Recirculating aquaculture systems, also known as water
reuse systems, have become more and more popular.
Recirculating systems are commonly found in aquaculture
facilities, wholesale and retail tropical fish facilities, and
public aquaria. However, in order to successfully and most
efficiently operate one of these systems, a good understanding
of fish health management considerations is critical.
Pathogens in Recirculating Systems
Water quality can be more unstable in recirculating systems
than in large ponds or flow-through systems. Water quality
fluctuations, such as temporary increases in ammonia or
nitrite, can, by themselves, result in disease or significant
losses. These environmental fluctuations often lead to
suppressed immune systems and greater susceptibility to
pathogens (i.e., disease-causing organisms, such as bacteria,
parasites, fungi, and viruses) and disease outbreaks.
Recirculating systems favor the growth of many disease causing
organisms and spread of disease. There are a number
of reasons for this tendency, including higher densities
of fish when compared to other culture systems; build up
of biofilms and sediment and subsequently pathogens in
tanks, sumps, or filtration components (especially mechanical
and biological filters); and slower turn over of water.
Over time, pathogens can become concentrated (i.e.,
present in high numbers). Most pathogens are considered
opportunistic, causing disease only in fish with suppressed
immune systems. However, if pathogens become sufficiently
numerous they can also cause disease in healthy
fish. In addition, the continuous flow of water throughout a
system can spread pathogens rapidly, especially in a system
lacking adequate disinfection protocols or components,
such as ultraviolet sterilization or ozone.
Bacteria, parasites, fungi and viruses can all become
concentrated in recirculating systems. Bacteria that seem
to increase in number in recirculating systems include
Aeromonas spp., Vibrio spp., Mycobacterium spp., Streptococcus
spp., and Flavobacterium columnare.
Parasites that tend to thrive and spread
relatively easily in recirculating systems include Trichodina,
Ichthyophthirius,Cryptocaryon, Amyloodinium, Costia and
Adequate control of pathogens in a system, and consequently
reduction of disease in these systems, requires an
understanding of where pathogens may be found, how they
can be transmitted to fish, and how their numbers may
be reduced. In addition, understanding the proper use of
chemicals to reduce or eliminate pathogens is an essential
part of good management.
The purpose of a biosecurity program
is to prevent entry of specific pathogens (disease-causing
organisms, i.e., bacteria, viruses, parasites, or fungi) that
may cause significant disease and are not present either in
the environment or on the fish in a given facility or system.
In some cases, this is achieved by extensive testing of fish
prior to receiving them from a supplier, or during isolation
and quarantine, prior to placing them in their intended
For some pathogens, this may not be an absolute elimination
of risk of entry, but primarily an overall reduction of
the number that do enter the facility, so that fish already on
the property do not receive an overwhelming load.
Biosecurity measures are important not only when bringing
new fish into a facility; these measures are also important
for reducing overall numbers of potential pathogens in a
given system, and to avoid transferring pathogens from
one system to another. For this reason, it is important to
understand where pathogens may be found (reservoirs),
and why quarantine, disinfection, and sanitation are
important to a good biosecurity program.
There are many areas within an aquaculture facility and
recirculating system that can act as reservoirs for pathogens.
The most important reservoirs are the fish themselves.
Fish can act as asymptomatic carriers of disease. In other
words, they may be immune to a specific pathogen but
still be able to shed the organism into the water or transfer
it to other fish by contact. Sick and dead fish are often
major reservoirs of disease-causing organisms. For this
reason, sick, moribund (dying), and dead fish should be
removed as soon as possible from a system and disposed of
according to county, state, or federal regulations. In most
instances, disposal can be as simple as placing the dead fish
in a plastic bag and putting it in a trash receptacle. Water
can also act as a reservoir. Water can spread pathogens to
anything it touches.
The ground (e.g., concrete slab) can contain pockets of
water that contains pathogens. Equipment, including nets,
siphon hoses and buckets, can also contain pockets of
disease-causing organisms. For this reason, disinfection
of floors, and use of footbaths (either small containers or
mats containing disinfectants) placed at entrances and exits
to system rooms is recommended, as is disinfection of all
equipment when used with fish in different tanks or vats or
systems. Nets should be kept off the floor and placed in an
appropriate clean location to avoid contamination.
Quaternary ammonium compounds are commonly used
to disinfect equipment but they must be rinsed adequately
prior to reuse because these compounds are toxic to fish.
Chlorine can be used but
will destroy nets and must be neutralized or rinsed off
adequately to avoid killing fish. Equipment disinfected
with iodine-containing compounds must also be rinsed
off prior to use because they can be toxic.
Contact a fish health or aquaculture specialist for recommendations on
disinfectants for equipment, floors, and footbaths.
System hardware, including sumps and filters, sediment,
and tank walls, are common sites for pathogens. Sumps and
tanks often contain a fine film (biofilm) or layer of sediment
that may harbor pathogenic organisms. Sediment on the
bottom of sumps and tanks should be vacuumed routinely.
Uneaten food lying on the bottom of tanks can also provide
areas for pathogens to flourish.
Filter beds, because of their particulate nature, concentrate
microorganisms. Mechanical filters should be backwashed,
as frequently as possible, to reduce the loads of the undesirable
(non-biofilter) bacteria, as well as other potential
Pathogens can be transmitted several ways within a recirculating system:
• in the water
• fish to fish
• by vectors and fomites
• in the food
Introduction of water used to ship fish can be a key source
of pathogens. Shipping water often contains high numbers
of bacteria and may also contain parasites or other pathogens.
These organisms are easily transferred from tank to
tank in the recirculating water, or by aerosolization (in mist
or spray) of water from one tank or system to another.
Within a single tank or vat, pathogens can be spread
directly from fish to fish. Higher stocking densities and
increased fish-to-fish contact (as seen in aggressive species)
can increase the rate of spread of pathogens.
Vectors are organisms that can transmit disease-causing
organisms from one animal to another. For example, the
crustacean parasite Argulus (“fish louse”) causes damage by
itself, but it is also believed to transmit bacteria and viruses
between fish. Leeches are another vector that can transmit
blood-borne parasites and bacteria between fish. Additionally,
people can act as vectors by transmitting water and
pathogens from one tank to another via their hands or
Fomites are inanimate objects that can transmit diseases.
Examples of fomites in aquaculture systems include equipment,
such as nets and siphon hoses, that are not properly
disinfected before being used in other tanks or vats.
Food can also be a source of disease. Frozen and live foods
can transmit bacteria, parasites, viruses, and fungi. In addition,
feeds that have been improperly stored can contain
pathogenic bacteria or mycotoxins, dangerous chemicals
produced by the growth of certain types of fungi in the feed.
System Disinfection or Sterilization
As described previously, water may spread pathogens and
also be a potential reservoir for them. Water from a tank
containing sick fish often carries numerous disease-causing
microorganisms. When this same water enters another tank
of fish, those fish are then exposed to the microorganisms
and they will have an increased risk of developing disease.
Disinfection helps to greatly reduce the spread of some
pathogens. Two techniques commonly used to disinfect
water in aquaculture systems are ultraviolet sterilization
Ultraviolet (UV) sterilizers typically consist of UV producing
lamps encased in a glass or quartz sleeve. Water
is passed over the lamps. The lamps emit ultraviolet light (a
wavelength of approximately 254 nm is considered optimal)
that penetrates cells and damages genetic material (DNA
and RNA) and proteins.
For each type of microorganism, a specific “zap dose,”
measured in microwatt seconds per square centimeter,
is required to selectively sterilize the system (i.e., kill the
unwanted organism). The zap dose is determined by the
intensity or wattage of the lamp, contact time or flow
rate of the water, water clarity, and size and biological
characteristics of the target organism. In general, larger
organisms require a larger zap dose
however, the specific structure of certain viruses (which
are generally much smaller than bacteria) makes some of
them more difficult to “kill” than other larger organisms. In
general, the zap dose required is lowest for gram-negative
bacteria, and it increases progressively for gram-positive
bacteria, viruses, spore-forming bacteria, and protozoans.
An aquaculture specialist or manufacturer of UV-sterilizers
can provide advice about the size of sterilizer required for
a specific system and specific pathogens. Maintenance and
regular bulb replacement are important, because UV-bulbs
quickly lose their initial strength. Most UV bulbs need
replacing every 6–9 months.
Bacterial counts, run on agar plates, can be used to determine
the effectiveness of UV sterilizers against bacteria
in the water. More user-friendly kits are also available
from some companies for bacterial count determination.
Consult a fish health specialist or aquatic microbiologist for
Ozone-disinfection systems introduce ozone, O3, a highly
reactive molecule, into a contact chamber (isolated from
the main system holding the fish). Ozone generators are
more complex than UV-sterilizing units, and they require
the presence of a high energy field through which dry
filtered air or pure oxygen flows. The ozone oxidizes (i.e.,
reacts with and breaks down) dissolved and suspended
molecules, as well as molecules within and on pathogens in
the water. In freshwater systems, ozone rapidly breaks down
or dissipates once it makes contact with the water; therefore,
water from a contact chamber can be reintroduced
into the system quickly, if the system is designed properly.
However, as ozone is so highly reactive, all ozone must be
eliminated from the water prior to its reintroduction. This
elimination can be accomplished in several ways including
off-gassing or removal by carbon filtration. Consult with an
aquaculture specialist or a manufacturer of ozone sterilizers
before purchasing a unit.
Ozone does not appreciably oxidize ammonia (i.e., convert
ammonia into nitrite). In recirculating systems, this
reaction is commonly accomplished by nitrifying bacteria
in the biofilter. Ozone does oxidize nitrite to nitrate, so it
augments the efforts of nitrifying bacteria in the biofilter. If
the ozone is turned off in a system adapted to its presence,
the nitrifying bacteria in the biofilter may not be present
in high enough numbers to prevent nitrite levels from
temporarily spiking in the system.
In addition to sterilizing water, ozone helps other parts of
the system. Ozone promotes water clarity by rapidly breaking
down dissolved and particulate organics that discolor
or cloud the water. Ozone improves biofiltration efficiency
by decreasing the organic load in the biofilter. This organic
load is a food source for bacteria known as heterotrophs.
Heterotrophs include many disease-causing bacteria that
often compete with nitrifying bacteria for space and oxygen
in the biofilter.
Ozone is more dangerous than UV sterilization. Small
amounts in the water can kill fish and residual amounts in
the air can be toxic to humans. In seawater, removal or dissipation
of ozone is typically slower than in freshwater, and
by-products of ozonation can increase the risk of disease in
fish. For example, chemical by-products of ozonation have
been suggested as one potential cause of head and lateral
line erosion, although, research to demonstrate this association
has not be completed. Also, some species are much
more sensitive to residual ozone levels than others. There
are different ways to monitor ozone levels in the water
holding the fish. Consult a specialist for details on proper
and safe use of ozone.
Effects of Chemicals on the Biofilter
If changes in management, such as improvements in water
quality, handling, or nutrition, cannot resolve a disease outbreak,
chemicals may be required. Water changes are always
recommended prior to placing tanks or vats containing the
treated fish back on-line with the rest of the system.
Several studies, conducted in the late 1970s using certain
chemicals, had different reported effects on biofilter capacity
Use of Antibiotics and Antibacterials
For species of food fish the use of antibiotics must be
undertaken with caution and guidance from an a suitable
experienced veterinary surgeon is important.
The chemical malachite green is explicitly
illegal for use in food fish, as are other chemicals. If in
doubt, contact a fish health specialist with regard to legal
use of treatments for the species you are raising.
Diagnosis of a bacterial disease should be verified by a fish
health specialist, and appropriate bacterial tests should be
run to determine which antibiotic will be effective. Ideally,
in ornamental fish, this antibiotic should be given in a
medicated food, although in some cases injections may be
warranted for valuable individuals.
In the ornamental fish industry and in public aquaria,
antibiotic bath treatments are used, under strict control,
when fish are not taking food or have external infections
Under certain conditions, veterinarians have the legal
right to prescribe antibiotics to their clients to be used in
an “extra-label” manner. “Extra-label” means using the
antibiotic in a way that is different from that for which it is
specifically labeled. Therefore, aquaculturists are encouraged
to work closely with a fish veterinarian during disease
outbreaks as well as during development of a fish health
Therefore, antibiotics should only be used in a bath under
the following conditions:
• the fish will not consume a medicated feed
• in consultation with a fish veterinarian or fish health
• proper culture and sensitivity tests have been run to
determine which antibiotic should be used
• the treated fish are “taken off line”, so the water is contained
and will not contact the biological filter
• the treated water is disposed of according to local
Studies (Collins et al 1976; Levine and Meade 1976; Spotte
1979) have demonstrated that use of antibiotics as a bath
treatment will negatively impact the biofilter, reducing its
ability to function by as much as 44–100%.
Use of Other Chemicals
Research has shown that there are some differences in the
inhibitory effects of formalin, malachite green (illegal for
use in food fish), methylene blue (methylene blue is not
recommended by fish health specialists and is illegal for
use with food fish), copper sulfate, and potassium permanganate
on the biofilter bacteria (Collins et al 1975; Levine
and Meade 1976).
Different studies show different effects. Formalin used in
one study, at 25 mg/L had no effect, whereas another study
showed reduction of biofilter bacterial activity by 27% when
used at 15 mg/L. As a rule of thumb, most aquaculturists
do not consider use of formalin at 15–25 mg/L to have a
major impact on the biofilter. However, when testing for
ammonia levels, formalin will react with Nesslers Reagent
(a component of most ammonia test kits) and can give a
falsely elevated ammonia reading. In systems treated with
formalin, the salicylate reagent test for ammonia is recommended
(Hach Company 2002) because it does not react
with aldehydes (e.g., formaldehyde found in formalin).
Malachite green (again, illegal for use in food fish) has been
shown to have no effect on the biofilter at 0.1 mg/L, combined
with or without formalin at 25 mg/L. Copper sulfate
at 1 and 5 mg/L likewise had no effect on biofiltration.
By contrast, potassium permanganate experiments have
been mixed. In one study, a 4-mg/L dosage resulted in
no inhibition of the biofilter, whereas in another study, a
1-mg/L dosage resulted in an 86% inhibition.
The actual impact on an individual system will most likely
depend upon many factors, such as chemical concentration,
length of time in treatment, organic load, pH, temperature,
alkalinity, filtration, oxygen levels, and stocking density;
and, although this will most likely be true for most chemicals,
this may better explain the differences in effect by
More work has to be conducted on the use of hydrogen
peroxide in recirculating aquaculture systems, especially its
safety and efficacy for use in various fish species and system
configurations, including effects on biofiltration. More
organics in the system lessen the likelihood that biofilter
bacteria will be damaged or killed by these chemicals.
However, too high an organic load will render these chemicals
ineffective as treatments.
If possible, affected fish should be treated in vats or tanks
that have been taken off-line from the remainder of the
system, and a 75–100% water change should be done in
those vats or tanks prior to their being placed back on-line.
It is important to reiterate that antibiotics are NEVER recommended
for use in system-wide bath treatments because
of the potential for development of antibiotic-resistant
strains of pathogens and severe detrimental effects on the
nitrifying bacteria within the biofilter. If a population of fish
in a recirculating system must undergo a specific antibiotic
bath treatment, that population should be isolated from the
rest of the system by shutting off water flow during treatment.
After treatment, 100% water changes for the treated
vats or tanks are recommended.
Salt (sodium chloride) Another chemical commonly
used in recirculating systems is salt (sodium chloride).
Salt can be useful in reducing certain parasite infections
in a system. Salt also helps reduce osmolarity stresses by
increasing the salt concentration in the water relative to
the normal concentration in the fish’s body (freshwater
fish have a higher body salt content than freshwater and so
must use energy to keep the body’s salt concentration – the
osmolarity – in balance). Most tropical fish can tolerate a
salt concentration of 1–3 g/L, and this level is not harmful
to the biological filter.
Before new fish are placed into a new system, or into
a system already containing fish, biosecurity protocols
(including quarantine, sanitation, and disinfection) should
Recirculating systems may promote the growth of certain
disease-causing organisms (pathogens). A good understanding
of where these pathogens (parasites, bacteria,
fungi, and viruses) may exist in a system and how they may
enter a system is important for the recirculating system
manager. This understanding is critical for good system
design and for the development of effective management
Pathogens can be found on fish in the system; in the water;
on system hardware including the facility floor; on surfaces
of tanks, sumps, and filter beds; and on husbandry equipment
such as nets and siphons. They can be transmitted by
water, from fish to fish, by vectors (other organisms including
people), by fomites (non-living things such as nets), and
by contaminated feed.
Ultraviolet and ozone sterilizing units can help reduce
overall pathogen numbers in a system, but they will not
prevent spread of pathogens within a system unit (e.g., tank
or vat). Sterilizing units must be sized properly, according
to manufacturer’s recommendations, and they also must
be strictly maintained. Only the water that contacts the
sterilizers will be affected. Poor husbandry (for example,
not dipping nets when using them between tanks) will
negate any benefits of these sterilizing systems. Also, ozone
can be dangerous to fish and humans.
Chemicals used in a system may have undesirable effects on
the water, biological filter, the fish, or employees. Therefore
the pros and cons of each chemical used in the system must
be understood. All chemicals should only be used in an
First published by the University of Florida