Managing Heart Rot in Live 

Trees for Wildlife Habitat in 

Young-Growth Forests of 

Coastal Alaska

Paul E. Hennon and Robin L. Mulvey

Pacific Northwest 

Research Station

General Technical Report 

PNW-GTR-890

February 2014

United States Department of Agriculture

Forest Service

DEPAR TMENT OF AGRICULT URE
Authors

Paul E. Hennon is a research plant pathologist, Pacific Northwest Research 

Station, Forestry Sciences Laboratory, 11175 Auke Lake Way, Juneau, AK 99801; 

Robin L. Mulvey is a plant pathologist, Alaska Region, State and Private Forestry, 

Forest Health Protection, 11175 Auke Lake Way, Juneau, AK 99801.

Cover photograph by Robin Mulvey.

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Abstract

Hennon, Paul E.; Mulvey, Robin L. 2014. Managing heart rot in live trees for 

wildlife habitat in young-growth forests of coastal Alaska. Gen. Tech. Rep. 

PNW-GTR-890. Portland, OR: U.S. Department of Agriculture, Forest Service, 

Pacific Northwest Research Station. 23 p.

Stem decays of living trees, known also as heart rots, are essential elements of 

wildlife habitat, especially for cavity-nesting birds and mammals. Stem decays are 

common features of old-growth forests of coastal Alaska, but are generally absent 

in young, managed forests. We offer several strategies for maintaining or restoring 

fungal stem decay in these managed forests that can be used to enhance specific 

types of wildlife habitat. 

Keywords: Stem decay, heart rot, cavity nest, wildlife habitat.
Contents

1 Introduction

1 Background

13 Silvicultural Techniques to Maintain and Restore Stem Decay

17 Conclusions and Key Points

18 Acknowledgments

18 Metric Equivalents

19 Literature Cited

23 Appendix
1

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Introduction

Stem decays (also known as heart rots) are specialized fungi that cause internal 

decay of living trees. These fungi are ubiquitous and important elements of the oldgrowth coastal rain forests in Alaska. Herein, we summarize some important contributions of stem decays in creating wildlife habitat and providing other ecological 

services. We then offer silvicultural techniques that can be used to retain or restore 

desirable amounts of stem decay in coastal Alaskan forests. These treatments could 

be prioritized where wildlife habitat or late-successional characteristics are primary 

resource goals in managed forests. Over time, measures taken to actively manage 

wood decay in young stands will facilitate predictable types of wildlife habitat and 

other desired features and processes of old-growth forests. 

Background

In coastal Alaska, stem decays cause about 30 percent loss of merchantable wood 

volume in mature forests (fig. 1) (Farr et al. 1976, Kimmey 1956). Timber cull studies are often the best or only source of information about the incidence and quantity 

of decay in live forest trees, and report results in terms of impacts on merchantable 

volume. Stem decay is especially prevalent in old-growth forests with infrequent 

fire, where long-lived trees are invaded by fungi that slowly consume wood. Beyond 

the considerable commercial losses to timber value, stem decay fungi also influence a number of important ecological processes. Carbon and nutrient cycles and 

forest structure are continually altered by these fungi in every old-growth forest 

in coastal Alaska. Stem decay fungi are important drivers of stand structure and 

dynamics by causing tree death and canopy gap formation through bole breakage 

(Hennon 1995, Hennon and McClellan 2003). In contrast, stem decays are generally 

absent or far less abundant in young, managed coastal forests (Tait et al. 1985). In 

southeast Alaska, there are 440,000 acres of young-growth on the Tongass National 

Figure 1—Stem decay fungi cause substantial losses to commercial timber resources (A) and drive a range 

of ecological functions, including canopy gaps caused by tree death, that maintain old-growth functions (B).

Stem decay is 

especially prevalent in 

old-growth forests with 

infrequent fire, where 

long-lived trees are 

invaded by fungi that 

slowly consume wood.

In contrast, stem 

decays are generally 

absent or far less 

abundant in young, 

managed coastal 

forests.

Paul HennonPaul Hennon
2

GENERAL TECHNICAL REPORT PNW-GTR-890

Forest, 245,000 ac on Alaska Native Corporation lands, and 45,000 ac on Alaska’s 

state lands. Some of these lands currently designated to be managed primarily for 

non-timber objectives offer opportunities for active management that promotes or 

accelerates characteristics of old-growth forests. The Tongass National Forest Land 

and Resource Management Plan emphasizes that management should consider 

wildlife and vegetation diversity implications on all land use designations. We 

recommend considering treatments to restore stem decay for wildlife habitat in 

stands or portions of stands that will persist over time (i.e., will not be harvested 

in the foreseeable future) to provide longer term habitat. This report focuses on the 

role of stem decays in providing habitat, and on management approaches that can be 

used to promote desired amounts of stem decay in managed stands of any age. 

Wildlife habitat—

In Pacific Northwest forests, 25 to 30 percent of bird and mammal species are 

dependent on decayed wood in trees to provide habitat for nests, dens, and roosts 

(Bunnell et al. 1999, Harestad and Keisker 1989, Li and Martin 1991, McClelland 

and Frissell 1975, Raphael and White 1984). In Alaska, it is estimated that 27 species are obligate cavity users. Birds, bats, and squirrels tend to use cavities obligatorily, while many mammals use cavities opportunistically (Bunnell et al. 1999). 

Lack of sufficient cavities for habitat is often considered a key threat to at-risk 

forest species, especially woodpeckers (Bunnell et al. 1999). Among cavity-nesters, 

primary cavity excavators are particularly important because the cavities that they 

create become legacy structures used by other wildlife in the decades that follow. 

In North America, up to 77 percent of nesting cavities used by nonexcavators are 

produced by primary excavator birds (rather than decay without excavation) and the 

majority of cavities persist for more than a decade (Cockle et al. 2011). 

In southeast Alaska, densities of cavity-nesting bird species were found to be 

significantly lower in young stands (35 years old) compared to old-growth stands in 

the two decades following thinning treatments (Matsuoka et al. 2012). This effect 

occurred regardless of thinning treatment density, probably because of the lack of 

large trees and snags with adequate decay for cavity-nesting habitat in the previously clearcut stands. Future monitoring of these stands may show that injuries 

caused by different logging treatment intensities may accelerate the rate of stem 

decay development and the return of cavity nesters.

Most research has evaluated the use of dead trees (snags) and snag cavities by 

bird species compared to the use of live trees with decay. Standing snags offer valuable habitat in old forests to cavity dwellers. In coastal Oregon and Washington, 

northern flying squirrels preferred den sites (cavities and other structures) in live 
3

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

trees to dead trees at a ratio of 2:1 (Carey et al. 1997), but use of cavities in live and 

dead trees was nearly equal on Prince of Wales Island in Alaska (Pyare et al. 2010).

In southeast Alaska, at least 12 species of birds relied on tree cavities for roosting 

or nesting in old forests (table 1; Kessler 1979), where usage was typically in the 

upper third of the tree bole (Hughes 1985). Wagner (2011) found that red-breasted 

sapsuckers on Kupreanof Island in southeast Alaska created nesting cavities in 

large-diameter spruce and hemlock snags, with an average cavity height and tree 

height of 58 ft and 90 ft, respectively. In a study that measured the number of dead 

trees in unmanaged old-growth stands in southeast Alaska, Hennon and McClellan 

(2003) reported a density of 17 to 22 large dead trees (diameter at breast height ≥ 

18 in) per acre; 20 to 35 percent of these were standing snags, while the rest were 

on the forest floor, having been uprooted or bole-snapped. These densities of dead 

tree structures in old-growth forests can be used as a reference condition to contrast 

with young-growth stands.

Table 1—Cavity-dependent bird species on Kosciusko Island in 

southeast Alaska (Kessler 1979) and bird species considered to 

be old-growth-dependent in southeast Alaska (Noble 1978)

Cavity-dependent Old-growth-dependent 

Boreal chickadee Sooty grouse

Boreal owl Brown creeper* 

Brown creeper* Chestnut-backed chickadee*

Chestnut-backed chickadee* Downy woodpecker*

Downy woodpecker* Golden-crowned kinglet

Hairy woodpecker* Hairy woodpecker*

Northern hawk-owl Audubon’s warbler

Northern saw-whet owl Red-breasted sapsucker

Red-breasted nuthatch Red-tailed hawk

Red-breasted sapsucker Ruby-crowned kinglet

Three-toed woodpecker* Sharp-shinned-hawk

Western screech-owl Three-toed woodpecker*

* = Indicates that species appear in both lists. Common names of birds have been updated.

Live trees with internal wood decay offer wildlife habitat similar to snags and 

downed trees, but there are a few important distinctions. First, live trees with stem 

decay generally remain standing longer than snags, providing longer-term habitat 

for species that use standing structures. Second, large hollows with a solid exterior 

are produced in live trees only when white rot stem decay fungi create a softened 

or hollow interior while the tree continues radial growth to provide sound outer 

wood. In contrast to a live tree that develops stem decay, a sound tree that is killed 

outright by cutting or that dies standing will decay from the outside in, and will not 

In contrast to a live 

tree that develops stem 

decay, a sound tree 

that is killed outright 

by cutting or that dies 

standing will decay 

from the outside in, 

and will not develop a 

distinctly decayed or 

hollow interior.
4

GENERAL TECHNICAL REPORT PNW-GTR-890

develop a distinctly decayed or hollow interior. Black bears prefer large hollows for 

hibernation, seeking out such structures in old-growth forests of southeast Alaska 

(DeGayner et al. 2005). Some of these hollow structures used by bears are present 

in dead trees, but were originally formed or initiated through the action of stem 

decay fungi while trees were still alive. These unique structures created in living 

trees can provide important habitat features that persist long after tree death. 

Stem decay fungi—

Stem decay is caused by fungi that invade and colonize the wood of living trees and 

decompose wood before the tree is dead. These fungi vary in appearance, specialization, infection biology, and type of decay produced (table 2; fig. 2). Some species 

require the exposed wood of wounds for entry, continue their decay after the tree 

dies, and are also general decomposers of dead trees (e.g., Fomitopsis pinicola). 

Other wood decay fungi initiate in the roots and spread to decay the tree’s lower 

bole as a butt rot (e.g., Phaeolus schweintizii). Several highly specialized fungi 

invade through small branches and are generally restricted to live or recently killed 

trees (e.g., Phellinus pini and Echinodontium tinctorium). In addition to the stem 

decay fungi that are adapted to infect live trees, others are particularly important 

for softening wood of dead trees for excavation in coastal Alaska (fig. 3). 

Table 2—Stem decay fungi on live conifer trees in southeast Alaska 

Heart and butt Western Mountain Western Sitka Lodgepole Type of

rot fungia hemlock hemlock redcedar spruce pine Rot/decay

Armillaria spp. X X X X X White

Ceriporiopsis rivulosa X White

Coniophora sp. X Brown

Echinodontium tinctorium R X Brown

Fomitopsis pinicola X X X Brown

Fomitopsis officinalis X Brown

Ganoderma spp. X X White

Heterobasidion annosum X X White

Laetiporus sulphureus X X R X Brown

Phaeolus schweinitzii X X Brown

Phellinus hartigii X R White

Phellinus pini X X X X White

Phellinus weirii X White

a Some root rot fungi are included because they are capable of causing both root and butt rot of conifers.

R indicates that the fungus is rare on this host.
5

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Figure 2—Conks (fruiting bodies) 

of several stem decay fungi of 

conifers in coastal Alaska. (A): 

Echinodontium tinctorium (paint 

fungus), (B) Ganoderma applanatum (artist’s conk), (C) Ganoderma tsugae (lacquer or varnish 

conk), (D) Phaeolus schweinitzii

(velvet-top fungus), (E) Laetiporus 

sulphureus (sulphur fungus), (F) 

Fomitopsis pinicola (red belt conk), 

(G) Phellinus pini (pini conk or red 

ring rot), and (H) Phellinus hartigii

(Hartig’s conk). Photos by Robin 

Mulvey.
6

GENERAL TECHNICAL REPORT PNW-GTR-890

The fruiting bodies of stem decay fungi (usually conks or mushrooms) disperse 

airborne spores, but the actual degradation of wood is by the threadlike vegetative 

part of the fungus (hyphae) inside trees. Two groups of stem decay fungi (brown 

and white rots) can be distinguished by their chemical degradation of wood cells, 

although both soften wood by breaking down cell walls. Brown rot fungi degrade 

only cellulose, leaving the other primary constituent of wood (lignin) as a considerably less dense but fairly stable residual structure that is suitable for excavation by 

woodpeckers. White rot fungi digest both cellulose and lignin, which can create 

hollows in trees that are considered to be a key habitat feature for some birds and 

mammals. Most of the internal wood decay of Sitka spruce is brown rot (84 percent), while most of the wood decay of western hemlock is white rot (63 percent) 

(Kimmey 1956; fig. 4). These striking differences in decay between tree species 

likely influence their use as habitat. 

Some fungi have preferences for different parts of the tree, most likely because 

of their manner of infection. The fungus Phaoelus schweinitizii resides in the lower 

stem and major roots. Fomitopsis pinicola can occur anywhere on roots or the stem, 

but it is most common low on the bole, where frequent wounds promote infection. 

Fomitopsis officinalis, a fairly rare brown rot fungus that produces large conks 

Figure 3—Fomitopsis pinicola (A) decays dead woody 

tissue of live or dead trees, 

softening snags for excavation 

and decomposing downed 

woody debris. Laetiporus sulphureus (B) and Ganoderma 

applanatum (C) also serve to 

prepare snags for excavation. 

Photos by Robin Mulvey.

Most of the internal 

wood decay of Sitka 

spruce is brown rot 

while most of the 

wood decay of western 

hemlock is white 

rot. These striking 

differences in decay 

between tree species 

likely influence their 

use as habitat.
7

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Figure 4—Contribution of fungi that cause brown rot (tan wedges) and white rot (white wedges) in living western hemlock and Sitka 

spruce in the forests of southeast Alaska. Adapted from Kimmey (1956). Note that Kimmey made classifications to fungal species 

primarily based on the visual appearance of wood decay, and these results should be validated by modern genetic techniques.

Armillaria spp.

(26%)

Heterobasidion annosum

(20%)

Ganoderma applanatum (1%)

Pholiota adiposa (9%)

Other brown rots (1%)

Phellinus pini (1%)

Phellinus hartigii (5%)

Fomitopsis

pinicola

(23%)

Hericium abietis (3%)

Phaoelus schweinitzii (5%)

Laetiporus

sulphureus 

(6%)

Western hemlock

38% brown rots

62% white rots 

Sitka spruce

84% brown rots

16% white rots 

Fomitopsis

pinicola

74%

Phellinus pini (9%)

Other white rots (1%)

Heterobasidion 

annosum (1%)

Armillaria spp. (5%) 

Other brown rots (2%)

 Laetiporus sulphureus (4%) 

Phaoelus 

schweinitzii (4%)

on live spruce, is most often found high on tree boles, perhaps because it infects 

through top breaks. As with the type of decay, the location of wood decay in trees 

probably influences wildlife use. For example, Hughes (1985) found that the majority (77 percent) of excavated cavities occurred in the upper one-third of tree boles 

on Admiralty Island, compared to 22 percent in the middle third and 1 percent in 

the lower third. 

Influence of tree age and species—

Increasing incidence and amount of decay with greater tree age is a consistent feature in forests worldwide, with the actual age-decay relationship differing by tree 

species, and, in some cases, geography (Boyce 1961). The term “pathological rotation” has been used to indicate the age at which a forest managed for timber begins 

to incur unacceptable heart rot losses (Meinecke 1916). This age was estimated to 

be 225 to 275 years for western hemlock in western British Columbia (Buckland et 

al. 1949) and 250 to 300 for Sitka spruce in the Queen Charlotte Islands, although 

there was little decay in spruce trees less than 200 years old (Bier et al. 1946).

There are marked differences in the amount of stem decay between young and 

old forests in coastal Alaska. Stem decay in very young trees cannot develop until 

trees begin producing heartwood. Even though young trees can initiate heartwood 
8

GENERAL TECHNICAL REPORT PNW-GTR-890

at 14- to 18-years old (Hillis 1987, Moore 2011), conifers less than 100 years old 

in southeast Alaska have little heartwood decay (Harris and Farr 1974). However, 

by 200 years old, 65 percent of western redcedar, 50 percent of western hemlock, 

and 20 percent of Sitka spruce trees have internal wood decay (Kimmey 1956). 

Decay incidence estimates can be misleading because there may be significant 

variation in the amount of decay per tree (Farr et al. 1976). For wildlife habitat, 

the quantity of decay (gross volume loss) may be a more meaningful estimate than 

decay incidence. Kimmey (1956) calculated percentage of volume decay in terms of 

percentage of board-foot cull and percentage of cubic-foot cull (fig. 5) and documented defect rates around 30 percent depending on the measure used. Cubic-foot 

calculations represent decay volume percentage more accurately than board-foot 

calculations, because board-foot cull calculations were rounded up more liberally. 

Board-foot calculations tend to be more useful for timber cruisers. Farr et al. (1976) 

calculated an overall percentage board-foot defect of 31 percent and confirmed 

Kimmey’s (1956) relationship between tree age and the percentage volume of decay 

in southeast Alaska (fig. 5). Surprisingly, western redcedar (not shown in fig. 5) has 

the greatest amount of stem decay of the conifer species in coastal Alaska. Western 

hemlock has more stem decay than Sitka spruce and generally acquires decay at an 

earlier age. This may result from differences in physiology between the two host 

species, or in the behavior of fungi that infect them.

Tree age (years)

0 100 200 300 400 500 600 700 800

Volume cull (percentage)

0

10

20

30

40

50

60

Sitka spruce

Western hemlock 

Figure 5—Influence of tree age on percentage of wood volume that is cull. Adapted using data from 

table 10 in Kimmey (1956) of mean gross volume cull values for dissected trees grouped by 50-year 

age intervals. Curves were fit with polynomial equations.

Western hemlock 

has more stem decay 

than Sitka spruce and 

generally acquires 

decay at an earlier age.
9

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Several factors are probably responsible for the high rate of defect in old-growth 

forests. During their growth from the understory to the upper canopy, large old 

trees have often experienced multiple, accumulated injuries from storms, neighboring trees falling, and animal damage. Visual indicators of past injuries (e.g., scars, 

wounds, frost cracks, broken tops) are positively associated with internal wood 

decay (Farr et al. 1976). The longevity of old trees provides adequate time for 

extensive decay to develop gradually following fungal infection through wounds 

and other infection courts (i.e., roots, branches, dead branch stubs). It is thought that 

the canopy status and vigor of trees may affect their susceptibility to certain decay 

fungi, because suppressed trees seal off old branch stubs and wounds more slowly 

than do vigorous trees. For example, Echinodontium tinctorium, which is rare in 

southeast Alaska, infects through small branch stubs; it more commonly affects 

suppressed trees, because branch stubs of these trees heal more slowly, providing greater time for infection to occur (Filip et al. 2009). Relative bark thickness 

may also influence tree species’ susceptibility to decay, as thin-barked species are 

more prone to larger and deeper wounds than species with thicker bark. Chemical 

defense compounds in the heartwood of some tree species may afford them relatively greater resistance to decay. However, even tree species with decay-resistant 

wood (e.g., western redcedar and yellow-cedar) can be highly defective as old trees, 

because a few specialized fungi can overcome their chemical defenses. 

The general relationship between decay incidence and volume and tree age 

translates to greater decay in old stands compared to young stands. The abundance 

of large snags is also reduced in young forests, unless they were retained at the 

time of harvest. There are few mortality agents that kill larger individual trees in 

young-growth stands (Tait et al. 1985). Instead, suppression mortality in young 

stands produces abundant small snags. Because western redcedar and yellow-cedar 

snags have decay-resistant heartwood, they probably do not offer significant cavitynesting habitat as snags unless they were decayed as live trees. Note that downed 

trees with hollows are common in young-growth stands, where they are a legacy of 

the cull trees left during the initial old-growth harvest. 

Influence of tree wounds—

Many important stem decay fungi, especially those of western hemlock, enter 

through mechanical wounds (fig. 6). For example, an estimated 65 percent of the 

stem decay in old-growth western hemlock in British Columbia is associated 

with natural injuries not caused by forest management (Buckland et al. 1949). 

Natural wounds to tree boles are common in coastal Alaska, and often originate 

from falling neighboring trees, internal cracks, splitting forks, or broken tops or 

branches (Hennon and McClellan 2003). Farr et al. (1976) found that trunk scars 

Many important stem 

decay fungi, especially 

those of western 

hemlock, enter through 

mechanical wounds.
10

GENERAL TECHNICAL REPORT PNW-GTR-890

extending into the heartwood are the most common injury to western hemlock and 

Sitka spruce, affecting 24 and 9 percent of trees, respectively, followed by basal 

scars for western hemlock and frost cracks for Sitka spruce. Animal feeding causes 

localized tree injury in specific regions of southeast Alaska. Porcupines feed on 

Sitka spruce and western hemlock forests close to the mainland (Eglitis and Hennon 1997), while brown bears damage yellow-cedar trees on several large islands 

(Hennon et al. 1990). The vertical position of wounding on tree boles is important 

to the creation of some forms of habitat, because some animals only use structures 

far from the ground. Lower bole wounds provide a form of habitat, and also may 

eventually lead to canopy gap formation as trees die through bole breakage. Natural 

top damage is mainly caused by wind or loading from snow and ice. 

Logging damage to trees during both falling and yarding activities produces 

tree injuries that mimic natural wounds. The tree species in coastal Alaska have 

thin bark (in part because of the absence of fire), so their boles and exposed roots 

are easily wounded. Precommercial thinning of small stems does not cause significant injury to retained trees, but any form of commercial logging with tree removal 

Figure 6— (A) Recent bole wound with sound, exposed wood and (B) older bole wound with extensive internal decay.

Logging damage to 

trees during both 

falling and yarding 

activities produces 

tree injuries that mimic 

natural wounds.

Paul Hennon

Robin Mulvey
11

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

will result in some tree injury. In a commercial thinning trial of young-growth 

stands (the Second Growth Management Program on the Tongass National Forest 

in the 1980s), approximately one-half of the residual trees were injured (Hennon 

1990). Most of these wounds were to the lower bole, although exposed roots and 

tops of some trees were also damaged or broken. Of the bole wounds, however, 

just over a quarter were large enough to lead to substantial decay (i.e., more than 1 

ft2 surface area of bark removed; Wright and Isaac 1956). The frequent lower bole 

wounds from logging are similar to common forms of natural tree injury in unmanaged forests. These wounds may eventually provide habitat for some animals, and, 

over the long term (>100 years), contribute to canopy gaps through bole breakage 

(Hennon and McClellan 2003). The less frequent logging wounds higher on tree 

boles may be particularly valuable for some species. Continued monitoring of tree 

injuries from commercial thinning will yield more information on the incidence 

and sizes of wounds that can be used to project decay, as described below. 

By dissecting and quantifying the amount of wood decay in wounds of different 

sizes and ages, equations were developed to predict future wood decay of wounded 

trees (Hennon and DeMars 1997). The development of wood decay is relatively 

slow in southeast Alaska, developing over the course of decades (fig 7). Wounds 

less than 5 years old are not significantly associated with decay (Farr et al. 1976). 

Larger bole wounds lead to more overall wood decay that develops at a relatively Stain and decay (ft3

)

3.0

2.5

2.0

1.5

1.0

0.5

0

Wound age (years)

0 10 20 30 40 50 60 70 80 

Sitka spruce

Western hemlock 

7 ft

2

5 ft

2

3 ft

2

1 ft

2

7 ft

2

5 ft

2

3 ft

2

1 ft

2

Figure 7—Predicted rate of stain and decay development in western hemlock and Sitka spruce 

with tree bole wounds of different sizes (given as wound surface area). Modified from Hennon and 

DeMars 1997.

The development 

of wood decay is 

relatively slow in 

southeast Alaska, 

developing over the 

course of decades.
12

GENERAL TECHNICAL REPORT PNW-GTR-890

faster rate. The pattern of wood decay differs between western hemlock and Sitka 

spruce. Once colonized by fungi, decay develops deep in the wood beneath wounds 

of hemlock, eventually creating a column of decay. In spruce, decay develops only 

in the outer wood, and the subsequent rate of advancement is very slow. These 

differences may explain the greater amount of stem decay in western hemlock than 

Sitka spruce in old forests. 

Harvest activities sometimes cause unintentional top breakage (fig. 8). We 

know less about decay development in top breaks compared to bole wounds, 

although more decay is expected to develop in larger diameter breaks. Farr et al. 

(1976) found that western hemlock trees with evidence of broken tops in the past 

had similar percentages of decay volume as trees with basal scars, but that broken 

tops were less common. When top breakage occurs low in the live crown, or below 

the live crown, the tree will probably die and have no chance of developing an 

internal decay column. 

Figure 8—Top breakage during logging provides large infection courts to fungi that 

eventually lead to extensive internal decay. Bole breakage that occurs near or below 

the live crown results in tree death (snag creation), which is less desirable than the 

development of an internal decay column in a tree that remains alive.

When top breakage 

occurs low in the live 

crown, or below the 

live crown, the tree 

will probably die and 

have no chance of 

developing an internal 

decay column.

Paul Hennon
13

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Silvicultural Techniques to Maintain and Restore Stem Decay

Strategies to encourage stem decay in managed forests (table 3) can enhance 

wildlife habitat but may not be appropriate in forests primarily managed for timber 

production. Landscape context can help to guide treatment decisions. For example, 

a small young-growth stand surrounded by old-growth forest may not require the 

same treatment as a large watershed with a history of extensive clearcuts. Within 

stands, the desired number of trees with stem decay, tree species with decay, and 

location of decay on tree boles need to be determined by wildlife biologists and 

weighed against potential loss to timber values, if timber production is a management objective. These decisions can be made in conjunction with forest pathologists 

to manage for specific types of wood decay or decay in specific parts of the tree. 

Stem decays can be maintained by selecting defective old trees to protect during 

green tree retention harvests of old-growth forests. In even-aged young-growth 

forests, restoration efforts through tree wounding or direct fungal inoculation may 

be needed to accelerate the return of stem decays and associated habitat features. 

Management favoring stem decay fungi could be one part of a young-growth 

restoration strategy, with other components focused on the creation of canopy gaps, 

multiple-canopy strata, snag recruitment, and other structural elements of oldgrowth forests.

Table 3—Strategies to maintain and restore stem decay

Management strategy Description

Maintain stem decay structures Trees with indicators of decay can be selected for

 through green tree retention harvests. retention during harvest, and buffered by other 

 retained trees, to maintain habitat refugia within 

 cut stands.

Wait for stem decay to return Stem decay will return to untreated young stands

 to young stands without treatment. through natural tree injury and fungal infection

 and growth over the course of centuries.

Wound trees through logging Intentional or unintentional injury during stand

 injury and top breakage. entries will create infection courts for stem decay 

 fungi, significantly accelerating decay development

 compared to untreated young-growth stands; 

 intentional injury with logging equipment or 

 explosives can target parts of the tree less 

 frequently wounded during logging operations 

 (upper boles) that are preferred by wildlife species.

Artificially inoculate select trees Particular tree species can be inoculated

 with stem decay fungi. strategically with specific species of decay fungi 

 that cause desired types of decay in targeted 

 locations on the tree bole; treatments can be 

 tailored to provide habitat for selected bird and 

 mammal species.

A small young-growth 

stand surrounded 

by old-growth forest 

may not require the 

same treatment as a 

large watershed with 

a history of extensive 

clearcuts. 
14

GENERAL TECHNICAL REPORT PNW-GTR-890

Maintain stem decay structures through green tree retention harvests—

Young trees that regenerate on clearcut harvest sites typically lack internal decay 

for 100 to 150 years or longer. To retain stem decays in managed forests, an option 

at the time of harvest is to conduct a green tree retention (partial) harvest, rather 

than a clearcut. Trees with conks, cracks, old top damage and other indicators of 

decay (Farr et al. 1976) could be targeted for retention, and even buffered by other 

retained trees. These alternative harvests will always result in some level of top, 

bole, and root injury to residual trees that remain, with damage (to as many as 30 

to 40 percent of residual trees) related to the harvest intensity, spatial distribution, 

and type of yarding (e.g., helicopter vs. ground based) (McClellan and Hennon 

2005). Minimizing these injuries during harvest entries is advisable because further 

injury to old residual trees is not required, as many of them will already contain the 

important stem decay structures for wildlife. 

Young trees growing adjacent to retained large trees are not expected to develop 

stem decay at a higher rate than young-growth trees that regenerate following 

clearcut harvests. Injuries and infection courts, rather than the quantity of airborne 

spore inoculum from nearby infected trees, drive the infection rates of young trees. 

Management activities that create infection courts through wounding have greater 

influence on the incidence of stem decay, as spore inoculum is ubiquitous in stands 

of all ages. Shading from the large retained trees may reduce the growth of neighboring young trees, but a greater infection rate is not anticipated. 

Wait for stem decay to return to young stands without treatment—

Young-growth stands in southeast Alaska generally lack damage agents and contain 

little stem decay. For example, a stand that regenerated after the oldest known 

industrial clearcut in Alaska, the Verstovia forest near Sitka, is now 160 years old 

and generally free of defect. Crown breakage from wind or snow and ice loading 

may be a source of injury that can lead to fungal infection in all young-growth 

stands. Figure 5 illustrates the relationship between stem decay (percentage volume) 

and tree age for the two predominant species, western hemlock and Sitka spruce 

in southeast Alaska. Long rotations will allow stem decay to be restored naturally, 

but stem decays will be lacking in forests scheduled for repeated short rotations in 

the absence of management (or other forms of disturbance) that might increase bole 

injuries and top breakage.

Wound trees through logging injury and top breakage—

Commercial thinning has multiple benefits, which include accelerating timber 

production and opening canopies for more understory growth and deer browse 

(Alaback 1982, Alaback and Tappeiner 1991, Tappeiner and Alaback 1989). Another 

benefit of thinning and tree removal may be the unintentional bole wounding and 

Young trees that 

regenerate on clearcut 

harvest sites typically 

lack internal decay 

for 100 to 150 years or 

longer.
15

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

top breakage of residual trees, which mimics natural wounding and favors the 

development of stem decay. In general, wounds greater than 1 ft2

 are considered 

large enough to lead to substantial decay (Hennon and DeMars 1997, Wright 

and Isaac 1956). Wounds can begin to lead to decay at any point after heartwood 

development, which normally occurs when trees are 14 to 18 years old. Stand-entry 

activities that wound trees may speed the restoration of wildlife habitat and other 

old-growth functions of stem decays by as much as a century compared to younggrowth stands that receive no treatment. In contrast to tree removal, precommercial 

thinning does not cause significant injury to residual trees.

Because unintentional logging wounds are most common in the lower crown, it 

may be appropriate to augment traditional logging injuries with intentional injury to 

the mid and upper boles of selected residual trees. The vertical position of wounding and subsequent decay affects the value and use of cavities as wildlife habitat 

(Hughes 1985). Some species only use structures far from the ground, while others 

are less restricted by cavity location. Lower bole injuries may develop into useful 

habitat features, eventually resulting in canopy gap formation when decayed lower 

boles snap. 

Unintentional top breakage occasionally occurs during harvest activities. Intentional top breakage using a feller buncher or placing explosives in the live crown are 

other management options that can increase stem decay in second-growth stands. 

If decay development is the goal, it is important to avoid top breakage in the lower 

live crown, because the tree will likely die and a decay column will fail to develop. 

Intentional wounding and upper-crown top breakage can be implemented during 

planned entries to young stands with standard equipment, thereby eliminating the 

need for costly supplemental entries. 

Artificially inoculate trees with decay fungi—

A recent review (Filip et al. 2011) discussed the results of direct inoculation of live 

trees with decay fungi in Oregon and Washington. Inoculations are accomplished 

by placing a substrate colonized with fungi into drilled holes in trees (Parks 

and Hildebrand 2002) or by firing shotgun or rifle shots loaded with fungi into 

trees (Baker et al. 1996, Manning 2008). These treatments have the advantage of 

introducing fungi that are known to cause rapid or a certain type of decay into 

desired parts of the tree. Filip et al. (2011), Bednarz et al. (2013), and Manning 

(2008) concluded that fungal inoculation is significantly more effective in causing 

decay than wounding without fungal inoculum. It is important to use native fungal 

species and to collect fungal inoculation materials close to the location where they 

will be used, as these fungi are best-adapted to the hosts and conditions in their 

local environment.

Stand-entry activities 

that wound trees may 

accelerate restoration 

of wildlife habitat 

and other old-growth 

functions of stem 

decays by as much as 

a century compared 

to young-growth 

stands that receive 

no treatment.
16

GENERAL TECHNICAL REPORT PNW-GTR-890

There may be concerns about the potential to increase stem decay in stands 

beyond the inoculated trees, especially in or near stands primarily used for timber 

production. Spores of stem decay fungi are abundant in all forest stands, even young 

stands with little or no decay. The quantity of stem decay differs among forests 

of different ages and conditions because the initiation of decay is dependent upon 

a viable spore landing on a wound, branch stub, or other suitable infection court, 

which requires time and chance. Fungal inoculation should not increase the likelihood of healthy, non-target trees becoming infected (Parks and Hildebrand 2002).

Few studies have evaluated fungal inoculations of Sitka spruce or western 

hemlock; one exception is a recent study from western Washington in which 

western hemlock and Douglas-fir trees were inoculated with Fomitopsis pinocola

(Bednarz et al. 2013). Nonetheless, protocols and lessons learned from inoculations 

of other tree species and in other locations in the Pacific Northwest have application in coastal Alaska. Although Parks and Hildebrand (2002) initially suggested 

that drilling and inserting multiple dowels at the same tree height might cause such 

extensive decay as to lead to bole breakage, Filip et al. (2011) recommended that 

three dowels be inserted at the same tree height (spaced evenly for trees <25 in 

in diameter, or clustered more tightly for larger trees). In contrast to inoculations 

spaced vertically on the tree bole a few feet apart, multiple inoculations at one 

height allow adjacent cultures to merge to form a decay column sufficient for cavity 

nesting more rapidly (<10 years). It is also advisable to insert a PVC (polyvinyl 

chloride) pipe at least 6 in long halfway into each drilled inoculation hole to prevent 

the tree from sealing the hole with resin or continued tree growth. Fast-growing 

trees will form a thicker annual ring around decay compared to slower-growing 

trees, which may make it difficult for primary excavators to access decay. This is 

less likely to present a problem in Alaska compared to Oregon and Washington, but 

is worth considering on particularly productive sites.

Filip et al. (2011) found that species of fungi caused considerably different rates 

of decay following inoculation. The fungus that caused the most rapid decay was 

Fomitopsis cajenderi, which is not native in Alaskan forests and should not be used 

there. Instead, other native species listed in this report that successfully caused 

decay in wet forest types, such as F. officianalis, F. pinicola, and Stereum sanguinolentum, would be good candidates. Phaeolus schweinitzii and Phellinus hartigii

were not evaluated, but are also native to Alaska and were recommended for trial in 

the research needs section of this review. Bednarz et al. (2013) found that F. pinicola inoculations were significantly more effective on western hemlock compared 
17

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

to Douglas-fir, which also suggests that it is important to carefully pair inoculation 

fungi with susceptible tree hosts. Manning (2008) found that Phellinus pini inoculations successfully caused decay of Douglas-fir on Vancouver Island within 5 years 

of inoculation, but indicated that other fungal species with more rapid growth may 

be more appropriate. Rifle inoculation methods resulted in slightly higher rates of 

decay compared to drilled holes in this study, and were less expensive because tree 

climbers were not needed. Filip et al. (2011) should be consulted to review and make 

recommendations for any trials in Alaska. Personnel in the Juneau Office of Forest 

Health Protection have the facilities to culture and develop inoculum of native fungi 

from Alaskan forests. 

Conclusions and Key Points

Stem decays, or heart rots, are caused by native species of fungi that create one of 

the defining characteristics of old-growth forests in coastal Alaska. They create 

unique wildlife habitat, and contribute to a number of other ecological processes, 

including canopy gaps and disturbance dynamics, nutrient cycling, and microbial 

biodiversity. Old forests are often described as “decadent,” but this term is too 

vague to be helpful in identifying the factors that should be managed to restore 

wildlife habitat or other old-growth characteristics. Trees in young stands typically 

lack stem decays, which usually take over 150 years to develop in forests that have 

few damage agents. 

Selection harvests of old-growth forests can target defective trees with existing 

stem decay for retention to serve as wildlife habitat in managed forests. Strategies 

to speed the reintroduction of stem decays in young-growth trees include unintentional and intentional tree injuries (lower and upper bole wounds, and top breakage) 

during silvicultural entries, as well as targeted artificial inoculation of trees with 

decay fungi.

The type and amount of wood decay in live trees differs considerable by tree 

species. Treatments that focus on western hemlock will produce a more rapid stem 

decay and there is considerably more “white rot” than in Sitka spruce. Some wildlife species might prefer to use Sitka spruce, however. The location of tree injuries 

in the lower or upper bole or as top breaks leads to different forms of wildlife habitat as decay develops and produces soft wood and cavities. This variation results in 

habitat diversification, and can also influence the length of time that a decayed tree 

remains alive and standing, which, in turn, affects other ecological processes. 

Strategies to speed 

the reintroduction of 

stem decays in younggrowth trees include 

unintentional and 

intentional tree injuries 

as well as targeted 

artificial inoculation of 

trees with decay fungi.
18

GENERAL TECHNICAL REPORT PNW-GTR-890

Specific actions to increase internal wood decay may be appropriate for younggrowth forests with management goals that favor wildlife habitat and the restoration 

of old-growth characteristics. However, promoting wood decay in trees is not necessary where defective old-growth trees are protected in green tree retention harvests 

or in young-growth stands scheduled for repeated short-rotation harvest. 

Acknowledgments

We thank Gregory Hayward, Sheila Spores, Catherine Parks, and Brian Logan for 

helpful suggestions and comments on early drafts of this report. 

Metric Equivalents

When you know: Multiply by: To find:

Inches (in) 2.540 Centimeters (cm) 

Feet (ft) 0.3048 Meters (m)

Acres (ac) 0.4047 Hectares (ha)

Square feet (ft2

) 0.0929 Square meters (m2)

Cubic feet (ft3) 0.0283 Cubic meters (m3)
19

Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

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Managing Heart Rot in Live Trees for Wildlife Habitat in Young-Growth Forests of Coastal Alaska

Appendix: Common and Scientific Names

Common name Scientific name

Plants:

 Mountain hemlock Tsuga mertensiana (Bong.) Carr.

 Shore pine Pinus contorta Dougl. ex Loud. var. contorta

 Sitka spruce Picea sitchensis (Bong.) Carr.

 Western hemlock Tsuga heterophylla (Raf.) Bong.

 Western redcedar Thuja plicata Donn ex D. Don

 Yellow-cedar Callitropsis nootkatensis (D. Don) Little

Birds:

 Boreal chickadee Poecile hudsonicus

 Boreal owl Aegolius funereus

 Brown creeper Certhia americana

 Chestnut-backed chickadee Parus refeschens

 Downy woodpecker Picoides pubescens

 Golden-crowned kinglet Regulus satrapa

 Hairy woodpecker Picoides villosus

 Northern hawk-owl Surnia ulula

 Northern saw-whet owl Aegolius acadicus

 Pine grosbeak Pinicola enucleator

 Audubon’s warbler Setophaga coronata

 Pine siskin Carduelis pinus

 Red-breasted nuthatch Sitta canadensis

 Red-breasted sapsucker Sphyrapicus ruber

 Red-tailed hawk Buteo jamaicensis

 Ruby-crowned kinglets Regulus calendula

 Sharp-shinned-hawk Accipiter striatus

 Sooty grouse Dendragapus obscurus

 Three-toed woodpecker Picoides tridactylus

 Western screech-owl Megascops kennicottii

Mammals:

 Black bear Ursus americanus

 Marten Martes americana

 Northern flying squirrel Glaucomys sabrinus

Fungi:

 Shoestring fungus Armillaria spp. 

 White butt rot Ceriporiopsis rivulosa

 Coral fungus Hericium abietis

 Coniophora decay Coniophora sp.

 Paint fungus Echinodontium tinctorium

 Red belt fungus Fomitopsis pinicola

 Quinine conk Fomitopsis officinalis

 Artist’s conk Ganoderma applanatum

 Heterobasidion conk Heterobasidion annosum 

 Chicken of the woods Laetiporus sulphureus 

 Velvet top fungus Phaeolus schweinitzii

 Hartig’s conk Phellinus hartigii 

 Pini conk Phellinus pini 

 Laminated butt rot Phellinus weirii

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