# Bacteria/biological starters



## Bolota

Hi,

What is your opinion on Bacteria starters (like green Bacter and others)? For my new setup I'm using new Tropica soil, new filter and only TC plants. Should I worry about the micro-flora and give it an additional push?
Is that just fish related issue?
Thanks


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## ian_m

One of the most brilliant ways of getting money from your wallet into the fish shop. Only beaten by test kits.


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## ceg4048

I agree with Ian. You can get billions of bacteria for free by simply digging up the largest weeds you find in your garden and scraping the soil from the roots. Mix it into the substrate as well as mixing it into the filter media. Job done.

Cheers,


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## kadoxu

Patience will do you wonders in this hobby... and saving you loads of money is also one of the nice things it does for you (I've learned this the hard expensive way)!


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## Nigel95

I didn't believe in bacteria bottles but someone gave me a tip to try bactostart from aquarium munster. Costs €7 and you dose it all at once. Works like a charm for me if you want cycle in a few days. And I used ada aqua soil which releases pretty much ammonia. The ammonia and nitrite peak did go really fast. But I also used a cycled filter... this may help as well. But I rescaped before with a cycled filter and the cycle of ammonia and nitrite did last much longer....

I am ok with 7 euro for a faster cycle... The green bacter is expensive IMO


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## dw1305

Hi all, 





kadoxu said:


> Patience will do you wonders in this hobby...


I agree with the others, none of the bacterial supplements are very useful. 

Have a look at <"Japanese Bonsai Gardens......"> and Dr Tim Hovanec's article <"Bacteria revealed">.

cheers Darrel


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## zozo

Nigel95 said:


> I didn't believe in bacteria bottles but someone gave me a tip to try bactostart from aquarium munster. Costs €7 and you dose it all at once. Works like a charm for me if you want cycle in a few days. And I used ada aqua soil which releases pretty much ammonia. The ammonia and nitrite peak did go really fast. But I also used a cycled filter... this may help as well. But I rescaped before with a cycled filter and the cycle of ammonia and nitrite did last much longer....
> 
> I am ok with 7 euro for a faster cycle... The green bacter is expensive IMO



Aren't you mixing things up? Bactostart is from Colombo..  And Münster has Aquavital Bactosprint.  I believe in neither of them or more to say non at all. And lab studies revealed that the survival rate of freeze dried bacteria products are rather very low when stored. Even the liquified ones didn't reveale any significant difference. There was no way to proof that the results were because of the extra added products. Well, never the less, even if few survive and wake up. <.It doesn't change the fact that you introduce sufficient life bacteria with the plants..> In some plants spp. these nitrifying bacteria are called <Rhizobiums>, these plants spp. develop special nodules at their roots bursting with these bacteria populations. Even in such high numbers these plants can grow on nitrogen poor soils and still survive on the nitrogen produced by the Rhizobiums. So if you want an absolute rocketing bactosprint burst, than make sure you have some <Fabales> in your garden, dig a few up and do what @ceg4048 says.

But these strains of bacteria actualy live in symbiosis with all plants, they are soil bacteria also found living in water.

Thus putting enough plants in a starting tank makes an extra additional boost not realy that more beneficial. Than you can safe the cash and buy yourself a nice diner for it..


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## Majsa

I read here at the forum that a starter bottle should contain Nitrospira species, such as Tetra Safe start...Although I am about to start a new tank with my "holiday method" the second year in a row, without bottled bacteria: 1) set up a tank in the spring / early summer 2) change water and mess with CO2 3) let it run and go on a summer holiday 4) add fish. Can't leave new fish unattended so the holiday gives me a nice "buffer" (last year 2 months exactly from start to fish).


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## Angus

I've never used them, i've seen anecdotal evidence on other forums that products such as Hagen's "cycle" make no difference in the time it takes to cycle a tank, best bet for speeding up a cycle is to try and find someone who can sort you out some filter mulm in my opinion.


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## dw1305

Hi all,
If you ignore whether these products contain active microbes or not, the main issue for me would actually be the method of production. They are produced commercially in environments with high ammonia loadings, meaning that even if they contain nitrifying bacteria they are likely not to be the ones that will survive in your tank.

If you look at Tim Hovanec's comments, towards the end of <"Bacteria revealed">, he says: 





> ......Finally, the results of the many tests I report in this paper demonstrate that Nitrobacter winogradskyi and its close relatives are not the nitrite-oxidizing bacteria in aquariums. Rather, this task falls to the Nitrospira-like bacteria.....


 He doesn't talk about are Archaea, but there is a lot of modern research  suggesting that they are the organisms you need.





dw1305 said:


> .... there are a number of papers specifically on the nitrifying organisms in aquarium filters which suggest that their assemblage shows a fluid response to varying ammonia loadings, with a stable core of archaea and an ever changing cast of nitrifying bacteria. This is described in <"Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing _Archaea_ and Comammox _Nitrospira"_>.


cheers Darrel


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## zozo

@dw1305 - Darrel do you know the numbers on this statement? Just curious what the values are..  


> Though water that is too rich in ammonia or has a pH that is too low will inhibit _Nitrospira'_s nitrifying activity


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## Tim Harrison

Bacterial communities cover every surface of the planet, often in biofilms. These communities are dynamic and change constantly according to available nutrition etc - for example, Darrel's fluid response to various ammonia loadings.

This response is very rapid - bacteria reproduce by binary fission. Most bacteria have generation times of one to three hours. Some species can double every 20 minutes, given optimal conditions. If that growth rate were sustained, a single cell would give rise to a colony weighing a million kilograms in just 24 hours. However, growth is checked by nutrient availability or accumulation of metabolic wastes etc.

Given those growth rates, even if the supplements contained the right bacteria, they wouldn't really be needed. I've never used them and my tank usually cycles in about a week.


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## zozo

Tim Harrison said:


> Bacterial communities cover every surface of the planet, often in biofilms. These communities are dynamic and change constantly according to available nutrition etc - for example, Darrel's fluid response to various ammonia loadings.
> 
> This response is very rapid - bacteria reproduce by binary fission. Most bacteria have generation times of one to three hours. Some species can double every 20 minutes, given optimal conditions. If that growth rate were sustained, a single cell would give rise to a colony weighing a million kilograms in just 24 hours. However, growth is checked by nutrient availability or accumulation of metabolic wastes etc.
> 
> Given those growth rates, even if the supplements contained the right bacteria, they wouldn't really be needed. I've never used them and my tank usually cycles in about a week.



Best example.  As many people experience(d) the all of a sudden cloudy and milky water appearing in minutes often after a drastic change in water parameters or soil disturbance and than doing a water a change but minutes later it's milkey again.. The famous bacterial explosion, in such vast numbers it clouds the water.


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## Nigel95

Yes I mean bactosprint.

I do plantless cycles from now on, so no plants at the start.


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## Aqua360

As I understand them, and my description here will be very rudimentary, aren't they supposed to bind ammonia to ammonium, or keep it at 1ppm to allow for the filter to "catch up", without killing the fish, instead only acting as a stressor?

In any case, using established media is 10x better, which shouldn't be too hard to procure if you know anyone or shops locally that can provide.


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## Aqua360

ceg4048 said:


> I agree with Ian. You can get billions of bacteria for free by simply digging up the largest weeds you find in your garden and scraping the soil from the roots. Mix it into the substrate as well as mixing it into the filter media. Job done.
> 
> Cheers,



I've never heard of this, but sounds intriguing!


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## zozo

They are soil bacteria and also live in wet conditions.. The name only implies where the are found in greatest numbers, but they are everywhere all around us, not only in the soil, just everywhere where they can nitrificate something or doramntly wait for something to nitrificate so to speak. Could very well be you have a few 1000 of them under your fingernails at the moment.

Even if you do absolutely nothing special for it, they will come on their own and find your tank. But they are actualy already in your tap water. In those days iron pipes were still used even more, because they seem to love to live in iron pipes.


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## ceg4048

Aqua360 said:


> I've never heard of this, but sounds intriguing!



Yes, as zozo mentions, the microorganisms that perform the nitrification live on land as well as in wetlands. They are the same and they function in exactly the same way. There is also a symbiotic relationship between plants and bacteria. 

Plants produce Oxygen via photosynthesis in the leaves and they transfer this gas to the roots. 
Root cells also need to breathe. The remaining Oxygen sent to the roots which is not consumed then escape out of the roots and out into the substrate.

The area within the vicinity of the roots is called the rhizosphere.
In Aquatic sediments however, there is usually a very poor Oxygen level and this would typically foster the development of anerobic microorganisms.

By sending Oxygen down to the roots the plant oxygenates the rhizosphere and so fosters the development of aerobic microorganisms. Terrestrial plants also transfer CO2 down to the roots.

This community becomes diverse and many of the microorganisms we depend on to detoxify the tank grow in abundance within the rhizosphere.
The roots feed the microorganisms with gasses and carbohydrates and the microorganism return the favor by fixing Nitrogen, Iron and other nutrients which the plant then uptakes.
The closer the soil is to the roots, the higher the Oxygen content tends to be and the richer the population of aerobic and beneficial microorganisms.

So if you pull up any weed, for example , and scrape off the sediment from the roots, you will actually have a rich source of  microorganism community with which to seed your substrate and your filter media. These are live and healthy population. The bigger and more robust the weed or grass, the better.

This is a much better source than the flimsy, freeze dried zombie bacteria that vendors pawn off on unsuspecting hobbyists, and it's free.
The same is true of your house plants. Grab some soil from those roots.

People are always fretting over"what kind of substrate do I need?", "How many layers of this product or that product?"

If you stop and think about it, you'll realize that plants grow in every type of sediment. They grow in the concrete of your driveway, or in rocks on a cliff. They grow in dirt.  That part is simple, but amazing and complex things happen in the dirt. Plants change the dirt into things that they need and that we need.




A nice little article in plain English: https://www.pacifichorticulture.org/articles/plants-are-in-control/

Cheers,


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## ceg4048

Aqua360 said:


> As I understand them, and my description here will be very rudimentary, aren't they supposed to bind ammonia to ammonium, or keep it at 1ppm to allow for the filter to "catch up", without killing the fish, instead only acting as a stressor?


Ammonia (NH3), which is highly toxic, and Ammonium (NH4) which is much less toxic are two Nitrogen species which coexist in equilibrium.
The do not bind in any way, but instead one can morph into the other if there is a change pH of the water.
At pH below 7 any NH3 released in the water will chemically change mostly into NH4. At pH above 7 the equilibrium shifts towards NH3.
No bottled zombie bacteria can suppress the pH of the water.



Aqua360 said:


> In any case, using established media is 10x better, which shouldn't be too hard to procure if you know anyone or shops locally that can provide.


Yep, I agree.

Cheers,


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## Bolota

Hi, 
Thank you all for the comments. However, in the context of the planted tank, and assuming that the time scale for the development of the microfauna is so short, why do we usually assume the tank is cycled not before a month or so? Also, in this respect, what is the definition of matured tank, and why do we usually expect that to happen only a few months after start? 
Because we (newbies and non-specialist) associate the concept "cycled" to the Nitrogen - cycle and this to bacteria communities... And what is "Matured" tank in this context? Why does it take so long?


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## Tim Harrison

I don't know...usual hokum maybe. Or perhaps folk are confusing tank cycling with substrate mineralisation, or the length of time it takes for substrates like AS to stop leaching ammonia.
Overall levels of ammonia, nitrite, and nitrate always seem to stabilise within acceptable levels quite quickly, often within a week or two because by then the filter has cycled and can handle the ammonia given off by the substrate.
So although it can take a few months for the AS to stop leaching ammonia, for instance, it's not usually necessary to wait anywhere near that long before adding critters.

As far as the tank becoming mature, there are probably a number of processes that contribute, assuming that it all goes according to plan. For example, after a few months or so the substrate stops leaching ammonia, plants have oxygenated the rhizosphere to one degree or other, and plant biomass will hopefully have increased greatly, along with healthy microbial activity. All these processes work synergistically to infer greater biological stability, making the whole system more robust.


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## ceg4048

Bolota said:


> Hi,
> Thank you all for the comments. However, in the context of the planted tank, and assuming that the time scale for the development of the microfauna is so short, why do we usually assume the tank is cycled not before a month or so? Also, in this respect, what is the definition of matured tank, and why do we usually expect that to happen only a few months after start?
> Because we (newbies and non-specialist) associate the concept "cycled" to the Nitrogen - cycle and this to bacteria communities... And what is "Matured" tank in this context? Why does it take so long?


Hi,
    The term "cycled" is a misused term and is often misunderstood. Many people believe that, as a result of the Nitrogen cycle, where NH3/NH4 is oxidized to NO2 and then to NO3, as soon as their test kit readings of NH3/NH4 subsides, then this automatically means that tank has completed it's initial buildup of important bacteria and that their filter is capable of sustaining the sewage created by the addition of fish.

This is a flawed belief because there are a lot more species and populations of microorganisms that are required to keep the system stable.

In effect, it's a number game. The tank water, sediment, and filter require trillions of trillions of  these species, and their reproduction rate takes time, i.e., one becomes two, becomes 4, becomes 8, and so on (this method of reproduction is called binary fission). The combination of their rate of reproduction and the numbers needed to fully handle the sewage requirement as a stable system means that it usually takes about 6-8 weeks for all this to occur. When the stable system is in place the tank is considered "mature". Even so, stable systems crash when mismanaged. Anoxic conditions, caused by poor maintenance, overfeeding and so forth can disrupt the populations of aerobic microorganisms and can destabilize the system.

As I mentioned, plants help with this maturation because they facilitate the development of aerobic microorganisms both in the sediment as well as in the water and by extension, the filter. 

Because a tank is NOT a natural system, despite clever marketing phrases such as "Natural Aquarium", it really can be a lottery as far as which combination of microorganisms inhabit the system. We want, as much as possible to foster the growth of the aerobic types because they are the ones that perform sewage treatment - however, plants also perform this same function. For example, plants uptake NH3/NH4. Most people focus on the fact that our preferred microorganisms uptake NH3/NH4 and they completely forget that these organisms require carbohydrates, Oxygen, Phosphate, Iron and other nutrients as much as, or in some cases, more so than they need NH3/NH4. In caring for your plants, you will also be helping to develop the desirable community of microorganisms and will be deterring the development of the undesirables.

Cheers,


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## sciencefiction

zozo said:


> @dw1305 - Darrel do you know the numbers on this statement? Just curious what the values are..


Tens of ppms of ammonia.... and the nitrifying population is apparently a lot more sensitive to pH than to ammonia levels, irreversibly so. They adapt to different ammonia levels. The levels that drasically change the populations are way higher than the ones in aquariums, even the ones used in fishless cycle.


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## richard brown

I just got a bottle of quick start by accident (sent missus for tap safe while she was out) and she came home with interpet quick start  not gonna use it in new tank, just gonna use water from my current tank and maybe squeeze some media.


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## dw1305

Hi all, 





zozo said:


> Darrel do you know the numbers on this statement? Just curious what the values are.


I'll have a go at these. 

The original paper on the complete oxidation of ammonia to nitrate by _Nitrospira_ spp. (complete ammonia oxidation; comammox) is Van Kessel _et al. _(2015) <"Complete nitrification by a single microorganism"> _Nature_. 2015 Dec 24; 528(7583): 555–559. 

The bacteria were identified in a bio-filter from Common Carp (_Cyprinus carpio_) RAS aquaculture, and this contained 0 - 75 µM NH4+. The RMM of NH4 is 18 (14+4), so a 0.75M solution of NH4+ would contain 18*0.75 = 13.5g NH4+ in 1 litre of water. 

Then we just need to do some sorting out with "powers of 10". A  "µM" is 10-6 Mol, so we use 13.5/1,000,000 (1*10^6) = 0.0000135 to give us a weight of NH4+ in grams. 

Then ppm is equivalent to mg/l, so we multiply 0.0000135*1000 (1*10^3) to give us 0.0135 ppm NH4+ (or we can take the two ^10 away from one another and divide 13.5/1000). In the paper they used a top ammonium loading of 500 µM NH4+ which (0.0135 * 6.667) gives 0.9 ppm NH4+. The reactor was maintained at pH7. 

There is probably a more modern reference, but the top level of NH4+ used may relate to the work of Kim, Lee & Keller (2006) <"Effect of temperature and free ammonia on nitrification and nitrite accumulation in landfill leachate and analysis of its nitrifying bacterial community..."> _Bioresour Technol_. 2006 Feb;97(3):459-68. 





> ......The activity of NOB was inhibited by NH3-N resulting in accumulation of nitrite. NOB activity decreased more than 50% at 0.7 mg NH3-N L(-1)....





sciencefiction said:


> Tens of ppms of ammonia.... and the nitrifying population is apparently a lot more sensitive to pH than to ammonia levels, irreversibly so. They adapt to different ammonia levels. The levels that drastically change the populations are way higher than the ones in aquariums, even the ones used in fishless cycle.


All the work I've read would strongly suggest that even small increases in ammonia loading drastically effect the microbial community. The initial reference would be Bartelme _et al._ (2017) <"Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox _Nitrospira_"> _Front Microbiol._ 2017; 8: 101. This had a top level of about 14 µM NH3 





> .......RAS operations data was examined from the beginning of a Yellow perch rearing cycle until ~6 months afterward. The mean biofilter influent concentrations of ammonia and nitrite were, respectively, 9.02 ± 4.76 and 1.69 ± 1.46 μM. Biofilter effluent ammonia concentrations (3.84 ± 7.32 μM) remained within the toxicological constraints (<60 μM) of _P. flavescens_ reared in the system.





Bolota said:


> However, in the context of the planted tank, and assuming that the time scale for the development of the microfauna is so short, why do we usually assume the tank is cycled not before a month or so? Also, in this respect, what is the definition of matured tank, and why do we usually expect that to happen only a few months after start?
> Because we (newbies and non-specialist) associate the concept "cycled" to the Nitrogen - cycle and this to bacteria communities... And what is "Matured" tank in this context? Why does it take so long?


It is like Clive @ceg4048 says the microbial community will always change dependent upon oxygen, ammonia, carbon etc. availability. If you just ignore the filter for a minute, and think about the substrate, as roots grow (and senesce) they will create gradients of carbon, oxygen and nutrient availability. As a general rule in ecology complexity brings stability and resilience, and species diversity (but not biomass) is highest in patchy, low nutrient situations. Since we had the ability to look at microbial DNA we've found thousands of "new" micro-organisms in bio-filters. From the Bartelme _et al._ paper ....





> ...We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by _Chitinophagaceae_ (~12%) and _Acidobacteria_ (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. _Archaea_ also were abundant, and were comprised solely of a low diversity assemblage of _Thaumarchaeota_ (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes.



You can create a low diversity microbial environment by having high ammonia loadings and a bare tank (no plants or substrate), and the biofilter will develop the bacterial community that we were told we needed to "cycle" our tanks. It is a black and white scenario, bacteria present = cycled, but it doesn't have to be like that and I'm personally convinced that it isn't the best option for 99% of fish keepers.

cheers Darrel


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## zozo

dw1305 said:


> I'll have a go at these.


Thanks, another night bussy...


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## dw1305

Hi all, 





zozo said:


> Thanks, another night busy


Another couple for you. The reference I couldn't find earlier is Kits _et al._ (2017)<"Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle"> _Nature_ 549, pages 269–272 (14 September 2017)





> ........Uncultured comammox _Nitrospira_ are highly abundant in biofilms from groundwater wells, drinking water treatment systems, and freshwater biofilters exposed to bulk concentrations of NH4+ from ~4 to 60 µM. Furthermore, recent _amoA_ qPCR data showed that comammox _Nitrospira_ were the most abundant ammonia oxidizers in a groundwater well containing on average 2 µM ammonium.....


The other paper is Cai, _et al._ (2018) "Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification" _Front Microbiol_. 2018; 9: 280.





> ..We used a culture-dependent approach to simulate the _in situ_ nitrification process in a freshwater biofilter to study the ecophysiology of the ammonia-oxidizing and nitrite-oxidizing guilds at a relatively low nitrogen concentration and the synergistic relationships between these guilds.
> 
> The cultured _N._ _vulgaris_ may be as competitive as _Nitrospira_-like NOB in oligotrophic environments. The nitrification kinetics of the cultures are influenced by NH4+ and/or NO2-, and HCO3- concentrations. Metagenomic sequencing indicated the draft genomes of the nitrifying partners (_Nitrosomonas_-like AOB and _Nitrobacter_-like NOB), and that their growth rate, substrates affinity, and lag duration strongly depended on the presence of each partner. Although the AOB and NOB could function independently, when both were present together, robust nitrification occurred.
> 
> Overall, the observations in this study indicate the competitiveness of the cultured _Nitrosomonas_-like AOB and _Nitrobacter_-like NOB in an oligotrophic environment and a strong dependence of their activities on the synergistic relationships between the two guilds. These results provide insights for possible manipulations of multi-species interactions to optimize nitrification treatment processes.


cheers Darrel


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## zozo

dw1305 said:


> Another couple for you.


Thanks again..


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## Zeus.

zozo said:


> Thanks again..



So if you could read the papers which Darrel has provided for you Zozo and then do a summary for the rest of us


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## zozo




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## dw1305

Hi all, 





Zeus. said:


> and then do a summary for the rest of us


Here is another one for Marcel (@zozo): Bagchi_ et al._ (2014) <"Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters">. _PLoS ONE_ 9(12): e113515. https://doi.org/10.1371/journal.pone.0113515.

In fact I would probably start with this one, it is a bit more _cute and cuddly_ than the other papers.





> .....Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (_amoA_) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable _amoA_ genes in three aquarium biofilters........These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.


cheers Darrel


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## zozo

Well first glans summary.. That's unexpectedly quite a lot...  But definitively give it a go to get a grasp..


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## sciencefiction

_Digestion of ammonia-oxidizer SSU rDNA with five restriction enzymes showed that a *high ammonium level resulted in a great community structure change that was reversible once the ammonium concentration was returned to its original level.* The smaller changes in community structure brought about by the two *pH extremes*, however, *were irreversible.*

Nitrifying bacteria exhibit different substrate concentration sensitivities (26). Media containing low substrate concentrations (10 mg of NH4+ liter−1) can give larger most-probable-number counts of ammonia oxidizers than media containing higher NH4+ concentrations (6, 26). *Also, ammonia oxidation is inhibited at high substrate concentrations. The growth rates of Nitrosomonas spp. cultures were reduced in the presence of 1,050 to 2,800 mg of NH4+-N liter−1*

In environments with high inputs of ammonium, such as wastewaters, biooxidation of this substrate increases the oxygen uptake and lowers the pH. Such modifications of the environment not only affect the production of nitrite and nitrate but can also select a different nitrifying community that is perhaps specialized for these new conditions. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106468/_


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## AverageWhiteBloke

After serious contemplation and taking everything into consideration I've carried out my own personal time,motion and feasibility study on the benefits of commercial bacteria cultures and the conclusion is that it would be quicker for me to go yank a dandelion out my back garden then spend the money on four cans of cider than to read the papers @dw1305 has provided. Then I would have to deal with the the stark reality that after reading them I wouldn't understand any of it. In fact, getting the Dandelion would be quicker than it's took for me to read this post never mind the papers.

What is baffling me though is why plantless cycle other than obviously if you never intend to keep plants in the tank ever and surely adding plants from an established system is probably THE best thing anyone can do to get the ball rolling on maturing an aquarium as well as all the other obvious benefits? The first month most people are still dialling in their setup which I find is best done without fish in, you can cock up without costing any fish its life.


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## dw1305

Hi all, 





sciencefiction said:


> _Digestion of ammonia-oxidizer SSU rDNA with five restriction enzymes showed that a *high ammonium level resulted in a great community structure change that was reversible once the ammonium concentration was returned to its original level.* The smaller changes in community structure brought about by the two *pH extremes*, however, *were irreversible.*
> 
> Nitrifying bacteria exhibit different substrate concentration sensitivities (26). Media containing low substrate concentrations (10 mg of NH4+ liter−1) can give larger most-probable-number counts of ammonia oxidizers than media containing higher NH4+ concentrations (6, 26). *Also, ammonia oxidation is inhibited at high substrate concentrations. The growth rates of Nitrosomonas spp. cultures were reduced in the presence of 1,050 to 2,800 mg of NH4+-N liter−1*
> 
> In environments with high inputs of ammonium, such as wastewaters, biooxidation of this substrate increases the oxygen uptake and lowers the pH. Such modifications of the environment not only affect the production of nitrite and nitrate but can also select a different nitrifying community that is perhaps specialized for these new conditions.
> 
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106468/_


Yes, this is the classic view of nitrification (the paper is from 1998). It is based upon the bacteria you could isolate, and grow, from a sample of waste water (because of the ammonia loadings it is has a large sewage component). It isn't really relevant when you move away from waste water treatment.

It is towards the start of the DNA based revolution in biological science, and is using PCR etc,. but on the cultures that were isolated and grown from the original waste water sample. 

Because we have much more extensive DNA libraries we can know look at the microbes _in situ, _meaning we've gone from a situation where we know about the few bacteria you can culture to one where we've found the thousand different organisms mentioned earlier in the thread.





AverageWhiteBloke said:


> Then I would have to deal with the the stark reality that after reading them I wouldn't understand any of it.


I'll be quite honest there is a lot of it that I don't fully understand, things move really quickly in genomics, it it the wild west frontier of biological sciences with a huge amount of time, money and effort being directed towards it. 

cheers Darrel


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## Zeus.

dw1305 said:


> I'll be quite honest there is a lot of it that I don't fully understand,



Good takes the pressure of us to try . Same in all specialties within Science eg chemistry, biology, physics and 'maths' a good understanding of the general principles and mechanisms etc can get you a long way, without the need off knowing all the details. 
Took years of study to get the Eureka moment of learning when a photon of energy is captured by a mitrocondria which results in an electron moving its orbit within ATP to provide the the main energy source of all life on earth.


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## Edvet




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## zozo

Zeus. said:


> Took years of study to get the Eureka moment of learning when a photon of energy is captured by a mitrocondria which results in an electron moving its orbit within ATP to provide the the main energy source of all life on earth.



I know i little of that part from my studying paramedics time over 30 years ago.. Physiology has a major part in it.. I remember the ATP/ADP cycle also intrigued me a lot.. But more to say, forgot most of it again since i only studied it and never realy worked in this field after that, than most if it all washes away again over the years. Also not realy that important, the books on my shelf, still available today as antiquebook, probably rather outdated since a lot ideas, theories etc. in this field need to be and are revised every 5 years anyway. So i have no idea what still holds value and what was completely wrong.

I remember one book in particular from Solomon H. Snyder, about Neuro Chemistry. It actualy was the only book in this erae stating in its epilogue. 

"All this is based upon generaly accepted theories and plausible hypothesis and should not be considered as absolute truth."

Made me look differntly at all literature from authors failing to state this. Probably something considered obvious, but still not for all that read it.


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## Zeus.

zozo said:


> But more to say, forgot most of it



Forgot most of my degree also, but we don't need/use the details on a daily basis. 
But the light/photons emmited by the sun to there capture in the ' baterial' entitys ie mitrocondria within living cells provided the soul energy source for complex life on earth was pretty mind blowing at the time, plus chemistry, biology and physics became one as they are OFC.


----------



## dw1305

Hi all, 





AverageWhiteBloke said:


> What is baffling me though is why plantless cycle other than obviously if you never intend to keep plants in the tank ever and surely adding plants from an established system is probably THE best thing anyone can do to get the ball rolling on maturing an aquarium as well as all the other obvious benefits? The first month most people are still dialling in their setup which I find is best done without fish in, you can cock up without costing any fish its life.


In the thread we had a while ago, using ADA aquasoil, <"Cycling without plants?"> it allowed the owner (@Cor) to "cycle" the tank with the light off. He didn't need to add any nutrients, because he was using Aquasoil. 





Edvet said:


>


Made me laugh, but I'm not sure <"Karl Popper"> would approve. 

This is something that I admire about Dr Tim Hovanec, even though he was scientifically (and economically invested) in the traditional view of nitrification, he has been willing to admit that <"_the past is another country">_ in light of more recent research into microbial filtration. 

cheers Darrel


----------



## sciencefiction

Thanks Darrel, very informative.

I don't know if you posted the below study but it's very readable for us simple mortals. I've picked a few quotes...


It basically says that in fresh water aquariums the dominant nitrifyers are "_ammonia-oxidizing archaea (AOA), belonging to the newly proposed phylum Thaumarchaeota"..._The amount of AOA compared to AOB is orders of magnitude higher in freshwater biofilters according to the study and its inversely related to the ammonia concentration. They suggest that the first nitrifyers in newly set up tanks could be AOB due to the higher ammonia levels and as the levels go down, there's a shift to AOA dominance. In my personal opinion. 

_This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoAgenes. 

For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration...

Neither hardness nor alkalinity correlated significantly with any other water chemistry parameters....

Although the detectable ammonia concentrations in established freshwater aquaria are typically low as a result of biological ammonia oxidation, a preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3), suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations._

_This study has identified that AOA are the dominant ammonia oxidizing microorganisms in freshwater aquarium biofilters. Aquarium ammonium concentrations were significantly and inversely correlated with AOA∶AOB ratios.

We also sampled from eight saltwater aquarium filters and two aquarium supplements for comparison (Table S1). Bacterial supplements (typically bottled liquid suspensions) are intended to aid in populating newly established aquaria with active nitrifying bacteria, to help ensure that ammonia and nitrite concentrations remain below toxic levels during the initial 1–2 months of aquarium filter colonization. The aquarium supplements included were Cycle (SP1; Rolf C. Hagen Inc., Montreal, Canada), and Bio-Support (SP2; Big Al's Distribution Centre, Niagara Falls, NY).

Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. _


----------



## sciencefiction

And the below one focuses on diversity of AOA.
*Partitioning of Thaumarchaeota populations along environmental gradients in high mountain lakes*
https://onlinelibrary.wiley.com/doi/full/10.1111/1574-6941.12047

Some quotes:

_Overall, this study provides strong evidence that, as for soil AOA, pH may be an important driver of aquatic AOA community composition with specific 16S rRNA and amoA gene lineages adapted to different pH ranges. Initially believed to be restricted to acidic soils, phylogenetic analyses revealed that AOA from the SAGMGC‐1 cluster are potentially important players in the nitrogen cycle of oligotrophic freshwater environments.

In recent years, environmental rRNA sequencing has shown that Archaea are extensively present in freshwater ecosystems and that most of them (excluding methanogens) are unrelated, or at best distantly related, to cultured counterparts (Auguet et al., 2010). Therefore, the metabolic potential of archaea in continental aquatic ecosystems and the impact in the freshwater biogeochemical cycling are largely unknown. There are, however, a few exceptions that have been recently explored. Among the archaeal phyla detected in freshwaters, Thaumarchaeota dominate in oligotrophic water assemblages, and harbour the amoA gene (Llirós et al., 2010; Auguet et al., 2011, 2012). Thus, increasing evidence suggests that Archaeamay play a major role in ammonia oxidation in lakes and rivers (Herfort et al., 2009; Merbt et al., 2011; Auguet et al., 2012).

We observed, however, that lakes with the highest DOC concentrations and, more generally, lakes with mesoeutrophic conditions apparently favoured Euryarchaeota instead of Thaumarchaeota. These freshwater euryarchaeotal lineages are largely unknown and certainly deserve further and specific research (Barberán et al., 2011).

For the AOA communities, the heterogeneity of the Pyrenean landscape allowed us to examine the influence of environmental gradients on the ecology and distribution of aquatic ammonia oxidizers. The results support the traditional species sorting concept in which local environmental gradients create spatial niches occupied by species with distinct environmental tolerances. Physicochemical variables, and particularly pH, were significant predictors of the 16S rRNA and amoA gene phylogenetic structure. The importance of pH in microbial assemblage abundance, composition and activity has been widely documented, particularly for soil microorganisms involved in nitrogen cycling (Fierer & Jackson, 2006; Bru et al., 2011; and references therein). In addition, lower nitrification rates have been reported with increasing water acidification (Rudd et al., 1988; Huesemann et al., 2002; Beman et al., 2011). Although AOA with different physiological and ecological niches (i.e. acidophilic, acidoneutrophilic and alkalinophilic) have been reported along pH gradients in soils (Nicol et al., 2008; Gubry‐Rangin et al., 2011; Pester et al., 2012), the influence of pH remains unclear as both negative and positive correlations between amoA gene abundance and pH have been observed. The results we have found in lakes agree with the findings in soils, suggesting specific selection and adaptation of AOA lineages to low pH. Interestingly, the AOA in the acidic Lake Aixeus (i.e. SAGMGC‐1 16S rRNA lineage, and Soil/Fresh 1 amoA clade) were similar to those found in acidic soils, and specifically to N. devanaterra, the first obligate acidophilic ammonia‐oxidizing Thaumarchaeota (Lehtovirta‐Morley et al., 2011), suggesting phylogenetic conservation for the adaptive mechanisms developed to cope with low pH conditions (Gubry‐Rangin et al., 2011). Under low pH the availability of NH3, the substrate for ammonia monooxygenase, is strongly reduced by protonization to 


 (Frijlink et al., 1992), and N. devanaterra shows the ability to grow at very low ammonia concentrations (0.18 nm, Lehtovirta‐Morley et al., 2011). It remains to be tested whether members of the aquatic SAGMGC‐1 may also have high ammonia affinity at low pH, which may explain the success of SAGMGC‐1 over I.1a Thaumarchaetoa in Lake Aixeus. In a recent study, we observed lineage segregation along the vertical gradient of a deep alpine lake (Auguet et al., 2012). Here, we show that pH is also an important environmental factor that may determine the composition of aquatic AOA assemblages._


----------



## sciencefiction

sciencefiction said:


> Thanks Darrel, very informative.
> 
> I don't know if you posted the below study but it's very readable for us simple mortals. I've picked a few quotes...
> 
> 
> It basically says that in fresh water aquariums the dominant nitrifyers are "_ammonia-oxidizing archaea (AOA), belonging to the newly proposed phylum Thaumarchaeota"..._The amount of AOA compared to AOB is orders of magnitude higher in freshwater biofilters according to the study and its inversely related to the ammonia concentration. They suggest that the first nitrifyers in newly set up tanks could be AOB due to the higher ammonia levels and as the levels go down, there's a shift to AOA dominance. In my personal opinion.
> 
> _This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoAgenes.
> 
> For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration...
> 
> Neither hardness nor alkalinity correlated significantly with any other water chemistry parameters....
> 
> Although the detectable ammonia concentrations in established freshwater aquaria are typically low as a result of biological ammonia oxidation, a preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3), suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations._
> 
> _This study has identified that AOA are the dominant ammonia oxidizing microorganisms in freshwater aquarium biofilters. Aquarium ammonium concentrations were significantly and inversely correlated with AOA∶AOB ratios.
> 
> We also sampled from eight saltwater aquarium filters and two aquarium supplements for comparison (Table S1). Bacterial supplements (typically bottled liquid suspensions) are intended to aid in populating newly established aquaria with active nitrifying bacteria, to help ensure that ammonia and nitrite concentrations remain below toxic levels during the initial 1–2 months of aquarium filter colonization. The aquarium supplements included were Cycle (SP1; Rolf C. Hagen Inc., Montreal, Canada), and Bio-Support (SP2; Big Al's Distribution Centre, Niagara Falls, NY).
> 
> Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. _



Timed out, can't put back the link to the study so here it is:

*Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters*
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023281


----------



## dw1305

Hi all, 





sciencefiction said:


> Although the detectable ammonia concentrations in established freshwater aquaria are typically low as a result of biological ammonia oxidation, a preference for high ammonia concentrations by AOB suggests a possible role for their involvement in first establishing an aquarium when ammonia concentrations may approach levels associated with fish toxicity. In addition, ammonium concentration was positively and significantly correlated with the number of fish per gallon of aquarium water (Tables S2 and S3), suggesting that AOB may also be important for heavily stocked tanks that experience chronic high ammonia concentrations.


The paper has been <"referenced a few times on the forum">, I think initially by @George Farmer, following mention in "Practical Fishkeeping". There is also some discussion of the possible advantages of initial  ammonia addition in <"Oxygen levels required"> and the linked <"PlanetCatfish thread">. Whatever side of the debate you stand on, I think the PlanetCatfish thread is worth reading. 





sciencefiction said:


> Here, we show that pH is also an important environmental factor that may determine the composition of aquatic AOA assemblages.


I think pH is relevant, and I would be very surprised if you didn't get greater rates of nitrification in neutral, or alkaline, water. 

cheers Darrel


----------



## sciencefiction

It seems that the verdict on ammonia toxicity and AOA is still not confirmed. The below study is about soils but I think it is still relevant.
There's more on pH influence on AOA and Carbon uptake in the link
*Drivers of archaeal ammonia-oxidizing communities in soil*

https://www.frontiersin.org/articles/10.3389/fmicb.2012.00210/full

*Ammonia or Ammonium as Substrate for Ammonia Monooxygenase*
Is ammonia (NH3) or the cation ammonium (NH4+) the substrate for the archaeal AMO enzyme? Ammonia is known to be the substrate of this initial step in bacterial ammonia oxidation (Suzuki et al., 1974; Arp et al., 2002). However, despite several studies dedicated to studying the biochemistry of AMO in bacteria, it still remains unknown whether ammonia or ammonium is the substrate for archaeal AMO (Martens-Habbena and Stahl, 2011). Bacterial oxidation of ammonia to nitrite (NO2-) is a two-step process. AMO oxidizes ammonia to hydroxylamine (NH2OH), and hydroxylamine oxidoreductase (HAO) catalyzes oxidation of hydroxylamine to nitrite (Arp et al., 2002). Structural differences in the archaeal AMO and bacterial AMO and the absence of genes encoding HAO and cytochrome _c_ proteins for recycling electrons suggest important differences between bacterial and archaeal ammonia oxidation. For example, nitroxyl (HNO) rather than hydroxylamine may be the intermediate in the AMO enzymatic reaction, or a different cytochrome system may be responsible for electron channeling in AOA (Walker et al., 2010).

The majority of AOA discovered to date were found in oligotrophic conditions (Hatzenpichler et al., 2008; Walker et al., 2010). The affinity of marine archaeon _Nitrosopumilus maritimus _for ammonium/ammonia was 200-fold higher than substrate affinity of AOB (Martens-Habbena et al., 2009; Martens-Habbena and Stahl, 2011). These microorganisms can obtain energy even under very low concentrations of substrate. It has been suggested that the differences in substrate affinities allow AOA and AOB to inhabit distinct niches separated by substrate concentration and thereby reduce competition (Martens-Habbena et al., 2009; Schleper, 2010; Martens-Habbena and Stahl, 2011; Verhamme et al., 2011). There are studies that suggest substrate inhibition of archaeal nitrification if high concentrations of ammonia are present (Di et al., 2010; Tourna et al., 2010).

Because AMO in AOA has a much higher affinity for substrate than the analogous process in AOB, it has been suggested that AOA dominate over AOB where ammonia concentrations are particularly low. This seems to be the case in oligotrophic environments such as sea water or hot springs (Hatzenpichler et al., 2008; Walker et al., 2010). For example, _Ca. Nitrososphaera gargensis_, which was first found in hot springs, fixes bicarbonate at lower levels when the ammonia concentration was higher than 3.1 mM. The optimal ammonia concentration for bicarbonate fixation was much lower, between 0.14 and 0.8 mM (Hatzenpichler et al., 2008). Some studies suggest that substrate concentration does not influence thaumarchaeal ammonia oxidation (Stopnisek et al., 2010; Verhamme et al., 2011). These authors showed that AOA grew similarly at low, medium, and high ammonia concentrations, whereas AOB grew best only with high ammonia concentrations. Other factors were suggested to be important in the growth of AOA. Di et al. (2009)observed in nitrogen-rich grassland soils neither AOA abundance nor their activity increased with the application of a large dose of ammonia substrate. In this study, AOA abundance was not quantitatively related to nitrification rates. Similarly, Ke and Lu (2012) did not see any changes in AOA in paddy field soils after urea was applied as nitrogen fertilizer.

In some studies, high ammonia appears to promote AOA growth and activity. Treusch et al. (2005)found considerably higher amounts of archaeal _amoA_ transcripts in those samples that had been amended with additional ammonia (10 mM). It was demonstrated that the soil archaea _Nitrososphaera viennensis_ strain EN76 grows well in media containing ammonium concentrations as high as 15 mM, but its growth is inhibited at 20 mM (Tourna et al., 2011). This is considerably higher than the inhibitory concentration of 2–3 mM reported for the aquatic AOA _Nitrosopumilus maritimus_ (Walker et al., 2010) and _Ca. Nitrososphaera gargensis_ (Hatzenpichler et al., 2008). Tolerance for ammonia toxicity of_ Ca. Nitrosoarchaeum koreensis_ strain MY1, isolated from an acidic agricultural soil, was slightly lower, 5 mM, than that of _Nitrososphaera viennensis_ (Jung et al., 2011). Park et al. (2006) found archaeal _amoA _in wastewater with 2 mM ammonia.

The source of substrate and its location can influence ammonia concentration in soil (Offre et al., 2009; Stopnisek et al., 2010; Verhamme et al., 2011). Ammonium production via mineralization, additions of ammonical fertilizers, animal wastes, and the atmospheric deposition of ammonium increases substrate supply, while competing consumptive processes include microbial assimilation (immobilization), plant assimilation, and ammonia volatilization reduce ammonia concentration (Norton and Stark, 2011). In addition, AOA do not respond to the addition of mineral nitrogen to soil (Di et al., 2009; Jia and Conrad, 2009; Stopnisek et al., 2010; Verhamme et al., 2011; Ke and Lu, 2012). In contrast, AOB increase in abundance after addition of ammonium sulfate or urine (Di et al., 2009, 2010; Jia and Conrad, 2009; Hofferle et al., 2010). Archaeal _amoA_ gene copies and nitrate concentration increased during incubation soil for 30 days (Offre et al., 2009). All ammonia in this soil was generated by nitrogen mineralization since no ammonia was added. Also, it was shown in upland field soils archaeal 16S rRNA gene was significantly affected by the class of fertilizer (chemical or organic fertilizer). In four different soil types 16S rRNA abundance of AOA was about 0.1–0.9 × 108 gene copy number higher in the plots where organic fertilizers were added than in the plots with chemical fertilizer addition.

Nitrate concentrations likely differ greatly both spatially and temporally under these two scenarios (Stopnisek et al., 2010). While ammonia from organic matter mineralization is slowly and constantly liberated resulting in low, but steady, levels of ammonia, an application of mineral nitrogen fertilizer promotes a burst of ammonia. Archaeal ammonia oxidizers should be expected to be in a higher abundance in the soils with high organic matter, which would provide a constant source of substrate (Stopnisek et al., 2010).

Adaptation to different concentrations of ammonia and the ability to survive even at extremely low concentrations of ammonia, together with other ecological factors, contribute to the ecological fitness and niche adaptation of AOA and AOB. The presence of different ecophysiological adaptations such as different concentrations of substrate suggests that a wide range of ecotypes can be expected to occur among soil AOA.
*Ammonia or Ammonium as Substrate for Ammonia Monooxygenase*
Is ammonia (NH3) or the cation ammonium (NH4+) the substrate for the archaeal AMO enzyme? Ammonia is known to be the substrate of this initial step in bacterial ammonia oxidation (Suzuki et al., 1974; Arp et al., 2002). However, despite several studies dedicated to studying the biochemistry of AMO in bacteria, it still remains unknown whether ammonia or ammonium is the substrate for archaeal AMO (Martens-Habbena and Stahl, 2011). Bacterial oxidation of ammonia to nitrite (NO2-) is a two-step process. AMO oxidizes ammonia to hydroxylamine (NH2OH), and hydroxylamine oxidoreductase (HAO) catalyzes oxidation of hydroxylamine to nitrite (Arp et al., 2002). Structural differences in the archaeal AMO and bacterial AMO and the absence of genes encoding HAO and cytochrome _c_ proteins for recycling electrons suggest important differences between bacterial and archaeal ammonia oxidation. For example, nitroxyl (HNO) rather than hydroxylamine may be the intermediate in the AMO enzymatic reaction, or a different cytochrome system may be responsible for electron channeling in AOA (Walker et al., 2010).

The majority of AOA discovered to date were found in oligotrophic conditions (Hatzenpichler et al., 2008; Walker et al., 2010). The affinity of marine archaeon _Nitrosopumilus maritimus _for ammonium/ammonia was 200-fold higher than substrate affinity of AOB (Martens-Habbena et al., 2009; Martens-Habbena and Stahl, 2011). These microorganisms can obtain energy even under very low concentrations of substrate. It has been suggested that the differences in substrate affinities allow AOA and AOB to inhabit distinct niches separated by substrate concentration and thereby reduce competition (Martens-Habbena et al., 2009; Schleper, 2010; Martens-Habbena and Stahl, 2011; Verhamme et al., 2011). There are studies that suggest substrate inhibition of archaeal nitrification if high concentrations of ammonia are present (Di et al., 2010; Tourna et al., 2010).

Because AMO in AOA has a much higher affinity for substrate than the analogous process in AOB, it has been suggested that AOA dominate over AOB where ammonia concentrations are particularly low. This seems to be the case in oligotrophic environments such as sea water or hot springs (Hatzenpichler et al., 2008; Walker et al., 2010). For example, _Ca. Nitrososphaera gargensis_, which was first found in hot springs, fixes bicarbonate at lower levels when the ammonia concentration was higher than 3.1 mM. The optimal ammonia concentration for bicarbonate fixation was much lower, between 0.14 and 0.8 mM (Hatzenpichler et al., 2008). Some studies suggest that substrate concentration does not influence thaumarchaeal ammonia oxidation (Stopnisek et al., 2010; Verhamme et al., 2011). These authors showed that AOA grew similarly at low, medium, and high ammonia concentrations, whereas AOB grew best only with high ammonia concentrations. Other factors were suggested to be important in the growth of AOA. Di et al. (2009)observed in nitrogen-rich grassland soils neither AOA abundance nor their activity increased with the application of a large dose of ammonia substrate. In this study, AOA abundance was not quantitatively related to nitrification rates. Similarly, Ke and Lu (2012) did not see any changes in AOA in paddy field soils after urea was applied as nitrogen fertilizer.

In some studies, high ammonia appears to promote AOA growth and activity. Treusch et al. (2005)found considerably higher amounts of archaeal _amoA_ transcripts in those samples that had been amended with additional ammonia (10 mM). It was demonstrated that the soil archaea _Nitrososphaera viennensis_ strain EN76 grows well in media containing ammonium concentrations as high as 15 mM, but its growth is inhibited at 20 mM (Tourna et al., 2011). This is considerably higher than the inhibitory concentration of 2–3 mM reported for the aquatic AOA _Nitrosopumilus maritimus_ (Walker et al., 2010) and _Ca. Nitrososphaera gargensis_ (Hatzenpichler et al., 2008). Tolerance for ammonia toxicity of_ Ca. Nitrosoarchaeum koreensis_ strain MY1, isolated from an acidic agricultural soil, was slightly lower, 5 mM, than that of _Nitrososphaera viennensis_ (Jung et al., 2011). Park et al. (2006) found archaeal _amoA _in wastewater with 2 mM ammonia.

The source of substrate and its location can influence ammonia concentration in soil (Offre et al., 2009; Stopnisek et al., 2010; Verhamme et al., 2011). Ammonium production via mineralization, additions of ammonical fertilizers, animal wastes, and the atmospheric deposition of ammonium increases substrate supply, while competing consumptive processes include microbial assimilation (immobilization), plant assimilation, and ammonia volatilization reduce ammonia concentration (Norton and Stark, 2011). In addition, AOA do not respond to the addition of mineral nitrogen to soil (Di et al., 2009; Jia and Conrad, 2009; Stopnisek et al., 2010; Verhamme et al., 2011; Ke and Lu, 2012). In contrast, AOB increase in abundance after addition of ammonium sulfate or urine (Di et al., 2009, 2010; Jia and Conrad, 2009; Hofferle et al., 2010). Archaeal _amoA_ gene copies and nitrate concentration increased during incubation soil for 30 days (Offre et al., 2009). All ammonia in this soil was generated by nitrogen mineralization since no ammonia was added. Also, it was shown in upland field soils archaeal 16S rRNA gene was significantly affected by the class of fertilizer (chemical or organic fertilizer). In four different soil types 16S rRNA abundance of AOA was about 0.1–0.9 × 108 gene copy number higher in the plots where organic fertilizers were added than in the plots with chemical fertilizer addition.

Nitrate concentrations likely differ greatly both spatially and temporally under these two scenarios (Stopnisek et al., 2010). While ammonia from organic matter mineralization is slowly and constantly liberated resulting in low, but steady, levels of ammonia, an application of mineral nitrogen fertilizer promotes a burst of ammonia. Archaeal ammonia oxidizers should be expected to be in a higher abundance in the soils with high organic matter, which would provide a constant source of substrate (Stopnisek et al., 2010).

Adaptation to different concentrations of ammonia and the ability to survive even at extremely low concentrations of ammonia, together with other ecological factors, contribute to the ecological fitness and niche adaptation of AOA and AOB. The presence of different ecophysiological adaptations such as different concentrations of substrate suggests that a wide range of ecotypes can be expected to occur among soil AOA.


----------



## sciencefiction

dw1305 said:


> Whatever side of the debate you stand on, I think the PlanetCatfish thread is worth reading.



Thanks Darrel. I have actually already read that thread. I will try not to "debate" over that  but from my point of view the AOA data available is consistent with annecdotal experience and empirical observation of aquarium cycling. And perhaps what we like to call a "matured tank" is simply the result of the process of establishing the most dominant nitrifyers, be it AOB or AOA of different types,  depending on the conditions of that particular tank. I think that process is gradual and how it happens and what exactly nitrifying AOA and AOB establishes is mostly irrelevant to mere fishkeepers as a tank always "matures" one way or another.


----------



## AverageWhiteBloke

dw1305 said:


> Hi all, In the thread we had a while ago, using ADA aquasoil, <"Cycling without plants?"> it allowed the owner (@Cor) to "cycle" the tank with the light off. He didn't need to add any nutrients, because he was using Aquasoil. Made me laugh, but I'm not sure <"Karl Popper"> would approve.
> 
> This is something that I admire about Dr Tim Hovanec, even though he was scientifically (and economically invested) in the traditional view of nitrification, he has been willing to admit that <"_the past is another country">_ in light of more recent research into microbial filtration.
> 
> cheers Darrel


Ahh OK,  I thought the point of the ADA soil was to give the plants the best start in life by loading up the column well in excess of nutrients many times EI values, last I heard was 100x. Just seems odd that one would "wash out" some of them in the dark before the plants get the benefit but clearly it's more complicated than that and above my pay grade. 

Sent from my STH100-2 using Tapatalk


----------



## dw1305

Hi all,





sciencefiction said:


> These microorganisms can obtain energy even under very low concentrations of substrate. It has been suggested that the differences in substrate affinities allow AOA and AOB to inhabit distinct niches separated by substrate concentration and thereby reduce competition (Martens-Habbena et al., 2009; Schleper, 2010; Martens-Habbena and Stahl, 2011; Verhamme et al., 2011). There are studies that suggest substrate inhibition of archaeal nitrification if high concentrations of ammonia are present (Di et al., 2010; Tourna et al., 2010).





sciencefiction said:


> ... And perhaps what we like to call a "matured tank" is simply the result of the process of establishing the most dominant nitrifyers, be it AOB or AOA of different types, depending on the conditions of that particular tank. I think that process is gradual and how it happens and what exactly nitrifying AOA and AOB establishes is mostly irrelevant to mere fishkeepers as a tank always "matures" one way or another.


I'd be pretty confident that those summarise the situation. 

Personally I'm always going to keep planted tanks with relatively low fish stocking, low nutrients and frequent water changes. If you like it is the <"oligotrophic approach">. I've corresponded a lot with <"Viktor Jarikov from PlanetCatfish">, we couldn't be more different in our approaches, but he understands what he is doing, and why he is doing it, and you have to say it works brilliantly for him.    

As an aside to this thread, @sciencefiction's  <"Round Indoor Pond Project"> is probably about as good as you can get in terms of fish welfare, the combination of the solid walled tub, the large water volume, water changes and emergent vegetation is absolutely ideal. 

cheers Darrel


----------



## sciencefiction

dw1305 said:


> As an aside to this thread, @sciencefiction's <"Round Indoor Pond Project"> is probably about as good as you can get in terms of fish welfare, the combination of the solid walled tub, the large water volume, water changes and emergent vegetation is absolutely ideal.



Thanks for mentioning it Darrel, I don't want it to sound like boasting, hence I refrained from posting initially but this particular tank is indeed doing extremely well. I dare say it's the best I ever got in terms of quality of fish keeping and it is something I am going to be aiming at from now on for any future fish pets  The fish are in top health and have great colors and even though I've had some of them for years, their behavior in this tank in comparison to before is like discovering a new continent. The fish are actually literally "playful" and very relaxed at the same time. There's no nervous or anxious swimming around, even during water changes. 
They're curious rather than skittish.   I am amazed at how well everything is working out. The water also remains crystal clear for some reason, not much effort from me on that part.  It's like glass and it actually has a very enthralling type of smell, like from a distant memory in my childhood when I was swimming somewhere nice and natural.  It's a sweet type of smell. I am not sure if its good or bad but I actually keep sniffing it when I sit over as I put my chin against the edge of the tank and watch the fish do their thing. For a change, they actually love seeing me there and keep bunching under my nose. Not all of them used to do that before 

If one has ever had a tank that makes them smile when they look at it, they'll know what I mean....I am a very anxious fish keeper and very observant person so I generally rarely see things as perfect but this tank makes me relax and think for at least a moment or two that everything I've done has indeed benefited the fish and its not a mirage of some sort


----------



## jaypeecee

Hi Folks,

I realize that this thread was started over a year ago. But I just want to add that I have had a lot of success with Tetra _SafeStart_ bottled bacteria. As many people will know, this product was developed by Dr Tim Hovanec. Using _SafeStart_, I have cycled a tank 'from scratch' in just six days. I use remineralized RO water with a few additional trace elements and it is very reliable. My source of ammonia is ammonium chloride.

JPC


----------



## dw1305

Hi all, 





jaypeecee said:


> was developed by Dr Tim Hovanec


Personally I've got a lot of time for Dr Hovanec, I don't have any practical experience of his products, but he has embraced <"the newer findings"> in his subject area.  





jaypeecee said:


> Using _SafeStart_, I have cycled a tank 'from scratch' in just six days.





jaypeecee said:


> My source of ammonia is ammonium chloride.


I'm not going there for either of those. I think @rebel's comments in <"Is it still cycled"> would be where I am with that one. 

Personally I'm pretty sure that the concept of <"cycling with ammonia"> has had its day in the planted tank, and in the future we will look back on it in the way that I look at <"aged tank water"> now. 

It was the convention in the 1970's that not changing your tank water was a good thing, and I never questioned it. Hind-sight is a wonderful thing, but it didn't make any more sense then, but we just never questioned it. 

cheers Darrel


----------

