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I recently wrote an article about soil and how the nutrients cycle through micro organisms, and bugs.   I was able to verify most of what I wrote,  but the two paragraphs below contain a couple statements shown in italic that I went out on a limb with.  I'd like your feedback as to the accuracy of what I am assuming.

In the first paragraph I'm assuming that when iron is converted in the anaerobic soil that it is converted to iron chelete and which is more soluble and easily washed away..

In the second paragraph I'd  like to add some chemistry math to describe this sentence " The plants exchange hydrogen H+ for nitrogen which also helps to return the pH to a higher level."

I assume that when the plants exchange H+ for nitrogen the pH is affected. 

Your help with this will be appreciated. 

-Bob


Minerals can influence the color of a well draining soil.  Red and yellowish tints are an indication of iron,  purple - black indicates manganese.  Gray can indicate a lack of organic matter, and an anaerobic condition due to the microbes having converted the iron to a more available form called iron chelate Fe2 which is easily leached away.   Organic matter produces very strong coloring agents as it decomposes.   Therefore gardeners are looking for dark soils the color of coffee.


Nitrification produces an acidic pH when oxidation occurs. This process is called reduction because there is a loss of electrons, and it releases energy that is used by the bacteria.  
Nitrifying bacteria do not generally like low pH, but fortunately other bacteria called denitrifying bacteria convert nitrogen salts created by the nitrification process back into nitrogen N2 which returns to the atmosphere.  The plants exchange hydrogen H+ for nitrogen which also helps to return the pH to a higher level.

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Ok, just letting you know that the direct question is way beyond my current knowledge, that being said; I have a few nitpicks. The most pedantic of them being you mixed up Reduction with Oxidization. You said " reduction...is a loss of electrons" (this is not of out of context for my purposes, but politicians should not be allowed to cut sentences like this...). Reduction is gaining electrons, while oxidization  is losing. There is a helpful mnemonic my AP Chemistry teacher taught me (actually, quite recently): OIL RIG--Oxidation is losing; Reduction is gaining.

Also, nitrogen based salts are not actually salts while dissolved in water. They are separate ions, because they are more attracted to water then the cation/anion. (That might be more pedantic, actually.)

Anyway, I have never heard of plants exchanging hydronium/hydrogen ions for nitrate. It doesn't really make sense to me, but then again, I'm not the one who researched it. I think Nate Storey or other Doctorates/Grad Students in the field will have a much better idea than me. Oh, and you are completely right about the color of various oxides (Mg, Fe, etc.).  Sorry for not being helpful, but I'll just call this "studying". 

Thanks I'm not good at chemistry and reduction always seems backwards to me.  Thanks for setting me straight.  I've changed it to

"Nitrification produces an acidic pH.  When oxidation occurs, an electron is lost, releasing  energy that is used by the bacteria."

Eric Warwick said:

Ok, just letting you know that the direct question is way beyond my current knowledge, that being said; I have a few nitpicks. The most pedantic of them being you mixed up Reduction with Oxidization. You said " reduction...is a loss of electrons" (this is not of out of context for my purposes, but politicians should not be allowed to cut sentences like this...). Reduction is gaining electrons, while oxidization  is losing. There is a helpful mnemonic my AP Chemistry teacher taught me (actually, quite recently): OIL RIG--Oxidation is losing; Reduction is gaining.

Also, nitrogen based salts are not actually salts while dissolved in water. They are separate ions, because they are more attracted to water then the cation/anion. (That might be more pedantic, actually.)

Anyway, I have never heard of plants exchanging hydronium/hydrogen ions for nitrate. It doesn't really make sense to me, but then again, I'm not the one who researched it. I think Nate Storey or other Doctorates/Grad Students in the field will have a much better idea than me. Oh, and you are completely right about the color of various oxides (Mg, Fe, etc.).  Sorry for not being helpful, but I'll just call this "studying". 


Thank you for compiling this! Yeah, reduction is weird.  
Bob Campbell said:

Thanks I'm not good at chemistry and reduction always seems backwards to me.  Thanks for setting that straight.  I'll change that ASAP.

Remember Bob that iron is a transition metal, so it comes in two flavors Fe2+ (called ferrous iron, also written as Iron(II), and Fe3+ (called ferric iron, also written as iron(III)...a chelate (or chelating agent) can be thought of as a "binding agent"...that keeps the iron from wanting to transition back to Fe3+ (or whatever the case may be). A chelate is a chemical compound in the form of a heterocyclic ring (usually an acid)...The 'thing' that it is 'chelating' (binding to itself) is anaerobically (or more correctly anoxically) redoxed Fe2+. This tends to happen in the slightly deeper strata of soil (40 to 80 cm I think...but you can look that up to make sure).

So Fe2+ in the soil isn't necessarily chelated.

And it's not necessarily 'leeched' away...Just wants to transition to Fe3+ in the presents of a predominately aerobic environment. (Like the upper strata of soil). Many other things may come into play in determining redox potentials. Here's run down on some of those things... http://lawr.ucdavis.edu/classes/ssc102/Section9.pdf

The portion about 'plants exchanging H+ for N'...I'm not really sure that it really pans out that way, but I could be wrong. I think your 'proton pump' model really only works for a cation displacement/exchange scenario. It wouldn't really explain N uptake in the form of NO3-...Which in my limited understanding can be accomplished by plants in one of two ways...By the releasing of hydroxide (OH) ions, or under certain circumstances, absorbing NO3- anions by simultaneously absorbing hydrogen ions, or releasing bicarbonate...So there are two different transport systems that co-exist and co-ordinate efforts to uptake NO3- nitrogen within most C3 plants. For the detailed mechanics of how this works exactly, you will have to consult the PhD's as it really is quite complex.

Good stuff Bob.

@Vlad,

Thank you,  I see I'm still using the term chelated incorrectly.  I have made corrections, and even described the process in further detail.

Minerals can influence the color of soil.  Red and yellowish tints are an indication of iron,  purple - black indicates manganese.  Gray can indicate a lack of organic matter, and an anaerobic condition due to the microbes having converted the iron to Fe2+.   Organic matter produces much stronger coloring agents as it decomposes, but in an anaerobic soil it can also provide food for anaerobic bacteria that reduce iron and manganese. Therefore gardeners are looking for dark soils the color of coffee.

 

I've also rewritten sentence concerning the exchange of H+ for N at the plant's roots.  Thanks for telling me about hydroxy.  I may make additions later about the NO3- exchange later, but here is what I have now.

"The roots take up negatively charged anions (H+) by exchanging hydroxy (OH-) anions.  This also helps to return the pH to a higher level"

 

I'll tell you the soil world is amazing.  It's got an economy with currency of it's own.  I hope you will read the entire article.

http://chicogardens.blogspot.com/2013/02/soil-web.html   This is really interesting stuff!   Most of what I have written was learned from reading Teaming with Microbes by Lowenfels & Lewis.  It began as notes I was taking as I read the book. I think the book is a masterpiece.

Here's the rewritten section I've been working on. 

Small particles of clay and humus carry positive electrical charges call ions.  Positive ions are called cations and negative charges are called anions. The positive ion (cations) of humus and clay attract the negative ions (anions) of calcium (Ca++),  potassium (K+), sodium (Na+), magnesium (mg++), iron (Fe+), ammonium (NH4+), and hydrogen (H+) so strongly that very little remains in solution.  The nutrients are held in clay and humus where roots exchange (H+) cation for a nutrient cation.

 

There are also anions of chloride (Cl-), nitrate (NO3-), sulfate (SO4-) and phosphate (PO4-) in the soil as well.  Since these are repelled by the humus and clay cations they are easily leached away.

 

Plant root hairs also have cations which are exchanged for the cations in the clay and humus.  The root hairs exchange one (H+) for every nutrient cation absorbed.  This occurs at the cation exchange site.  The Cation Exchange Capacity (CEC) is a measurement of how many exchange sites there are in the soil.  Higher CEC measurements indicate that the soil can store large amounts of nutrients, which is why gardeners like a high CEC.  But the clay and humus which give the soil this quality also prevents good drainage and aeration so a  mixture with good soil texture is important.

 

Each cation exchange, as well as some fungal and bacterial exchanges effect the pH of the soil.  Knowing the pH is important because different microbes prefer different soil pH and depending on the plant certain microbes may be required for nutrient exchange.

 

Bacteria come in two basic types.  Anaerobic which lives without oxygen and produces offensive odors, and aerobic which lives with oxygen and produces pleasant fresh odors.  Bacteria are responsible for recycling carbon, sulfur, and nitrogen.  CO2 is a by product of aerobic bacteria, and sulfur is recycled by anaerobic bacteria. 

 

Nitrogen found in the atmosphere can not be used directly by plants. It must be 'fixed' through a process called nitrification where aerobic bacteria combine nitrogen with either oxygen or hydrogen to form  nitrite (NO2-), and eventually nitrate (NO3-) ions from the ammonium (NH4+) waste of protozoa and nematodes which consume other bacteria and fungi.  

 

Nitrification produces an acidic pH.  When oxidation occurs, an electron is lost, releasing energy that is used by the bacteria.   Nitrifying bacteria do not generally like low pH, but fortunately other bacteria called denitrifying bacteria convert nitrogen salts created by the nitrification process back into nitrogen N2 which returns to the atmosphere.  The roots take up negatively charged anions (H+) exchanging hydroxy (OH-) anions.  This also helps to return the pH to a higher level. 

 

Hydrogen is the root's currency. They sell sell OH- for H+, and then exchange H+ for nutrient cations.  Also consider this - even microorganisms carry their own charges, and are also influenced by the anions an cations of the roots and soil."

 

 

Vlad Jovanovic said:

Remember Bob that iron is a transition metal, so it comes in two flavors Fe2+ (called ferrous iron, also written as Iron(II), and Fe3+ (called ferric iron, also written as iron(III)...a chelate (or chelating agent) can be thought of as a "binding agent"...that keeps the iron from wanting to transition back to Fe3+ (or whatever the case may be). A chelate is a chemical compound in the form of a heterocyclic ring (usually an acid)...The 'thing' that it is 'chelating' (binding to itself) is anaerobically (or more correctly anoxically) redoxed Fe2+. This tends to happen in the slightly deeper strata of soil (40 to 80 cm I think...but you can look that up to make sure).

So Fe2+ in the soil isn't necessarily chelated.

And it's not necessarily 'leeched' away...Just wants to transition to Fe3+ in the presents of a predominately aerobic environment. (Like the upper strata of soil). Many other things may come into play in determining redox potentials. Here's run down on some of those things... http://lawr.ucdavis.edu/classes/ssc102/Section9.pdf

 

The portion about 'plants exchanging H+ for N'...I'm not really sure that it really pans out that way, but I could be wrong. I think your 'proton pump' model really only works for a cation displacement/exchange scenario. It wouldn't really explain N uptake in the form of NO3-...Which in my limited understanding can be accomplished by plants in one of two ways...By the releasing of hydroxide (OH) ions, or under certain circumstances, absorbing NO3- anions by simultaneously absorbing hydrogen ions, or releasing bicarbonate...So there are two different transport systems that co-exist and co-ordinate efforts to uptake NO3- nitrogen within most C3 plants. For the detailed mechanics of how this works exactly, you will have to consult the PhD's as it really is quite complex.

Good stuff Bob.

While doing research I came across this site with calculations for redox.

I think you guys might like it.

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