Low Ph Stalling Cycle?

[waterdrop]

Neale,

"Saprotrophic bacteria" is a new term to me, different from the familiar "Heterotrophic" and "Autotrophic (or the longer, more specific Chemolithoautotrophic also used for our two nitrifying species)" so I've been taking a look at some soil science articles in the scientific literature since reading your post up there, in an effort to educate myself a tiny bit. About the best one I found, by the way, is an article by Hogberg and Read called "Towards a more plant physiological perspective on soil ecology" in "Trends in Ecology & Evolution" Volume 21, Issue 10, October 2006, Pages 548-554 (for those of you also hunting for material.)

At this point I can't tell whether saprotrophic is simply a different name, basically, for the bacteria we've been (here in the "New to the Hobby" forum anyway) collectively labeling as the "heterotrophs" (of course meaning they consume organic material rather than inorganic, like the autotrophs) which we've understood to be composed of any number of unspecified species that typically remain more waterborn than the autotrophs and are the primary means by which fish waste, excess fishfood, plant debris and other organics are broken back down into ammonia. We also know them as the primary constituents of milky white bacterial blooms. Do you have any insight into whether the term "saprotrophic" you've used refers to the same species we've used the "heterotrophic" term for, or perhaps already know this to be a *different* category of aquarium bacteria that we should know about and understand.

Excuse all the writing here but I'm quite surprised not to have come across this term in my two years here and my exploration of Hovanec's three articles on the autotrophs and numerous articles since those that OM47 and I have periodically looked at in the waste water treatment plant scientific literature. (Perhaps I've missed some coverage of this in the Scientific subforum as I've not had time to keep up with that one.. OM, please tip me off if that's the case.)

I've never had reason, so far, to think of the waterborn heterotrophs to be a bacteria that we need to "develop." My understanding was that these were so completely ubiquitous in non-chlorinated, air-exposed water systems like aquaria that no special effort was ever put forth in quantifying or encouraging them per se. They are simply expected to be present in large numbers, both in a just-filled, dechlored tank and later in an operational, cycled tank.

WD ( so much more to say, so little time, sigh)

 

[nmonks]

Briefly (I HAVE to go shopping now or I'll have nothing for dinner) the word "saprotrophic" is applied to organisms that break down organic matter, and thereby get the energy they need. Fungi are the classic example. They don't "eat" in the same way as animals, by catching and consuming other organisms (actually, some do, but we'll let that pass) but instead wait for something to die and break that down instead. The blue mould in a nice bit of Stilton cheese is a saprotrophic fungus breaking down complex organic materials (the protein in the cheese) to get the energy and amino acids it needs to survive. The break down is outside fungus, and the fungus absorbs the products of digestion. Again, this is different to animals, which consume prey (plants or animals) and break them down inside their bodies.

A heterotrophic organism is simply one that needs to get its energy from something else. It is different from an autotroph (like a plant) that "makes" the energy it needs via some chemical process driven by light energy. Plants make complex molecules from simple ones using light energy, and then break them down to release energy whenever they need it. Animals can only break things down to release energy, and rely on plants to make the complex molecules (sugars for example) in the first place.

Heterotrophic organisms can be predators (like animals) or saprotrophs (like fungi). Both depend on someone else having made the complex organic molecules in the first place.

So, all saprotrophs are heterotrophs, but not all heterotrophs are saprotrophs. Example of heterotrophs that aren't saprotrophs would be carnivores, herbivores, and parasites.

To a degree though, the boundaries are fluid. Aeromonas are saprotrophic bacteria when doing its thing in the gravel, breaking down bits of fish skin and other such things. But these bacteria are mindless, and some will attack living tissues too. Normally, the immune system of a healthy fish fends them off without the least bother, and does this all the time, every day. However, if the fish is stressed and its immune system isn't working, Aeromonas overwhelm the living tissues and eat the cells there instead. In doing so they grow in numbers, clog up blood vessels, and cause further cell death. Lo and behold, Finrot.

In any case, yes, saprotrophic bacteria are ubiquitous, but not necessarily in equal numbers in all places. A clean, new aquarium surely won't have many. It'll take time for them -- just like any other population of organisms -- to ramp up to the numbers allowable by whatever energy source (in this case, fish wastes) is available. I have no idea how long it takes, probably not long at all, but it's a factor worth considering.

Cheers, Neale

 

[dudleyd]

Thanks very much all of you. I'll keep you posted.

DD

 

[Emma*]

This is my first go at posting so please be gentle with me.

I have an Interpet fixbox 64l tank and have been doing a fishless cycle for 23 days.

The problem i'm having is i'm not getting any ammonia drop at all so far. It is dosed up to 4ppm. Nitrite is 5.0 and nitrate is about 10. Temp is 28 degrees C. Added interpet filter start for the first week as instructed. Substrate and ornaments are all in, had murky water (in the tank) for about a week and has been crystal clear ever since. I'm using an API master test kit for testing. Water is treated with interpet tap safe to remove metals.

Having read some of the threads on this forum i think maybe my ph was a bit low at maybe just below 7. Went to lfs and got some API ph up.

So my questions are, what ph is optimal for the cycling process?

is anything else affecting the cycle?


Thanks in advance.

I have exactly the same tank as you! The same equipment and testing kit. Im having problems with my fishless cycle, except my ammonia and nitrite levels are 0 and my nitrate is 40, ph level is 7.6. My tank went a cloudy colour for a few days, its now crystal clear. Im only day 8 with my cycle, when did you first get ammonia? Ive been putting fish food in but its not doing anything!

 

[dudleyd]

Hi emma. I've added household ammonia avaiable from boots for 49pence. In my opinion and after reading most of the fishless cycle methods i decided this would give me more control on the level of ammonia in the tank, i.e. i can dose it to exactly 4ppm.

Todays results from my tank are,

Ammonia 4ppm
Nitrite 5 ppm (probably more)
Nitrate 20ppm (this has risen)

So still no ammonia drop

How is everyone reding the results from their own tests using the API master kit? Where do you hold the test tube, right next to the card with the colours on ar an inch away so the light shines through it? the 2 different ways give very different results.
It's not that i've got bad eyes or anythiing but some of the colours look almost the same to me e.g. ammonia 2.0 and 4.0

DD

 

[Emma*]

I have the same problem with the kit, the colour never looks exactly like it does on the card! I hold it up in the light against the card. I checked the levels today, the Nitrate has gone down to 20ppm. Ammonia is 0.25 - 0.50ppm. Nitrite is still 0.25ppm. Think i may have to buy some ammonia, is it pure ammonia?
Are you using filter start that came with the tank? Im using it as it says, dose every 2 days for 2 weeks but it says it gets rid of bacteria which is good when you have fish but I think its stopping me getting ammonia because its keeping the tank clean and getting rid of the bacteria!

 

[dudleyd]

Yes make sure you get pure ammonia, some places sell perfumed stuff but this is BAD. Ask someone helpfull in boots and they'll direct you to the good stuff, it's in a white and blue bottle with a red child proof cap.
I used the filter start, it obviously hasn't decreased my cycle time as i don't think i'm even close to finish. Some people swear by it but largely people think it's a waste of money, if it comes free though with the tank then whats the harm?

If i hold my ammonia test right next to the card then i get somewhere near 4ppm, if i hold it a centimeter away and let the light through it then it's 1ppm.

 

[Emma*]

Thank you. I will buy some ammonia and see how I get on, how long before the ammonia starts to go down again? Do I add it everyday?

 

[dudleyd]

I'm no expert emma. click here for one that is on this forum, i think if you follow these instructions then you're not going to go far wrong.

Should i be doing water changes during the cycle or not?

 

[Emma*]

I just read all of that! I dont think you have to do water changes till nearer the end of the cycle when ammonia and nitrites are 0ppm and nitrate is high thats when you water change to keep the nitrate down, also plants help keep it down aswell

 

[nmonks]

They really don't. Unless you have a very light stocking of fish, and a very dense stocking of fast-growing plants under intense lighting, the impact plants have on nitrate is minimal.

This isn't to say that things like algae (or vegetable) filters can't work, they can, but the design and use of such units is far beyond the abilities of most aquarists.

Cheers, Neale

also plants help keep it down aswell

 

[waterdrop]

OK Neale and Dudley, I'm back to add more comments and questions:

Dudley, thank you for being patient with us, its rare that a normal fishless cycle thread becomes the conduit for biology class and discussion of methodologies but its happened here in your thread and we'll just keep it going if you don't mind as sometimes it kills the feel of it if we yank it out to the scientific section or something. As thread owner I'll give you a comment first:

You asked "Should I be doing water changes during the cycle (fishless cycle, that is) or not?" In your immediate situation the answer is no. If we descriptively divide the fishless cycle into 3 phases (before nitrite spike, during nitrite spike, after nitrite spike) then you are somewhere within the first two phases, your nitrate(NO3) level is not high and I assume your pH is still artificially raised up near 8. All of this should mean you have no current need for a water change. Overall there's nothing wrong per se with water changes during fishless cycling, assuming you recharge the ammonia back to proper level afterwards, but they do momentarily slow the cycle down a bit, so we avoid them until necessary. They are much more often needed in the third phase, after the nitrite spike is over and we are waiting for nitrite to be able to drop in 12 hours. The most common reasons they are needed is to raise the pH and because nitrate(NO3) has skyrocketed. Both of those sometimes happen in the last phase.

Neale, many thanks for the very interesting info about the definitions of saprotrophs, heterotrophs and autotrophs. You are a better biology teacher than some of my former professors.

It does appear that we've been applying the broader term "heterotroph" to the bacteria that break down organic material like flake into ammonia, which can then be consumed by the autotrophs on the biomedia of the filter that constitute the biofilter. Everything I've seen so far agrees with what you said, that saprotroph is a more specific category for these bacteria that break down organic debris. You went beyond simple definitions and made it clear how the different categories fit together in the big picture.

I like the way you have spoken openly about the different techniques of using organic matter, like fishfood flakes, versus using household ammonia for the fishless cycling process. It strikes me that for someone obviously used to and experienced with the flake method, you've tried to be fair in your assessment of the ammonia method.

Hobbies like this are funny things in that bits of science get used and add to the interest, but seldom are the studies that would apply any science directly to the hobby topics at hand, despite plenty of us grasping at "nearby" science, in microbiology, fish farms, waste water treatment plant literature, biology and botany. It sure would be fun to have some serious scientists chalking up the pH, temperature, mineral content, materials, lighting or lack of it and dosing patterns of ammonia and organic debris and laying out nice results for us, but its hard to imagine it ever happening.

My own perspective is biased in all its own odd ways: After having my basements full of tanks and playing at keeping all sorts of fish and some breeding, I came away as a young person with little real knowledge to show for it. Many years went by and I missed many intervening practices in the hobby. When my son's tank renewed my interested I was fascinated to find the ammonia method, not to mention many other changed aspects of fishkeeping and planted tanks.

Deep in my first ammonia-based fishless cycle I was treated to plenty of days of introspection about whether I was "being had" by this new information I had come across so widely on the internet. When everything played out just about exactly as had been laid out, I knew it was for real and subsuequent experiences have reinforced it. I'm sure my bias is to be a bit over-enthusiastic about it, but we've really had large numbers of successful fishless cycles here in the subforum over the last two years.

Its pretty clear that the progress of a fishless cycle will play out as a pretty similar sequence of events regardless of the ammonia source. The significant difference to me is that I feel there is more control in the careful dosing of liquid ammonia and verification of the dosed level via a followup ppm measurement. Fishfood or prawn loading, I feel, carries much greater variability due to different food makeups and less measurable dosing and delayed timing of conversion to ammonia. I know to some extent we've got a case here of each of us sitting on the outside looking in at the others preferred method, when both have their idiosyncrasies but both can work.

There are cases we get of people using fishfood or prawns and having all sorts of problems with it and we say "ahah!" and label it problematic. I'm aware that likewise we have our percentage of ammonia method cases that seem to veer off into long time-consuming stalls at one or another stage. It certainly seems likely that there are other major factors we are unaware of regardless of method. I know in the bacterial growth for WWTP (waste water) they've only belatedly realized that the nitrite oxidizing species is Nitrospira and not Nitrobacter, something that we found out in freshwater aquaria quite a while ago. The WWTP researchers also seem to be quite interested in dosing frequency ("pulsing" of the ammonia) as a possible significant factor.

I have never seen evidence of a concern that would indicate a problem with heterotroph(saprotroph) development. I would think this would show up as some sort of poor performance of the biofilter -after- the big water change and addition of fish, when organic waste would increase. I would be interested in your thoughts on this. Instead, fishless cycles that pass their qualifying week of dropping 5ppm of ammonia to zero each day seem to provide an environment that fish find comfortable and even stimulating. What I mean is that the fish adapted quickly and showed color and movement of the best sort and of course we see optimal NH3, NO2 and NO3 numbers continue. I just think I will continue to recommend the ammonia method for its greater control except in cases where ammonia can't be had or easily used for some reason.

~~waterdrop~~

 

[dudleyd]

Thankyou WD

I don't mind the thread being hijacked a bit, it's all very interesting.

I have now decided (when comparing the coulour of the liquids in the test tubes to the ones on the comparison cards) to hold the tube about a centimeter away from the card and allow the light to shine through it. If i hold the nitrITE test next to the card then it is almost black where as if i hold it a little distance away then it reads 5ppm.

Is this method right?

 

[nmonks]

Neale, many thanks for the very interesting info about the definitions of saprotrophs, heterotrophs and autotrophs. You are a better biology teacher than some of my former professors.

Thank you.

Its pretty clear that the progress of a fishless cycle will play out as a pretty similar sequence of events regardless of the ammonia source. The significant difference to me is that I feel there is more control in the careful dosing of liquid ammonia and verification of the dosed level via a followup ppm measurement. Fishfood or prawn loading, I feel, carries much greater variability due to different food makeups and less measurable dosing and delayed timing of conversion to ammonia.

When all is said and done, it's probably six of one, half a dozen of the other. The difference really comes down to the "precise" approach adding ammonia works, versus the "idiot-proof" approach of using flake food. I'm sure you could identify the sources of potential problems using both methods. In the case of adding flake food, the usual problem is not adding enough. You need to be using enough to replicate the quantity of fish being kept, and if that means a fair old pinch, then that's the way it is! On the other hand, dosing ammonia is fiddly, and I'm sure many times it seems to fail it is because the aquarist didn't add enough (or perhaps so much they poisoned the tank).

I have never seen evidence of a concern that would indicate a problem with heterotroph(saprotroph) development. I would think this would show up as some sort of poor performance of the biofilter -after- the big water change and addition of fish, when organic waste would increase. I would be interested in your thoughts on this.

It may come down to the types of fish being kept. If you're keeping small tetras that eat all the food added to the tank, and excrete most of their ammonia via their gills, then the denitrification bacteria are probably the ones that matter. But if you have a big catfish that eats chunks of meat, defecates a great deal, and is prone to regurgitating some of its food, then the saprotrophic bacteria probably matter a good deal. This is purely speculation though.

I just think I will continue to recommend the ammonia method for its greater control except in cases where ammonia can't be had or easily used for some reason.

To be honest, I recommend people don't cycle aquaria at all. Instead, I prefer to tell people to clone existing filters. If you take live media from one filter and stick it in another, within reason you can instantly and safely cycle a new aquarium without putting any of your fish at risk. A mature filter can lose 50% of its biological media without causing any problems, and obviously the live media put into the new filter will support a similar quantity of livestock to what the old filter was supporting in the other aquarium.

Cheers, Neale

 

[waterdrop]

To be honest, I recommend people don't cycle aquaria at all. Instead, I prefer to tell people to clone existing filters. If you take live media from one filter and stick it in another, within reason you can instantly and safely cycle a new aquarium without putting any of your fish at risk. A mature filter can lose 50% of its biological media without causing any problems, and obviously the live media put into the new filter will support a similar quantity of livestock to what the old filter was supporting in the other aquarium.

Cheers, Neale

Oh yes, we certainly recommend cloning whenever possible. Most of the context of our fishless cycling advice is just about the small but special fraction of cases where its a new beginner, out of reach of mature media and starting from scratch.

You should consider giving it a shot sometime on some tank, just to file some more experience for yourself if you haven't already had reason to give it a try. A fair number of seemingly pretty experienced old-timers have given the opinion that it perhaps constitutes a step forward in the reliable, repeatable prep of a good biofilter prior to fish introduction. rdd1952 prepared a pretty good paper from a pretty wide array of other sites and sources and then in the last couple of years MW, BTT, rabbut, OM47 and myself, along with others have refined a few details here and there with what I've felt was some general consensus that the process itself was getting a little more reliable and the language to describe it was improving some too. It hasn't seemed like just a fashion thing. It seems arguable that 3 approaches (fish-in/planted, fishfood-fishless and ammonia-fishless) broadly have the ability to satisfy different needs among different hobbyists not having access for mature media for one reason or another.

An example of where each of our approaches probably sounds "fiddly" to the other person is probably the actual ammonia or "flake pinch" itself. To me the ammonia dosing doesn't seem fiddly. Its true you have to understand the aqueous ammonia may have a different concentration from what the bottle says once its been opened, so you get a number from TFF calculator and then start lower than that number and test the ammonia up to something that is pretty close to 4ppm. We recommend using graduated droppers (etc.) and noting what amount that 4-5ppm turned out to be. From then on the day to day add to feed the cycle requires no fiddling.

Likewise, to us, looking at you, the "big pinch" vs. "even bigger pinch" seems very unquantified, especially given potential differences in brands of fishfood even if the food was weighed. And then on top of that there seems no clear time period to wait to later test and determine whether you were under or overdosing (underdosing too much potentially slowing the overall time it takes to cycle or overdosing potentially getting you up to 8ppm where a different species of autotroph messes things up.) BUT, I'm sure all those things could be quantified and explained to better communicate the flake method to beginners.

~~waterdrop~~