Forest and Shade Tree Pathology

Root Diseases

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Root and butt rots

These are wood-decay diseases, and overlap with stem decays. Most are caused by Basidiomycota. They may get in through wounds in the lower part of the tree or penetrate roots directly. They involve the roots and in some cases the butt also.

They may be found killing cambial tissues or growing in the inner wood:

  1. For cases where the fungus kills cambium at the root collar, the tree will die when the root collar is girdled (killed all the way round). This is quickly lethal.
  2. In other cases, the fungus decays the inner wood at the base of the stem (heartwood). This is called butt rot. A tree can live with butt rot for many years, just as it can with stem decay in the main stem. Very often the tree dies because it is uprooted or snapped (physical failure) rather than direct mortality from killing tissues.

Cortical root rots

Cortex is the outer tissues of roots. The cortex is the succulent outer tissue of young roots. As the root becomes woody, the cortex gets squashed, and instead we have cambium and phloem (inner bark), which is also succulent and rich in nutrients. Many of the fungi that can attack the cortex of young roots can move into the cambium and phloem of woody roots.

This group overlaps with nursery diseases, many of which are cortical root rots. Here we just consider those that are known to be important in big trees.

Most of the well-known pathogens of mature trees in this group are water molds (Oomycota).

Vascular wilts

A vascular wilt is a disease in which the pathogen moves in the active xylem, disrupting the flow of xylem sap, causing wilting and other drought-like symptoms.

These could be better grouped with the other vascular wilts that we'll learn about later, but some infect through the roots and can spread from tree to tree by mycelial growth the way many root diseases can, so we think of them more as root diseases. They do not cause root "rot."

Most are caused by Ascomycota or Deutermycota.

Disease Cycle

We'll go through that with each fungus, as it varies slightly. But one thing you should keep clearly in mind: in addition to airborne dispersal by spores (which most of them can do), they can usually grow as mycelium from one tree to another, across root contacts or grafts. So there are two kinds of inoculum: airborne (spores) and soilborne (infested stumps and root systems).

Host Specialization

This is a fascinating aspect of root pathogens, especially root- and butt-rot fungi, that we have only learned in the last 10-20 years. In many of the major pathogens, we have been finding that there are host-specialized groups within what has been considered a single, uniform species. In most cases these groups are morphologically very similar. But there are different populations, which often cannot interbreed, on different host groups. The details vary with disease, so we'll consider it as we discuss examples. Keep this phenomenon in mind and try to imagine explanations in terms of biology, ecology, genetics, etc.

Root and Butt Rots

Imagine you are in the forest and come upon an opening. You observe:

Diagram of disease center

You have entered a mortality center due to root and butt rot. How do you know?


How do you diagnose root rot? How do you distinguish a tree that went down from root rot vs. windthrow? Think of your observations as you stand among the trees. First, if there is a mortality center, look for evidence of a chronosequence of mortality (i.e., trees died long ago near the center and more recently as you approach the margin). Centers of mortality from bark beetles, lightning, wind, etc. won't have that. Look for trees that have snapped at about stump or soil height or uprooted due to root and butt rot. The center may be a few trees or a few hectares.

Then, whether there is a center or not (there often isn't!), look at the uprooted ones closely. Wood that was sound when it broke has jagged, splintery breaks, whereas wood that was decayed when it broke has "brash" breaks, where failure is across the grain and less splintery.

Butt Rot Other
Chronosequence of mortality. Simultaneous mortality (blowdown, patch kill by bark beetles, lightning).
Butt-rotted trees have evidence of stem or root failure. Lower stem snaps or roots fail near root collar. Wind-thrown trees don't usually have failure of main roots or stem. Instead the soil fails, and some usually adheres to the roots. Snapping of sound stems near the base is rare.
Failures of roots or snapped stems have evidence of decay on the broken surface (brash failure, breaks easily across the grain), even long after the failure and after subsequent decay occurs. Wood that does break is sound on the broken surfaces, leaving evidence of a splintery fracture surface.
In a mortality center due to root and butt rot, downed trees usually point in all directions like "pick-up-sticks." When trees are windthrown in a group (blowdown), they are usually oriented in more or less the same direction.

For confirmation, fell a dying or recently killed tree, or cut a fallen tree, and look for decay. You may need to excavate some roots and cut into them.

Bark beetles: If you find bark beetles or ecologically similar insects in a tree, consider the possibilty that they killed it. But recognize that, although many bark beetles can kill healthy trees, a tree that dies from other causes usually has them too. In conifers the resinous response to beetle attacks and the presence of mass attacks can be used to diagnose bark beetle mortality.

Crown symptoms may or may not be seen, and are not diagnostic (specific):

Diagnosis of specific diseases: One can learn to recognize the decays based on type, texture, zone lines, visible mycelium, etc. Of course, the easiest way is to find a conk. You should be so lucky!


The pathogens in these cases are almost all basidiomycetes, usually polypores (Aphyllophorales). But there is one important one that forms gilled mushrooms (Agaricales), and even a few in the Ascomycota (perithecial), such as Hypoxylon deustum.


In many areas these are the most important diseases.

For root diseases in general, impact is often unrecognized. Slow, steady, consistent, not epidemic outbreaks. Widespread, well distributed. Detection difficult and uncertain. Levels of root rot are always higher than can be estimated by above-ground symptoms.

Root and butt rots have three distinct kinds of economic impact: mortality, cull, and growth loss.

Their ecological impact is also important.

Armillaria Root Rot

Please see the separate page on this important disease.

Annosum Root Rot


This disease occurs across the northern hemisphere in temperate regions. Most conifers can be attacked. Most serious on West Coast and in SE. The disease is very different in pines vs. non-pines. Pines tend to be killed outright; the fungus grows in the cambium and girdles the root collar. Non-pines (true fir, spruce, hemlock) tend to get butt rot and hang on quite a while before death. You usually get disease centers with it, but they tend to peter out before they get very big. We don't know why.


The pathogen is Heterobasidion annosum. It forms annual or perennial conks. In many climates, they tend to be hard to find, grow under duff or in stumps. On living or dead trees. Has an asexual stage, but not very important in disease. No rhizomorphs. Specialization: There are at least two kinds of the fungus (still one species). We recognize the P-type, primarily found on pines; and the S-type, primarily found on spruce and other non-pines. (The difference between hosts in tissues attacked is apparently not function of pathogen differences.) The types are practically intersterile.

Stumps are non-selective, may find either type in stumps. Also, host specialization is not absolute; crossovers happen.

Eastern North America to the Rocky Mountains has only the P-type, and the disease is only significant on pines. The west coast has both S- and P-types and serious disease on both. What controlled the distribution of the types? What would happen if the S-type were introduced to the east coast? I don't know!

Disease Cycle, Epidemiology

The disease cycle of H. annosum differs from Armillaria in two respects: 1) spores play a much bigger role in the disease cycle, and; 2) no rhizomorphs - requires root contacts or grafts for secondary spread. The greater role of spores is the most important difference. Stress is not really an issue.

Spores commonly infect stumps after a thinning. In this way it can get into a completely new stand that doesn't yet have it. It grows down the roots of the stump, crosses over to contacting roots of living trees, and attacks. Stumps are susceptible for several weeks after cutting.

Spores may also infect wounds, but only in non-pines. Thus logging scars can be infection court for establishment of new centers.

Spores can directly infect roots in the soil, but we don't know how common this is or how big a role it plays in disease cycle. Probably can be ignored for practical matters.

Longevity of inoculum in stumps is an issue here. Big stumps in the West may sustain fungus for well over 50 yrs. Major threat from one rotation to the next. In the Southeast, pine plantations, because of the heat and humidity the fungus consumes a stump in less than 10 years. So when a stand is cut, the fungus starts, seedlings are planted. But the seedlings take time to contact the roots of the old stumps. By that time, the fungus is a goner. So H. annosum is not a threat between rotations, though it is within a rotation after thinning.


FIDL icon(western US) FIDL icon(eastern US)

Laminated Root Rot


Laminated root rot is a typical root and butt rot. It leads to expanding centers of mortality. Small trees die standing, and bigger ones fall over. It is restricted in distribution to the Pacific Northwest and Inland Empire area, but it occurs on a variety of important conifers there and causes very significant losses (60 million cu. ft./yr. in WA+OR). Advanced decay is laminated and has white mycelium with brownish hairs in it.


Phellinus weirii. Polypore, produces brown, unremarkable conks that are resupinate (flat on substrate, all pore surface with no upper cap), but they are not commonly found.

It has become increasingly obvious that there are two forms of the pathogen, one on western redcedar and the other on Douglas-fir, true fir and hemlock. More and more information has come to light, and recently the two forms were formally recognized as distinct species. Unfortunately, the traditional name, P. weirii, went with the less important one (on redcedar). The more important one on Douglas-fir is called P. sulphurascens. They do cross hosts sometimes but for management purposes that can be ignored.

Disease Cycle, Epidemiology

This is another one, like Armillaria, where the spores don't seem to play much of a role. All the inoculum of significance comes from infected stumps and roots. It can't grow through soil like Armillaria, but root contacts and grafts are sufficient to get it around. Stress is not an issue.


Laminated root rot is a major management problem in some of the most productive forests in North America. Several approaches can be used.

Resistance. There are usually discrete infection centers with this disease. As described above, infection centers can be regenerated to resistant species. There is a range of resistance. Pines, cedars and hardwoods are most resistant (to the Doug-fir form). They should be favored around infection centers.

Inoculum Reduction. As described above, this may involve stump removal or fumigation. Stumping is limited by terrain for equipment. Fumigation is more experimental.

Host removal. There is one other approach that can be tried in sapling stands. Cut all trees with symptoms and adjacent nonsymptomatic trees that are susceptible. The idea is to remove host material from the developing infection centers so the fungus dies out. It won't invade dead roots. However, the pathogen can survive for many years in old stumps.

Early harvest. In older stands, salvage symptomatic trees where possible and consider final harvest earlier than usual. Thinning is not good if the disease is dispersed because there will be asymptomatic, infected trees left as crop trees, and windthrow will be more likely.

Management of this disease may be expensive, but it is a lot better than doing nothing in severely infested stands on average or good sites. FIDL icon

Cortical Root Rots - Littleleaf Disease


Occurs in Piedmont region of South. 15 million acres of shortleaf pine. Loblolly also affected but less so. Starts at about 20 years and gets progressively worse. Chlorosis, shorter needles, thinning crown, reduced needle complement. Feeder roots in bad shape. Death in about 6 yrs.


Phytophthora cinnamomi, an Oomycete with typical life cycle. Also, species of Pythium and even nematodes may get involved.


This disease only occurs under environmental conditions peculiar to this region. Some of these conditions result from land abuse long ago by humans. Extensive cotton cropping depleted the nutrients (esp. nitrogen) and led to severe erosion. Also, soil is clay, and there is a hardpan, so soil drainage is poor. Soil gets too wet, then during dry conditions roots can't get down (moisture extremes). Can see graying and mottling of soil as indications of poor aeration. Clearly not an ideal place for tree growth. Younger trees don't have that problem.

So environmental factors are of great importance. On good sites, the disease is not a problem.


Cortical Root Rots - Port-Orford Cedar Root Rot


Disease only of Port-Orford cedar, which has very limited distribution on OR/CA border. Important because the wood is extremely valuable. Disease appeared in a nursery in 1923, got into ornamental plantings, eventually reached native range in 1952. Now moving within that range.

Fungus infects fine roots like good cortical rotter, then moves up to bigger roots and even a bit up the stem. Phloem and cambium turn from creamy to dark cinnamon brown. Crowns fade through yellow to red to brown. Trees die quickly, in a few weeks for small trees and a few years for large trees.


Phytophthora lateralis, typical Oomycete. Probably introduced from Eurasia.


The fungus is soilborne and waterborne. Propagules include mycelium in organic matter, sporangia, zoospores, oospores, or chlamydospores. Sporangia germinate to produce hyphae or zoospores (Δ). Zoospores are short-lived and can swim only a few centimeters, but they can be transported in streamwater and attack roots adjacent to streams. The pathogen survives periods unsuitable for growth as mycelium or as oospores or chlamydospores. Chlamydospores may survive up to 7 years in dead organic matter.

Disease can enter new areas when soil is carried on vehicles, animals. Then, movement locally is clearly associated with drainages, downhill. Along streams, likelihood of infection increases with tree size and proximity to the stream (Δ). Larger trees present a larger target and those closest to the stream are most likely to be exposed to inoculum.


Impacts of this disease have been great. It has destroyed the ornamental cedar industry, estimated at up to 1 million dollars annually. Port-Orford cedar is extremely valuable, and timber losses have been estimated at 250 million to nearly 1 billion dollars. Ecosystem effects are also considerable.

At this point, there are not many options for management.

Exclusion: Focus production of Port Orford cedar in areas where the disease is absent and it may reasonably be excluded. Examples are hilltops and flats, where infection is unlikely to come down with water drainage. Various operational details are conducted with this in mind: road construction, hydrology, landings, etc. Vehicles are cleaned before entering the exclusion zone. Restrict entry into areas with Port Orford cedar where practical.

Eradication: If hosts are absent for 3-5 years, the fungus will apparently die out. Kill trees in high hazard sites: along roadbeds, along streams, in potholes, wet areas. Keep these areas free of cedar. Keep spacing of cedar such that the fungus cannot grow from tree to tree.FIDL icon


Root-Infecting Vascular Wilt - Black-Stain Root Disease


Various western conifers, trees develop thin, chlorotic crowns, eventually die, in groups. Cut into roots and lower stem to find dramatic streaks of black stain.


Leptographium wageneri, a deuteromycete. Closely related to Ophiostoma stain fungi. Dark hyphae, grows in tracheids, probably insect vectored for long-distance dispersal. Grows root-to-root for secondary spread.

3 types have been described as subspecies. They are physiologically and, to a slight degree, morphologically distinguishable. Important point is they are host-specialized:


In Douglas-fir, vectors are known, root-feeding weevils. They are attracted to fresh wounds and stumps, so thinning initiates disease in some stands. In pines, damage is associated with slightly wetter conditions, flats and drainages.


Current approaches to management of this disease are probably not fully effective or satisfactory. Avoid undo wounding or disturbance, avoid creating wet areas, avoid or delay precommercial thinning, conduct operations in summer to avoid peak times of vector activity.

Manage for nonhosts of the type on the site. FIDL icon

Funny picture "Wow! I get tickled pink thinking about root and butt rots!"

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Last modified 22 Feb, 2015