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Basic plant biology

3 months ago

12 min read

This section comments briefly on the major parts of the plant and then discusses plant nutrition (Figure 6.3). Further discussion is outside the scope of this publication, but more information can be found in the section on Further Reading.

Basic plant anatomy and function


Roots absorb water and minerals from the soil. Tiny root hairs stick out of the root, helping the absorption process. Roots help to anchor the plant in the soil, preventing it from falling over. Roots also store extra food for future use. Roots in soil-less culture show interesting differences from standard in-ground plants. In soil-less culture, water and nutrients are constantly supplied to the plants, which are facilitated in their nutrient search and can grow faster. Root growth in hydroponics can be significant for the intense uptake and the optimal delivery of phosphorus that stimulates their growth. It is worth noting that roots retain almost 90 percent of the metals absorbed by the plants, which include iron, zinc and other useful micronutrients.


Stems are the main support structure of the plant. They also act as the plant's plumbing system, conducting water and nutrients from the roots to other parts of the plant, while also transporting food from the leaves to other areas. Stems can be herbaceous, like the bendable stem of a daisy, or woody, like the trunk of an oak tree.


Most of the food in a plant is produced in the leaves. Leaves are designed to capture sunlight, which the plant then uses to make food through a process called photosynthesis. Leaves are also important for the transpiration of water.


Flowers are the reproductive part of most plants. Flowers contain pollen and tiny eggs called ovules. After pollination of the flower and fertilization of the ovule, the ovule develops into a fruit. In soil-less techniques, the prompt delivery of potassium before flowering can help plants to have better fruit settings.


Fruits are developed parts of flower ovaries that contain seeds. Fruits include apples, lemons, and pomegranates, but also include tomatoes, eggplants, corn kernels and cucumbers. The latter are considered fruits in a botanical sense because they contain seeds, though in a culinary definition they are often referred to as vegetables. Seeds are the reproductive structures of plants, and fruits serve to help disseminate these seeds. Fruiting plants have different nutrient requirements than leafy green vegetables, especially requiring more potassium and phosphorous.


All green plants are designed to generate their own food using the process of photosynthesis (Figure 6.4). Photosynthesis requires oxygen, carbon dioxide, water and light. Within the plant are small organelles called chloroplasts that contain chlorophyll, an enzyme that uses the energy from sunlight to break apart atmospheric carbon dioxide (CO2) and create high-energy sugar molecules such as glucose. Essential to this process is water (H2O). This process releases oxygen (O2), and is historically responsible for all of the oxygen in the atmosphere. Once created, the sugar molecules are transported throughout the plant and used later for all of the physiological processes such as growth, reproduction and metabolism. At night, plants use these same sugars, as well as oxygen, to generate the energy needed for growth. This process is called respiration.

It is vital to locate an aquaponic unit in a place where each plant will have access to sunlight. This ensures adequate energy for photosynthesis. Water should always be available to the roots through the system. Carbon dioxide is freely available from the atmosphere, although in very intensive indoor culture it is possible that plants use all of the carbon dioxide in the enclosed area and require ventilation.

Nutrient requirements

In addition to these basic requirements for photosynthesis, plants need a number of nutrients, also referred to as inorganic salts. These nutrients are required for the enzymes that facilitate photosynthesis, for growth and reproduction. These nutrients can be sourced from the soil. However, in the absence of soil, these nutrients need to be supplied another way. In aquaponics, all of these essential nutrients come from the fish waste.

There are two major categories of nutrients: macronutrients and micronutrients. Both types of nutrient are essential for plants, but in differing amounts. Much larger quantities of the six macronutrients are needed compared with the micronutrients, which are only needed in trace amounts. Although all of these nutrients exist in solid fish waste, some nutrients may be limited in quantity in aquaponics and result in deficiencies, e.g. potassium, calcium and iron. A basic understanding of the function of each nutrient is important to appreciate how they affect plant growth. If nutrient deficiencies occur, it is important to identify which element is absent or lacking in the system and adjust the system accordingly by adding supplemental fertilizer or increasing mineralization.


There are six nutrients that plants need in relatively large amounts. These nutrients are nitrogen, phosphorous, potassium, calcium, magnesium and sulphur. The following discussion outlines the function of these macronutrients within the plant. Symptoms of deficiencies are also listed in order to help identify problems.

Nitrogen (N) is the basis of all proteins. It is essential for building structures, photosynthesis, cell growth, metabolic processes and the production of chlorophyll. As such, nitrogen is the most common element in a plant after carbon and oxygen, both of which are obtained from the air. Nitrogen is therefore the key element in the aquaponic nutrient solution and serves as an easy-to-measure proxy indicator for other nutrients. Usually, dissolved nitrogen is in the form of nitrate, but plants can utilize moderate quantities of ammonia and even free amino acids to enable their growth. Nitrogen deficiencies are obvious, and include yellowing of older leaves, thin stems, and poor vigour (Figure 6.5a). Nitrogen can be reallocated within plant tissues and therefore is mobilized from older leaves and delivered to new growth, which is why deficiencies are seen in older growth. An overabundance of nitrogen can cause excess vegetative growth, resulting in lush, soft plants susceptible to disease and insect damage, as well as causing difficulties in flower and fruit set.

Phosphorus (P) is used by plants as the backbone of DNA (deoxyribonucleic acid), as a structural component of phospholipid membranes, and as adenosine triphosphate (the component to store energy in the cells). It is essential for photosynthesis, as well as the formation of oils and sugars. It encourages germination and root development in seedlings. Phosphorous deficiencies commonly cause poor root development because energy cannot be properly transported through the plant; older leaves appear dull green or even purplish brown, and leaf tips appear burnt.

Potassium (K) is used for cell signalling via controlled ion flow through membranes. Potassium also controls stomatic opening, and is involved in flower and fruit set. It is involved in the production and transportation of sugars, water uptake, disease resistance and the ripening of fruits. Potassium deficiency manifests as burned spots on older leaves and poor plant vigour and turgor (Figure 6.5b). Without potassium, flowers and fruits will not develop correctly. Interveinal chlorosis, or yellowing between the veins of the leaves, may be seen on the margins.

Calcium (Ca) is used as a structural component of both cell walls and cell membranes. It is involved in strengthening stems, and contributes to root development. Deficiencies are common in hydroponics and are always apparent in the newest growth because calcium is immobile within the plant. Tip burn of lettuces and blossom-end rot of tomatoes and zucchinis are examples of deficiency. Often, new leaves are distorted with hooked tips and irregular shapes. Calcium can only be transported through active xylem transpiration, so when conditions are too humid, calcium can be available but locked-out because the plants are not transpiring. Increasing air flow with vents or fans can prevent this problem. The addition of coral sand or calcium carbonate can be used to supplement calcium in aquaponics with the added benefit of buffering pH.

Magnesium (Mg) is the centre electron acceptor in chlorophyll molecules and is a key element in photosynthesis. Deficiencies can be seen as yellowing of leaves between the veins especially in older parts of the plant. Although the concentration of magnesium is sometimes low in aquaponics, it does not appear to be a limiting nutrient, and addition of magnesium to the system is generally unnecessary.

Sulphur (S) is essential to the production of some proteins, including chlorophyll and other photosynthetic enzymes. The amino acids methionine and cysteine both contain sulphur, which contributes to some proteins' tertiary structure. Deficiencies are rare, but include general yellowing of the entire foliage in new growth (Figure 6.5c). Leaves may become yellow, stiff and brittle, and fall off.


Below is a list of nutrients that are only needed in trace amounts. Most micronutrient deficiencies involve yellowing of the leaves (such as iron, manganese, molybdenum and zinc). However, copper deficiencies cause leaves to darken their green colour.

Iron (Fe) is used in chloroplasts and the electron transport chain, and is critical for proper photosynthesis. Deficiencies are seen as intervenous yellowing, followed by the entire foliage turning pale yellow (chlorotic) and eventually white with necrotic patches and distorted leaf margins. As iron is a non-movable element, iron deficiencies (Figure 6.5d) are easily identified if new leaves appear chlorotic. Iron has to be added as chelated iron, otherwise known as sequestered iron or FeIEDTA, because iron is apt to precipitate at pH greater than 7. The suggested addition is 5 millilitres per 1 m2 of grow bed whenever deficiencies are suspected; a larger quantity does not harm the system, but can cause discolouration of tanks and pipes. It has been suggested that submerged magnetic-drive pumps can sequester iron and is the subject of current research.

Manganese (Mg) is used to catalyse the splitting of water during photosynthesis, and as such, manganese is important to the entire photosynthesis system. Deficiencies manifest as reduced growth rates, a dull grey appearance and intervenous yellowing between veins that remain green, followed by necrosis. Symptoms are similar to iron deficiencies and include chlorosis. Manganese uptake is very poor at pH greater than 8.

Boron (B) is used as a sort of molecular catalyst, especially involved in structural polysaccharides and glycoproteins, carbohydrate transport, and regulation of some metabolic pathways in plants. It is also involved in reproduction and water uptake by cells. Deficiencies may be seen as incomplete bud development and flower set, growth interruption and tip necrosis, and stem and root necrosis.

Zinc (Zn) is used by enzymes and also in chlorophyll, affecting overall plant size, growth and maturation. Deficiencies may be noticed as poor vigour, stunted growth with reduced inter-nodal length and leaf size, and intravenous chlorosis that may be confused with other deficiencies.

Copper (Cu) is used by some enzymes, especially in reproduction. It also helps strengthen stems. Deficiencies may include chlorosis and brown or orange leaf tips, reduced growth of fruits, and necrosis. Sometimes, copper deficiency shows as abnormally dark green growth.

Molybdenum (Mo) is used by plants to catalyse redox reactions with different forms of nitrogen. Without sufficient molybdenum, plants can show symptoms of nitrogen deficiency although nitrogen is present. Molybdenum is biologically unavailable at pH less than 5.


The availability of many of these nutrients depends on the pH (see Section 6.4 for pH-dependent availability), and although the nutrients may be present they may be unusable because of the water quality. For further details on nutrient deficiencies outside the scope of this publication, please refer to the section on Further Reading for illustrated identification guides.

Aquaponic sources of nutrients

Nitrogen is supplied to aquaponic plants mainly in the form of nitrate, converted from the ammonia of fish waste through bacterial nitrification. Some of the other nutrients are dissolved in the water from the fish waste, but most remain in a solid state that is unavailable to plants. The solid fish waste is broken down by heterotrophic bacteria; this action releases the essential nutrients into the water. The best way to ensure that plants do not suffer from deficiencies is to maintain the optimum water pH (6-7) and feed the fish a balanced and complete diet, and use the feed rate ratio to balance the amount of fish feed to plants. However, over time, even an aquaponic system that is perfectly balanced may become deficient in certain nutrients, most often iron potassium or calcium.

Deficiencies in these nutrients are a result of the composition of the fish feed. Fish feed pellets (discussed in Chapter 7) are a complete food for the fish, meaning they provide everything that a fish needs to grow, but not necessarily everything needed for plant growth. Fish simply do not need the same amounts of iron, potassium and calcium that plants require. As such, deficiencies in these nutrients may occur. This can be problematic for plant production, yet there are solutions available to ensure appropriate amounts of these three elements.

In general, iron is regularly added as chelated iron in the aquaponic system to reach concentrations of about 2 mg/litre. Calcium and potassium are added when buffering the water to the correct the pH, as nitrification is an acidifying process. These are added as calcium hydroxide or potassium hydroxide, or as calcium carbonate and potassium carbonate (see Chapter 3 for more details). The choice of the buffer can be chosen based on the plant type being cultivated, as leafy vegetables may need more calcium, and fruiting plants more potassium. In addition, Chapter 9 discusses how to produce simple organic fertilizers from compost to use as supplements to the fish waste, ensuring that the plants are always receiving the right amount of nutrients.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, Reproduced with permission.

Food and Agriculture Organization of the United Nations