Writing Prompt: Nitrifying bacteria are undesirable in a reef tank

[Dburr1014]

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?

As you see in post #157, my Hanna checker does not see any nitrate for months now.
Would it be useful information for me to check for nitrite? It's been years since I have, lol.

 

[jda]

I don't know about blue light inhibiting nitrite oxidation, but sunlight or Metal Halides have more blue light than most LEDs. The LEDs just look more blue to our eyes since much of the other spectrums are not there. There is a massive amount of blue light that covers the ocean.

I think that it might be more likely that you have a bad nitrite test. Have you verified with a few other good test kits like LaMotte or Hach? IIRC, and I might not, that .1 to .2 is in the margin of error in most cheap nitrite test kits.

 

[biom]

I don't know about blue light inhibiting nitrite oxidation, but sunlight or Metal Halides have more blue light than most LEDs. The LEDs just look more blue to our eyes since much of the other spectrums are not there. There is a massive amount of blue light that covers the ocean.

I got the information from here, yes it is for wastewater treatment but still :

Light as a Novel Inhibitor of Nitrite-Oxidizing Bacteria (NOB) for the Mainstream Partial Nitrification of Wastewater Treatment

Conventional biological nutrient removal processes in municipal wastewater treatment plants are energy-consuming, with oxygen supply accounting for 45–75% of the energy expenditure. Many recent studies examined the implications of the anammox process in sidestream wastewater treatment to reduce...

www.mdpi.com

"...It was found that blue light illumination effectively inhibited NOB rather than ammonia-oxidizing bacteria due to their different sensitivity to light, resulting in partial nitrification..."

I think that it might be more likely that you have a bad nitrite test. Have you verified with a few other good test kits like LaMotte or Hach? IIRC, and I might not, that .1 to .2 is in the margin of error in most cheap nitrite test kits.

It is Salifert, tested against fresh mixed salt - zero nitrite - clear solution, my son tested his cycling new tank - it was above 2.5 ppm - quite purple. So I would say the test is ok. Of course it is not precise as all colorimetric tests with visual determination.

 

[jda]

Don't you think that you can probably put that one away as just academic? I just skimmed that article, but I did not see the blue spectrum that was used - what nm wavelength? They did indicate about 100 umol/m2, which is about 100 PAR which nearly every tank has that is lit for corals has, and many have WAY more than this. Even if this is a thing, nearly every reef should have these issues in the light. Even if every reef had these issues, they have sumps and areas shaded by rock and corals that have no light.

Even bad test kits can measure zero and high values pretty well... it is the small gradient between barely detectable and zero that have the most room for error. IME, exactly what you are testing.

I am just curios, but do academic studies for AOB for freshwater translate well to saltwater? I most put aside freshwater studies when I am reading, but maybe I should not.

 

[biom]

more on light inhibition:

Influence of light intensity on bacterial nitrifying activity in algal-bacterial photobioreactors and its implications for microalgae-based wastewater treatment

The influence of irradiance on the nitrifying activity in photobioreactors of a bacterial consortium enriched from a wastewater treatment bioreactor w…

www.sciencedirect.com

 

[Hans-Werner]

I just skimmed that article, but I did not see the blue spectrum that was used - what nm wavelength?

Blue LEDs were used. Without more details you can expect that it were "normal" 450 nm blue LEDs. At the same time 450 nm is the most effective wavelength for most biological processes that are either activated or inhibited by blue light.

 

[biom]

AOA are oxidizing the ammonia to nitrite and this accumulates because of lower affinity of nitrifying bacteria for nitrite

I kind of put that hypothesis in a test - two days ago I have started increasing feeding and to add small amount of NH4 (0.2 ppm) and a drop of KZ Amino acids. And surprisingly today ammonia is still undetectable, nitrite dropped to 0.025 (from 0.05 yesterday and 0,1 the day before yesterday), and nitrate raised to 2.5 ppm from practically zero yesterday. So yes, it looks possible in a underfed tank and competition for ammonia, ammonia oxidizing bacteria/ archaea are not producing enough nitrite for NOB to kick in and oxidize it to nitrate.

Just as a side note, during this two weeks of zero nitrate and ammonia and nitrite at 0.2 ppm all my corals looked totally fine. So @Dburr1014 I think it worth it to measure nitrite just for the test.

 

[Hans-Werner]

ammonia oxidizing bacteria/ archaea are not producing enough nitrite for NOB to kick in and oxidize it to nitrate.

Hi Stoyan, I do not completely understand this part of your reply. There seems to be an increase in nitrate and even an decrease in nitrite.

 

[biom]

"Hi Stoyan, I do not completely understand this part of your reply. There seems to be an increase in nitrate and even an decrease in nitrite.

Hi Hans-Werner, yes, that was the surprise, there was clear trend of decreasing nitrite after added ammonia and increased feeding and then nitrate appeared this morning. Don't have clear explanation as of yet but could be NOB need certain higher nitrite concentration threshold to "wake up" (and maybe intensive blue light doesn't help) but once awake they could oxidize NO2 even to lower concentrations before going back into dormant phase? The other explanation is NOB they also need at least some nitrogen in different form (NH4 / aminoacids?) as "building blocks". Very interesting and deserves more scientific approach (better tests and setup) but still quite interesting.

Tank is 20 gal water, no sump, siporax 400ml, skimmer, PO4 = 0.015 ppm (a bit low but stabile) 0.25 ml nopox/day.

 

[Subsea]

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.

Randy,
With a 25 year mature tank, I dose ammonia every day. While I do feed heavy with both live food and flakes, I can grow out much coral. I am all about nutrient recycling, however, fraging and selling coral is easily achieved for nutrient export.

 

[jda]

Blue LEDs were used. Without more details you can expect that it were "normal" 450 nm blue LEDs. At the same time 450 nm is the most effective wavelength for most biological processes that are either activated or inhibited by blue light.

I think that it is a bad assumption to assume 450nm. I have read studies with blue light and they used 380nm and others at 420nm. I would rather an actual scientific paper tell us so that we don't have to assume anything.

They are many chromo proteins that react in the blue range are not most effective at 450nm, so there is not even a parallel here.

 

[Anemone_Fanatic]

I have a scientific hypothesis. If you fill your tank with epoxy instead of water, corals/fish will keep their color forever!

 

[Subsea]

I counter pose: nitrifying bacteria are unavoidable in the common reef tank. First to come life forms, absolute last to go, associated with all life forms we keep by direct unremovable attachment, the denizens must be accepted with open arms

Kudoes to this post.

@brandon429
Because my goal is to achieve as much diversity in filter feeding community of mixed garden high nutrient lagoon, I also sought a diversity of micro fauna & fana to feed different size particles to different filter feeders. No filter socks or protein skimmers to restrict the microbial loop.

 

[Hans-Werner]

I think that it is a bad assumption to assume 450nm. I have read studies with blue light and they used 380nm and others at 420nm. I would rather an actual scientific paper tell us so that we don't have to assume anything.

They are many chromo proteins that react in the blue range are not most effective at 450nm, so there is not even a parallel here.

420 nm and more so 380 nm is not really blue but violet. While 420 nm is at the border to blue 380 nm is almost UV. 450 nm is a standard wavelength for LED, it is the excitation light for most white LEDs.

The fact that there are other chromoproteins doesn't change the fact that ~ 450 nm blue light is the most effective blue light in regulating biological processes. Literature about cryptochromes and blue light effects fills several thick books.

P. S.: Fig. 4B is on inhibition of nitrite oxidzing activity.

 

[Belgian Anthias]

In a small closed natural environment one must provide food and enough nitrogen ( nitrate) consumption and carbon import. One must create a balance between fast and slow growers, between heterotrophs and autotrophs, mainly driven by the C:N ratio of feed, the internal food cycle. One must provide enough and balanced growth to keep the dissolved nutrients levels low. One must be able to direct this growth in order to keep the balance. And most important, one must provide balanced export of growth to prevent overload.
Every life cycle a lot off organic carbon in the feed is exported decreasing the C:N ratio of the feed, constantly increasing the need for nitrifying capacity ( nitrate production) to avoid toxic ammonia accumulation. If using high protein food the nitrate level may increase fast., which in the situation is a good thing. In a mixed tank often fish are target fed with high protein food. Fish and most other organisms taking up that food release +- 80% of the nitrogen in the food directly into the environment in the form of ammonia. A skimmer constantly removes released organic waste ( including organic carbon) but not produced ammonia, this way increasing the importance for nitrifiers to remove toxic ammonia. It is often said a skimmer prevents nitrate accumulation. Does it?

This can be solved very easily by assimilating produced nitrate-nitrogen by importing CO2 using photo-autotrophic growth in a refuge. The export of dissolved nutrients is crucial especially in the long term and then the use of growth driven by light energy is a welcome addition, maintaining the C:N balance due to C import and stabilization of the buffering capacity through NO3-N assimilation. With active management and targeted nutrition, each nutrient can be controlled as desired by harvesting growth.


Good nitrogen and carbon management starts with what is going in, the food added, which should have a high C:N ratio. Commercial fish food for aquarium fish may have a very high protein content ( very high nitrogen content, very low C:N ratio) this way increasing the need for a very effective nitrifying capacity, in particular if a skimmer is used to harvest organic waste ( carbon) leaving inorganic nitrogen compounds behind.

Keeping a marine aquarium without a skimmer, no problem. Without a nitrifying capacity, without all 3 pillars supporting the carrying capacity, yes, no problem, for how long?

 

[Belgian Anthias]

NOB are very sensitive for high ammonia availability. They are inhibited when the ammonia availability reaches a certain but too high level . AOB need a lot of oxygen and always are competing with NOB for oxygen. A battle they both can not win as long enough organic carbon is available for much faster growing ( logarithmic) heterotrophs consuming oxygen fast. That is where archaea play there important role as they are able to function in low oxygen conditions consuming produced ammonia, providing growing conditions for NOB ( lowering ammonia availability by producing nitrite) or for ANAMMOX depending on where in the biofilm the action takes place. On the other hand NOB also are sensitive too high nitrite availability which availability can be lowered by ANAMMOX.

A lot of nitrifiers are able to oxidize ammonia to nitrate, taking over the function of AOB and NOB, mainly in oxygen saturated conditions.

I use availability, not level. Availability of nutrients depends on local activity and local growth rates ( logarithmic) with fast changes, there where the action takes place. One may have high levels but not enough local availability to support high local growth rates and visa versa. At a dept of one mm in a biofilm life and competition is completely different compared to its surface and may be mainly anaerobic, depending on the oxygen consumption and growth rates on and in the outer layers.

Most natural nitrification processes take place in the outer layers of local biofilms (, there where a lot of remineralization takes place, and in which the conditions are completely different as one is able to measure in the water column. One may have a very active nitrifying biofilm combined with a very active remineralization capacity without elevated nutrient levels in the water column. It is this active growth which keeps the nutrient levels low or is responsible for increasing levels. In case of a too low C:N ratio in the feed nitrite and nitrate levels must increase to avoid toxic ammonia levels. This may cause problems from one day to an other if it goes wrong. if the balance is lost it will show in the nutrient levels and the nitrite level then is an important parameter.

When it comes to light, most nitrifiers are very active in the dark. They do not like to be exposed to direct sunlight. That is why AOB, NOB, AOA, function best in a biofilm, in a biofilter, in soil etc...

They do play an important role in managing the holobiont of corals and other organisms.

Nitrate is your friend, not an enemy. In case of doubt, know your enemies.

 

[kecked]

I didn’t read all 9 pages but I just experience an odd one. I messed my tank up by washing my live rock in tap and pulling a heavy layer of algae off the rocks. Tank was dead anyway as the heater failed. I observed that the ammonia spiked no duh there. But when I added a heavy does of bacteria to drop it something odd happed that I did see in my tank before the die off but not always. My nitrates dropped from around 10pm to zero and my phosphate also dropped significanton. That stopped and now ammonia sits there and I see no nitrites or nitrate Despite daily doses of bacteria. Fish seem happy. I did use prime in desperation to save the fish which worked. Alk went to 20. 50% water change coming today. Anyway the nitrate drop was the point of the post.

 

[kecked]

thought….was my oxygen so low that the anerobic bacteria to convert nitrate to nitrogen where working in the open! Poor fish.

 

[Belgian Anthias]

I didn’t read all 9 pages but I just experience an odd one. I messed my tank up by washing my live rock in tap and pulling a heavy layer of algae off the rocks. Tank was dead anyway as the heater failed. I observed that the ammonia spiked no duh there. But when I added a heavy does of bacteria to drop it something odd happed that I did see in my tank before the die off but not always. My nitrates dropped from around 10pm to zero and my phosphate also dropped significanton. That stopped and now ammonia sits there and I see no nitrites or nitrate Despite daily doses of bacteria. Fish seem happy. I did use prime in desperation to save the fish which worked. Alk went to 20. 50% water change coming today. Anyway the nitrate drop was the point of the post.

Why bacteria ( heterotrophs) are added daily? Assuming they do well they grow at a logarithmic rate using up available nutrients. (heterotrophs do not produce nitrite or and nitrate) There will be plenty of these fast growing bacteria everywhere waiting for opportunities. What reason there can be to add bacteria daily?

You must have been very desperate. Seachem claims "prime" does Removes chlorine, chloramine and Detoxifies ammonia, nitrite, and nitrate. Is it a kind of ionizator ? I do not know. Clorine and cloramine should have been removed before using the water for making the salt mix. How ammonia , nitrite and nitrate is detoxified? These are elements triggering enzyme production in bacteria and other organisms to do there job and when needed.
Ammonia toxicity is PH related, NH3 to NH4, and related to the way biological membranes can be penetrated. This also is about local PH, before and after the membrane ( the skin of cells, bacteria and other organisms), the PH difference outside and inside the cells. It is about how these organisms are able to retrieve nitrogen.

Ammonia is produced and consumed constantly. Heterotrophs are the main producers ( remineralization) and consumers and the consumption is related to the C:N ratio of the food which is used and is minerelized. Normally not all produced ammonia and building materials can be used up and then nitrifiers will use the ammonia heterotrophs where not able to use due to growth limitations ( limited availability of dissolved organic carbon. Most is released as CO2 after being used for energy production) Photo-autotrophs can use up produced nitrate ( stabilizing alkalinity this way) and use up all by heterotrophs produced building materials, this way clearing the water of nutrients and introduce organic carbon restoring the C/N ratio of total available feed.

If ammonia sits there and no nitrite is produced, this is a dangerous situation. Why ammonia is not used up? Why nitrite is not produced? Nitrate is safely stored and usable nitrogen. if it is not produced it will be used up relatively fast explaining the nitrate drop.
I have no clue what " prime" contains or what exactly are the so called "bacteria ". What I do know is that using products of which one does not know what they contain or and without knowing how they do what they are supposed to do is NOT the way which will lead to a balanced closed bio-system.

Nitrogen management of a closed system starts with what is going in, the C/N ratio of food added. Using high protein fish food increases the need for an efficient and high nitrate production, certainly if a skimmer is in use. Nitrate is never the enemy but your best friend.

 

[Randy Holmes-Farley]

Seachem claims "prime" does Removes chlorine, chloramine and Detoxifies ammonia, nitrite, and nitrate. Is it a kind of ionizator ? I do not know. Clorine and cloramine should have been removed before using the water for making the salt mix. How ammonia , nitrite and nitrate is detoxified? These are elements triggering enzyme production in bacteria and other organisms to do there job and when needed.

Seachem does claim it, but provides no evidence whatsoever, and independent testing shows it does nothing for ammonia. It also cannot detoxify nitrate and they claim, and likely does nothing useful for nitrite.