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Plant anatomy

Plant anatomy describes the structure and organization of the cells, tissues and organs of plants in relation to their development and function. Flowering plants are composed of three vegetative organs: (i) roots, which function mainly to provide anchorage, water, and nutrients, and to store sugars and starch; (ii) stems, which provide support; and (iii) leaves, which produce organic substances via photosynthesis. The roots grow down in response to gravity. In general, a seedling produces a primary root that grows straight down and gives rise to secondary lateral roots. These may produce tertiary roots, which in turn may branch, with the process continuing almost indefinitely. Growth occurs at the root tip or apex, which is protected by a root cap. Roots grow and branch continually, in their search for minerals and water. The efficiency of the root as an absorbing organ depends on its absorptive surface area relative to its volume, which is created by the root hairs and the complex system of branches.

Figure 7 illustrates the basic anatomy of a plant. The hypocotyl is the portion of the stem which at its base links with the root. At the other end of the stem is the terminal bud, or apical bud, which is the growing point. The stem is normally divided into nodes and internodes. The nodes hold one or more leaves, which are attached to the stem by petioles, as well as buds which can grow into branches with leaves or flowers. The internodes distance one node from another. The stem and its branches allow leaves to be arranged to maximize exposure to sunlight, and flowers to be arranged to best attract pollinators. Branching arises from the activity of apical and axillary buds. Apical dominance occurs when the shoot apex inhibits the growth of lateral buds so that the plant may grow vertically. The shoots, which bear the leaves, flowers and fruit, grow towards a light source. The leaves usually contain pigments and are the sites of photosynthesis (see The leaves also contain stomata, pores through which water exits and through which gas exchange occurs (carbon dioxide in and oxygen out).


Figure 7: The anatomy of a plant

  1. The Shoot System. 2. The Root System. 3. Hypocotyl. 4. Terminal Bud. 5. Leaf Blade. 6. The Internode. 7. Axillary Bud. 8. Node. 9. Stem. 10. Petiole. 11. Tap Root. 12. Root Hairs. 13. Root Tip. 14. Root Cap\_anatomy\#/media/File:Plant\_Anatomy.svg

Plant physiology

Plant physiology is a vast subject, covering fundamental processes such as photosynthesis, respiration, plant nutrition, plant hormone functions, tropisms, photoperiodism, photomorphogenesis, circadian rhythms, environmental stress physiology, seed germination, dormancy, stomata function, and transpiration. Here we will focus on the most important physiological processes and how they are affected by growing conditions.


All green plants generate their own food using photosynthesis. Photosynthesis is the process by which plants are able to use light to produce energy and carbohydrates through the fixation of CO2:

$ 6 𝐶𝑂2 + 6 𝐻2𝑂 → 𝐶6𝐻{12}𝑂6 + 6 𝑂2$

Although photosynthesis occurs in all green parts of a plant, the main site for this process is the leaf. Small organelles called chloroplasts contain chlorophyll, a pigment that uses energy from sunlight to create high-energy sugar molecules such as glucose. Once created, the sugar molecules are transported throughout the plant where they are used for all the physiological processes such as growth, reproduction, and metabolism. Photosynthesis requires light, carbon dioxide, and water.


The process of respiration in plants involves using the sugars produced during photosynthesis plus oxygen to produce energy for plant growth:

$ 𝐶6𝐻-{12}𝑂6 + 6 𝑂2 → 6 𝐶𝑂2 + 6 𝐻_2𝑂 + 𝑒𝑛𝑒𝑟𝑔𝑦$

While photosynthesis takes place in the leaves and stems only, respiration occurs in all parts of the plant. Plants obtain oxygen from the air through the stomata, and respiration takes place in the mitochondria of the cell in the presence of oxygen. Plant respiration occurs 24 hours per day, but night respiration is more evident since the photosynthesis process ceases. During the night, it is very important that the temperature is cooler than during the day because this reduces the rate of respiration, and thus allows plants to accumulate glucose and synthesise other substances from it that are needed for the growth of the plant. High night temperatures cause high respiration rates, which could result in flower damage and poor plant growth.

Osmosis and plasmolysis

Osmosis is the process by which water enters the plant’s roots and moves to its leaves (Figure 8). In most soils, small quantities of salts are dissolved in large quantities of water. Conversely, the plant cells contain lesser amounts of water in which salts, sugars and other substances are concentrated. During osmosis, water molecules attempt to equalize their concentration on both sides of cell membranes. Thus, when water moves from the soil, where it is most abundant, it ‘seeks’ to dilute the solution in the cells. Water entering a cell is stored in a large, central vacuole. When a cell becomes turgid (fully inflated) the rate of water uptake is slowed. Cell turgor gives firmness to water-filled tissues. The difference between crisp and wilted lettuce leaves illustrates the nature of turgid and non-turgid (flaccid) cells. Most plant species wilt in soils where significant quantities of salts have accumulated, even when adequate water is present. Such saline soils have a lower water content than the root cells, so the roots lose water as the direction of osmotic flow is reversed. This process is called plasmolysis. A cell starts to shrink without adequate internal water. After prolonged water loss, the cell begins to collapse without any internal water for support. Complete cellular collapse is rarely reversible. When the cells start to collapse from water loss, the plant is usually doomed because its cells die.


Figure 8: Turgor pressure on plant cells


Transpiration is the loss of water from a plant in the form of water vapour. This water is replaced by additional absorption of water through the roots, leading to a continuous column of water inside the plant. The process of transpiration provides the plant with evaporative cooling, nutrients, carbon dioxide entry, and water to provide plant structure. When a plant is transpiring, its stomata are open, allowing gas exchange between the atmosphere and the leaf. Open stomata allow water vapour to leave the leaf but also allow carbon dioxide (CO2), which is needed for photosynthesis, to enter. Temperature greatly influences transpiration rate. As air temperature increases, the water holding capacity of that air increases sharply. Warmer air will therefore increase the driving force for transpiration, while cooler air will decrease it.


Phototropism is a directional response that allows plants to grow towards, or in some cases away from, a source of light. Positive phototropism is growth towards a light source; negative phototropism is growth away from light. Shoots, or above-ground parts of plants, generally display positive phototropism. This response helps the green parts of the plant to get closer to a source of light energy, which can then be used for photosynthesis. Roots, on the other hand, will tend to grow away from light. The hormone controlling phototropism is auxin. Its principal function is to stimulate increase in cell length, especially near stem and root tips. In stems illuminated from above, cells undergo equal rates of elongation, resulting in vertical growth. But when lit from one side, stems change direction because auxin accumulates in the shaded side, causing the cells there to grow faster than those toward the light. Phototropism can therefore cause plants to grow tall and thin as they stretch and bend to find an adequate light source.


Photoperiodism is the regulation of physiology or development in response to day length, which allows some plant species to flower – switch to reproductive mode – only at certain times of the year. Plants generally fall into three photoperiod categories: long-day plants, short-day plants, and day-neutral plants. The effect of photoperiodism in plants is not limited to when they will flower. It can also affect the growth of roots and stems, and the loss of leaves (abscission) during different seasons. Long-day plants generally flower during the summer months when nights are short. Examples of long-day plants are cabbages, lettuces, onions and spinach. On the other hand, short- day plants flower during seasons that have longer periods of night. They require a continuous amount of darkness before flower development can begin. Strawberries are short-day plants. The flowering of some plants, referred to as day-neutral plants, is not connected to a particular photoperiod. These include chillies, cucumbers and tomatoes. Commercial growers can take advantage of knowledge about a plant’s photoperiod by manipulating it into flowering before it would naturally do so. For example, plants can be forced to flower by exposing or restricting their access to light, and can then be manipulated to produce fruit or seeds outside of their usual season (Rauscher 2017).

  1. Growing requirements

The primary environmental factors that affect plant growth are: light, water, carbon dioxide, nutrients (see Chapter 5), temperature, and relative humidity. These affect the plant’s growth hormones, making the plant grow more quickly or more slowly.


Light transmission, of the appropriate quantity and quality, is crucial for optimal photosynthesis, growth, and yield. The sun produces photons with a wide range of wavelengths (Figure 9): UVC 100- 280 nanometres (nm), UVB 280-315 nm, UVA 315-400 nm, visible or photosynthetically active radiation (PAR) 400-700 nm, far-red 700-800 nm, and infrared 800-4000 nm. Within the visible range of the spectrum the wavebands can be further divided into colours: blue 400-500 nm, green 500-600 nm, and red 600-700 nm.


Figure 9: Chlorophyll absorption spectrum[email protected]/29979758460

There are two different types of chlorophyll – chlorophyll a and chlorophyll b. Chlorophyll a is the most common photosynthetic pigment and absorbs blue, red and violet wavelengths in the visible spectrum. It participates mainly in oxygenic photosynthesis in which oxygen is the main by-product of the process. Chlorophyll b primarily absorbs blue light and is used to complement the absorption spectrum of chlorophyll a by extending the range of light wavelengths a photosynthetic organism is able to absorb. Both of these types of chlorophyll work in concert to allow maximum absorption of light in the blue to red spectrum.

Plant light responses have evolved to help plants acclimatise to a wide variety of light conditions. All plants respond differently to high and low light conditions, but some species are adapted to perform optimally under full sun, while others prefer more shade. In darkness, plants respire and produce CO2. As the light intensity increases, the photosynthetic rate also increases, and at a certain light intensity (the light compensation point), the rate of respiration is equal to the rate of photosynthesis (no net uptake or loss of CO2). In addition to light intensity, the colour of light also influences the rate of photosynthesis. Plants are able to use wavelengths between 400 nm and 700 nm for photosynthesis. This waveband is called photosynthetically active radiation (PAR) (Davis 2015).

The amount of light available for plants is highly variable across the globe and through the seasons. For example, at low solar elevations the light must pass through a larger volume of atmosphere before it reaches the earth’s surface, which causes changes in the spectrum, as the atmosphere filters proportionately more of the shorter wavelength of light, so it filters more UV than blue, and more blue than green or red. Changes in spectral composition with season and location influence plant light responses (Davis 2015).


The availability of many nutrients depends on the pH of the water. In general, the tolerance range for most plants is pH 5.5-7.5. If the pH goes outside of this range, plants experience nutrient lockout, which means that although the nutrients are present in the water, the plants are unable to use them. This is especially true for iron, calcium and magnesium. However, there is evidence that nutrient lockout is less common in mature aquaponic systems than in hydroponics, because aquaponics is an entire ecosystem, while hydroponics is a semi-sterile undertaking. Consequently, in aquaponic systems there are biological interactions occurring between the plant roots, bacteria and fungi that may allow nutrient uptake even at higher levels than pH 7.5. However, the best course of action is to attempt to maintain slightly acidic pH (6–7), but understand that higher pH (7–8) may also function (Somerville et al. 2014c).

Most plants need high levels (> 3mg/L) of dissolved oxygen (DO) within the water. This oxygen makes it easier for the plant to transport nutrients across its root surfaces and internalise them. Without it, the plants can experience root rot, where the roots die and fungus grows. Also, many plant root pathogens operate at low dissolved oxygen levels, so if the water is low in oxygen it can give these pathogens the chance they need to attack the roots (Pantanella 2012).

The ideal water temperature range for most vegetables is 14-22 ⁰C, though the optimal growing temperatures varies between different plant species (see Chapter 7). Generally, it is the water temperature that has the greatest effect on the plants, rather than the air temperature. The bacteria and other micro-organisms that inhabit aquaponic systems also have a preferred temperature range. For example, the nitrification bacteria that convert ammonia to nitrate prefer an average temperature of approximately 20 ⁰C (Pantanella 2012; Somerville et al. 2014c).

Carbon dioxide (CO2)

During photosynthesis, plants use CO2 to make food, and release oxygen as a result. Increased concentrations of CO2 increase photosynthesis, spurring plant growth. Fresh air contains CO2 at about 0.037%, but in a tightly enclosed greenhouse or growroom, ambient CO2 can get used up quickly. For example, in a plastic greenhouse, CO2 levels can be reduced to less than 0.02 % just 1-2 hours after sunrise. At levels below 0.02%, plant growth will be greatly limited, and at levels below 0.01%, plants will stop growing altogether. By increasing CO2 levels to 0.075-0.15%, growers can expect a 30-50% increase in yields over ambient CO2 levels, and time to fruiting and flowering can be reduced by 7-10 days. However, excessive levels of CO2 enrichment can have adverse effects. Levels above 0.15% are considered wasteful, while levels above 0.5% are harmful. Excessive levels will cause the stomata on plant leaves to close, temporarily stopping photosynthesis, and since plants are no longer able to transpire water vapour adequately when the stomata are closed, leaves can become scorched.


Temperature is the major environmental factor that influences the vegetative growth processes in plants from the initial stages of development to flower formation. Each plant species has its own optimal temperature range. Plants ‘seek’ to reach their optimal temperature, and a balance between air temperature, relative humidity and light is important in this. If light levels are high, the plant will heat up, resulting in a difference between plant temperature and air temperature. To cool down, the plant's transpiration rate must increase. Very low or high temperatures in the growth environment may be detrimental to various metabolic processes such as nutrient uptake, chlorophyll formation, and photosynthesis. Generally, an increase or decrease in temperature above or below the optimal level is known to alter several physiological processes in plants and damage the plant cells, thus altering growth.

Relative humidity

Relative humidity (RH) is the amount of water vapour present in air expressed as a percentage of the amount needed for saturation at the same temperature. Relative humidity directly influences the water relations of a plant, and indirectly affects leaf growth, photosynthesis, and the occurrence of diseases. Under high RH the transpiration rate is reduced, turgor pressure is high, and plant cells grow. When RH is low, transpiration increases, causing water deficits in the plant which may result in plant wilt. The water deficits cause partial or full closure of the stomata, thereby blocking entry of carbon dioxide and inhibiting photosynthesis. The incidence of insect pests and diseases is high under high humidity conditions, and high RH also favours easy germination of fungal spores on plant leaves.

Copyright © Partners of the [email protected] Project. [email protected] is an Erasmus+ Strategic Partnership in Higher Education (2017-2020) led by the University of Greenwich, in collaboration with the Zurich University of Applied Sciences (Switzerland), the Technical University of Madrid (Spain), the University of Ljubljana and the Biotechnical Centre Naklo (Slovenia).

Please see the table of contents for more topics.

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