant roots. A metal paper clip opened up should work fine.

*Reference: Barko JW and Smart RM. 1986. Sediment-related mechanisms of growth limitation in submersed macrophytes. _Ecology_ 67: 1328-1340.


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## hoppycalif (Apr 7, 2005)

And, with that, we now have the 541st alternative use for paper clips!!


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## mysiak (Jan 17, 2018)

Very interesting information about the substrate compaction. This might explain why I see very strong roots growth in the cap, but only very few roots reaching into the soil area which is "fluffy" by sight (naturally released gas bubbles are either completely without any smell, or with faint smell of sulfur). Interestingly enough, plants are growing like crazy anyway, so nutrients must be reaching plants. Or is it just that plants do not "need" to use longer roots if they have enough nutrients in the top layer of the substrate? In each case, I will try to release bubbles from one area in the tank and observe the reaction of plants to it.


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## Dude (Nov 14, 2018)

Huh, I would have thought a compacted substrate would be more likely to lead to anaerobic conditions due to it being more stagnant. I wonder how this relates to the 1-1.5" depth recommendation for soil substrates. Surely an inch and a half of densely packed dirt would have a different outcome from a loose inch and a half.


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## dwalstad (Apr 14, 2006)

mysiak said:


> Very interesting information about the substrate compaction. This might explain why I see very strong roots growth in the cap, but only very few roots reaching into the soil area which is "fluffy" by sight (naturally released gas bubbles are either completely without any smell, or with faint smell of sulfur). Interestingly enough, plants are growing like crazy anyway, so nutrients must be reaching plants. Or is it just that plants do not "need" to use longer roots if they have enough nutrients in the top layer of the substrate? In each case, I will try to release bubbles from one area in the tank and observe the reaction of plants to it.


I will be interested to hear your results. If roots aren't going to the bottom, it's probably that faint smell of H2S. The roots stay up in the more aerobic upper layer where it's "safe".

In my well-established (1-9 years) tanks, roots go down to the bottom glass.

In your tank with its robust, established, and copious plant growth, I suspect that upwelling nutrients and CO2 more than make up for an anaerobic bottom layer. The plants stay safe and still get the nutrients they need to thrive.

One cannot help but admire plant adaptation and accommodation.


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## dwalstad (Apr 14, 2006)

Dude said:


> Surely an inch and a half of densely packed dirt would have a different outcome from a loose inch and a half.


Yes, for sure. But organic soils are not only fluffy and loose, but filled with organic matter (~50%) that bacteria feed on. In a new tank setup, the organic matter is fresh and the bacteria go wild, consuming all oxygen and other respiratory compounds (e.g., electron acceptors like nitrates, sulfates, carbohydrates, etc). Lots of gas generated, much of it CO2. After a few months, the soil settles down as all the "fast food" is used up.

A mineral soil is mostly inert. It has just a small amount of organic matter (~5%), so it is much less likely to go anaerobic.

So in a new tank setup, 1.5 inches of a mineral soil, tightly packed and dense, would never go as anaerobic as 1.5 inches of fresh, fluffy potting soil.

By poking the soil, you introduce oxygenated water into the substrate. It alleviates the severely anaerobic conditions that generate H2S and the organic acids of fermentation. It compresses the soil particles bringing nutrients in closer contact to plant roots. It releases inhibitory compounds (organic acids) and toxic gases (H2S) from the substrate.

Some hobbyists "mineralize" a new organic soil and allow it to decompose in a bucket for a few weeks before putting it in the tank. It's another solution for the same problem. I let the soil mineralize in the tank, but help it along--if there are problems--with poking, water changes, etc.

With many of my new tank setup, I had no problems. Plants took off within days. But if you see signs of plant die-back in a tank with a fresh organic soil that has started bubbling, then I would consider timely counter-measures.

I hope this makes sense. (My book _Ecology of the Planted Aquarium_ has an entire chapter on submerged soil chemistry.)


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## mysiak (Jan 17, 2018)

dwalstad said:


> I will be interested to hear your results. If roots aren't going to the bottom, it's probably that faint smell of H2S. The roots stay up in the more aerobic upper layer where it's "safe".
> 
> In my well-established (1-9 years) tanks, roots go down to the bottom glass.
> 
> ...


In my bigger tank, cryptocorynes have roots up to the bottom, I'm not very concerned about substrate going too anaerobic - at least in parts with rooted plants. Situation might be different in the back, where I have mainly stem plants floating above the substrate with hardly any roots going into the substrate. Although when I poked in there, no bubbles came out, so I assume that situation is under control.

In my small tank, I can clearly see that only a very few roots are reaching the bottom. I poked the substrate close to the glass gently yesterday and about half of the bubbles were odorless (nitrogen? CO2? ..), the other half had a very faint H2S smell. As far as I know, H2S gas is extremely smelly, so I suppose that I have a very little concentration of it in the substrate. Nevertheless, I will continue to release these bubbles every few days mainly to see the impact on plants and their roots.


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## Dude (Nov 14, 2018)

dwalstad said:


> I hope this makes sense. (My book _Ecology of the Planted Aquarium_ has an entire chapter on submerged soil chemistry.)


 It does.

So for a soil with a high amount of organic material like mine, I need to be more vigilant about preventing/alleviating anaerobic conditions. I did some poking the other day as you suggested and quite a lot of bubbles were released all across the tank. Mostly near plants that were struggling. I'll try to do it regularly until no more bubbles come out and then less often afterwards just in case.


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## dwalstad (Apr 14, 2006)

This all sounds good. I will be interested if Dude's plants respond. (I'm thinking I might need to add a Q&A to next printing of my book on this poking business.)

Mysiak, plant growth in your tanks is so exuberant that I don't see how you could ever tell one way or the other.


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## Bwooster (Apr 4, 2018)

Hello everyone,

Thank you for this interesting thread. I lately saw on the internet that some people mix their soil with aquarium gravel, or sand, when doing "El natural" set-ups. It made me wonder if this might help prevent or alleviate anaerobic conditions in the substrate, since the organic, fine-grained particles would have a lesser tendency to "clump".

What do you think?

Enviado desde mi Lenovo P2a42 mediante Tapatalk


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## Michael (Jul 20, 2010)

When I use highly organic soil I mix it 50/50 with the cap material, usually Safe-T-Sorb or something similar. It was a valuable tip from an experienced aquarist when I was first starting. I've never had problems with anaerobic substrate when the soil is prepared in this way. If you are using a natural top soil you probably don't need to do this because natural soils are rarely more than 5%-10% organic matter.


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