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Tank cycling and biological maturity in planted aquariums

November 17, 2023 20 min read

Tank cycling and biological maturity in planted aquariums

Biofiltration 101

The decomposition of waste products in a tank happen 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, cellular lining, dead cells, fiber, urea and other organic by products. 

shrimp planted tank

Snails, shrimps and other detritus feeders 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 sized fecal matter from fish and feed off the microbes that populate on it. Bacteria also produce bio-film that capture particulate matter - this is very important in ensuring water clarity and in clumping pollutants together. Protozoans and larger micro-organisms breakdown the waste further into simpler nitrogenous compounds. Bacteria, fungus, and archaea break these down further, and a large portion of the waste ends up as ammonia (NH3) and Carbon dioxide (CO2). Bacteria and archaea further oxidize ammonia (NH3) to nitrite (NO2), and to Nitrates (NO3). If anaerobic bacteria is present in the ecosystem, Nitrates can further be reduced to Nitrogen gas (N2), completing the nitrogen cycle. Nitrates (NO3) or Nitrogen gas (N2) are the common end points of the decomposition chain for nitrogenous waste in an aquarium. Nitrogen gas will off gas into the atmosphere naturally in an open system, while Nitrates are taken up by growing plants or removed during water changes. 

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

Hobbyists do not have established testing methods for gauging organic waste levels at earlier stages of decomposition - other than visually being able to observe fish feces and build up of organic detritus at the substrate level, or observe 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 keenly aware of the importance of keeping it at bay. Principally, this is done by having a matured filter that contains enough bacteria and archaea to oxidize ammonia and nitrites quickly as it is produced. The process of establishing a filter with bacteria and other microbes is called tank cycling. 

​Cycling a planted tank means building up these colonies of bacteria before adding livestock. This is so that any toxic ammonia produced by livestock can then be processed swiftly into relatively benign nitrates.

However, ammonia oxidation is not the only function of filtration. As mentioned above, while hobbyists can test for ammonia easily, they do not have good testing methods for gauging organic waste levels at earlier stages of decomposition - other than visually being able to 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 does have a negative impact on fish and plant health. It is also the filter's job to capture such particulate matter. A sure sign that the filter is not working optimally is when the tank water is observed to be cloudy.

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

The substrate zone has a ton of surface area if aquasoil and smaller sized gravel is used. The substrate is an important capture point for debris and particulate matter to settle. 

Creating an ideal environment for microbial growth

The first step to tank cycling is by making sure you are providing a favorable environment for microbial colonization and propagation. Most microbes live on surfaces, with the two most populous locations being in the filter and substrate as these two areas have high surface area. However, surface area is not the only factor at play.

Optimizing filter media

Bacteria (Nitrosomonas and Nitrosococcus​ among others) & archaea in the filter & substrate converts ammonia (NH3) to nitrite (NO2). Different strains of microbes (Nitrobacter and Nitrospira) converts nitrite (NO2) to nitrate (NO3). These bacteria are most populous on tank surfaces, where they will create bio-films which serve as bacteria housing units protecting them from twitches in external environmental conditions. They are most populous in the substrate and filter - as such, the main goal of filter media is to provide good housing for bacteria colonies.

Filter media that has more surface area theoretically provides more surface for bacteria colonization. However, ammonia oxidizing bacteria also requires access to flow of water and oxygen in order to do their job. Good filter media strives to have 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 capture finer particles more quickly, but also clog more quicker - and the opposite is true 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 large variability in the efficacy of the media/filter, but can be mitigated by using a pre-filter (more on this in the section on filter layout below) to capture particulate matter. 

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

Some brands will boast having 1000 times the surface area compared to simple filter sponges. While that claim may be theoretically true, the real world performance of upmarket filter media is often not significantly better compared to using cheap, boring, common filter foam. Having a ton of surface area that does not have good access to water flow and oxygen similarly does not achieve much with regards to ammonia oxidation. Bacteria bio-film and waste organic matter clog up fine pores of upmarket media that claim to have very large porous surfaces. Bio-films and organic matter also add colonization surfaces to coarser media that may not have as much theoretical surface area. 

Many commercial brands upsell ceramic/sintered glass media that claims to have a huge surface area - however, the ultra-fine pores are clogged easily by detritus and bio-film. On the other hand, the large spacing between individual ceramic/sintered glass pieces means that it is hard to get complete clogging of the media, unlike sponge media that can get very badly clogged if not serviced.

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

Some ceramic media such as Biohome (pic above) and Seachem Matrix are advertised have anaerobic interiors that allow Nitrate reducing bacteria to thrive. These bacteria reduce Nitrates (NO3) to Nitrogen gas (N2) by extracting the oxygen for respiration, fully completing the denitrification process. The nitrogen gas off-gases into the atmosphere. This is one method of removing residual Nitrates in the water column, but it requires quite a lot of filter media to be effective as anaerobic bacteria work much more slowly compared to their aerobic cousins.  In typical hobbyist sized filters, their nitrate reducing impact is not always significant. Nitrates are much more effectively removed through water changes, which are also useful for diluting other dissolved pollutants in the tank. Nitrates are also readily consumed by plants in a planted aquarium. 

Beyond ammonia oxidation

Ammonia oxidation is not the only role that filter media microbes play. The volume of filter media needed purely for ammonia oxidation is surprisingly small. However, ammonia is not the only form of pollutant in aquarium water. Large organic waste particulate matter give rise to pathogenic microbes if they are not broken down quickly. Filter media house microbes that form bio-films that clump fine organic waste matter and other pollutants together. The filter also serves as a capture point for large organic waste particles. This is what keeps the water crystal clear in a matured aquarium that has adequate filtration. Even very fine filter media by itself would have a hard time clarifying water without the help of microbial bio-films. Having more filter media is thus 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 large variety of media on the market has been a result of commercial firms looking for more angles to upsell hobbyists, and most do not produce any significant difference in working efficacy. However, if you do choose a variety of different media, there are a few principles to adhere to. 

Optimally, if ceramic or bio-media is used, we do not want the fine pores of the surfaces of the ceramic media to get clogged with organic debris, so ceramic media should be used after a foam layer that filters out coarser particles. Foam coarser than 30ppi work less well as a filter for finer particles, so preferably 30-45ppi foam is used as a shield before the ceramic media. When this foam layer clogs, you can rinse it without disturbing the bio-media layers there after.

Layout 1: Finer foam as a first layer

The finest layer is placed at the first layer, this layer will clog quickly and require regular servicing (every 2 to 4 weeks) to prevent slow down of flow for the whole filter. The middle foam layer serves both as bio-media and a capture point for fine particles. The bio-media is kept free of large particulate matter by being at last stage.


  • 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.


  • 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 folks that are lazy and want to minimize cleaning 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 time to clog as the layers filter out particulate matter progressively, and need the least servicing. However, once it clogs, you will need to rinse out most of the layers at the same time, which may lead to some disruption of the microbial colonies.


  • 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.


  • 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?

Since all foam media eventually clogs, some hobbyists have used ceramic media exclusively in their filters. The large spacing between individual pieces means that the filter will never clog fully. This layout is thus also less efficient at capturing fine particulate matter. While there is no direct mechanical capturing of fine particulate matter by fine filter media, bacteria bio-film still clumps fine particulate matter and detritus together. The coarse nature of the media means that detritus clumps will likely settle in the tank rather than the filter. In tanks where water changes are done frequently, or there is no significant generation of fine particulate matter, this filter layout can work well. 


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


  • 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 it is meant to be serviced regularly. The pre-filter keeps the main chamber from accumulating larger waste particles. This design allows the main chamber to work undisturbed for long periods of time (up to a year), while the easily accessible pre-filer chamber is cleaned more often (every 3-6 weeks).

Due to the finer filter foam used in the pre-filter, fine particulate matter is easily filtered out. This achieves both easy high water clarity, as well as leaving bio-media undisturbed. Some filter models on the market come with build-in pre-filters. Pre-filter units can also be installed separately before the main filter.


  • 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.


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

For filters such as the Oase Biomaster series (as shown below), the fine pre-filter foam allows the main chamber to work smoothly without being serviced for more than a year. The pre-filter can easily be removed without touching the main chamber. This is the design that we at 2hr Aquarist prefer to run on our own tanks. 

Flow and oxygenation, trace elements

In order to propagate and decompose waste, microbes require good oxygen levels. In an aquarium, having a clean water surface and good water circulation is essential to maintain good oxygen levels. In aquariums, gaseous exchange happens only on the water surface - so making sure the water surface is clear of oils and that surface water is constantly exchanged with deeper water in the tank is important.

Buying a good sized filter to drive the flow, with outlet/inlets set up in a good position to give good flow across the entire tank makes a big impact. The flow setup should also take into consideration hardscape positions.

Wet/dry filters with chambers that have access to air flow are especially effective where ammonia cycling is concerned. While aquatic plants can produce a lot of oxygen during the light window, aquariums are mostly only lighted for 1/3 of the day or less. When the plants are not photosynthesizing, they become net consumers of oxygen. Good gaseous exchange and oxygen levels should be maintained consistently 24/7.

In additional to oxygen, ammonia reducing bacteria also require Magnesium, phosphates, carbonates and organic carbon in small amounts. To this end, seeding an empty aquarium with purely just bacteria culture and ammonia is not sufficient to kick start the cycling, the other elements mentioned above must be present as well. In aquariums where soil substrates are used, these elements tend to be available. However, for tanks using inert substrates, they may be lacking.

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

pH, carbonates and other water parameters

For ammonia oxidizing bacteria to work, they require other components besides pure ammonia; the bacteria also require carbonates(CO3), Magnesium(Mg) and phosphates(PO4) to be present. These elements are often available in trace amounts from tap water and are also emitted from active substrates such as aquasoil. For commercially popular strains of ammonia oxidizing bacteria such as Nitrosomonas and Nitrosococcus, they function optimally in alkaline pH ranges between 7.5 - 8.0. In acidic tanks, especially low pH aquasoil tanks below pH 6, thaumarchaeota or archaea may form the dominant ammonia oxidizers in the system and not bacteria. (see more below on this topic).

Reduced toxicity of ammonia below pH 7

In biological systems, ammonia can occur in two types - ionized form (NH4+) and as the unionized form (NH3). How much ammonia exists in one form or the other is largely dependent on the pH range of the aquarium. Ionized ammonium (NH4+) is much less toxic. Therefore, ammonia toxicity is reduced significantly in lower pH environments as most of the ammonia present will be in the ionized ammonium (NH4+) format.

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. 

low pH planted tank

Bacteria does not work below pH 6 ?

Persistent anachronistic thinking in the aquarium hobby will often spread the rumour that tanks cannot cycle below pH 6 or that bacteria oxidization of ammonia stops when the pH drops below a certain level. While commonly known ammonia oxidizing bacteria such as Nitrosomonas and Nitrosococcus function optimally in higher pH ranges, they are not the only ammonia oxidizing organisms in aquatic systems. In acidic environments, archaea, thaumarchaeota and other organisms, rather than bacteria, may form the primary ammonia oxidizers in the system. Scientific studies such as this one also show that bacteria nitrification still happens in low pH environments as they form a protective biofilm where the micro-environment is conducive for their work.

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

Cycling tanks in low pH environments entirely on the typical strains Nitrosomonas and Nitrosococcus will be slower than in higher pH tanks, however, different forms of microbial life will eventually develop to take on the ammonia oxidizer roles in such systems. If the natural pH point of your tank is below 6, there is no need to modify your tank's water chemistry. However, the tanks may take longer to fully cycle compared to tanks with with more alkaline water. On the flip side, almost all ammonia exists as ammonium (NH4+) at lower pH ranges, which makes it non-toxic.

Softwater 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 sees a pH of 5.0 when CO2 is turned on.

Kick starting cycling with starter bacteria / established media

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

New tanks are largely devoid of micro-fauna. Bacteria and other microbes do enter the system piggy bagging on plants and fish that are added. Soil substrates tend to come seeded with more microbes than inert substrates. Below are a few common ways to seed the system with micro-organisms, so that the tank cycles faster.

1. Introduce mulm/matured filter media from a matured tank to the new filter. This introduces a large amount of seed microbes quickly. This can be done by siphoning mulm found at the bottom of the substrate of a matured tank and transferring it directly onto the new tank's substrate. It can also be done by mixing aged substrate from an older tank with new substrate in a new setup. Placing aged filter sponges from an older filter into a newly setup filter also works. Squeezing the organic detritus from older established filter sponges into a new tank/or filter also works. This is the best method of seeding a new tank as it introduces a large variety of active microbes directly into the new tank system.

2. Dosing bottled or powered commercial bacteria into a new system helps 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. But care must be taken to collect it from a location that is not polluted. 

Once the initial batch of microbes have been introduced, tank cycling can begin.

Cycling a tank - old school fish in method

The old school method of cycling a tank is by adding fish gradually over time. A few hardy fishes are added right from the start. The waste products from these fish will feed the bacteria cycle. Over weeks, more fish are added gradually as the bacteria in the filter develop over time. Large weekly water changes are still done to prevent build-up of waste products. This method has worked very well in the past as long as regular water changes are done to prevent large build up of ammonia. However, it has also been criticized for being cruel - and that while fish may not display outward signs of stress, that is still have implications on their organ health and lifespan if ammonia levels are not monitored carefully.

By testing ammonia and nitrite levels in the aquarium, one can gauge whether biological waste is being reduced at a sufficient rate, and whether ammonia is building up to toxic levels. This method is less suitable for higher pH (8+) tanks where ammonia toxicity occurs readily due to ammonia existing predominantly in the toxic NH3 format. In higher pH ranges, ammonia toxicity occurs quite quickly. Ammonium is much less toxic in lower pH ranges. It is common to see low pH (pH 6+) tanks measuring a couple of ppm of total ammonia that still hold healthy looking fish, much to the puzzlement of observers.

How much ammonia is acceptable in such a method?

Ammonia burns gills and causes internal organ damage and death at high doses. In low doses, it can still cause stress and shortened lifespan in fish. For practical purposes, if you see fishes having poor coloration, not feeding well or hiding when they are supposed to be swimming out in the open, it can be a sign that the water quality has deteriorated and that a water change should be done.

Smaller fishes produce very little waste, especially in a large tank that is lightly stocked. As the tank grows in with plants, they also add an additional buffer by taking in 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 adding liquid ammonia regularly into a new tank; fully setup except for livestock or plants, to grow the bacteria colonies. Follow these 3 steps:

  1. A dose of 2ppm of ammonia is added, then the water is tested after a couple of days (takes about 3 days or so from a cold start to even see levels change). When ammonia levels start to decline, one would start seeing 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 every day to feed the bacteria (add enough to raise levels back to around 2ppm). After many more days, nitrite levels would fall, and one can then measure nitrate levels rising as the bacteria converting nitrite to nitrate has populated. This takes longer than step 1 as the bacteria responsible for nitrite conversion to nitrate populates more slowly.
  3. Eventually, even with additions of ammonia, nitrites and ammonia would measure at 0 after a 6hr period, while nitrates accumulate. The ammonia cycling process for the tank is now complete. The entire process can take 2-8 weeks depending on tank parameters.

Typically, we would change 80% of tank water to reduce nitrates before adding livestock. Adding starter bacteria cultures at step 1 greatly speeds up the process.

In a tank where ammonia is added at a steady rate, ammonia oxidizing microbes will establish first, transforming the ammonia to nitrites. As nitrites build up, microbes that oxidize nitrites to nitrates propagate, and over time, nitrites are converted to nitrates. For most tanks, nitrates is the end product of microbial action, and excess nitrate is removed through large water changes. All three processes happen continuously in a matured tank. In a planted aquariums where other parameters are fulfilled, plants will uptake ammonia and nitrates through the water column.

Cycling with aquasoil:

In a tank with aquasoil, ammonia is usually emitted by new soils so there is no need to dose additional ammonia.

After filling the tank, we recommend to do a 100% water change before running the filter. This removes 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 intake. Then we recommend letting the tank run for a couple of weeks without plants or fish or lights on. The only thing that is running is the filter. This is often called a 'dark start' method of starting a planted tank.

The aquasoil should emit ammonia for quite awhile upon initial submergence. This will provide food for the bacteria to feed on. Bacteria propagates at an exponential rate. However, it can still take many days for the colonies to reach good size and there is an appreciable impact on ammonia readings. If you do not use starter bacteria products, it is a good idea to add mulm or used filter media to kickstart the cycle. Without the use of starter bacteria products, full cycling of the tank can take up to a month or more. With the use of starter bacteria products, cycling time can be shortened to a week plus. 

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

Tests can be done every few days to monitor the ammonia level. When both ammonia and nitrite readings read zero, it means that the tank is cycled. For tanks that have been seeded with starter bacteria, cycling can kick in as quickly as within a week. For most tanks, it takes 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 reduce ammonia toxicity as most of the ammonia exists as less toxic ammonium(NH4+) format in low pH (below 7). This allows hardy plants to be planted and grown even in early stages where ammonia levels are detectable. However, more sensitive plants, such as Utricularia gramminifolia, and tissue culture plants in general, should only be planted after the tank is cycled - they melt easily in fresh soil. Other plants that are vulnerable to algae and adapt better to matured tanks include Bucephalandra species, Hygrophila Chai, Eriocaulon species.

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

Is ammonia really great as plant food? Head here 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 tank cycling's first goal is to get ammonia cycling done.

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

Microbes and decomposers also participate in consuming organic waste. A biologically matured system is one where there is enough microbial life to break down harmful organic pollutants quickly into benign substances. This creates a more favorable environment for both livestock and plants. The faster waste gets broken down, the less triggers there are for algae to spawn. This is why biological maturity is important even in tanks with no livestock. It takes time for a tank to be biologically mature (a few weeks), even though ammonia cycling itself may be done. Hobbyists do not have established testing methods for gauging organic waste levels at earlier stages of decomposition - other than visually being able to observe fish feces and build up of organic detritus at the substrate level. Only when waste has been broken down into ammonia format does it show up on hobbyist's ammonia test kits. So having a zero ammonia reading does not automatically mean that the water is free from other forms of organic pollutants. 

The tank needs to be viewed as a ecosystem as a whole. For planted tanks, having a large portion of the tank planted with healthy, growing plants stabilizes the system faster. 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. Having the plants settle in and grow is an important part of stabilizing a planted tank's ecosystem.

Some plant species such as Utricularia gramminifolia and Bucephalandra acclamatize much smoother in tanks that are biologically matured. These species should never be planted in a fresh setup. Both species face more algae and melting issues in a new setup, even though they do not have very demanding growth requirements.

Some signs that the tank is biologically matured;

  • Ammonia tests come in at 0 consistently.
  • Water clarifies quickly even after substrate has been disturbed.
  • Water is clear (micro-particles are clumped up by bio-film).
  • Dead livestock disappears quickly (presence of larger sized detritus feeders like shrimp).
  • Aquarium is not foul smelling (larger organic molecules are broken down quickly).
  • Sensitive livestock such as shrimps have high survival rate and reproduces regularly.

Some signs that a tank is not biologically matured;

  • Cloudy water in new tanks.
  • Positive ammonia readings.
  • Frequent triggers of algae; green dust algae and diatoms are especially common.
  • Melting plants even though parameters seem alright.
  • Unable to keep sensitive livestock alive (Shrimps, sensitive fish).

Presence of brown, stringy diatoms in a new setup is a strong sign that the tank is not biologically matured yet. In most healthy tanks, diatoms disappear by themselves over time without any extra intervention.

Tank is a micro-ecosystem; avoid disturbing the balance

Tanks can easily have their bio-filter community disturbed. These micro-organisms are sensitive; as a good gauge, we would say any action that can harm sensitive fish or shrimp can hurt the microbial community. If you are perpetually unable to keep shrimps alive in your tank - chances are you have a system that is not biologically stable.

  • Frequent usage of harsh chemicals such as algicides.
  • Too frequent washing of the filter.
  • Ammonia spikes due to abuse of terrestrial fertilisers or bad tap water.
  • Heavy metals or poor quality tap water during water changes.
  • Large fluctuations in tank parameters such as alkalinity.
  • Failure to use dechlorinator in tap water that contain chloramines. (newbie mistake)

The bio-filter tends to grow to accommodate the amount of waste that the system produces, but it does not easily compensate for spikes in the system. For example, if you feed your fish an amount of food that produces 1ppm of ammonia a day, your tank's microbial community will grow to digest that amount on a regular basis. The day that you triple feed and get a spike of 3ppm of 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 apply to water changes. For tanks that are run on a weekly water change schedule, often skipping it letting the tank run say 3 weeks without water changes will often cause algae to trigger.

Head here to learn how to control algae in a new tank setup