# Biological filtration - one for Darrel, Clive and co.



## George Farmer (12 Feb 2012)

http://www.plosone.org/article/info%3Ad ... ne.0023281

A bit over my head but the gist is that a lot of filters don't actually contain bacteria!

If someone cleverer than me could put the article into laymans terms, that would be great. 

Another interesting article - http://www.practicalfishkeeping.co.uk/m ... p?sid=4780


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## BigTom (12 Feb 2012)

Don't have much time so only given it a skim read, but yes, the paper suggests that archaea, rather than bacteria, seem to be the most prevalent agents of nitrification in most the aquariums sampled.

"The results of this study revealed that, based on amoA gene abundances, AOA (ammonia-oxidizing archaea) were the dominant putative ammonia oxidizers in the majority of freshwater and saltwater aquaria".

Will leave it to Clive and Darrel for more insightful comment!


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## Ady34 (12 Feb 2012)

Practical fishkeeping article:
"AOBs die in low oxygen content – nope.
We all know that oxygen content is a key player in the conversion of ammonia (NH3) to nitrite (NO2) - the clue is right there in the O part of NO2. Typically, the thinking has been that high oxygen yields high AOB’s, and that low oxygen brings about their demise. 

However, as much as we consider the ‘safe’ level of oxygen in water to be around 6mg/l (pending temperature) our AOB bacteria can be found at considerably lower levels. What varies is the prevalent lineage of bacteria found. In the research highlighted, Nitrosomonas europa can be found in sludge communities with a dissolved level of a scant 1.2 – 2.4mg/l O2, although at higher levels of oxygen the lineage gives way to Nitrosomonas oligotropha.

But it doesn’t even stop there. The lay argument goes that in the confines of a bottle, beneficial AOB’s in absence of any oxygen will surely perish. Even this is not the case, with studies suggesting that nitrifying bacteria can switch their metabolisms, resulting in resting cells, or even by switching from nitrifying to denitrifying behaviour.

One study cited reports how Nitrosomonas europa can bide its time with nitrite denitrification using molecular hydrogen, organic matter and hydroxalmine – producing N2O and N2 in its wake. The exact mechanisms of this activity have yet to be explained but it’s hinted that the procedure may be a response to the negative effects of high nitrite in the environment – AOBs may well convert it to protect themselves".

This is generally way over my head, but it did always make me wonder about the 'filter off for no more than half an hour' rule in relation to aerobic bacterial die off due to oxygen depletion..... my tank never seems to suffer after a power cut of a few hours, sometimes you dont even know the power has been off.
Ady.


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## dw1305 (14 Feb 2012)

Hi all,
It is an interesting article, I'm not a microbiologist and I've only had a quick skim, but my suspicion would be that it is about right. I think the main problem is that people want simplified linear "black and white" solutions in a complex "shades of grey" world, and microbial ecology is very rarely simple and linear. It is only really with this sort of rigorous scientific experimentation that we can advance our knowledge.


> The results of this study revealed that, based on amoA gene abundances, AOA (ammonia-oxidizing archaea) were the dominant putative ammonia oxidizers in the majority of freshwater and saltwater aquaria


I can do this bit, it doesn't mean these aren't "bacteria" in layman's terms, it is just that scientists don't call them bacteria, in the same way they don't have "fish" or "reptiles" as a category, but they do have "birds" and "mammals", it is all to do with phylogeny and being monophyletic <http://tolweb.org/Life_on_Earth/1>. 


> Although they are simple, microscopic organisms, Archaea are quite distinct from more commonly encountered Bacteria, having branched off from the latter very early in evolutionary history (probably >3.5 billion years ago.) In fact, Archaea are more similar to humans than to Bacteria in many important ways, and are probably more closely related to us as well!


 from "The Tree of Life" <http://tolweb.org/Crenarchaeota/9>.

cheers Darrel


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## plantbrain (14 Feb 2012)

Issues with O2 seem to cause havoc in planted tanks due to higher organic matter, and biomass, if these die back much.....plants.........and their roots......which pump O2 into the sediment............so that sediment is a gaint filter essentially, then like Ady suggest, you(the aquarium) will pay........

Whenever I do large trims etc, I always do large water changes, it might be due to O2, or some other factor, but O2 seems to be a biggy.

If you are a small microscopic bacteria, archaea etc..........NH4 is a hot commodity. So you are going to use a lot of O2 to oxidize and get all that reducing energy out of the NH4. That's fine if there is a stable supply of NH4 and.........plenty of O2 around..........but that's often rare.

Many of these bacteria like to live in the O2/no O2 interface where the NH4 leaches up through the sediment.
They are close to the source of NH4 production..........and right at the limits of O2 to oxidize NH4. So having lower O2 tolerance is typical. While our filters will often have high O2, once we turn them off, in perhaps less than 10-15 minutes, many cnaister filters will have zero ppm in the water.

Sumps seem to have much less issue with shutting the filter off vs a sealed canister, and it's fairy obvious if you consider O2.


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## dw1305 (14 Feb 2012)

Hi all,


> If you are a small microscopic bacteria, archaea etc..........NH4 is a hot commodity. So you are going to use a lot of O2 to oxidize and get all that reducing energy out of the NH4. That's fine if there is a stable supply of NH4 and.........plenty of O2 around..........but that's often rare. Many of these bacteria like to live in the O2/no O2 interface where the NH4 leaches up through the sediment. They are close to the source of NH4 production..........and right at the limits of O2 to oxidize NH4. So having lower O2 tolerance is typical.


That is pretty much what I think, it is back to the schematic from the trickle filter 


 or the Winogradsky column <http://www.biology.ed.ac.uk/research/groups/jdeacon/microbes/winograd.htm>, but instead of the boundaries being the artificial drawn straight lines, they are diffusion gradients of gases and nutrients that move backwards and forwards as conditions change, with the gases and organic compounds being utilised by an ever changing microbial assemblage. 

Additionally because inside the canister we are in the dark, we don't have any light utilising autotrophs, everything has to get its energy by chemical means and oxygen is likely to be in short supply.

cheers Darrel


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## sWozzAres (13 May 2012)

The most interesting thing about that article is...



> In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3)...


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## hinch (13 May 2012)

this seems to promote an idea I pushed a few months ago in another thread, its perfectly possible to have a filterles tank and still have adequate "filtration" with the correct plant biomass and substrate. the filter its self if added becomes not a biological filtration function but instead simply a mechanical filtration system for removing particles from the water.

not saying it always works like that but in the right circumstances I believe you can go filterless and have perfectly good quality water and fish.


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## Alastair (13 May 2012)

Take big toms bucket of mud, he has no filter on it what so ever, all his plants below and above water clearly provide adequate filtration alone 


Sent from my iPhone using Tapatalk


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## BigTom (13 May 2012)

It's worth noting though that I have a massive surface area and plant biomass, along with fast growing emergent and floating plants and a very light fish stocking, so not something I would recommend for the average community aquarium.


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