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Bacteria/biological starters

Tim Harrison

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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.
 

ceg4048

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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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@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.
 

richard brown

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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 :banghead: not gonna use it in new tank, just gonna use water from my current tank and maybe squeeze some media.
 

dw1305

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Hi all,
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)....
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.
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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dw1305

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Hi all,
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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dw1305

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Hi all,
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
 

zozo

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

dw1305

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Hi all,
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.
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
 

Zeus.

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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 :oops:. 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.
 

zozo

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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.
 

Zeus.

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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

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Hi all,
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.
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
 
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