Best way to cycle a second filter

[dw1305]

Hi all,
This comes up a lot on some other forums.

There is a fairly full discussion (from all sides of the argument) at <"PlanetCatfish: Cycling Question"> and <"PlanetCatfish:Using deep gravel....">.

These references are from the "Cycling Question" thread.

"...........New DNA/RNA techniques for investigating microbial communities are discovering a whole raft of different organisms that oxidize ammonia. I think the evidence is stacking up all the time that the Archaea are the primary oxidizers of ammonia.

"Relative contribution of of archaea and bacteria to aerobic ammonia oxidation in the environment" <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.328.2761&rep=rep1&type=pdf>

"Evaluation of autotrophic growth of ammonia-oxidizers associated with granular activated carbon used for drinking water purification by DNA-stable isotope probing"<http://www.sciencedirect.com/science/article/pii/S0043135413008464>,

"Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant" <http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02786.x/full>

"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#pone-0023281-g004>
&
"Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants"<http://www.nature.com/ismej/journal/v9/n3/full/ismej2014158a.html>......."

The problem from my point of view is that a whole mythology has grown up around "cycling", and for some of the "adding ammonia" adherents it doesn't really matter what new evidence comes up, they know that they are right and everyone else is wrong.

cheers Darrel

 

[AndyMcD]

Firstly, I cannot believe how much you are all picking on me😉!

Alto, the website I directed you to has both the words 'bio' and 'labs' in their domain name. How can they not be a reputable source of scientific data?

I do take your point about reading scientific papers and I do try to do this (but perhaps not enough in this particular area). I was struggling to think of a better source of data which discussed the colour of bacteria. I just thought everyone had brown stains on their filter media. I'm beginning to feel embarrassed about talking about this on a public forum.

The other piece of information which led to me going down this path is the following from The Book of ADA. However, what this does not include is the rate at which the aerobic organisms will deplete their energy stores and die once oxygen is depleted. My assumption was that if oxygen is depleted after 1.5 hours, in 24 hours only anaerobic heterotrophic bacteria would be thriving.



James O, it seemed a bit inappropriate to be talking about how tiny my tank is in comparison to TGM's huge tank and their massive bio load. I thought on this forum what you did with your tank mattered more than what size it is, but apparently not!

I've now filled the new tank and begun cycling the new filter and ADA Aquasoil. I'm doing this to minimise the number of water changes I carry out in the first three weeks. After that, I'll add new plants plus move my fish (and a second mature filter) from my old (even smaller at 70L) tank. I didn't fancy the alternative of doing water changes daily for weeks. Also, I preferred doing the hardscape and substrate layout dry.



Ian_m, is there anyone you haven't sent a gunked up filter foam to😉? I think this may be the best way of transferring organisms from one filter to another.

However, I've had big issues with BBA in my old aquarium, my concern was that it would be a good way of transferring spores also.

My main concern was that the bacteria in my filter were submerged, without any oxygen for 24 hours. In a bag, they may have had some (limited) access to oxygen.

Also, the new filter was rattling and I was concerned it was because the mature media was disintegrating, so I took it out. It turned out that the propellor was inserted incorrectly.

Hopefully, I'm wrong and the new and old media being in contact for 24 hours means some of the organisms have transferred from old to new.

At least I've got 3 weeks for the new system to cycle. Also, once I move my (small) bio load of fish with the already mature filter, I'll have sufficient filtration even if the new hasn't cycled, whatever cycling really means!

Darrel, thank you for the links. I'll have a go at reading them all.

 

[alto]

I'm beginning to feel embarrassed about talking about this on a public forum.

don't feel that!
so not my intention to cause any embarrassment etc

You ask questions & get discussions going & people contributing ... that's what makes forums live.
😀

 

[AndyMcD]

Absolutely agree!

 

[dw1305]

Hi all,

Ian_m, is there anyone you haven't sent a gunked up filter foam to😉? I think this may be the best way of transferring organisms from one filter to another.

Kudos to "Ian_m", it is a good method.

However, I've had big issues with BBA in my old aquarium, my concern was that it would be a good way of transferring spores also.

I think BGA, Diatoms, Green Algae etc will always colonise any suitable water body fairly rapidly. If you have a look with a microscope at a plant leaf, some tank substrate etc, you will find a <"huge array of different organisms">.

The other piece of information which led to me going down this path is the following from The Book of ADA. However, what this does not include is the rate at which the aerobic organisms will deplete their energy stores and die once oxygen is depleted. My assumption was that if oxygen is depleted after 1.5 hours, in 24 hours only anaerobic heterotrophic bacteria would be thriving.

No, they are right about the oxygen depletion, but it is back to the "shades of grey" argument really. If you read through the PlanetCatfish threads it covers this subject in quite a lot of detail, but the major findings have been that nitrification is a carried out by a much wider range of microbes (including a lot of ammonia oxidising archaea (AOA)) than was originally thought.

We know from the work with waste water that AOA are very flexible and resilient organisms, which can survive in environments <"with low and fluctuating dissolved oxygen levels">. This is from <"Aquarium nitrification re-visited" >:
"That AOA are better adapted to low ammonia environments is supported by the present study with aquarium biofilters, where ammonium concentrations are maintained at consistently low concentrations, and certainly well below 1 mg N L−1 in all sampled aquaria"

The black and white scenario - canister filters
One of the big problems with canister filters is that, because they don't have a gas exchange surface, the water in them quickly becomes de-oxygenated. Where people keep a large bioload, in a tank without plants (Mbuna etc), this can happen even in normal operation.

If you use your filter as a syphon, or fill it with floss, or try to balance aerobic oxidation of NH3 with anaerobic out-gassing of N2 within the same filter canister, you are always teetering on the brink of a biological filtration catastrophe. You have a "positive feedback loop" where increasing ammonia levels deplete oxygen, which decreases nitrification, which increases ammonia which further depletes oxygen etc.

This is the reason for pouring 95% of the water out of the filter, and opening the taps, if it stops working. This is also one of the advantages of a sump with floating cell media, a HMF, or a "wet & dry" trickle filter, gas exchange still occurs when there is no water flow.

If you are in the circumstance where you have no substrate, or structure, in your tank, and are entirely dependent upon the canister filter bacteria for nitrification, then a loss of power can be terminal. I'm never going down the bare tank/canister filter route, and I strongly advise others against it, because you have a "single point of failure", "a severe risk" and a "significant likelihood of occurrence".

In most cases what limits microbial nitrification is lack of oxygen and not lack of sites for nitrification or lack of ammonia. Dissolved oxygen is the key metric, which is why biologists are primarily interested in <"Biochemical Oxygen Demand (BOD)">.

Plant and microbe systems
In a tank with plants and a substrate you have mitigated for single point of failure straight away, because you have a separate reservoir of nitrifying bacteria/archaea in the upper layers of the sediment, and in the rhizosphere around plant roots. In addition plants are net producers of oxygen and convert NH4+/NO3- into plant material, removing fixed nitrogen from the water column.

We are now in a "negative feedback loop", where increased levels of ammonia lead to increased plant growth, which increases the oxygen supply and the area where nitrification can occur, and directly decreases the level of fixed nitrogen in the system. Because of these factors plant/microbe systems are potentially about an order of magnitude more efficient than microbe only systems.

The end result of all this is that a new, or "cleaned" filter sponge etc. will quickly be colonised from the reservoir of microbes within the system.

cheers Darrel

 

[AndyMcD]

Darrel, thank you very much for such a detailed reply!


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[dw1305]

Hi all,

Darrel, thank you very much for such a detailed reply!

No problem, I haven't really made 4,000 posts, I've just posted the same thing 4000 times. There are plenty more references and details in <"PlanetCatfish: Cycling Question"> and <"PlanetCatfish:Using deep gravel....">.

I still get a regular stream of what can only be described as "hate mail" about the cycling posts. If I'd known the level of animosity that they were going to generate I probably would have kept my thoughts to myself.

cheers Darrel

 

[AndyMcD]

Darrel, I noted TwoTankAmin's tone. He might as well have been typing in bold red with caps lock on!


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[ian_m]

The other "emergency" way of cycling your tank, if you have fish and no dirty/cycled filters, is to use things like Prime and AmQuel daily to neutralise the ammonia and nitrite. I have done this before, works well.

I bought a tank from Ebay and when I turned up to collect it, the tank had been taken down (a couple of weeks before for an Ebay'er non payer) and all the gravel/sand had been washed and dried, filters & media all cleaned and dried and fish all in another tank on a tiny filter that the seller was keeping. So I have to start again with completely un-cycled water/tank. I just added AmQuel each day and performed frequent water changes, using AmQuel as dechlorinator. Testing reveal zero ammonia and zero nitrite. Couldn't test nitrate as AmQuel interferes with nitrate tests. Anyway some of the fish survived and lasted years....Actually about 2003 to 2012 for the plec's.

 

[alto]

I don't know about the "hate mail" aspect - that argues a certain instability 😉 - but I didn't find anything really objectionable in TTA's tone (he did mention the sarcasm & apologized in advance ... likely I get this, as I'm also apparently guilty of poor internet communication skills 😳 ... oh ... and the sarcasm 😳😳😳)

Both fishless cycling & plant cycling work.
I've only had decent results with the named test kits,Seachem & Salifert - I ran standard curves & known "test" samples for ammonia, nitrite, nitrate, pH (I was in a research lab at the time) with several branded kits, most do a reasonable job (there were a few outliers that performed poorly most of the time, some that performed poorly occasionally); when it comes to other parameters such as phosphate, iron etc, fewer test kits perform reasonably, those that do are very expensive (& I feel unnecessary for most freshwater applications).

I like planted tanks but when I lived in an area where there was not a single aquatic plant within a 3 hour drive (each way) & no online vendor wanted to ship me anything (not even books!), I went back to fishless cycling with ammonia & "single point failure" canister filter system ... except bacteria colonize all surfaces of the tank & décor & substrate, so while the effects of the wind driven power outages weren't ideal, I also didn't lose any fish, if at home, I isolated the filter & just kept it damp to maintain oxygen levels - I kept tanganyikans so fish stocking levels were low (a significant factor).
Eventually I found a marine shop that would order from Tropica etc & put everything on the train for me (I only needed to drive an hour to meet the train at a junction where they'd unload my stuff if I was already there & reminded them 😉) so back to planted tanks 🙂
I lived there for 3 years & helped a friend set up a small aquarium "zone" in his shop, I did a planted display tank, but never convinced anyone coming in to venture planted 🙂 (though they were very polite & listened 😀 ) but I did manage to get some fishless cycling (we'd run the tests) - most people just want to buy a tank & take home a few fish - same day! - at least we could convince them to come back later for the fish (OK we insisted 😉 .. . as did the other local "garden & lifestyles" shop that had set up a small aquarium section).

I think BGA, Diatoms, Green Algae etc will always colonise any suitable water body fairly rapidly.

While I agree with this statement, there is also the idea/reality of threshold "inoculation" levels (not saying that well at all) ie a minimum number of organisms must be introduced into a system, before a "disease" state or stable population may establish - this varies very much with the organism introduced & the inherent properties of the resident system to maintain (existing) balance.

Andy - as I tried to communicate, skip the mucky bits & any debris/mulm (where heterogeneity of organisms is likely much greater) & just use seemingly "clean" media to cycle your new tank.
Similarly, when transferring stuff over, limit visible algae etc as much as possible - not much can be done about the bits fish/shrimp may release - but clean wood/rocks etc will likely improve your odds of not immediately seeing the same old issues in the new tank; also establishing the new tank with it's own varied flora will tend to make "invasions" more difficult.





(note that TTA is correct when pointing out the possibility of bias in the papers/articles all sharing a single name - this may be more prevalent in some areas of research than others)

 

[dw1305]

Hi all,

I don't know about the "hate mail" aspect - that argues a certain instability 😉 - but I didn't find anything really objectionable in TTA's tone

Same applies, I've no objection to TTA, or his posting style. We have a fundamental difference of opinion about cycling, but we have other areas where our views coincide. He has kept and bred a fabulous range of fish.

cheers Darrel

 

[rebel]

Hi Darrel, I've read the planetcatfish references that you provided (with thanks!).

In a nutshell, what's your recommendation for cycling a planted tank? [ You can write a one-liner and that's kool ]

From my POV, cycling is different for different situations
1. high load fish only tank - no plants
2. planted tank - expert level, active substrate, high density high quality plants, CO2, proposed HIGH fish loading
3. planted tank - newbie - inactive substrate (gravel), poor quality low density planting, proposed HIGH fish loading
4. 2 with low fish load like ADA tanks
5. 3 with low fish load - usually never happens - usually ends up with lots of rams, BN, tetras, gouramis coming out of the ears... 😉
6. COLD water (non tropical temps less than 18 degrees)
7. Ponds (tropical)
8. Cold water ponds
9. Ponds with no circulation (ie static container)

In summary, I think cycling can't just be generalised into any situation.

Any thoughts?

 

[BruceF]

What happens if one simply sets up a tank with a light a filter and a substrate. How long would it take to cycle itself? Would it cycle at all?

 

[rebel]

What happens if one simply sets up a tank with a light a filter and a substrate. How long would it take to cycle itself? Would it cycle at all?

To figure this out, you need to define how you define and measure 'cycle'. Part of the issue is the unreliability of test kits also. I am unsure how unreliable the 0 readings in the cheap ammonia/nitrite test kits which are main ones needed to check for 'cycling'. The nitrate test kit is unreliable as shown many times elsewhere and probably needs frequent calibration which is out of scope of any newbie.

 

[alto]

What happens if one simply sets up a tank with a light a filter and a substrate. How long would it take to cycle itself? Would it cycle at all?

Yes, it will cycle - it may've been Hovanec that was part of a group that measured tank "cycling" when various commercial "Cycle" products were used vs plain water, as I recall, all tanks cycled eventually, the tanks with added "Cycle" product cycled somewhat faster but this was put down to the solutions (likely) acting as a food source rather than actually supplying live N-cycle bacteria (that are active in aquaria). Various parameters were measured to determine cycle stage of the tanks, including isolating bacteria from water column vs biofilm etc.
Sorry I don't recall how much slower the "water only" tanks were ... maybe think in terms of 6-8 weeks rather than 4-6 weeks ... if you look hard enough, you may find this paper online 🙂

Of course the populations of N-cycle bacteria present in this "water only" tank will be very low compared to a tank that has been prepared with ammonia.

If you want to check the accuracy of a test kit, just prepare a solution of known concentration & run the test ... I've done this with ammonia, nitrite & nitrate: some of the kits yield reasonably accurate results.
Some manufacturers include a reference solution which can be tested to confirm kit is working as expected (eg, Seachem Nitrite/Nitrate MultiTest)

 

[AndyMcD]

In layman's terms (because I've most definitely read far less than everyone else), here's my opinion.

The population size and diversity of Microorganisms in a planted tank has a profound affect on how habitable the environment is for fish and may have an impact on the maintenance of the aquarium.

The cycling process is about waiting for the population of certain Microorganisms to increase to a size that they can process the ammonia and nitrites created, due to fish excretion and organic compounds being broken down.

Many of these Microorganisms are transferred into an aquarium either via the water supply or on an object that is added. This means that given time most aquariums should go through the cycling process, providing the Microorganisms are provided with the nutrients they require to reproduce.

Steps can be taken to increase the initial population size by adding filter media or floss from a mature aquarium or commercially available products. This will also help to ensure that a more diverse population of Microorganisms are introduced into the aquarium.

For example, nitrifying bacteria require a source of ammonia. Like plants, nitrifying bacteria are autotrophic, which means that they convert the most basic dissolved gases and salts into the organic compounds they need to grow. One population of bacteria oxidise ammonia to nitrates, releasing energy which they use to create organic carbon molecules from carbon dioxide. Relatively speaking, using CO2 as the main source of carbon for growth requires a great deal more energy than utilising organic carbon molecules created by other organisms (how heterotrophs consume carbon for growth).

A second population of nitrifying bacteria convert the nitrites to nitrates (e.g. Nitrobacter or Nitrospira). The population of these bacteria do not multiply significantly until sufficient ammonia is being converted to nitrites. This serial rather than parallel growth of the two populations of bacteria extends the length of time it takes for the process to complete.

This means that the growth of the population size of nitrifying bacteria is a slow process, typically taking several weeks to complete.

The environment and availability of nutrients can affect the growth of the bacteria population. Ammonia is required by one group of nitrifying bacteria, but to process this, it must also have a supply of oxygen for oxidation and CO2 for carbon for growth. Other environmental factors can affect growth, e.g. Temperature. At lower temperatures the population size increases less rapidly, which is why cold water aquariums can support a lower density of fish.

The autotrophic bacteria compete with heterotrophic bacteria for oxygen. Organic carbon (e.g. Dying plants or excess food) acts as a food source for the heterotrophic bacteria. As it requires less energy for them to convert organic carbon to grow, they can out compete the autotrophic bacteria. Keeping a well maintained aquarium will help to reduce the availability of organic carbon, making it easier for the nitrifying bacteria to compete.

The nitrifying bacteria can exist in the water column, but will inhabit suitable surfaces. They create a biofilm from cellulose, which adheres to the surface, providing protection against flow, for example. Over time, this biofilm will be populated by other Microorganisms and can act as a substrate for algal spores, for example.


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[dw1305]

Hi all,

1. high load fish only tank - no plants
3. planted tank - newbie - inactive substrate (gravel), poor quality low density planting, proposed HIGH fish loading

This is the real problem, I want to persuade people that these scenarios are untenable, and that even with micro-management disaster is inevitable in the longer term. If people really are set on following this route, the best hope for success is a "wet and dry" trickle filter.

I think for all other scenarios it really is a "one size fits all" solution and that "plants and time" are all you need.

What happens if one simply sets up a tank with a light a filter and a substrate. How long would it take to cycle itself? Would it cycle at all?

Yes it will, depends upon the planting, but 6 weeks should be plenty. If you have plants with access to atmospheric CO2 (Diana Walstads <"aerial advantage"> ) then that time period is shortened further.

it may've been Hovanec that was part of a group that measured tank "cycling" when various commercial "Cycle" products were used vs plain water, as I recall, all tanks cycled eventually, the tanks with added "Cycle" product cycled somewhat faster but this was put down to the solutions (likely) acting as a food source rather than actually supplying live N-cycle bacteria (that are active in aquaria).

This is right, Dr Hovanec has carried on with his work on biological filtration, and in <"Bacteria revealed"> he talks about why they couldn't find any Nitrobacter (NH4+ > NO2-) in aquarium filters (although Nitrospira (NO2- > NO3-) was present. It is a good read and an objective review of his earlier work.

Because scientists have access to libraries of DNA (and RNA) for bacteria and archaea it is now possible to actually look at the micro-organisms that are present in filters etc. Archaea and Bacteria are quite different at the molecular level (<"they form two of the three kingdoms of life">)

Older microbiological techniques relied upon culturing bacteria and then identifying them with gram stains etc, which meant that you were only looking at a tiny sub-sample of the microbial diversity that was present.

I think the research (from <"earlier in the thread">) have shown pretty clearly that a much greater diversity of organisms is involved in nitrification that was originally thought, and diversity brings resilience.

If you want to check the accuracy of a test kit, just prepare a solution of known concentration & run the test ... I've done this with ammonia, nitrite & nitrate: some of the kits yield reasonably accurate results.

This is good practice, I spent my "day job" yesterday with the students constructing standard curves and solving linear/non-linear equations.

The real problem with monovalent anions (like NO3-) comes with interference from other anions (often chloride Cl-). A particular problem with NO3 is that nearly all nitrate containing compounds are soluble, so you can't easily use spectrophotometry or colorimetry. Colorimetric methods for NO3 (like <"cadmium reduction">) are reliant on reducing the NO3- to nitrite (NO2-), as some nitrite compounds are both coloured and insoluble. Nitrate testing in sea-water is easier, mainly because you have a known chloride ion concentration.

We use <"ion selective electrodes"> for ammonium and nitrate in non-polluted water, but even then it isn't always straightforward to get comparable and repeatable results. It would be purely speculation, but my suspicion would be that very few of the reported results from test kits for ammonia, nitrate etc are anywhere near right, and a lot are likely to be wrong by an order of magnitude.

It is possible to keep heavily stocked, non-planted tanks, to have simultaneous nitrification and de-nitrification in a filter, to judge water quality based upon test kits results etc. but the key word is "possible", and I'm much more interested in "probable".

cheers Darrel

 

[alto]

I suppose it rather depends on one's expectations from these kits, as an example, suppose tank has a "measured" 20ppm nitrate - kit can't possible show a level of 200 ppm as there's insufficient reagent, perform a 10X dilution on tank sample with tap water, RO water, DI water & tank water & check readings
In my case tap water is very soft, slightly acidic ... & so run the tanks as I have low stocking levels with at least 50% weekly water changes, I used various branded kits, generated a standard curve with each, tested additional samples, then tank water at various dilutions with mentioned dilutents ...

Results ran something like this
20ppm +/- 5 pm
(10 X dilution) 2 ppm - 5ppm (no zero readings & not possible to distinguish 1,2 or 3 ppm with reasonable accuracy/precision)

I also took tank water (with it's presumed (measured) 20ppm nitrate) & spiked with additional nitrate ... again results fell within expected ranges ... so I fail to comprehend how that ~20ppm nitrate level can be orders of magnitude off 😕

I was sceptical of these kits, hence the playing about.


All I'm looking for from these kits is absence/presence of ammonia, nitrite & reasonable amounts of nitrate
- given local tap water, I keep soft, acidic water fish, often wild caught so I want low nitrates etc.

I would not use these kits to add reagents to "known" levels, calculations are better suited for that ... OTOH having added nitrate etc to a level of 10ppm, why not run a test kit sample & see what reading you get 😉

 

[dw1305]

Hi all,

I suppose it rather depends on one's expectations from these kits, as an example, suppose tank has a "measured" 20ppm nitrate - kit can't possible show a level of 200 ppm as there's insufficient reagent, perform a 10X dilution on tank sample with tap water, RO water, DI water & tank water & check readings
In my case tap water is very soft, slightly acidic ... & so run the tanks as I have low stocking levels with at least 50% weekly water changes, I used various branded kits, generated a standard curve with each, tested additional samples, then tank water at various dilutions with mentioned dilutents ...

Results ran something like this
20ppm +/- 5 pm
(10 X dilution) 2 ppm - 5ppm (no zero readings & not possible to distinguish 1,2 or 3 ppm with reasonable accuracy/precision)

I also took tank water (with it's presumed (measured) 20ppm nitrate) & spiked with additional nitrate ... again results fell within expected ranges ... so I fail to comprehend how that ~20ppm nitrate level can be orders of magnitude off

This is it in a nutshell, I'd be confident that your measured nitrate values are pretty accurate, because you have performed serial dilutions, generated a standard curve, have water that is low in solutes etc.

Again it is purely conjecture but my suspicion would be that you are very much in a minority of testers who follow lab. protocols.

The problem for me is that you can't then compare the values you've recorded with the values from some-one who has more solute rich water, hasn't followed the same methodology etc.

cheers Darrel

 

[alto]

Yeah but all this chatter about possible interference re aquarium water testing - what about urine testing 😉 ... those multitest strips work surprisingly well 😀
(unfortunately aquarium grade test strips are mostly low quality - despite the high end pricing)

I did all the serial dilutions & standard curves etc as I was sceptical of the aquarium test kits (& some definitely provided "creative" results) but was overall impressed with what was on the market.
I looked at the chemistry behind each test kit method, noted the interfering compounds etc - I'm far from convinced that they are so significant & frequent as to invalidate "most" test kits ...

(questionable technique, sure, 😉)

I rarely test these days, but do recommend novice aquarists "test" - if they get results A +/- a, then suddenly result Z, there's something that needs investigating ... people can't bring their aquaria into the shops, but they can bring water samples ... assign something a name & number & it's a more level playing field for discussion than qualitative observations - especially with someone that has limited knowledge of fish behaviour, appearance etc