Writing Prompt: Nitrifying bacteria are undesirable in a reef tank

[ReefGeezer]

True. No Scientific tests just a couple years of use about 2 times a month getting 50 or so bags of fish from the airport. Prior to use a few(maybe a 1/3) of those fish would die in the tanks after being added(with in a day) with no apparent damage or disease. After we started using prime and acclimating them to the tank parameters in their shipping water unexplained deaths diminished greatly. Just so you all know I dont currently use or advocate the use of prime especially in tanks and have seen or at least thought it may have caused issues with cycling of ammonia, which would mean its doing something. Is it just snake oil? I have no proof either way and no skin in the game.

When I owned an LFS, I initially acclimated 20-30 boxes per week of transshipped fish without Prime back in the day. It was a simple float to establish temp... Open bags and dump into 5 gallon buckets... and drip acclimate. There was an expected mortality rate, but I don't remember it being anywhere close to on-third. I tried products that claimed to "neutralize ammonia or help the fishes slime coat, but nothing seemed to help. Eventually, after talking to several wholesalers, I learned that unless the water in the bags was a lower salinity than that of my system, salinity acclimation was an unnecessary risk. IF I REMEMBER CORRECTLY... Osmotic shock was only an issue when going from a lower salinity to a higher one. I kept my fish systems at 1.018. Transshipped fish, repackaged at LAX, usually came in at or maybe slightly higher. Fish loss decreased greatly once I stopped drip acclimating transshipped fish unless the salinity of the shipment was lower than my system.

If the salinity was lower in the shipping water we would place the fish immediately in water from our system that was diluted to match, or be slightly lower than the shipping water, and then drip acclimate accordingly. I might prefer transferring fish into fresh, ammonia free water to trusting Prime to somehow neutralize, remove, or otherwise lock it up just because Seachem says it does.

I am NOT advising everybody to quit acclimating fish though. Transshipping, or even shipping wholesale fish from LA or Tampa, is different than bringing one fish home from the LFS or even shipping a couple overnight.

 

[BigMonkeyBrain]

Interesting thread that got quite some attention since Friday, so I only scanned through the posts yet. Some very interesting turns.

I just wanted to add that there is a kind of empiric proof that (much) nitrification is not necessary: Oxidating filters like the canister filters used for freshwater aquaria, sponge filters etc. which are very effective substrates for nitrifying bacteria never really prevailed in reef tanks.

In the very early reef keeping a brand, Dupla, tried to advertise trickle filters with plastic "bio balls" but after some initial success reefers soon (largely) gave up using any oxidating filters.

Do you agree? Is this generally accepted?

Regarding nitrifying bacteria (excluding the AOA, ammonia oxidizing archaea): These are chemoautotrophs, so they really need something they can metabolize, ammonia for the ones and nitrite for the others. They also need some concentrations. If they don't get them they just will starve. In most tanks ammonia oxidizing bacteria just won't get enough ammonia to survive or at least to form a substantial population.

However, for ammonia oxidizing archaea this seems not be just as true since they populate not only surfaces and water column but also animals like sponges, corals and fishes.

Interesting ! You stopped short of giving us the okay to dose ammonia


Probably happens !

 

[Hans-Werner]

Interesting ! You stopped short of giving us the okay to dose ammonia

In this regards Randy is right, it is okay.

I personally am not convinced yet that it is necessary, at least not for tanks with some fish or crustaceans which are fed. Additionally, with organic carbon available some bacteria can fix dissolved N2 nitrogen, bacteria called diazotrophic, although the importance of this nitrogen source seems not scientifically proven.

 

[biom]

OK, so the world of reefing is loaded with folks talking about nitrifying bacteria as good bacteria, and some other bacteria are bad.

I think it's a perfectly valid hypothesis that cannot be easily dismissed that nitrifying bacteria are bad for a fully stocked reef aquarium.

Here's the step by step rationale:

1. Corals prefer to take up ammonia instead of nitrate, and will preferentially take ammonia when both are present.

2. Nitrate requires extra energy to use as a source of N, relative to ammonia.

3. When nitrifying bacteria are present, they can grab up ammonia present in the water and convert it to nitrate, leaving less ammonia for corals.

4. Corals, seeing inadequate ammonia then need to take up nitrate, causing reefers to want to raise nitrate above natural levels to ensure corals have at least something as a source of N.

5. Studies show that elevated nitrate can cause detrimental effects on corals.

Hypothesis: Contrary to popular belief, nitrifying bacteria are undesirable in an operating and fully stocked reef aquarium where there are plenty of ammonia consumers.

I don’t think nitrifying bacteria are bad for the reef tank, for sure not that bad as “really bad” bacteria like pathogens or some cyanobacteria.

They could be considered "undesirable" in a reef tank only if there is a proof they could outcompete corals for ammonia. This is unlikely I think, having in mind AO Bacteria are not very effective in processing ammonia and according @taricha experiment it looks like nitrification doesn’t happen in the water column.

I also don’t think it is possible to get rid of them. Even you try to kill them with antibiotics (which I find crazy and dangerous idea), they will return in matter of days, they are everywhere - in soli, in dust, in water, in air on our hands.

 

[biom]

I just wanted to add that there is a kind of empiric proof that (much) nitrification is not necessary: Oxidating filters like the canister filters used for freshwater aquaria, sponge filters etc. which are very effective substrates for nitrifying bacteria never really prevailed in reef tanks.

In the very early reef keeping a brand, Dupla, tried to advertise trickle filters with plastic "bio balls" but after some initial success reefers soon (largely) gave up using any oxidating filters.

Do you agree? Is this generally accepted?

I agree - pure oxidation/nitrification filters like sponges and plastic bio balls were largely abandoned, but other bio medias that offer larger surfaces and potentially low oxygen areas like siporax and bio blocks are still used maybe because they also offer suitable environment for denitrification?

 

[Hans-Werner]

I agree - pure oxidation/nitrification filters like sponges and plastic bio balls were largely abandoned, but other bio medias that offer larger surfaces and potentially low oxygen areas like siporax and bio blocks are still used maybe because they also offer suitable environment for denitrification?

Funny suggestion: Dosing nitrate to feed denitrification.

By the way, here something interesting comes to my mind: There are two kinds of denitrification in which bacteria use nitrate as electron acceptor, the denitrification to N2, dinitrogen gas, and the denitrification to ammonia. Nitrate dosing with subsequent denitrification could be a way to supply ammonia and a little bit of alkalinity and pH increase. It is just the reverse process of nitrification.

I am not sure whether Siporax or bio block filtration are very popular and will remain so. Some promises are made about filter substrates, but I can't assess whether they make sense in reef tanks.

 

[Belgian Anthias]

OK, so the world of reefing is loaded with folks talking about nitrifying bacteria as good bacteria, and some other bacteria are bad.

I think it's a perfectly valid hypothesis that cannot be easily dismissed that nitrifying bacteria are bad for a fully stocked reef aquarium.

Here's the step by step rationale:

1. Corals prefer to take up ammonia instead of nitrate, and will preferentially take ammonia when both are present.

2. Nitrate requires extra energy to use as a source of N, relative to ammonia.

3. When nitrifying bacteria are present, they can grab up ammonia present in the water and convert it to nitrate, leaving less ammonia for corals.

4. Corals, seeing inadequate ammonia then need to take up nitrate, causing reefers to want to raise nitrate above natural levels to ensure corals have at least something as a source of N.

5. Studies show that elevated nitrate can cause detrimental effects on corals.

Hypothesis: Contrary to popular belief, nitrifying bacteria are undesirable in an operating and fully stocked reef aquarium where there are plenty of ammonia consumers.

Autotrophic growth ( nitrification) is one of the 3 essential pillars supporting the bioload of the system. responsible for the carrying capacity.

1. As do most organisms and bacteria. Nitrifiers are essential for turning toxic ammonia not used up by fast growers into safely stored and usable nitrogen. They produce the nitrogen source used by slower growing organisms responsible for restoring and keeping the C/N in balance. In a closed environment after each live cycle less organic carbon is available and less ammonia can be used up by fast growers. What happens without nitrifiers ?
2. That is why fast growing heterotrophs only use ammonia as a nitrogen source using up available organic carbon very fast, needing nitrifiers to remove ammonia not used up. ( Vodka dosing, adding pure organic carbon, first removes all available ammonia much faster as nitrifiers are able , removing the nitrifying capacity this way)
3. Nitrifying bacteria use ammonia not only to grow, their growth rate is low. Carbon is constantly exported to produce energy and nitrifiers are needed to remove all ammonia left over, to prevent a toxic level can be reached. Nitrifiers need 40 times less nutrients than, for example, corals and heterotrophic bacteria to render the same amount of toxic ammonia harmless. They mainly use ammonia which cannot be used by the faster growing heterotrophs due to lack of organic carbon.
4. This has nothing to do with nitrifiers! Reefers doing that are not good informed. This only can be caused by an unnatural C/N ratio ( high protein food, carbon dosing?) which is responsible for the availabilty of ammonia in the watercolumn and maybe too high growth rates within the coral holobiont. Corals are able to mange the C/N ratio and growth rates within the coral-holobiont. They are able to import carbon and produce organic carbon ( symbiodinium) and release mucus. An unnatural C/N ratio makes this management imposible. Using nitrate as a nitrogen source the growth rate of heterotrophs is slowed down by +- factor 8 wich prevents coral bleaching due to lack of phosphorus, mainly caused by too high growth rates within the holobiont due to a C/N ratio out of balance . Dinoflaggelates ( symbiodinium) are effective Nitrate consumers as are most photo-autotrops, although they prefer ammonia as a nitrogen source.
5. More and recent studies have shown this is not true at all, only at very high levels effecting all organisms. Nitrate is safely stored usable nitrogen and is easily removed or reused. It is not dangerous at all. Coral bleaching is caused by abnormal high growth rates, certainly not by nitrate availability. Nitrate reduces the calcification of stony corals but that is normal as nitrate absorption is much slower with lower growth rates as a result. more energy is needed, but energy caption is not a problem for photo-autotrophs. Heterotrophs need organic carbon.

Hypothesis: Keeping a reef without nitrifiers is possible but only in the short term. In most reefaquaria not enough carbon is imported by autotrophs and food with high C:N ratio must be used ( low protein) . Using high protein feed, If ammonia is not used up fast enough it will reach toxic levels fast and nitrifiers will not be available for turning it into harmless nitrate. Nitrate is not the enemy, it is your friend. And for those thinking other wise, know your enemies.

 

[MnFish1]

OK, so the world of reefing is loaded with folks talking about nitrifying bacteria as good bacteria, and some other bacteria are bad.

I think it's a perfectly valid hypothesis that cannot be easily dismissed that nitrifying bacteria are bad for a fully stocked reef aquarium.

Here's the step by step rationale:

1. Corals prefer to take up ammonia instead of nitrate, and will preferentially take ammonia when both are present.

2. Nitrate requires extra energy to use as a source of N, relative to ammonia.

3. When nitrifying bacteria are present, they can grab up ammonia present in the water and convert it to nitrate, leaving less ammonia for corals.

4. Corals, seeing inadequate ammonia then need to take up nitrate, causing reefers to want to raise nitrate above natural levels to ensure corals have at least something as a source of N.

5. Studies show that elevated nitrate can cause detrimental effects on corals.

Hypothesis: Contrary to popular belief, nitrifying bacteria are undesirable in an operating and fully stocked reef aquarium where there are plenty of ammonia consumers.

1. There is constantly ammonia being produced - enough for coral. The ammonia requiring bacteria will go dormant for a while and eventually perhaps die if there is not enough feeding (though judging by the number of people supplementing multiple things into their tanks daily there is probably plenty of ammonia for everyone)
2. Requires extra energy for 'what'
3. See # 1. I'm not sure there is a lot of data that suggest that corals are obligate ammonia users. Since I believe they can use N2, etc etc via symbiotic bacteria (not ammonia requiring)
4. Many people have kept low PO4 and Nitrate tanks for a while now.
5. True (though many people dose it)

Hypothesis - your hypothesis is incorrect - And if it were, the corals, etc would use the ammonia before the nitrifying bacteria - in all likelihood. The nitrifies would go dormant/die and it is a non-issue.

 

[Randy Holmes-Farley]

Hypothesis - your hypothesis is incorrect - And if it were, the corals, etc would use the ammonia before the nitrifying bacteria - in all likelihood. The nitrifies would go dormant/die and it is a non-issue.

Is there evidence to support that hypothesis (that corals get all they want before nitrifiers take it)?

 

[Randy Holmes-Farley]

1. As do most organisms and bacteria. Nitrifiers are essential for turning toxic ammonia not used up by fast growers into safely stored and usable nitrogen.

That may often be true, but it is obviously not always true since it depends on the balance between ammonia input and uptake.

A tank with a deficit for N (such as those where nitrate or ammonia or other N source is regularly dosed) need not fit your description at all.

 

[MnFish1]

Is there evidence to support that hypothesis (that corals get all they want before nitrifiers take it)?

I'm not sure what kind of evidence you would want - i.e. I'm not even sure quite how to design a protocol to test it. So if you mean a study - no. However - it becomes even more complicated - since 'nitrifiers' can include many more bacteria, than most people consider, it. becomes difficult to quantify it.

 

[Randy Holmes-Farley]

I'm not sure what kind of evidence you would want - i.e. I'm not even sure quite how to design a protocol to test it. So if you mean a study - no. However - it becomes even more complicated - since 'nitrifiers' can include many more bacteria, than most people consider, it. becomes difficult to quantify it.

Ok, thanks.

 

[Hans-Werner]

I think this discussion is a bit "unterkomplex" (not complex enough) without the ammonia oxidizing archaea (AOA), please see here and here.

There are some indicators that the main ammonia oxidation in reef aquaria is done by AOA. Besides ammonia oxidation at low total ammonia concentrations it is in my eyes the buildup of nitrite in quite some reef aquaria.

I have experienced it several times that reefers complain about high indication of nitrate test with words like "this can't be, I have low nutrient concentrations". When I told them to please check for nitrite it frequently turned out it was a false-high indication due to some low nitrite concentration.

AOA are oxidizing the ammonia to nitrite and this accumulates because of lower affinity of nitrifying bacteria for nitrite and because of competitive inhibition by chloride ions. This is at least my interpretation at the moment.

I guess we can't finally solve the problems only theoretically by discussion. We may have to wait for better knowledges about the role of AOA and maybe for better observations by reefers.

(By the way, >> THE<< AOA, Nitrosopumilus marinus, was discovered in a marine aquarium.)

 

[BigMonkeyBrain]

Hans-Werner​

"I guess we can't finally solve the problems only theoretically by discussion. We may have to wait for better knowledges about the role of AOA and maybe for better observations by reefers."

In my reading I've found studies that show many different ratios of AOA to AOB in Aquaria ?

"Archaea in Aquaria: Tiny Organisms, Huge Discovery"​

'http://aquariumkids.org/archaea/'

Probably happens !

“So let it be written, so let it be done”

 

[PeterEde]

And with that theory the hobby takes a step forward. Or does it

 

[BigMonkeyBrain]

And with that theory the hobby takes a step forward. Or does it

Discussions open the mind not necessarily change it.

Zager and Evans - In The Year 2525​

"Everything you think, do, and say, is in the pill you took today"

Probably happens !

“So let it be written, so let it be done”

 

[Dburr1014]

I have really enjoyed the discussion.
I don't have much to add to it other than I did start to dose ammonia a few months ago. Not on a regular basis, more of when I think about it. Chronic low NO3 in my testing and PO4 has been pretty stable at 0.1 +/- 0.02
Nothing has died in the past 4 months.
I was dosing calcium nitrate. Stopped after that 8ppm reading and switched to the ammonia.

 

[Randy Holmes-Farley]

FWIW, moving out of the theoretical to the actual, some folks dosing ammonia do report apparent benefits, but those are single reef tank experiments, not controlled studies, and the question always arises, compared to what being done before dosign ammonia (e.g., better than dosing nitrate, and at what levels, or better than not dosing anything with low nitrate, etc.).

 

[Hans-Werner]

In my reading I've found studies that show many different ratios of AOA to AOB in Aquaria ?

"Archaea in Aquaria: Tiny Organisms, Huge Discovery"​

I know some studies about this theme including this one. Unfortunately it does not typify the saltwater tanks. There are no data on the total ammonia concentrations of the saltwater tanks, which would have been interesting.

Other research papers go even further and report or speculate that AOA may play important roles in the marine organisms themselves and internal nutrient cycling. Nitrification by AOA and nitrite oxidizing bacteria is known from sponges and ammonia oxidation might also take place in corals and in and on many other marine organisms. Here it gets really complicated to speculate which effect symbionts may have and how much of the ammonium that surrounds the coral is oxidized to nitrate before it is taken up by the corals.

An interesting tool might be simvastatin, a medication against high blood cholesterol, that is reported to selectively inhibit AOA. Antibiotics are selective for bacteria and don't affect archaea. So in theory it would be possible to inhibit one of both or both and look what happens. The article also gives interesting details about the differences between AOA and ammonia oxidizing bacteria (AOB).

It is really an astonishing career archaea have made, from "strange bacteria" that only occur under extreme conditions of pressure and temperature at volcanic hot spots in the deep sea to an own domain of organisms that are similarly ominipresent as bacteria. Today there are three accepted domains of organisms, Archaea, Bacteria and Eukarya (all other organisms).

 

[biom]

Besides ammonia oxidation at low total ammonia concentrations it is in my eyes the buildup of nitrite in quite some reef aquaria.

I have experienced it several times that reefers complain about high indication of nitrate test with words like "this can't be, I have low nutrient concentrations". When I told them to please check for nitrite it frequently turned out it was a false-high indication due to some low nitrite concentration.

AOA are oxidizing the ammonia to nitrite and this accumulates because of lower affinity of nitrifying bacteria for nitrite and because of competitive inhibition by chloride ions. This is at least my interpretation at the moment.

That is exactly what happening with my experiment right now. I have almost zero (Salifert) Nitrate and Ammonia but .1-.2 ppm Nitrite for two weeks!
I was asking myself same questions why would this happen and why my nitrite-oxidizing bacteria (NOB) are not dealing with Nitrite?
a) lower affinity of nitrifying bacteria for nitrite - that is interesting but in NSW nitrite level is quite low often below .005 and still NOB are thriving.
b) competitive inhibition by chloride ions - I know this is valid for fish but never heard if valid for bacteria NOB will check
c) Inhibition by (blue) light - There is information that oxidation of nitrite is light inhibited especially by blue light
d) skimming - I was wondering since most of the NOB are inhabiting water column may be they are skimmed out and given their very slow reproduction rate might be a problem?