Research carried out over many years by the United States Forest Service has demonstrated that many old pruning ideas and practices are no longer valid. Botanists now know that healthy trees have the intrinsic ability to resist invasion of wood-decaying organisms. Trees can close off pockets of decay and prevent its spread into neighboring wood by a process called compartmentalization.
The structure of the branch connection to the trunk plays an important role in decay resistance. A swollen branch collar is usually visible at the point where a side branch connects to the woody parent stem or trunk. This collar results from the meeting of two patterns of growth: the branch and the trunk. The side branch probably developed from a lateral bud in its second season. As the season progressed, the annual growth ring of bark on the parent stem or trunk began to expand and surround the base of the new shoot.
This phenomenon resembles a mechanical ball-and-socket connection. With each passing year the branch collar continues to grow around the base of the branch, strengthening the attachment. As the collar grows, it may compress the bark causing a visible ridge, called the branch bark ridge, to form where the branch tissue and the trunk tissue meet.
For woody plants the branch collar has special significance. It is a storehouse for chemicals known as phenols that are highly toxic to fungi. Phenols help prevent decay-causing organisms from moving from injured or dying branches into healthy tissue.
If a branch is cut off flush with the parent branch or trunk — and the collar is removed, as was once advised — the tree loses its natural protective barrier and decay organisms can more readily enter the wound. The latest advice employs a pruning method called natural target pruning.
The branch is severed from the trunk at the edge of the branch collar where the concentration of phenolic compounds is high. A wound at the edge of the collar heals fastest and is most effective in repelling decay organisms.
Trees are able to shed dead branches, closing over their wounds with callus tissue to help prevent decay. Callus also forms over the surface of wood exposed by a pruning cut. Cuts made on the outside edge of the collar appear initially as a circle and later, when callus forms, as a doughnut. Each subsequent year the hole in the doughnut grows smaller until the wound is completely closed. An improper flush cut not only leaves an oval wound or larger area for callus to close but also removes the protective branch collar.
The speed of the healing process depends upon the health and vigor of the individual tree or shrub, as well as the quantity of food reserves in the plant. Trees that are long-lived are better able to compartmentalize, resist decay, and quickly close injuries than are weaker, short-lived species.