edX course

MOOC
Aquaponics - the circular food production system

Course reader
Week 2 – Fish Biology, Feeding and Growth, Health and Welfare

ZHAW Zurich University of Applied Sciences, Wädenswil, Switzerland

Based on and adapted from Junge, R., Antenen, N., Villarroel, M., Griessler Bulc, T., Ovca, A., & Milliken,
S. (Eds.) (2020). Aquaponics Textbook for Higher Education. Zenodo.
http://doi.org/10.5281/zenodo.3948179
CONTENTS
CONTENTS ............................................................................................................................................................. 1

2.1 FISH ANATOMY & PHYSIOLOGY ............................................................................................................................ 2

2.1.1 General external anatomy....................................................................................................................... 2
2.1.2 General internal anatomy ....................................................................................................................... 6
2.1.3 Respiration physiology ............................................................................................................................ 9

2.2 FISH FEEDING AND GROWTH ............................................................................................................................. 10

2.2.1 Energy requirements ............................................................................................................................. 11
2.2.2 Main interactions between ingestion and environmental factors ........................................................ 12
2.2.3 Abiotic factors ....................................................................................................................................... 12
2.2.4 Biotic factors.......................................................................................................................................... 13
2.2.5 Proximate composition of fish feeds and essential nutrients ................................................................ 14
2.2.6 Types of feeds ........................................................................................................................................ 15
2.2.7 Feeding strategies ................................................................................................................................. 16
2.2.8 Automatic feeders ................................................................................................................................. 18
2.2.9 Production plan and monitoring the evolution of the farm .................................................................. 19
2.2.10 Designing feeds for aquaponics ........................................................................................................ 21

2.3 FISH WELFARE ................................................................................................................................................ 23

2.3.1 Introduction ........................................................................................................................................... 23
2.3.2 Legislation in the EU .............................................................................................................................. 23
2.3.3 Specific measures to evaluate welfare .................................................................................................. 24
2.3.4 The HPI axis and the stress response ..................................................................................................... 24
2.3.5 Operational welfare indicators.............................................................................................................. 25
2.3.6 Tools to use on-site ................................................................................................................................ 26

2.4 REFERENCES .................................................................................................................................................. 27

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2.1 Fish anatomy & physiology
2.1.1 General external anatomy
The aim of this section is to introduce important anatomical features of fish and to relate them to function
and physiology. There are more than 34,000 species of freshwater and marine fishes on our planet, each
with specific requirements and ecological niches, which has led to specific body adaptations
(fishbase.org). However, many of the fish, especially teleosts (bony fish with a moveable pre-maxilla),
share some common features. Although the number of species used in aquaculture is probably over 200,
the number used in aquaponics is narrower, and mostly restricted to freshwater fish (Table 1). Each fish
species has different requirements on their environment in terms of water quality, temperature, and
tolerance stresslevels.

Table 1: Summary of the fish species used in aquaponics, including those cited in two
international surveys on aquaponic practitioners
(Love et al. 2014; Villarroel et al. 2016)

Common name Species Family Order

Tilapia Oreochromis niloticus Cichlidae Cichliformes
Pangasius Pangasius pangasius Pangasiidae Siluriformes
Catfish Silurus glanis Siluridae Siluriformes
European carp Cyprinus carpio Cyprinidae Cypriniformes
Trout Oncorhynchus mykiss Salmonidae Salmoniformes
Bass Morone saxatilis Moronidae Perciformes
Pike perch Sander lucioperca Percidae Perciformes
European perch Perca fluviatilis Percidae Perciformes

Most of the fish used in aquaponics follow a basic anatomical outline (Figure 1). Looked at longwise, there
are three main regions of the body: the head, the trunk region, and the tail (Canada Department of
Fisheries and Oceans 2004). In terms of possible abnormalities, veterinarians tend to focus on problems
related to the eyes, fins and skin. Apart from those, there are other parts of the external anatomy that
are important in terms of indirect measures of fish welfare, fish quality, and health problems, and one
should be able to locate these. For example, blood sampling usually involves injecting a needle
underneath the lateral line in the tail region to find the caudal vein. To tag individuals, passive integrated
transponder tags (PIT tags) are normally injected into the muscle under the dorsal fin. Some other plastic
paints can be injected on or near the mouth and eyes, but any type of exterior tags often cause problems
since they affect the very delicate skin and can cause infections. If nothing else, basic knowledge of some
species-specific anatomy can also help to avoid fish fraud when purchasing them commercially.

Eyes and nose

As opposed to some cartoon characters, real fish have no eyelids and have no way of 'closing' their eyes.
Their light sensitive eyes are in direct contact with the surrounding water at all times, giving an idea of
the importance of water quality. Many fish are not used to direct sunlight and congregate in locations
with shade. The Mexican cavefish (Astyanax mexicanus) is one example of a blind fish, but most fish used
in aquaponics can see very well. While alive, bilateral exophthalmia (the bulging of both eyes from their
sockets) is often used as a general indicator of infection. Unilateral exophthalmia is probably the result of

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a contusion. After slaughter, the whiteness of the eye is used as a quality indicator (see Council Regulation
(EC) 2406/96). For example, a high-grade, very fresh fish have a convex eye with a black and shiny pupil,
while fish with a concave eye, grey pupil, and a 'milky' cornea should be discarded. Close to the eyes are
two small openings (nares) which lead to an area with olfactory sensors which can be quite sensitive in
many fish. For example, salmonids use their olfactory sensors during migration in order to return to their
original breeding grounds. In order to be able to smell anything, a current has to be established in and out
of the nares, normally while fish are swimming but, unlike in mammals, the holes do not lead to the throat.

Figure 1: Basic external anatomy of a fish (from http://anatomyhumanbody.us)

Opercula and gills

The operculum is a bony cover that shields the gills, the lungs of the fish which capture the rather limited
supply of oxygen dissolved in water. The opercular frequency, or the rate at which the opercula open and
close over a period of time, can be used to verify whether fish are breathing correctly or may be overly
stressed. In anesthetized or dead fish, veterinarians often 'check under the hood' by lifting up the opercula
to examine the gills, which should be bright red and moist, and not covered in mucus, white, or smelly.
External observation of the gills can also provide information about possible bacterial or parasitic
infections. Compared to mammals, fish gills are thus more of an external organ than an internal one, again
underlining the importance of water quality to protect this delicate and important organ (e.g. correct
water pH). Finally, apart from oxygen absorption and CO2 release, the gills are an important outlet for
nitrogenous waste (Figure 2). Hoar & Randall (1984) calculated that more than 80% of ammonia (NH3) is
excreted via the gills, while only trace amounts are passed as urine.

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Figure 2: The gills work according to the counter flow principle: water and blood flow in opposite directions. The O2
content in blood can therefore rise to the same concentration as that in the surrounding water
(source: https://338373gasexchange.weebly.com/fish.html)

Skin
The skin is one of the most important organs in fish. It has three basic components: the dermis (inner
layer), the epidermis (outer layer), and the scales. The scales are embedded in the dermis, which is
responsible for providing colour. Mucus is made by the epidermis and helps to protect the cells. It has
anti-fungal and anti-bacterial properties and plays a role in immune function (Wainwright & Lauder 2017).
Any type of skin lesion or scale loss can have serious consequences for fish, since healing in an aqueous
environment can take a long time and wounds can get waterlogged. Just imagine, for example, trying to
heal a paper cut on your finger by keeping it submerged in a glass of water for a week. The whole healing
process would take much longer, and you would be more exposed to bacterial infections. For all these
reasons, when handling live fish, one has to keep the fish wet all of the time and also use plastic gloves so
as not to damage their skin.

The lateral line is part of the skin organ and consists of perforated scales with cilia (short microscopic hairs
that can move) that are connected to the nervous system and provide information about water
movement around the fish and pressure (constituting a sense organ not found in mammals). This allows
fish to hunt at night or move in very opaque water by sensing the vibrations around them.

Finally, as a curiosity, several recent studies have related skin colour to fish personality. For example, the
colour of the dermis on the dorsal area of salmon (between the dorsal fin and the head) is darker or has
more dark spots in fish that are more aggressive (Castanheira et al., 2017).

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Fins
Fins can be used as indicators of fish health and welfare. We want to avoid fraying of the fins (when the
skin comes apart between the rays), fin erosion (white colouring at the tips of the fins), necrosis (dead
cells on the fins), or discoloured spots, the latter of which may indicate the presence of parasites or
bacterial infection.

Dorsal fin
Normally fish have one dorsal fin, but they can have up to three (one after another, as in cod). There are
two types of dorsal fin rays, spiny and soft. The dorsal fin is mostly used to help maintain the fish in an
upright position. It is supported by rays which are often erectile to allow the fish to 'open or close' it
depending on signalling requirements. Tilapia has a large dorsal fin with pointed rays that can easily cut
hands that want to grab it out of the water. The number of rays per fin can also be used to identify the
species of fish. For example, rainbow trout have between 10-12 rays on their dorsal fin while brown trout
(not normally grown in aquaponics) have around 13-14.

Adipose fin
This is a rather short and fat fin which is common in salmonids, but whose function is unclear. It is full of
fat and appears to have sensory neurons. Sometimes it is cut off in farmed salmon to differentiate them
from wild salmon but Reimchen & Temple (2004) found that fish without an adipose fin have a higher tail
beat amplitude, indicating that it has a role in natural swimming behaviour, and that cutting it off probably
has a negative effect on welfare.

Caudal fin
This is the largest and most powerful fin and is directly connected to the spine. It is used to thrust the fish
forward. Sometimes, it can also be nibbled by other fish or get eroded by being rubbed on different
surfaces. The tail is also important for measurement purposes (Figure 3). Apart from weighing the fish,
aquaculturists often measure the standard length (from mouth to the beginning of the tail) and fork length
(from mouth to the fork at the tip of the tail).

Anal fin
This fin is posterior (behind) the anus and urogenital pore on the ventral side of fish. Sometimes referred
to as the cloacal fin, it is also important in stabilizing fish when swimming, so that they do not roll over
onto their sides.

Pectoral and ventral fins

Close to the operculum fish have pectoral fins, which roughly correspond with the arms of terrestrial
mammals, and below them are the ventral or pelvic fins. In some fish, generally those considered to be
'less evolved' (i.e. those which have changed less over time compared to their ancestors), like salmonids,
the ventral fins are further down the trunk region, while they are closer together in more modern fish
(such as tilapia). The pectoral fins help fish to move up and down while the ventral fins are more important
in stopping movement.

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Figure 3: Example of fish length measurements for a tarpon fish. For standard weight equations, the total length is
used, which includes the caudal fin (source: http://www.nefsc.noaa.gov/lineart/tarpon.jpg).

2.1.2 General internal anatomy

In this section we will outline the most important internal organs of fish (Figure 4), underlining the main
differences with mammals and some important facts that influence how fish should be maintained.

Figure 4: General internal fish anatomy (source: http://www.animalsworlds.com/internal-

anatomy.html).

Brain
Fish have small brains compared to terrestrial vertebrates. For example, the human brain weighs
approximately 1.4 kg and represents around 2% of the total body mass, but fish brains only represent
0.15% of their body mass. Nonetheless, unlike many vertebrates, fish brains are quite adaptive and
maintain the ability to grow and change throughout life (they maintain the ability to produce new
neurons; Zupanc 2009). Fish brains have three main regions: the forebrain (with the olfactory lobes and

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telencephalon), the mid-brain (optical lobes), and the hind-brain (cerebellum). Fish do not have a
neocortex, which some scientists think is necessary to be fully conscious of pain, but other important
structures exist that suggest they can feel pain, such as the amygdala, the analogue neurons, the
cerebellum, and the pallium (outer layer of the telencephalon; for more information see Braithwaite
2010).

Hearing in fish
Although fish do not make sounds, detection of sound provides invaluable information about objects at
distances beyond that provided by vision and in all directions.

The hearing system of vertebrates first arose in fishes, who have two independent sensory systems to
detect sound. The primary system is the inner ear, that is surrounded by the skull bone. The inner ear
contains structures, called otoliths, which are much denser than water and a fish’s body. Otoliths are
made of calcium carbonate and their size and shape is highly variable among species. Because of the
density difference between the fish’s body and the otoliths, the otoliths move at a different amplitude
and phase in response to sound waves than the rest of the fish. The difference between the motion of the
fish’s body and the otoliths results in bending of the cilia on the hair cells that are located in the inner ear.
This differential movement between the cilia and the otolith is interpreted by the brain as sound.

The sound detection also involves, to a lesser extent, the lateral line system, which is generally used to
detect vibration and water flow.
For more details on hearing in fish see https://dosits.org/animals/sound-reception/how-do-fish-hear/.

Heart
The heart is located just underneath the gills. Like the brain, it is quite small and relatively simple
compared to terrestrial vertebrates, normally only weighing a few grams. It has a contractile ability to
collect blood from the body and send it to the gills in a one-loop system which will be commented on
more below under the section on respiration. It is a simple circuit with one atrium, one ventricle, and a
conus which leads directly to the gills. There is no double circuit as in mammals, where the blood sent to
the lungs returns to the heart to get pumped back to the body. In fish the blood is 'pumped' out of the
gills to the body without sending it back to the heart.

Digestive system
The general makeup of the digestive system in fish is similar to other vertebrates, with a mouth,
oesophagus, stomach, small intestine, large intestine, and anus. However, there is little demarcation
between the different sections of the small intestine, nor is there an ilea-caecal valve separating the small
from the large intestine.
Generally carnivorous fish have bigger stomach while carp-like fishes (Cypriniformes) have none, the food
pulp gets processed almost exclusively in the long intestines. Fish with a stomach have the pyloric caeca,
while fish with no stomach don’t have them. The caeca are derivations of the digestive tract, which help
to increase the total surface area for digestion and extract essential nutrients.

Abdominal fat
An important difference between wild and cultured fish is the amount of abdominal fat that accumulates
in the latter. For example, sea bream from aquaculture will typically accumulate more visceral fat than

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wild sea bream, while fish that are fasted for longer periods have less fat than fish fasted for less time
(Mozanzadeh et al. 2017).

Spleen
The spleen is normally a dark red circular organ attached to the intestine. It helps to clean the blood,
contains white blood cells, and is an important part of the immune system.

Liver and gall bladder

The liver is quite large and reddish, and beginners sometimes confuse it with the heart. It plays a vital role
in detoxifying any organic or inorganic contaminants from the food or water, as well as participating in
protein synthesis, and fat and glycogen storage. Underneath the liver is the yellowish green gallbladder.
Most fish do not have a distinguishable pancreas but rather Brockmann bodies, a collection of endocrine
cells found along the digestive tract which can produce insulin.

Swim bladder
This organ is unique to fish. It can be filled or emptied to control buoyancy, and thus affects the amount
of energy needed to swim. It can also be used to produce or receive sounds. Fish can be either
physostomous (like trout), who can fill up their swim bladder via a pneumatic duct which is connected to
the gut, or physoclistous (like bass), with no direct connection between the oesophagus and the entry to
the swim bladder, so it must be filled up using a gas gland. Physostomous fish are better prepared for
sudden changes in water height while it will take longer for physoclistous species. For all fish it is important
to fill the swim bladder with air at an early stage of development, in order to assure proper growth and
avoid spinal deformities (Davidson et al. 2011).

Kidneys
The kidneys are paired organs that are quite long and narrow, and dorsal to the swim bladder. They play
an important role in blood homeostasis (i.e., maintaining appropriate levels of dissolved ions), which
explains their substantial size. As in mammals, they are needed to 'clean' the blood, which is especially
important in an aqueous medium where the concentration of different ions must be monitored
continuously. It should be noted that fish from fresh- and saltwater have adopted opposing methods to
maintain appropriate levels of blood electrolytes. Freshwater fish have a higher concentration or ions in
their blood than the surrounding water. Therefore, due to osmosis, the gills and kidneys of those fish must
work to avoid absorbing too much water (H2O) and losing too many ions (they drink little and 'urinate' a
lot). In saltwater the opposite occurs: fish drink/ingest more water and urinate little since the
concentration of ions in their blood is lower than the surrounding water. In aquaponics, care should be
taken to ensure that the nutrient solution for plants is not having a negative effect on the fish due to
inappropriate ion levels. At the end of the kidney there is a bladder to store urine, but it is very small
compared to mammals, mostly because little urine is produced in comparison (as mentioned above, much
of the nitrogenous waste is excreted by the gills).

Testes and ovaries

Most of the fish used in aquaponics will be used as food and will not mature sexually (breeders are kept
in a separate installation). However, it is useful to know that sexual reproductive organs in fish are internal
and start to develop deep inside the dorsal region of the fish near the head kidney. As fish mature, the
gonads grow drastically towards the urogenital pore near the anus. During breeding season semen or eggs

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will be expelled for external fertilization. Sexual maturity of the fish often has an adverse effect on the
immune system of the fish making them less robust towards stress and parasite loads.

2.1.3 Respiration physiology

The air we breathe is mostly nitrogen (78%) and oxygen (21%). The water that fish 'breathe' also contains
oxygen, but at a much lower concentration, less than 1%. In addition, since water is 840 times denser than
air and 60 times more viscous, it takes more effort for fish to 'breathe' to extract oxygen, around 10% of
their metabolic energy. In comparison, terrestrial animals only use about 2% of their metabolic energy to
extract oxygen from air. For example, rainbow trout need to move approximately 600 ml of water past
their gills per minute per kg weight while, in comparison, terrestrial reptiles such as turtles only need to
move 50 ml air min-1 kg-1. As a result, even though fish gills are quite efficient, obtaining enough oxygen
from the surrounding water can be difficult.

Fish capture oxygen using their gills which are in direct contact with the surrounding water and are easy
prey for parasites and bacterial infections. The total surface area of the gills is approximately 10 times the
surface area of the whole body. Gills are also important in ion exchange (maintaining the acid-base
balance) and waste elimination, such as ammonia. Thus, fish basically urinate via their gills as well as
breathe through them. To obtain oxygen, water is drawn into the mouth cavity and then the mouth is
closed to force water out through the two opercula. This pumping movement creates a unidirectional
flow of water, unlike the inhaling and exhaling through the same orifice in terrestrial mammals. Some fish,
such as sharks, can keep their mouth open while swimming, which apparently provides enough flow of
water over the gills to breathe normally. If your tanks allow it, you can try to measure the heart frequency
of your fish indirectly by counting the opercular frequency – the times that the opercula open and close
per one minute. This measurement can be used as an indirect indicator of animal welfare since stressed
fish have high opercular frequencies.

From the buccal cavity water flows through two gills, one on each side of the fish’s head. In most fish the
gill, protected by the gill cover or operculum, consists of four vertical bony rods. On each rod two v-
shaped primarily gill lamellae are attached, floating horizontally in the water stream that flows towards
the caudal/posterior end. Each primary lamella is equipped with numerous secondary lamellae i.e. very
fine tissue sections that allow maximum surface and a close proximity of the water flow and the blood
stream.
The primary filaments or primary lamellae are red since they are full of blood. Each primary lamella has
secondary lamellae which cross it perpendicularly and carry individual blood cells to facilitate gas
exchange (release CO2 and capture O2 using the haemoglobin in the red blood cells). The flow of the blood
runs against the flow of water, which increases its efficiency. In addition, fish can open or close the set of
primary filaments to expose more secondary lamellae to the water, effectively taking deeper breaths.
After filling up with oxygen the blood cells continue to move through the body via arteries.

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2.2 Fish feeding and growth
Feeding and fish nutrition are fundamental aspects of aquaculture, both in terms of fish growth and of
economics. Proper feeding depends on the development and choice of quality feeds and on choosing
appropriate methods to distribute the feed to the fish in the tanks. Apart from affecting growth, feeding
can also affect fish health and welfare, which depends in turn on how much we know about the
requirements of each species. Each species has its own natural history and well-defined stages of
growth, which should be understood in order to provide optimal care.

The candidate fish species for aquaponics occupy defined ecological niches in their natural habitat.
Therefore, we need to provide adequate conditions for proper development, including housing
conditions, which means defining the correct temperature, salinity, water quality, light conditions, and
speed of water flow. Normally the most demanding phases are the maintenance of breeders and the
fertilization/incubation of ova or eggs and rearing of larvae. Aquaponic production will normally be
dealing with later stages, usually called 'on-growing'. As the scale of aquaculture and aquaponic farms
increases, it becomes more complex to maintain a large number of production phases in the same
installation, so companies become specialized in one or two stages, such as breeding and rearing of larvae
or on-growing. In the case of aquaponics, where fish are maintained in recirculating aquaculture systems
(RAS), we normally use juveniles which are grown to adults, aiming to simplify the fish production part of
the system with only one or two phases, if possible.

Feeding in aquaculture differs fundamentally from feeding the terrestrial mammals. Livestock on land
normally self-feed using what are known as ad libitum feeders (each animal can choose when to approach
the feeder and how much to eat at any given time of the day). In that case it is relatively easy for the
farmer to detect the ration that was really ingested. In aquaculture and aquaponics, fish can also use self-
feeders, but it is much more difficult to judge how much feed they actually consume. The danger is that
any extra feed that falls into the water and is not ingested becomes waste that 'pollutes' the system.
Efforts need to be made, therefore, to estimate the feed to be distributed and the precise ration that the
fish need.

One way to distribute the feed manually from outside the tanks, spread over the whole surface area of
the water, observing the behaviour of the fish until they seem to be satiated, and then feeding is stopped.
Since the fish are feeding underwater, it is not that easy to know when they stop feeding or how much
they ate, or even if some fish ate more than others. The more we know about a species, the more we
know about their feeding habits. For example, Nile tilapia in the wild are omnivorous when young
(juveniles), eating both zooplankton and phytoplankton, while they become more herbivorous as they get
older (> 6 cm long) (FAO 2018). Trout, on the other hand, are mostly carnivorous throughout their lives,
with a diet almost exclusively based on insects and any smaller fish they can manage to catch. In any case,
the perception and knowledge of the people who are in charge of feeding is very important. For more
information on the feeding habits of different species, see the Aquaculture Feed and Fertilizer Resources
Information System, run by the Food and Agriculture Organization of the United Nations (FAO 2018).

Another way is to use automatic feeders. Here we might depend on technological developments such as
underwater cameras to detect when the fish are no longer eating. All the feed that goes into the tank
becomes a part of the system, whether it is eaten or not. Indeed, fish feed is the main external element
of any aquaponic system and should be carefully controlled. Non-ingested feed remains in the tank and

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causes two problems, one associated with its cost and another associated with its elimination. These two
problems underlie the need for adequate designs.

The hydraulics of the system should facilitate the removal of the uneaten feed. If the design is deficient,
cleaning will be more complex, and the fish may be bothered by the frequency of maintenance routines.
Any decrease in the sanitary conditions of the tanks will have immediate consequences on the welfare of
the fish, and on the profitability of the farm. So, even if we know the nutritional needs of the species, a
poorly designed installation will make it difficult to provide adequate requirements for good fish welfare,
and feed will be wasted.

2.2.1 Energy requirements

As all living organisms, fish require energy, and that energy is provided by the oxidation of the organic
components in feed. Fish require energy to carry out their daily activities, such as breathing and
swimming, and to transform, restore, and grow their body tissues. The energy requirements of fish
depend on their physiological state and on the environmental conditions. In general fish make a more
efficient use of the energy ingested compared to terrestrial mammals, due to the following reasons:

1. Aquatic species are poikilotherms, which means that their body temperature is the same as the
surrounding water, so they do not need to spend energy heating up their body or keeping it at a
constant temperature, as occurs with terrestrial livestock;
2. Since they live in water, fish do not require a strong body skeleton to support their weight under
the full pressure of gravity, as in terrestrial livestock, nor do they require the costly metabolic
processes required to maintain that skeleton;
3. Nitrogenous waste in fish is eliminated as ammonia directly from the gills which consumes less
energy than having to make urea or uric acid and then eliminate it, as is done by mammals and
birds.

Figure 5 provides an overview of the balance of nutrients and energy in fish. If we assume that it has
ingested all the feed provided, the energy is distributed percentage-wise among different physiological
processes, within ranges. If maintained under stressful conditions (poor lighting, low water quality,
inadequate stocking densities), where the fish are alive but not comfortable, about 40% of the feed energy
will be consumed just to cope with the stress, leaving only 30% for growth. On the other hand, under
optimal conditions, fish will use up to 40% for growth. Obviously, the economic viability of an aquaponic
system will depend on the optimal use of the energy provided. To do that we have to ensure that they
ingest all of the feed, and that we provide optimal housing conditions so that the fish are not overly
stressed.

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 Figure 5: Balance of nutrients and energy for fish kept in recirculating systems.
2.2.2 Main interactions between ingestion and environmental factors
As commented above, we should be able to house each species according to its requirements. For that
we first need a profound knowledge of the species that we are going to work with before we begin to
grow the fish or start the installation. Once we have this information, we should be able to maintain the
adequate housing conditions in our system, which in this case is related to aquaponic systems.

2.2.3 Abiotic factors

The main environmental aspects to consider and that have a direct effect on production are the following:

1. Physico-chemical parameters of the source water, which are independent of the aquaculture
activity itself:
a. Water temperature, which regulates the speed of all metabolic processes.
b. Water salinity or conductivity
c. pH
d. Turbidity and total suspended solids
e. Any potentially toxic compounds in the source water. The initial quality of the water is
one of the basic success factors in the installation.
2. Physico-chemical parameters of the tank water:
a. Dissolved gases: fundamentally oxygen, which should be monitored continuously and is
required by fish for normal function. In parallel, carbon dioxide is produced by fish
respiration, and other gases are present in the circuit, such as nitrogen (that can appear
during the over-saturation of pumped water), or hydrogen sulphide or methane from the
anaerobic decomposition of sediments.
b. Dissolved micro- or macronutrients, which are related to the feed, including several
elements vital for the development of the fish, such as phosphorus, iron, and especially
the nitrogenated substances excreted by the fish.

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2.2.4 Biotic factors
Different species of fish are extraordinarily diverse in terms of their social requirements, such as stocking
density. Historically, fishes chosen for aquaculture are robust under different conditions, which makes it
easier to choose adequate management, including carrying out daily tasks on the farm without generating
many sanitary complications in the fish. This is also the case for aquaponics, where the most popular fish
is tilapia, well known for its wide tolerance range.

However, in the beginning, we first had to domesticate wild species, which were normally difficult to
manage, reproduce, and grow, but had a high economic value. That high value covered the costs of
production of delicate species. A clear example is rainbow trout, which in the beginning was a very
complex species, hard to produce and manage, even though now it seems relatively simple. Any poor
management and inadequate movement of the fish produced stress and damages to the skin which led
to infections that brought on or facilitated disease and other common problems of fish that are stressed.
Examples of species that are currently being domesticated, and have not reached their full potential in
aquaculture, are burbot (Lota lota) and white fish (Coregonus sp.). Technological development and
accumulated knowledge have drastically improved the techniques used in the routine operations on
farms, such as sampling of the fish, counting the fish, movement of live fish, etc. The main aspects that
will influence the welfare of the fish in the tanks include:
1. Social structure: For example, trout are quite territorial, and that they require frequent size
grading during the initial phases of growth in order to avoid the appearance of dominant fish that
will damage the smaller fish. In that case it is better to keep the fish within a narrow size range in
separate tanks in order to improve production. We also know that tilapia and Clarias species show
two different modes of behaviour: territorial if at low densities, and swarming/schooling if at high
densities. Thus, low densities are not always better for all fish species.
2. Fish density: each species has a minimum and maximum stocking density below or above which
problems may arise and fish welfare will be jeopardized. Density is normally measured in kg/m3
and varies depending on the system. Some high output industrial RAS systems grow tilapia above
60 kg/m3 but normally aquaponic systems use lower densities, around 20 kg/m3 (see for example
the Aquaponic Gardening Rules of Thumb), although values can range widely depending on fish
size and RAS system set-up.
3. Human disturbance: this depends on the species. Tench (Tinca tinca), for example, are quite
flighty, and can hurt themselves by bumping into the tank walls when disturbed or even when
they notice human shadows. One solution is to put curtains around the tanks to avoid being seen,
or to set tanks on rubber supports to minimize vibrations from human steps or machines.
4. Prey or feed: the size of the feed should be appropriate for the size of the fish and distributed
throughout the tank so as not to promote dominant fish. Otherwise less proactive fish will not
gain weight and tanks will need to be size sorted more often, which is stressful.
5. Predators: The presence of predators, such as cats, dogs or birds close to the tanks, can stress the
fish a lot, and contact needs to be avoided by using artificial boundaries such as fences.
6. Loud noises: Music or loud pumps can be stressful for fish as well.

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2.2.5 Proximate composition of fish feeds and essential nutrients
When research began on fish feeds more than 50 years ago, scientists first analysed the natural diets of
the species in question. Trout, as an example of a carnivorous fish, had a natural diet that consisted of
50% protein, 15% fat, 8% fibre, and 10% ash, which is high in protein compared to terrestrial mammals.
Ever since then researchers have been trying to find the right balance of protein, carbohydrates, fats,
fibre, vitamins and minerals for fish used in aquaculture (Bhilave et al. 2014).
One of the most important components of any fish feed is protein. All proteins are composed of amino
acids in different proportions. Thus, modern nutritionists tend to look at protein requirements in terms
of amino acid requirements and aim to identify the ideal levels of the most important ones. This makes
the whole system more efficient since fish are not getting any extra amino acids (that are then wasted),
and have enough of the essential amino acids to grow healthy. Usually the level of protein is the first and
most important question to ask when designing a diet. This is also a key issue in aquaponics since the
protein in feed is the source of all the nitrogen waste that will later be used by plants.
Carbohydrates are composed of glucose, the main energy source for animals. In fish feed the most
commonly found carbohydrate is starch, which helps to hold feed pellets together and provides an
inexpensive source of energy. Although typically found in low amounts in fish feed, recent developments
have led to an increase in its use. Now, in an effort to spare protein, that is, to reduce the amount of
amino acids that are broken down to make energy, fish nutritionists are supplying more carbohydrates,
with the advantage that the latter are also cheaper than protein (e.g., Lazzarotto et al. 2018). The only
drawback is that this approach effectively makes many carnivorous fish more herbivorous, or vegetarian,
since the extra carbohydrates are mostly of plant origin. Many studies in the past five years have been
analysing how this can affect fish growth and welfare, and the results are promising.
Fats are made up of triglycerides or fatty acids which, like carbohydrates, provide energy to fish and,
unlike carbohydrates, can be stored in different organs. Many fish, especially from colder waters, rely on
high levels of fat in their diet (less than 15%), including omega-3 and omega-6 fatty acids. Fatty acids are
also needed to transport fat-soluble vitamins. The relatively high levels of fat in most fish diets means that
anti-oxidants are required to maintain their stability, avoiding degradation during processing and storage
of the feed (Harper & Wolf 2009).
Crude fibre is the indigestible or difficult to digest part of feed that helps to promote gut motility
(peristalsis). Ash represents the minerals in feed, such as potassium, phosphorus, copper and zinc.
Exceeding the minerals that can be assimilated by the fish means that the extra minerals will be dissolved
in the water. This is also important in aquaponics since we can design feeds that provide excess minerals
that will end up being excreted by the fish and will therefore be available for the plants. However, it is
usually a good idea to optimize feed for fish first.
An important concept in fish nutrition is the digestible protein to digestible energy ratio, often
abbreviated as DP/DE. If the diet given to the fish is healthy and balanced, they will stop eating when they
'feel' their energy budget is reached. Energy can come from fat, carbohydrates or protein. As seen above,
the most accessible source of energy is carbohydrate, followed by fat, and lastly protein. If the diet is high
in protein compared to easily accessible energy (a high DP/DE), fish will have to eat more protein than
they need to grow. Thus, that extra protein will not turn into muscle but will be broken down and used
for other metabolic purposes, or simply wasted. On the other hand, if the DP/DE is low, then the fish will
stop eating before then have enough to grow properly, and will be debilitated (Oliva-Teles 2012).

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 Table 2: Summary of feed composition (as percentage of dry weight) for a carnivore (trout) and a herbivore
(tilapia). The remaining 10% includes ash with vitamins and minerals
Trout1 Tilapia2

Protein 50 30

Carbohydrates 17 46

Fat 15 9

Fibre 8 5
1
FAO 2018; 2Tran-Ngoc et al. 2016
In summary, Table 2 provides the general composition of a diet for adult trout (carnivore) and adult tilapia
(herbivore), the latter being the most commonly used fish in aquaponics. The amount of vitamins and
minerals is low compared to the other main components, and depends on the vitamin/mineral mix used
by the feed producer. For example, the aquaponic system at the Arizona State University that is used to
grow tilapia uses feed with 5 mg/kg of folic acid and 66 mg/kg of vitamin E in terms of vitamins, and 7
mg/kg of phosphorus and 0.5 mg/kg of magnesium in terms of minerals (see Fitzimmons 2018), among
others.
2.2.6 Types of feeds
In Europe, intensive aquaculture began at the end of the 19th century, when governments decided to
breed fish to obtain fingerlings which were used to restock lakes and rivers (Polanco & Bjorndal 2018).
Those fish represented an important source of protein for villages and communities near the river and
helped to alleviate hunger. Efforts were made to promote the most appreciated species, such as
salmonids, which are carnivorous. As production increased and fish were kept under intensive care for
longer periods, farmers began to formulate feeds. In the beginning they captured macroinvertebrates
(mostly insect larvae) in nearby water bodies, but that was seasonal and in limited supply. Later, fish were
fed using waste products from slaughterhouses, which were chopped up into small pieces and thrown in
the water directly. As a result, many salmon farms were established close to slaughterhouses.

Fish farms near ports used discarded fish from the fisheries but the supply was not always constant and
was more difficult to organize as production increased. Farmers began making a paste with discarded fish
that was blended to make fish meal, to which they sometimes added plant protein. The paste could also
be shaped into pellets, which facilitated spreading over tanks, but since it was quite humid it could not be
kept for very long periods before going bad. Around the middle of 20th century, fish nutritionists started
to develop granulated feeds. They were drier and were easier to adapt to the nutritional requirements of
each species and were much easier and cheaper to store.

Those first granulated or compound dry feeds facilitated the expansion of fish farms. Since then there has
been intense research on the most appropriate and economically profitable raw materials to use in feed
formulas. The whole process was improved by introducing the technique of extrusion, which applies high
pressure to the feed paste during short intervals, increasing the temperature, making the granule lighter
(allowing it to float in the water for longer periods) and allowing the incorporation of more fish oil. It also
improved the compactness of the granules so that they did not dissolve immediately upon contact with
water.

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More recently efforts have been made to produce feeds that are more sustainable and organic. As
mentioned above, for carnivores that means reducing the amount of fish meal in fish feed (and replacing
it with plant or insect protein) and fish oil. For vegetarian tilapia it also means reducing or eliminating any
fish meal or fish oil, while maintaining flesh quality. Recent research has focused on alternative protein
sources for many types of fish, including the use of algae or insect meal.

2.2.7 Feeding strategies

Apart from using adequate feeds, we need to ensure that the pellets provided are the right size for the
mouth of the fish. For small fish this usually means a fine powder and for larger fish a round pellet that
can be several mm in diameter. For example, Aquaponics USA suggests using powder for tilapia from
hatching to 3 weeks old, and then a fingerling crumble (1/32 inch or 0.9 mm) until they grow to about 2
cm in length, fingerling pellet (1/16 inch or 1.6 mm) until about 4 cm in length, and grow-out-pellet (3/16
inch or 4.8 mm) after about 6 cm in length.

It is also necessary to distribute the feed adequately. Normally feed is thrown onto the surface of the tank
and personnel perceive how the fish react – whether they move to the surface and begin to eat (generally
a good sign), or whether they remain on the bottom of the tank (generally a bad sign). However, in neither
case is it obvious whether they are eating properly, how much ends up in their mouths, and how much is
wasted. Due to these problems it is quite easy to overfeed.

In general, feed is distributed to the fish according to feeding tables that are prepared by the feed
producer in terms of water temperature and growth stage. But the perception of the feeder, the
personnel giving out the food, is very important since he/she can tell how hungry the fish are, and that is
related to season, daytime and health and welfare. More and more efforts are being made to automate
the process, and systems have improved considerably, but we cannot underestimate the importance of
observing the fish, which is probably the best and most direct method of understanding their current
status. While much research has been performed to optimize feeding for maximum growth, it is obvious
that if we provide less feed than they need, they will grow less, and the producer will lose money.

In order to understand the feeding, we need to define some concepts, based on Figure 6, which was
developed by Skretting, a large feed company. We need to define the concept of maximum ration, which
is the theoretically ideal ration to be given to the fish. However, it is specific to each farm since it depends
on external conditions such as water quality and temperature, as well as tank design. The main concepts
and indices used commercially include the following:
1. Feed conversion rate (FCR): this is the ratio between the amount of feed ingested (in kilograms or
grams) divided by the live weight increase (in kg or g). On a commercial level we sometimes use
an 'industrial FCR' which is an approximate figure based on all the feed provided over a period of
time divided by the tonnes of fish produced during that same period. In that case, if there was
mortality, we do not subtract the feed consumed by the fish before their death. This industrial
FCR provides an idea of the real production costs. Another similar index is the biological
conversion factor (BCF), which is the kg of feed really consumed by the fish divided by kg gained.
It is harder to calculate the BCF at an industrial level since the fish have to be handled and the
feed put down their throats, but is useful when we want to know the maximum efficiency of newly
developed feeds. FCR describes the amount of feed needed for one kg weight gain by the fish:

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 𝐹𝑜𝑜𝑑 𝑓𝑒𝑑 𝑡𝑜 𝑡ℎ𝑒 𝑓𝑖𝑠ℎ [𝑘𝑔]
𝐹𝐶𝑅 =
𝐿𝑖𝑣𝑒 𝑤𝑒𝑖𝑔ℎ𝑡 𝑔𝑎𝑖𝑛 [𝑘𝑔]
This ratio reflects the nutritional and economic value of a feed. An FCR of 1 means that you have
a live weight gain of 1 kg if you feed 1 kg of feed. The higher the FCR is, the higher your feed
expenses are. Young fishes have a lower FCR (between 0.4 – 0.8), while adult fishes have an FCR
between 0.9 – 2. The FCR depends on fish species and feed manufacturer. Sometimes you get
more economic value with high quality feed and the related better growth of the fish, in
comparison to cheaper feed with a lower FCR.

2. Specific growth rate (SGR): this represents the percentage daily growth of fish. It is specific for
each species and related to fish size and water temperature. Like the FCR it is dimensionless (no
units) and is useful for comparing data between farms or species. The SGR shows the daily average
growth of a fish in percentage of its bodyweight:
% 𝑙𝑛𝑊2 − 𝑙𝑛𝑊1
𝑆𝐺𝑅 [ ] = ( ) ∗ 100
𝑑 𝑇2 − 𝑇1
where W1 and W2 denote the weight of fish at the beginning and at the end of the growth
period, respectively, and (T2-T1) denote the duration of growth period in days.

3. The daily feed rate (DFR): the percentage of feed provided expressed as a percentage of fish
weight (% fish weight per day). Normally this percentage is higher for younger fish (around 10%)
and lower for older fish (around 1-2%).

4. Ration consumed: the ration really consumed by the fish.

5. Maintenance ration: the precise ration needed in order to maintain the fish at a constant weight
without growth.

6. Maximum ration: the ration needed in order to obtain the maximum possible growth.

In Figure 6 we can visualize the concept of the maximum ration, which provides maximum growth of the
species under culture. This maximum ration will be specific to each farm and depends on local conditions.
As we get nearer to the maximum ration, growth will increase, but if we go over the limit, we are wasting
feed. However, in general terms it is advisable to feed small fish more than the maximum ration, since
the waste will be small due to the small existing biomass, and we will tend to maximize growth. But in the
case of final growth, we tend to be more prudent, since there is a large biomass in the water, and any
extra feed that is lost will be costly and will increase the negative environmental impact, making it
necessary to clean it up.

Following Figure 6, with a small ration the fish will use all the energy for their daily activities and may even
lose weight (where the FCR will be infinite). If we increase the ration, the fish will improve their growth as
well as the FCR. At the point of maximum growth, any feed provided in excess will be an economic and
environmental problem, with no benefits for production. For that reason, we have to adjust the feed
ration to the growth of the fish to a point that is close to the maximal ration but being careful not to go
past that point.

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 Figure 6: Evolution of specific growth rate (SGR), feed conversion rate (FCR) and ration of
feed provided to the fish in terms of the percentage of feed per live-weight of the fish
per day.

The control of biological processes involved in aquaculture requires close supervision in order to
anticipate possible problems. It is important to be able to fix problems as far in advance as possible, which
implies detecting very mild symptoms at the outset. All that will help reduce production costs and improve
efficiency. As a result, the aquaculture sector understands that it needs to train personnel adequately and
continuously, especially those in charge of feeding.

Even in modern aquaculture systems such as RAS, which are increasingly computerized and automated,
personnel need to be aware of the sophisticated biological processes occurring within the unit.
Technological developments are increasing but should be accompanied by adequate training in the use
of available techniques to improve production on all levels. Those concepts are a foundation for success.
Indeed, the continuous training of personnel involved in feeding is a very important aspect of farm
operations. The supervisor of feeding determines, to a large degree, the profitability of the farm, since
he/she provides the energy for the fish to grow. Any changes in feeding habits, however small, can be a
symptom of problems in the system which, if uncorrected, can become serious sanitary problems.

2.2.8 Automatic feeders

The automation of feeding requires knowledge about the feeding habits of the species in question. We
also need to know technical details, such as the number of fish in each tank and their sizes. Manual feeding
has advantages, as mentioned above, and is still used to 'keep in touch' with the fish. Nonetheless,
technological developments can facilitate this labour. Nowadays there are many types of automatic
feeders, especially for large-scale projects with a large biomass. Here we focus on the different types of
automatic feeders used in RAS.

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Normally the feed to be distributed is dry and pelleted, and placed directly into the tank where it may
float for a time, but eventually it will tend to sink to the bottom. Most fish eat the feed on the surface or
on its way down the water column, before it reaches the floor of the tank. Many aquaculture species are
predators in the natural habitat and show aggressive behaviour when eating, which can lead to problems.
Most modern automatic feeders take this fact into consideration, since poor feeding with inadequate
feeders can lead to populations with dominant individuals who eat in excess, while the more submissive
individuals go without. The immediate consequence is a higher variety of sizes in the tank, which makes
it necessary to classify it more often, in order to break the social hierarchy and increase feed efficiency.
Automatic feeders can be divided into two large groups, related to the biomass of fish and the quantity
of feed to be distributed:
1. Feeders for juveniles: these distribute small rations at a high frequency (10-60 times a day). The
pellet is very small, and feed can be stored directly on the feeder and refilled by hand.
2. Feeders for on-growing: these distribute large quantities of feed at a relatively low frequency (3-
30 times a day). Pellets are large and feeders are refilled by hand or automatically.

The cost of manually feeding fish is quite high in terms of time dedication needed to distribute it. The
following company web sites provide details of feeder designs available for different species and
aquaculture farms (http://www.acuitec.es, www.akvagroup.com; www.aquacultur.de). The basic parts of
on-growing feeders are:
1. Storage or deposits for different types of pellets which originate from feed bags or silos delivered
by truck.
2. Distribution of feed from the deposit onto the distribution site at the tank. Tubing runs from the
storage site to the automatic feeder, which in turn has a small deposit. At this stage pellets are
moved using mechanical systems or compressors and air injection. This equipment is quite
specialized to ensure correct supply and adequate hygiene. Examples of the degree of
sophistication of the feeding systems used in intensive aquaculture can be found at AKVA group.
Some companies also use feeding robots for fingerlings in RAS, which is an automated way to fill
up deposits near the tank. The robots move throughout the building using guides or rails that
hang from the ceiling (see for example Crystalvision).
3. Distribution site
This is the final part of the automatic feeding system. Here the feed is spread out on the surface
of the tank all at the same time, thereby allowing all the fish to feed simultaneously, which is
better than placing the pellets in one small location. Thus, the distribution site is important for
keeping the tank population homogeneous.
4. Monitoring the consumed feed
Recent technological developments allow one to detect when fish stop eating, which sends a
signal to the automatic feeders to stop providing feed. These systems work with subaquatic
cameras or acoustic and laser detectors, which let the feeder know when the appetite of the fish
is waning.

2.2.9 Production plan and monitoring the evolution of the farm

All aquaponic farms need well defined production goals and a plan to fulfil those goals. Specifically, it is
helpful to define the following aspects well in advance:
1. The species to be used

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 2. The size of fingerlings needed initially and the target size of the adults to be sold at the end. This
will help to define the productive cycles on the farm (types of tanks, etc.)
3. The growth curve of the fish species to be able to keep a growth log so that the fish can be fed
adequately and the growth targets can be checked and achieved.
4. The optimal densities and housing conditions for each stage of growth. This will help to define the
maximum load of live biomass in the installation, and annual production
5. The health management to be used to maintain optimal conditions for the fish
6. The level of training of the personnel involved

The welfare of the fish and the economic viability of the installation will depend on compliance with the
objectives that are budgeted in the project. We need to know whether fish are reaching their expected
growth and transforming feed adequately, and whether mortality is higher than expected. We should
know the expected growth curve in relation to the water temperature. That, along with the duration of
the production system, will help to design a production plan that will be the basis for the operating costs.
Once production has begun, it should be monitored adequately.

There should be clear traceability back to the source of the fish. We need to know the number of fish and
their initial size on the first day that they were housed. Daily we register each of the production activities
that were carried out, such as the daily source of feed, the cleaning mode, and measures of physical and
chemical parameters. In Figure 7 we present an example of the control sheet. These data are collected
daily for each of the tanks and should be stored in the monthly report and processed in order to be able
to determine the evolution of farm production. Regularly we should weigh a sample of fish to estimate
growth in each tank. We should capture enough fish to represent the tank, normally at least 10-15
individuals per 100 fish. Feeding is then adjusted periodically according to that average fish weight.

Figure 7: Data sheet to note details about the tanks and the fish on a daily basis

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2.2.10 Designing feeds for aquaponics
Fish feeds for aquaponics can be home-made or bought from specialized feed companies that formulate
specific diets depending on the species and age of the fish. Normally commercial producers use
specialized feeds since they are guaranteed to meet all the nutritional needs of the fish, and tend to be
more cost effective compared to making and formulating one’s own feed. However, formulated feeds are
not always perfect and may have varying effects on the quality of the water where fish live and excrete
waste. Only recently have scientists and engineers begun to look at specific diets for fish in recirculation
systems and in aquaponic units. Theoretically, it seems possible to provide fish with pelleted feed, which
will help them to grow quickly, while providing enough nutrients for the plants that will later 'feed' on this
water. In practice, however, things are more difficult, and depend on many complex parameters such as
the temperature and pH of the recycled water, as well as microbiota in fish intestines and in biofilters. An
aquaponics practitioner should know the basics of feed composition in order to have some way to judge
which feed would be best to start off with. Although it may not be necessary to design feeds from scratch,
one should be able to choose the best feed for this system after reading the following sections.

Fish growth and nitrogen retention

The nitrogen that will eventually be eliminated as ammonia by the fish originates from the protein in the
feed. Although there is some nitrogen in other components of feed, almost all nitrogen absorbed by fish
and eliminated as waste is from amino acids, which are the building blocks of proteins.

If we know the percentage of nitrogen in the feed, we can then calculate the approximate amount that
will be excreted as ammonia into the water. That ammonia will later be turned into nitrate which will be
provided to the plants. It should be noted here, however, that fish do not really urinate but, as opposed
to most mammals, they eliminate nitrogenous waste through their branchia (similar to our lungs). In the
following sections we will follow the source and fate of nitrogen in an aquaponic system, based on
Seawright et al. (1998), who were one of the first groups to publish studies on nutrient cycling in
aquaponic systems. In their paper they provide an equation for calculating the nitrogen balance in the
system, which we will use as a guide. After calculating the nitrogen present in the feed, we calculate how
much is retained in the fish, lost as uneaten feed, and lost in faeces, to end up with the concentration of
ammonia in the surrounding water.

Nitrogen source
Feed is the main nitrogen source in our aquaponic system. In order to calculate the total amount of
nitrogen placed into the tank via the feed we first need to know the exact amount of feed used, in grams
or kilograms. Next, we need to know the percentage of protein in the feed. This is normally shown on the
feed label or available from the feed producer. As mentioned in previous sections, fish feeds have high
proportions of protein, normally between 25% and 50%. Once we know the protein percentage, we can
calculate the percentage of nitrogen by multiplying it by 0.16. We use that number since nutritionists
assume that approximately 16% of all protein is nitrogen. Thus, for a feed for tilapia with 35% protein we
know it has 35% * 16% = 5.6% nitrogen. If we added, for example, 120 grams of feed to the tank in one
day, we are adding 120 g * 5.6% = 6.72 g of nitrogen.

Nitrogen absorption by the fish

The fish will absorb nitrogen into its protein deposits, which is mostly its muscle. However, most of the
fish body weight is water, so that weight has to be discounted since the nitrogen is only present in what

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can be called the 'dry weight of the muscle'. Generally, and based on results in our lab and findings from
the literature (e.g., Seawright et al. 1998), the dry weight of tilapia is about 27% of its body weight or, put
another way, 73% of tilapia muscle is water.

Next, we need to know the feed conversion rate (FCR). The FCR is the ratio between the feed provided
divided by the weight gained (see section 2.2.6). The inverse of the FCR is called the feed efficiency, or the
weight gain divided by the feed ingested (1/FCR). That is, for a FCR of 1.5, the feed efficiency is 1/1.5 =
66.73%.

Of course, it would be better to have a high feed efficiency: the higher it is, the more economically
advantageous it is. However, fish have a maximum limit for how much muscle they can accrue over time.
As muscle grows, the amount of protein will grow (as well as the amount of total nitrogen in the muscle),
but the proportion of protein in the muscle will remain more or less stable. The total percentage of
nitrogen with respect to body weight is around 8.8% in tilapia. This may vary among species, but is a good
approximate number.

So, depending on the feed provided, we can estimate how much nitrogen will be retained in the fish. If
we provide 120 g of feed using the values suggested above, then the nitrogen retained in fish will be found
by multiplying the feed by the dry weight, by the feed efficiency and by the percentage of nitrogen in fish
muscle, i.e., 120g * 27% * 66.73% * 8.8% = 1.90 grams of nitrogen from the feed will stay in the fish.

Nitrogen lost in solids

Apart from being lost as urine, nitrogen waste can be lost via faeces. We can measure the protein or
nitrogen content of faeces since it accumulates in the solids filter of our system, or we can siphon it up
daily and store it. The solid waste could also contain feed that was not ingested but, as mentioned above,
it is difficult to measure exactly how much feed was not consumed by the fish, so we lump together faeces
and feed not consumed as solid waste. Before analysis, the solid waste is dried to calculate the dry weight,
and then the nitrogen content is measured. In a RAS system the total amount of solids is around 10%, i.e.,
10% of the feed provided to the fish ends up as solid waste (including fish faeces and pellets that are not
ingested). When analysed we found that the nitrogen content of the faeces was 4.8%.

Finally, to calculate the total grams of nitrogen lost in solids per the amount of feed we provide to the
tank, we need to multiply the amount of feed (120 g) by the percentage of feed that is lost in solids (faeces
and feed not eaten), and the percentage of nitrogen in the solids (4.8%). Say that the percentage of feed
lost in solids is 10%, the nitrogen lost in solids in that case would be: 120g * 10% * 4.8% = 0.576 g of
nitrogen in the feed is lost as solids. Again, this is only an example, and that percentage can vary depending
on the system and other conditions.

Nitrogen dissolved in water as total ammonia nitrogen (TAN)

Next, we can use the above calculations to quantify the nitrogen dissolved in the water, which is
essentially lost as ammonia waste. This means: Nitrogen excreted (dissolved) as TAN exctreted = Nitrogen
in Feed – Nitrogen incorporated in fish – Nitrogen in feaces.
In the case above, 6.72 – (1.90 + 0.576) = 4.24 g NH3-N. That is, 63.1% (4.24/6.72) of the nitrogen from
the feed is converted into NH3-N. It is excreted by the branchia as NH3-N but, depending on the water pH,
it is converted into NH4-N. The term TAN denotes total ammonia nitrogen, or the combination of NH3-N+
NH4-N.

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2.3 Fish welfare
2.3.1 Introduction
Aquaculture is one of the few types of animal farming that has grown continuously over recent decades,
by about 10% annually on an international level (Moffitt & Cajas-Cano 2014). However, as production
increases and new technologies, such as aquaponics, appear, we have been witness to more problems
related with fish health and welfare. Although it may seem surprising, more than 1300 scientific articles
have been published on fish welfare since 1990 (see Table 2). Not all those studies deal with commercially
produced species, but in general the number for all fish is comparable to or higher than some other
species like sheep, horses or poultry.

Table 2: Summary of publications on animal welfare for different species of

farm animals (based on a search in the Web of Science for the years 1990-2017).

Species Papers
Fish 1295
Trout 550
Sheep 1149
Cattle 2417
Pig 2638
Horse 926
Poultry 1078

One of the first scientific reviews of fish welfare was by Conte (2004) from the University of California at
Davis, followed a few years later by two groups from the United Kingdom (Huntingford et al. 2006 and
Ashley 2007). In his review, Conte (2004) underlines that fish farmers already know that welfare is
important and that stress must be minimized since fish have specific requirements in terms of handling
and environment outside of which they will not thrive or survive. Compared to terrestrial animals, fish are
more demanding in terms of growing conditions and can be stressed easily, so much so that they can also
die easily. Huntingford et al. (2006) summarize the main arguments for believing that fish can feel pain.
Fish are complex beings that develop sophisticated behaviour, so the authors believe they can probably
suffer, although it may be different in degree and type than for humans. That review ends up identifying
four main critical areas when considering fish welfare: assuring that fish are not kept without water or
food; assuring that producers provide good water quality and equipment; that their movements or
behaviour are not restricted; and that mental and physical suffering be avoided. In his review, Ashley
(2007) starts with a description of the industry and the critical points that may compromise fish welfare,
including fish density in cages and problems with aggression. For example, some species, like tilapia, are
more aggressive when kept at low densities than at higher densities. Importantly, Ashley (2007) provides
a table of the main welfare problems in fish which is seven pages long. In conclusion, there is a lot of
scientific literature about fish welfare and several critical areas have been identified. However, regarding
aquaponics, there are very few studies about the welfare of fish bred together with plants, but we can
learn from other studies about the welfare of fish kept in small-scale recirculation systems.

2.3.2 Legislation in the EU

In Europe, any animal kept for the purpose of farming must comply with Directive 98/58/EC, which is a
law that sets down several minimum conditions for adequate animal welfare for vertebrates. Although

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fish are technically included in that Directive, they are practically exempt due to our lack of knowledge
about fish welfare, so there are no specific requirements for minimum conditions for fish used in
aquaculture. Since 2006, several reports have been published in Europe, for example by the European
Council of the European Food Safety Authority (EFSA), which give scientific recommendations for the most
common species used in aquaculture. Overall, at least in Europe, there seems to be general agreement
that fish undergo stress when oxygen levels are low and when they are taken out of water, and that
chronic stress in fish compromises the immune system and can make them more vulnerable to disease.

2.3.3 Specific measures to evaluate welfare

Studies on fish welfare began later than for other farm animal species, in part because aquaculture is a
younger animal production science and also since it was unclear whether fish can feel pain. Until recently,
fish were not considered to be sentient animals, but that situation has been changing. Sneddon (2003)
was one of the first to prove that trout have pain receptors (nociceptors) on their face and jaw. She proved
that those receptors respond to stimuli which are potentially damaging and send nervous signals to the
spinal cord and brain. In addition, it appears that trout are aware of pain since they change complex
behaviour when given a noxious substance, but revert to normal behaviour when given morphine (which
essentially eliminates the pain). Those findings have also been confirmed in other species such as goldfish,
where anxiety and fear decrease when they are given doses of morphine (Nordgreen et al. 2009). On the
other hand, other scientists like Rose (2002) argue that fish cannot feel pain like humans since they lack a
neocortex. Thus, they are probably not conscious about their pain in the same way as we are, although
they react to pain in a similar manner. Whatever the case may be, both sides agree that fish can be
stressed and that they have evolved a complex physiological response to stressors. Dawkins also makes
the important point that everyone should worry about animal welfare whether or not they are conscious,
simply because poor animal welfare leads to diseased and unhealthy fish, which has negative effects on
farmers and consumers (Dawkins 2017).

2.3.4 The HPI axis and the stress response

When fish are subjected to stress the so-called stress axis or HPI-axis is activated (hypothalamo-pituitary-
interrenal axis, Sumpter et al. 1991). This cascade of physiological processes that follow a stressful
stimulus are categorised into three consequitive parts. First, the stressor is perceived as such in the brain
initiating the 'primary response'. Within seconds (neuronal response) and minutes (endocrine response)
the brain, the pituitary and the interrenal gland react to the stress. The hypothalamus produces
corticotropin releasing hormone (CRH) which stimulates the production of adrenocorticotropic hormone
(ACTH) by the pituitary, also called the adenohypophysis. ACTH is released into the blood stream and
simulates the production of cortisol by the interrenal gland (also associated with the kidneys in fish), which
corresponds with the adrenal cortex in mammals (Okawara et al. 1992). These substances trigger the
'secondary response' which includes amongst others an increase in heart rate, oxygen uptake and in
glucose concentration in plasma via glucogenolysis (Pickering & Pottinger 1995). Both the primary and
secondary response systems help to restore homeostasis after a stress by providing energy and oxygen
to the body to adjust and return to normal or basal metabolic function, usually within hours.
If the stressful stimulus persists, the stress axis stays activated and cannot restore a normal level. A
chronically activated HPI axis leads to a 'tertiary response' where, due to the long-term stress, the function
of the immune system gets impaired, the growth is reduced, the behaviour altered, and reproduction
compromised.

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Although there is no simple relationship between stress and welfare, low stress levels are correlatied with
good welfare. Unstressed fish are assumed to experience good welfare and with this are more robust
towards diseases, have lower background mortality rates and a better growth.

Figure 8: The HPI axis in fish and the cascade of responses after a stressor (source: Schreck & Tort 2016) (CRH =
corticotropin releasing hormone, ACTH = adrenocorticotropic hormone).

2.3.5 Operational welfare indicators

On an industrial level, a new approach is being developed to analyse fish that involves interactions
between scientists studying animal welfare and companies that strive to be more efficient. Together they
are developing operational welfare indicators (OWI). A good example are the manuals presented by the
Nofima (for salmon Noble et al. (2018) and trout Noble et al. (2020) that instruct farmers how to evaluate
on a commercial level the immediate environment, different groups of fish, and individual fish. As
mentioned above, many scientific articles have been published on fish welfare, most of which are based
on observations made in the lab. OWIs are practical indicators that are used on the farm and can be easily
explained and repeated. OWIs can be separated into two large groups: those more related to the
environment; and those related to the fish. The latter can be applied to groups of fish, or individually.
Finally, indicators can include laboratory analyses which are less operational per se but can provide useful
information in the short term (see Figure 9). OWIs can provide an idea of the current status of production
in terms of the needs of the fish and their welfare. In parallel, they can be used to help develop good
practice and to identify critical points that can have a negative effect.

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 Figure 9: Summary of the operational indicators (source: Noble et al. 2018) used on fish
farms, including indicators that vary with the environment and the animal. The animal-
based indicators can be based on groups of fish or on individuals, and individual indicators
can include laboratory analyses.

One of the most relevant indicators for stress and welfare is the behaviour of the fish. First and foremost,
this includes the swimming and feeding behaviour. The former should be calm and continuous, ideally the
fish should swim in a shoal well distributed over the whole tank. The latter should be enthusiastic but not
aggressive. Although there is plenty of equipment that can be purchased to feed fish automatically, it is
recommended to feed fish at least once a day by hand in order to get an idea about how they are doing.
Another operational indicator that is common in fish farms is the coefficient of condition in live weight
(the live weight in grams divided by the standard length cm3). It indicates nutritional status (Bavčević et
al. 2010), proportion of fat storages and growth performance.

2.3.6 Tools to use on-site

A different approach was published by our research group (Tschirren et al. 2021), where the focus was on
the development of a digital tool that is applicable by the fish farmers on-site. To assist this we first
developed a model to assess fish welfare. A network of information was created to link needs, i.e.,
fundamental requirements for welfare, with parameters, i.e., quantifiable aspects of welfare. From this
so-called ontology, 80 parameters that are relevant for welfare, have practicable assessment methods
and deliver reliable results were selected and incorporated into a model. The model, named MyFishCheck,
allows the evaluation of welfare in five distinct modules: farm management, water quality, fish group
behaviour, fish external and fish internal appearance, thereby yielding five individual grades categorising
welfare ranging from critical, to poor, to acceptable, and good. To facilitate the use of the model, a
software application was written. With its adaptability to different fish species, farming systems,
regulations and purposes as well as its user-friendly digital version, MyFishCheck is a next step towards
improved fish welfare assessment and provides a basis for ongoing positive developments for the
industry, the farmers and the fish.

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 1. Ontology
Creation of a fish welfare ontology with needs (black) and
parameters (grey and white) to store, manage and handle
the information.

2. Modules
Selection of welfare parameters that are relevant, reliable
M W FG FE FI and applicable (grey).
18 × 18 × 20 × 18 × 10 × Definition of the five modules of the model with their
respective parameters.

3. Intervals and weights

Parameter Parameter intervals PS SW PW Literature review for the 80 welfare parameters to define
Optimum: … 0 1 the intervals (details in supplementary Table S2).
Allocation of the parameter scores (PS) and the score
Oxygen Within target range: … - 0.33 2.33
weights (SW) according to the number of intervals.
5
saturation Within tolerance range: … - 0.66 3.66 Expert survey for the 80 welfare parameters to define their
Outside the tolerance range: … -1 5 relative importance resulting in the parameter weights
(PW) (details in Appendix B).

4. Equation
𝑆 𝑆𝑊 𝑊 Summation of the scores of the used parameters within
𝐺 = 1 each module. After a normalisation, a transformation and
𝑆𝑊 𝑊
an offset the equation delivers a module grade (MG) that
assesses fish welfare in the given module.

5. Applications
Development of a Microsoft Excel version and a software
application (Android app) to facilitate the use of the
model.

Figure 9: Flow chart of the MyFishCheck model development process by Tschirren et al. 2021.

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