# Anaerobic soil?



## boopsie (Apr 22, 2013)

I think I might have anaerobic soil. All my plants are getting squishy and rotting away, and my water is all cloudy. I have three MTS in the tank, so I didn't bother to poke the soil. What do I do? Do I have to remove the dirt and start fresh?


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## RiceFish (Feb 9, 2013)

try poking the sand a bit and see if that solves the problem with anaerobic soil. There are many reasons why plants couldn't be thriving lighting, fertilizer, etc. What are you using for lighting?


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## Gallium (May 14, 2013)

Poke the soil with a chopstick or knife. If bubbles come out of it, you have a buildup of toxic gas. I don't normally associate cloudy water with anaerobic bacteria, it's usually just the bubbly substrate that confirms their presence.


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## boopsie (Apr 22, 2013)

I poked the soil in a few places and lots of bubbles came out. If I just poke it all over will that solve the problem? 

I have a zoomed 6500K bulb for lighting. My plants were doing fine for a while, it's just suddenly going down hill. Also, there's some sort of film forming on top of the water. I'm at a loss.


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## Gallium (May 14, 2013)

Do NOT poke all over! The gas in those bubbles is VERY toxic and diffuses into the water quickly. It can kill fish in a matter of hours.

I would remove the fish, invertebrates, etc you have into a clean tub of water, drain the tank, and remove the dirt. You don't have a balance at the moment, and at this point you can't really fix it without tearing the tank apart and starting over. If you want to use dirt, you should mineralize it before use. I also suggest mixing it half and half with sand, clay chips, and fine gravel before you cap it to reduce the chance of anaerobic pockets forming.

Edit;

If you have a betta in that tank you need to remove it asap. The scum forming on the surface will coat the betta's labyrinth organ and possibly kill it.


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## boopsie (Apr 22, 2013)

I've moved my fish etc. into the hospital tank with clean water. I'm so glad I saw your post before I went and did something stupid. :shock: I'm in the process of cleaning out the planted tank. I'm very discouraged over this, but I'd like to give it another go. How do I mineralize the soil?


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## Gallium (May 14, 2013)

For now, you can poke the soil up as much as possible and then change the water completely, but you'll build up the gas pockets again fiarly quickly so your best bet is to restart the substrate. Just be sure to keep your filter running on the tank with your fish in it so you don't have to re-cycle.

Sorry, links to other goes are not allowed.
~Redchigh


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## boopsie (Apr 22, 2013)

Thank you for the information. I have no idea where to go to get dolomite or muriate of potash, though. Does this method work better than just dirt and cap plus poking the soil frequently?


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## Gallium (May 14, 2013)

Usually, yes. The base idea behind mineralized soil is that it mimics the processes found in nature, thus eliminating the need for water column dosing. A properly mineralized soil tank setup will have it's own carbon, iron, and sulfur cycle. Anaerobic bacteria are necessary for a healthy tank, and they are natural, but not in the numbers or concentration that causes the bubbles to form. 

If the post above is too hard to follow, you can basically just use pure humus, which is available by the bag for pretty cheap. To set up a true NPT that actually mimics natural biological processes you need to use other elements than only dirt, since just the dirt alone won't be able to provide the cycles needed and usually hosts too much bacteria and compacts too easily. If dirt must be used it should really be a low nutrient, or a high nutrient (of the proper proportions) mixed with clays or inert substrates. 

Alternatively you can place dirt in a bucket or several buckets of water (for larger amounts of dirt) and frequently stir up the dirt. Twice a week dump out the buckets (but retain the dirt) and refill it. Continue for a minimum of 5 weeks. It will speed up a little if there is some water current so adding an airstone to the bucket will help a lot. You'll get compaction and anaerobic bacteria even after doing this, but the number will be reduced. Adding sand to the bucket will help host bacteria that break down the soil further to lessen the buildup of anaerobic bacteria. After you add the soil to the tank, add MTS right away so they can begin burrowing. You'll want at least one or two per gallon of tank in order to keep the substrate aerated enough. 

This is a simplified method and it does work in most cases, the things you really cannot skip on is adding the snails right away in decent numbers. Adding too few snails will allow some parts of the soil to compact quickly leading to the pockets of bacteria.


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## boopsie (Apr 22, 2013)

I see...that makes sense. I think that's what I'll do, then. Do you know where I can buy the dolomite and muriate of potash? And will any old pottery clay from the craft store do?


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## redchigh (Jan 20, 2010)

I've used oil-dri, a clay absorbant sold in Walmart automotive as an additive. Its a pure clay product that I've also used as a cap before.


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## boopsie (Apr 22, 2013)

I'm having the worst time trying to find dolomite and can only find muriate of potash in giant bags. Can anyone point me in the right direction?


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## RiceFish (Feb 9, 2013)

Try looking in an arts and crafts store like Michaels or a store that specializes in pottery


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## VJM (Feb 7, 2013)

I hear a lot about "toxic substrate gas can kill your fish", but I have never seen anyone post that this has actually happened. Does anyone have any legit source to prove this point? 

My substrate gets pockets wherever there aren't roots. I poke, bubbles come out, fish are 100% fine.


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## Nicci Lu (Jan 7, 2013)

Bubbles are pretty normal in Walstad tanks- it's just normal decomposition. It's when they smell like sulfur that they are anaerobic- this is more uncommon. boopsie, if your soil had anaerobic pockets you would have been smacked in the face by rotten egg odor when the bubbles came out. Just keep poking the soil once a week, and you'll be fine.

VJM, I have only seen maybe one or two people say they've actually had anaerobic pockets, so I suppose it can happen. But I am beginning to suspect that this threat has been rather exaggerated. The pink Christina Aguilera monsters of the aquarium hobby.

I still poke my substrate, though, even with my MTS.


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## Nicci Lu (Jan 7, 2013)

One of my tanks has flourite mixed with the soil, and the other has plain Hartz pH 7 clay kitty litter (non-clumping, non-scented) in the soil. But, as far as I know, the purpose of these (or any clay mixed with soil) is to provide CEC (cation exchange capacity). The clay is able to store the nutrients that are being released by the decomposing soil, thereby keeping those nutrients within the soil and available to plant roots. As a bonus, the CEC of clay keeps those nutrients from being released into the water column.

EDIT: Even with these additions, I still get bubbles. But not the _bad_ bubbles.

EDIT #2: Not sure if Gallium mentioned this, but a good rule to follow to avoid the formation of anaerobic pockets is to make sure that the soil layer is only 1-1 1/2 inches deep. Too deep substrate is said to be a cause of anaerobic pockets.

I'm wondering how clay or an inert substance like sand would help avoid anaerobic pockets?


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## Stone (Jan 6, 2013)

the bubble that come out are nitrogen gas, that has been fixed by nitrogen fixing bacteria, which is a process that's anaerobic, nitogrn gas is toxic even to us mamals unless it has been "fixed" by the nitrogen fixing bacteria, I have not checked in a few years to see if they have solved this "fixing" process, it was an unknown


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## Stone (Jan 6, 2013)

@Nicci you can not avoid nature look up nitrogen fixing bacteria it will explain the process, it is basically how things are broken down so plants can use them, ammonia nitrites and so on, it's kind of the nitrogen cycle that happens in soil/dirt if you sit on the shore of a lake/pond/swamp toy will see bubbles coming up from the soil, it's just a part of nature


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## Nicci Lu (Jan 7, 2013)

@Stone- Um, I think possibly you misunderstood me? I don't mind the bubbles at all, at least not the ones that come from normal decomposition, or bacterial denitrogenation if you will.  These bubbles are the ones that release nitrogen.

Actually, anaerobic pockets release hydrogen sulfide, not nitrogen. This is what is toxic to fish, and why it smells like sulfur. There is always some anaerobic activity occurring in the soil, but a buildup of anaerobic decay in a pocket where it gets trapped results in an accumulation of hydrogen sulfide. Usually plant roots are enough to supply oxygen to the soil- anaerobic bacteria can only live in oxygen depleted areas, and so where there is oxygen there are no anaerobic pockets. This is why a substrate that is too deep can cause this problem.


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## VJM (Feb 7, 2013)

Well, my tanks all have bubbles that smell like sulfur. I poke and release them. All fish are absolutely fine. 

If anyone can point me to any first hand info, anywhere, that indicates this has ever been responsible for a fish death, I would love to check it out.


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## Stone (Jan 6, 2013)

@VJM you will not find any, just like you won't find anything about bettafix killing bettas. lots of myths and legends floating around the net


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## itsme (Jun 4, 2013)

I have been worried about anaerobic soil since I set my NPT 10 gallon tank up on May 3,2013. The picture is about 2 weeks ago and I have got more plant growth since then. I have had one baby betta in there since 5/3/13 and 3 turbo snails and 2 RCS and 2 ghost shrimp. In the beginning I poked the soil twice a day and then after a month I stopped doing that since plants were growing and thought it wouldn't be needed anymore. Last week I started seeing the big bubbles coming out of the soil in different areas of the tank but it does not seem to be affecting anything and not really smelling anything. I do 40 % water changes once or twice a week. I do still have tannins in the water, but my worry is that somehow the sand and dirt now seem to have shifted where there is a lot in the front and less in the back. I do see pockets in the deep part of the soil. I started with 2 inches of organic potting soil and 1 inch of play sand. That front part is what I am worried about but I do not see bubbles coming from that area. Is that a concern for the anaerobic soil? If I poke it now I would worry it would be anaerobic. Sorry if this is too long but I am new to all of this and I worry a lot.


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## Nicci Lu (Jan 7, 2013)

Well, VJM and Stone, you guys have inspired me to do some research on this mystery. Not from aquarium hobby sites, where myths do abound, but from scholarly articles, and, er, Wikipedia (because we all know that Wikipedia is never wrong, right? ;-)). My faculty with scientific language is rather poor, however, so you might to do some digging on your own.

First off, hydrogen sulfide is toxic to fish. Perhaps this was never in question, but it's a good place to start. "Hydrogen sulfide inhibits oxidative phosphorylation by blocking the reoxydation of reduced cytochrome by molecular oxygen. The overall result is inhibition of energy metabolism by cells, similar to the effect of hypoxia.... Fish exposed to acutely lethal levels of hydrogen sulfide exhibit increased ventilation rates, followed by rapid cessation of ventilation, then death."

*Actual data*
-Egg survival and fry development of northern pike limited by exposure to as little as .006 mg/L hydrogen sulfide (henceforth abbreviated as h-s because I'm lazy).
-Acute toxicity in bluegill eggs after 72 hours at .019 mg/L.
-Acute toxicity in bluegill fry after 96 hours at .013 mg/L.
-Acute toxicity in juvenile bluegill after 96 hours at .048 mg/L.
-Acute toxicity in adult bluegill after 96 hours at .045 mg/L.
-Chronic exposure to .002 mg/L for 826 days did not cause mortality in bluegill.
-Growth of adult bluegill retarded by exposure to .011 mg/L.
-Acute toxicity in channel catfish after 3 hours occurred with 1.4 mg/L exposure.
-Acute toxicity in channel catfish fingerlings after 3 hours occurred with 1.0 mg/L exposure.
-High concentrations of h-s responsible for poor growth in channel catfish in acidic waters. (_What is a 'high concentration'? I don't know..._)
-The EPA "suggests a maximum [h-s] concentration of .002 mg...for fish and other aquatic life."

*How is it produced
*The production of hydrogen sulfide is part of the sulfur cycle. Anaerobic bacteria (bacteria that requires the absence of oxygen) decomposes organic sulfur, using it for energy. This process creates hydrogen sulfide as a waste product. Organic sulfur comes from animal/fish and plant residue. High rates of microbial activity lead to anaerobic conditions within mud.

*The Big Question
*So, what we really want to know is how much hydrogen sulfide is typically created in a closed environment (i.e., our home aquariums) and whether this amount is enough to cause toxic conditions in our fish. I'm not sure. Most scholarly studies and literature focus on ponds and lakes. If anyone knows of a _scholarly_ study that addresses hydrogen sulfide in home aquaria, I would love to see it. However, I have come across these facts. Check them out and decide for yourself.

-Photosynthetic bacteria can oxidize h-s to sulfur and sulfate in the presence of light and the absence of oxygen.
-H-s is oxidized by oxygen, creating first sulfur dioxide and then sulfate. This may occur readily in surface waters. Both waste products are "eventually" _(wish I knew how long "eventually" was) _removed through absorption by plants and soil.
-Hydrogen sulfide is readily soluble in water.
-In water, h-s is a weak acid yielding bisulfide ions and sulfide ions. At a pH of 7, the ratio of bisulfide ions to sulfide ions is 1:1. As pH increases, the ratio of bisulfide ions to liquid hydrogen sulfide increases. Only above pH 12 will the sulfide ions be at a 50% concentration.
-Several species of soil, aquatic and marine microorganisms oxidize h-s to elemental sulfur.
-*"Because it is a gas under ambient conditions, bioconcentration and food chain biomagnification are unlikely to occur."* _(This might be different in a closed environment?)_

It would appear that there are conditions in our home aquaria that encourage the oxidization of h-s. But what would happen if a fish were directly hit by one of these bubbles before it has become soluble and/or oxidized?

*Sources
*Boyd, Claude E. _Pond Aquaculture Water Quality Management_. Norwell, Massachusetts: Kluwer Academic Publishers, 1998. 145-147.
_Toxicological Profile for Hydrogen Sulfide_. Washington DC: Agency for Toxic Substances and Disease Registry, nd. 115-118.
"Hydrogen Sulfide." Wikipedia.


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## Nicci Lu (Jan 7, 2013)

itsme- The depth of your soil from the picture is somewhat of a concern. It looks rather deep to me. Also, I'm not sure that you have enough plant coverage for an NPT. If you look down from the top, you should only be seeing 20% max of your substrate.

That being said, bubbles are normal and if you aren't smelling sulfur, you should be okay. Keep poking- just make sure that there is no livestock above the area where you're poking, in case you do release an anaerobic pocket. Better to release them than to let them be, if they do exist. If your water params are okay and you're not smelling sulfur, then I don't think you have to consider a tear down. Just keep a close eye on things. Sometimes, I use the flat of my hand to press down on the substrate- you can release a lot of bubbles that way.


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## itsme (Jun 4, 2013)

Thank you for the reply. This is how my tank looked the first day, coudy, but the soil and sand were even,









This a picture I took today









I just got some big bubbles come out of this thick area in front a few minutes ago.


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## itsme (Jun 4, 2013)

I was also reading about it and found this article:
Anaerobic decay can result in the accumulation of a gas called hydrogen sulphide (H2S). In theory, because this gas is toxic to fish, any bubbles of H2S can harm or kill your fish. However, in practise H2S oxidises very rapidly, and once it is in contact with oxygenated water the H2S gets converted to plain old sulphur (or as the Americans spell it, sulfur). This reaction is so fast that it is for all practical purposes instant, so small amounts of H2S will be rendered harmless long before the concentration in the water reaches dangerous levels. Marine aquarists have learned to embrace anaerobic decay, and routinely set up filters (e.g., deep sand beds and mounds of living rock) that perform anaerobic decay. I also have yet to see a pond that *didn't* have masses of anaerobic decay going on in the thick, gooey mud at the bottom of the pond. But for whatever reason, freshwater aquarists are still skeptical. So let's put things into perspective. Anaerobic (or at least dysaerobic) conditions are normal in muddy freshwater substrates, and most plants actually prefer them to the clean, oxygenated plain gravel substrates we usually give them. Under anaerobic conditions the mineral ions they want are "reduced" and more easily absorbed than they would in their "oxidized" states. Plant roots carry oxygen into the substrate via a tissue called aerenchyma, which you can think of as being a bit like a snorkel. Some of the oxygen carried down to the roots escapes and immediately around the roots the conditions are partially, but not completely, oxygenated (i.e., dysaerobic rather than anaerobic). So wherever plants are growing, the actual risk of dangerous levels of H2S developing becomes even smaller. Occasionally poking the substrate with a stick to stir things up a little won't do any harm, and I always add Malayan livebearing snails to planted tanks because they do this automatically, behaving rather like earthworms do on land. In my view, these snails are indispensable and as you probably know they never, ever harm plants. I took it from here http://www.wetwebmedia.com/plantedtkssubwebindex/soilagfaqs.htm


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## jaysee (Dec 9, 2009)

I agree that the whole "gas bubbles killed my fish" problem is primarily myth. Either that or it is the ONE problem that everyone manages to avoid...


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## VJM (Feb 7, 2013)

Awesome discussion you guys! 

I can answer the question about what happens if a fish gets hit directly by a bubble- absolutely nothing. I shoo them away when I am poking, but do they listen? Of course not. One was being nosy, and a bubble burst right on his nose. He is fine.


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