The Physiology of trees

Although you can successfully keep bonsai without any real knowledge of how trees grow, limiting yourself to maintaining your trees by feeding and removing any unwanted growth, anyone who has an interest in trees is bound to want to know a little of how they grow.

Trees and Shrubs are defined as woody plants, that is a plant which produces a permanent stem, or in the case of shrubs, stems, with buds at least 25cm above the roots. There are however exceptions to this rule, with some trees having evolved to cope with sub-arctic conditions and the need to keep low, avoiding searing winds. Those plants can also tolerate being buried in snow for long periods, the snow protecting them from the worst conditions.

They are also termed 'Vascular', plants, having a system of tubes, not unlike our own, to transport energy to and from those parts of the body (tree) needing them and to and from those parts of the body designed to produce, or store them. Those veins are present throughout the tree, from the tips of the roots, to the tips of the leaves.

Cooksonia an early vascular plant from about 420 million years ago grew to about 5cm.

The first true plants (alga) evolved in the sea about 570 million years ago, but it was only some 430 million years ago, that conditions on Earth became suitable for the evolution of plants on land.

Several factors have driven the evolution of trees, not least of which was the appearance of plant eating reptiles. As the reptiles started eating the then small plants, they (plants) evolved. In line with Darwin's theory of evolution those plants having a trait that, say made them taller, keeping the foliage out of reach of the predators and providing better access to light, passed on their genes to the next generation.

Another factor is that those trees that grew taller were able to 'shade out' their rival's, reducing those rival's ability to reproduce.

About 375 million years the club mosses and tree ferns were the major plant groups, with examples reaching 50 meters tall. It is the remains of these plants that now form the coal we use.

As plants got taller, predators followed suit with taller reptiles evolving and the race was on!, culminating, although not at the same time, in the Sauropod dinosaurs reaching some 40' tall, 90' long and the two big Redwood trees. The Sequoiadendron Gigantium, capable of reaching over 350' tall, prime specimens weighing in at about 500 tons (making them by far the largest living things on the planet) and the coast redwood, Sequoia Sempervirens, a lighter tree, but measured at 367'. Of course not all trees, or reptiles evolved to that size, with plants and their predators evolving to fill environmental niches. Nor should it be forgotten that a large part of plant evolution has taken place since the end of the Dinosaurs and the coming of plant eating Mammals. The battle goes on even today.

Trees are divided into two types. The Gymnosperms represented by conifers. The Gymnosperms date back to about 300 million years ago. The other group are the Angiosperms, the flowering plants, which arose about 150 million years ago. All deciduous and non-deciduous broadleaved plants, with the exception of the Ginkgo, are Angiosperms.

In order to support taller trees they needed something to strengthen the stems, while allowing the passage of nutrients up and down the tree. The solution was to grow a hard core with any growth taking place under the trees skin or bark.

How do plants grow?


Plant growth takes place in response to external stimulation, usually the lengthening, or shortening of the photoperiod (length of daylight), although factors such as drought will obviously have an effect on the plants ability to grow. We of course affect the distribution of hormones when we prune the trees. These factors affect the production of hormones such as absisic acid, controlling the withdrawal of sugars from the leaves and their subsequent drop.

Pruning encourages buds left further down the shot to develop, which they might not under normal circumstances. The auxins which cause growth are targeted towards the shoot tips, pruning redirects them to the other buds on the shoot. Auxins are the hormones that promote stem and root growth in plants, they influence many aspects of plant growth and development, including the enlargement of cells, they inhibit the development of auxiliary buds, tropisms and the production of roots.

Man-made auxins are used in rooting powders and gels for cuttings and some weed killers. The high auxin levels cause such rapid growth that the plants die. The most common naturally occurring auxin is indoleacetic acid, or IAA. It's produced in the shoot tips and transported to other parts of the plant.


Tropism is the directional growth of a plant. This happens in response to a stimulus such as gravity, light, or contact. The movement is either positive, or negative depending on whether the growth is towards, or away from the stimulus. Geotropism, the response of plants to gravity, causes the root (positively geotropic) to grow downwards and the stem (negatively geotropic) to grow upwards.

Phototropism causes the plant to grow towards light and hydrotropism towards water. Although not significant in bonsai, thigmotropism, or haptotropism, is the response to physical contact, as with the tendrils of climbing plants when they touch a support and then wrap around it.

Tropic movement is the result of greater rate of growth on one side of the plant than the other.

Growth takes place in 'Meristems', regions of rapidly dividing cells, which as they mature will change into the specialised cells of the leaves, roots, trunk, flowers or fruit. The whole process is fuelled by the sugars in the sap.

One of the major sites of meristems are the Cambium layers.

Beneath the Bark

A number of complex processes take place in and beneath the bark of your bonsai and to understand how your tree grows, you will need to understand them.

There are six layers forming the outer skin of a tree. In this section we will look at what each layer does.

The outer layer of the bark, or leaves is the Epidermis. This forms a waxy, waterproof skin, helping the plant to retain moisture. This skin is also present on the leaves.

The epidermis is peppered with small holes, called stomata. These holes are used, both to breathe and vent excess moisture into the atmosphere.

The Bark is the next layer in. Bark is formed by the bark cambium. The cells produced, are designed to be impervious to both moisture, and gasses. They soon harden and die.

The expansion of the living tree beneath the bark stretches and cracks the dead layers, causing the bark to fissure. This gives the familiar textures to the bark of our trees.

The Bark Cambium is the next layer in. The bark is formed by its own layer of cambium, fed by the sugars in the phloem.

The Phloem comes next. It is the pathway in which the sugar bearing sap is transported around the tree, powering its growth. It is the region of the tree responsible for the development that takes place in the two cambium layers that sandwich it.

The Cambium layers are where most of the growth takes place.

In periods of growth, it is the cambiums which use most of the energy (sugars) contained in the sap, powering the development of the layers on either side of the cambium, of new shoots, roots and the repair of any parts of the tree that become damaged.

Cells produced in the cambium layer move either inward, forming the Xylem, or outwards as the Phloem and the layers on either side of them.

The Xylem is the part of the tree that carries the nutrient rich water to the top of the tree.

As the new xylem is created by the cambium, older cells forming the tubes in which the water moves die, forming the wood.

The cells of the xylem contain large amounts of a substance called lignin and it is that lignin which forms the wood.

The bark, like the leaves has Stomata, pores through which it breathes. These holes will eventually clog up. As a way of freeing up the stomata the tree sheds the outer layer of bark. Out own skin goes through a similar process.

Here we see a wonderful example of bark shedding on a London Plane. the tree is growing right next to the Telecom tower in central London and with all the dirt and fumes, needs to keep it's stomata open

The Leaves

The powerhouse for all this growth had been laid down at the very beginning of plant evolution, with the process of photosynthesis, using the energy of the Sun to produce sugars from available minerals. This process is dependent on the green pigment chlorophyll, present in all leaves, even when masked in coloured leaved cultivars of plants.

As with the Bark, the leaves are covered in the Epidermis, which is peppered with Stomata, the pores through which the tree breathes.


Is the process by which chlorophyll containing plants and some bacteria capture energy as light and convert it to chemical energy. The energy produced is used to drive a series of chemical reactions, which produce simple sugars, which provide the food for your trees and indeed all life. The plant must have a supply of carbon dioxide, light and water for photosynthesis to occur.

Photosynthesis takes place inside chloroplasts, which are found in leaf cells of plants.

Oxygen is a by-product of photosynthesis, almost all oxygen in the atmosphere has been produced by photosynthesis.

Chlorophyll is the green pigment common to all photosynthetic cells, it absorbs all wavelengths of visible light with the exception of green, which it reflects. This reflected green light is detected by our eyes, giving leaves their colour.

Daylight may be considered to be made up of the three primary colours Red, Green and Blue, although blue is by far the largest component and the best suited to photosynthesis.

The Red/Blue elements of light are absorbed by the leaf, passing into the palisade cells in the leaf and fuelling Photosynthesis in the chloroplasts. The green light is reflected.

Normal (tungsten) household lights emit a lot of red light and little blue, this means that, although to our eyes a room is well lit with white light, the plant is getting little blue light and is unable to photosynthesise. Normal fluorescent lights are if anything worse as the following diagrams illustrate.

Tungsten filament lamps emit a continuous spectrum peaking in the red area and falling away in the blue, the colour most suited to Photosynthesis, reducing the plants ability to turn light into energy.

Fluorescent lamps emit a different spectrum, with peaks at varying wavelengths depending on the type of lamp. Some tubes, particularly those made for the Aquarist trade will give a good approximation of daylight.
The impact of unsuitable lighting on trees kept indoors cannot be understated. If you must keep bonsai indoors please talk to your local garden centre about appropriate lighting.

Although the two graphs above are crude representations of actual Spectral Emission Diagrams they are as accurate as my memory allows, having spent five years studying photography.

Rotate your trees


The main function of leaves is to turn light into food for the tree. The tree will not put energy into producing, or maintaining branches and leaves where they will get no light, they will in fact shed those branches. To maintain a tree with 'depth' you will need to rotate you trees so that both the front and back get an adequate amount of light.

This may mean turning the tree around for a week or so every month, but it's better to look at the back of a tree with a full set of branches, than something with all the visual 'depth', of a cardboard cut-out.

The Illustration to the left shows the sun's passage around a tree, with little light getting to the branches at the back. This, in a tree kept indoors will usually be on the room side of the tree, foliage and branches there will die if not given enough light.

The leaf is a complex structure, having a number of specialist functions. In this section we will look at how leaves work.

The epidermis is the outer layer of the tree, being present on both the bark and leaves. It provides a waxy layer, reducing the amount of water the tree loses through evaporation. In the leaves this layer is about one cell thick, allowing maximum sunlight to get into the leaf, powering the process of photosynthesis.

The palisade cells are directly under the skin (epidermis) of the leaf, they contain the chloroplasts, which are the site of photosynthesis. Being close to the surface of the leaf they are able to obtain as much sunlight as possible.



Chloroplasts are photosynthetic organelles found in the leaf cells of higher plants.

Chloroplasts contain the green pigment chlorophyll along with the enzymes and other products needed for photosynthesis. However the green chlorophyll may be masked by other pigments such as phycoerythrin, or phycocyanin, giving red or blue colours to the leaves.

A 'Deshojo' Maple

Even red leaved cultivars of species have chlorophyll, although it may not be that obvious

As with all other living parts of the tree, the leaves contain the tubes of the xylem, bringing water and chemicals to the chloroplasts in the palisade cells, to convert to sugars. They also contain the phloem, the tubes that distribute the sugar rich sap around the tree, they are however carried in bundles rather than the layered rings of the trunk/branches.

Carbon dioxide is essential to the process of photosynthesis and this gets into the leaves through the Stomata. These holes are opened and closed when needed by the guard cells.

The guard cells will open or close the stomata to allow Carbon dioxide in and when used allow Oxygen out, oxygen being a waste product of photosynthesis. They will also close if the tree becomes dry, stopping water evaporating out through them.

Stomata exist on both leaves and bark, exessive covering with either moss, or lichens on the trunk can harm trees.

In conifers the stomata are often closely grouped along the underside of the needles, creating light coloured bands. As with this Western Hemlock


A maple leaf (in autumn colour), showing the veins. Those veins contain the same vascular tissues, the xylem and phloem that are present in the trunk and roots.

A normal and an Etiolated shoot.

Lack of light, or long exposure to unsuitable light will cause growth to become thin and pale. This is called 'etiolated growth' and such growth has a greatly reduced potential for photosynthesis and limits the plants ability to produce food.

Bonsai kept indoors, in inadequately lit places, will be prone to this.

Leaf fall


Leaf drop in deciduous trees is controlled by a process called Abscission, which is also responsible for the shedding of flowers and fruit.

Should your bonsai suffer a trauma, such as drying out, Abscission can be triggered as a self-defense mechanism, as reducing the tree's surface area reduces the amount of water it 'perspires'

As with most processes in plants, abscission is brought about by the release of hormones, Absisic acid and Ethylene, a type of hydrocarbon that can act as a plant hormone. Production of these is usually triggered by the decreasing amount of light and lowering of temperature as the year ends. These hormones modify cells at the base of the leaf petiole, creating two layers of cells.

In the upper layer, the cells breakdown, allowing the leaf to separate. The lower, or protective layer seals the wound.

At the base of each leaf you will find a dormant bud, waiting to produce next years shoot.

Here we see a leaf with the petiole (green). In Autumn after abscission

The Roots

The roots perform two functions in the life of the tree, they are the foundation on which the tree grows, providing stability against winds and of course they supply the tree with the water and chemicals it needs to produce sap and hence feed the tree.

All plants have a major root that grows down into the soil. This is the taproot and provides the main anchorage to the ground. A tree in a shallow bonsai pot will usually have had the taproot removed, or reduced.

As with the shoots, pruning the roots will produce side roots, although these roots can appear anywhere along the root, as the production of roots is not limited to where there are latent buds.


The roots spread out about as far as the tree is wide, adding to the stability of the tree.

They also provide the tree with the resources it needs to grow. This can require a massive root structure and you can usually assume that what you see of the tree above ground, is echoed in volume below ground.

The roots themselves are a complex structure, as you can see from this illustration.

Here we have the Vascular tubes. As with all parts of the tree, the veins of the xylem and phloem are present in the roots. They are however in bundles, rather than the rings of the upper parts of the tree.

The root hairs perform two functions. Firstly they massively increase the roots surface area, increasing its ability to absorb water and chemicals.

Secondly their travels out into the surrounding soil, make a better anchorage for the root to move forward and further fix the tree into the ground.

Should the roots be allowed to dry out, either while repotting, or through under watering, the root hairs will die. This will significantly reduce the trees ability to take up water and hence delay its recovery.

Root hairs do not grow into roots and only live for a few weeks.

The cells of the region of maturity were formed by the ageing of cells in the region of elongation. This region is often referred to as the 'Region of differentiation', implying that as the cells mature, they become different, some developing into root hairs, some forming the vascular tissue and others may form the beginnings of root buds and hence new roots.

The region of elongation contains cells recently produced by the meristematic cells behind the root cap. These cells continue to expand pushing the root tip forward. As these cells age they join the region of maturity.

The meristematic zone is where the roots growth takes place.

The cells of the meristematic zone are constantly dividing, with those older cells, towards the back of the zone rapidly elongating, this elongation pushes the root cap forward. Those cells at the front of the zone replacing damaged cells of the root cap.

The root cap could be described as the 'Crash helmet' of the root. It protects the meristematic zone, while shedding cells to lubricate the roots passage through the soil.

The root cap is sensitive to the earth's gravity and it is this sensitivity that ensures the roots primarily grow downward into the soil. This sensitivity is called geotropism

Not all roots are negatively geotropic, species that evolved in wet environments, like the Mangrove, or the Swamp Cypress shown here develop 'Air roots', or Pnumataphores.

Sap Flow

We are all aware of sap, and understand that it moves up and down the tree, performing a similar function to our own blood.

The roots absorb both water and nutrients. This cocktail travels up the tree through the tubes in the xylem. As it reaches the top of the tree the mixture finds its way out through the branches and shoots to the leaves.

Having passed through the leaves and the process of photosynthesis, the sugar rich sap moves throughout the tree in the tubes of the phloem, fueling the process of growth.

The Wood

You can still see the growth rings on this piece of chain-sawed wood

Let's start by looking at what wood is.

The wood is formed as the inner layers of the xylem are replaced by new growth.

The cells that form the tubes of the xylem, as with all cells in plants have a membrane of cellulose. The cells of trees and shrubs however have an extra component, lignin. Lignin is what gives woody plants their strength.

To the left we see a section through a twenty-four year old Scots pine, felled for timber in Norfolk, England. Counting the trees growth rings gives its age.

Close inspection of the distances between the rings shows larger gaps in the centre and hence faster growth when the tree was young.

Commercial timber is classified as two types, Hardwoods and Softwoods and this classification parallels the division of Gymnosperms, the conifers, producing softwood and the Angiosperms, the hardwood trees, the flowering broadleaved trees.

Hardwoods are much stronger than their Softwood cousins. The reason for this increased strength is that the tubes in a hardwood are generally smaller than softwoods and there is more wood between the tubes.

A hardwood cross section

A Softwood cross section




Maple seeds (Samara)

All reproduction serves two purposes. Firstly it increases the number of individuals of a particular species, thus providing a larger gene pool for the naturally occurring genetic changes. These changes enable species to cope with and take advantage of new, or changing environments. This process will often result in the evolution of a new species. Secondly it provides a food source for predatory, or parasitic species.

The higher plants usually reproduce sexually, with the joining of the sets of the parent plant's genes one of the main occasions for the genetic change to occur. However sexual reproduction is not the only way plants propagate, or can be propagated as we shall see.

Trees are divided into two types, Gymnosperms, the conifers and Angiosperms, the broadleaved trees. They are classified by the covering (or lack of) of their seeds.

An Angiosperm a Peach and a Gymnosperm a Pine

Mosses, Liverworts, Fungi and Ferns do not produce flowers and seed, but rely instead on 'spoors'. These spoors are self-fertile and are often small enough to be carried on the wind.

The higher plants have flowers, with both male and female parts to distribute their genetic code and produce seed. Unusually however some trees, Pines being an example, have the male and female reproductive parts on separate flowers, often carried on different branches.

An Angiosperm flower

A typical Angiosperm flower consists of the male, pollen-producing stamen. The female pollen receptors, the stigma and the seed producing ovary.

The petals are really only there to attract pollen eating and of course distributing insects.

The fruit that develops around seeds serves two purposes. Firstly it proves attractive to fruit eating animals and birds, the seeds are generally resistant to the gastric juices of both and will pass out of the diner, pre packaged in its own little pile of compost.

If the fruit should, perhaps as a windfall, end up on the ground, it is yet again surrounded by its own compost heap.

Fertilisation may be carried out by a number of agents. Insects, particularly bees are the best known pollinators, however birds, wind and some animals such as fruit eating bats also play their part.

The pollen is carried from stamen of one flower to the stigmas of another. To avoid self-fertilisation most plants have the stigma and stamen mature at different times.

On reaching the stigmas, the pollen is transported down the tube they are mounted on, to join with the female seed, fertilising it

Female and male Gymnosperm flowers

Gymnosperms, the conifers differ in that flowers are either male, pollen producing, or female, seed producing.

The female flower will develop into the cone, the male will drop off after shedding its pollen.

The pollen of Gymnosperms is usually distributed by wind and anyone who has been in a pine forest at pollen time will be familiar with the clouds of yellow, dust like pollen.

Not all gymnosperms have cones. Some such as the Yew and Ginkgo have fleshy covered seeds called 'arils'.

The seed of a yew tree

Most non fruiting trees rely on the wind to distribute their seeds, often over long distances.

A popular way of keeping the seed in the air to cover greater distances, is with a wing like structure, as with Pine, or Maple seeds, wing like seeds are called 'Samara'

Pine seeds are carried in pairs, on each of the cones segments.

A natural raft style tree

We are able to force the issue of tree reproduction by creating new trees from cuttings, or by layering a tree. Certainly layerings occur naturally, As branches mature they get heavier, this weight will often cause them to touch the ground. Prolonged contact with the ground will cause roots to develop, creating what we in bonsai call a Raft style tree.

The parent tree may eventually die but the rooted layering will go on and live out its natural life span, of perhaps several hundred years.

Another way that plants reproduce is to produce 'suckers'. These grow from adventitious buds that develop on the roots.

These suckers will grow on to be mature trees.

Cuttings, layerings and suckers are asexually reproduced and hence carry only the genes of the plant they were taken from. The advantage of this in bonsai is that asexually produced trees, when planted in a group all exhibit the same growth characteristics such as leaf colour and size.


Trees can live for a long time, (the Bristlecone pine of Arizona, in the USA has specimens over 5,000 years old), however everything comes to an end. If you are successful in keeping your bonsai, they should outlive you by several hundred years, leaving a legacy that future generations can enjoy, in much the same way we are able to enjoy the many ancient bonsai there are.

Allen. C. Roffey June 13, 2018 3:31