# Will filter bacteria survive and function under 6 Ph?



## Michal (10 Nov 2016)

Hi everyone,

I keep Chocolate and Samurai Gouramis in RO water and when I add peat to the aquarium, the PH drops to 5,2 - 5,5 in a few days, until the next water change. Then it will rise up a little.
I´ve been searching the internet for the answer, but what I found is either too technical for me or it´s lab testing.
So I need to know for sure. Does nitrifying bacteria survive and work at 5 Ph or just survive or even start dying?

Michal


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## AverageWhiteBloke (10 Nov 2016)

De-nitrifying bacteria are found in some really hostile places including very acidic conditions so my guess would be that they should be fine. Don't know if there's a lower limit of PH on the strains found in our aquariums. Interesting question, unfortunately I don't have the answer but I'm sure someone who has will be along shortly.


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## Manisha (10 Nov 2016)

Hi Michal, welcome to ukaps ☺ in post 34 http://www.ukaps.org/forum/threads/how-to-know-if-your-tank-is-cycling.43253/page-2#post-464120 a member explains their thoughts on how a low pH can effect bacteria when cycling. I have soft water and at pH5, my tank seemed not to be making any progress when starting up. I can't link any scientific evidence - this is just based on my observations. I understand extremes of temp & pH can denature enzymes so wonder if it may be a similar process?


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## Michal (11 Nov 2016)

Thanks very much for your replies. 

My tank is running for almost two years now. Chocolate gouramis are in about a year and Vaillanti for few months. Problem is, that every time the pH drops bellow 5,5, I get stressed and do daily RO water changes until the pH rise again. 
It´s common knowledge (between fishkeepers around here) that de-nitrifying bacteria stops working at pH bellow 6. (I don´t know if that is the true or not. I have read that they stop or that they don't.) 

I just can´t use chocolates as the subjects for testing. 

I am thinking of stopping to add any peat or oak leaves to the water, but it wouldn't be like their home anymore


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## EnderUK (11 Nov 2016)

Why are you worried about bacteria? Grow plants, not bacteria, problem solved.


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## Michal (11 Nov 2016)

Thanks for the answer. 

As simple as that?


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## dw1305 (11 Nov 2016)

Hi all,





Michal said:


> My tank is running for almost two years now. Chocolate gouramis are in about a year and Vaillanti for few months.


OK the important bit there is "_Chocolate Gouramis are in about a year_", showing that conditions are good.





Michal said:


> Problem is, that every time the pH drops bellow 5,5, I get stressed and do daily RO water changes until the pH rise again.


Just ignore pH, it isn't a very useful parameter in very soft water. pH is a ratio, and when you have very pure water it is pretty much meaningless. 





Michal said:


> It´s common knowledge (between fishkeepers around here) that de-nitrifying bacteria stops working at pH bellow 6. (I don´t know if that is the true or not. I have read that they stop or that they don't.)


No it doesn't, but nitrification does slow down when carbonates are in short supply. In these acid environments nitrification will overwhelmingly be carried out by Archaea, not Bacteria, and they are much more tolerant of low pH. 

This is for soils, but exactly the same processes will occur in the filter <"Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils">. Also because the pH is acidic the ammonia is in the form of the ammonium ion NH4+, and much less toxic than NH3.





EnderUK said:


> Why are you worried about bacteria? Grow plants, not bacteria, problem solved.





Michal said:


> As simple as that?


Pretty much, "plant/microbe" nitrification is much more efficient than "microbe only" biological filtration.

cheers Darrel


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## Manisha (11 Nov 2016)

dw1305 said:


> Hi all,OK the important bit there is "_Chocolate Gouramis are in about a year_", showing that conditions are good.Just ignore pH, it isn't a very useful parameter in very soft water. pH is a ratio, and when you have very pure water it is pretty much meaningless. No it doesn't, but nitrification does slow down when carbonates are in short supply. In these acid environments nitrification will overwhelmingly be carried out by Archaea, not Bacteria, and they are much more tolerant of low pH.
> 
> This is for soils, but exactly the same processes will occur in the filter <"Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils">. Also because the pH is acidic the ammonia is in the form of the ammonium ion NH4+, and much less toxic than NH3.Pretty much, "plant/microbe" nitrification is much more efficient than "microbe only" biological filtration.
> 
> cheers Darrel



Oh dear, now I'm really confused again! Is low pH not a problem because ammonia is usually ammonium under these circumstances? Even if you had a wet/dry filter with more oxygenation - does pH have no effect on bacteria?


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## Michal (11 Nov 2016)

Thank you Darrel very much!

Why I didn't ask sooner


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## dw1305 (12 Nov 2016)

Hi all, 





Manisha said:


> Is low pH not a problem because ammonia is usually ammonium under these circumstances? Even if you had a wet/dry filter with more oxygenation - does pH have no effect on bacteria?


Yes pH has an effect on the ammonia oxidising bacteria that were thought to be responsible for nitrification in aquariums. This article is by Dr Tim Hovanec, <"Bacteria revealed">, and it summarize what we know now. This is the paper which first indicated that the Archaea are the primary oxidising organisms in aquariums:  <"Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters">. The Archaea are much less constrained by low pH, but they still need a source of CO2 (usually from dissolved HCO3-).

All decomposition is slowed in acidic water, if you put dead leaves into a fish tank with oxygenated alkaline water they will much more quickly oxidise via bacterial activity, when compared with a tank with acidic water.

This is the pH response curve of total ammoniacal ammonia (TAN). Oxygen becomes quite relevant here, because it is a base, and even water that is naturally acidic may become alkaline if oxygen saturation is at, or above, 100%, so there are risks involved in assuming pH will protect your livestock.





It is really back to plants again, plants are a massive plus in biological filtration, they really are the <"goose that lays the golden egg">, and a lot of this is to do with their positive effect on oxygen levels.

As long as the oxygen supply exceeds the oxygen demand biological filtration will carry on at any pH level. Plants give you "belt and braces" and particularly plants with access to aerial levels of CO2 and dissolved oxygen.

The ideal situation is to have emergent plants, because these engender more suitable conditions in the substrate for microbial colonisation, but floating plants are a very good alternative and their root structure still supports microbial activity, as well as the direct uptake of NH4+ from solution (details in the quoted text). 





dw1305 said:


> From Gilroy, S & Jones, L. (2000) "Through form to function: root hair development and nutrient uptake" _Trends in Plant Science_, 5:2, pp56–60.
> Available at <http://www.sciencedirect.com/science/article/pii/S1360138599015514>


cheers Darrel


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## Manisha (13 Nov 2016)

Thanks for the detailed information & links - I'm getting there, I think ☺


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## dw1305 (13 Nov 2016)

Hi all,





Manisha said:


> Thanks for the detailed information & links - I'm getting there, I think ☺


The really strange thing is that there are loads of papers on <"constructed wetlands">, <"aquaculture"> and <"sewage treatment"> which look at the processes that underlie biological filtration, but the traditional ideas are about aquarium cycling are like a multi-headed hydra, as soon as you provide evidence to debunk one part, it just pops up again. 

I know that oxygen is the prime metric in biological filtration, and that plants are the single most important factor in maintaining water quality, but I can't convince the majority of aquarium keepers. 

cheers Darrel


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## Michal (13 Nov 2016)

Yes, I agree. The aquarium keepers around here work mostly with very old myths. I had to go to the foreign forums to get some fresh info.
Thanks again.

 I knew about the importance of oxygen, thats why I built wet and dry sump filter. Didn't know about the plants though.
Now I just need to find some more plants for very soft and acidic water.

I wonder if orchid hanged above the aquarium with the roots reaching to the water will work any good?


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## dw1305 (13 Nov 2016)

Hi all,





Michal said:


> Didn't know about the plants though.


I think plants are still regarded as ornaments by many aquarists. Often, even when they realize that they can improve water quality, they are seen as very much a minor player compared to microbial filtration.

The reason why plants are net oxygen producers is just a simple chemistry. During photosynthesis one molecule of oxygen is released for every molecule of CO2 taken up. When the light levels reach light compensation point plants become net oxygen producers, when light levels are below light compensation point plants are oxygen consumers, due to respiration, but plants must be net oxygen producers, after respiration is taken into account, because they grow, and that growth (the carbohydrate produced from photosynthesis) is a measure of the extra oxygen production.





The same applies to nitrification, it is an oxygen intensive process. Every ion of NH4+ that plants take up doesn't enter nitrification and doesn't consume any oxygen.






Michal said:


> Now I just need to find some more plants for very soft and acidic water.


_Ceratopteris thalictroides_ is a good one.





Michal said:


> I wonder if orchid hanged above the aquarium with the roots reaching to the water will work any good?


It won't really grow quickly enough to have much effect, but a plant like a _Philodendron_ would work. If you did want an orchid something like a _Vanda_ would enjoy life.

Have a look at "Hydrophyte"s <"threads on this forum">.

This is a tank featured on <"PlanetCatfish">




cheers Darrel


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## Aqua360 (13 Nov 2016)

I have no idea if pothos or as it's also known as devil's ivy does well in acidic, but it will devour nitrates and generally seems to contribute to healthy tanks whenever I utilise it


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## Michal (14 Nov 2016)

Beautiful!

I always wanted plants hanging over the aquarium. This is perfect. I think I start with orchids, which I've got and then I get some Philodendrons as well. 
Also, lucky bamboo would looks nice. And help I think.


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## dw1305 (15 Nov 2016)

Hi all,





Aqua360 said:


> I have no idea if pothos or as it's also known as devil's ivy does well in acidic, but it will devour nitrates and generally seems to contribute to healthy tanks whenever I utilise it





Michal said:


> I always wanted plants hanging over the aquarium. This is perfect. I think I start with orchids, which I've got and then I get some Philodendrons as well. Also, lucky bamboo would looks nice. And help I think.


Pothos (_Epipremnum aureum_) and Lucky "Bamboo" (_Dracaena sanderiana_) are both good ones. Umbrella papyrus (_Cyperus alternifolius_) is another option. 

Have a look at <@Iain Sutherland's>  _<"Copella_ riparium">.

cheers Darrel


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## sciencefiction (15 Nov 2016)

Michal said:


> Beautiful!
> 
> I always wanted plants hanging over the aquarium. This is perfect. I think I start with orchids, which I've got and then I get some Philodendrons as well.
> Also, lucky bamboo would looks nice. And help I think.



I love emersed plants....In most cases they need extra light besides room light. I never had pothos but its one of those that does well on room light. It is very low light tolerant. The ones I've tried require tank light additionally to room light to stay healthy and grow. Otherwise they slowly wither and die. But if the room is very bright or the plants get plenty of window light, a lot of species will work. Just look for plants that like being watered a lot and also ones that require moderate humidity, not high humidity like aquatic plants.  There's a period of adaptation though, if they haven't previously grown in water. It may take a few months for them to adapt but they should not be dying while adapting. Their growth is just stopped in time and then all of a sudden they take off. They also flower quite well once established. Plants that don't like too much water, will eventually start melting in aquarium, including the roots. You'll be able to smell the pot  when that happens...


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## Michal (15 Nov 2016)

Hi everyone,

Thank you.

I'm thinking (I already started to build it actually) that I hang wooden beam (small one) or big oak branch, by chains from the ceiling. Then I can attach plants to that beam somehow.
Problem will be the humidity in the room, specially during the winter. I'll have to put some acrylic around, up to the ceiling. There will be 250W HPS lamp, which I already use, during the winter, when light from the outside is low, for my house plants. So, light won't be a problem. Only acrylic, which is three time more expensive than normal glass.

But I will get there.

I've got one question though. It might be from different circle, but still is about filters.

Recently I built wet and dry sump filter (with foam and bio balls) and I'd like to ask if anyone know how long does it takes for bacteria or Archaea to colonize the sump filter, so I can give away my canister filters?

Thank you again for your answers. It's priceless 

Michal


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## dw1305 (16 Nov 2016)

Hi all,





Michal said:


> I'm thinking (I already started to build it actually) that I hang wooden beam (small one) or big oak branch, by chains from the ceiling. Then I can attach plants to that beam somehow.
> Problem will be the humidity in the room, specially during the winter. I'll have to put some acrylic around, up to the ceiling. There will be 250W HPS lamp, which I already use, during the winter, when light from the outside is low, for my house plants. So, light won't be a problem. Only acrylic, which is three time more expensive than normal glass.


 I'm at RBG Kew next week, I'll try and get a shot of the water lily pool in the <"Princess of Wales Conservatory">. It used to have a great epiphyte branch above it, but it has gone now.






Michal said:


> Recently I built wet and dry sump filter (with foam and bio balls) and I'd like to ask if anyone know how long does it takes for bacteria or Archaea to colonize the sump filter, so I can give away my canister filters?


If you can move some of the media from the canister filter to the sump it should only take a few days. Sponges are really good for transferring microbial communities. You can swirl the sump sponge in the rinsings from the canister filter media and it will start functioning straight away.

If you have plants they will take up any "spare" ammonia. For those who don't own Diana Walstad's <"book">, there is a useful summary in <"_Plants vs Filters_">.

Can you run the filter and sump simultaneously? If you can I would. Longer is nearly always better.

Have a look a this article by Stephan Tanner <"Aquarium biofiltration">.

cheers Darrel


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## Lindy (16 Nov 2016)

Michal said:


> Thanks very much for your replies.
> 
> My tank is running for almost two years now. Chocolate gouramis are in about a year and Vaillanti for few months. Problem is, that every time the pH drops bellow 5,5, I get stressed and do daily RO water changes until the pH rise again.
> It´s common knowledge (between fishkeepers around here) that de-nitrifying bacteria stops working at pH bellow 6. (I don´t know if that is the true or not. I have read that they stop or that they don't.)
> ...



 I know i'm late to this party but what I'd like to suggest is that you prepare water in a container that has peat in it or are filtering through peat with an external. When it gets to the desired ph then use it to water change the tank the fish live in. This way you avoid the swings you are having. It was in this way I prepared water for my liquorice gourami while breeding them. I never added peat directly to their tanks.


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## Michal (16 Nov 2016)

I run both, filter and sump for a week now, and I'll continue for another two. Just to be sure.



dw1305 said:


> I'm at RBG Kew next week, I'll try and get a shot of the water lily pool in the <"Princess of Wales Conservatory">. It used to have a great epiphyte branch above it, but it has gone now.



Well, that is amazing. 



dw1305 said:


> If you have plants they will take up any "spare" ammonia. For those who don't own Diana Walstad's <"book">, there is a useful summary in <"_Plants vs Filters_">.



From what I've just read I can understand that biofiltration by bacteria might be even bad for plants (for those preferring ammonium over nitrate). I've got around 15 plant species in my aquarium, but none of them is on the list in the summary. (I haven't got the book - yet). Does that mean that my plants prefer nitrate? 
I also understand that if I keep aquarium filled with plants which prefer ammonium I don't need filtration. Just water movement.




dw1305 said:


> Have a look a this article by Stephan Tanner <"Aquarium biofiltration">.



I think I know how substrate must be important in biofiltration. Once I changed all the substrate, keep plants, run the filters in barrel, keep most of the water, but after two weeks I had ammonia spike which killed third of the fish.


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## Michal (16 Nov 2016)

Lindy said:


> I know i'm late to this party but what I'd like to suggest is that you prepare water in a container that has peat in it or are filtering through peat with an external. When it gets to the desired ph then use it to water change the tank the fish live in. This way you avoid the swings you are having. It was in this way I prepared water for my liquorice gourami while breeding them. I never added peat directly to their tanks.



Thank you Lindy.

Yes, I used to do that. Peat and RO water in a barrel. 
Now just pure RO water straight to the aquarium. I change only 10% of water.  I've got peat in a sump filter and oak leaves in the aquarium. 
I don't worry about pH too much anymore (not after what I've read past few days).

Since you've got experience with breeding delicate fish I'd like to ask you something. If you be so kind?

My female chocolate has the eggs in her mouth now. I think it's fifth day. She is hiding all day, doesn't eat, just moving with her mouth sometimes. Do you think it's clever to take her out and put her into sump, where I keep cherry shrimps. I'm afraid that it will stress her, but I probably won't be able to find any fry and feed it. There are too many hiding places in the aquarium.


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## dw1305 (17 Nov 2016)

Hi all,





Michal said:


> I also understand that if I keep aquarium filled with plants which prefer ammonium I don't need filtration. Just water movement.


 I don't look on plants as an alternative to microbial filtration, I look on plants and microbes as two essential, synergistic, components of a whole system.





Michal said:


> From what I've just read I can understand that biofiltration by bacteria might be even bad for plants (for those preferring ammonium over nitrate). I've got around 15 plant species in my aquarium, but none of them is on the list in the summary. (I haven't got the book - yet). Does that mean that my plants prefer nitrate?


 Microbial biofiltration isn't bad for plants. Microbial nitrification produces nitrate (NO3-), and even though it looks like most plants will preferentially take up ammonium (NH4+), all plants will utilise any form of fixed nitrogen, including nitrite (NO2-).  

Fixed nitrogen is always a scarce resource in nature, because it takes a lot of energy to split the stable triple bond of the N2 molecule  to liberate two reactive nitrogen atoms, that can form biologically active compounds. Organisms have evolved to make use of any form of fixed nitrogen. For plants it takes less energy to take up ammonium, but a lot of fixed nitrogen is going to be NO3 and it will still be taken up and utilised.

cheers Darrel


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## Michal (17 Nov 2016)

Thank you,

So it is about balance between microbial nitrification and plants. I am on the right path then


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## dw1305 (17 Nov 2016)

Hi all, 





Michal said:


> So it is about balance between microbial nitrification and plants. I am on the right path then


Yes you are.

As well as the direct nitrogen uptake by the plants they also provide additional oxygen and more niches for microbial colonisation (often from "leaky" roots), and these <"epiphytic nitrifiers"> are known to be particularly important in <"Constructed wetlands"> etc. 

It is always plant/microbe filtration, a lot of the criticism of the cycling posts has ignored this, and unfavourably contrasted "_filtration by plants_" with "_filtration by bacteria_", as if they are mutually exclusive. 





> .....In addition, nitrogen in the ammonia form is not readily taken up by plants, so no matter how high the ammonia levels get in your fish tank; your plants will not be getting much nutrition from it.


 This really p*sses me off, but on a lot of forums and <"web pages"> (where the quote above came from) there are statements that "_plants don't take up ammonia, only nitrate_" and are "_really just an alternative to water changes_", and don't have any _"part to play in the important bits of biological filtration_". 





> ...Not quite accurate. While plants do consume some ammonia and nitrate, the amount of intake is puny. You’d have to cover every square inch of a 30 gallon fish tank just to take care of the ammonia produced by two tiny Neon Tetra.  <"So the plants are irrelevant here.>"


Nothing could be further from the truth, and even the most cursory "Google" would <"provide plenty of evidence to the contrary">, but the same "facts" are continually re-cycled, and seem to have a life of their own.

cheers Darrel


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## Nelson (17 Nov 2016)

dw1305 said:


> This really p*sses me off,


Oh Darrel ,I'm shocked.Someone needs to go sit on the naughty stair .


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## Michal (17 Nov 2016)

dw1305 said:


> This really p*sses me off, but on a lot of forums and <"web pages"> (where the quote above came from) there are statements that "_plants don't take up ammonia, only nitrate_" and are "_really just an alternative to water changes_", and don't have any _"part to play in the important bits of biological filtration_".



I believe it could be annoying sometimes.

But for me personally, this website and information I found here, are extremely helpful.


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## sciencefiction (19 Nov 2016)

Plants are essential for fish well being as Darrel says, in many ways and in conjunction with the other type of filtration.

I was reading recently about phytoremediation of plants. You can find many papers about its positive affect, by different species of plants.  Here is one about floaters.

http://www.tandfonline.com/doi/abs/10.1080/15226514.2016.1183567?journalCode=bijp20

_"*Phytoremediation of wastewater toxicity using water hyacinth (Eichhornia crassipes) and water lettuce (Pistia stratiotes)"*_

_This paper elucidates the phytoremediation potential of water hyacinth and water lettuce on the reduction of wastewater toxicity......

Results:

Phytoremediation reduced 58.87% of ammonium content, 50.04% of PO43−, 82.45% of COD and 84.91% of BOD. After 15 days of the experiment, metal contents in treated wastewaters decreased from 6.65 to 97.56% for water hyacinth and 3.51 to 93.51% for water lettuce tanks._


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