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Pruning determines the basic design of the tree.

Bonsai must always have a natural shape. The tree should remind the viewer of the growth habits of trees that might be found in nature.
Many years ago when cultivation of bonsai became established in Japan, the classic styles of bonsai evolved. These styles are not arbitrary or artificial, but they are abstractions and simplifications of the many forms that trees growing wild adopt.
Although the shaping of a bonsai does not require that it be a faithful copy of classic styles, the precepts involved provide guidance for the basic patterns for shaping the trunk, relationships of branches and the overall silhouette.—Masahiko Kimura

Heavy (Creation) Pruning

Creation pruning is the process of turning an ordinary piece of nursery stock into a pre-bonsai. It is a very stressful process for the tree, and so should only be done when the tree is dormant, at the end of winter. If it is done too late in spring, the stress could kill the tree.
For some trees, the process could include reducing the height of the tree by cutting off the trunk just below the final visualized height of the tree. But for all trees, it will include removing unwanted or ugly branches. With a deciduous tree, this could include removing up to eighty percent of the tree’s foliage areas, but for evergreen trees, such drastic pruning can mean certain death, so trees may need to be reduced in stages.

Light (Maintenance) Pruning

Light pruning includes thinning of secondary branches, maybe the removal of some branch or the restructuring of the apex, and it includes pinching back and leaf removal, or defoliation. It is limited to improving the appearance of the structure already established by an earlier heavy pruning.
Because it is not so stressful for the tree, thinning of the branches can be done at the beginning of spring. Pinching back can be done throughout the season (depending on the species), and leaf pruning can be done in summer.

Pruning to Shape the Trunk (Trunk Chop)

Creation pruning on young trees can include cutting back the trunk, sometimes as far as the trunk base (drastic pruning). This is typically done on trees grown in the ground, in order to create more taper. For some deciduous trees, this can be done by simply removing the unwanted trunk, cleaning up the cut, and waiting for new buds to form to choose a new leader. It is usually best to leave an inch or more of stub above the desired new leader to allow for dieback. There is no need to protect the stub from dying out. This will allow the new leader to become strong enough to survive after the cut is cleaned up. These photos show the technique for cleaning up that stub of a trident maple. Notice that the stub was sawed off cleanly horizontally. This is done to allow us to use the best leader from the new buds that erupt. If we cut the tree at an angle, the sap recedes and we have to repeat the process. Pretty soon we can run out of tree!

The size of the trunks can make it a little more difficult to know just how to proceed. For a very large trunk, a pruning saw can be a great asset. Remember that the Japanese saws cut on the pull stroke, and leave more wood than you think you will want, so that the cut can be reduced and shaped. Once you have the main part of the trunk removed, use concave or spherical knob cutters to reduce the cut. Be careful not to reduce the cut too much, that can be worse than not cutting enough!

When you get the cut to the proper shape, clean up the edges with a grafting knife or razor blade and seal the cut. I recommend purchasing a good grafting knife and learning how to sharpen it. Properly sharpened, it cuts far more cleanly than a razor blade, and the imperative here is not to damage the living tissue. With a grafting knife, thin slices of the extremely hard maple can be shaved off. Trim this to a gentle, rounded curve that will heal naturally. Do not make this a concave cut, as it is too large to heal properly and can hold water and promote rot. Finally protect the cut with a good putty type wound sealer. The paste type in a tube is actually grafting sealer and can prevent the cut from cicatrizing properly.

Pruning to Select the Main Branches

How do we reconcile the notion of a bonsai having a natural shape with the traditional rules of branch placement? How does first branch, second branch, back branch fit into the ideal of a naturalistic tree?
The first thing to remember is that the “rules” of bonsai style are not rigid laws written in stone. They are observations about what makes certain trees beautiful. With that in mind, we can tell that it takes more than just numbered branches to make a beautiful tree.

Even though every bonsai has a front, it is important to note that the famous trees have both front and back branches as well as branches at the side. These provide a fullness and balance to any tree. A common mistake is to cut a piece of nursery stock until one has just a few twigs left at all the “proper” places. This makes for a long time of wondering why the tree looks so bare, if it even survives. Remember to leave more branches than you may ultimately use, because they can always be removed, but cannot be put back.

Basic Technique for Pruning Branches

Always be sure to use the tool that fits the job you are doing. It is better to use a bigger tool, if the right one is not available. That may mean using a saw to cut a branch, but that is preferable to splitting the bark or breaking your tool.

Always leave a stub when cutting a branch. If you are going to jin the branch, leave the stub long. If not, leave the stub short. For a pine, it is an excellent idea to leave the stub for a few months until it stops bleeding, then reduce it. For deciduous trees, it can be reduced immediately with your knob cutters using several strokes. This prevents splitting of the branch down into the trunk. For larger cuts, a sharp gouge can do a better job of shaping the cut. After shaping the cut roughly, use your grafting knife to smooth the edges of the live material–the cleaner the cut, the quicker it will heal.

Once you have the cut flush, hollow it out just a little, and seal the cut. In this photo taken a week after making some larger pruning cuts (vigorous trident maple), you can already see the edge of the healing wound under the cut putty.

Utilizing Open Spaces

When selecting branches, it is sometimes better to train yourself to see the empty (“negative”) space surrounding them. Often it is easier to see what is holding us back by looking at it in a completely different way.
Not only does a tree take up space; it also has places that don’t. Just as a forest planting should have some open space “to let the birds fly through,” so should any bonsai make use of both the positive and negative. When the two are balanced, the whole tree takes on a sense of balance.

Pruning to Shape Branches

Once the main design of the tree has been established, maintenance and renewal pruning combined with wiring will continue to advance the style of the tree until it is “complete.”
The branches should mirror the trunk. As we select branches at the outside curve of the trunk, we also select sub-branches on the outside curve of the branches. If the trunk has drastic angles or gentle curves, the branches should do the same. With most deciduous trees, this is accomplished more with pruning than wiring, although some wiring may be necessary.
To prune to develop branches, you must understand the budding habits of your tree. Does it bud opposite the branch, or does it alternate? Also, does it tend to die back by one bud, or can you prune it closely to the bud you want? This is where specific species knowledge is necessary. Generally, you will want to prune back to a bud that is growing in the direction you want the new growth to go. You will want to remove any growth downward or straight up, and on trees that grow with opposite buds (maples, for example), you will want to prune to just two buds at each branching.

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