# Where is the Bacteria?



## Jaseon (15 Apr 2021)

I believe myself or did believe that beneficial bacteria is everywhere in an established tank, but not the water column. My question is in what quantities is the bacteria in lets say the substrate compared to the decor, and obviously any biological filtration you may have. So how do we know unless using a microscope to actually see them over the rocks substrate and elsewhere?, or do we just assume its there, and go with that?


----------



## anewbie (15 Apr 2021)

There was a paper and i can't find it but you might if you search - that demonstrated the vast majority is typically in the filter - specifically sponge or bio media. There is also a bit in the substrate and i suppose it matters a great deal what type of substrate you have and what type of bacteria you wish to count. can't recall any analysis on rocks and driftwood.


----------



## dw1305 (15 Apr 2021)

Hi all,


Jaceree said:


> . My question is in what quantities is the bacteria in lets say the substrate compared to the decor, and obviously any biological filtration you may have.


It is difficult to quantify, because there are a lot of potential variables.


Jaceree said:


> So how do we know unless using a microscope to actually see them over the rocks substrate and elsewhere?, or do we just assume its there, and go with that?


We have to make some assumptions and even a microscope isn't very useful. The recent findings of a whole kingdom of unknown nitrifying organisms was done by <"looking at microbial RNA for Ammonia oxidising genes">. This was how people found COMAMMOX _Nitrospira_ and the Ammonia Oxidising Archaea (AOA) in Aquarium filters. What <"they didn't find"> were the ammonia oxidising bacteria _Nitrobacter _etc which were thought to be responsible for aquarium nitrification.

The <"nitrifying micro-organisms"> are potentially anywhere there is a surface and oxygen as "a biofilm". In a <"nutrient rich"> highly oxygenated environment the "surface" could actually be other microbes where <"microbial flocs may build up">.

The exact nature of the <"microbial assemblage"> will depend upon the <"amount of oxygen"> and <"the supply of ammonia">. 


anewbie said:


> that demonstrated the vast majority is typically in the filter - specifically sponge or bio media. There is also a bit in the substrate


It is all down to oxygen, so if you don't have plants the substrate is likely to be largely de-oxygenated and that will limit nitrification. If you <"have plants"> then the situation is different in that a larger area of the substrate will be oxygenated and the potential for nitrification increased.

Plants modify the substrate because their roots are leaky structures and <"leak both oxygen"> and <"carbon compounds">. 

This is from: <"_Myriophyllum aquaticum_ Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater">.


> ........ However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of _Myriophyllum aquaticum_ to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha-1 d-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial _amoA_) and denitrifying genes (_nirS_, _nirK_, and _nosZ_) were increased significantly by _M. aquaticum_ in the sediments, and the strongest effects were observed for the archaeal _amoA_ (218-fold) and _nirS_ genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that _M. aquaticum_ greatly changed the microbial community, and ammonium oxidizers (_Nitrosospira_ and _Nitrososphaera_), nitrite-oxidizing bacteria (_Nitrospira_),.........


cheers Darrel


----------



## Jaseon (15 Apr 2021)

I got to get reading on all that its excellent stuff.


----------



## anewbie (16 Apr 2021)

dw1305 said:


> Hi all,
> 
> It is difficult to quantify, because there are a lot of potential variables.
> 
> ...




I think the substrate+plants are more complicated - because sometime you get sulfur and sometime nitrogen gas - sometime rot and decay and sometime healthy growth. Naturally I believe some of it has to do with if the substrate compacts and prevent oxygen flow but even that doesn't seem to fully explain the dynamics. I lack the scientific equipment to actually test the chemical reaction taking place but observation as i experiment with different substrates seem to indicate there are certain conditions that become quite undesirable and produce a lot of negative side effects across the tank.


----------



## dw1305 (16 Apr 2021)

Hi all,


anewbie said:


> I think the substrate+plants are more complicated - because sometime you get sulfur and sometime nitrogen gas


That is right, you can potentially get substrates that are anaerobic and N2 gas is produced from the <"anaerobic denitrification of NO3">. If you go a stage further you can get an anoxic substrate where <"hydrogen sulphide (H2S) is produced">.

I don't want my substrate going anoxic, but I'm not particularly bothered by <"what happens in the substrate"> as long as I have good plant growth, it is the plants that matter.

If you did want to create an anoxic substrate, you could do by incorporating a large amount of <"easily decomposable organic matter">, which is why we advise against using any substrate with <"composted green waste"> in it.

Personally I'm always willing to trade short term optimal plant growth for <"long term stability">, so I use a 90% silica sand substrate with a <"small amount of clay and leaf mold added">.

cheers Darrel


----------



## anewbie (16 Apr 2021)

dw1305 said:


> Hi all,
> 
> That is right, you can potentially get substrates that are anaerobic and N2 gas is produced from the <"anaerobic denitrification of NO3">. If you go a stage further you can get an anoxic substrate where <"hydrogen sulphide (H2S) is produced">.
> 
> ...


I'm a bit confused by what causes the transition from anaerobic to anoxic as both seem to be without oxygen breakdown of waste however in my specific case i ended up with a very nasty anoxic situation with an innate substrate but waste matter managed to get mixed into the lower level of the substrate so i think simply using silica  substrate is not sufficient solution.
-
In my specific situation i think what happened is that when the tank broke i shoveled the substrate out replaced the tank and put it in and the shoveling mixed organics in the upper level to the lower level - however one could imagine that over a longer period of time the organic matter on the upper layers will eventually mix to the lower levels creating an issue. In my specif case the tank was around 16 months old when it sprung a leak in the bottom seal.


----------



## dw1305 (16 Apr 2021)

Hi all, 


anewbie said:


> specific case i ended up with a very nasty anoxic situation with an innate substrate but waste matter managed to get mixed into the lower level of the substrate so i think simply using silica substrate is not sufficient solution.


It is back to variables really. 

With sand the waste material tends to sit on top, but with traditional aquarium gravel, uneaten food etc. can fall through the interstices (gaps). 

You can ameliorate for this to some degree by keeping Malaysian Trumpet Snails (_Melanoides tuberculata_), but if you have a large bioload (for example a <"large messy carnivorous Cichlid"> (like an Oscar or a Midas Cichlid) in a relatively small volume tank) you are still likely to have problems with low substrate aeration.   

If you don't have plants you can remove some of this material via "gravel vacuuming", but then you are reliant on nitrification in the filter and if you use your <"filter as a syphon">, or you attempt to have <"simultaneous aerobic nitrification/anaerobic denitrification in the filter">, disaster is almost inevitable. 

cheers Darrel


----------



## anewbie (16 Apr 2021)

dw1305 said:


> Hi all,
> 
> It is back to variables really.
> 
> ...


The substrate was extremely fine grain size approx 0.3-0.4 mm. In fact I think coarser substrate while allowing foods are less likely to develop anoxic situation since they 'breath' due water being able to move between the larger grain sizes. All of my tanks are heavily planted - not quite as heavy as this tank since it was low tech but similar layout (this is my 40B). The 40B does have trumpet snail but this 29 does not. My test solution was actually to replace the 0.3mm substrate with one that is closer to 0.6mm to test my theory that 'breathing' is a better long term solution. I still doesn't understand that transition from anaerobic to anoxic but in the case of the 40B it is largely anaerobic judging from the odor less gas release.


----------



## dw1305 (16 Apr 2021)

Hi all, 


anewbie said:


> The substrate was extremely fine grain size approx 0.3-0.4 mm. In fact I think coarser substrate while allowing foods are less likely to develop anoxic situation since they 'breath' due water being able to move between the larger grain sizes.


Fair enough, I'm really not sure then. Maybe some-one else will be able to pass comment. I'll cc. in @Soilwork (or possibly @sciencefiction)? 

cheers Darrel


----------

