# study & questions



## Flear (Oct 5, 2012)

i hope to use this thread to get feedback if i'm understanding things right

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in high pH iron is removed (i think around 8.0 all iron is removed - those notes are at home, i'm not 

i have notes on the most basic of redox, only enough to understand it's got some value (still learning)
-sounds interesting to get into 

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iron, in a high redox environment (tends to coincide with high pH environments)
-converts iron from ferrous iron(2+) into ferric iron(3+) (i still don't understand this about iron, so i'm just going with it) which is not soluble, and falls out of suspension

this leaves out rust, but at the moment i'm not concerned

in a low O2 environment, (eg. anoxic substrate) iron may be converted back into ferrous form, and be returned to the nutrient cycle.

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leaves me with more questions than answers, but sharing and curious if i got that much right at the moment


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## Mikaila31 (Dec 18, 2008)

Redox potential and pH do not correlate with eachother. pH deals with hydrogen ions, redox is electrons. You can have high pH and low redox, you can have low pH and high redox. Some molecules can have pH dependent redox potentials 

Iron changes form under oxidizing conditions because it of how its electrons are arranged. An oxidizing environment has a higher number of electrons present. This changes energy requirements for many compounds and allows them to take an oxidized state. Every chemical change effects the physical properties of that chemical. For iron the +3 oxidized state is mostly insoluble because it looses that attraction it had to the water molecules. Redox has an effect on many chemicals and compounds other then iron as well.

The first thing to come to terms with flear is chemical and biological systems are dynamic. There are usually no straight lines and always more questions then answers.


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## Flear (Oct 5, 2012)

so redox and pH correlations are coincidental, got it, ... (still need to learn more)

i red that before but tried to overly simplify it 

i could ask all kinds of questions on that iron 3+ vs iron 2+ relating to redox and pH, ... but it would really be frustrating for everyone if the answer was on the next page, ... back to reading. this will be one of those questions i'll wait till i'm done the book and either have the answer or not, ... but better to read first instead of get distracted.


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## Flear (Oct 5, 2012)

"High levels of dissolved O2 can inhibit photosynthesis."

does this mean pearling is bad ? (it looks neat, never thought beyond that)

needs more water circulation ?


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## pop (Aug 29, 2012)

Hello Flint:
Photosynthesis is the process by which plants, some bacteria, and some protistans use the energy from sunlight to produce sugar, which cellular respiration converts into ATP, the "fuel" used by all living things. The conversion of unusable sunlight energy into usable chemical energy, is associated with the actions of the green pigment chlorophyll. Most of the time, the photosynthetic process uses water and releases the oxygen 
We can write the overall reaction of this process as: 
*6H2O + 6CO2 ----------> C6H12O6+ 6O2*​ Most of us don't speak chemicalese, so the above chemical equation translates as:
*six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar plus six molecules of oxygen

oxygean is a by-product and not used in photosynthesis 
I would not worry about pearling dissolved oxygen on leaves, my plastic plants pearl dissolved oxygen all the time.
pop
*


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## Flear (Oct 5, 2012)

*not related to study*

aside from toxicity levels (without actually being toxic, just present in quantities too high)

animals and plants just poop out what they don't use don't they ? (yes, generalized)
(or whatever it's called with plants and bacteria do this)

---

-back to study (having a difficult time today - but working on it)


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## Mikaila31 (Dec 18, 2008)

Flear said:


> "High levels of dissolved O2 can inhibit photosynthesis."
> 
> does this mean pearling is bad ? (it looks neat, never thought beyond that)
> 
> needs more water circulation ?


The only natural scenario where high or supersaturated levels of dO2 happen would be in a very high photosynthesis environment where O2 production is in considerable excess of the systems O2 demand and O2 diffusion into the atmosphere. Basically its not highly common and would be temporary and localized if it does happen. Circulation would help but you need to realize there isn't much water movement in natural heavy planted waters. Its not going to have much effect on the plants since its a issue of their production. Photosynthesis is energy input. They can still respire under high O2, after all respiration requires oxygen. Simply because light is present doesn't mean a plant has to only photosynthesize. Too much light will also inhibit photosynthesis, tho the actual levels depend on the plant species. Everything that is a variable to plant growth... nutrients, light, environmental conditions all have ideal levels and can be too high or two low. But this is all relative to a specific species, which leads on to the basis of resource competition between species. 

Pearling happens under the right conditions. Flow certainly does have an effect. The layer of water on the leaves is the first thing to get super saturated. Any object in water will have drag on the water moving around it. This means where the leaves and water meet will have the slowest water movement. On the other hand pearling doesn't mean the water is super saturated. It could just be an effect of circulation and diffusion. If the plant is producing O2 faster then it can dissolve into the water it will pearl regardless of O2 content of the water.


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## Flear (Oct 5, 2012)

*slight distraction from studies*

correct me if i'm wrong, ... 

is redox related to oxygen or potential chemical energy ? (i'm thinking the later)

everything i'm readings talks about oxygen, (current text), ... but also talks about the potential energy gained in reactions...

(i wish i had a bigger list)... things like fluorine, cobalt, gold, chlorine all have higher energy values that oxygen


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## Mikaila31 (Dec 18, 2008)

Flear said:


> correct me if i'm wrong, ...
> 
> is redox related to oxygen or potential chemical energy ? (i'm thinking the later)
> 
> ...


As far as we care in this situation redox is related to oxygen. An oxic environment pushes towards oxidation (Ammonia to nitrate as we know). Anoxic the energy potential is different and pushes towards reduction (nitrate to ammonia). Oxygen is common and is an oxidizer, there are many other oxidizers but in a biological system oxygen is the main one. Flourine are chlorine are both oxidizers and they are both highly toxic to biological systems. 

Potential energy varies widely and is specific to each reaction and changes based on environmental conditions and fluxes. I'm not sure what you mean by other ions having higher energy values.... Its not to say they don't, but there are a couple different types of energy when talking about chemistry. Potential energy is the stored energy in a molecule or system. There is also activation energy which is what is required to initiate the reaction. If activation energy can not be met the reaction will not happen unless it is somehow reduced. This doesn't matter if potential energy is high or not. Not all reactions result in an energy gain, especially biological ones. Photosynthesis requires energy input, that mostly being sunlight but some comes from the plant as well. The energy input drives the synthesis of sugars. The sugars are now stored energy for the plant. Only when it respires and breaks down the sugars it made does it get energy out of them.


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## pop (Aug 29, 2012)

Hello Mikaila31
“An oxic environment pushes towards oxidation (Ammonia to nitrate as we know). Anoxic the energy potential is different and pushes towards reduction (nitrate to ammonia).” I am not disagreeing with you but only asking a question would not a anoxic environment tend to reduce nitrate to a form of nitrogen gas completing the nitrogen cycle instead of ammonia restarting the nitrogen cycle which is an oxygen intense process.

“Photosynthesis requires energy input, that mostly being sunlight but some comes from the plant as well. The energy input drives the synthesis of sugars. The sugars are now stored energy for the plant. Only when it respires and breaks down the sugars it made does it get energy out of them” again I am not disagreeing with you but I thought that oxygen (respiration) is produced by photosynthesis during the light dependent reaction creating ATP’s glucose sugars are created during the light independent reaction using CO2 the calvin-benson cycle and not part of plant respiration.
In #7 “Any object in water will have drag on the water moving around it. This means where the leaves and water meet will have the slowest water movement” are you talking about the unstirred area that is sometimes called the boundary layer in fluid dynamics created by friction.

I have been learning up.
pop


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## Mikaila31 (Dec 18, 2008)

pop said:


> Hello Mikaila31
> “An oxic environment pushes towards oxidation (Ammonia to nitrate as we know). Anoxic the energy potential is different and pushes towards reduction (nitrate to ammonia).” I am not disagreeing with you but only asking a question would not a anoxic environment tend to reduce nitrate to a form of nitrogen gas completing the nitrogen cycle instead of ammonia restarting the nitrogen cycle which is an oxygen intense process.


Yes in an anoxic environment nitrate can be reduced all the way to N2. This certainly does happen to some extent. Tho ammonia is not converted to N2 from what I know. It is nitrate to nitrite to N2(most common at least), but I'm not entirely sure of that. Some Nitrite will go to ammonia some to N2. This nitrogen(as N2) is basically lost to the system in a freshwater environment. N2 is rarely usable by aquatic plant as very few can nitrogen fix, some bacteria can fix nitrogen but again its only going to happen in an anoxic environment were nitrogen is limiting, as its very demanding. So any N2 produced in an anoxic substrate will eventually move back into the oxic layers and eventually into the atmosphere and leave the system, or it will eventually bubble out when physics allow it to. If you have ever paid attention to substrate of a semi-clear lake gases regularly bubble out especially if you disturb them. Nitrogen gas is one component other gases also form in an anoxic substrate due to other nutrient cycles. Nitrate that enters an anoxic environment may leave it before being fully reduced, similarly if nitrite enters an anoxic environment it will still be reduced. 


pop said:


> “Photosynthesis requires energy input, that mostly being sunlight but some comes from the plant as well. The energy input drives the synthesis of sugars. The sugars are now stored energy for the plant. Only when it respires and breaks down the sugars it made does it get energy out of them” again I am not disagreeing with you but I thought that oxygen (respiration) is produced by photosynthesis during the light dependent reaction creating ATP’s glucose sugars are created during the light independent reaction using CO2 the calvin-benson cycle and not part of plant respiration.


Yes you are very correct. The light and dark reactions are what make up photosynthesis in that manner. Water is cleaved to produce the O2, I'm not sure if that is considered a type of respiration or not. By respiration I mean, or was referring to, cellular respiration(glycolysis) which is what happens to the glucose created during photosynthesis(unless they are stored as starch) they under go glycolysis and basically broken back down into water and CO2 again. 


pop said:


> In #7 “Any object in water will have drag on the water moving around it. This means where the leaves and water meet will have the slowest water movement” are you talking about the unstirred area that is sometimes called the boundary layer in fluid dynamics created by friction.
> 
> I have been learning up.
> pop


Yes the boundary layer is exactly what I am referring to. 

One should always be learning:-D


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## Flear (Oct 5, 2012)

there are some bacteria that can convert ammonium directly to N2. - yes, definitely not common
they were discovered in sewage treatment plants, and i think the bacteria themselves are toxic.

easy to see why not desirable

i stopped looking into that direction when the suggestion that these bacteria are toxic. so i don't remember too much, and when i try to look it up i keep forgetting what it's called. Anammox if curious (i hate looking up that word, i can never spell it right 

---

bits i have found for nitrogen fixing bacteria point me towards cyanobacteria, ... much of which is toxic (there are non-toxic strains out if curious - spirulina comes to mind), i'm not sure at all, but i think cyanobacteria convert N2 to ammonia.


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## beaslbob (Oct 17, 2012)

I deep sea bed (DSB) was all the rage 10 years ago. And is still in use with many reef type tanks.

But then about 5 years ago some reported all the sudden crashes.

So people started talking much more about refugiums with macro algaes. and also algae turf scrubbers (again).

the DSB works with anoxic bacteria to reduce nitrates to nitrItes then to nitrogen gas.

But if it is not work correctly some evil bacteria can actually further reduces the nitrItes to ammonia.

So you wind up with an aerobic cycle ammonia->nitrItes->nitrates.

and an anaerobic nitrates->nitrItes->ammonia. (plus possibly releaseing some sulfur in the process)

And to top all that off the surface of the substrate has low oxygen (high carbon dioxide) and nitrogen gas. The exact requirements for cyano bacteria. so after a few months of operation, nitrates drop down and then here comes a huge cyano bloom.

so some like me just use FW plants and marine macro algaes so the cycle is:

ammonia->nitrItes->nitrates->plant tissue. :lol:


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## Flear (Oct 5, 2012)

bob, it doesn't sound like you know why DSBs were used, ... nor does it sound like you're familiar with why they were abandoned as a good alternative to keeping reef aquariums healthy. (i could be wrong, don't care, not getting into it farther here)

otherwise, this is a topic that was covered in excessive depth and detail in a thread on another forum to understand and share what was going on.

not something i'm going to get into on here at all. (pending text material - and even then, i'm 'currently' satisfied with what i know to rest assured a DSB is a waste of time & space)


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## Flear (Oct 5, 2012)

is it right to view biochemical activity (nitrates, CO2, sugars, etc.) as little more than stores of energy ?

a particular chemical has a specific energy value stored within it's bonds, ... to make use of this, enough energy has to be applies to break down or change the chemical to have a predictable energy output that is used by organisms.

would that be right or make it harder for me to understand things later on ?


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## Mikaila31 (Dec 18, 2008)

BSD is something really only discussed for reefs/SW which I know nothing about. FW wise I do keep fairly deep substrates and some are initially quite anoxic due to soil breakdown. I feel typically they stay anoxic but gas production drops off quickly. Most of these tanks are straight topsoil with a sand cap, but one is just 2" of uncapped topsoil. It varies from soil to soil on how they respond and how quickly they establish. You do not need an excessively deep soil to get it go anoxic. Its a natural thing to happen and IMO nothing to be too concerned about. Only difference between sand and topsoil is topsoil has that high initial nutrient breakdown since I don't mineralize them. I've never had issues with cyano bact. except in the exact opposite.... my bare bottom tanks will get cyano sometimes. Main reason in FW at least is cyano loves little to no nitrates, it can out-compete in those conditions because as mentioned above it can nitrogen fix. No matter how anoxic my soil tanks get I make sure the nutrients stay high since my tanks are high demand - high production.

Plants are not a long term nitrogen sink. To assume this you have to assume they are always growing and never limited by any specific nutrient as that can easily slow uptake of others. Also assuming they never die back. The only way this works in nature is from grazing herbivores, which typically are non-aquatic but waterfowl and some mammals. If you think about it, temperate lakes like in the midwest were I live loose most all their plants every winter once the ice sets in. The dieback is down to basically the roots as ice and snow cut out most sunlight as well. Then come mid summer there are some amazing 'towers' of plants easily 20ft tall on one of the clearer lakes I love. 

@ flear Yes that is the chemical basis of how an organism works no matter how small or large. Additionally molecules prefer to have lower energy there does not always need to be a biological process involved. Take the ammonia-ammonium association. This happens because at lower pH there is a greater abundance of H+ ions in the water, this changes potential energy of the ammonia. At lower pH/higher conc. of H+ ammonium is more stable and the activation energy to go between the two is low enough it can happen spontaneously on its own. Food webs also follow the basis of energy transfers, so it is a trend throughout the entire system.


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## Flear (Oct 5, 2012)

*acidic conditions in fermentive processes*

is it just under anoxic conditions that the substrate is expected to acidify while organics break down ?

i have no idea what is going on in my substrate (nor do i know how it could be tested without messing with it, causing inaccurate readings)

i may be asking a little early, but for things to adicify, wouldn't nutrients be changed and/or displaced in another area that would be more alkaline/base reading ?


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## Flear (Oct 5, 2012)

*Anoxic Environments*

the intestines (not to sound gross)
do these count as anoxic environments for potential nutrient cycling ?

(i assume more for larger fish)
i would guess only if the fish have eaten critters that for whatever reason (including hypothetical) have consumed nutrients that would otherwise be removed from whatever nutrient cycle it is a part of due to pH & redox.


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## beaslbob (Oct 17, 2012)

_Posted via Mobile Device_


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## beaslbob (Oct 17, 2012)

Just reread page 1 on oxygen.
Always wondered on my tanks with plants and no circulation why i have high ph yet fish do fine.
Perhaps there is much higher o2 and much lower co2 then if i had circulation.
_Posted via Mobile Device_


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## Mikaila31 (Dec 18, 2008)

Acidifying of the substrate is going to be a relative process I believe. In a lake the bedrock is an input of buffers as well as runnoff and groundwater. The substrate is only going to acidify if the buffers allow it to and that depends on acid production and the input of buffers. If it is biological activity that is causing the acidification then no there does not need to be a proportional amount of basic molecules produced in the system. Its typically the addition of hydrogen that increases acidity, this is reduction and more prone to an anoxic environment. 

Digestive system is aerobic and anaerobic.

The food chain doesn't really consume nutrients. Some become the makeup of of the fish while others are broken back down from complex molecule to basic nutrient then excreted for energy production. Every event of consumption, plant to fish, fish to fish, fish to bigger fish, ect. There is high energy loss each time. Much of what is consumed goes towards biological functions and is broken down then expelled as waste. Chapter 19 covers this in detail. 

Bob thats guessing again. No circulation simply means diffusion between air and water is what will depend on O2 and CO2 conc. If the aquatic environment is consuming both faster then diffusion then they will be lower then equilibrium. If it is producing them at a faster rate they may be slightly higher. If the tank is overall not very productive they will likely be at equilibrium. But again its all just speculation unless you bother to test them. I have tanks with plants and usually no circulation as well, and nothing all to amazing about them. Currently my soil, planted uncirculated tank has significantly lower pH then my soil planted circulated/filtered tank, by almost a full degree using the same tap and similar water changes. But that doesn't really say a whole lot, there are many ways to effect the pH.


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## Flear (Oct 5, 2012)

Mikaila, ... 

i didn't even consider food being consumed just for it's energy value/content, so obvious now.

thanks for the heads up


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## Flear (Oct 5, 2012)

*page 249 - nitrogen*

maybe i'm slow or something, ...

i look at this and can't help but think "the energy is backwards", ... 

to me, it looks like ammonium has the lowest energy, and nitrate has the highest
this is backwards to my familiarity with bacteria & whatnot looking at the nitrogen cycle trying to obtain energy from ammonia, and releasing nitrite, and obtaining energy from nitrite and releasing nitrate.

i'm sure it's some mental stumbling block but i look at this and can't wrap my head around it, it just seems backwards

my head says Ammonia/ammonium should have the highest energy

am i just daft here and missing the obvious or is there something going on i'm just not getting ?


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## beaslbob (Oct 17, 2012)

Mikaila31 said:


> ...
> 
> Bob thats guessing again. No circulation simply means diffusion between air and water is what will depend on O2 and CO2 conc. If the aquatic environment is consuming both faster then diffusion then they will be lower then equilibrium. If it is producing them at a faster rate they may be slightly higher. If the tank is overall not very productive they will likely be at equilibrium. But again its all just speculation unless you bother to test them. I have tanks with plants and usually no circulation as well, and nothing all to amazing about them. Currently my soil, planted uncirculated tank has significantly lower pH then my soil planted circulated/filtered tank, by almost a full degree using the* same tap and similar water changes*. But that doesn't really say a whole lot, there are many ways to effect the pH.


 
Perhaps it is the combination of no water changes and lack of circulation.


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## Mikaila31 (Dec 18, 2008)

Flear said:


> maybe i'm slow or something, ...
> 
> i look at this and can't help but think "the energy is backwards", ...
> 
> ...


What you are missing is that figure shows nitrogen assimilation. Basically plants (macrophytes) and other photosynthetic organisms can only uptake ammonia/ammonium, I recall we discussed this in another thread. They do use nitrate and nitrite but as mentioned they have to convert it back to NH3/NH4. Ammonia does have higher energy so they are working against the energy flow and the plants do have to put in energy to make this conversion. The diagram shows the enzymes required to make these reactions and the number of electrons used to get nitrate and nitrite to a usable form. This is the reason plants prefer NH3/NH4. They will only use nitrate and nitrite if they need to as they can not gain as much energy in comparison to ammonia. The only exception to this is nitrogen fixation which is also depicted there along with its very high energy requirements.


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## Flear (Oct 5, 2012)

redox isn't necessarily equal to potential energy content ?

i think that's the part i was missing

Edit:
i'm familiar enough with plants preferring Ammonium over nitrate, although they can take in both, ... and ammonium is preferred as the plants have to work extra hard to convert nitrate backwards till it reaches ammonium

i've also stumbled across the internal pH of plants ensures the presence of ammonium (over ammonia) so plants have ammonium to use at their disposal.


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## Flear (Oct 5, 2012)

*Iron - Redox vs pH*

Iron is really screwing with me. (not counting chelates)

i'm left to guess that Ferric iron is oxidized, ... but i'm not sure.
-if oxidized it would make sense to me to list it as Fe2O3
instead what i am seeing mention of is Fe3+

in the presence of O2 it's supposed to turn into ferric iron, ... k
ferric iron isn't water soluble, ... k

for hydroponics pH availability says iron is available all the way through up to pH 8 about. it tapers off as the pH climbs, but it's there

redox says otherwise. that the presence of O2 alone will remove iron from the system.

---

i missed something or something is poorly explained
or i'm looking at both pH & redox and wondering why they are arguing like this on nutrient availability in a soilless solution.

ammonia/ammonium changes are easy, it's a basic ratio, as the ph shifts one way, more is converted that way, as the ph shifts the other way, more move back, ... easy

iron is really screwing with me.


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## Mikaila31 (Dec 18, 2008)

Pretty sure as far as iron goes plants produce chelating compounds to get the iron. Usually most all aquarium fertilizers come chelated. Iron is also a trace nutrient its not in very high demand.


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