United States

Department

of Agriculture

Forest Service

Rocky Mountain

Research Station

Research Paper 

RMRS-RP-47

July 2004

Roles of Woody Root-Associated 

Fungi in Forest Ecosystem 

Processes: Recent Advances in 

Fungal Identification

Jill A. Hoff, Ned B. Klopfenstein, Jonalea R. Tonn, Geral I. McDonald

Paul J. Zambino, Jack D. Rogers, Tobin L. Peever, Lori M. Carris
Rocky Mountain Research Station

Natural Resources Research Center

2150 Centre Avenue, Building A

Fort Collins, CO 80526

Abstract

Hoff, Jill A.; Klopfenstein, Ned B.; Tonn, Jonalea R.; McDonald, Geral I.; Zambino, Paul J.; Rogers, Jack D.; 

Peever, Tobin L.; Carris, Lori M. 2004. Roles of woody root-associated fungi in forest ecosystem processes: recent advances in fungal identification. Res. Pap. RMRS-RP-47. Fort Collins, CO: U.S. Department of 

Agriculture, Forest Service, Rocky Mountain Research Station. 6 p.

Interactions between fungi and woody roots may be critical factors that influence diverse forest ecosystems processes, such as wood decay (nutrient recycling); root diseases and their biological control; and endophytic, epiphytic, and mycorrhizal symbioses. However, few studies have characterized the diversity and the spatial and 

temporal distribution of woody root-associated fungi in forest ecosystems. Molecular genetic techniques that facilitate fungal identification are now available to help investigate complex and dynamic interactions of these fungi.

Key Words: Ascomycetes, Basidiomycetes, fungi, endophyte, polymerase chain reaction, root rot, 

Zygomycetes.

The Authors

Jill A. Hoff is a Forest Pathologist with the West Virginia Department of Agriculture. She completed an A.S. degree 

in Wildlife Technology at Penn State University–DuBois, a B.S. degree in Wildlife Resources at the University of 

Idaho, and an M.S. degree in Plant Pathology at Washington State University. Current address: Plant Industries 

Division, West Virginia Department of Agriculture, 1900 Kanawha Blvd., E, Charleston, WV 25302-0191 U.S.A.

Ned B. Klopfenstein is a Research Plant Pathologist with the USDA Forest Service, Rocky Mountain Research 

Station at the Forestry Sciences Laboratory, 1221 South Main Street, Moscow, ID 83843 U.S.A.

Jonalea R. Tonn is a Forester with the USDA Forest Service, Rocky Mountain Research Station at the Forestry 

Sciences Laboratory in Moscow, ID.

Geral I. McDonald is a Research Plant Pathologist Emeritus with the USDA Forest Service, Rocky Mountain 

Research Station at the Forestry Sciences Laboratory in Moscow, ID.

Paul J. Zambino is a Research Plant Pathologist with the USDA Forest Service, Rocky Mountain Research 

Station at the Forestry Sciences Laboratory in Moscow, ID.

Jack D. Rogers is a Professor with the Department of Plant Pathology at Washington State University, P.O. Box 

646430, Pullman, Washington 99164-6430 U.S.A.

Tobin L. Peever is an Assistant Professor with the Department of Plant Pathology at Washington State 

University-Pullman.

Lori M. Carris is an Associate Professor with the Department of Plant Pathology at Washington State UniversityPullman.

Acknowledgments

The authors are grateful for comments contributed by Dr. Paul Hessburg, Dr. Deborah S. Page-Dumroese, Dr. 

Mee-Sook Kim, Bryce A. Richardson, Raini C. Rippy, Joanne M. Tirocke, Jane E. Stewart, and John W. Hanna 

to an earlier version of this manuscript. Funding for this work was provided by the USDA Forest Service, Rocky 

Mountain Research Station, Microbial Processes as Ecosystem Regulators in Western Forests Research Work 

Unit, Moscow, ID, and the USDA Forest Service, Pacific Northwest Research Station, Wenatchee, WA. This is 

Contribution Number 52 of the National Fire and Fire Surrogate Project (FFS), funded by the U.S. Joint Fire 

Science Program. Use of trade names does not constitute endorsement by the USDA Forest Service.
USDA Forest Service RMRS-RP-47. 2004. 1

Root Fungi: Neglected Biological 

Components of Forest Ecosystems

In recent years, ecologists have increased their efforts 

to understand belowground, biological interactions in 

forest ecosystems. Interactions that occur among plant 

roots, animals, and microorganisms are dynamic and 

substantially influence ecosystem processes. Ecologists 

have just begun to study the biota contributing to these 

interactions (Copely 2000).

Among belowground biota are the fungi, which are 

tremendously diverse and play wide-ranging roles in 

forest ecosystem processes (Rossman and others 1998). 

A primary role of fungi is the degradation of plant and 

animal matter, which allows recycling of resources 

(Rossman and others 1998). Fungi are aided in this role 

by their ability to obtain nutrients through absorption. 

Their capacities for growth on various substrates depend on their abilities to: (1) degrade complex nutrient 

sources extracellularly; (2) transport simple nutrients 

across cell membranes for metabolic processes (nutrition though absorption); and (3) tolerate or deactivate 

compounds that inhibit fungal growth.

Studies of fungal biodiversity in forest ecosystems 

can provide baseline information for determining interrelationships among organisms and indicate potential roles of fungi in forest ecosystem dynamics. 

Understanding the role of fungi in forest ecosystem processes is key to characterizing stability and succession 

of biological components (for example, trees), while information on fungal biodiversity can provide insight on 

sustaining fungi as beneficial resources (Rossman and 

others 1998).

Due to the widespread distribution of fungi and their 

association with diverse organic and inorganic substrates, the actual number of fungal species in existence 

is difficult to assess (Rossman and others 1998). Fungi 

isolated from wood include such diverse groups as mucoraceous species (zygomycetes), ascomycetes, basidiomycetes, and deuteromycetes (asexual fungi). Fungi 

associated with woody roots have not been well studied, 

in part because roots are not readily observed without 

excavation. In addition, root substrates vary temporally 

and spatially within the soil profile over the life span of 

a tree. This paper addresses the potential diversity and 

ecological functions of fungi associated with woody 

roots of forest trees.

Wood Decay Fungi

Wood decay fungi are commonly associated with 

woody roots. In the forest, decay fungi play an important role in carbon and nitrogen cycling, while helping 

to convert organic debris into humus. Some fungi attack living trees; others invade dead or down timber and 

slash on the forest floor. Wood-decaying basidiomycetes 

colonize and degrade wood using enzymatic and mechanical processes. Brown-rot fungi preferentially attack and rapidly depolymerize structural carbohydrates 

(celluloses and hemicelluloses) in the cell wall leaving 

the modified lignin behind. White-rot fungi can progressively utilize all major cell wall components, including 

both carbohydrates and lignin (Jasalavich and others 

2000).

Although wood decay fungi are primarily basidiomycetous, some ascomycetous fungi cause rapid white-rot 

of various hardwood trees (Nilsson and others 1989). A 

comprehensive review of decay fungi in trees has been 

presented by Gilbertson (1980). Species surveys of fungi in coniferous forests are usually based on the distribution of fruiting bodies (sporocarps) (fig. 1). Because 

fruiting bodies only develop under specific environmental conditions, such inventories may span several years 

but still not accurately reflect the abundance of fungal 

species (Johannesson and Stenlid 1999).

Pathogenic Fungi

Pathogenic fungi are also common associates of 

woody roots. Various pathogenic heart-, butt-, and 

root-rot fungi kill living trees by attacking functional 

Roles of Woody Root-Associated Fungi in Forest 

Ecosystem Processes: Recent Advances in Fungal 

Identification

Jill A. Hoff, Ned B. Klopfenstein, Jonalea R. Tonn, Geral I. McDonald

Paul J. Zambino, Jack D. Rogers, Tobin L. Peever, Lori M. Carris
2 USDA Forest Service RMRS-RP-47. 2004. 

vascular and cambium tissues. They enter roots by direct 

penetration or by stump- or bole-to-root colonization. 

Although some pathogenic fungi are not predictably 

distributed within a forest, others (for example, rootand butt-rot fungi) can kill trees in slowly expanding 

mortality centers that create gaps in the forest canopy. 

Well-known examples of root pathogens include some 

Armillaria species (basidiomycetous fungi that can 

cause “shoestring rot”; fig. 2), Phellinus sulphurascens

and P. weirii (causal agents of laminated root rots), and 

Heterobasidion annosum (causal agent of annosus root 

rot). Infection centers of root pathogens can be widespread and locally abundant, and the centers persist 

from centuries to millennia. Root- and butt-rot pathogens are among the most influential agents of forest disturbance in some conifer ecosystems, and they shape the

structure and composition of natural and managed forests (Hansen and Goheen 2000). H. annosum is a complex of biological species specialized to pine, spruce, 

and fir hosts. Colonization of stumps and wounds initiates infection centers, but tree-to-tree spread along 

roots expands centers of infection and mortality on the 

appropriate host (Garbelotto and others 1997; Stenlid 

and Redfern 1998). Like Heterobasidion, the genus 

Armillaria also contains a number of poorly differentiated species, and more studies are needed to fully understand the ecological role of many such species.

Endophytic Fungi

A fungal endophyte lives asymptomatically within plant parts (intercellularly or intracellularly) for at 

least part of its life cycle (Saikkonen and others 1998). 

Endophytic fungi usually occur in aboveground plant 

tissues but are also found in roots. Unlike mycorrhizal fungi, fungal endophytes of roots lack extraradical 

(outside the root) hyphal networks and mantles (sheaths 

around the roots).

While much information is available on pathogens 

and mycorrhizal fungi, little is known about symptomless (possibly neutral or mutualistic) endophytes 

of plants. Endophytic fungi are often divided into two 

groups: the “clavicipitaceous system” (ascomycete family Clavicipitaceae), which contains endophytes of grass 

that often confer resistance to herbivory and pathogens, 

and endophytes representing all other fungal groups on 

diverse herbaceous and woody hosts (Petrini 1997). 

Fungal endophytes have been found in all woody plants 

studied to date. Trees and shrubs usually contain numerous fungal species; however, there has been little attempt to correlate ecological and evolutionary aspects 

of fungal endophytes of grasses versus woody plants 

(Saikkonen and others 1998). Based on the endophytic 

fungi of grasses, some endophytic fungi of woody roots 

may have potential for biological control of pathogens 

and/or insects.

Epiphytic Fungi

The external plant surface provides an environment 

for fungal growth that varies spatially and temporally 

and can also be unique to the host. New surfaces become progressively available for colonization as the 

Figure 1. Fruiting body of Boletus mirabilis, a mycorrhizal fungus that is frequently associated with decomposing woody 

debris (photo by L.M. Carris).

Figure 2. Armillaria ostoyae causes root and butt rot on a diverse host tree species. (A) mycelial fan beneath the bark 

is a sign of Armillaria disease on Douglas-fir (photo by J.D. 

Rogers). (B) Fruiting bodies help to identify the species of 

Armillaria, but fruiting is typically sporadic in nature (photo by 

G.I. McDonald).
USDA Forest Service RMRS-RP-47. 2004. 3

plant grows (Andrews and Harris 2000), and plant organs differentiate and undergo developmental processes. Each aspect of plant growth and development can 

affect microbial flora on the surface. Many researchers have noted seasonal patterns in the composition 

of phyllosphere (leaf surface) microbial communities. 

Epiphytic fungi of woody roots are not well documented and warrant further study. It is also not known if root 

epiphytes may also occur as endophytes.

Ectomycorrhizal Fungi

Ectomycorrhizal (EM) fungi are typically associated 

with feeder roots; however, the potential interactions of 

these fungi with woody roots is unknown. EM symbioses are important on a global scale because most trees 

throughout the world’s boreal, temperate, subtropical, 

and tropical forests are ectomycorrhizal. For host trees, 

these fungi gather nutrients and scavenge nitrogen, 

phosphorus, and trace elements from both inorganic 

and organic pools in the soil, while extracting fixed carbon from the tree (Horton and Bruns 2001). These mutualistic fungi also provide host plants with increased 

access to water and protect plants from pathogens, 

chemical extremes (for example, high pH), and heavymetal contamination (Cullings and others 2000). Until 

the mid-1990s, knowledge of EM fungal community 

structure and the degree to which species assemblages 

show predictable colonization patterns in space and 

time was almost exclusively based on sporocarp surveys (Dahlberg 2001). EM fungi are generally basidiomycetes (for example, species of Russula, Cortinarius, 

Chroogomphus, Lactarius, Suillus, Paxillus) (Cullings 

and others 2000; Horton and Bruns 2001).

Mycoparasitic Fungi

Mycoparasitic fungi obtain at least part of their nutrients from other fungi. Some are being investigated 

for their roles in the biocontrol of plant pathogens in 

the rhizosphere (root surface) and spermosphere (seed 

surface) (Whipps 2001). Mycoparasites are extremely 

common in soil, where they can act as natural regulators of fungal populations. They can be biotrophic on 

their host fungus, with the host fungus showing few 

symptoms other than reduced growth rate, or necrotrophic, with host cells killed under some conditions. 

Commercial formulations of some mycoparasitic fungi 

(for example, Trichoderma spp.) are available for use 

against certain plant pathogens including root rot pathogens, such as Pythium spp. and H. annosum.

Identification, Species Concepts, 

and Ecological Roles of Fungi

Morphological identification of the diverse fungi 

isolated from wood is difficult and tedious. Moreover, 

many fungal species that grow in wood may not be culturable under laboratory conditions (Johannesson and 

Stenlid 1999). Of those that are culturable, the woodrotting fungi present an additional problem: Petri plate 

cultures of most basidiomycetes do not produce fruiting 

bodies that supply critical characters for identifying genera, families, and species (Nobles 1948).

The species concept is central to biology, and yet 

a universally useful definition of species is elusive.

Though much of the discussion of variability within 

species has centered on animals and plants, surveys of 

fungal diversity must also consider the species concept. 

Fungal species definitions have been based on overall 

phenotypic similarity, ecological distributions, reproductive isolation versus cohesion, evolutionary divergence, 

and combinations of the above (reviewed by Harrington 

and Rizzo 1999). In practice, fungal species concepts 

have evolved from strictly morphological descriptions, 

to biological (reproductive) species concepts, to phylogenetically (deoxyribonucleic acid, DNA, divergence) 

based species concepts. Morphological, ecological, and 

pathological species are all defined from phenetic (observable) characters, most of which relate directly to 

structures and functions (Harrington and Rizzo 1999). 

For example, some ecological species have been based 

on adaptation to a particular niche, or on disease symptoms and host association for some plant pathogens. 

To facilitate fungal identification and examine relationships among fungal groups, a molecular tool called 

the Polymerase Chain Reaction (PCR) can be used to 

amplify (produce numerous copies of) specific fragments of DNA. Such fragments must contain conserved 

(less variable) sequences at either end of the fragment 

that correspond to short, artificially constructed “primer” sequences that “prime” the process of generating 

new copies of the target region by a DNA polymerase 

enzyme. DNA fragments are analyzed by comparing 

differences in sequences, which allows analyses of relationships within and among phenetically defined species (Bridge and others 1998). Sequence analysis may 

reinforce or invalidate phenetic species definitions while 

providing valuable insights into their evolutionary history. DNA-based analysis can be especially important 

for species complexes where major defining characters 

relate to environmental adaptation, as is the case for 
4 USDA Forest Service RMRS-RP-47. 2004. 

ecological species (Bridge and others 1998). Molecular 

techniques are currently used to identify fungi from 

plants for diverse ecological studies (examples include 

Horton and Bruns 2001; Johannesson and Stenlid 1999; 

Vandenkoornhuyse and others 2002) and have also revealed evolutionary relationships among major groups 

of fungi (Klich and Mullaney 1992).

In general, conserved DNA regions are used to resolve broad evolutionary relationships among fungi (for 

example, at the family, order, and class levels), but more 

variable DNA regions are used to resolve relationships 

among or within species. Ribosomal DNA (rDNA) is 

well suited for both purposes. The fungal genome (a 

haploid set of all DNA within the cell nucleus) contains 

roughly 200 tandem and nearly identical repeats of the 

rDNA region (Berbee and Taylor 2001). This rDNA region typically contains genes for the Small Subunit (= 

SSU, 17S), 5S, 5.8S, and Large Subunit (= LSU, 25S) 

ribosomal subunits, Internal Transcribed Spacers (ITS), 

and Intergenic Spacers (IGS) (Horton and Bruns 2001). 

The high proportion of rDNA in the genome usually 

enables amplification of rDNA targets from even lowquality DNA preparations (Berbee and Taylor 2001).

The ITS region is well suited for identification because unknown organisms can usually be identified to 

the species or species group level by comparing ITS sequence data from unknown isolates to the extensive ITS 

fungal data currently deposited in electronic databases 

(for example, GenBank, EMBL, and DDBJ). Because 

ITS sequences typically vary with species, closely related taxa should show close sequence similarity (Horton 

and Bruns 2001). The major limitations to this approach 

are the inability of a researcher to be certain that a fungus whose sequence has been entered in the database has 

been accurately identified, and the low representation of 

fungi from some substrates.

For the purposes of assessing fungal diversity associated with woody roots, utilizing ITS data can contribute to a more comprehensive assessment than surveys 

based solely on morphology, by allowing identification 

of fungal species that are nonsporulating and nonsporocarp forming. PCR and DNA sequencing, combined with 

morphological verification can greatly facilitate surveys 

of fungal diversity by validating taxonomic identification (fig. 3 and 4). One such study on endophytes of 

woody roots has found 27 fungal genera associated with 

Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] and 

ponderosa pine (Pinus ponderosa Douglas ex Lawson & 

C. Lawson) (Hoff 2002). An unexpected finding from 

that study was that the two predominant groups of isolated fungi corresponded to an ascomycetous genus of 

heat-resistant fungi (Byssochlamys) that may be active in 

bioprotection, and a zygomycetous genus (Umbelopsis) 

that is a common soil fungus not previously detected in 

living roots of these tree species. Whether frequency and 

intensity of wildfires or prescribed burns affect levels 

of such root fungi is currently unknown, but the implications for fire and host succession effects on disease 

through these or other previously overlooked fungi are of 

great interest. Future studies will determine if prescribed 

burning could be used to favor beneficial, root-associated 

fungi that are heat resistant, while discriminating against 

fungal pathogens that are less heat tolerant.

Implications

The diversity of fungi occupying ecological niches on 

and in woody roots of forest trees is largely unexplored. 

Figure 3. Fungal isolation, culture, and DNA amplification using PCR. (A) Root increment core. (B) Isolation of fungi by 

growth on a selective culture medium. (C) Fungal culture 

initiating from a root core. (D) A pipette tip gently scraped 

across a fungal culture provides suitable template DNA for 

PCR. (E) Reaction tubes are placed in a temperature cycler 

for PCR. (F) Electrophoresis gel showing DNA products 

produced by PCR.
USDA Forest Service RMRS-RP-47. 2004. 5

Berbee, M.L.; Taylor, J.W. 2001. Fungal molecular evolution: 

gene trees and geologic time. P. 229-245 in McLaughlin, D.J; 

McLaughlin, E., eds. The Mycota Vol. VIIB, Systematics 

and Evolution. Springer-Verlag, Berlin, Germany.

Bridge, P.D.; Arora, D.K.; Reddy, C.A.; Elander, R.P., 

eds. 1998. Applications of PCR in Mycology. CAB 

International, Wallingford, United Kingdom. 376 p.

Copely, J. 2000. Ecology goes underground. Nature. 406: 

452-454.

Cullings, K.W.; Vogler, D.R.; Parker, V.T.; Finley, S.K. 2000. 

Ectomycorrhizal specificity patterns in a mixed Pinus 

contorta and Picea engelmannii forest in Yellowstone 

National Park. Applied and Environmental Microbiology. 

66: 4988-4991.

Dahlberg, A. 2001. Community ecology of ectomycorrhizal 

fungi: an advancing interdisciplinary field. New 

Phytologist. 150: 555-562.

Garbelotto, M.; Lee, H.K.; Slaughter, G.; Popenuck, T.; Cobb, 

F.W.; Bruns, T.D. 1997. Heterokaryosis is not required for 

virulence of Heterobasidion annosum. Mycologia. 89: 

92-102.

Gilbertson, R.L. 1980. Wood-rotting fungi of North America. 

Mycologia. 72: 1-49.

Hansen, E.M.; Goheen, E.M. 2000. Phellinus weirii and other 

native root pathogens as determinants of forest structure 

and process in western North America. Annual Review 

Phytopathology. 38: 515-539.

Harrington, T.C.; Rizzo, D.M. 1999. Defining species in the 

fungi. P. 43-71 in Worrell, J.J., ed. Structure and Dynamics 

of Fungal Populations. Kluwer Press, Dordrecht, The 

Netherlands.

Hoff, J.A. 2002. Fungal diversity in woody roots of east-slope 

Cascade ponderosa pine (Pinus ponderosa) and Douglasfir (Pseudotsuga menziesii). M.S. thesis, Washington State 

Univ., Pullman, WA: 76 p.

Horton, T.R.; Bruns, T.D. 2001. The molecular revolution 

in ectomycorrhizal ecology: peeking into the black-box. 

Molecular Ecology. 10: 1855-1871.

Jasalavich, C.A.; Ostrofsky, A.; Jellison, J. 2000. Detection 

and identification of decay fungi in spruce wood by 

restriction length polymorphism analysis of amplified 

genes encoding rRNA. Applied and Environmental 

Microbiology. 66: 4725-4734.

Johannesson, H.; Stenlid, J. 1999. Molecular identification 

of wood inhabiting fungi in an unmanaged Picea abies

forest in Sweden. Forest Ecology and Management. 115: 

203-211.

Klich, M.A.; Mullaney, E.J. 1992. Molecular methods for 

identification and taxonomy of filamentous fungi. P. 35-

55 in Arora, D.K.; Elander, R.P.; Mukerji, K.G., eds. 

Handbook of Applied Mycology. Marcel Dekker, Inc., 

New York.

Nilsson, T.; Daniel, G.; Kirk, T.K.; Obst, J.R. 1989. 

Chemistry and microscopy of wood decay by some higher 

Ascomycetes. Holzforschung 43: 11-18.

Nobles, M.K. 1948. Studies in forest pathology VI. 

Identification of cultures of wood-rotting fungi. Canadian 

Journal of Forest Research. 26: 281-431.

Petrini, O. 1997. Ecological and physiological aspects of hostspecificity in endophytic fungi. P. 87-100 in Redlin, S.C.; 

Carris, L.M., eds. Endophytic Fungi in Grasses and Woody 

Plants: Systematics, Ecology and Evolution. APS Press, 

St. Paul, MN.

Figure 4. DNA sequencing of PCR products, comparisons with 

sequence data bases, and morphological characterization 

for species identification. (A) Example of a DNA sequence 

chromatogram showing portions of the DNA sequence of a 

PCR product. (B) Results of a GenBank Blast search identifying fungal DNA sequences with the most similarity to a 

sequence from an unknown fungal isolate. (C) Additional 

information from GenBank Blast showing percent identity 

of sequences from the unknown fungal isolate with the database sequence that it most closely matches. (D) Microscopic 

observations are used to verify genus and species identification. (E) Example of microscopic structure used for 

morphological verification of sequence-assisted species 

identification.

Unexpected results from recent studies (Hoff 2002) 

indicate a great need to further explore the diversity and 

ecological roles of fungi associated with woody roots of 

various forest trees in diverse ecosystems. As the role 

of fungal diversity in ecosystem processes is better understood, information should become available to improve sustainable forest practices.

For more information on terminology used in mycology, the reader is referred to: Ulloa, M.; Hanlin, R.T. 

2000. Illustrated dictionary of mycology. APS Press, St. 

Paul, MN. 448 pp.

References

Andrews, J.H.; Harris, R.H. 2000. The ecology and 

biogeography of microorganisms on plant surfaces. Annual 

Review of Phytopathology. 38: 145-180.
6 USDA Forest Service RMRS-RP-47. 2004.

Rossman, A.; Tulloss, R.E.; O’Dell, T.E.; Thorn, R.G. 1998. 

All Taxa Biodiversity Inventory of Fungi in a Costa Rican 

Conservation Area. Parkway Publishers, Inc., Boone, NC. 

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plants. Annual Review of Ecology and Systematics. 29: 

319-43.

Stenlid, J.; Redfern, D.B. 1998. Spread within the tree and 

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Hütterman, A., eds. Heterobasidium annosum: Biology, 

Ecology, Impact and Control. CAB International, New 

York. 125-141.

Vandenkoornhuyse, P.; Baldauf, S.L.; Leyval, C.; Straczek, 

J.; Young, J.P.W. 2002. Extensive fungal diversity in plant 

roots. Science. 295: 2051.

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the rhizosphere. J. Experimental Botany. 52: 487-511.
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