Since we have two separate stickies on using plants to help with removing nitrates and a lot of pages for people to dig through to find the information they are looking for, I thought I would take the time to speak in detail about the symbiotic relationship fish, plants, bacteria, and waste have and how to use it. This will also discuss cycling in detail and the pros and cons different methods. Much of what is contained below is directly related to the cycle we have in any aquarium setup and thus quite useful to know.
In a traditional aquarium environment we use pumps and some sort of mechanical filtration. The pumps provide water exchange and encourage waste to get trapped within the mechanical filtration. Lots of things are happening here that for the basic hobbyist might seem a bit at first. This is understandable considering scientists dedicate their careers to one aspect of the many that occur in fish keeping. The following information will hopefully demystify much of what happens. It focuses on bacteria in an aquaponics system. Aquaponics in its most basic definition is Plants and Fish. A little more detailed description includes why it works thus the bacteria article below.
This may be found here: http://www.fao.org/3/a-i4021e/i4021e05.pdf It is available publicly. The entire paper can be found here: http://www.fao.org/3/a-i4021e.pdf
5. Bacteria in aquaponics
Bacteria are a crucial and pivotal aspect of aquaponics, serving as the bridge that
connects the fish waste to the plant fertilizer. This biological engine removes toxic
wastes by transforming them into accessible plant nutrients. Chapter 2 discussed
the nitrogen cycle, especially the critical role of nitrifying bacteria, and outlined the
essential parameters for maintaining a healthy colony. Chapter 4 discussed the aspects
of biofilter materials that host these same bacteria. This brief chapter serves as a review
of the bacteria, including details of the important bacterial groups. Heterotrophic
bacterial activity is more fully discussed in terms of its role in the mineralization of
solid fish waste. Unwanted bacteria are discussed, including: denitrifying bacteria,
sulphate-reducing bacteria and pathogens. Finally, the timeline of bacterial cycling is
discussed in regard to the establishment of a new aquaponic system.
5.1 Nitrifying bacteria and the biofilter
Chapter 2 discussed the vital role of nitrifying bacteria in regard to the overall aquaponic
process. The nitrifying bacteria convert the fish waste, which enters the system mainly
as ammonia, into nitrate, which is fertilizer for the plants (Figure 5.1). This is a twostep
process, and two separate groups of nitrifying bacteria are involved. The first step
is converting ammonia to nitrite, which is done by the ammonia-oxidizing bacteria
(AOB). These bacteria are often referred to by the genus name of the most common
group, the Nitrosomonas. The second step is converting nitrite to nitrate is done by
the nitrite-oxidizing bacteria (NOB). These are commonly referred to by the genus
name of the most common group, the Nitrobacter. There are many species within
these groups, but for the purposes of this publication, the individual differences are
not important, and it is more useful to consider the group as a whole. The nitrification
process occurs as follows:
1) AOB bacteria convert ammonia (NH₃) into nitrite (NO₂-)
2) NOB bacteria then convert nitrite (NO₂-) into nitrate (NO₃-)
Nitrification and, therefore, a healthy bacterial colony is essential to a functioning
aquaponic system. Nitrifying bacteria are relatively slow to reproduce and establish
colonies, requiring days and sometimes weeks, and therefore the patience of the
farmer is one of the most important management parameters when establishing a new
aquaponic system. Many aquariums and aquaponic systems have failed because too
many fish were added before the colony of bacteria was fully developed. There are
several other key parameters to support nitrifying bacteria. Generally, bacteria require
FIGURE 5.1
a large, dark location to colonize with good water quality, adequate food and oxygen.
Often, nitrifying bacteria form a slimy, light brown or beige matrix on the biofilter, and
have a distinctive odour that is difficult to describe, but does not smell particularly foul
which could indicate other micro-organisms.
5.1.1 High surface area
Biofiltration material with a high specific surface area (SSA) is optimal to develop
extensive colonies of nitrifying bacteria. SSA is a ratio defining the surface area
exposed from a given volume of media, and is expressed in square metres per cubic
metres (m2/m3). In general, the smaller and more porous the particles of the media, the
greater is the surface available for bacteria to colonize. This results in more efficient
biofiltration. There are many such materials used in aquaponics, either as growing
media or for biofiltration, e.g. volcanic gravel, expanded clay, commercial plastic
biofilter balls, and plant roots. The volcanic tuff and Bioballs® considered in this
manual have, respectively, 300 m²/m³ and 600 m²/m³, which is an adequate SSA to
enable bacteria to thrive. Further characteristics and SSA of the different media used
in aquaponics are summarized in Table 4.1 and Appendix 4. If the biofilter material
is not ideal and has a lower surface area to volume ratio, then the biofilter should be
larger. An oversized biofilter cannot harm an aquaponic system, and although overly
large biofilters would add unnecessary expense, excess biofiltration capacity has saved
many systems from collapse.
5.1.2 Water pH
Nitrifying bacteria function adequately through a pH range of 6–8.5. Generally, these
bacteria work better at higher pH, with the Nitrosomonas group preferring a pH of
7.2–7.8, and the Nitrobacter group preferring a pH of 7.2–8.2. However, the target pH
for aquaponics is 6–7, which is a compromise between all of the organisms within this
ecosystem. Nitrifying bacteria function adequately within this range, and any decrease
in bacterial activity can be offset with a larger biofilter.
5.1.3 Water temperature
The optimal temperature range for nitrifying bacteria is 17–34 °C. This range
encourages growth and productivity. If the water temperature drops below this range,
the productivity of the bacteria will tend to decrease. In particular, the Nitrobacter
group is less tolerant of lower temperature than is the Nitrosomonas group, and as such,
during colder periods nitrite should be more carefully monitored to avoid harmful
accumulations.
5.1.4 Dissolved oxygen
Nitrifying bacteria need adequate levels of DO in the water at all times to grow healthily
and maintain high levels of productivity. Nitrification is a reduction/oxidation (redox)
reaction, where the bacteria derive the energy to live when oxygen is combined with
the nitrogen. Optimum levels of DO are 4–8 mg/litre, which is also the level required
for the fish and the plants. Nitrification does not occur if the DO concentration drops
below 2 mg/litre. Ensure adequate biofiltration by dedicating aeration to the biofilter,
either through flood-and-drain cycles in media beds, air stones in external biofilters, or
cascading water return lines to the canals and sump tanks.
5.1.5 UV light
Nitrifying bacteria are photosensitive until they fully establish a colony, and sunlight
can cause considerable harm to the biofilter. Media beds already protect the bacteria
from sunlight; but if using an external biofilter, be sure to keep it shaded from direct
sunlight.
5.1.6 Monitoring bacterial activity
If all of these five parameters are respected, it is safe to assume that the bacteria are present
and functioning properly. That said, bacteria are so important to aquaponics that it is
worth knowing the overall health of the bacteria at any given time. However, bacteria
are microscopic organisms, and it is impossible to see them without a microscope.
There is a simple method to monitor the bacterial function; testing for ammonia, nitrite
and nitrate provides information on the health of the bacterial colony. Ammonia and
nitrite should always be 0–1 mg/litre in a functioning and balanced aquaponic unit. If
either is detectable, it indicates a problem with the nitrifying bacteria. There are two
possible, common reasons for this to occur. First, the biofilter is too small for the
amount of fish and fish feed. Therefore, there is an imbalance and there are too many
fish. To rectify, either increase the biofilter size or reduce the number of fish, or the
fish feeding regime. Sometimes, this problem can occur when the system started out
balanced when the fish were smaller, but gradually became unbalanced as the fish grew
and were fed more with the same size biofilter. Second, if the system is balanced in
size, then the bacteria themselves may not be functioning properly. This could indicate
a problem with the water quality, and each parameter listed above should be checked.
Often, this can occur during winter seasons as the water temperature begins to fall and
bacterial activity slows.
5.2 Heterotrophic bacteria and mineralization
There is another important bacteria group, as well as other micro-organisms, involved
in aquaponics. This bacteria group is generally called the heterotrophic group. These
bacteria utilize organic carbon as its food source, and are mainly involved in the
decomposition of solid fish and plant waste. Most fish only retain 30–40 percent of
the food they eat, meaning that 60–70 percent of what they eat is released as waste.
Of this waste, 50–70 percent is dissolved waste released as ammonia. However, the
remaining waste is an organic mix containing proteins, carbohydrates, fats, vitamins
and minerals. The heterotrophic bacteria metabolize these solid wastes in a process
called mineralization, which makes essential micronutrients available for plants in
aquaponics
FIGURE 5.2
These heterotrophic bacteria, as well as some naturally occurring fungi, help
decompose the solid portion of the fish waste. In doing so, they release the nutrients
locked in the solid waste into the water. This mineralization process is essential because
plants cannot take up nutrients in solid form. The wastes must be broken into simple
molecules in order to be absorbed by plants’ roots. Heterotrophic bacteria feed on any
form of organic material, such as solid fish waste, uneaten fish food, dying plants, dying
plant leaves and even dead bacteria. There are many sources of food available for these
bacteria in aquaponic units.
Heterotrophic bacteria require similar growing conditions to the nitrifying bacteria especially
in high levels of DO. The heterotrophic bacteria colonize all components of the unit, but are
especially concentrated where the solid waste accumulates. Heterotrophic bacteria grow much
faster than the nitrifying bacteria, reproducing in hours rather than days. In media beds, the
wastes collect on the bottom, permanently wet zone and many heterotrophic bacteria are found
here. In other systems, the main colonies are found on the filters and separators, and in the
canals. Mineralization is important in aquaponics because it releases several micronutrients that
are necessary to plant growth. Without mineralization, some plants may experience
nutrient deficiencies and would need supplemental fertilizer.
Heterotrophic bacteria are aided in the decomposition of solid waste by a
community of other organisms. Often, earthworms, isopods, amphipods, larvae and
other small animals can be found in aquaponic systems, especially within media beds.
These organisms work together with the bacteria to decompose the solid waste, and
having this community can prevent accumulation of solids.
5.3 Unwanted bacteria
5.3.1 Sulphate reducing bacteria
Nitrifying and mineralizing bacteria are useful to aquaponic systems, but some other
types of bacteria are harmful. One of these harmful groups of bacteria is the sulphatereducing
group. These bacteria are found in anaerobic conditions (no oxygen), where
they obtain energy through a redox reaction using sulphur. The problem is that this
process produces hydrogen sulphide (H2S), which is extremely toxic to fish. These
bacteria are common, found in lakes, saltmarshes and estuaries around the world, and
are part of the natural sulphur cycle. These bacteria are responsible for the odour of
rotten eggs, and also the grey-black colour of sediments. The problem in aquaponics
is when solid wastes accumulate at a faster pace than the heterotrophic bacteria and
associated community can effectively process and mineralize them, which can in turn
lead to anoxic festering conditions that support these sulphate-reducing bacteria. In
high fish density systems, the fish produce so much solid waste that the mechanical
filters cannot be cleaned fast enough, which encourages these bacteria to multiply and
produce their noxious metabolites. Large aquaponic systems often contain a degassing
tank where the hydrogen sulphide can be released safely back to the atmosphere.
Degassing is unnecessary in small-scale systems. However, even in small-scale systems,
if a foul odor is detected, reminiscent of rotten eggs or raw sewage, it is necessary to
take appropriate management action. These bacteria only grow in anoxic conditions, so
to prevent them, be sure to supply adequate aeration and increase mechanical filtration
to prevent sludge accumulation.
5.3.2 Denitrifying bacteria
A second group of unwanted bacteria are those responsible for denitrification. These
bacteria also live in anaerobic conditions. They convert nitrate, which is the coveted
fertilizer for plants, back into atmospheric nitrogen that is unavailable for plants.
These bacteria are also common throughout the world, and are important in their own
right (see Figure 2.4). However, within aquaponic systems, these bacteria can decrease
efficiency by effectively removing the nitrogen fertilizer. This is often a problem with
large DWC beds that are inadequately oxygenated. A problem could be suspected
when plants show signs of nitrogen deficiencies despite the system being in balance,
and when there is a very low nitrate concentration in the water. Investigate possible
areas within the DWC canals that are not circulating properly, and further increase
aeration with air stones.
Some large aquaponic systems deliberately use denitrification. The feed rate ratio
balances the nutrients for the plants but usually results in high nitrate levels. This nitrate
can be diluted during water exchanges (suggested in this publication for small-scale
systems). Alternatively, controlled denitrification can be encouraged in the mechanical
filter. This technique requires careful attention and off-gassing, and is not recommended
for small-systems. More information can be found in the section on Further Reading.
5.3.3 Pathogenic bacteria
A final group of unwanted bacteria are those that cause diseases in plants, fish and
humans. These diseases are treated separately in other parts of this publication, with
Chapters 6 and 7 discussing plant and fish disease, respectively, and Section 8.6 discussing
human safety. Overall, it is important that there are good agricultural practices (GAPs)
that mitigate and minimize the risk of bacterial diseases within aquaponic systems.
Prevent pathogens from entering the system by: ensuring good worker hygiene;
preventing rodents from defecating in the system; keeping wild mammals (and dogs
and cats) away from aquaponic systems; avoiding using water that is contaminated; and
being aware that any live feed can be a vector for introducing alien micro-organisms
into the system. It is especially important not to use rainwater collection from roofs
with bird faeces unless the water is treated first. The major risk from warm-blooded
animals is the introduction of Escherichia coli, and birds often carry Salmonella spp.;
dangerous bacteria can enter the system with animal faeces. Second, after prevention,
never let the aquaponic water come into contact with the leaves of the plants. This
prevents many plant diseases as well as potential contamination of fish water to human
produce, especially if the produce is to be eaten raw. Always wash vegetables before
consumption, aquaponic or otherwise. Generally, common sense and cleanliness are
the best guards against diseases from aquaponics. Additional sources for aquaponic
food safety are provided throughout this publication and in the section on Further
Reading.
5.4 System cycling and starting a biofilter colony
System cycling is a term that describes the initial process of building a bacterial colony
when first starting any RAS, including an aquaponic unit. Under normal circumstances,
this takes 3–5 weeks; cycling is a slow process that requires patience. Overall, the
process involves constantly introducing an ammonia source into the aquaponic unit,
feeding the new bacterial colony, and creating a biofilter. The progress is measured
by monitoring the nitrogen levels. Generally, cycling takes place once an aquaponic
system is built, but it is possible to give the biofilter a head start when creating a new
aquaponic system. It is important to understand that during the cycling process there
will be high levels of ammonia and nitrite, which could be harmful to fish. Also, make
sure all aquaponic components, in particular the biofilter and fish tank, are protected
from direct sunlight before starting the process.
Once introduced into the unit, the ammonia becomes an initial food source for
the AOB, a few of which are naturally occurring and recruit to the system on their
own. They can be found on land, in water and in the air. Within 5–7 days after the
first addition of ammonia, the AOB start forming a colony and begin to oxidize the
ammonia into nitrite. Ammonia should be continuously, but cautiously, added to
ensure adequate food for the developing colony without becoming toxic. After another
5–7 days the nitrite levels in the water will have started to rise, which in turn attracts the
NOB. As the NOB populations increase, the nitrite levels in the water will start to decline as
nitrite is oxidized into nitrate. The full process is illustrated in Figure 5.3, which shows the trends
of ammonia, nitrite and nitrate in the water over the first 20–25 days of cycling.
The end of the cycling process is defined as when the nitrate level is steadily increasing,
the nitrite level is 0 mg/litre and the ammonia level is less than 1 mg/litre. In good conditions,
this takes about 25–40 days, but if the water temperature is cool, complete cycling may take
up to two months to finish. At this point, a sufficient bacterial colony has formed and is
actively converting the ammonia to nitrate.
FIGURE 5.3
The reason this process is long is because nitrifying bacteria grow relatively slowly,
requiring 10–15 hours to double in population. However, some heterotrophic bacteria
can double in as little as 20 minutes.
Aquarium or aquaculture retailers sell various products containing living nitrifying
bacteria (in a bottle). Once added to the unit, they immediately colonize a system
thus avoiding the cycling process explained above. However, these products may be
expensive or unavailable and ultimately unnecessary, as the cycling process can be
achieved using organic means. Alternatively, if another aquaponic system is available,
it is extremely helpful to share part of the biofilter as a seed of bacteria for the new
system. This greatly decreases the time necessary for cycling the system. It can also
be useful to separately start a biofilter medium by continuously trickling a solution
containing 2–3 mg/litre of ammonia for a few weeks in advance. The media would
then function as a primer by simply incorporating it into the new aquaponic biofilter.
A simple trickling system can be built by suspending a wide plastic crate of medium
above a small tank containing the ammonia solution that is being circulated by a small
aquarium pump.
Many people use fish as the original source of ammonia in a new tank. However,
these fish suffer the effects of high ammonia and high nitrite throughout the cycling
process. Many new aquarists do not have the patience to allow a tank to fully cycle and
the result is that the new fish die, commonly referred to as “new tank syndrome”. If
using fish, it is recommended to use a very low stocking density (≤ 1 kg/m3). Instead of
using fish, there are other sources of this initial ammonia to start feeding the biofilter
colony. Some possible sources include fish feed, sterilized animal waste, ammonium
nitrate fertilizer and pure ammonia. Each of these sources has positives and negatives,
and some sources are far better and safer to use
than others.
The best ammonia source is finely ground fish food because it is a biologically safe product,
and it is relatively easy to control the amount of ammonia being added. Be sure
to use fresh, unspoiled and disease-free fish feed only. Chicken waste, despite being an
excellent ammonia source, can be very risky and can introduce dangerous bacteria into the
aquaponic system. Escherichia coli and Salmonella spp. are commonly found in
chicken and other animal manure and, therefore, any manure must be sterilized before use.
Household ammonia products can be used, but be sure that the product is 100 percent ammonia
and does not include other ingredients such as detergents, colourants or heavy metals that
could ruin the entire system. Once the ammonia source has been selected, it is important to
add the ammonia slowly and consistently, and to monitor the nitrogen levels every 2–3 days. It is useful to record levels on a graph to track the process of the cycling. It is important not to add too much ammonia, and it is better to have a little bit too little than too much. The target level is 1–2 mg/litre. If
ammonia levels ever exceed 3 mg/litre, it is necessary to do a water exchange to dilute the
ammonia in order to prevent it from inhibiting the bacteria.
5.4.1 Adding fish and plants during the cycling process
Plants and fish should be added only after the cycle is complete. Plants can be added a little
bit earlier, but expect nutrient deficiencies in these early plants during this period because
other nutrients take time to reach optimal concentrations.Only once the ammonia and nitrite levels are
below 1 mg/litre it is safe to start stocking the fish. Always start stocking the fish slowly. Once
fish have been stocked, it is not uncommon to see a secondary and smaller ammonia and nitrite
spike. This happens if the ammonia created from the newly stocked fish is much greater than
the daily ammonia amounts added during the cycling process. Continue to monitor the levels
of all three types of nitrogen, and be prepared to do water exchanges if ammonia or nitrite levels
rise above 1 mg/litre while the system continues to cycle.
5.5 Chapter summary
• In aquaponics, ammonia must be oxidized into nitrate to prevent toxicity to fish.
• The nitrification process is a two-step bacterial process where ammonia-oxidizing bacteria convert ammonia (NH3) into nitrite (NO2-), and then nitrite-oxidizing bacteria convert nitrite into nitrate (NO3-).
• The five most important factors for good nitrification are: high surface area media for bacteria to grow and colonize; pH (6–7); water temperature (17–34 °C); DO (4–8 mg/litre); cover from direct exposure to sunlight
• System cycling is the initial process of building a nitrifying bacteria colony in a new aquaponic unit. This 3–5 week process involves adding an ammonia source into the system (fish feed, ammonia-based fertilizer, up to a concentration in water of 1-2 mg/litre) in order to stimulate nitrifying bacteria growth. This should be done slowly and consistently. Ammonia, nitrite and nitrate are monitored to determine the status of the biofilter: the peak and subsequent drop of ammonia is followed by a similar pattern of nitrite before nitrate starts to accumulate. Fish and plants are only added when ammonia and nitrite levels are low and the nitrate level begins to rise.
• Ammonia and nitrite tests are used to monitor the function of the nitrifying bacteria and the performance of the biofilter. In a functioning system, ammonia and nitrite should be close to 0 mg/litre. High levels of either ammonia or nitrite require a water change and management action. Usually, poor nitrification is due
to a change in water temperature, DO or pH levels.
• Another class of micro-organisms naturally occurring in aquaponics is that of heterotrophic bacteria. They decompose the solid fish waste, releasing some of the nutrients into the water in a process called mineralization.
In a traditional aquarium environment we use pumps and some sort of mechanical filtration. The pumps provide water exchange and encourage waste to get trapped within the mechanical filtration. Lots of things are happening here that for the basic hobbyist might seem a bit at first. This is understandable considering scientists dedicate their careers to one aspect of the many that occur in fish keeping. The following information will hopefully demystify much of what happens. It focuses on bacteria in an aquaponics system. Aquaponics in its most basic definition is Plants and Fish. A little more detailed description includes why it works thus the bacteria article below.
This may be found here: http://www.fao.org/3/a-i4021e/i4021e05.pdf It is available publicly. The entire paper can be found here: http://www.fao.org/3/a-i4021e.pdf
5. Bacteria in aquaponics
Bacteria are a crucial and pivotal aspect of aquaponics, serving as the bridge that
connects the fish waste to the plant fertilizer. This biological engine removes toxic
wastes by transforming them into accessible plant nutrients. Chapter 2 discussed
the nitrogen cycle, especially the critical role of nitrifying bacteria, and outlined the
essential parameters for maintaining a healthy colony. Chapter 4 discussed the aspects
of biofilter materials that host these same bacteria. This brief chapter serves as a review
of the bacteria, including details of the important bacterial groups. Heterotrophic
bacterial activity is more fully discussed in terms of its role in the mineralization of
solid fish waste. Unwanted bacteria are discussed, including: denitrifying bacteria,
sulphate-reducing bacteria and pathogens. Finally, the timeline of bacterial cycling is
discussed in regard to the establishment of a new aquaponic system.
5.1 Nitrifying bacteria and the biofilter
Chapter 2 discussed the vital role of nitrifying bacteria in regard to the overall aquaponic
process. The nitrifying bacteria convert the fish waste, which enters the system mainly
as ammonia, into nitrate, which is fertilizer for the plants (Figure 5.1). This is a twostep
process, and two separate groups of nitrifying bacteria are involved. The first step
is converting ammonia to nitrite, which is done by the ammonia-oxidizing bacteria
(AOB). These bacteria are often referred to by the genus name of the most common
group, the Nitrosomonas. The second step is converting nitrite to nitrate is done by
the nitrite-oxidizing bacteria (NOB). These are commonly referred to by the genus
name of the most common group, the Nitrobacter. There are many species within
these groups, but for the purposes of this publication, the individual differences are
not important, and it is more useful to consider the group as a whole. The nitrification
process occurs as follows:
1) AOB bacteria convert ammonia (NH₃) into nitrite (NO₂-)
2) NOB bacteria then convert nitrite (NO₂-) into nitrate (NO₃-)
Nitrification and, therefore, a healthy bacterial colony is essential to a functioning
aquaponic system. Nitrifying bacteria are relatively slow to reproduce and establish
colonies, requiring days and sometimes weeks, and therefore the patience of the
farmer is one of the most important management parameters when establishing a new
aquaponic system. Many aquariums and aquaponic systems have failed because too
many fish were added before the colony of bacteria was fully developed. There are
several other key parameters to support nitrifying bacteria. Generally, bacteria require
FIGURE 5.1
a large, dark location to colonize with good water quality, adequate food and oxygen.
Often, nitrifying bacteria form a slimy, light brown or beige matrix on the biofilter, and
have a distinctive odour that is difficult to describe, but does not smell particularly foul
which could indicate other micro-organisms.
5.1.1 High surface area
Biofiltration material with a high specific surface area (SSA) is optimal to develop
extensive colonies of nitrifying bacteria. SSA is a ratio defining the surface area
exposed from a given volume of media, and is expressed in square metres per cubic
metres (m2/m3). In general, the smaller and more porous the particles of the media, the
greater is the surface available for bacteria to colonize. This results in more efficient
biofiltration. There are many such materials used in aquaponics, either as growing
media or for biofiltration, e.g. volcanic gravel, expanded clay, commercial plastic
biofilter balls, and plant roots. The volcanic tuff and Bioballs® considered in this
manual have, respectively, 300 m²/m³ and 600 m²/m³, which is an adequate SSA to
enable bacteria to thrive. Further characteristics and SSA of the different media used
in aquaponics are summarized in Table 4.1 and Appendix 4. If the biofilter material
is not ideal and has a lower surface area to volume ratio, then the biofilter should be
larger. An oversized biofilter cannot harm an aquaponic system, and although overly
large biofilters would add unnecessary expense, excess biofiltration capacity has saved
many systems from collapse.
5.1.2 Water pH
Nitrifying bacteria function adequately through a pH range of 6–8.5. Generally, these
bacteria work better at higher pH, with the Nitrosomonas group preferring a pH of
7.2–7.8, and the Nitrobacter group preferring a pH of 7.2–8.2. However, the target pH
for aquaponics is 6–7, which is a compromise between all of the organisms within this
ecosystem. Nitrifying bacteria function adequately within this range, and any decrease
in bacterial activity can be offset with a larger biofilter.
5.1.3 Water temperature
The optimal temperature range for nitrifying bacteria is 17–34 °C. This range
encourages growth and productivity. If the water temperature drops below this range,
the productivity of the bacteria will tend to decrease. In particular, the Nitrobacter
group is less tolerant of lower temperature than is the Nitrosomonas group, and as such,
during colder periods nitrite should be more carefully monitored to avoid harmful
accumulations.
5.1.4 Dissolved oxygen
Nitrifying bacteria need adequate levels of DO in the water at all times to grow healthily
and maintain high levels of productivity. Nitrification is a reduction/oxidation (redox)
reaction, where the bacteria derive the energy to live when oxygen is combined with
the nitrogen. Optimum levels of DO are 4–8 mg/litre, which is also the level required
for the fish and the plants. Nitrification does not occur if the DO concentration drops
below 2 mg/litre. Ensure adequate biofiltration by dedicating aeration to the biofilter,
either through flood-and-drain cycles in media beds, air stones in external biofilters, or
cascading water return lines to the canals and sump tanks.
5.1.5 UV light
Nitrifying bacteria are photosensitive until they fully establish a colony, and sunlight
can cause considerable harm to the biofilter. Media beds already protect the bacteria
from sunlight; but if using an external biofilter, be sure to keep it shaded from direct
sunlight.
5.1.6 Monitoring bacterial activity
If all of these five parameters are respected, it is safe to assume that the bacteria are present
and functioning properly. That said, bacteria are so important to aquaponics that it is
worth knowing the overall health of the bacteria at any given time. However, bacteria
are microscopic organisms, and it is impossible to see them without a microscope.
There is a simple method to monitor the bacterial function; testing for ammonia, nitrite
and nitrate provides information on the health of the bacterial colony. Ammonia and
nitrite should always be 0–1 mg/litre in a functioning and balanced aquaponic unit. If
either is detectable, it indicates a problem with the nitrifying bacteria. There are two
possible, common reasons for this to occur. First, the biofilter is too small for the
amount of fish and fish feed. Therefore, there is an imbalance and there are too many
fish. To rectify, either increase the biofilter size or reduce the number of fish, or the
fish feeding regime. Sometimes, this problem can occur when the system started out
balanced when the fish were smaller, but gradually became unbalanced as the fish grew
and were fed more with the same size biofilter. Second, if the system is balanced in
size, then the bacteria themselves may not be functioning properly. This could indicate
a problem with the water quality, and each parameter listed above should be checked.
Often, this can occur during winter seasons as the water temperature begins to fall and
bacterial activity slows.
5.2 Heterotrophic bacteria and mineralization
There is another important bacteria group, as well as other micro-organisms, involved
in aquaponics. This bacteria group is generally called the heterotrophic group. These
bacteria utilize organic carbon as its food source, and are mainly involved in the
decomposition of solid fish and plant waste. Most fish only retain 30–40 percent of
the food they eat, meaning that 60–70 percent of what they eat is released as waste.
Of this waste, 50–70 percent is dissolved waste released as ammonia. However, the
remaining waste is an organic mix containing proteins, carbohydrates, fats, vitamins
and minerals. The heterotrophic bacteria metabolize these solid wastes in a process
called mineralization, which makes essential micronutrients available for plants in
aquaponics
FIGURE 5.2
These heterotrophic bacteria, as well as some naturally occurring fungi, help
decompose the solid portion of the fish waste. In doing so, they release the nutrients
locked in the solid waste into the water. This mineralization process is essential because
plants cannot take up nutrients in solid form. The wastes must be broken into simple
molecules in order to be absorbed by plants’ roots. Heterotrophic bacteria feed on any
form of organic material, such as solid fish waste, uneaten fish food, dying plants, dying
plant leaves and even dead bacteria. There are many sources of food available for these
bacteria in aquaponic units.
Heterotrophic bacteria require similar growing conditions to the nitrifying bacteria especially
in high levels of DO. The heterotrophic bacteria colonize all components of the unit, but are
especially concentrated where the solid waste accumulates. Heterotrophic bacteria grow much
faster than the nitrifying bacteria, reproducing in hours rather than days. In media beds, the
wastes collect on the bottom, permanently wet zone and many heterotrophic bacteria are found
here. In other systems, the main colonies are found on the filters and separators, and in the
canals. Mineralization is important in aquaponics because it releases several micronutrients that
are necessary to plant growth. Without mineralization, some plants may experience
nutrient deficiencies and would need supplemental fertilizer.
Heterotrophic bacteria are aided in the decomposition of solid waste by a
community of other organisms. Often, earthworms, isopods, amphipods, larvae and
other small animals can be found in aquaponic systems, especially within media beds.
These organisms work together with the bacteria to decompose the solid waste, and
having this community can prevent accumulation of solids.
5.3 Unwanted bacteria
5.3.1 Sulphate reducing bacteria
Nitrifying and mineralizing bacteria are useful to aquaponic systems, but some other
types of bacteria are harmful. One of these harmful groups of bacteria is the sulphatereducing
group. These bacteria are found in anaerobic conditions (no oxygen), where
they obtain energy through a redox reaction using sulphur. The problem is that this
process produces hydrogen sulphide (H2S), which is extremely toxic to fish. These
bacteria are common, found in lakes, saltmarshes and estuaries around the world, and
are part of the natural sulphur cycle. These bacteria are responsible for the odour of
rotten eggs, and also the grey-black colour of sediments. The problem in aquaponics
is when solid wastes accumulate at a faster pace than the heterotrophic bacteria and
associated community can effectively process and mineralize them, which can in turn
lead to anoxic festering conditions that support these sulphate-reducing bacteria. In
high fish density systems, the fish produce so much solid waste that the mechanical
filters cannot be cleaned fast enough, which encourages these bacteria to multiply and
produce their noxious metabolites. Large aquaponic systems often contain a degassing
tank where the hydrogen sulphide can be released safely back to the atmosphere.
Degassing is unnecessary in small-scale systems. However, even in small-scale systems,
if a foul odor is detected, reminiscent of rotten eggs or raw sewage, it is necessary to
take appropriate management action. These bacteria only grow in anoxic conditions, so
to prevent them, be sure to supply adequate aeration and increase mechanical filtration
to prevent sludge accumulation.
5.3.2 Denitrifying bacteria
A second group of unwanted bacteria are those responsible for denitrification. These
bacteria also live in anaerobic conditions. They convert nitrate, which is the coveted
fertilizer for plants, back into atmospheric nitrogen that is unavailable for plants.
These bacteria are also common throughout the world, and are important in their own
right (see Figure 2.4). However, within aquaponic systems, these bacteria can decrease
efficiency by effectively removing the nitrogen fertilizer. This is often a problem with
large DWC beds that are inadequately oxygenated. A problem could be suspected
when plants show signs of nitrogen deficiencies despite the system being in balance,
and when there is a very low nitrate concentration in the water. Investigate possible
areas within the DWC canals that are not circulating properly, and further increase
aeration with air stones.
Some large aquaponic systems deliberately use denitrification. The feed rate ratio
balances the nutrients for the plants but usually results in high nitrate levels. This nitrate
can be diluted during water exchanges (suggested in this publication for small-scale
systems). Alternatively, controlled denitrification can be encouraged in the mechanical
filter. This technique requires careful attention and off-gassing, and is not recommended
for small-systems. More information can be found in the section on Further Reading.
5.3.3 Pathogenic bacteria
A final group of unwanted bacteria are those that cause diseases in plants, fish and
humans. These diseases are treated separately in other parts of this publication, with
Chapters 6 and 7 discussing plant and fish disease, respectively, and Section 8.6 discussing
human safety. Overall, it is important that there are good agricultural practices (GAPs)
that mitigate and minimize the risk of bacterial diseases within aquaponic systems.
Prevent pathogens from entering the system by: ensuring good worker hygiene;
preventing rodents from defecating in the system; keeping wild mammals (and dogs
and cats) away from aquaponic systems; avoiding using water that is contaminated; and
being aware that any live feed can be a vector for introducing alien micro-organisms
into the system. It is especially important not to use rainwater collection from roofs
with bird faeces unless the water is treated first. The major risk from warm-blooded
animals is the introduction of Escherichia coli, and birds often carry Salmonella spp.;
dangerous bacteria can enter the system with animal faeces. Second, after prevention,
never let the aquaponic water come into contact with the leaves of the plants. This
prevents many plant diseases as well as potential contamination of fish water to human
produce, especially if the produce is to be eaten raw. Always wash vegetables before
consumption, aquaponic or otherwise. Generally, common sense and cleanliness are
the best guards against diseases from aquaponics. Additional sources for aquaponic
food safety are provided throughout this publication and in the section on Further
Reading.
5.4 System cycling and starting a biofilter colony
System cycling is a term that describes the initial process of building a bacterial colony
when first starting any RAS, including an aquaponic unit. Under normal circumstances,
this takes 3–5 weeks; cycling is a slow process that requires patience. Overall, the
process involves constantly introducing an ammonia source into the aquaponic unit,
feeding the new bacterial colony, and creating a biofilter. The progress is measured
by monitoring the nitrogen levels. Generally, cycling takes place once an aquaponic
system is built, but it is possible to give the biofilter a head start when creating a new
aquaponic system. It is important to understand that during the cycling process there
will be high levels of ammonia and nitrite, which could be harmful to fish. Also, make
sure all aquaponic components, in particular the biofilter and fish tank, are protected
from direct sunlight before starting the process.
Once introduced into the unit, the ammonia becomes an initial food source for
the AOB, a few of which are naturally occurring and recruit to the system on their
own. They can be found on land, in water and in the air. Within 5–7 days after the
first addition of ammonia, the AOB start forming a colony and begin to oxidize the
ammonia into nitrite. Ammonia should be continuously, but cautiously, added to
ensure adequate food for the developing colony without becoming toxic. After another
5–7 days the nitrite levels in the water will have started to rise, which in turn attracts the
NOB. As the NOB populations increase, the nitrite levels in the water will start to decline as
nitrite is oxidized into nitrate. The full process is illustrated in Figure 5.3, which shows the trends
of ammonia, nitrite and nitrate in the water over the first 20–25 days of cycling.
The end of the cycling process is defined as when the nitrate level is steadily increasing,
the nitrite level is 0 mg/litre and the ammonia level is less than 1 mg/litre. In good conditions,
this takes about 25–40 days, but if the water temperature is cool, complete cycling may take
up to two months to finish. At this point, a sufficient bacterial colony has formed and is
actively converting the ammonia to nitrate.
FIGURE 5.3
The reason this process is long is because nitrifying bacteria grow relatively slowly,
requiring 10–15 hours to double in population. However, some heterotrophic bacteria
can double in as little as 20 minutes.
Aquarium or aquaculture retailers sell various products containing living nitrifying
bacteria (in a bottle). Once added to the unit, they immediately colonize a system
thus avoiding the cycling process explained above. However, these products may be
expensive or unavailable and ultimately unnecessary, as the cycling process can be
achieved using organic means. Alternatively, if another aquaponic system is available,
it is extremely helpful to share part of the biofilter as a seed of bacteria for the new
system. This greatly decreases the time necessary for cycling the system. It can also
be useful to separately start a biofilter medium by continuously trickling a solution
containing 2–3 mg/litre of ammonia for a few weeks in advance. The media would
then function as a primer by simply incorporating it into the new aquaponic biofilter.
A simple trickling system can be built by suspending a wide plastic crate of medium
above a small tank containing the ammonia solution that is being circulated by a small
aquarium pump.
Many people use fish as the original source of ammonia in a new tank. However,
these fish suffer the effects of high ammonia and high nitrite throughout the cycling
process. Many new aquarists do not have the patience to allow a tank to fully cycle and
the result is that the new fish die, commonly referred to as “new tank syndrome”. If
using fish, it is recommended to use a very low stocking density (≤ 1 kg/m3). Instead of
using fish, there are other sources of this initial ammonia to start feeding the biofilter
colony. Some possible sources include fish feed, sterilized animal waste, ammonium
nitrate fertilizer and pure ammonia. Each of these sources has positives and negatives,
and some sources are far better and safer to use
than others.
The best ammonia source is finely ground fish food because it is a biologically safe product,
and it is relatively easy to control the amount of ammonia being added. Be sure
to use fresh, unspoiled and disease-free fish feed only. Chicken waste, despite being an
excellent ammonia source, can be very risky and can introduce dangerous bacteria into the
aquaponic system. Escherichia coli and Salmonella spp. are commonly found in
chicken and other animal manure and, therefore, any manure must be sterilized before use.
Household ammonia products can be used, but be sure that the product is 100 percent ammonia
and does not include other ingredients such as detergents, colourants or heavy metals that
could ruin the entire system. Once the ammonia source has been selected, it is important to
add the ammonia slowly and consistently, and to monitor the nitrogen levels every 2–3 days. It is useful to record levels on a graph to track the process of the cycling. It is important not to add too much ammonia, and it is better to have a little bit too little than too much. The target level is 1–2 mg/litre. If
ammonia levels ever exceed 3 mg/litre, it is necessary to do a water exchange to dilute the
ammonia in order to prevent it from inhibiting the bacteria.
5.4.1 Adding fish and plants during the cycling process
Plants and fish should be added only after the cycle is complete. Plants can be added a little
bit earlier, but expect nutrient deficiencies in these early plants during this period because
other nutrients take time to reach optimal concentrations.Only once the ammonia and nitrite levels are
below 1 mg/litre it is safe to start stocking the fish. Always start stocking the fish slowly. Once
fish have been stocked, it is not uncommon to see a secondary and smaller ammonia and nitrite
spike. This happens if the ammonia created from the newly stocked fish is much greater than
the daily ammonia amounts added during the cycling process. Continue to monitor the levels
of all three types of nitrogen, and be prepared to do water exchanges if ammonia or nitrite levels
rise above 1 mg/litre while the system continues to cycle.
5.5 Chapter summary
• In aquaponics, ammonia must be oxidized into nitrate to prevent toxicity to fish.
• The nitrification process is a two-step bacterial process where ammonia-oxidizing bacteria convert ammonia (NH3) into nitrite (NO2-), and then nitrite-oxidizing bacteria convert nitrite into nitrate (NO3-).
• The five most important factors for good nitrification are: high surface area media for bacteria to grow and colonize; pH (6–7); water temperature (17–34 °C); DO (4–8 mg/litre); cover from direct exposure to sunlight
• System cycling is the initial process of building a nitrifying bacteria colony in a new aquaponic unit. This 3–5 week process involves adding an ammonia source into the system (fish feed, ammonia-based fertilizer, up to a concentration in water of 1-2 mg/litre) in order to stimulate nitrifying bacteria growth. This should be done slowly and consistently. Ammonia, nitrite and nitrate are monitored to determine the status of the biofilter: the peak and subsequent drop of ammonia is followed by a similar pattern of nitrite before nitrate starts to accumulate. Fish and plants are only added when ammonia and nitrite levels are low and the nitrate level begins to rise.
• Ammonia and nitrite tests are used to monitor the function of the nitrifying bacteria and the performance of the biofilter. In a functioning system, ammonia and nitrite should be close to 0 mg/litre. High levels of either ammonia or nitrite require a water change and management action. Usually, poor nitrification is due
to a change in water temperature, DO or pH levels.
• Another class of micro-organisms naturally occurring in aquaponics is that of heterotrophic bacteria. They decompose the solid fish waste, releasing some of the nutrients into the water in a process called mineralization.
