# Foul smell and yellow water



## SOulGirL (1 May 2022)

Hi there,

so I've been having a very strange problem with my new tank.
I recently started a new setup where I used about 12L of brand new Amazonia substrate (the original, not the V2) and for hardscape I used Seiryu stone, previously washed before placing in the tank.
I did a dark start, meaning, only the scape and substrate, filled with water and filter running for about 2 or 3 weeks.
No lights and no plants while cycling.
The filter is an Oase Biomaster 350 that had previously been working in my last setup so was more or less cycled.
Had a few weeks with ammonia super high, then came the nitrites peak and then nitrates. After that I did a big 90% WC and apparently the tank was cycled.
The thing is, the water started turning very yellow after a few days of the dark start and the it smelled reallty bad. Smells a bit like Prime, when the bottle is already running low.
I do use Prime for water conditioning, but never had this problem before.

Last week I added new plants, all from 1 2 Grow from Tropica, lights Twinstar 600S at 60% for 6 hours and also CO2 2bps (on 2 hours before lights on and off 1 hour before lights.)
I also did a 60% WC when I added the new plants.
Since the water is still very yellow and with a bad smell I added carbon to the filter about 3 days ago, but no change. Still looks yellow and has a foul smell.
Does anyone have any idea what might be happening? And what I can do to solve it?
WC's doesn't seem to work either, since after 1 or 2 days of a big WC the water is yellow again.

Adding a pic so you can see how yellow the water was before adding the plants. And now it's not as yellow but not much better either.


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## plantnoobdude (1 May 2022)

SOulGirL said:


> Hi there,
> 
> so I've been having a very strange problem with my new tank.
> I recently started a new setup where I used about 12L of brand new Amazonia substrate (the original, not the V2) and for hardscape I used Seiryu stone, previously washed before placing in the tank.
> ...


is it a musty soil/forest smell( Idk how to describe it)? ada amazonia has lots of peat in it aswell, so that is staining the water. I had the same experience. you can do a couple water changes, it should reside.


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## MirandaB (1 May 2022)

Sounds like you've got some anaerobic issues,try poking a skewer into the substrate in places and see if any bubbles come out.


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## dw1305 (1 May 2022)

Hi all, 
@SOulGirL, nice name, I still <"keep the faith">. 


SOulGirL said:


> Had a few weeks with ammonia super high, then came the nitrites peak and then nitrates. After that I did a big 90% WC and apparently the tank was cycled.
> The thing is, the water started turning very yellow after a few days of the dark start and the it smelled really bad. Smells a bit like Prime, when the bottle is already running low.
> 
> 
> ...


Unfortunately the filter wouldn't have been cycled for your new tank <"with super high ammonia levels." We know <"much more about nitrification now"> and most of what you read on FB and forums  is just utter b*llocks.

My guess is that it is one or both of the reasons that @MirandaB  and @plantnoobdude give. 


SOulGirL said:


> WC's doesn't seem to work either, since after 1 or 2 days of a big WC the water is yellow again.


I think you are obliged to carry on with the water changes. While you don't have any fish I wouldn't use a conditioner.  

Seachem won't tell you how "Prime" works, but <"it is this mechanism"> and it is just shuffling any ammonia around. In terms of chlorine (Cl2) it will just outgas, neither ammonia (NH3) or chlorine (Cl-) are an issue for the plants (at the levels in UK tap water).

cheers Darrel


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## SOulGirL (1 May 2022)

plantnoobdude said:


> is it a musty soil/forest smell( Idk how to describe it)? ada amazonia has lots of peat in it aswell, so that is staining the water. I had the same experience. you can do a couple water changes, it should reside.


No, it is actually more of a sulphur smell. Wish it was the earthy smell, that would be a lot better news since I actually like that smell... I already did several WC's, mostly 50% but also some other bigger ones, 70% and even 90%. And still after 1 or 2 days the water is yellow again.


dw1305 said:


> Hi all,
> @SOulGirL, nice name, I still <"keep the faith">.
> 
> Unfortunately the filter wouldn't have been cycled for your new tank <"with super high ammonia levels." We know <"much more about nitrification now"> and most of what you read on FB and forums  is just utter b*llocks.
> ...



Sorry to disagree with you, but the tank is indeed cycled. Had really high ammonia for several weeks, than really nigh nitrites and after that nitrates. Have been testing for about 2 weeks now with zero ammonia and nitrites and nitrates around 25 or so....



MirandaB said:


> Sounds like you've got some anaerobic issues,try poking a skewer into the substrate in places and see if any bubbles come out.


Yep, tried that too, nothing came out...

The plants are doing ok though...here are pics of when first planted and then, today. In less than a week and they have already shown some nice growth.


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## GHNelson (1 May 2022)

Try poking under the rocks!


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## KirstyF (1 May 2022)

Hi Ya

Timeline is a bit confusing.

You mention you did a dark start for 2 or 3 weeks and you then mention that you had high ammonia for several weeks then nitrites, then nitrates. You have been running with no nitrites (nitrates around 25ppm) for 2 weeks now, but you’ve only had plants in for a week!

Has there been a period of time where you had lights on but no plants?? 

Also, what water changes have been done and when in the timeline, if you can remember!  

This may help people to figure out what’s going on for you. 😊


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## dw1305 (1 May 2022)

Hi all,


SOulGirL said:


> ........No, it is actually more of a sulphur smell. Wish it was the earthy smell, that would be a lot better news since I actually like that smell... I already did several WC's, mostly 50% but also some other bigger ones, 70% and even 90%. And still after 1 or 2 days the water is yellow............
> 
> Sorry to disagree with you, but the tank is indeed cycled. Had really high ammonia for several weeks, than really nigh nitrites and after that nitrates. Have been testing for about 2 weeks now with zero ammonia and nitrites and nitrates around 25 or .......


It maybe cycled now, but it definitely isn't quite where it needs to be, mainly because of the colour and smell.

Personally  I don't particularly like the binary switch cycled concept and I'd like to move away from it.

What I do like is the <"Seasoned Tank Time"> concept that Cory at Aquarium Co-Op talks about.

There are also some issues with testing for both dissolved gases and monovalent ions which was one of the reasons for the development of both Estimative and Duckweed indices.

Cheers Darrel


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## Aleman (1 May 2022)

Could it be Anaerobic conditions in the substrate causing hydrogen sulphide to develop??


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## Simon Cole (1 May 2022)

@SOulGirL - can I just say you are very talented when it comes to designing rock formations.

@Aleman - sulphidogenesis is rather rare in nature.  I do review the literature every few years to see whether there is any new evidence of it forming in fens, bogs and other wetland environments. It does turn up in small or undetectable traces occasionally. There is good evidence that it forms deep underneath certain rice paddy fields.  I'm fairly open minded that it may yet be detected in certain natural wetland environments. I am less open minded to the possibility that it could form in aquariums because I tend to think that substrates are likely to be permeable to dissolved oxygen and that the chemical conditions for microbial sulphidogenesis are unfavourable and would probably take a very long time to develop. It seems more likely to be olfactory resonance from organic molecules (possibly also containing sulphur), which is far more common in environmental pollution events. If it were generated due to the interaction of sulphur in water conditioners with substrates for instance, then I see that as a largely chemical interaction as opposed to an the product of microbial anaerobic activity, and it is hard to imagine how this might prevail outside anoxic water conditions. When you dissolve sodium metabisulphite in water even in considerable doses, it is hard to get it to produce detectable hydrogen sulphide. I guess that would be a very easy test to perform to see whether aquarium water has the potential to emit hydrogen sulphate, as people have noted it is easy to smell in relatively low concentrations.


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## SOulGirL (2 May 2022)

KirstyF said:


> Hi Ya
> 
> Timeline is a bit confusing.
> 
> ...


I'm sorry, I do realize that the way I explained it is indeed confusing, I'm gonna try to explain as best I can, since I didn't actually keep a super strict record of times/days, etc.
I know the tank had ammonia for about 2 weeks after I started the dark start. Then slowly ammonia started to decrease and the nitrites appeared as well as high nitrates.
This went on for about 2 more weeks.
During the first 7 days I also added bacteria to the tank, in the form of Aquavitro Seed. (don't know if this makes any difference)
It was just last week that I did the planting, so at this point the tank is around 1 month and a half, more or less, from my account...

I only turned the lights ON and CO2 when I planted. No lights or anything else during the previous month.
The smell though actually appeared right at the beginning, where there was no plants or light, as well as the yellowing of the water.

Something I forgot to mention and may have some effect on this, I had the filter stopped for a few days, filled with water and biomedia from last setup, before I started this new tank.
Once the smell appeared (basically almost as soon as I turned it on, I panicked thinking it was something rotting in the filter and emptied the filter and rinsed everything under tap water. Then added it to the tank again, and also did a huge 90% WC.
The weird thing is that nothing in the filter smelled bad...I have no idea what is happening here.



Simon Cole said:


> @SOulGirL - can I just say you are very talented when it comes to designing rock formations.
> 
> @Aleman - sulphidogenesis is rather rare in nature.  I do review the literature every few years to see whether there is any new evidence of it forming in fens, bogs and other wetland environments. It does turn up in small or undetectable traces occasionally. There is good evidence that it forms deep underneath certain rice paddy fields.  I'm fairly open minded that it may yet be detected in certain natural wetland environments. I am less open minded to the possibility that it could form in aquariums because I tend to think that substrates are likely to be permeable to dissolved oxygen and that the chemical conditions for microbial sulphidogenesis are unfavourable and would probably take a very long time to develop. It seems more likely to be olfactory resonance from organic molecules (possibly also containing sulphur), which is far more common in environmental pollution events. If it were generated due to the interaction of sulphur in water conditioners with substrates for instance, then I see that as a largely chemical interaction as opposed to an the product of microbial anaerobic activity, and it is hard to imagine how this might prevail outside anoxic water conditions. When you dissolve sodium metabisulphite in water even in considerable doses, it is hard to get it to produce detectable hydrogen sulphide. I guess that would be a very easy test to perform to see whether aquarium water has the potential to emit hydrogen sulphate, as people have noted it is easy to smell in relatively low concentrations.


Thank you! I really appreciate it 
It took quite a long time of testing and trying to find the right rocks etc, but I do like the end result.



dw1305 said:


> Hi all,
> It maybe cycled now, but it definitely isn't quite where it needs to be, mainly because of the colour and smell.
> 
> Personally  I don't particularly like the binary switch cycled concept and I'd like to move away from it.
> ...



For sure it isnt't where it's supposed to be. I am really upset with this, cause I tried my best to do everything right and still I'm having problems.
And the worst of it all, is that I have no clue how to fix it.
Thanks for the help though!


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## GHNelson (2 May 2022)

Hi
Keep up the water changes and try this application below!
You can also plant some of these fast growing stems and remove them at a later date!








						Using stem plants as a filtering aid at Start Up!
					

The subject of using fast-growing stem plants as part of a filtering aid has cropped up a few times recently. This idea has been around for a long time so not new,....it has benefits especially for a new set - up. I try and cover at least 50% of the water surface minimum.  1. Improves water...



					www.ukaps.org
				



hoggie


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## dw1305 (2 May 2022)

Hi all,


SOulGirL said:


> I am really upset with this, cause I tried my best to do everything right and still I'm having problems.
> And the worst of it all, is that I have no clue how to fix it.


I don't see them as insurmountable problems, you just need to carry on changing some water and add some fast growing plants. <"I like a floating plant">, but <"other options"> are available.  Soon or later things will settle down and plant growth will make the <"tank suitable for livestock">.  

What I can't tell you is how long that process will take.



You don't need to test the water, if you have a <"reasonable mass of growing plants"> your tank is "cycled". You can carry on testing the water if you feel happier doing that, but don't make decisions based purely on the test kit results.

cheers Darrel


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## SOulGirL (2 May 2022)

GHNelson said:


> Hi
> Keep up the water changes and try this application below!
> You can also plant some of these fast growing stems and remove them at a later date!
> 
> ...





dw1305 said:


> Hi all,
> 
> I don't see them as insurmountable problems, you just need to carry on changing some water and add some fast growing plants. <"I like a floating plant">, but <"other options"> are available.  Soon or later things will settle down and plant growth will make the <"tank suitable for livestock">.
> 
> ...



Regarding floating plants I have access to these 2, which one do you recommend?
Phyllanthus fluitans​LIMNOBIUM LAEVIGATUM​Also, how much water do you guys recommend me to change then? And how often?
I was thinking of the usual 50% once a week, but will do whatever is needed ofc!  Thank you for all your help!


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## GHNelson (2 May 2022)

Hi
I would do two or three smaller ones over the week to re-fresh the aquarium!
hoggie


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## SOulGirL (2 May 2022)

GHNelson said:


> Hi
> I would do two or three smaller ones over the week to re-fresh the aquarium!
> hoggie


About 20 or 30%? Is that ok?


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## GHNelson (2 May 2022)

Yes, that will be good!
Might take a few weeks to get the aquarium fully cycled as Darrel stated, but better safe than sorry!


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## SOulGirL (2 May 2022)

GHNelson said:


> Yes, that will be good!
> Might take a few weeks to get the aquarium fully cycled as Darrel stated, but better safe than sorry!


Sounds great! Oh and I'm not in any hurry. Just want things working as smoothly as possible.
Will definitely do that then  Thanks so much!

Will update as soon as I have any news!


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## dw1305 (2 May 2022)

Hi all,


SOulGirL said:


> Regarding floating plants I have access to these 2, which one do you recommend?
> Phyllanthus fluitans​LIMNOBIUM LAEVIGATUM​


<"Probably Amazon Frogbit"> (_Limnobium laevigatum_), it is a chunkier plant than _Phyllanthus_, and <"it is green">.

Cheers Darrel


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## SOulGirL (2 May 2022)

dw1305 said:


> Hi all,
> 
> <"Probably Amazon Frogbit"> (_Limnobium laevigatum_), it is a chunkier plant than _Phyllanthus_, and <"it is green">.
> 
> Cheers Darrel


Ok! Thank you!


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## _Maq_ (28 Jul 2022)

Simon Cole said:


> sulphidogenesis is rather rare in nature.


I'm perplexed. I too regularly read scientific papers on natural ecology, and in my opinion sulfate reduction occurs wherever sulfates are present. In the oceans, it ubiquitous. It occurs in ponds regularly.
Yes, in peat bogs it may be insignificant if the water is very sparsely mineralized, and therefore sulfates are present in meager quantity. Methanogenesis occurs in such places instead.


Simon Cole said:


> I am less open minded to the possibility that it could form in aquariums because I tend to think that substrates are likely to be permeable to dissolved oxygen and that the chemical conditions for microbial sulphidogenesis are unfavourable and would probably take a very long time to develop.


I hate to disagree with you, @Simon Cole , really. Oxygen penetrates as deep as biological oxygen demand allows. Other factors like coarseness of the sediment or water flow above the sediment are secondary factors.
In commercial substrates containing lots of easily degradable organic matter BOD is very high, oxygen cannot penetrate very deep and anaerobic activity is huge. Sulfate reduction (to sulfide) occurs.
When hydrogen sulfide moves upward it gets oxidized either biotically (faster) or abiotically *before* it reaches the water column. That's the normal state of affairs. But if the BOD is too high, the boundary between oxic and suboxic zone is *above* the sediment and the disaster happens - hydrogen sulfide leaks into water column. Obviously, this is what happened to thread starter.
In our tanks, sulfate reduction is often relegated to very deep zones not because of deep oxygen penetration but because *nitrates* are abundant, nitrate reduction zone (denitrification) is huge and only below this zone sulfate reduction may occur.


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## Simon Cole (28 Jul 2022)

As I wrote, I am still open-minded about magnitude of this process natural freshwater ecosystems, but I am not convinced that there is adequate <evidence>.
Direct evidence for atmospheric hydrogen sulphide emissions from natural freshwater systems can be rather sporadic, and often these measurements are either undetectable or very low.
There is also the suggestion that <plants are emitting most of these gases> as opposed to the water itself.

In terms of aquariums, I am still sceptical. As I proposed, test the potential for your aquarium water to generate hydrogen sulphide, then make assumptions.
I would expect that most ionic sulphur species can diffuse readily into the water column where they are oxidised. I do not foresee aquarium water columns as having the correct reducing conditions to enable hydrogen sulphide to survive for very long when it can diffuse between zones. I think it is plausible that sulphate esters and other organic sulphate molecules (including methyl mercaptans, carbonyl sulphide, dimethyl sulphide, carbon disulphide, dimethyl disulphide) can cause these smells, if sulphidogenesis is the mechanism.

My historical perception does not typically diminish in the face of introduced conjecture. We may well hold different opinions over time, but I am not that bothered about agreeing over a hypothesis, and it's not very fair to imply that a disagreement exists simply because my historical perception does not support a particular position that you hold today. If I had to form an agreement with you, then it would be that I am dubious, sceptical, unresolved, open-minded, and ambivalent, in that order. The academic community is a long way off persuading me that there are obvious disasters waiting to happen. I am uncertain whether what you have said is even hypothetically possible. No offence taken, I am still grateful for your comment


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