Nitrifing/denitrifing misconceptions

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mojoreef

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I thought I would start up a little thread to keep the blood flowing, hehehe. Thier is a huge misconception about the N cycle. Most hobbists think of the N cycle in the following way.
Nitirfing bacteria living in a aerobic zone break ammonia down to nitrite then to nitrate, Then denitrification, where bacteria living in a anaerobic zone take the nitrate and process it down to nitrogen gas.
Now in reality it is quite different. Denitrification occurs in a ll zones, both aerobic/anaerobic/anoxic and so on. That and the pathways (as in ammonia to nitrite to nitrate to gas) are pretty much bunk also. It would be like showing the roads of a city by only showing the major highways and not all the other roads in streets in the town.

So anyone want to play??????



Mike
 

NaH2O

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That and the pathways (as in ammonia to nitrite to nitrate to gas) are pretty much bunk also.
Hmmm.....I don't follow this. I figured a chemical reaction is a chemical reaction....unless you referring to the "nitrate to gas" part?? I understand that there are various branches taking place during denitrification, but the nitrification part, too?
 

mojoreef

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Nikki what I am saying is that this is only one pathway. Thier are like 40 strains of what we call amonia reducing bacteria alone. Some do the same things but the vast majority all have unique methods and pathways.
In the aerobic conditions, ammonia can be converted to nitrite, or it can be converted to dinitrogen monoxide or nitrogen monoxide or to nitrate. Its not a carved in stone thing as most percieve, but really a very complex biochemical system.


Mike
 

Maxx

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Okay, I'm intrigued. You will most likely need to speak S-L-O-W-L-Y and use your hands when describing the complex stuff. I slept too much during my chemistry class.
Nick
 

mojoreef

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Nick thier is a common thought that it is a linear system, one thing leading to another, but it gets alot deeper. Most folks think that denitrification only occurs in and on aerobic enviroments, well not true it can occur in aerobic, ananerobic, anoxic and oxic enviroments. Sam thng can be said for nitrification, it can occur in all those places to. Its all determined by conditions within each area. Food source, bacterial strain, enzyme typing and so on. neat stuff actually


Mike
 

NaH2O

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Sorry if I'm skewing the thread, but I'm trying to understand this pathway.

In the aerobic conditions, ammonia can be converted to nitrite, or it can be converted to dinitrogen monoxide or nitrogen monoxide or to nitrate.

Dinitrogen monoxide = N2O = nitrous oxide
Nitrogen monoxide = NO = nitric oxide

I thought these were processes of denitrification more often seen in anaerobic conditions.

HNO3- (nitrate) + H2 (hydrogen gas) ----> NH3 (ammonia) + N2O (nitrous oxide)

Then N2O can be converted to NO. My understanding is NO is unstable and converts back to N2O and NO2 quite readily?
 

mojoreef

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Nikki yes it is also a anaerobic process to. But it is not limited to anaerobic zones, it can happen at atmospheric levels of O2. It all has to do with the enzymes used, the bacteria that inhabit the area and the food source that causes the inhabitation.
What I am trying to say is that thier is not just one set pathway. But in reality thier are many pathways, pretty much for every element along the way. Denitrification is not reserved for just the anaerobic zone and thus nitrification is not reserved for just aerobic. Their are bacterial strains that inhabit all zones, and can perform these tasks. each of them have thier own pathway and byproducts that result from the job they do.

Boy I hope I didnt muddy that up to much.


Mike
 

Maxx

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Denitrification is not reserved for just the anaerobic zone and thus nitrification is not reserved for just aerobic. Their are bacterial strains that inhabit all zones, and can perform these tasks. each of them have thier own pathway and byproducts that result from the job they do.
Okay,
I understand this, but is there bacteria strains that we prefer to do this over others? Is the one type of bacteria that we would like above all others, and can we realistically recreate the habitat necessary for that bacteria in our tanks?
I think I se where you're going w/ this Mike, the concept being that if we're not tied down to one strain of abcteria, then we are not tied down to one type of environment for it, ie DSB vs BB vs SSB, and consequently have a little more latitude when planning our tanks.
Or I could be wrong......
Nick
 

NaH2O

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I see it as, whatever food is available, then the organism that eats that food will be there doing its thing. By controlling the "food" we are controlling the bacteria and therefore the pathways, which leads to whichever endproduct.

LOL - I feel like I just spoke in a circle!
 

Maxx

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Nikki,
Limiting the food supply is part of it, however the major limiting factor in bacteria, as I recall from my Bio classes is actually competition as opposed to food availability. Food availability has alot to do w/ it, but its more indirect. Whatever organism is able to starve out the competition will win the turf wars, and control the food supply. I hope that makes sense.
Nick
 

NaH2O

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It is almost like the chicken and the egg. Whatever food source is available will be eaten up by the particular bacteria that eats it. Yes, competition plays an important role - and food availability will allow for degree of competition, as well as say what bacteria are present. If the organisms don't eat the same things, then they wouldn't be competing for food, as much as space, I guess.
 

Witfull

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also dont forget the "tween zones",,,different strains will survive in different layers. as the DSB get deeper and available 02 reduces...it doesnt mean less bacteria at that level,creating a dead zone..other strains that can live and do there thing will inhabit that zone.
 

MikeS

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mojoreef said:
Denitrification is not reserved for just the anaerobic zone and thus nitrification is not reserved for just aerobic.
Agreed...but isn't the large majority of denitratification occuring in the anerobic zones, and the large majority of nitrification taking place in arobic zones?

As a newcomer I was handed down the bare bones process of ammonia-nitrite-nitrate-gas, as I continue to hand it down to newcomers...what would you say are the implications of the obviously more complex bioreduction process to the average aquarium keeper?

MikeS
 

NaH2O

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Wit - true. The facultative anaerobes take care of that "area". Don't forget, though, that all of these processes take place in more than just a DSB.

In regards to anoxic vs. oxic - Mike, how do you define these areas....are these not the same as anaerobic vs. aerobic, or is anoxic "nearly" void of oxygen?

Agreed...but isn't the large majority of denitratification occuring in the anerobic zones, and the large majority of nitrification taking place in arobic zones?
This is where I'm at, too.

MikeS, I'm not sure the average aquarium keeper needs to know the deep side of the processes, as much as just understanding how the process works and where it is taking place.
 

mojoreef

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I understand this, but is there bacteria strains that we prefer to do this over others?
yea I guess, but its not like we have a say in that.
Is the one type of bacteria that we would like above all others, and can we realistically recreate the habitat necessary for that bacteria in our tanks?
Again it doesnt really pertain to much as they dictate not us.
I think I se where you're going w/ this Mike, the concept being that if we're not tied down to one strain of abcteria, then we are not tied down to one type of environment for it, ie DSB vs BB vs SSB, and consequently have a little more latitude when planning our tanks.
Hmm no not really Nick. Most folks have been led to believe that it is some kind of domino principle, one stain following another each feeding on the byproduct of the last. In reality its alot different and not even close to the domino effect. Also they create thier won enviroment and/or enviroments are created by thier presence so its a total flux.

Nikki food source plays a role for sure in the everychanging state of flux.

also dont forget the "tween zones",,,different strains will survive in different layers. as the DSB get deeper and available 02 reduces...it doesnt mean less bacteria at that level,creating a dead zone..other strains that can live and do there thing will inhabit that zone.
Ahhh finally some one to pick on, lol. This is the line of thinking I want to get rid of. The whole concept of zones doesnt really pertain. This is the heart of the problem that we need to get past in order to truely understand what is going on in thier. We need to get away from this zonal line of thinking. Thanks Dave,

As a newcomer I was handed down the bare bones process of ammonia-nitrite-nitrate-gas, as I continue to hand it down to newcomers...what would you say are the implications of the obviously more complex bioreduction process to the average aquarium keeper?
Yes Mike, but your not a new comer anymore so I get to pick on you now, lol.
The bare bones line of thinking was handed down to you as a source of information about the nitrogen cycle that is involved with the initial cycle of the tank. For that no problemo, good enough. But now we are falling back onto the nitrogen, sulfur, iron, carbon cycles as a means of biological filtration. here is where we should have a better understanding, reduction is but one form, thier are many. Man Corals denitrify Mike if we really want to take a peek at things, hehehe.
Here is a quick example. Thier are 40 strains of ammonia oxidizing bacteria (AOB) some bacteria types will convert ammonia to nitrite, some to nitrate, some to a multitude of gases. Some of these baceterias live in aerobic zones, some live in anaerobic zone, some in anoxic and so on. Each of them uses a particular type of enzyme/microbes in order to do thier reduction or conversion or oxidization. Each enzyme will make it or break it as to weather or not another form of bacteria will be able to use its enzyme. Each enzyme will create its own enviroment just by its creation, so what will happen it that enviroment?? What happens when all these formed enzymes are all in one area??? what does that do to the equation, does it change the food source and thus the whole enviroment of each particular micro enviroment?? Alot of bacteria use a varity of stuff as electron exceptors, so how does that pertain to any given micro enviroment at any given time? Example a bacterial strain converts ammonia to a gas directly, so now that area is loaded with a form of nitrogen gas, Hmmm What bacteria can play with the gas?? Which now brings our friend cyano bacteria into play, It likes Nitrogen gas right.

Just a couple of things to thnk about. rofl


Mike
 

NaH2O

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I'm on bacterial/enzymatic/biogeochemical cycle informational overload. Sulfate reducing bacteria, sulfur reducing bacteria, sulfur oxidizing bacteria, the phosphorous cycle, all of the enzymes, and different ways the processes can lead - it was an overload for sure. I did find in some of my literature that Cyanobacteria are free-living nitrogen fixers, and they can fix nitrogen by using hydrogen from hydrogen sulfide, which would increase nitrogen's availability in sulfurous environments. I also found that chemolithotrophs oxidize iron and/or manganese, and are responsible for deposits of minerals on the ocean floor.

One thing I discovered was that NO3- and NH3 get assimilated back to NH2 groups of proteins. Also, Nitrate being converted back to ammonium, so the "cycle" never seems to have an end.

I picture all of these microenvironments, and obviously the environment controls the diversity and quantity of microbes....but it is becoming evident that the microbes also control their environment?

I did find the following quotes interesting when doing a little research. They are taken from this study. Not sure if they pertain, but a neat tidbit of info to say the least: Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments

Ammonia oxidation is generally ignored in traditional models of geochemical cycling in anoxic marine sediments, despite the demonstration of bacterial oxidation of ammonia under anoxic conditions in laboratory culture. The aim of this study was to determine the potential for ammonia oxidation in anoxic environments by characterization of communities of organisms capable of anoxic ammonia oxidation in marine sediments in Loch Duich. Ammonia oxidation in anoxic environments has been demonstrated in comparable marine systems (56) and in previous studies of Loch Duich sediments from the same site (40). Evidence for ammonia oxidation in anoxic sediments analyzed in this study is provided by pronounced nitrate peaks in anoxic regions (Mortimer, personal communication) and by15N-based techniques (J. Barnes, personal communication). Three bacterial groups were targeted. ß-Proteobacterial ammonia oxidizers utilize NO2 in anaerobic oxidation of ammonia (50), while planctomycetes include the Anammox organisms, which carry out anaerobic ammonia oxidation in wastewater treatment systems (12, 22).
Established pathways for anaerobic oxidation by ß-proteobacterial ammonia oxidizers and planctomycetes require substrates (NO2 or NO2-) derived from aerobic processes, which are unlikely to penetrate to the depths sampled in this study. Luther et al. (33) and Hulth et al. (21), however, provided indirect evidence for the potential for coupled anoxic nitrification-denitrification and manganese oxidation-reduction in marine sediments whereby Mn2+ was oxidized by nitrate and ammonia was oxidized by manganous oxides. Mortimer et al. (40) suggested that these processes occur throughout the iron reduction zone of the Loch Duich sediments and that the observed pronounced nitrate peaks may result from locally uncoupled nitrification-denitrification processes or locally increased concentrations of manganous oxides. The demonstrated presence and activity of ammonia oxidizers in these environments add further evidence for coupled anoxic nitrification-manganese reduction processes and have significant implications for descriptions and predictions of nitrogen turnover and geochemical cycling in marine sediments.
 

mojoreef

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I'm on bacterial/enzymatic/biogeochemical cycle informational overload. Sulfate reducing bacteria, sulfur reducing bacteria, sulfur oxidizing bacteria, the phosphorous cycle, all of the enzymes, and different ways the processes can lead - it was an overload for sure.
Now now Nikki remember it is as easy as falling off a log...remember???


MIke
 

MzWeazelle

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My lord - where do you come up with these threads at 7:42 on a Sunday morning? Ouch!

What I'd REALLY like to know is what neat things can I put into my tank that will reduce the ammonia - nitrite - nitrate "pollution problem" in the first place? Populate the tank & clean it - kill two birds with one stone!
 
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