how biological filtration works

how biological filtration works
(or, the enlightenment of poo and its eventual transformation into a new state of being)

Many people get into fish-keeping only to realise that they got into a hobby which is actually a lot more complex than they realised ... they lose a lot of fish by not understanding, not having any help and not having any basic sources to draw from. In the process they may lose a lot of fish, often expensive ones, freak out, tear their beards, gnash their teeth, yell about what a pooey hobby fish-keeping is ... and, disappointed, give it up ... which is always a great loss to the fish-keeping community. Biological filtration is the most grassroots principle in fishkeeping, and without doubt the most important to understand.
The vast majority of filtration systems in aquariums utilise biological filtration as their mainstay of converting harmful waste products into less harmful ones, however, there are certain conditions in which biological filtration will not work, which we will get to later. In tanks which house discus, the conditions will be ideal for biological filtration. The PH is around 7 and the water quite soft.
When setting up a new tank, a running-in or "cycling" period is needed before introducing its occupants. This generally takes 4 - 6 weeks.
Here's why:
When a new system is ready to start there are very few microscopic organisms living in it. Usually we use tap water which has been chlorinated, and a lot of bacteria and micro-organisms die from chlorine/chloramine poisoning, including those which are active in biological filtration (poor suckers, but lucky for us it kills he nasties, too, although, who knows what the chlorine does to us!). Thus the tank is quite sterile.

The Nitrogen Cycle utilises two species of bacteria, which will form in sequence as the system begins to cycle. The first of which to appear is the Nitrosomona bacteria. Fish generate waste which is quite high in ammonia content and the first stage in biological filtration is for the Nitrosomona bacteria to consume the ammonia and convert it into nitrites. This very important, because ammonia, even in relatively small concentration is quite a deadly substance for your fish. Nitrites, are somewhat less toxic, but are still very dangerous. It takes about 1 to 3 weeks for this to begin to happen effectively, but it doesn't finish here.
This is where the second stage of your biological filtration will come in. The second stage of biological filtration will kick in once there are enough nitrites present for our second type of bacteria to thrive on. These hard little workers are called Nitrobacter. Nitrobacter consume the nitrites and convert them into relatively harmless nitrates. This process takes another 2 to 3 weeks to occur naturally.
Both these bacteria are of a type called "aerobic" ... which doesn't mean they dance around a lot and play silly music ... it does mean that they need oxygen to function. There are many different ways to oxygenate your water effectively, but that's another subject.
Traditionally, a couple of cheap fish (guppies, feeder-goldfish) can be used to start the Nitrogen Cycle, utilising their waste products, however there are some enzyme based products available which can be used to "kick-start" this cycle and with these methods the cycle time is cut down quite a bit. Here is a good link if you want to learn about fishless cycling :
www.discusforums.com/forum/viewtopic.php?t=895
Another method is to use some of the media from an already established filter. Lucky you, if you have multiple tanks or a friend who will give you some established filter medium ... but be quick, in getting this into your new set-up, as the bacteria will begin to die within 1 - 2 hours, unless kept moist and in contact with air.
In nature, the end product of all this hard work are nitrates. Plants use nitrates in their growth process, and heavily planted aquariums with very few fish in them can be balanced, where the plants use all the nitrates present in the water. This isn't practical in most discus tanks, however, as many are bare bottomed, have no plants and have too high a population of fish for this to be a viable thing.
This is why we do water changes, often and conscientiously. Although nitrates are a lot less toxic than nitrites or ammonia, it still builds up and can pose a problem to fish, especially to fish like discus. So change your water, your fish will love you for it and smile whenever you come into the room ... I promise ... and just maybe they will dance :)
Examples of filters using biological filtration include under-gravel filters, fluid-bed filters, canister filters, hang-on filters, trickle-filters, sump filters, sponge filters, box filters, top filters, power filters etc, etc

As mentioned earlier, there are conditions of extremes where biological filtration becomes non-functional, as the bacteria cannot survive. One such instance is the kind of condition in which blackwater fish, such as some Apistogramma species need to spawn. This water can be as low as 3.5 ph and have extremely low, if any, hardness. Some species come from water so soft, it rivals Reverse Osmosis filtered water. Such extreme acidity will not be conducive to the survival of bacterial cultures in a biological filtration system and thus .... back to many many water changes (did I mention your fish will love you for those? and maybe, if you're lucky, get the newspaper for you in the morning and your flippers, too! .... but you gotta be very lucky).

One word of advice, also on stocking your tank ... when the biological filter is set up, try not to dump 50 gillion fish into your tank at once, but increase the load slowly and steadily, as the bacteria need time to increase as the waste products increase.

enjoy your fish :)

Fantastic explanation, and a great read too.

All those new to aquariums (and a few who missed Biology 101), read, learn, and enjoy :book

Thanks Wickedglass,

Awesome explanation. Let me ask you this. There seems to be a lot of discus keepers who have a variety of water changing schedules.

For example: i bought two discus from someone on the forum, he had barebottom tanks, backdrop filter and he changes the water once a month.

Oakleigh Aquarium also change the water once a month and he feeds the fish 3-4 times a day. Now, Oakleigh pretty much only sell discus and his fish are nice and healthy. He tells me there are two ways to keep your water 'safe'. 90-100% water changes every day (like they do in Malasia) or well-established biological filtration (like he has). He doesn't seem to be worried about the build-up of nitrates.

Another example: i bought another two fish from someone in the forum who changes 90% of the water daily. He had nothing except one of those black round sponges in the water, no external filtration i could see.

What is the deal with once a month water changes?

The nitrate build-up in Oakleigh Aquarium happens like in any other system. Nitrates are way not as harmful to fish as are ammonia and nitrites. Fish usually can handle quite a build up of nitrates in their water before things go cock-eyed and you really urgently need to do a waterchange. By that time it may be too late. The reason for more frequent water change is to prevent a shock to the fish. Nitrates build up slowly, the fish get used to having more nitrate in their water and adapt over time. Then you do a 90% waterchange and the chemistry of the water has all of a sudden changed in the matter of less than 1 hour. Discus tend to be somewhat sensitive to quick-changing conditions. An aquarium shop like Oakleigh is merely a half-way station and most of the fish will get sold before the end of the month, so I'm guessing he does water changes when his stocks are low and before he gets new stock in, I've never talked to him about it, but I might ask him next time I'm there.
In Malaysia where they do daily 90% water changes, they probably have little or no filtration and the luxury of good quality water, at the right temperature, in abundance, so changing the water daily keeps the system nice and clean of nasty waste products.
When doing such large waterchanges you will need to bring the new water up to temperature before adding it, as cold water would be too much of a shock to the system of the fish. Small water changes more frequently means you don't need to pre-heat the water.
The amount of water changes depends also on the density of your fish. more fish in the tank the more waste, the more of either filtration and/or waterchanges you will need. many people think waterchanges are a known quantity and regimen. This is not so, it all depends on ... size of your tank in relation to density of fish, how much you feed them, what your filtration is like, how much waste your fish create (some types of fish create more metabolic waste than others) and personal philosophy.
Also, believe it or not, those black sponge filters can act as a quite effective biological filter, although I think daily 90% water changes are somewhat excessive, considering the water shortage here in australia. In my community tank I tend to change the water every 2 weeks, but many many years ago, I had a tank going for almost a year before I heard about the necessity of water changes, only topping it up when the water evaporated, I didn't lose a fish. When I did read about waterchanges, I stupidly changed a lot of it and a bunch of my fish died ... I was young (9 years old) and uneducated in the ways of the fishkeeper then. I don't recommend doing that though :)
I hope that helps somewhat

Thanks dude!

You've been a great help.

awesome explanations wickedglass

i give it to you man!
you make it sound simple.

thanks

Very well expalined - good job!

Also, could I ask what your opinion is on doing a fishless cycle using bottled ammonia? Or would you use this as a bacteria-food if you add bacteria?
ie. Are there any contaminants etc in bottled ammonia that could cause a problem?

I know this is an older post, but I thought that still may be of interest. It's a pictorial explanation of the maturing process for a biological filter.

Excellent graph. Thanks for that BN.

...and nobody mentioned that bacterial activity is temperature dependant. Or did I just miss it? About every 8 degrees centrigrade bacterial activity doubles. Within reason of course since water can store less oxygen at higher temperatures. You will generally get maximum bacterial activity at 32 degrees centrigrade. Don't want to over complicate things. Just thought it was worth mentioning