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Just a note, anything I posted recently about Nitrospira is invalid to us, as that is not the same as Nitrosonomas and Nitrobacter.

I'll compile all the articles that seem any good post all of the links together, give me a few.

Almost your bedtime Caliban? Some nice dry reading to put you to sleep ;)
 
I know, but if we can gather enough information, we can at LEAST either confirm or deny the "too high ammonia is bad! too high nitrite is bad!" thing that goes around and demands lots of water changes during a fishless cycle.
I've found even MORE articles. I am definitely on the right track. Unfortunately, my brain is going into a kind of overload. I think I need to look over these articles one by one, take notes elsewhere (instead of brain dumping here) and then come back and post some summaries of the relevant information I've culled.

I've just read some really interesting stuff that I think you might be interested in because of our conversation yesterday where you posited that "if you grow too much nitrosonomas[ammonia eating], there isn't room for the nitrobacter[nitrite eating] to grow". This current paper I'm looking at implies that nitrite itself is inhibitory to the growth of nitrosonomas, which would mean that as soon as the nitrobacter starts to grow, the nitrosonomas STOPS growing. Basically implying there should be "room enough for everyone"
... you following all this?

My brain is turning to mush. I need to go play a video game or something and take a break from this lol


Although this could also indicate why some people report that ammonia stays where it is for some time. I've heard people claim that ammonia has hung at 2ppm for example for days. This could be because nitrite I think you mean nitrospira? Eating bacteria has started to grow. This to me would indicate that the bacterias are working TOGETHER.
 
The articles I just read conclude that nitrobacter is not the bacteria responsible for the breakdown of nitrite. It is nitrospira in freshwater aquaria unless I am mistaken nitrospira is very valid to us.
 
OK here comes my link dump. I have not read all of these, no way. These are just everything that I have bookmarked to read and research.

The following are links resulting from my google search "nitrosomona inhibition high ammonia":
http://ftp.mpi-bremen.de/pub/moleco.../Gieseke_EM2003.pdf?origin=publication_detail
Loss of Ammonia Monooxygenase Activity in Nitrosomonas europaea upon Exposure to Nitrite
Nitrite as a stimulus for ammonia-sta... [Appl Environ Microbiol. 2002] - PubMed - NCBI
http://www.environmental-expert.com/Files%5C5306%5Carticles%5C12678%5C401.pdf
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http://www.thewaterplanetcompany.com/docs/WPC_Nitrification & Denitrification .pdf (Delapool's link)
Nitrite as a Stimulus for Ammonia-Starved Nitrosomonas europaea
Strict and Facultative Anaerobes: Medical and Environmental Aspects - Google Books
Microbial Granulation Technology for Nutrient Removal from Wastewater - Yu Liu, Lei Qin, Shu-Fang Yang - Google Books

The following are links resulting from my google search "nitrobacter inhibition high nitrite":
Nitrogen Compounds: Advances in Research and Application: 2011 Edition - Google Books
http://www.isws.illinois.edu/pubdoc/CR/ISWSCR-326.pdf
Limited impact of free ammonia on Nitrobac... [Bioresour Technol. 2010] - PubMed - NCBI
The Prokaryotes: A Handbook on the Biology of Bacteria - Stanley Falkow, Eugene Rosenberg, Erko Stackebrandt - Google Books
Lesson 21: Nitrates and Nitrites
The Nitrogen Cycle - How Ammonia and Nitrite are Controlled in Wastewater and Aquatic Environmentsetc.
Total Nitrification balance
 
Wow I just read the follow-up article by Dr Tim and I'm flabbergasted, this is not what we have been taught at all!
That article he wrote was excellent - still technical, but presented a bit more conversationally so it was easier to follow his process and results.

So our 2nd bacteria (nitrite to nitrate) are nitrospira?? Not nitrobacter?
Are there other articles out there asserting/proving/confirming his results?
This is huge. This means that bacterial additives are SCIENTIFICALLY BUNK unless they have nitrospira instead of nitrobacter.

/ugh now i need another search entirely. Inhibition of high nitrites on nitrospira!
 
OK it's not like it hasn't been said before elsewhere in different years (and swept under the rug), but do you guys realize that we just discovered why bottled bacteria never works (at least not instantly), and we have SCIENTIFIC DATA to back that up?

It only speeds up the growth of the nitrite-eating bacteria (Nitrospira) a little bit and it's probably ONLY because the Nitrosomonas added can help produce some nitrites very early on (before they die) that the Nitrospira can start eating/growing with.

This is huge. We need to keep this up, we can really contribute something to the hobby if we can take all of these scientific papers and studies and condense them into some practical application to share.
 
http://www.ceric.net/wonmun3/ksee/04712722.pdf
This one is about the inhibition of BOTH Nitrobacter and Nitrospira at different levels of free ammonia. Interesting and useful as it may imply that the colony of nitrite-eating bacteria could be of different composition depending how much ammonia and nitrites are present. Pub 2008

https://ftp.kdis.edu.cn/211-xkkr-13/doc/Influence%20of%20physicochemical%20and%20operational%20parameters%20on%20Nitrobacter%20and%20Nitrospira%20communities%20in%20an%20aerobic%20activated%20sludge%20bioreactor.pdf
Influence of parameters on Nitrobacter AND Nitrospira communities. Pub 2010. This is an interesting one which tries to optimize conditions to grow a particular bacteria because they don't have the same environmental needs.

I'm finding now that our aquarium may grow different nitrite-eating bacteria depending on our ammonia, nitrite, temperature levels. MAYBE. This is a theory, I still need to read all of these (although it is becoming too daunting)
 
I saw an interview of Dr tims creator about his bottled bacteria. He basically stated that most bottled bacteria is the type that comes from waste treatment plants which is more suited to live in super high nutrient environments where ammonia and nitrite is off the charts rather than our low nutrient systems. This is apparently why a lot of people have issues using bottled bacteria.
I have only now realized that Dr Tim is Dr Tim who co-authored the paper on Nitrospira.

I'm looking more into his papers and research now.
Here is another paper co-authored by Dr Tim. This one is about the ammonia oxidizing bacteria.
http://www.drtimhovanec.com/Publications/ScientificPapers/files/page8_1.pdf

I actually got excited for a little while, thinking Dr Tim might actually be accessible for contact and discussion, but I imagine he is out of my reach. I would have to pay him for consulting services. In addition, since he has a line of aquarium additives, that would make it difficult for me to trust that he doesn't have an agenda. A shame!
 
OK.
Breakthrough. BIG BREAKTHROUGH.

The ammonia that inhibits nitrifying bacteria is FREE AMMONIA ONLY (NH3)
But MOST AMMONIA in our system at a time is AMMONIUM
http://www.aquariumadvice.com/forums/f12/your-guide-to-ammonia-toxicity-159994.html (Mebbid provided this link)

Therefore when it is reported and perpetuated that high ammonia inhibits nitrifying bacteria, in actuality only free ammonia (NH3) and not the sum total of ammonia and ammonium do this (which is what test kits report - they report SUM TOTAL)
Meaning our cycle can tolerate a FAR HIGHER reading of ammonia on our test kits than people have been led to believe and perpetuate (depending on pH).

Here's a quote
"
Free ammonia and ammonium:

Ammonia is far more toxic than ammonium the pH and temperature will determine the percentage of ammonia to ammonium found in the aquatic environment.
At 24C:
pH 7 - 0.5% of total ammonia is NH3
pH 8 - 5% of total ammonia is NH3
pH 8.2 - 7.7% of total ammonia is NH3
pH 8.4 - 11.6% of total ammonia is NH3
pH 8.6 - 17.3% of total ammonia is NH3
Free ammonia (NH3) will inhibit nitrification at the following levels: Nitrosomonas marina/biospira 10 mg/ and for nitrobacter/nitrospira just 0.1 mg/l. This has implications if you are trying to cycle a marine tank or a freshwater tank with a high pH for African cichlids for example and using the standard internet recommendation of 4 mg/l of ammonia.
Because the free ammonia level will be approx 0.4 mg/l and this substantially inhibit the rate at which nitrite is converted to nitrate. "
Source: Nitrifying bacteria


I will find some additional sources that are more "original" (i.e. the actual paper studies) but I hope that you guys following see what a breakthrough this information is to what we think we "know"

On a side note this explains how/why I can cycle successfully with 18ppm ammonia. Using the above information as an example, at 18ppm NH3+Nh4 I actually only have .495ppm of ACTUAL FREE AMMONIA which is WELL under the 10ppm that the Nitrosomonas can actually tolerate. Given my pH, I would have to have 100ppm of NH3+NH4+ to have even 2ppm of free ammonia. And keep in mind, nitrosomonas can actually tolerate up to 10ppm free ammonia (NH3)

You may ask, what makes ammonia be ammonium? pH. Just pH. I lost my source but I have a paper/article about this. Ammonia likes to team up with "something"(forget what) to make ammonium. The lower the pH, the more of the "somethings" in the water. When there is an available "something", the ammonia pairs with it and becomes ammonium. Simple as that.

OK so WHY do we perpetuate a particular level of ammonia in the cycle? This is the next question. This one DOES have a theory, which is that the nitrIte eating bacterias cannot tolerate ammonia nearly as well.
More research required.

However, I am going to make the following statement: Your nitrosomonas (ammonia eating bacteria) cannot/will not stall due to excessively high ammonia (within reason).
MYTH #1 BUSTED!

Rebuttals welcome. I realize I still need to post some higher qualified sources.

By the way, the bacteria responsible for ammonia oxidation in aquaria is called Nitrosomonas Marina. In this study they studied aquaria bacteria and you can also see that they kept the level of NH3 (again, free ammonia) at 5-10ppm while growing the ammonia oxidizing bacteria for study.
 
A claim from a non-chemist:
"PPM is an expression of mg/L, so in other words, it is a relationship by weight. 1 PPM of ammonia means that each liter contains 1 mg of ammonia. With a molar mass of 17.031 g/mol (1 mol = 6.022 * 10^23 ) that means that that mg of ammonia contains (6.022 * 10^23 / 17.031) / 1000 = 3.536 * 10^19 molecules of ammonia. When those molecules of ammonia get the three hydrogen atoms replaced by two oxygen atoms to become a nitrite ion, all of a sudden we have 46.0055 / 17.031 = 2.7 times the original weight (1 mg) of nitrite in that liter of water, so now we have 2.7 PPM of nitrite. Same number of molecules, but each one weighs more. When those nitrite ions get an extra oxygen atom added to turn them into nitrate, we now have 62.0049 / 46.0055 = 1.35 times more weight yet again, for a total of 3.64 PPM of nitrate."
Source: 1 ppm ammonia = 1 ppm nitrite = 1 ppm nitrate?

If this person's napkin math is correct, 1ppm ammonia converts to 2.7ppm nitrIte.

I can use this to make my own napkin math to estimate the TAN (total ammonia NH3 + NH4) in my system, and then figure out my bad ammonia (NH3).
The day I had .5 nitrites, my TAN went from 18 to 17.81
Next day I had 3ish nitrites, so we'll say I dropped 1ppm ammonia, to 16.81
Next day 5 nitrites, so we'll say I dropped another 1ppm, 15.81
Next day, well, nitrites are capped out. But surely the bacteria is doubled, so let's say I lost 2ppm ammonia, plus a little extra. Let's call it 13.5

We'll say based on the NH3 to NH4 math that the free ammonia (Nh3) in my system is .37125

This should be toxic to my second-level bacteria. But, my nitrite eating bacteria ARE reproducing. I know this because I HAVE nitrates.
So what gives? This is the next part of the research.
 
I wish I could access the entire paper I want to cite, but the abstract may be enough.

Nitrite-eating bacteria, primarily Nitrospira, are NOT affected or inhibited until 10ppm of free ammonia (NH3). Now as we have learned, we don't get levels of NH3 that are this high in aquaria because most of our ammonia reading is actually ammonium.

2006 scientific paper. Source

"Batch tests were carried out with Nitrospira in mixed and pure cultures using concentrations of free ammonia widely believed to be inhibitory to nitrite-oxidizing organisms. The mixed culture batch tests were conducted with mixed liquor from a bench scale completely stirred tank reactor (CSTR) treating a synthetic wastewater having a low C:N ratio. Nitrospira were confirmed as the dominant nitrite oxidizers via RNA slot blotting. Nitrospira moscoviensis were used for the pure culture trials. The results from this study suggest that free ammonia (NH3-N) concentrations of up to 10 mg/L were not inhibitory to Nitrospira either in situ or in pure culture."

Nitrobacter, on the other hand, IS inhibited by free ammonia NH3, starting at levels somewhere from .1-1.0
Source: http://ftp.mpi-bremen.de/pub/moleco.../Gieseke_EM2003.pdf?origin=publication_detail Page 9, section "Inhibition by Free Ammonia"

So far, we have confirmed that ammonia levels that we actually see in our cycle process will not inhibit either first phase or second phase bacterial production.

Now to tackle: How/why does the cycle stall out due to high Nitrites? This will be the focus of my next research.
 
Ok first of all, I was having a nice dream then woke up to this so thanks for that. I am going to read all articles now however, first thing that springs to mind to me from what I have read is that if our test kits are measuring sum ammonia, this would mean that a reading of 0.25ppm ammonia during a fish in cycle is actually much less! since my pH is 7.6 Which makes fish in cycling a bit more appealing ;) we also know that when adding ammo lock we turn the ammonia in to ammonium. You could have a look at how ammo lock does this. Our test kits still read high ammonia even after ammo lock is added.

Now you could also fishless cycle 2 ways. You could lower the ph and dose more ammonia since only a small percentage would be free or you could increase ph and dose less ammonia to get a higher percentage of free ammonia.

My question is this. I have read that nitrosomonas still convert ammonium but nitrospira do carry on this may be due to ph since I believe thst below a certain ph value ammonia becomes ammonium.

Sent from my SM-T210 using Aquarium Advice mobile app
 
Both the free ammonia (NH3) and ammonium (NH4) seem to be converted to nitrite, it is just the question of how much of it is toxic (the NH3) to both the nitrosomonas and nitrospira. The nitrospira is just converting nitrite so it doesn't care about the ammonium as a food source.
I *think*, not 100% certain on that claim, cannot recall.

Overall I think it's best to cycle with the lowest pH reasonable in order to keep the free ammonia low, because the nitrosomonas can convert it either way, and this may allow more Nitrobacter to grow (in addition to Nitrospira)

I decided not to work on the nitrite oxidizing bacteria today because I just don't have any more brain bandwidth lol
It's 2:20 AM here, off to sleep.
 
Growth at low ammonium concentrations a - PubMed Mobile

Ok this article claims that nitrosomonas bacteria does not die off when subjected to low ammonium. It is outcompeted but goes dormant and recovers10 weeks after the last dose of ammonium and continues to convert the ammonia 48 hrs after new dosing

Sent from my SM-T210 using Aquarium Advice mobile app

That is really interesting. Where are you going with this?

Challenging the assumption that our bacteria die off if we make "too much" with the cycle? I've always heard that the excess will die off but apparently it just goes dormant for weeks at a time?
 
That's according to this article yes. I've always questioned the the fact the bacteria die off without food. Without oxygen yes if course but bacteria have survived millions of years if be a bit disappointed if it gave up since it number 1 aim is survival.
 
There are also claims that high levels of nitrite does inhibit ammonia nitrifying bacteria although not massively and there is a suggestion that ammonia dosing should be low in order to let the nitrospira catch up as not to allow nitrites to build up.

What I am interested to know is. At 4ppm ammonia according to api test kit. How much of that is free ammonia? We read that it depends on ph levels but if at my ph of 7.5. The articles claim I would have 0.5% free ammonia which works out at 0.02ppm

This doesn't make sense though as I'm sure dark green ammonia 4ppm on API has killed people's fish before now. Unless of course these were people with a high ph increasing the percentage of free ammonia? Does this sound right?

I read a hell if a lot this morning I need help lol.
 
Ahh we got moved :(

That's a good question re: the free ammonia levels. I follow your statements

I think the link that Mebbid posted is actually more accurate than that quote I posted [regarding free ammonia levels in our total ammonia reading] because free ammonia level is related to BOTH temp and pH. I think that article I quoted from wasn't quite as accurate since it was not taking temperature into account.
So in your example at pH 7.5 assuming a standard-ish temp of 26C then 4.0ppm TAN has free ammonia in the toxic range, at .075ish
According to the charts in the link.
I can't edit out that quote I posted or I would, as I think the charts in the link are more accurate.
 
On another practical application note re: my bucket cycle, the cycle is coming along really fast. TAN(ammonia+ammonium) dropped into readable levels and I have tons of nitrates. Based on the nitrates I think I'm down to 5ppm TAN from my estimated high of 18ppm.
I saw the pH was starting to crash, it was down to about 6.5. So I added a dab of baking soda, although I haven't tested again yet because I wanted it to circulate.
 
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