Basic Bonsai Botany

Sometimes when I mention that I practice bonsai I find myself explaining how a tree or plant grows. Mostly I am explaining how to miniaturize the tree in the aspect of pruning. This information is just the basics when it comes to the botany of plants or our bonsai, but it is a good start to understanding just how plants work. Enjoy the read, click the images to see a larger version and be sure to check out the sources that I used.

Why do you cut the roots? Won’t that kill it? How, at certain times of the year that are pretty predictable, many plants and trees flower in response to specific day lengths. What causes branching to occur when branch tips are removed? In deciduous trees what is the reason for them to drop their leaves in fall and awaken from dormancy each spring? There are a ton of questions on how plants function.

This is a list of names for the different parts of trees and what they do.

  • Leaves produce food for the tree and release water and oxygen into the atmosphere.
  • Chloroplasts are the chlorophyll bodies within the cells of leaves in which photosynthesis takes place in order to manufacture carbohydrates (starches and sugars) for the tree. They give the green color to leaves.
  • Stomata are specialized “breathing” pores in the leaves through which carbon dioxide enters and water and oxygen are released. They close when water is limited
  • The Trunk is the main support of the tree to better expose leaves to the sun. The bark is the “skin” of the tree and provides an external protective layer.
  • Inner bark (Phloem) located just under the bark, is part of the circulatory system, carrying compounds manufactured in the leaves, down throughout the tree where needed.
  • The Cambium is a layer only a single cell thick between the inner bark (phloem) and the sapwood (xylem). It produces the cells that allow both the phloem and xylem to grow.
  • The sapwood (Xylem) is produced by the cambium and carries water and nutrients up from the roots to the leaves.
  • The Heartwood is essentially inactive sapwood. It gives the tree strength and rigidity and serves as a depository for stored food and waste.
  • Main branches are the large limbs on the trunk that give the tree it’s basic shape and structure.
  • Secondary branches are mainly horizontal on the main branches that create the outline of the tree.
  • Tertiary branches (twigs) on the secondary branches have the leaves.
  • The Root system can be quite extensive depending primarily on soil texture and depth. Availability of moisture and nutrients also affect the extent of the root system.
  • Some trees may have an initial Taproot, but as the tree grows, other more horizontally growing roots predominate. It serves as the initial anchor for the tree.
  • Lateral roots develop from the base of the trunk and spread, forming an extensive network that serves to anchor the tree. They also provide storage for carbohydrates.
  • Feeder roots grow from the lateral roots and serve to transport water and nutrients absorbed by the root hairs. They tend to be concentrated within the “dripline” (where the rain drips off the tree canopy) but may extend great distances if searching for adequate moisture and nutrients.
  • Root hairs are microscopic appendages to the feeder roots that along with a symbiotic relationship with mycorrhiza, absorb the water and nutrients the tree needs in order to live and grow.
  • Mycorrhiza is a fungus that grows in association with the roots of a plant in a symbiotic or mildly pathogenic relationship. They help break down nutrients into a form that the roots can use.

So if we put this together we end up with this.

The roots collect the water and nutrients that are transported to the leaves by the xylem in the roots, trunk and branches. Then the leaves take in carbon dioxide through the stomata and the chloroplasts , using energy from the sun, they convert the nutrients into carbohydrates. Those carbohydrates are transported throughout the tree by the phloem.

Leaves
How do leaves work? On both sides of the leaf there are layers called epidermis; sandwiched in the middle are chloroplast containing cells where the photosynthesis process takes place. This middle layer is called mesophyll (Greek meso-middle, phyll-leaf). Mesophyll cells are similar to veins in that they wind their way through the leaf. Each of the veins contain xylem cells to supply the mesophyll with water and nutrients while the phloem cells remove newly made foods. The upper epidermis is usually smooth and dense to reduce water loss. Some plant leaves are covered with hairs that help reduce loss of water. The lower epidermis contains stomata. The stomata is how the plants breath (Greek stoma- mouth). The stomata is located in the lower epidermis to help prevent them from becoming clogged with dust that can normally gather on the top surface and prevents harmful air borne fungal spores from entering. Leaves that tend to stand upright, such as Iris, have stomata on both leaf surfaces.

The openings in the stomata allow gases to enter the leaf and water vapor to escape. With most plants, the stomata routinely close at night because the absorption of carbon dioxide is not necessary when photosynthesis is not taking place. Other reasons or times the stomata may close is on hot, dry days, in heavy winds or when the soil gets to dry or when the uptake of water can’t keep up with the rate of water loss.

Each stoma is bordered by two guard cells. The guard cells control the size of the opening of the stoma. The guard cells inner walls, next to the openings of the stoma, are thicker than the outer walls. While in a relaxed state, the guard cells lie parallel to each other with no opening between them. When the plant pumps water into the guard cells, the thin walls stretch, the shape of the cells change, curving away from each other, and the stoma opens. Loss of water to the guard cells reverses the process. The anatomy of leaves is designed to bring the ingredients together for the chemistry of photosynthesis.

When the part of the leave come together this is how they work. Water and dissolved minerals flow through the plant’s xylem, connecting roots and stems with leaf petioles, midribs, and veins. Carbon dioxide enters the leaf through open stomata, then diffuses into the mesophyll cells, where the gas collects. Finally, in the chloroplasts, light and raw materials converge in the process upon which all life depends.

The photosynthesis process

The chloroplasts collect sunlight and this leads to a series of events where water and carbon dioxide are used to synthesize simple molecules that will be used to build substances of increased molecular complexity. Several types of sugars are the first product created by the process: ribulose diphosphate, glucose, fructose, and sucrose.

Thousands of glucose molecules are joined in long chains creating molecules of starch and cellulose. Starch is the food that is stored in the plant cells until needed as energy or for conversion into other plant products by specialized enzymes. Cellulose, once formed and incorporated into cell walls is not available for other purposes. The photosynthesis process utilizes hydrogen from the water and releases oxygen back to the atmosphere.

Following the production of sugars, the biochemistry of plants leads in many directions, some of which involve the introduction of mineral elements from the soil, into the structure of certain molecules. These will be discussed later.

The Root System

The root system of plants usually receive little to no attention from gardeners, kind of “out of sight, out of mind”. When a plant is root bound and needs to be transplanted is when most gardeners become aware of the root system. The root system does three things for the plant.

  • Roots anchor the plant in the soil
  • They absorb water and nutrients
  • Store excess food for future needs

There are two ways that roots anchor the plant.

  • The first is to occupy a large volume of shallow soil around the plant’s base with a fibrous root system consisting of many thin, profusely branched roots. Because they grow close to the soil surface, they effectively hold soil in place and lessens soil erosion. Fibrous roots capture water as it begins to soak into the ground and must draw their mineral supplies from the surface soil before the nutrients are leached to lower levels.
  • The second way is a tap root system.  The taproot is one or two rapidly growing roots that go straight down into the soil with little branching to draw water and minerals from deep water tables.

A few species grow both root systems, others adopt one or the other, depending on the soil and water conditions. Fibrous roots grow when the surface soil is moist and tap roots grow when it is dry.

Trees distribute their roots in a wide circle in an area beyond the leaf canopy where rain is channeled from the foliage above. This is called a “drip-zone”.

The main purpose of the roots is to probe the soil for water and minerals at a distance from the plant, so the primary growth is their most important growth process. Most of the new cells produced are laid down behind the growing tip. There, they augment the length of the root and when the cells elongate, the root tip pushes its way through the soil. To protect the root tip, cells are produced to create a protective barrier called a root cap. This barrier is readily rubbed off but is quickly replaced, much like our skin when it dries and peels off from the surface. When the root cap cells are ruptured by sharp soil particles, their protoplasm forms a slimy coat lubricating the root tip as it works its way through the soil and around objects like rocks. The root’s primary growth activity is concentrated about 1/4” along its tip.

Absorption of water and nutrients takes place a short distance back from the root tip, in an area where thousands of root hairs form a fuzzy band around the root. These root hairs are extensions of the outer root cells and increase the absorption area of the root by several hundred times. The zone where the root hairs grow remains constant. During the growth of the root, new hairs form just above the growing tip, while old ones, at the top of the group, shrivel and die.

Branching of the roots begins in the slightly older parts of the root, some distance from the tip. Branching roots tend to grow at right angles to the parent root, to explore other regions of the soil around the plant. Each branch of a root works just like the root that produced it, with the same methods of growth, a set of root hairs has the capacity to form branches of its own.

When a root tip comes in contact with the air, the root cap harden and the root stops growing in length. To prevent the root from growing upwards the root cap contains a tiny ball of clay in its hollow end that gravity acts upon and keeps the root tip growing downward.

Growth controls

Biologists have found that plants produce special substances to regulate the processes of plant growth and development. We call these substances hormones. Five plant hormones, or plant growth regulators have been identified in plants.

Growth Responses to Light

The first hormone to be discovered in plants was the one that causes stems to grow toward the light. This process is called Phototropism, (Greek tropos, to turn), This hormone is a growth response to external stimuli. When stems are illuminated from above, the cells undergo equal rates of growth vertically. When stems are lit from one side they change direction because cells on the shaded side grow faster than those on the side of the light. Phototropism is a common response in sun-loving species. Most shade-loving species display little or no phototropic response. The hormone controlling phototropism is named auxin, after a Greek word meaning “to increase”.

The main function of Auxin is to increase cell length in stems and root tips, where it concentrates. When one side of a stem is in light, auxin accumulates in the side that is shaded. This causes the cells to grow faster on the shaded side and the stems bend towards the light. This allows the plant’s food factories (leaves) better exposure to harvest the light. Some leaf petioles also experience phototropism.

The hormone gibberellin is responsible for the growth of stem internodes, the space between leaves. Light intensity is responsible for the action of gibberellin on internode cells. When a plant is in full sun, the hormone’s effect on growth creates shorter internode length. This means that in low light or shade, gibberellin becomes more active, causing the internodes to stretch, raising leaves to a position where they are better able to locate light. Shade-loving species show no such reaction.

Growth Responses to Gravity

Roots and stems react differently to the gravitational fields of the earth by growing in opposite directions. Geotropism is the name given to this process. (Greek: ge, earth)

Not all but most roots grow down in the direction of the pull of gravity. Stems, for the most part, grow opposite to the gravitational pull. If a stem is placed on its side, the shoots will soon turn and begin to grow upward. Auxins collect on the underside, stimulating those cells to grow more rapidly than those on top. The mechanism of auxin migration is still a mystery to this day.

Geotropism plays a role in seed germination. In the soil, the embryos of randomly scattered seeds point in any of the many directions. Soon as the roots and shoots start to grow and their orientation is recognized and sets them on the right course. Imagine how it would be for gardeners to have to plant each seed in a “correct position” for them to germinate and grow properly.

Hormones and Plant Functions

Plant physiology is dependent on hormones to initiate various actions that control growth functions. Examples are auxins and gibberellin hormones that react to external stimuli and light.

The Aging Process

When fruits ripen or leave prepare to separate from their stems they undergo aging or senescence. This process is also controlled by hormones. Once senescence or aging has started, it is irreversible, so plants must possess strict control over this process to prevent the premature death of tissues, organs or the whole plant.

Another hormone is Cytokinin. It is responsible for promoting cell division. It also plays a role, along with auxin and gibberellin, in inhibiting senescence by maintaining the structural integrity of cells.

Acting against these three hormones are two other hormones that promote the aging process. The senescence promoting substances are ethylene, a gas, and abscisic acid, so named because it is the primary agent that promotes leaf abscission.

Ethylene and abscisic acid are produced when fruits ripen and result in changes in cell structure, such as the breakdown of membranes and the softening of cell walls. When leaves age (senescence), prior to dropping (abscission), they go through the breakdown of chlorophyll and weakening of cell walls at the base of the petiole. In the spring and summer, auxin is produced in the leaf keeps these cells intact. But, low night temperatures and short days in autumn cue the leaves to produce less auxin and increase the production of ethylene and abscisic acid. In evergreens, sequential abscission in the oldest leaves occurs by way of the same series of biochemical events. In a like manner, abscission of fruits and flowers takes place at appropriate times.

Branching and Root Formation

We know that in order for plants to fill out, the stem tips must be removed periodically. As long as buds are present at the stem tips (apical buds) they suppress the growth of buds (axillary buds) further back on the branch. Auxin that is produced in the tip of the stems, exerts the inhibiting effect on axillary bud growth. By trimming a plant we are simply removing the source of auxin.

There is a difference between species’ abilities to form adventitious roots on cuttings. Root development in cuttings of some species is promoted by auxin naturally present, while other species must be treated with a rooting compound, a preparation of synthetic auxin.

With the roles played by the five hormones described above, this can be added. Gibberellins control seed germination; ethylene promotes stem thickening, especially in seedlings; abscisic acid brings on dormancy where gibberellin revives them from winters sleep.

Plant Defenses

Over time plants have evolved and developed natural defenses to help them survive in stressful situations. We have already discussed how plants react in non stressful situations so let’s look at what plants do when they are stressed.

Dormancy

When a plant becomes dormant, it is preparing for the approach of environmental conditions that will limit growth or threaten death. The onset of dormancy requires a reduction of physiological activities to the minimum necessary for survival. Deciduous trees typically discard their leaves that would be damaged by frost, low temperatures, strong cold winds, cloudy days and snow cover. Annual plants die before the seasonal extremes arrive. These species
survive in the form of dormant seeds that germinate when conditions become favorable again for their growth. Perennials typically die back above ground with the underground portions ready to begin growth after the extremes of winter pass.

Different environmental extremes of nature dictate small plant size among native species in the arctic tundra and high on the mountains in the alpine zone. Their low, compact form provides protection against the weight of snow covers in winter, and after the snows have melted, against the impact of strong winds, in their exposed habitats.

Plants in any habitat constantly struggle to adjust to the changing environment.

Mechanical Protection

Have you ever brushed up against a rose bush, cactus or a hawthorn? If you have then you know how well some plants defend themselves. The protective structures these species bear are classified by botanists into three categories:

• Thorns are found on hawthorn trees, blackthorn trees, and pyracantha. They are modified, short branches grown from axillary buds terminating in sharp, hard points.

• Spines, as found on cactus and hollies, are modified leaves or parts of leaves, such as projections from leaf margins. Since spines are modified branches or leaves, they develop at nodes on stems.

• Correctly called prickles, the rose’s protective structures are arranged in irregular patterns within the internodes. Prickles are short, woody outgrowths with many species being recurved (having tips pointing downward) Such a shape hinders small animals trying to climb the stem to reach the leaves. They also provide a secondary, supportive role, as in climbing roses where the recurved prickles become hooked on the support structure as well as its branches.

This same role is played by recurved thorns like those on the stems of bougainvillea.

Chemical Protection

There are two parts to the biochemistry of plants. One involves life-sustaining chemistry of basic metabolism and includes photosynthesis, the extraction of foods by cellular respiration and the construction of cellulose, starch, fats, and proteins. Pathways branching away from these essential processes lead to the synthesis of secondary products including those that function as chemical defenses.

Tannins is one of these secondary products. The protein-binding, enzyme- inactivating capacity of tannins make them superior deterrents to insects and herbivores. They contain substances that also effectively inhibit fungal and bacterial growth.

One of the most interesting of the secondary products is called alkaloids. When introduced into animals (human), they have a wide-ranging physiological effect. They protect against predators because of their bitter taste. Some alkaloids have mild or strongly addictive side effects: caffeine in coffee and tea or nicotine in tobacco for example.

Alkaloids, when ingested act as cardiac and respiratory stimulants. They also act as muscle relaxants, blood vessel constrictors, and pupil dilators. When ingested in uncontrolled quantities, they can cause violent illness, coma or even death.

Wound Healing

The surface tissues of plants are called epidermis and cork and they act as barriers between a plant’s interior and external environment. Cutin, produced and superimposed on epidermal cells prevents water loss from the leaves and stems and prevents entry of fungal spores into the plant. Suberin is a substance in the walls of cork cells. This inhibits water loss from woody stems; whereas tannin, another chemical present in cork, acts as a natural fungicide and insecticide.

Injury to either the epidermis or cork results in uncontrollable water loss and the formation of openings through which unwelcome organisms find easy access to the plant’s interior.

An opening made in plant tissues is initially sealed by the exposed cells on the wound surfaces which collapse and die. Then a waxy substance, similar to cutin and suberin, form a callus or parenchyma tissue, over the exposed wound. Cork then slowly encroaches from the area around the wound. A few years after a branch is trimmed from a tree, cork development may have completely obliterated the wound. For healing to be effective, it is important that woody branches be cut close to the supportive trunks, since it is difficult for the cork to grow over stubs.

In many species, exudates form effective barriers between injured and healthy tissues. Conifers produce a sticky, aromatic fluid called resin that oozes from resin canals when they are broken. It is insoluble in water and hardens on exposure to air. Gums are different from resins in their chemical composition and are water-soluble, viscous liquids, that also dry to form hard coats on wounds. Latex is a white or colorless exudate that contains, among other components, rubber particles that effectively seal scars and wounds.

Latex, resins and some gums are known to have bacterial, fungicidal and anti-herbivore properties.