# Help: investigating soil mechanics



## atc84 (May 18, 2013)

So as i have learned and helped others, i didn't know why certain things go about.

I know how a lack of oxygen in the substrate leads to anaerobic soil from decomposing organics, but have no idea the process/function to it. Does it have to do with nitrifying bacteria? Do roots release oxygen through their roots? 

I feel like i've seen somewhere it went over this, but can't recall.


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## Tugg (Jul 28, 2013)

Yes, plants release O2 via the roots. That allows the bacteria to breath and decomp the organic material for the plants to then "eat". If a substrate is too thick or the root density too low, anaerobic pockets form where the bacteria can't breath O2. Instead anaerobic bacteria begin to reduce nitrate and sulfate to steal their oxegen until its completely anoxic.

Small pockets are inevitable and not a real problem, its when you get a buildup of the H2S (Hydrogen sulfide - Sulfate that has been reduced) that you have a problem. H2S is a toxic poison.


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## atc84 (May 18, 2013)

Ah ok, thanks for the details. And the only way to remove H2S is for it to bubble out of the substrate?


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## Zapins (Jul 28, 2004)

I agree with most of what you talked about Tugg, but I have to disagree with roots releasing O2. Roots take up O2. Only green plant tissue can make and release O2. Roots have no chlorophyll and therefore cannot produce oxygen. The only metabolic process that goes on inside them is the breakdown of sugars that are transported from the leaves to the roots in order to keep them alive. Breaking down sugars is part of normal respiration, and respiration requires oxygen. Therefore, unless the substrate has enough oxygen in it roots will die. 

This is part of the reason swamp trees have those hollow "knees" that stick up out of the water. They are there to pipe down oxygen from the air into the root and soil area. Many other aquatic plants have hollow tubes that travel from the surface of the water down to the roots to provide oxygen to the root tissue as it grows. 

Anaerobic soil happens because there are basically two general kinds of bacteria that each rely on a different type of metabolism to get by. Aerobic bacteria need oxygen to live and without oxygen they cannot produce energy from breaking down oganics in the soil. Anaerobic bacteria usually cannot survive in oxygen environments (because oxygen is surprising quite damaging and toxic to cells), these bacteria only live in small pockets of anaerobic soil usually. When the soil becomes anaerobic the pockets of anaerobic bacteria spread out and start decomposing the organic material there and at the same time the aerobic bacteria die back due to a lack of oxygen. Soil can become depleted of oxygen if the cap on the soil is too thick, or too fine. This is why fine sand is not a good cap for soil tanks. Also, high clay content in a soil will also prevent oxygen from diffusing through and keeping it aerobic. 

H2S is made by the anaerobic bacteria. So as long as you keep oxygen in the substrate by using low clay % soil, and by keeping the soil cap fairly thin and coarse-grained you shouldn't have issues.

To remove H2S, just reintroduce oxygen into the soil in some way (poking holes, changing the soil cap). Oxygen will kill the anaerobic bacteria that produces the H2S.


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## SBS (Feb 26, 2013)

Hi Zapins, are you certain plants don't release oxygen via the roots? Here are at least two articles talking about oxygen released via the roots:

http://mit.biology.au.dk/~biohbn/cv/pdf_files/Aquatic Botany 61 (1998) 165-180.pdf

http://www.jstor.org/discover/10.23...id=2129&uid=2&uid=70&uid=4&sid=21104171956203

http://digitalcommons.unl.edu/dissertations/AAI3070121/


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## Tugg (Jul 28, 2013)

I may have misread or misunderstood, but I was under the impression that plants transport it down into the roots. Isn't this why soil tanks are heavily planted, to prevent the soil from going anaerobic?


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## atc84 (May 18, 2013)

Just today i noticed a root from either a water sprite or jungle val was pearling. Does this prove it releases oxygen?


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## Zapins (Jul 28, 2004)

Thanks for the interesting articles SBS.

Though producing oxygen and transporting it from elsewhere are two different things. Roots cannot make oxygen in any appreciable quantity. Some species can transfer it from the water column or surface via hollow structures called aerenchyma, but this is variable and depends on the species. The middle link you posted mentions the variability that plants produce.

Aerenchyma:








From:​http://upload.wikimedia.org/wikipedia/commons/d/d3/Aerenchyma2.JPG​


Zapins said:


> This is part of the reason swamp trees have those hollow "knees" that stick up out of the water. They are there to pipe down oxygen from the air into the root and soil area. Many other aquatic plants have hollow tubes that travel from the surface of the water down to the roots to provide oxygen to the root tissue as it grows.


The third paper you posted is interesting since it mentions how deep the oxygen from the roots penetrates into surrounding substrate. I knew there was some amount of oxygen released around roots, but did not realize it was only 760-1160 μm thick.



> A layer of oxygen was detected around the lateral roots, and its thickness (760-1160 μm) also increased with bulk BOD


My first post was probably a minute detail in the grand scheme of things, but I find the distinction interesting and important. My general point is that roots should not be viewed in the same way as plant leaves (in terms of making O2) and simply having plants rooted in the substrate doesn't guarantee that there will be enough O2 in it to prevent it from becoming anaerobic.

There are several examples of aquatic plants being rooted into the substrate but then rot away because the soil becomes anaerobic with time. I suppose a lot of this depends on other factors, like the species in question or how organic rich the substrate is and how quickly the bacteria digests it (and uses up the oxygen from the surrounding soil). If the rate the bacteria uses the oxygen up exceeds the rate that fresh oxygen reaches the soil and roots then anaerobic conditions occur which in turn damage roots.

If you've got some free time here is an interesting summary paper that discusses whether roots of aquatic plants can get enough O2 from transported O2 rather than the surrounding soil, or if they experience oxygen deficiency: http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1937.tb06904.x/pdf


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## SBS (Feb 26, 2013)

> Though producing oxygen and transporting it from elsewhere are two different things. Roots cannot make oxygen in any appreciable quantity.


I wasn't thinking roots "produce" oxygen as obviously they have not contact with light, but along the lines of roots releasing oxygen/transporting oxygen to the substrate taken from other areas of the plant.
I guess, it would depend on species of plants in regards to roots and oxygen.

However, judging by my immersed plants planted in see through pots, plenty of long rooted plants in the soil would play some role in preventing the soil from compacting and becoming anaerobic.
And a lot of other factors play a role whether oxygen reaches the soil or not, whether there's enough oxygen in the water to start with, to suffice all oxygen demands. Is that oxygen reaching the required parts of the tank(for example if you don't supply oxygenated water to an external filter it will end up smelling of rotten eggs obviously, so same can happen in the soil, at least at lower layers or if little oxygen is going into the soil for one or another reason)

Fish need oxygen, plants need oxygen at night, nitrification, decomposition, and so on. Everything needs oxygen, not everything needs co2.
Do you have a thick soil layer, or thin one, what is it capped with, thickness again?.......Is flow with oxygenated water reaching the soil? Do you have shredders to prevent large organic material from piling up faster than it can be decomposed, are organics too much for the tank to handle?....etc.. Many factors would have an effect on oxygen levels and healthy stable tank.


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## dymndgyrl (Jan 22, 2007)

Read Diana's book - 
Chapter VIII section F, titled "Effect of Aquatic Plants on Substrates":

First line- "All plant roots release considerable oxygen and organic compounds as part of their normal functioning ..."

And Chapter IX section 4a titled "Root Release of Oxygen by Aquatic Plants":

First line - "The roots of all aquatic plants release oxygen into thier environment...."


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## Tugg (Jul 28, 2013)

I nodded of a few pages in, but the summary was worth the read:



zapins link said:


> (Leaf types noted earlier in the paper)
> Type A: Not more than 5 mm. high, rudimentary.
> Type B: Varying in height, but all growing at the same rate.
> Type C: Still green, but growing slowly or not at all.
> ...


Basically, in a healthy plant, the new growth provides little to no O2 to tissue outside of it's own leaves. The older growth that has matured provides a great deal of O2, and the older dying leaves provide just a little (as to be expected since they are dying).

This shows the importance of healthy older leaves for a plant to maintain it's roots. When new growth shades the old, and there is insufficient lighting, roots can suffocate and die.

As for supplying the surrounding area, I would argue that within 760-1160μm is a great deal of oxygenated volume, especially in a moderate to heavily planted tank. If this is the area of equal O2 levels as the root, then there is an even wider range or lower levels that support bacterial life. Something like a sword can spread out wide and breakup potential anaerobic pockets, keeping them VERY small and safe.

Its no wonder why plants float with this much gas flowing inside of them.


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## atc84 (May 18, 2013)

I wasn't assuming that roots create oxygen, since they don't have chloroplasts in the root cells. Since the root itself was releasing oxygen (visibly noticeable), whether it be in the soil or not (since it's not photosynthetic), it must be releasing oxygen in the soil if it was buried. 

This would make sense, since in the early stages of an aquarium, decomposition, bacteria growth, etc, a lot of O2 is being used in the substrate. When non-established plants are introduced into the aquarium, they are not able to create enough oxygen to fulfill the needs of the bacteria. This leads to anaerobic substrate, which is common in high organic soils.

In contrast, the DSM involves establishing plants before the decomposition of the soil is trapped in the substrate since air flow occurs much faster without a deep water level. It is noticed by people who try this find plants accumulate much faster to being submersed, since the "older growth that has matured provides a great deal of O2"(this post confused me, i hope im using this correctly) towards the substrate.


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## Phoenix1307 (Jun 1, 2014)

I would only add that for growth, plants need abundant Carbon. As Walstad points out, plants would rather get this from Ammonia in the water rather than through their root systems as organic compounds. Fish produce Ammonia. And, broad-leaf plants have a much higher leaf-area than stem plants. Healthy plants equate to healthy root systems which help to keep the soil aerobic.

In a new tank, stem plants help to stabilize the entire ecosystem quickly, growing at a rate of as much as 1/2" per day, with adequate light, sucking up the available carbon (ammonia). As the broadleaf plants root systems become established (2-4 weeks) they then begin new leaf growth, as much as 1/2-1" per day, again, with adequate light. At this time, the stem plants can become "outreached" by the ability of the broadleaf plants to suck up nutrients, and their growth can slow, by comparison. My estimation is that one broadleaf plant is equal in leaf area to perhaps 50-100 stem plants, but that may be high.

With enough plants, it is hard to overpopulate a tank with vertebrates (within reason, of course), so long as there enough invertebrates to manage the mulm that settles. You'll know by "how much" and "what" comes up when you vacuum. "Not so much," you probably have a good balance. "Too much" and "too many" fish. "Nothing," and you can probably safely add more fish.

For plant growth, lighting is the key factor that governs the whole process, and when it comes to the "amount" of light, LEDs provide the best return on space and efficiency, and their initial high cost is more than paid for by their efficiency and the savings on electricity usage compared to fluorescents and MH bulbs, and even CFLs. But beware. Not all LEDs are equal, some fixtures with .2 watt LEDs and others, 3 watts and higher. 60 Watts (20x3) in my 29g high tank seems adequate judging by plant growth, which is about 1.5 watts LED/gal, if that helps establish a baseline.


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## SBS (Feb 26, 2013)

> I would only add that for growth, plants need abundant Carbon. As Walstad points out, plants would rather get this from Ammonia in the water rather than through their root systems as organic compounds.


How do plants get carbon from ammonia? Ammonia is a chemical compound, not organic and has a forumula of NH3.

Organic compounds on another hand contain carbon. Decomposition of organics creates a source of carbon for the plants in the form of CO2(though some plants can take other types of carbon in the lack of co2)


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## Skizhx (Oct 12, 2010)

Walstad mentions that plants would rather get nitrogen from ammonia, not carbon... 

I think this is sort of debatable though...

As far as I'm aware, ammonia uptake is a passive cellular mechanism (no energy required). Once it's taken into the plant it's converted and stored as ammonium (or used immediately). Nitrate uptake on the other hand requires active mechanisms (requires energy), and more energy is required to convert nitrates into ammmonium for storage than to convert ammonia to ammonium.

So, unless I'm mistaken, plants take in ammonia more than nitrates because the intake is easier energy wise, and there's no regulatory mechanisms to slow/prevent uptake of ammonia. Further, ammonia is more easily converted to a storable form of nitrogen.

I wouldn't go as far to say this means that plants "prefer" ammonia though, just that it's a more easily accessed form of nitrogen, and they will take it in more consistently than other forms.


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## busymomv (May 25, 2014)

Hi all! Great and informative thread here. I'm in the beginning stages of a dirted / Walstad style tank and trying to figure out the balance of it all.

Tank specs:
1" MGOCPM w 1" gravel cap
36g 
8.5 hrs light from USA Current Satellite + LED (Split schedule 4.5 hrs on; 5 hrs off; 4 hrs on)
Mix of rooted, stem, and floating plants
3 or 4 small MTS (I think) and 1 large nerite snail
3 platys
1 betta

Its just about the end of week 3 and plants have grown for sure, nitrogen cycle is just about complete. (NH4/NH4=0; NO2=0.1; NO3=5) However, I noticed the plants weren't doing as well as I'd hoped at the beginning of this week - many of them had leaves that seemed to be decomposing, or holes in them, and some that were doing great initially seemed to be going "bad"; or the new growth slowed significantly. AND I noticed a few bubbles coming up from the substrate. 

So all week I've been poking the substrate 1 or 2 times a day, releasing bubbles I assume are H2S, and the plants seem to be much happier. From what I've read on this thread, and in D.W.'s book, I'd like to think that eventually the roots of the rooted plants will become established and the anaerobic soil will be less of a hazard to the plants and fish. How long should I expect that to take? If the H2S is being released by poking the substrate, and goes straight up via bubbles, is the water very contaminated? I'm happy to do water changes to be safe, but I'm not sure how toxic this situation actually is. Fish still seem well, behaving normally and have good appetites. Plants look much healthier and the decomposing has not continued since I started releasing the bubbles from the substrate / bringing O2 to the substrate/roots via poking it every day. 

Should I be doing anything else? or am I doing anything wrong that I should stop?

As always, thanks for your help!


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