Biofiltration 101

The decomposition of waste products in a tank occurs in many stages. Fish & plants (yes, plants too, in the form of old leaves and old plant parts) excrete organic waste in the form of waste proteins, amino acids, cell membranes, dead cells, fibre, urea and other organic by-products.

Snails, shrimps and other detritivores also help by consuming detritus and breaking down organic material into smaller particles.

Shrimps, snails, isopoda and other small aquatic organisms mechanically break down larger fish faeces and feed on the microbes that live on them. Bacteria also produce a biofilm that traps particulate matter - this is very important in maintaining water clarity and clumping pollutants. Protozoa and larger microorganisms further break down the waste into simpler nitrogen compounds. Bacteria, fungi and archaea break these down further and much of the waste ends up as ammonia (NH3) and carbon dioxide (CO2). Bacteria and archaea further oxidise ammonia (NH3) to nitrite (NO2) and nitrates (NO3). If anaerobic bacteria are present in the ecosystem, nitrates can be further reduced to nitrogen gas (N2), completing the nitrogen cycle. Nitrates (NO3) or Nitrogen gas (N2) are the common endpoints of the decomposition chain for nitrogenous waste in an aquarium. Nitrogen gas is naturally released into the atmosphere in an open system, while nitrates are taken up by growing plants or removed during water changes.

Tiny micro-organisms are involved in the various stages of decomposition and these important processes are largely invisible to the naked eye.

Hobbyists have no established test methods for measuring organic waste levels at earlier stages of decomposition - other than visually observing fish faeces and organic detritus accumulation at substrate level, or observing that the water is cloudy due to particulate matter.

At the stage where ammonia (NH3) is produced, hobbyist test kits are readily available to test for ammonia (NH3), nitrites (NO2) and nitrates (NO3) in the water column. As elevated ammonia levels are toxic to livestock, most hobbyists are aware of the importance of keeping them at bay. The main way to do this is to have a mature filter that contains enough bacteria and archaea to quickly oxidise ammonia and nitrites as they are produced. The process of building up a filter of bacteria and other microbes is called tank cycling.

Cycling a planted tank means building up these colonies of bacteria before adding animals. The idea is that any toxic ammonia produced by the animals can then be rapidly converted into relatively harmless nitrates.

However, ammonia oxidation is not the only function of filtration. As mentioned above, while hobbyists can easily test for ammonia, they do not have good testing methods for measuring organic waste levels at earlier stages of decomposition - other than being able to visually see cloudy water or particulate matter floating around the tank. Having large amounts of organic waste and pathogenic microbes floating around in the water column is detrimental to fish and plant health. It is also the job of the filter to capture such particulate matter. A sure sign that the filter is not working optimally is if you notice that the tank water is cloudy.

One observation is that many hobbyists claim that their 'water parameters are perfect' with no measurable ammonia or nitrite, yet they continue to lose fish or have fish that are frequently sick. This is because water quality can be poor and full of other contaminants even when ammonia or nitrate is not detectable. For example, the tank water may contain high levels of pathogenic bacteria due to high levels of organic waste.

The substrate zone has a large surface area when aquasoil and smaller gravel are used. The substrate is an important collection point for debris and particulate matter.

Creating an ideal environment for microbial growth

The first step in aquarium cycling is to ensure that you are providing a favourable environment for microbial colonisation and growth. Most microbes live on surfaces, with the two most populated areas being the filter and substrate, as these two areas have a high surface area. However, surface area is not the only factor at play.

Optimizing filter media

Bacteria (including Nitrosomonas and Nitrosococcus) & Archaea in the filter & substrate convert ammonia (NH3) to nitrite (NO2). Various strains of microbes (Nitrobacter and Nitrospira) convert nitrite (NO2) to nitrate (NO3). These bacteria are most abundant on the surface of the aquarium, where they form biofilms that act as a bacterial shelter, protecting them from external environmental conditions. They are most abundant in the substrate and filter - so the main objective of filter media is to provide good housing for bacterial colonies.

Filter media with a larger surface area theoretically provide more surface area for bacterial colonisation. However, ammonia oxidising bacteria also need access to water flow and oxygen to do their job. Good filter media strive to provide a balance of both. Common forms of filter media include sponge or ceramic type media.

Good quality 20-30ppi filter foam will work well as a general filter media in most scenarios. Finer foam (40-60ppi) may trap finer particles more quickly, but will also clog more quickly - and vice versa for coarser foam. Foam media will clog progressively over time, with the media closest to the filter inlet clogging the fastest. This clogging leads to a large variability in media/filter efficiency, but can be mitigated by using a pre-filter (more on this in the filter layout section below) to trap particulates.

Commercial companies have been creative in using ceramics, sintered glass and other exotic materials to create new forms of filter media to upsell the customer.

Some brands will boast that they have 1000 times the surface area of basic filter sponges. Whilst this claim may be true in theory, the real world performance of high-end filter media is often not significantly better than using cheap, boring, ordinary filter foam. Similarly, having a lot of surface area that does not have good access to water flow and oxygen will not achieve much in terms of ammonia oxidation. Bacterial biofilm and organic waste clog the fine pores of high-end media that claim to have very large porous surfaces. Biofilm and organic matter also add colonisation surfaces to coarser media that may not have as much theoretical surface area.

Many commercial brands upsell ceramic/sintered glass media that claim to have a huge surface area - but the ultra-fine pores are easily clogged by debris and biofilm. On the other hand, the large spacing between the individual ceramic/sintered glass pieces means that it is difficult for the media to become completely clogged, unlike sponge media which can become very clogged if not maintained.

The main advantage of ceramic media is that it lasts forever and will not collapse or compress over time, and the large spacing between the individual pieces means that it will not completely clog over time. However, it does not trap finer particles as well as finer filter foam.

Some ceramic media, such as Biohome (pictured above) and Seachem Matrix, have an anaerobic interior that allows nitrate-reducing bacteria to thrive. These bacteria reduce nitrates (NO3) to nitrogen gas (N2) by extracting the oxygen for respiration, thus completing the denitrification process. The nitrogen gas is released into the atmosphere. This is one method of removing residual nitrates from the water column, but it requires quite a lot of filter media to be effective, as anaerobic bacteria work much more slowly than their aerobic cousins. In typical hobby size filters, their nitrate reducing effect is not always significant. Nitrates are much more effectively removed by water changes, which are also useful for diluting other dissolved contaminants in the tank. Nitrates are also readily consumed by plants in a planted aquarium.

Beyond ammonia oxidation

Ammonia oxidation is not the only role played by filter media microbes. The amount of filter media required for ammonia oxidation alone is surprisingly small. In acidic aquarium environments where the pH is less than 7, most of the ammonia is in the ammonium form, which makes it non-toxic.

Ammonia is not the only form of pollutant in aquarium water. Large particles of organic waste give rise to pathogenic microbes if they are not broken down quickly. Filter media harbor microbes that form bio-films that clump together fine organic waste and other contaminants. The filter also acts as a trap for large organic waste particles. This is what keeps the water crystal clear in a mature aquarium with adequate filtration. Even very fine filter media alone would have a hard time clarifying the water without the help of microbial bio-films. Having more filter media is therefore important for maintaining good water quality.

Most of the tanks in the 2hr Aquarist gallery run on boring 30ppi filter foam, we do not use any branded filter media.

Filter media layouts

Complex filter media layouts tend to give the aquarist a feel-good factor without any significant increase in actual performance.

The wide variety of media on the market is the result of commercial companies looking for more ways to upsell hobbyists, and most do not make a significant difference in working efficiency. However, if you do choose to use a variety of different media, there are a few principles to follow.

Optimally, when using ceramic or bio media, we do not want the fine pores of the ceramic media surfaces to become clogged with organic debris, so ceramic media should be used after a layer of foam to filter out coarser particles. Foam coarser than 30ppi works less well as a filter for finer particles, so 30-45ppi foam is preferred as a shield before the ceramic media. If this foam layer becomes clogged, it can be flushed out without disturbing the subsequent layers of bio-media.

Layout 1: Finer foam as a first layer

The finest layer is placed on the first layer, this layer will clog quickly and requires regular maintenance (every 2 to 4 weeks) to prevent slowing down the flow of the whole filter. The middle foam layer acts both as a bio-media and a fine particle trap. The bio-media is kept free of large particles by being the last layer.

Pros:

• Fine layer of foam prevents bio-media segments from clogging up.
• Only the first layer has to be serviced regularly, the rest of the filter can be left undisturbed for long periods.
• Great for stability of the bio-media's microbial community.
• Fine particulate matter is captured well.

Cons:

• Finer layer foam layer will clog quickly.
• Clogging of the first layer will slow down flow for the whole filter.
• Unsuitable layout for folks that are not regular on maintenance.

Layout 2: Lowest maintenance layout

For people who are lazy and want to minimise the cleaning of the filter. The layout should start with the coarsest media and progress to the next finer media, with the last layer being the finest. This filter layout will take the longest to clog as the layers progressively filter out particulate matter, and will require the least maintenance. However, once clogged, you will need to flush most of the layers at the same time, which may cause some disruption to the microbial colonies.

Pros:

• Less servicing required, filter will take an extended period to clog.
• Fine particulate matter is captured well due to the mix of coarse and fine layers.

Cons:

• Maintenance will likely require servicing of all layers at the same time.
• Bio-media layers may clog more easily, and not have optimal water flow

Layout 3: No maintenance layout?

As all foam media will eventually clog, some hobbyists have used ceramic media exclusively in their filters. The large spacing between the individual pieces means that the filter will never clog completely. This layout is also less efficient at capturing particulate matter. While there is no direct mechanical capture of particulate matter by fine filter media, the bacterial biofilm still clumps particulate matter and debris. The coarse nature of the media means that clumps of detritus are more likely to settle in the tank than in the filter. In tanks where water changes are frequent, or where there is no significant generation of particulate matter, this filter layout may work well.

Pros:

• Almost no maintenance.
• No slow down of water flow due to large spacing between ceramic pieces.

Cons:

• Fine particulate matter will likely settle on the tank substrate rather than filter.
• Fine pores of the bio-media will clog more easily.
• Best used in tanks with frequent water changes.

Layout 4: Pre-filter before main chamber

This is a similar layout to layout 1, except that the fine foam layer is in a separate pre-filter chamber. The pre-filter chamber is separated from the main chamber to keep it accessible and should be serviced regularly. The pre-filter prevents larger waste particles from accumulating in the main chamber. This design allows the main chamber to operate undisturbed for long periods (up to a year), while the easily accessible pre-filter chamber is cleaned more frequently (every 3 to 6 weeks).

The finer filter foam used in the pre-filter easily filters out fine particles. This makes it easy to achieve high water clarity without disturbing the bio-media. Some filter models on the market come with integrated pre-filters. Pre-filters can also be installed separately before the main filter.

Pros:

• Fine particulate matter is captured well, great water clarity.
• Bio-media does not clog.
• Bio-media layers are left undisturbed for extended periods of time, ensuring continuous stability of the biological system.

Cons:

• Most filters on the market do not come with a build-in pre-filter.
• Pre-filter needs to be serviced regularly.

In filters such as the Oase Biomaster range (shown below), the fine pre-filter foam allows the main chamber to operate smoothly for over a year without maintenance. The pre-filter can be easily removed without touching the main chamber. This is the design we at 2hr Aquarist prefer to use on our own tanks.

Flow and oxygenation, trace elements

Microbes need good oxygen levels to grow and break down waste. In an aquarium, a clean water surface and good water circulation are essential to maintain good oxygen levels. In aquariums, gas exchange only takes place at the surface of the water, so it is important to keep the surface free of oil and to ensure that surface water is constantly exchanged with deeper water in the tank.

Buying a good size filter to drive the flow, with the outlet/inlets well positioned to give good flow throughout the tank, will make a big difference. The flow arrangement should also take into account the position of the hardscape.

Wet/dry filters with chambers that have access to air flow are particularly effective where ammonia cycling is concerned. While aquatic plants can produce a lot of oxygen during the light window, most aquariums are only lit for 1/3 of the day or less. When plants are not photosynthesising, they become net oxygen consumers. Good gas exchange and oxygen levels should be maintained consistently around the clock.

In addition to oxygen, ammonia reducing bacteria require magnesium, phosphates, carbonates and small amounts of organic carbon. Simply seeding an empty aquarium with a bacteria culture and ammonia is not enough to start the cycle, the other elements mentioned above must also be present. In aquariums where soil substrates are used, these elements are usually available. However, in tanks using inert substrates, they may be lacking.

A clean water surface with some surface agitation is important for maintaining oxygen levels. We use surface skimmer inlets for all tanks in the 2hr Aquarist gallery. This keeps the water surface clear and directs oxygen-rich surface water into the filter. Similarly, the filter outlet is positioned near the top of the tank to mix the oxygen-rich surface water with the rest of the tank water.

pH, carbonates and other water parameters

For ammonia-oxidising bacteria to work, they need other components besides pure ammonia; the bacteria also need carbonates (CO3), magnesium (Mg) and phosphates (PO4) to be present. These elements are often present in trace amounts in tap water and are also released from active substrates such as aquasoil. For commercially available strains of ammonia oxidising bacteria such as Nitrosomonas and Nitrosococcus, they function optimally in alkaline pH ranges between 7.5 - 8.0. In acidic tanks, particularly low pH aquasoil tanks below pH 6, thaumarchaeota or archaea may be the dominant ammonia oxidisers in the system rather than bacteria. (see more on this topic below).

Reduced toxicity of ammonia below pH 7

In biological systems, ammonia can occur in two forms - ionised (NH4+) and unionised (NH3). The amount of ammonia present in either form depends largely on the pH range of the aquarium. Ionised ammonia (NH4+) is much less toxic. Therefore, the toxicity of ammonia is greatly reduced in lower pH environments as most of the ammonia present will be in the form of ionised ammonium (NH4+). In aquasoil tanks where high levels of ammonia are emitted, one can escape most of the disadvantages of elevated ammonia due to the strong buffering capacity of the soil, which lowers the pH below 7.

The majority of tanks in our 2hr Aquarist gallery run between pH 5 and pH 6, due to the combination of soft tap water and aquasoil. 

Bacteria does not work below pH 6 ?

Persistent anachronistic thinking in the aquarium hobby often spreads the rumour that tanks cannot be recirculated below pH 6, or that bacterial oxidation of ammonia stops when the pH drops below a certain level. While commonly known ammonia oxidising bacteria such as Nitrosomonas and Nitrosococcus function optimally at higher pH ranges, they are not the only ammonia oxidising organisms in aquatic systems. In acidic environments, archaea, thaumarchaeota and other organisms, rather than bacteria, may be the primary ammonia oxidisers in the system. Scientific studies such as this onealso show that nitrification by bacteria still occurs in low pH environments because they form a protective biofilm where the microenvironment is conducive to their work.

Many natural lakes and rivers have pH ranges below 6 (some in the 3+ range) and they thrive with microbial life.

Cycling tanks in low pH environments entirely on the typical strains of Nitrosomonas and Nitrosococcus will be slower than in higher pH tanks, but other forms of microbial life will eventually develop to take over the ammonia oxidiser roles in such systems. If the natural pH of your aquarium is below 6, there is no need to change the water chemistry of your aquarium. However, tanks may take longer to fully cycle than those with more alkaline water. On the other hand, at lower pH ranges, almost all ammonia is present as ammonium (NH4+), which makes it non-toxic.

Soft water tanks with Aquasoil often see very low pH ranges due to the combination of Aquasoil lowering the KH and CO2 injection lowering the pH. The tank above has a pH of 5.0 when CO2 is switched on.

Kick starting cycling with starter bacteria / established media

Once the filter and tank have been set up, the cycling process can begin ~.

New tanks are largely devoid of micro-fauna. Bacteria and other microbes enter the system by piggybacking on plants and fish that are added. Soil substrates tend to be seeded with more microbes than inert substrates. Below are some common ways to seed the system with micro-organisms to speed up tank cycling.

1. Introduce sludge/mature filter media from a mature tank into the new filter. This will quickly introduce a large amount of seed microbes. This can be done by siphoning mulm from the bottom of the substrate of a mature tank and transferring it directly to the substrate of the new tank. It can also be done by mixing aged substrate from an older tank with new substrate in a new set-up. Transferring aged filter sponges from an older filter to a newly installed filter will also work. Squeezing the organic detritus from older established filter sponges into a new tank and/or filter will also work. This is the best method of seeding a new tank as it introduces a wide variety of active microbes directly into the new tank system.

2. Dosing bottled or powered commercial bacteria into a new system will help seed the system with beneficial bacteria.

3.Adding sediment collected from a natural lake. This can introduce a large and diverse amount of micro-organisms. However, care must be taken to collect it from an uncontaminated location.

Once the first batch of microbes has been introduced, tank cycling can begin.

Cycling a tank - old school fish in method

The old school method of cycling a tank is to add fish gradually over time. A few hardy fish are added from the start. The waste products of these fish will feed the bacterial cycle. Over a period of weeks, more fish are gradually added as the bacteria in the filter develop over time. Large weekly water changes are still carried out to prevent a build-up of waste products. This method has worked very well in the past as long as regular water changes are made to prevent large ammonia build ups. However, it has also been criticised for being cruel - and although fish may not show outward signs of stress, it can still affect their organ health and lifespan if ammonia levels are not carefully monitored.

By testing ammonia and nitrite levels in the aquarium, it is possible to assess whether biological waste is being removed at a sufficient rate and whether ammonia is building up to toxic levels. This method is less suitable for higher pH tanks (8+) where ammonia toxicity is more likely to occur because ammonia is predominantly in the toxic NH3 form. At higher pH ranges, ammonia toxicity occurs quite rapidly. Ammonium is much less toxic at lower pH ranges. It is common to see low pH (pH 6+) tanks with a few ppm of total ammonia still containing healthy looking fish, much to the bewilderment of observers.

How much ammonia is acceptable in this method?

Ammonia burns gills and causes internal organ damage and death at high doses. At low doses it can still cause stress and shorten the life of the fish. In practical terms, if you see fish with poor colouration, not eating well or hiding when they should be out in the open, it may be a sign that the water quality has deteriorated and a water change is needed.

Smaller fish produce very little waste, especially in a large, lightly stocked tank. As the tank becomes overgrown with plants, they will also provide an additional buffer by taking up ammonia as a nitrogen source.

Cycling a tank before adding fish (Fishless cycling)

Fishless cycling became popular when folks realize that they do not need to risk fish health and that they can provide the ammonia necessary by other means.

Cycling by dosing ammonia:

This involves regularly adding liquid ammonia to a new tank that has been completely set up, except for livestock or plants, to allow the bacteria colonies to grow. Follow these 3 steps:

1. A dose of 2ppm ammonia is added, then the water is tested after a few days (it takes about 3 days from a cold start to see any change at all). When the ammonia levels start to drop, you would see a build-up of nitrite. The first step of the ammonia oxidation cycle is started (but not necessarily completed).
2. Additional ammonia is then added each day to feed the bacteria (add enough to bring levels back up to around 2ppm). After many more days, nitrite levels would fall and you can then measure nitrate levels rising as the bacteria that convert nitrite to nitrate have colonised. This takes longer than step 1 because the bacteria responsible for converting nitrite to nitrate are slower to populate.
3. Eventually, even with the addition of ammonia, nitrites and ammonia would be measured at 0 after 6 hours, while nitrates would accumulate. The ammonia cycling process for the tank is now complete. The whole process can take 2-8 weeks depending on the tank parameters.

Typically we would change 80% of the tank water to reduce nitrates before adding animals. Adding starter bacterial cultures at step 1 will greatly speed up the process.

In a tank where ammonia is added at a steady rate, ammonia-oxidising microbes will establish first, converting the ammonia into nitrites. As nitrites build up, microbes that oxidise nitrites to nitrates will proliferate and over time nitrites will be converted to nitrates. In most tanks, nitrate is the end product of microbial action, and excess nitrate is removed by large water changes. All three processes occur continuously in a mature aquarium. In a planted aquarium where other parameters are met, plants will take up ammonia and nitrates through the water column.

Cycling with aquasoil:

In a tank with Aquasoil, ammonia is normally released by new soil, so there is no need to add ammonia.

After filling the tank, we recommend a 100% water change before running the filter. This will remove organic debris and dust and prevent the filter from taking up a lot of debris at the start. After starting the filter, dose the starter bacteria culture into the filter inlet. We then recommend that you run the aquarium for a couple of weeks with no plants, fish or lights on. The only thing running is the filter. This is often referred to as the 'dark start' method of starting a planted aquarium.

The aquasoil should give off ammonia for a while when first submerged. This will provide food for the bacteria to feed on. Bacteria multiply exponentially. However, it can take many days for the colonies to reach a good size and have a noticeable effect on the ammonia levels. If you are not using starter bacteria products, it is a good idea to add mulch or used filter media to get the cycle started. Without the use of starter bacteria products, a full tank cycle can take up to a month or more. With the use of starter bacteria products, the cycle time can be reduced to a week or less.

In tanks where the aquasoil is very rich in ammonia, ammonia levels can rise very rapidly. Water changes can be made to bring it down if it exceeds 5ppm, as excessive ammonia can slow down the cycle.

Tests can be carried out every few days to monitor ammonia levels. If both ammonia and nitrite readings are zero, the tank is cycling. For tanks that have been seeded with starter bacteria, cycling may take as little as a week. For most tanks it will take at least 2 to 3 weeks for cycling to be complete.

How soon can one add plants/fish ?

The lowered pH of the tank water due to the buffering capacity of Aquasoil reduces ammonia toxicity as most of the ammonia is present in the less toxic ammonium (NH4+) format at low pH (below 7). This allows hardy plants to be planted and grown at early stages where ammonia levels are detectable. However, more sensitive plants such as Utricularia gramminifolia, and tissue culture plants in general, should not be planted until the tank has been cycled - they melt easily in fresh soil. Other plants that are susceptible to algae and adapt better to mature tanks are Bucephalandra species, Hygrophila Chai, Eriocaulon species.

Similar to plants, fish are best added after the tank has been cycled. Hardier fish can be added earlier for the fish-in cycle; most commercially available tetras and cheaper fish from aquarium shops fall into this category. However, as mentioned above in the section on fish-in cycling, you should monitor them for signs of distress and carry out a water change if necessary.

Go tohere to read about why you should or should not cycle a tank before planting.

Tank maturity beyond ammonia cycling

Ammonia cycling is just one form of organic waste in the tank. However, it is the one that affects livestock and algae the most, so the first goal of tank cycling is to get ammonia cycling done.

Journey to the micro-cosmos has very good videos of microbes consuming algae.

Microbes and decomposers are also involved in the consumption of organic waste. A biologically mature system is one in which there is sufficient microbial life to rapidly break down harmful organic pollutants into harmless substances. This creates a more favourable environment for both animals and plants. The faster waste is broken down, the fewer triggers there are for algae to spawn. This is why biological maturity is important even in unstocked tanks. It takes time for a tank to become biologically mature (a few weeks), even though the ammonia cycle itself may be complete. Hobbyists have no established test methods for measuring organic waste levels at earlier stages of decomposition - other than visually observing fish faeces and the accumulation of organic detritus at substrate level. It is only when waste has decomposed into ammonia form that it will show up on hobbyist ammonia test kits. Therefore, a zero ammonia reading does not automatically mean that the water is free of other forms of organic pollutants.

The tank must be considered as a whole ecosystem. For planted aquariums, the system will stabilise more quickly if the majority of the aquarium is planted with healthy, growing plants. Healthy plants oxygenate the water, absorb harmful ammonia and provide a healthy habitat for microbes. Deteriorating plants pollute the environment by contributing detritus and organic waste. Allowing plants to establish and grow is an important part of stabilising the ecosystem of a planted aquarium.

Some plants such as Utricularia gramminifolia and Bucephalandra acclamate much more quietly in biologically mature tanks. These species should never be planted in a new aquarium. Both species have more problems with algae and melting in a new setup, although they do not have very demanding growth requirements.

Some signs that the tank is biologically matured;

• Ammonia tests are consistently 0.

• Water clarifies quickly even after substrate disturbance.

• Water is clear (micro-particles are clumped together by bio-film).

• Dead animals disappear quickly (presence of larger detritivores such as shrimp).

• Aquarium does not smell bad (larger organic molecules are broken down quickly).

• Sensitive animals such as shrimps have a high survival rate and reproduce regularly.

Some signs that a tank is not biologically matured;

• Cloudy water in new tanks.

• Positive ammonia readings.

• Frequent algae outbreaks; green dust algae and diatoms are particularly common.

• Melting of plants although parameters appear to be fine.

• Inability to keep sensitive animals alive (shrimps, sensitive fish).

The presence of brown stringy diatoms in a new set-up is a strong indication that the tank is not biologically mature. In most healthy tanks, diatoms will disappear on their own over time without any intervention.

Tank is a micro-ecosystem; avoid disturbing the balance

Tanks can easily have their bio-filter community disturbed. These microorganisms are fragile; as a good rule of thumb we would say that anything that can harm fragile fish or shrimp can also harm the microbial community. If you are consistently unable to keep shrimp alive in your aquarium - chances are you have a system that is not biologically stable.

• Frequent use of harsh chemicals such as algaecides.

• Washing the filter too often.

• Ammonia spikes due to misuse of terrestrial fertilisers or poor tap water.

• Heavy metals or poor quality tap water during water changes.

• Large fluctuations in aquarium parameters such as alkalinity.

• Failure to use a dechlorinator in tap water containing chloramines. (beginner's mistake)

The bio-filter will tend to grow to accommodate the amount of waste produced by the system, but it will not easily compensate for spikes in the system. For example, if you feed your fish an amount of food that produces 1ppm of ammonia per day, your tank's microbial community will grow to digest that amount on a regular basis. The day you triple the feed and get a spike of 3ppm ammonia - there will be a short term ammonia spike as the microbial community is not used to dealing with that amount of input. So whether you feed your fish more or less, it should be a relatively regular amount.

This concept also applies to water changes. In tanks that are run on a weekly water change schedule, skipping water changes will often result in algae blooms.

Go to here to learn how to control algae in a new tank setup.