The root and shoot both form in the dividing tissues at
each end and grow like mirror reflections of each other.
The part of stem where buds grow is
called node. The part between two buds
is called internode. Since a bonsai is a
miniaturization of a natural plant, you
should shrink the internode. However,
internode can grow overlong where the
growth is vigorous. Such branches are
known as coarse and vigorous branches.
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We present here research findings on plant physiology and include their
explanations for you to better understand the various operations in bonsai
making. We summarize the general principles, and we will keep the
explanations simple. However, the knowledge we include here is not required
directly on a pragmatic basis when making a bonsai.
Of course, there are many exceptions, for the diverse nature contains
countless varieties of plants. Whatever the exceoptions there may be, you
will learn to single them out after knowing the general principles.
Perhaps you have already or will read professional instructions and heard
or will hear excerpts' explanations before you start making a bonsai. But
have you understood or will you understand the meaning of those
explanations?  If not, you may not be able to fully apply the knowledge, and
you can easily forget what is written there. Also, when making a bonsai you
should know whether your daily work fits the plant's physiological needs and
how your work suits the plant's vital activity. Knowing these will add more
fun to your bonsai making experience. In addition, when new problems arise
and you solve them by trials and errors, the knowledge of the physiology of
your plant can help you solve these puzzles.
We hope the materials described here will become Ariadne's Thread in
guiding your bonsai experience.
- Physiology Describes the Secret -
Principle of Plant's Shape
Unit of plant's shape --The Shoot
A “shoot” botanically refers to the pair of stem and leaves growing on the
stem. This set of two things forms the basic unit of a plant's shape. A plant
begins with one shoot and grows more shoots as it develops. In this way a
plant gradually forms its complex shape.
A plant consists of the shoots.
Shoot formed in the bud
A shoot is first formed by the cell division and regeneration of the shoot
apical meristem in the buds. It then gradually grows. In this process, cells in
the shoot, i.e. the stem, and cells in the leaves and the buds (lateral buds or
axillary buds) are formed. Newly formed stem, leaf, and lateral bud are
compressed and folded in the bud.
A cabbage is a giant shoot grown
directly from the bud
The development of the stem, leaf, and lateral bud during the shoot's
As water is absorbed from outside the cells to the vacuoles inside the cells,
it increases the volume of each cell and enlarges the cell. By the time cells
mature, the volume of each cell will increase longitudinally by tens of times.
Insufficient water in vacuoles and cells lowers the water pressure in each cell,
which is unable to hold up the plant in the same way flat tires cannot hold up
a vehicle. Therefore, not watering the plant on time will cause it to wither. As
this process goes on, the folded stem, leaf, and lateral bud grow larger and
stretch in the vertical direction.
Starting in the bud, shoot tissues
including the stem, leaf, and bud
develop gradually.
Two units of plant ― The correspondence between the shoot and root
Besides the shoot, the root forms another unit in a plant's structure. The
shoot mainly grows upwards. In contrast, the root mainly grows downwards.
However, there are many exceptions. Some plants grow their roots above
the ground, while other plants grow their shoots underground.
The root and shoot both form in the dividing tissues at each end and grow
like mirror reflections of each other. The cell division is the most active around
both ends (cell division site). The cell division frequency decreases as one
moves away from each end to the cell development site, where cells grow
larger and stretch in vertical directions instead of dividing. Far away from each
end, cells will not grow too large but they form distinct shapes according their
functions. This is the cell maturation site.
The balance between the shoot and root
1.Balance in water
The sizes of the root and shoot are determined by the balance between the
amount of water absorbed in the root and that used for transpiration and
photosynthesis in the shoot (mainly in the leaves). Water is mainly used for
photosynthesis and cell growths.
2.Balance in nutrients
Plants grow by cell divisions in the buds. For cell divisions to occur, nutrients
such as minerals absorbed from the roots and carbohydrates produced by
photosynthesis in the shoots (mainly in the leaves) are necessary. The root
and shoot will grow larger until they can supply the plant with enough
3.Balance in mechanics
The root will grow thicker and larger from the taproot in the center until it can
support the shoot and prevent it from leaning. Conversely, the shoot only
grows as large as the root does.

For a plant growing in moist soil, its roots absorb plenty of water, so its
shoots will keep growing. This will cause the plant to form coarse and
vigorous branches. On the other hand, more branches and leaves will result
in more transpiration from the shoot. So the roots will grow to balance. If
you over-pruned or injured the roots during repotting, this sudden decrease
in the amount of roots will disturb the balance between the roots and shoots.
Then, the tree may defoliate or let part of the shoots wither to recover the
balance. But failure to recover the previous balance will cause the entire plant
to wither.
The growths of the shoot and root
are balanced.
The root grows larger according to the needs of the
shoot, and the shoot grows until the root can fully
support it. The two parts are mutually dependent. The
larger one part grows, so will the other part develop
Specifically, the balance between the shoot and root
signifies the balance in the supply and demand of the
following three factors in the plant. These factors
determine the sizes of the shoot and root.
The leaves of deciduous trees fall in late autumn, and the leaves do not
yet develop in early spring. So late autumn and early spring are the best
seasons to root-prune plants in temperate zones. In these periods, leaves of
evergreen trees are inactive, so the requirement of water and nutrients in the
shoot lowers. Thus, the damage to the balance between the root and the
shoot is minimal even if you prune the roots. Should you prune the roots,
since the soil temperature has not dropped in late autumn or early spring,
the roots are still active and are capable of healing the wounds after being
pruned. For the same reasons as above, the best time to prune tropical
plants is during their dormancy.
If you prune your plant's roots at other times, you need to prune some
leaves as well. You should also supply the plant with enough water after
pruning. It should be mentioned that after pruning the roots on the left side
of the plant, the leaves on that side may sometimes begin to wither to an
extent. This suggests that specific part of the roots supply water and
nutrients to specific part of the shoots.
What is coarse and vigorous branch?
In order to reproduce a tree's natural shape, the bonsai tree should have
a thick trunk that tapers upwards. The branches and leaves should be
thinner and finer compared to the trunk, and they should grow amply. All
these can be achieved by controlling and adjusting the root-shoot balance.
When training your bonsai tree from a seeding or a young tree, you
should first let the roots grow as large as possible in order to let the trunk
grow thick. Since the amount of water and nutrients needed in the shoot is
equal to that provided by the root, you should let the roots grow fully so
that the shoot can fulfill its needs. In this stage, to ensure the roots will grow
freely, you should either grow the plant in a large flowerpot or grow it in the
To make the shape of your bonsai, you need to repeatedly prune the
stems, leaves, and buds on the shoot. The bonsai's shape is made by
pruning the shoots and adjusting the balance between the root and the
shoot. By pruning large amount of shoot under an existing root-shoot
balance, you reduce more rapidly the consumption of water and nutrients in
the shoot than the supply by the root. Under such stimulation, the extra
water and nutrients supplied by the root will flow to the hitherto dormant
lateral buds and activate their growths.
Specifically, when stems are pruned, the buds will of course be cut off as
well. This will stop the growth of the stems in the vertical direction. Water
and nutrients supplied by the root to the buds will then flow to the lateral
buds and make them grow. Therefore, after you prune the stems above the
lateral buds, new shoots will branch out near the cuts.
If the lateral buds have already developed into a new shoot, the new shoot
will diverge more. The stems on the new shoot will be thinner than those on
the old shoots. You can make use of this and prune the trunk and branches
to make tapers. You can also make bends in the trunk and branches. In
addition, you can apply this when pruning the coarse and vigorous branches
to grow new branches.
After each leaf pruning, water and nutrients that has been previously
supplied to the leaves will now flow to the lateral buds. Just like in stem
pruning, the lateral buds on the stems will be activated and develop into a
new shoot and keep growing.
Pruning all the leaves once will cause huge imbalance between the
water-and-nutrient supply by the root and the demand for it in the shoot. As
a result, new shoots will develop in most abundance. For example, when you
prune all the leaves after the buds have developed into a shoot and the
leaves have matured, the tree will grow equal amount of leaves to restore the
balance. This then activates the hitherto dormant lateral buds that will grow
into new shoots. In that case, the tree in fact has completed a
two-year-growth within one year. So you have reduced the time and have
completed within one year a two-year training of your bonsai tree. If you can
prune three times in one year, then you will accomplish three-year's training.
In bud pruning, the shoots will stop growing like in stem pruning, and the
lateral buds will be activated and grow into new shoot. Depending on the tree
species, or if the tree is old or the momentum of its growth is low, some
lateral buds may not be easily activated after stem pruning. Also, after
leaf-pruning conifer trees, the leaf shape can deteriorate or the trees can
easily wither. As you will probably spend the most energy in bud-pruning, the
bud-pruning is used mainly in the above-mentioned trees, or uncommon
trees, or deciduous trees whose branches and leaves you want to beautify.
Buds are essential for training new branches and making a bonsai.
Buds grow out at the end or in the middle of a shoot. A bud growing at
the end of a shoot is called apical bud, terminal bud, or end bud. That
which grows in the middle of a shoot is called lateral bud, or axillary bud
for it grows at the same place as the leaves do. The lateral buds grow to
produce new shoots and become apical buds, so new shoots are also
called lateral branches.
In addition, buds can sometimes grow out on trunk, roots, and leaves.
These buds are called adventitious buds.
Flowering plants have flower buds or floral buds of slightly different
shapes. So to differentiate from them, buds are sometimes called leaf
buds or foliar buds.
In naturally growing trees, the shoots including the stems, branches and
leaves develop larger upwards and stretch outwards as they grow. The
opposite should happen in a bonsai, the tree must remain small while it
grows. So you must prune the stems, branches, and leaves that have grown
upwards or outwards to make a bonsai. Then relatively more water and
nutrients are supplied by the roots, and new shoots will grow. Water and
nutrients now are supplied to the lateral buds on the inner side of the tree.
These buds will be activated and grow in horizontal direction.
As the lateral buds on the inner side grow, you can add more branches
and leaves to the bonsai tree while keeping its original size. In addition, as
the growth period is short, new branches and leaves are thin and small.
You should observe the most upward and outward stretches at the shoot
tips, i.e. the buds on the outside of the tree and on the coarse and vigorous
branches. So you need to prune these parts often. In doing so, water and
nutrients supplied by the roots will be transferred to other parts of the tree,
which in turn accelerates the growth of the branches and leaves that have
been growing slowly. Thus, the tree as whole has a balanced growth.
Therefore, reducing the bonsai tree's size is intimately related to
reproducing the tree's natural beauty.
The above-mentioned tips will only work when sufficient water and nutrients
are supplied by the roots. According to botanical research findings, the size
and quantity of leaves and the height of a tree in nature are determined by
water and nutrients absorbed in soil and the total energy obtained from
You need to prune the roots to ensure they supply enough water and
nutrients. The roots absorb water and nutrients in soil by root hair at the
root tips. Root hair has a rather short life span, and new root hair constantly
replaces old withering one. The most important factor in increasing water and
nutrient absorption is not to have thick and long roots but to increase their
total amount. Indeed, more roots can absorb more water and nutrients.
For naturally growing trees, large and thick roots such as the taproots are
necessary for supporting the shoots. But a bonsai tree does not need thick
roots including the taproot. On the contrary, the taproot will inhibit the
growth of finer roots. So during root pruning, you should focus on pruning
the taproot and the thick roots.
Like the shoots, new lateral roots will grow out after root pruning, which
increases the total number of roots. More roots will provide more water and
nutrients to the tree, which is advantageous to the development of lateral
buds after shoot pruning. On the other hand, without root pruning there will
be few roots, and so the shoots will be poor. Therefore, root pruning is
indispensable to achieving the effect of shoot pruning.
Plant hormone
Pruning makes the lateral buds grow, so the shoots and roots can grow
to adjust their mutual balance. All these activities are due to the effects of
plant hormones such as auxins and cytokinins. Plant hormores are
chemicals that regulate the growth of the plant. There are several
categories of them, but until now many aspects of these hormones have
not been understood.
Auxins and cytokins are not just two specific hormones, but they refer
to two families of chemicals. They have various effects, and their main
effect is to promote cell divisions. The most typical one is in forming the
scab-looking knobby calluses which cover the wounds after the tree is cut
or wounded in order to keep out germs and prevent tree juices from
flowing out.
Mutual effects of auxins and cytokinins in the growth of the shoots and roots
Auxins are primarily synthesized in the apical buds in the shoots. They
reach the roots through phloem in the stem and trunk. When the auxins
concentration in the roots has reached a certain threshold, many lateral
roots will grow out. Thus, a plant with active apical buds will form many
branching roots. On the other hand, auxins can also inhibit the roots from
growing larger. According to the results, as the auxins concentration
increases, the plant grow out many tiny roots.
Cytokinins are mainly synthesized in the apical meristem in the root tips.
They are transported from the roots to the shoots with water and
nutrients through xylem in the stem and trunk. Cytokinins will accumulate
in the apical buds. This boosts the vigor of cell divisions there and thereby
increases the vitality of the shoots and leaves. Therefore, it is correct to
say more roots or more apical meristems poduce more cytokinins, and so
shoots will grow more vigorously. Moreover, vigorously growing shoots will
increase the amount of auxins synthesized in the apical buds and sent to
the roots, which further boosts cytokinins synthesis there.
These findings are scientific explanations of the fact that the trees with
ample roots have abundant shoots.
They also explain why plants stop growing in winter. As the soil
temperature drops in winter, the roots become less active and so
cytokinins synthesis decreases. Consequently, cell divisions stop in the
apical buds.
The reason why the lateral buds grow after being
pruned――Apical dominance
Usually the apical buds alone are stimulated into growing, whereas the
growth of all lateral buds below them is suppressed. This is called apical
dominance. Shoots do not grow in lateral direction but grow outwards.
Pruning is to cut off apical buds so as to remove the apical dominance.
We consider the following hypotheses to explain the effects of auxins,
cytokinins, and apical dominance.
Dormant lateral buds will grow immediately after being applied
cytokinins. Also, if we spray cytokinins to the entire tree, germination of
the lateral buds will be evidently be boosted. Thus we can conclude that the
apical dominance occurs because the cytokinins concentration in the apical
buds is too high.
In other words, the cytokinins concentration is the highest in the roots
where they are synthesized, their concentration gradually lowers as they
are transported upwards through xylem. In the topmost apical buds where
cytokinins accumulate, their concentration is especially high. Auxins
produced in the apical buds promote cells' absorption of cytokinins, so
cytokinins accumulate especially in the apical buds with active auxins
production. In contrast, cytokinins do not accumulate in the lateral buds,
so the growth of the lateral buds is suppressed.
The optimal auxins concentrations for promoting the growth of the apical
buds and lateral buds differ. We have seen high concentration of auxins
promotes the growth of the apical buds but suppress that of the lateral
buds. We may consider a second hypothesis that lower auxins
concentration is needed to promote the growth of the lateral buds. Indeed,
if we prune the apical buds and place agar gel containing auxins on the
wounds immediately after the lateral buds grow out, we will observe the
growth of the lateral buds are suppressed. This confirms our hypothesis.
In addition, the growth of the lateral buds after pruning the apical buds
is the results of both the decrease in auxins and the increase in cytokinins.
Besides the above mentioned plant hormones, other new chemicals have
been discovered and identified more recently.
All plants develop from a single shoot and grow new shoots, on which new
shoots grow out. As the shoot ends develop and branch for several times,
the plant grows bigger. Meanwhile, the stems grow thicker to support the
increased weight of the plant, and to transport more water and nutrients.
Similarly, the roots keep growing.
For the shoots and roots to grow thicker, cell reproduction must occur in
the horizontal direction. This is called the secondary growth. It occurs in the
cell division tissue known as the vascular cambium in the stems. It should be
noted that some plants do not have secondary growths. But almost all plants
used for bonsai have secondary growth. As the cells develop in vascular
cambium, their cell walls thicken. After the cell die, their cell walls remain and
harden, and become firm supportive tissue. Grass has  short secondary
growth, whereas trees have extended secondary growths. In this way trees
make most of their stems, which are known as wood. Secondary growth
occurs both in shoots and roots.
Water, nitrogen, and inorganic minerals in soil are absorbed by root hair and
then transferred upwards through the vessels in xylem to the main root,
trunk, branches, and eventually leaves and buds at the shoot ends. Water is
broken down into oxygen and hydrogen by the energy in sunlight in the
leaves, and photosynthesis produces carbohydrates such as sugar and
starch by combining the hydrogen with the carbon dioxide absorbed from the
stoma in the leaves. About 20% of water is not used in this process, instead
it evaporates from the stoma in the leaves.
A plant is composed of cells and fibers. Cells support various vital life
activities of the plant by cell divisions. Fibers build and shape the cell walls
surrounding cells. Indispensable to all these life activities are carbohydrates.
There are two types of cell activities. One concerns the growth of the
plant, i.e the enlargement of its size, and the other its reproduction. For the
plant to grow larger, the ends of the stems and branches will bud and the
tree will grow taller. The branches will grow longer and the leaves will grow
denser. As the roots penetrate deeper into the soil, the trunk and branches
will grow thicker. The tree's wounds are also healing as it repairs itself. To
produce offspring, the tree will flower and eventually bear fruit.
Fibers make up the cell walls that surround the cells and make them rigid.
In their development, cells first divide to produce more cells. Then the cell
walls thicken to fix the plant tissues. The support provided by the cell walls
enable the vessels transporting water and nutrients to maintain their shapes.
The leaves and branches can keep their shapes for the same reason. Indeed,
a plant can support itself on the ground because of the cell walls. Most
tissues in the trunk and branches are composed of thick layers of cell walls
left by dead cells.
Carbohydrates are the building materials for cells and fibers.
Carbohydrates combine with each other to form fibers. They react with
nitrogen absorbed from roots into amino acids and proteins, which construct
the shapes of plant cells. All above-mentioned processes require
carbohydrates that are produced in the leaves and stored in the trunk and
For trees growing in nature, the stem size is determined by the amount of
water and nutrients transported through the vessels in xylem and that of
carbohydrates transported through sieve tubes in phloem. In addition, the
stem size should have enough wood to support the tree's weight. For a
bonsai plant, you may neglect the weight issue, so the other two factors are
more important.
Here are some findings from the botanical research.
  1. When a single stem branches into two, the cross section area of the
    stem before branching is more or less the same as the sum of the
    cross section areas of the two branches.
  2. The cross section area of a stem is proportional to the total amount of
    leaves on the stem up to its end.
Simply put, the more a shoot branches out upwards, the thicker the shoot
grows. So if you want to thicken a shoot, you should increase the number of
branching at that shoot and increase the amount of leaves on it.
For example, to thicken trunk while making “kokejun” (taper), you can just let
more branches grow out of the trunk and let the leaves grow denser.
Meanwhile, you should gradually reduce the amount of branches and leaves
on the shoots as you move up the trunk, and cut off the topmost branches
and leaves. As shoots grow via branching, this method can be applied to any
part of a tree.
Carbohydrates produced in
the leaves move to the
branches, stems, and roots
through sieve tubes in
phloem. Eventually, they are
transported to the buds and
root tips where cell division is
active, or to the reserve
tissue in the roots and the
stems to be stored. The
opposite can also happen as
carbohydrates move from the
storage tissues in the stems
and roots to the leaves and
buds. Water, carbohydrates,
and other nutrients are
transported through xylem
and phloem via changes in
osmotic pressure and the
capillary phenomenon.
6. Leaf Pruning
Physiology of Shaping
End of shoot
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A Guide to Bonsai Basics
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For a change
Making a bonsai by controlling and adjusting the root-shoot balance
Bud types and their names
Realizing “keisho-sodai” by controlling the root-shoot balance
Secondary growth