Factors affecting stem decay in stands (epidemiology)

Age of Stand

Stand age is such an important and complex factor affecting the amount of decay, it gets (part of) its own page!

But there are obviously factors other than age that influence level of stem decay. What accounts for such variation among stands in the amount of decay?

Stand History

Events and conditions in the life of a stand, especially those that create infection courts, can cause dramatic increases in the level of stem decay.

  • Fire causes basal scars.
  • Ice and snow storms break off tops and branches.
  • Logging often causes felling wounds and basal scars from skidders and logs.
  • Density is not so obvious. Assume a fungus gets in through large branch stubs. If the stand is dense, branches are shaded out while they are still small, and infection courts are not created. An open stand will have larger branch stubs. But remember that some fungi use small twigs as infection courts, so the dense young stand may favor them.
  • Animals, especially ungulates can create infection courts, particularly when the stand is young. Therefore the history of animal management on the site can influence decay.

Stand Composition

As mentioned, species vary greatly in their susceptibility to decay, so stand composition is an obvious factor determining the level of decay. The percent of defect in a mixed stand should be roughly a composite of that expected for the species represented.

This has obvious management implications: we can influence the amount of decay in a stand by influencing composition. In the West, Douglas-fir is often clear cut. Clear-cut stands can come back to Douglas-fir, which generally has relatively low levels of decay. If we engage in partial cutting, as many argue we should for esthetic reasons, we favor an understory of shade-tolerant hemlock and true firs, which are more susceptible to decay than Douglas-fir. Worse, the understory is often wounded by the logging. Obviously, a manager has many factors to consider, and decay is just one of them.


Relationships of stem decay to site are not very consistent, and no sweeping generalizations can be made. In an enormous study of red ring rot, caused by Porodaedalea pini in Pseudotsuga menziesii (Douglas-fir), Boyce & Wagg found that decay begins at a younger age and reaches higher levels on good sites compared to poor sites ​[3]​. However, they also found it more common in central and southern Oregon (dry) than in other parts of the Pacific Northwest; also more common on southern slopes than northern. There is a general tendency for levels of stem decay to be greater in the drier parts of a tree’s range. The higher temperatures may be more important than moisture in these cases. Dichomitus squalens is much more serious on ponderosa pine in Arizona and New Mexico (10-50% cull) than in California. This is thought to be because the first states get summer rains with high humidity, allowing infection in the dead branches. In pine regions of California, summers are dry.


Here’s another concept. We generally feel that the factors outlined above are more important in determining infection than the availability of spores. We assume that the spores will usually be there. However, in many cases, we do not have hard evidence for this.


Indicators are the external signs and symptoms of the presence of decay. They are very useful in diagnosis, but also in management. Knowledge, skill, and experience in recognizing and understanding indicators is essential in working with and managing stem decays.  Indicators vary among tree species and decay fungi.  Traditionally, forest pathologists and/or mensurationists would conduct a cull study in a given forest region to quantify losses associated with given categories of indicators.  These were then used to produce local cull manuals that foresters could use when cruising a stand to calculate defect and estimate net merchantable volume. Cull guides or manuals (e.g., ​[1]​) provide valuable information to foresters, especially cruisers, in managing forests with stem decays.

Fruiting. It often happens that only a small portion of trees with decay have fruiting, but it’s a great indicator when it occurs. Depending on the fungus, this may be big beautiful conks, small conks, mushrooms, or fruiting flat on the surface, with or without pores. Some fungi fruit only after the tree or infected branches fall to the ground. A few produce so-called “sterile conks”, which are not conks at all, but black fungal masses protruding from the stem.

Punk knots. Not many fungi result in punk knots, but they include Porodaedalea pini, the most important cause of stem decay in conifers in the northern hemisphere. A punk knot is a knot where at least the inner wood is decayed and replaced by fungal tissue that looks like the context (flesh) of the conk. The tissue is not visible at the surface, but only when the bark is shaved away. Such knots may be swollen or not. Boyce termed those “swollen knots” vs. “punk knots”, respectively ​[2, 3]​. Since they are the same except for swelling, it is perhaps less confusing to refer to the former as swollen punk knots ​[9]​. Less commonly, punk knots may be sunken.

Exposed decay. Decay may be exposed at branch stubs, wounds, and cavities. That’s a pretty good indicator of decay, don’t you think?

Sounding. When decay is advanced near the base of a tree, typically one can hear the low-pitched, hollow sound when striking the bark with a heavy tool. This can be considered an indicator.

Infection courts. These include lightning scars, fire scars, frost cracks, and mechanical injury from trees falling, wind damage such as broken tops, logging damage, etc. Dead tops, broom rusts that infect the stem, and old dwarf mistletoe cankers can also be infection courts. They are not definite evidence of decay, only that decay is more likely than in a tree without indicators. The larger the infection court, the more likely is decay. Likelihood also depends greatly on the tree species.

Stem decay impacts

Because losses increase with stand age, they were generally highest in the days of cutting old-growth stands and lowest in young, managed stands.

In the 1940s, it was estimated that stem decays caused an annual loss of 1.5 billion board feet in commercial forests of the US ​[4, 10]​.

Management to reduce decay

Decayed trees should be removed

In thinnings and other partial cuts, decayed trees should be removed. This is less an issue of reducing inoculum than of improving the residual stand and giving healthy trees more room to grow.

An exception is in cases where wildlife, particularly endangered species, are a consideration. Many animals nest in decayed trees. For instance, red cockaded woodpecker in southern pines. One reason for their endangerment is the shortage of such trees in intensively managed forests.

Cuts whose main goal is to remove such defective trees are called sanitation cuts. Those marking the trees, in fact for any cut other than clear-cut, should be trained to recognize indicators of decay in the particular tree species.

Also, salvage cuts after a fire or storm damage can be done to remove trees that have fresh infection courts that will certainly lead to decay.

A common practice in old days and no doubt still done in some cases today, was to leave decayed, defective trees as seed trees. The idea was that they weren’t worth harvesting anyway, let’s get some use out of them. But susceptibility to decay probably has a significant genetic component, so in doing that you could reduce the quality of future stands.

Wounding should be prevented

There are many approaches that can be used to reduce wounding:

  • Clear-cutting, where otherwise possible is advantageous in this regard.
  • Plan logging roads carefully to avoid damage to residual stand. Their are techniques for this. Use trees to be harvested as bumper trees, then harvest them last.
  • Keep stand entries to a minimum, avoid frequent light cuts.
  • Keep vehicles away from trees.
  • If pruning is practiced, do it early, when branches are less than few inches diameter.

For cases where animal wounds are damaging, exclude or reduce cattle or deer. For cases where fire scars are important, protect against fire.

Other infection courts

For cases where larger branch stubs are infection courts, maintain stand density to reduce their size, consider pruning early. I’m not aware of any operational tests of this or actual cases where it was used, but it should be effective.


Stump sprouts can be infected via heartwood through the stump. In pruning excess sprouts, favor lower sprouts that are less likely to be infected this way.

Favor sprouts that are alone. When sprouts are large (>3″) clumps of very close sprouts should be treated as a unit, either all cut or all left.

Pathological Rotation

Total and merchantable wood volume of Abies balsamea (balsam fir) over the life of a stand in the Lake States. Each measure of wood volume is separated into gross, decay, and net (gross minus decay/cull). Based on data from ​[5]​.

Yield tables are often used in forestry to predict wood volume produced in a stand of given species, age, and site quality. They usually predict gross yield. However, yield may be much less when you account for decay. At right is an example, shown in terms of both total volume and merchantable volume (or what would be merchantable without decay).

The practical length of time a stand should grow for timber production (rotation age) may be influenced by decay. This is referred to as pathological rotation. The concept had been bubbling up in the literature, but Meinecke in 1916 was apparently the first to use that term ​[6]​. He stated “. . . the upper limit of this range [of cutting ages] should not lie beyond the period at which the gain from increment is offset by loss from decay . . .” The data of Kaufert ​[5]​, using balsam fir, provide a good example (data are graphed at right). Pathological rotation should really be based on volume and growth on an area basis rather than tree basis. It may be defined variously:

  • The absolute upper limit, as Meinecke wrote in the quote above, is the age at which volume added by growth = volume lost to decay. At this point, the slopes of the decay/cull and gross curves at right are equal, and the stand is at maximum net volume (peak net volume in graphs). Carrying the stand longer will result in reduced sound volume.
  • In practice, it is the age beyond which carrying the stand is not economically feasible because net volume growth is flat or decreased by decay ​[7]​. This is somewhere between the peak net growth rate (also known as maximum net periodic increment) and peak net volume.

Pathological rotation may need to be factored into a manager’s decision to determine the actual rotation based on all considerations. In some species, such as aspen, pathological rotation is usually limiting. Here are some examples of fairly short pathological rotation ages:

aspenMinnesota40-50 ​[8]​
 Utah80-90 ​[7]​
yellow birchNova Scotia120
balsam firNew York70


  1. 1.
    Aho PE. 1982. Indicators of cull in western Oregon conifers.  General Technical Report GTR-PNW-144. U.S. Department of Agriculture, Forest Service, Pacific Northwest Forest and Range Experiment Station <10.2737/pnw-gtr-144>.
  2. 2.
    Boyce JS. 1961. Forest Pathology, 3rd ed. New York: McGraw-Hill Book Company. 572 pp.
  3. 3.
    Boyce JS, Wagg JWB. 1953. Conk Rot of Old-Growth Douglas-fir in Western Oregon.  Bulletin 4. Oregon Forest Products Laboratory and Oregon State Forestry Department <https://ir.library.oregonstate.edu/downloads/k35695737>.
  4. 4.
    Hepting GH, Kimmey JW. 1949. Heart Rot. In: Yearbook of Agriculture. Trees 1849:462–465. Washington DC, USA: US Department of Agriculture <https://naldc.nal.usda.gov/download/IND43895085/PDF>.
  5. 5.
    Kaufert F. 1935. Heart rot of balsam fir in the Lake States, with special reference to forest management. University of Minnesota Agric. Exp. Station Technical Bulletin 110:1–27 <https://conservancy.umn.edu/bitstream/handle/11299/204039/mn1000_agexpstn_tb_110.pdf>.
  6. 6.
    Meinecke EP. 1916. Forest Pathology in Forest Regulation. Bulletin (Contributions from the Bureau of Plant Industry) vol. 275. Washington, D.C.: United States Department of Agriculture <https://www.google.com/books/edition/_/p1cDAAAAYAAJ>.
  7. 7.
    Meinecke EP. 1929. Quaking Aspen: A Study in Applied Forest Pathology.  Technical Bulletin 155. Washington, D.C.: United States Department of Agriculture <https://www.google.com/books/edition/_/Qwck7ovwX1wC>.
  8. 8.
    Schmitz H, Jackson LWR. 1927. Heart rot of aspen with special reference to forest management in Minnesota. Technical BuIlletin 50. University of Minnesota Agricultural Experiment Station <https://conservancy.umn.edu/bitstream/handle/11299/203990/mn1000_agexpstn_tb_050.pdf?sequence=1>.
  9. 9.
    Tainter FH, Baker FA. 1996. Principles of Forest Pathology. New York: John Wiley & Sons, Inc. 805 pp.
  10. 10.
    Wagener WW, Davidson RW. 1954. Heart rots in living trees. The Botanical Review 20(2):61–134 <https://pdfslide.net/documents/heart-rots-in-living-trees.html>.