Botany for Beginners

By Carl Morrow

Although this title contains attractive alliteration it is a very tricky topic for discussion due to its extreme generality. Botany includes the study of the physiology, structure, genetics, ecology, distribution, classification and economic importance of plants. It often also includes the study of seaweeds and fungi, two related kingdoms of life. So you can see it is a very broad topic and many of the processes are closely interlinked and in trying to make it "basic" often results in the simplification and loss of many of the beautiful subtleties that occur in plants.

This subject also has the potential to be extremely dry and boring to people who are not interested in it, but I can assure you that by having some insight into the way in which plants work really enhances your bonsai experience. It allows you to understand more clearly WHY certain things happen to your plants and HOW you can use these processes to your advantage.

In this article I am going to focus on water and its path through a bonsai. The reason for this choice is that water is the most important nutrient in plants and because bonsai growers always seem to be obsessed with water and watering regimes, thus highlighting its critical importance. Water is the one resource that most dramatically restricts land plants. It serves many important functions within plants. It is an important transport medium, it dissolves many chemicals which allows them to react together in a controlled way and it provides very effective support to the soft tissue in the plant body in the form of turgor pressure within the cells.

Very large amounts of water are needed for normal plant growth. Less than 1% of the water taken up by the roots is turned into "stuff"; sugars, proteins, cells, wood and other biomass. The rest of the absorbed water is lost via transpiration through the leaves. This loss is essential and good for the plant, so that the plant can absorb Carbon Dioxide for photosynthesis. When the plant is photosynthesizing it opens up the pores in its leaves (stomata) in order to allow carbon dioxide to be taken up by the leaves. Because water is a very much smaller molecule than CO2 it is very easily lost from the leaf when these pores are opened up. The water loss is good for the plant as the evaporation cools the leaf and the tremendous flow of water through the plant allows its roots to take up enough nutrients from the soil and concentrate them in the leaves.

The process of water moving from the soil through the roots, stems then leaves and finally being lost to the atmosphere is called the Soil-Plant-Atmosphere-Continuum, SPAC for short. This process is driven by water's tendency to move down moisture gradients. If regions of high moisture content are connected to patches of low moisture content then the water will move from the high to the low in an attempt to make everywhere uniform. The actual mechanisms involved are horribly complicated and only explainable using detailed physical and mathematical theories and formula. It is only necessary to remember the general process that is occurring. The flow of water through the plant is fundamentally driven by the loss of water from the surface of the leaf This is the transition that contains the steepest moisture gradient and so it has the power to drive the rest of the process. This is a very confusing concept that hopefully will be more understandable by the time you reach the end of this article.

Water availability in the soil

Clay and organic matter have a structure that allows them to hold water very strongly meaning that the soil may appear damp but the water is actually unavailable to the plant's roots. Sand, on the other hand, has a coarse, granular structure that causes it to have a very weak hold on water. The hold is so weak that the force of gravity is strong enough to remove it and so water drains very rapidly out of the sand. For water to be successfully stored in a plant-available form, the spaces between the soil particles need to be in a size range of 0.2 to 30 micrometers (um) in diameter. How big is a um? There are 1000 um in 1 mm, a relatively thin piece of paper is in the order of 50 um thick.

Along with particle space size, the density of the soil is also an important feature. Roots grow best in intermediate density soil that is friable and uniform with no hard or particularly soft patches in it. The soil needs to be soft enough for good root penetration but compact enough to allow good root-soil contact that allows liquid water to be absorbed. As mentioned previously, the spaces allowing for adequate absorption are very small indeed. It is, however, easier to add water to a soil than to take it away and so I use a more open, freely drained potting medium that is frequently watered rather than one that holds a lot of water. In bonsai, one needs to consider other soil properties such as the necessity of the soil setting properly so that the tree is firmly anchored into its pot and the presence of gritty material to encourage fine root ramification.

As soil dries it shrinks and this shrinkage can cause a lot of damage to plants because the contact between the soil and the roots is lost and so the plant cannot absorb moisture. Plants combat this effect by the presence of mucilaginous root sheaths and myccorhizal fungi. Both of these methods ensure a continued contact between the roots and soil so that the plant is able to continue absorbing the moisture that it requires. In addition, it has been shown that these sheaths and fungal associations help the plant to acquire the nutrients that it needs from the surrounding soil.

Water in the roots

Roots fulfill many important functions for the plant. They anchor the plant; they store nutrients and water and they also absorb water and dissolved nutrients from the soil and ensure that they are passed up to the top of the plant where these chemicals are needed.

It is important to know something about plant cell structure if one is to understand how a root manages to absorb water. On the outside of a plant cell is the cell wall. Although rigid, it has an open, fibrous structure somewhat like a sponge. Inside the cell wall one finds the living cell membrane and inside this is the cytoplasm otherwise known as the cell sap.

When a root is in an area where it is able to absorb water, there are two pathways that the water can follow. The first is called the apoplastic pathway where the water flows through the spongy cell wall while the other pathway is called the symplastic pathway where the water is actually absorbed by the cell. Following the symplastic route, the water is taken up by the cell and passed through special little connections between the cells (plasmodesmata) until it arrives at the middle of the root. Once here, the water is transferred into the xylem and it is transported up to the top parts of the plant.

If the water follows the apoplastic route then it moves through the cell walls of the cortex of the root until it arrives at the endodermis of the root The endodermis contains waterproofing in its cell walls (Casparian strip) that forces the water to be absorbed across the cell membrane into the cell. This apoplast water then joins the other water that has followed the symplastic route in its journey up the stem. By forcing the water to cross a membrane the plant is able to control its water uptake.

If soil is waterlogged then there is an unexpected decrease in the uptake of water by the plant. The plants experience a "physiological drought" with all the usual symptoms one associates with dry plants - wilting, leaves shrivel etcetera. It is important to keep this symptom of water logged soils in mind so that you think twice before immediately watering a wilted plant. Investigate it first to make sure that is the soil is dry. The main effect of flooded soils is to starve the roots of oxygen and so they are not able to respire and release energy to grow. The physiological drought symptom of flooded soils is also interesting because it shows that water uptake is an active process that requires energy released from the oxidation of sugars. From this one can see that the presence of oxygen around the roots is critically important for the health of the plant. This is further support for the trend to use open, freely draining growing media for your plants.

"Root burn" as a result of over fertilization is also caused by an upset in the water balance of the plant when using too high a concentration of fertilizer. Also, if you fertilize a tree and then allow the soil to dry out, the dissolved salts are greatly concentrated and may cause root burn. In this situation, water will flow out of the root into the salty solution in the soil rather than from the soil into the root. This will cause the plant to suffer due to lack of water. You can observe this effect if you take a celery stalk or strip of potato and place it in concentrated salt or sugar solution. Within a few hours the plant will become soft and flexible indicating a loss of turgor from the cells.

Most plants are adaptable to the environment in which they find themselves. They do however take time to adjust to new surroundings and so one of the keys to successfully cultivating plants is to be consistent with your watering regime. Plants can manage most watering programs as long as it is constant and not varying all the time.

Water in the stems

The function of a plant stem is threefold. It is a big tube carrying water, mineral salts and sugars between the roots and the leaves. It also serves to hold the leaves in the correct position to capture as much sunlight as possible. The third function is one of competition and being able to push leaves up, past neighbors so that you capture the sunlight and not your competing neighbors. Keeping up with the Jones's so to speak!

The bulk of a woody stem is made up of xylem, which is responsible for transporting water from the roots to the leaves. Its structure is basically a large bundle of straws that have small connections between them. When water is streaming up the stern it can be thought of as many separate tubes, each behaving more or less independently.

One of the big, popular questions about sterns is how are trees able to get the water that has been absorbed by the roots, all the way up to the top of the tree? We have plenty of evidence that it does work (just look at a Redwood tree standing at 110m tall); while the current theories are not good enough yet to explain it adequately. One thing that is known is that an unbroken column of water has an extremely high tensile strength. The traditional theory states that the leaves are responsible for sucking the water up the stem from the roots. On closer investigation there are indications that this does not completely explain the process and so new theories are being proposed.

It is interesting to note the speed of water transport through a stern. In evergreen plants, like conifers, the water travels at 1.8 to 3.6 cm per minute while in deciduous trees the speed is 6.6 to 7.3 cm per minute. This gives a good reason why deciduous trees need more water than conifers and why conifers can survive in drier soils.

The secret of successful water transport is a continuous column of water. As I have said earlier, the water stream in the stem is made up of a whole lot of small water columns inside their "straws". What happens if one of these columns breaks? The breaks are called embolisms or the tube has cavitated. These breaks can be caused by drought conditions. Due to the lack of water around the roots of the plant the column of water in the stem gets stretched. The water explosively evaporates due to the low pressure and the column snaps. This snapping can actually be heard and scientists can record these sounds to monitor the rate of cavitation. Freezing and thawing can have a similar effect and even strong shocks and vibrations can cause damage to water columns under tension. Embolisms are important because they reduce the ability of the stem to transport water and in extreme cases they can even limit growth.

Plants have two ways of coping with this cavitation. Some plants are able to refill the broken water columns. This usually occurs at night when there is a lower water demand from the leaves. There are also indications that the plants have some kind of stem pressure and root pressure that forces water into the vessels. A demonstration of this root pressure can be seen in the "bleeding" of cut trunks and the droplets of water that appear on the edges of strawberry leaves in the early morning. If there are small bubbles in the vessels they can dissolve in the surrounding water. Once the tubes have been refilled, they can start conducting water again.

Some plants cannot repair these embolisms and so once the vessel has cavitated it becomes useless and the plant has to rely on new wood growth to replace these damaged tubes. This is one of the main reasons why woody plants have to continuously grow fatter in order to maintain a functioning set of vessels.

Plants can adapt to reduce the amount of cavitation occurring. The vessels can be made thinner which makes the water columns stronger and the wood becomes denser. It has also been shown that drought tolerant species are more resistant to cavitation. It would be interesting to see if there was any relationship between a tree's resistance to cavitation and its suitability to collecting for bonsai due to the water stress that a newly collected tree is exposed to.

Stems can also store water for the plant. If the root uptake of water and loss of water through the leaves are monitored, one will see that there is a lag period between the increase in transpiration and increase in root uptake. Among other reasons, stems store water to allow for this lag period. This volume of water is small compared to a tree's daily water use but it does serve as an important buffer in the water relations of the plant ego in freezing weather conifers needles can continue losing water while the roots cannot absorb water because the soil is frozen. The stem-stored water will prevent the needles suffering desiccation damage. This stored water becomes useful in times of stress for the plant and so may be helpful in bonsai when one collects or repots a tree. At this stage the roots are not functioning properly and so the stem-stored water can act as a small buffer during the day to keep the leaves water filled.

This storage capacity of the stems also needs to be kept in mind when one is creating shari on a trunk. If you expose wood and notice that it is wet then you need to remember that this moisture is coming from somewhere and so the wood needs to be protected until the tree has had a chance to create a new barrier to this uncontrollable loss of water. Rudi Adam recommends a layer of latex or stone sealer (bonding liquid) on the exposed wood.

Water in the leaf

Leaves are very much more familiar to people. The primary function of leaves is photosynthesis the conversion of carbon dioxide and water into high energy sugars using the energy from sunlight. Most of the structures of the leaf are related to maximising the efficiency of this function. The vessels that run up the trunk extend into the leaves and form a network of veins that support the flat leaf. These vessels also carry the water that entered the plant at the roots all that time ago I The surface of the leaf is covered with a waxy cuticle that prevents excess, uncontrolled water loss from the leaf. The loss of water from the leaf is controlled by tiny pores called stomata that are scattered over the surface of the leaf, particularly on its underside. The hole in the stoma is surrounded by two guard cells that can control how wide the hole is. Compared to the atmosphere, the cells in the leaf are very wet. This causes tremendous amounts of evaporation from these cells (as happens when you hang washing out to dry). This water diffuses from the surface of the cell s and out of the leaf through the stomata. This lost water is replaced by more water that is present in the vessels of the leaf which, in turn draws water out of the stem and eventually this unbroken chain ends up at the surface of the root where more water is drawn into the root. So now, armed with all this background information that you have read, it is possible to understand the Soil-Plant-Atmosphere-continuum (SPAC) that was mentioned at the beginning of this article, a little more clearly!

I hope that you have gained something from this article. Plants are enormously complicated, but any knowledge that one does have about their functioning is useful in explaining why certain things are done in bonsai. It should also give you the tools to asses horticultural activities and decide for yourself which ones make no sense whatsoever and which ones will enhance the growth of your trees.


  1. Campbell N.A. (1990) Biology (2nd Edition) The Benjamin / Cummings Publishing Company, Inc., Redwood City, California.
  2. Eames AJ. and MacDaniels L.H. (1947) An introduction to plant anatomy (2nd Edition) McGraw-Hill Book Company, Inc., New York & London.
  3. Kramer PJ. and Kozlowski T.T. (1960) Physiology of trees. McGrawwHill Book Company, Inc., New York.
  4. Lambers H., Chapin F.S. and Pons T.L. (1998) Plant Physiological ecology. Springer-Verlag, New York.

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Random Bonsai Tip

You can bend thick, hardened branches by undercutting. A wedge is cut underneath where the bend is needed and then the branch is eased down anw wired into place. Thick, coarse branches could also be removed completely and replaced with new branches by thread grafting or approach grafting