Fish Health Management Considerations in Recirculating Aquaculture Systems

Fish Health Management Considerations in Recirculating Aquaculture Systems

In order to successfully and most efficiently operate RAS, a good understanding of fish health management considerations is critical.

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.

Pathogen Reservoirs

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


Pathogen Transmission

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

and ozonation.

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

management program.

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

potassium permanganate.

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

be followed.

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

appropriate manner.

First published by the University of Florida

Written by:  - Updated 7 Apr, 2020  
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