New Nitrate theory

[Paul B]

It seems this notion of a new nitrate theory is based on the assumption that some new formerly unknown strain of bacteria may exist that fixes this free nitrogen.

It is not a new unknown strain of bacteria but the regular airobic bacteria that is all over a tank which converts ammonia to nitrate.
I think he is saying that this process can go back and fourth between the different types of bacteria. At first in the shallow layers of a substrait the ammonia is converted to nitrate which we all know. Then in the lower layers the nitrate is converted to nitrogen. The nitrogen can again be converted back to ammonia which in turn gets turned back to nitrate.
Too many processes for me to get my mind fully around. But I do know that many people with DSBs have nitrate problems, maybe this is why

 

[Aquarist007]

<a href=showthread.php?s=&postid=14941561#post14941561 target=_blank>Originally posted</a> by Paul B
It is not a new unknown strain of bacteria but the regular airobic bacteria that is all over a tank which converts ammonia to nitrate.
I think he is saying that this process can go back and fourth between the different types of bacteria. At first in the shallow layers of a substrait the ammonia is converted to nitrate which we all know. Then in the lower layers the nitrate is converted to nitrogen. The nitrogen can again be converted back to ammonia which in turn gets turned back to nitrate.
Too many processes for me to get my mind fully around. But I do know that many people with DSBs have nitrate problems, maybe this is why

I thought there were three strains
aerobic converting ammonia to nitrites
anerobic converting nitrites to nitrates
anoxic converting the nitrates to nitrogen gas.

 

[tmz]

<a href=showthread.php?s=&postid=14941561#post14941561 target=_blank>Originally posted</a> by Paul B
It is not a new unknown strain of bacteria but the regular airobic bacteria that is all over a tank which converts ammonia to nitrate.
I think he is saying that this process can go back and fourth between the different types of bacteria. At first in the shallow layers of a substrait the ammonia is converted to nitrate which we all know. Then in the lower layers the nitrate is converted to nitrogen. The nitrogen can again be converted back to ammonia which in turn gets turned back to nitrate.
Too many processes for me to get my mind fully around. But I do know that many people with DSBs have nitrate problems, maybe this is why

Hello Paul.

To be clear, it is generally understood that nitifiers(the bacteria that take waste material and make nitrate ) are aerobic and denitrifiers(those that break down nitrate NO3) are anerobic.

Many people have nitrate problems with bare bottom tanks, shallow substrates and deep substrates.Many don't . There are too many other variables to conclude one type of substrate is better than an other for a particular system.

One turn this debate has taken is wether or not depth of sand bed is an advantage for anerobic denitrifying bacteria. In a well kept bed with proper fuana , it could be in my opinion.This debate has been going on for years and is nothing new.

The second related point for debate is the claim to this newly found or newly mused strain of anerobic bacteria that fixes free nitrogen gas to hydrogen and thus adds it back to the organic pool as ammonia/ammonium. Does this non photosynthetic bacterium exist or is it merely a contrivance to support a position opposing the use of deep substrate ? Has it been seen under microscope? How much ammonium does it produce.How does it do that? If it's been identified some facets of it's behavior or chemistry must have been observed;what are they? Without more definitive information, this doesn't seem to be a very complete or useful theory to me.

 

[tmz]

OK , it's been a while ; so I reread the whole article again.

There is a lot of"possibly", "feasible" and"may be" mixed in with seemingly more assertive sentences about a 2nd pathway for anaerobic bacterial activity which are then subtlety qualified.

My original take on it as reasoned speculation was generous. It's mostly a restatement of denitrification as we know it with a confusing side trip attempting to distinguish between anaerobic and anoxic areas.
Areas are full of oxygen or anoxic(devoid of oxygen to a greater or lesser degree). Metabolism/bacterial activity is either aerobic(using oxygen for energy) or anaerobic (occurring in the absence of oxygen)or degrees in between.BTW,Whys noted this in an earlier post.
There are no anaerobic areas; there are anoxic areas in which anaerobic bacterial activity predominates. So a strategy encouraging more anaerobic areas and less anoxic areas, as the author suggests in one of his central positions, makes no sense at all to me.Perhaps he means areas that are not totally anoxic but I don't really know.

There is also nothing in the article to suggest that the existence of the second pathway nitrogen fixing bacteria deep in the sandbed is anything but pure imagination. The argument that algae persist at low nitrate levels is attributable to some unknown bacteria creating ammonium in an anoxic area is thin and ignores the whole issue of phosphate limitation in microalgae growth. Even if phosphate didn't play such a central role in nuisance algae growth , any ammonium or ammonia could simply come from decomposition of organic materials anywhere in the tank.

Nothing new here; and, the old is not very clearly stated nor comprehensive as well as a bit obfuscatory and misleading,in my opinion.

 

[Paul B]

Nothing new here; and, the old is not very clearly stated nor comprehensive as well as a bit obfuscatory and misleading,in my opinion.

Yes, but if it was clear, we would have nothing to talk about :lol:

 

[Aquarist007]

"obfuscatory " I love reading your posts Tom--there is always a neat new word in it.

I'm going to change my avitar to Capn' Obfuscatory much more fitting personally and I am sure there are alot of others on here that would agree

 

[Paul B]

"obfuscatory

That ain't a word, it's a disease, I once went out with a girl that had a bad case of odfuscatory

I knew I should have went to college :eek1:

 

[Aquarist007]

<a href=showthread.php?s=&postid=14943894#post14943894 target=_blank>Originally posted</a> by Paul B
That ain't a word, it's a disease, I once went out with a girl that had a bad case of odfuscatory

I knew I should have went to college :eek1:

oh my you went out with her because she was a

oops I better pm you:lol:

 

[tmz]

I met lots of obfuscating young ladies in college. Plenty of professors too.

 

[Aquarist007]

<a href=showthread.php?s=&postid=14944586#post14944586 target=_blank>Originally posted</a> by tmz
I met lots of obfuscating young ladies in college. Plenty of professors too.

too much information:lol:

 

[Paul B]

OK I looked it up. Yep I did go out with some girls like that

"To make so confused or opaque as to be difficult to perceive or understand"

 

[herring_fish]

There seems to be a lull here.

There seems to be a lull here.

Let’s set aside ammonia, nitrite, nitrate and phosphates for just one moment. Let use instead thing about pH KH Calcium and trace elements. Does anyone have any thoughts on a bed that is placed in the tank for the stabilization of water chemistry only?

Bacteria still works to brake down and dissolve a potion of the sand which serves to stabilizes these parameters regardless of whether the nutrients are processed. Is that assumption true?

How can I best take advantage or that?

 

[Paul B]

Bacteria still works to brake down and dissolve a potion of the sand which serves to stabilizes these parameters regardless of whether the nutrients are processed. Is that assumption true?

My substrait of dolomite had been in the tank for longer than 40 years, I don't notice any of it breaking down yet. If it did it would certainly not be enough to affect water chemistry.

 

[tmz]

Re: There seems to be a lull here.

Re: There seems to be a lull here.

<a href=showthread.php?s=&postid=14948282#post14948282 target=_blank>Originally posted</a> by herring_fish
Let’s set aside ammonia, nitrite, nitrate and phosphates for just one moment. Let use instead thing about pH KH Calcium and trace elements. Does anyone have any thoughts on a bed that is placed in the tank for the stabilization of water chemistry only?

Bacteria still works to brake down and dissolve a potion of the sand which serves to stabilizes these parameters regardless of whether the nutrients are processed. Is that assumption true?

How can I best take advantage or that?

I don't think bacteria break down aragonite. The sand is largely precipitated calcium carbonate. It will dissolve at lower ph. Ph drops may occur in a bed as the water in the bed becomes more acidic from waste that is processing.

 

[tmz]

<a href=showthread.php?s=&postid=14947072#post14947072 target=_blank>Originally posted</a> by Paul B
OK I looked it up. Yep I did go out with some girls like that

"To make so confused or opaque as to be difficult to perceive or understand"

Thanks for clearing that up Paul. Scott was getting me in trouble.

 

[herring_fish]

Re: Re: There seems to be a lull here.

Re: Re: There seems to be a lull here.

<a href=showthread.php?s=&postid=14948539#post14948539 target=_blank>Originally posted</a> by tmz
I don't think bacteria break down aragonite. The sand is largely precipitated calcium carbonate. It will dissolve at lower ph. Ph drops may occur in a bed as the water in the bed becomes more acidic from waste that is processing.

Yes that is what I mean. I know that the Upside Down Sand Bed does have noticeable dissolution of aragonite that has to be replenished periodically.

 

[MattL]

<a href=showthread.php?s=&postid=14942032#post14942032 target=_blank>Originally posted</a> by capn_hylinur
I thought there were three strains
aerobic converting ammonia to nitrites
anerobic converting nitrites to nitrates
anoxic converting the nitrates to nitrogen gas.

It seems there is a general misconception in this thread.

When dealing with the nitrogen cycle in a reef, it may be assumed that there are nitrifiers and denitrifiers*.

Nitrifiers oxidize ammonia to nitrite, and then separately nitrite to nitrate. These bacteria are aerobic autotrophs. They are aerobic in that oxygen is the terminal electron acceptor, and autotrophic in that they use inorganic carbon (alkalinity) as their carbon source. Ammonia or nitrite, depending on the bacteria, are the electron donors. These bacteria are always aerobic, as oxygen must be the terminal electron acceptor.

Denitrifiers use a variety of pathways to reduce nitrate to ammonia or nitrogen gas. These bacteria are anaerobic bacteria, in that nitrate (and not oxygen) is the terminal electron acceptor. I will have to go check, but from a reefkeeping perspective, these bacteria are also likely to be exclusively heterotrophs, meaning they must use organic carbon as their carbon source. The organic carbon also serves as the electron donor and energy source.

While denitrifying bacteria are anaerobic, they live in anoxic (not anaerobic regions). This is where people tend to get confused.

Microorganisms are aerobic or anaerobic depending on whether they use oxygen or another oxidized molecule as the terminal electron acceptor. Waters are oxic or anoxic depending on whether dissolved oxygen is present.

Waters that are anaerobic not only lack dissolved oxygen, but a suitable electron acceptor. So in our tanks, this would have to be a region depleted of nitrate and sulfate and iron and so on, which is highly unlikely. So from a reefkeeping perspective, our waters are oxic or anoxic (and not likely anaerobic).

I hope this clears things up,

Matt

* The chances of there being nitrogen fixing bacteria actually fixing nitrogen are small, simply due to the prevalence of organic and inorganic nitrogen in our tanks. Nitrogen fixers, if given the chance, will rely on any other nitrogen source other than dinitrogen simply because nitrogen fixation is such an energy intensive process. Someone else mentioned the ammonox process a while back, but this process requires super high concentrations of ammonia that are unlikely to be seen in our reefs.

 

[Aquarist007]

<a href=showthread.php?s=&postid=14949072#post14949072 target=_blank>Originally posted</a> by MattL
It seems there is a general misconception in this thread.

When dealing with the nitrogen cycle in a reef, it may be assumed that there are nitrifiers and denitrifiers*.

Nitrifiers oxidize ammonia to nitrite, and then separately nitrite to nitrate. These bacteria are aerobic autotrophs. They are aerobic in that oxygen is the terminal electron acceptor, and autotrophic in that they use inorganic carbon (alkalinity) as their carbon source. Ammonia or nitrite, depending on the bacteria, are the electron donors. These bacteria are always aerobic, as oxygen must be the terminal electron acceptor.

Denitrifiers use a variety of pathways to reduce nitrate to ammonia or nitrogen gas. These bacteria are anaerobic bacteria, in that nitrate (and not oxygen) is the terminal electron acceptor. I will have to go check, but from a reefkeeping perspective, these bacteria are also likely to be exclusively heterotrophs, meaning they must use organic carbon as their carbon source. The organic carbon also serves as the electron donor and energy source.

While denitrifying bacteria are anaerobic, they live in anoxic (not anaerobic regions). This is where people tend to get confused.

Microorganisms are aerobic or anaerobic depending on whether they use oxygen or another oxidized molecule as the terminal electron acceptor. Waters are oxic or anoxic depending on whether dissolved oxygen is present.

Waters that are anaerobic not only lack dissolved oxygen, but a suitable electron acceptor. So in our tanks, this would have to be a region depleted of nitrate and sulfate and iron and so on, which is highly unlikely. So from a reefkeeping perspective, our waters are oxic or anoxic (and not likely anaerobic).

I hope this clears things up,

Matt

* The chances of there being nitrogen fixing bacteria actually fixing nitrogen are small, simply due to the prevalence of organic and inorganic nitrogen in our tanks. Nitrogen fixers, if given the chance, will rely on any other nitrogen source other than dinitrogen simply because nitrogen fixation is such an energy intensive process. Someone else mentioned the ammonox process a while back, but this process requires super high concentrations of ammonia that are unlikely to be seen in our reefs.

Thank you for accepting my invitation to join this thread Matt.

From what I have just read I am interpreting(from a very basic knowledge) that our deep sand beds are not anoxic and therefore can't support detrifying bacteria. Further is they can't support the dentrfiers then they are not doing the job they are reported to do--reduce nitrates.
This could explain the failure of deep sand beds overtime in that nitrates simply saturate the deep layers gradually moving up to the top layers where the nitrates start being introduced back into the water column?

 

[MattL]

<a href=showthread.php?s=&postid=14949317#post14949317 target=_blank>Originally posted</a> by capn_hylinur
Thank you for accepting my invitation to join this thread Matt.

From what I have just read I am interpreting(from a very basic knowledge) that our deep sand beds are not anoxic and therefore can't support detrifying bacteria. Further is they can't support the dentrfiers then they are not doing the job they are reported to do--reduce nitrates.
This could explain the failure of deep sand beds overtime in that nitrates simply saturate the deep layers gradually moving up to the top layers where the nitrates start being introduced back into the water column?

Before I begin, bear in mind there was a small error in the copy of this response I sent you personally that I corrected here, so for the last few sentances, use what I wrote here.

Just to clarify, sand beds are most likely lacking in dissolved oxygen (anoxic). Casual observance and probing with an ORP meter can verify this.

Sand beds are not anaerobic. Again, anaerobic means a lack of all suitable electron acceptors, not just oxygen. I'm going to guess that between the nitrate, sulfate, and iron in our tanks, our sand beds are only anoxic, not anaerobic.

Just to summarize, for bacteria:

• Aerobic Bactera live in Oxic waters
• Anaerobic Bacteria live in Anoxic waters
• Anaerobic Bacteria live in Anaerobic waters

For waters

• Oxic: O2, SO4--, NO3-, Fe+++
• Anoxic: SO4--, NO3-, Fe+++
• Anaerobic: None.

As for the failure of deep sand beds, there can be many reasons. Anaerobic bacteria are notoriously finicky and difficult to culture, grow, and control. Back in 2001, I wrote about the shallow sand bed on another message board and my preference for using it, as I feared that creating large anoxic zones in my tank with a deep sand bed could lead to potential catastrophe. I still use a fairly shallow sand bed, and rely on other means to get rid of nitrate.

Also, denitrifers are heterotrophs. Unlike our autotrophic nitrogen oxidizers, they cannot take alkalinity from the water to use as a carbon source for cell synthesis. If the deep sand bed is carbon limitting, then denitrification would be limitted. The whole philosophy behind ethanol dosing (which, for the record, I swore would never work, but I now realize I was wrong and that our tanks are carbon limitted) is that denitrification is being inhibited by the lack of a readily available carbon substrate, such as ethanol.

Matt

 

[Aquarist007]

boy nothing like an excellent on line class in microbiology--great posts Matt or Dr. Matt.

Can one assume then that the anerobic bacteria that live in the anoxic areas of the dsb and live rock perform both reduction reactions of nitrites to nitrates and then nitrates to nitrogen?
Or are there two strains of anerobic bacteria that perform these two functions?