Advances in agronomy volume 73

Agronomy

DVANCES I N

VOLUME

73


Advisory Board
Martin Alexander

Ronald Phillips

Cornell University

University of Minnesota

Kenneth J. Frey

Larry P. Wilding

Iowa State University

Texas A&M University

Prepared in cooperation with the
American Society of Agronomy Monographs Committee
John Bartels
Jerry M. Bigham

Jerry L. Hatfield
David M. Kral

Diane E. Stott, Chairman
Linda S. Lee
David Miller
Matthew J. Morra
John E. Rechcigl
Donald C. Reicosky

Wayne F. Robarge
Dennis E. Rolston
Richard Shibles
Jeffrey Volenec


Agronomy

DVANCES IN

VOLUME

73

Edited by

Donald L. Sparks
Department of Plant and Soil Sciences
University of Delaware
Newark, Delaware

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2001 by ACADEMIC PRESS

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Contents
CONTRIBUTORS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
PREFACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

vii
ix

INTERACTIONS AMONG ROOT-INHABITING FUNGI AND
THEIR IMPLICATIONS FOR BIOLOGICAL CONTROL
OF ROOT PATHOGENS
David M. Sylvia and Dan O. Chellemi
I.
II.
III.
IV.
V.

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Functional Diversity in the Root Zone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interactions among Root-Inhabiting Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Opportunities for Pest Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Research Priorities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2
3
13
17

21
24

DWARFING GENES IN PLANT IMPROVEMENT
S. C. K. Milach and L. C. Federizzi
I.
II.
III.
IV.
V.
VI.
VII.

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Biochemical Basis of the Dwarf Phenotype . . . . . . . . . . . . . . . . . . . . . . . .
Dwarfing Genes and Their Use for Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . .
Breeding Challenges and Varieties Developed . . . . . . . . . . . . . . . . . . . . . . . . . .
Pleiotropic Effects of Dwarfing Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Molecular Mapping of Dwarfing Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

36
38
43
45
48
51
55
56

A REVIEW OF THE EFFECT OF N FERTILIZER TYPE
ON GASEOUS EMISSIONS
Roland Harrison and J. Webb
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
II. The Processes Controlling Emissions of Nitrogen Gases
from Fertilizers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
III. Measurements of Ammonia Emission Following Nitrogen
Fertilizer Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v

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69
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CONTENTS

IV. Ammonia Emission Factors for Nitrogen Fertilizers . . . . . . . . . . . . . . . . . . .
V. Measurements of Nitrous Oxide Emissions Following Nitrogen
Fertilizer Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
VI. Nitrous Oxide Emission Factors for Nitrogen Fertilizers. . . . . . . . . . . . . .
VII. Nitric Oxide Emissions from Nitrogen Fertilizers . . . . . . . . . . . . . . . . . . . . .
VIII. Summary and Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

88
90

97
99
99
103

RHIZOBIA IN THE FIELD
N. Amarger
I.
II.
III.
IV.
V.
VI.

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Diversity in Rhizobia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Rhizobium Systematics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Natural Populations of Rhizobia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Introduction of Rhizobia into Soil . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

110
112
123
129
143
147
148

INDEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

169


Contributors
Numbers in parentheses indicate the pages on which the authors’ contributions begin.

N. AMARGER (109), Laboratoire de Microbiologie des Sols, Institut National de
la Recherche Agronomique, 21065 Dijon, France
DAN O. CHELLEMI (1), USDA, ARS, Horticultural Research Laboratory, Ft.
Pierce, Florida 34945
L. C. FEDERIZZI (35), Universidade Federal do Rio Grande do Sul, Faculdade
de Agronomia, Departamento de Plantas de Lavoura, Porto Alegre, Brazil
ROLAND HARRISON (65), ADAS Consulting Ltd., ADAS Boxworth, Boxworth, Cambridge CB3 8NN, United Kingdom
S. C. K. MILACH (35), Universidade Federal do Rio Grande do Sul, Faculdade
de Agronomia, Departamento de Plantas de Lavoura, Porto Alegre, Brazil
DAVID M. SYLVIA (1), Soil and Water Science Department, University of Florida,
Gainesville, Florida 32611
J. WEBB (65), ADAS Consulting Ltd., ADAS Wolverhampton, Wolverhampton
WV6 8TQ, United Kingdom

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Preface
Volume 73 contains four excellent chapters on contemporary and important topics in the agronomic sciences. Chapter 1 is a thoughtful review of interactions

among root-inhabiting fungi and their implications for biological control of root
pathogens. The fungi are defined, their distribution and abundance are discussed,
and their role in agroecosystems is presented. Chapter 2 discusses advances in the
role of dwarfing genes in plant improvement. Emphasis is placed on breeding and
genetics aspects. Chapter 3 covers a topic that is of great environmental interest—
the effect of nitrogen fertilizers on gaseous emissions. Processes controlling and
measurements of emissions of nitrogen gases are fully discussed. Chapter 4 is a
comprehensive review of Rhizobia, including diversity, systematics, natural populations, and field introduction of Rhizobia.
I thank the authors for their first-rate reviews.
DONALD L. SPARKS

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INTERACTIONS AMONG ROOT-INHABITING
FUNGI AND THEIR IMPLICATIONS
FOR BIOLOGICAL CONTROL
OF ROOT PATHOGENS
David M. Sylvia1 and Dan O. Chellemi2
1

Soil and Water Science Department
University of Florida
Gainesville, Florida 32611
2

UDSA, ARS

Horticultural Research Laboratory
Ft. Pierce, Florida 34945

I. Introduction
II. Functional Diversity in the Root Zone
A. Classification Schemes for Functional Groups
B. Clinical Pathogens
C. Subclinical Pathogens
D. Arbuscular Mycorrhizal Fungi
E. Additional Nonpathogenic Fungi
III. Interactions among Root-Inhabiting Fungi
A. Interactions among Pathogens
B. Interactions of AM Fungi with Pathogenic and Nonpathogenic Fungi
C. Interactions between Pathogenic and Nonpathogenic Fungi
D. Application of Island Biogeography Theory to Root–Fungal Interactions
IV. Opportunities for Pest Control
A. Current and Future Control Strategies
B. Role of Biological Control
C. Obstacles to Implementing Biological Control
V. Research Priorities
References

Soil fungi impact plant health because they grow in, on, and around roots, infecting healthy tissues and colonizing senescent materials. We review the literature
concerning these fungi and discuss the various interactions that occur among the
root-inhabiting fungi and their diversity at the community level. Root-inhabiting
fungi are classified as clinical and subclinical pathogens, mycorrhizal fungi, and
additional nonpathogenic fungi. We define each group, present data on abundance
and distribution, and describe their roles in agroecosystems.We also discuss the
1
Copyright

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Advances in Agronomy, Volume 73
2001 by Academic Press. All rights of reproduction in any form reserved.
0065-2113/01 $35.00


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SYLVIA AND CHELLEMI
application of island biogeography theory to the understanding of fungal species
diversity in the root zone. Our goal is to contribute to a better understanding of the
complex ecology of root-inhabiting fungi so researchers can formulate reasonable
and testable hypotheses concerning the roles these fungi play in maintaining the
delicate balance between plant health and disease. We describe the implications of
fungal interactions for biological control strategies of root pathogens using three
diverse approaches: single tactic, integrated pest management, and proactive pest
management. We conclude that it is the very complex nature of the rhizosphere
that makes it imperative that we invest resources into fundamental research of
C 2001 Academic Press.
rhizosphere ecology.

I. INTRODUCTION
Fungi contribute significant biomass to soils where they have important functions in nutrient cycling (Harley, 1971) and microaggregate formation (Tisdall
et al., 1997). Soil fungi also encounter plant roots; they grow in, on, and around
roots and infect healthy tissues and colonize senescent materials (Parke, 1991).
In his classic tomes, Garrett (1960, 1970) characterized the edaphic fungal flora
as either soil or root inhabiting. He further characterized the root-inhabiting fungi as
either unspecialized or specialized parasites. The unspecialized parasites, such as

species of Pythium and Rhizoctonia, generally grow on juvenile root tissue. In
contrast, the specialized parasites may grow on more mature tissues and result in
vascular wilts as well as root rots.
The parasitic nature of these associations does not imply that all root-inhabiting
fungi are pathogens. In fact, many fungi growing with roots are beneficial, as
exemplified by mycorrhizal symbionts (Smith and Read, 1997) and nonpathogenic
parasites associated with roots (Deacon, 1987). Here we use “parasite” to describe
an organism that infects roots in order to obtain food for energy and growth, while
the term “pathogen” is used of an organism that specifically incites plant disease—
“the injurious alteration of one or more ordered processes of energy utilization in
a living system” (Bateman, 1978).
Our objectives for this chapter are to review the extant literature concerning fungi
growing on and in roots and to discuss the various interactions that occur among
these fungi. We begin by describing functional classifications of fungi that occur
with roots and then discuss the ecological roles of each major group (clinical and
subclinical pathogens, mycorrhizal fungi, and additional nonpathogenic fungi).
Next we discuss interactions that occur among these root-inhabiting fungi and their
diversity at the community level. Our goal is to contribute to a better understanding


ROOT-INHABITING FUNGI

3

of the complex ecology of root-inhabiting fungi so that researchers will be in a
better position to formulate reasonable and testable hypotheses concerning the
roles these fungi play in maintaining the delicate balance between plant health and
disease. Thus, we conclude this chapter by describing the implications of these
fungal interactions for biological control strategies of root pathogens and propose
further research priorities to achieve this end.

II. FUNCTIONAL DIVERSITY IN THE ROOT ZONE
A. CLASSIFICATION SCHEMES FOR FUNCTIONAL GROUPS
Winogradsky (1924) attempted to classify soil microorganisms on the basis of
their growth habit and modes of nutrition. Those that grow rapidly when nutrients
are readily available were described as zymogenous and those that grow slowly
on recalcitrant material as autochthonous. This is similar to the r-K life strategies
proposed by MacArthur and Wilson (1967) for animal systems. Pugh (1980),
following the reasoning of Grime (1979), expanded on and applied these concepts
to fungi, separating them into four broad life strategies:
1. ruderals, which have high sporulation and fast growth rates on simple, exogenous substrates;
2. competitors, which maintain growth over a longer time period by maximizing
capture of available resources;
3. stress-tolerants, which have low sporulation and slow growth rates as nutrients
are depleted resulting in a stable population; and
4. survivors-escapes, which occupy unique habitats such as the phylloplane or
rhizosphere of roots in waterlogged soils.
The rhizosphere has been defined as the soil adjacent to roots with altered physical, chemical, and biological characteristics compared to the bulk soil (Bowen and
Rovira, 1999). The input of inorganic and organic nutrients from actively growing
roots stimulates microbial growth, resulting in rapid increases in populations of
bacteria, fungi, and protozoa (i.e., the ruderals). Theoretically, establishment of
competitors should follow the ruderals and, as nutrients are depleted, stress-tolerant
organisms should predominate.
Some have divided the rhizosphere into the ectorhizosphere (zone outside the
root), rhizoplane (the root surface), and endorhizosphere (zone inside the root)
(Balandreau and Knowles, 1978). Though semantically incorrect (Kloepper et al.,
1992), an understanding of the physical, chemical, and biological properties of
these adjacent, but dissimilar, locations should help one understand the growth
habitat and life strategies of root-associated fungi. Unlike most bacteria, the

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SYLVIA AND CHELLEMI

majority of fungi are filamentous organisms and their expanding vegetative structures may easily span, and influence, life processes across these zones.
Biodiversity is an important issue and is gaining scientific, as well as political, attention. Biodiversity may be viewed as comprising taxonomic, genetic, and
functional components (Solbrig, 1991). Most research has focused on taxonomic
diversity and, with the advent of the new molecular tools, increasing emphasis is
being placed on genetic diversity. However, there are few studies that focus on the
manner by which genetic or taxonomic diversity affects ecosystem function (Zak
et al., 1994). The challenge for soil ecologists is to understand the impact of these
fungi on root function and plant health.
A classification scheme for root-inhabiting fungi may include clinical and subclinical pathogens, mycorrhizal fungi, and additional nonpathogenic fungi (suggesting our lack of knowledge of many fungi that occur in the root). In the remainder
of this section we summarize the natural histories and agroecosystem functions of
these groups.

B. CLINICAL PATHOGENS
1. Definition
Clinical pathogens can be defined as root-inhabiting fungi that cause visual
symptoms of disease. Typically these include mortality or elimination of the reproductive potential of the host plant, where reproductive potential is inclusive of
both sexual (seed) and asexual (vegetative) propagation. Thus, clinical pathogens
have the potential to dramatically impact the survivorship of plant populations.
While this definition addresses the functional role of the fungus in the ecosystem, it does not differentiate the parasitic nature or host specificity of the fungus. This functional group contains fungi which require living tissue of a specific
plant host to grow and reproduce (obligate parasites), as well as fungi which can
survive for extended periods of time in the soil on organic matter (facultative
parasites).
2. Abundance and Distribution
Clinical pathogens are found throughout the ecological range of terrestrial
plants, and epidemics of plant disease occur in a wide array of ecosystems ranging from the subarctic to the equatorial tropics. Their population dynamics within

crop production systems have been studied extensively. Typically, populations of
clinical pathogens are present at low levels, bordering on the lower detectable
range, until presence of the host coupled with favorable environmental conditions
create an explosion of the pathogen population resulting in an epidemic of plant


ROOT-INHABITING FUNGI

5

disease (Flowers and Hendrix, 1972; Kannwischer and Mitchell, 1981; Mitchell,
1978; Smith and Snyder, 1971). Under most conditions, they probably constitute
a small proportion of the community of root-inhabiting fungi and contribute little
to the total fungal biomass in the soil. Considerably less information exists on the
abundance of clinical pathogens in natural ecosystems (Alexander, 1992; Burdon,
1987).
3. Role in Agroecosystems
While comprising a small percentage of the total fungal biomass in soils, clinical
pathogens perform a major functional role in the ecosystem because they are primary regulators of plant density and diversity. This is most evident in agroecosystems where large-scale monoculture is practiced (Burdon and Chilvers, 1982).
Epidemics of plant diseases in natural systems have also been observed (Dinoor
and Eshed, 1984; Newhook and Podger, 1972; Schmidt, 1978; Weste and Ashton,
1994). In a study conducted over 4 years in permanent plots, root infection by
Rhizoctonia solani or Pythium irrgulare significantly reduced plant populations of
the annual legume Kummerowia stipulacea (Mihail et al., 1998). The reductions
were more severe at high plant densities. Computer simulation of epidemics caused
by Phytophthora spp. and Fusarium oxysporum have indicated that initial increase
of the pathogen population requires that the host density be above a threshold level
(Thrall et al., 1997).

C. SUBCLINICAL PATHOGENS

1. Definition
Subclinical pathogens invade root tissue and cause localized cell death and
disruption of vascular functions. However, visual symptoms are often difficult to
discern as subclinical pathogens do not cause mortality or eliminate the plants
ability to reproduce. Fungi placed in this classification have been referred to as
“minor pathogens” by Salt (1979). However, unlike Salt’s definition, which limited
this group to fungi that only parasitize root-tips or cortical cells, assignment to the
status of subclinical pathogen does not place any restriction on the type or location
of host tissue colonized within the root. Included in this group are fungal species
belonging to a diverse grouping of genera, including Pythium, Mucor, Fusarium,
and Cylindrocarpon. Subclinical pathogens can negatively impact plant health in
many ways. Through localized necrosis they disrupt vascular function in the root
and alter morphology and limit nutrient uptake or availability in the plant host
(Larkin et al., 1995), which results in a reduction in plant vigor and decline in
plant health. Infection by subclinical pathogens may predispose plants to injury


6

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by other plant pests or environmental stress. Their effects on plant health may be
synergistic when they parasitize root tissue in conjunction with other soil microbes,
such as plant pathogenic nematodes or bacteria. Their effects on the host make the
plant more vulnerable to drought, flooding, or other unfavorable environmental
conditions. Finally, subclinical pathogens can serve as vectors for plant viruses
(Campbell and Fry, 1966; Gerik and Duffus, 1986).
The fact that some fungal species can exist as both clinical and subclinical
pathogens muddies the distinction between these groups. For example, at ambient
temperatures of 28◦ C or less, Pythium aphanidermatum and Pythium myriotylum

function as subclinical pathogens on pepper and tomato (Chellemi et al., unpublished data), parasitizing root cells and causing significant reductions in growth,
but not limiting the plants ability to survive and reproduce. However, at ambient
temperatures near 34◦ C these fungi cause extensive plant mortality in the same
host.
2. Abundance and Distribution
Subclinical root-inhabiting fungi are distributed throughout the range of terrestrial plants. Their diversity and abundance remains relatively unknown due in part
to the fact that their status as subclinical pathogens remains largely undetermined.
Demonstrable reductions in plant growth or yield in fulfillment of Koch’s postulates are required to confirm their status as plant pathogens. These procedures are
time consuming and labor intensive and, therefore, determination of pathogenic
status has been typically reserved for those fungi suspected of inducing plant
mortality. Thus, investigations to determine the status of subclinical pathogens
are usually undertaken for alternative reasons (i.e., suspicion of vectoring a plant
virus or interaction with other clinical pathogens). In crop production systems, the
abundance of subclinical pathogens has been investigated in replant diseases of
perennial crops (Mazzola, 1999) and citrus declines of unknown etiology (Graham
et al., 1983; Nemec et al., 1980).
3. Role in Agroecosystems
Subclinical pathogens also function as regulators of plant density, though to
a lesser extent than the clinical pathogens. They do so by affecting the relative
fitness of plant populations. This is accomplished by reducing the competitive
ability of plants through reductions in vigor or reproduction. There is evidence for
this role in natural plant systems (Augspurger, 1983; van der Putten et al., 1993).
In a study by Holah and Alexander (1999), root-inhabiting fungi unique to soils
associated with Chamaeerista fasciculata (an annual legume) were detrimental
to Andropogon geradii (a native tallgrass and one of the dominant perennials in
the ecosystem). Subclinical pathogens can also initiate processes leading to the


ROOT-INHABITING FUNGI

7

breakdown of plant tissue and recycling of carbon in the soil, as they are present
in root tissue at the time of plant senescence (Waid, 1974).

D. ARBUSCULAR MYCORRHIZAL FUNGI
1. Definition
Mycorrhizae are symbiotic associations of specific fungi with the fine roots
of plants. Several mycorrhizal types have been described, and one or more of
these plant–fungus associations are found in nearly every biome on Earth (Smith
and Read, 1997). The arbuscular mycorrhizal (AM) type is the most widespread
mycorrhiza found on plant roots in agroecosystems. The diagnostic feature of arbuscular mycorrhiza is the highly branched arbuscules that develop within root
cortical cells. The fungus initially grows between cortical cells but soon penetrates
the host cell wall and grows within the cell lumen. Neither the fungal cell wall nor
the host cell membrane are breached (Bonfante and Perotto, 1995). As the fungus
grows, the host cell membrane invaginates and envelops the fungus, creating a
new compartment where material of high molecular complexity is deposited. This
apoplastic space prevents direct contact between the plant and fungus cytoplasms
and allows for efficient transfer of nutrients between the symbionts. The arbuscules
are relatively short lived and are often difficult to observe in field-collected samples.
Other structures produced by AM fungi include vesicles, auxiliary cells, extramatrical hyphae, and spores. Vesicles are thin-walled, lipid-filled structures that
usually form in intercellular spaces. Their primary function is thought to be for
storage; however, vesicles can also serve as reproductive propagules for the fungus. The term vesicular–arbuscular mycorrhiza or VAM was originally applied to
this group, but because a major suborder lacks the ability to form vesicles in roots,
AM is now the preferred acronym. Auxiliary cells are formed in the soil and can
be coiled or knobby. The function of these structures is not known. Spores can be
formed either in the root or more commonly in the soil. Spores produced by AM
fungi are asexual, formed by the differentiation of vegetative hyphae. For some
fungi (e.g., Glomus intraradices), vesicles in the root undergo secondary thickening, a septum (cross wall) is laid down across the hyphal attachment, and a spore is
formed, but more often spores develop from hyphal swellings in the soil. The AM

fungi may produce an extensive network of extramatrical hyphae (Sylvia, 1990)
and can significantly increase phosphorus-inflow rates of the plants they colonize
(Jakobsen et al., 1992).
The AM fungi are currently classified in the order Glomales (Morton, 1988).
The order is further divided into suborders based on the presence of (i) vesicles
in the root and formation of chlamydospores borne from subtending hyphae for
the suborder Glomineae or (ii) absence of vesicles in the root and formation of


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auxiliary cells and azygospores in the soil in the suborder Gigasporineae. The order
Glomales is further divided into families and genera according to the method of
spore formation. The spores of AM fungi are very distinctive and range in diameter
from 10 to >1000 ␮m. The spores can vary in color from hyaline to black and in
surface texture from smooth to highly ornamented. More than 150 species of AM
fungi have been described; however, taxonomy at the species level is currently
going through extensive revision. The reader may visit the INVAM webpage
( to obtain current information on AM taxonomy.
2. Abundance and Distribution
Most crop plants are colonized by AM fungi and, in fact, it is much easier
to list the predominately nonmycorrhizal plant families—the Caryophyllaceae,
Chenopodiaceae, Cruciferae, Juncaceae, Polygonaceae, and Proteaceae—than the
mycorrhizal ones. Surveys of field-grown crops reveal wide ranges in the extent
of colonization of roots by AM fungi (Table I). Many edaphic factors, such as soil
type (Frey and Ellis, 1997), soil fertility (Bolgiano et al., 1983), and pH (Clark,
1997), affect the extent of colonization but the conspicuous fact is that the majority
of agronomic crops grown under a wide range of conditions consistently have a

significant portion of their root systems colonized by AM fungi. It is clear that
the critical question for the agronomist is not whether their crops are colonized by
AM fungi but rather what impact these fungi have on crop and soil productivity.
We have incomplete knowledge of the species of AM fungi associated with
agronomic crops because numerous difficulties are encountered when attempting
to characterize diversity of these fungi in the field; spores are difficult to identify,
some species do not sporulate, and there is little relationship between functional
and morphological diversity (Douds and Millner, 1999). The few surveys that
quantify AM fungal spore densities or species richness (Table I) suggest that
there are often less than 10 spores g−1 soil and between 5 to 10 species of AM
fungi present in a given agronomic soil. What these numbers mean relative to soil
productivity is unclear because spores may represent only a small proportion of
the total mycorrhizal propagules in the soil [colonized roots and hyphae may also
initiate new mycorrhizae (Friese and Allen, 1991)]. Furthermore, AM species,
and even isolates, may differ dramatically in their effect on plant growth (Boerner,
1990; Boucher et al., 1999), and with current knowledge it is impossible to predict
which propagules will have the greatest impact on crop response.
Even though AM symbioses are among the best known examples of compatibility between plants and microbes we have little understanding of the factors that contribute to the specificity of these compatible interactions. The AM symbioses are
often considered nonspecific (Gianinazzi-Pearson, 1984; Sanders, 1993). Nonetheless, there is mounting evidence that “host preference” is an important characteristic of AM symbioses (Dhillion, 1992; Giovannetti and Hepper, 1985). By this


9

ROOT-INHABITING FUNGI
Table I
Examples of AM Fungal Associations of Agronomic Crops

Crop
Aeschynomene
americana

Allium cepa
Apium graveolens
Capsicum annuum
Cucumis melo
Eleusine coracana

Location

Max. root
Max. spore Species
colonization (%) densitya richness

Florida

30b

Israel
Israel
Australia
Israel
Israel
India

Minnesota
Pennsylvania
Gossypium hirsutum Texas
Helianthus annuus India
Glycine max

Reference

3

6

Medina et al. (1988)

ca. 50b
ca. 50b
58b
ca. 50b

nac
na
na
na

na
na
na
na

Krikun et al. (1990)
Krikun et al. (1990)
Olsen et al. (1999)
Krikun et al. (1990)

>50b
30b, d

na
6

na
na

25b
9,b 67d
70b
23b, d

67e
<1,b 1d
na
5

14
na
na
na

Krikun et al. (1990)
Harinikumar and
Bagyaraj (1989)
Johnson et al. (1991)
Douds et al. (1993)
Zak et al. (1998)
Harinikumar and
Bagyaraj (1989)

Hordeum vulgare

Demark

50b

2

na

Jakobsen and
Nielsen (1983)

Lycopersicon
esculentum

Florida

52d

4

4

Unpublished data

Oryza sativa

Japan

55b

3

na

Solaiman and
Hirata (1997)

Pisum sativum

Denmark

80b

2

na

Jakobsen and
Nielsen (1983)

Solanum tuberosum

England

53b

Triticum aestivum

Pennsylvania
Pennsylvania
Kansas

15d
35,b 45d
27b

Denmark

50b

Australia

20,b 70d

na

na

Minnesota
S. Dakota

34b
10,b 43d

71e
na

14

na

Pennsylvania
Quebec
India

84d
71b, d
29b, d

na
21
4

na
na
na

Zea mays

a

3

na

Hayman et al. (1975)

8
<1,b 4d

3

na
na
6

2

na

Boswell et al. (1998)
Douds et al. (1993)
Hetrick and Bloom
(1983)
Jakobsen and
Nielsen (1983)
Ryan et al. (1994)

Data variously presented as spores per gram or per milliliter.
Conventional system.
c
na = data not available.
d
Organic/sustainable system.
e
High value due to an abundance of Glomus aggregatum.
b

Johnson et al. (1991)
Vivekanandan and

Fixen (1991)
Boswell et al. (1998)
Kabir et al. (1998)
Harinikumar and
Bagyaraj (1989)


10

SYLVIA AND CHELLEMI

we mean that different species, strains, or isolates of AM fungi colonize plant roots
to different degrees and have variable effects on plant growth and development.
Here it is important to distinguish among specificity (innate ability to colonize),
infectiveness (amount of colonization), and effectiveness (plant response to colonization). The AM fungi differ widely in the levels of colonization they produce
in a root system and in their impact on nutrient uptake and plant growth.
Host preference may be under the genetic control of the host, the fungus, or, most
likely, a complex interactive effect of both symbiotic partners with soil edaphic
factors. Much of the extant literature emphasizes the role of the plant in the interaction. Johnson et al. (1991) found that cropping history (maize vs soybean) and soil
type altered the communities of AM fungi in soil, Bever et al. (1996) demonstrated
host-dependent sporulation among common lawn plants, and Zhao et al. (1997)
reported differential development of AM fungi with two legume species. Host
genotype variation in root colonization and plant response also has been demon◦
and Rydberg,
strated for citrus (Graham and Eissenstat, 1994), pea (Martensson
1995), wheat (Hetrick et al., 1996), barley (Baon et al., 1993), and tomato (Barker
et al., 1998).
Less is know about the effect of the fungal genotype on root colonization and
plant response. Inoculum density can be a confounding factor when one attempts
to differentiate fungal affects (Clapperton and Reid, 1992; Daft and Nicolson,

1969). However, when inoculum densities are not limiting or have been equalized,
important ecotypic variation among AM fungi has been reported (Boyetchko and
Tewari, 1995; Douds et al., 1998; Graham et al., 1996; Hepper et al., 1988; Monzon
and Azcon, 1996; Stahl et al., 1990; Sylvia et al., 1993b). These studies support
the hypothesis that the fungal ecotype will have an important impact on root
colonization, sporulation, and host plant response
3. Role in Agroecosystems
We are becoming increasingly aware of the important multifunctional roles of
AM fungi in ecosystems (Newsham et al., 1995b). Besides improving uptake of
poorly mobile nutrients (George et al., 1992), AM symbioses may impact drought
tolerance (Schellenbaum et al., 1998) and pathogen interactions (Azc´on-Aguilar
and Barea, 1997) and contribute to soil quality by channeling carbon to the soil
and thereby improve soil aggregation (Jastrow et al., 1998). Furthermore, there is
mounting evidence that AM fungi are important determinants of plant community
structure and plant succession (Allen et al., 1995; Gange et al., 1993). van der
Heijden et al. (1998) concluded that below-ground diversity of AM fungi is a
major factor contributing to the maintenance of plant biodiversity and ecosystem
function.
The function of AM fungi in highly managed agroecosystems is less certain
(Hayman, 1987). Under nutrient (Bagyaraj and Sreeramulu, 1982; Beyene et al.,


ROOT-INHABITING FUNGI

11

1996; Osonubi et al., 1995) or moisture stress (Sylvia et al., 1993a), they can
significantly increase crops yields. However, in highly managed, high-input systems, it is possible to demonstrate growth reductions due to AM colonization
(Graham and Eissenstat, 1998; McGonigle and Miller, 1996). Furthermore,
Hetrick et al. (1993) found that modern breeding practices have reduced mycorrhizal dependency of wheat. Indeed, in those cases where colonization occurs in the absence of a demonstratable growth enhancement of the plant, the

net cost of the symbiosis may exceed the net benefit (Johnson et al., 1997).
Nonetheless, when one takes a more holistic view of the plant–soil continuum,
the “cost” of the symbiotic association may turn out to be an important benefit
(Schreiner and Bethlenfalvay, 1995). For example, Wright and Upadgyaya (1997)
have described a high-molecular-weight glycoprotein (termed glomalin) that is
produced in abundance by AM fungi. This material accumulates in soil and is
positively correlated with aggregate stability (Fig. 1) (Wright and Upadhyaya,
1998).
Conventional agronomic practices may adversely affect the diversity and abundance of AM fungi in agroecosystems (Johnson and Pfleger, 1992; Thompson,
1994). Large applications of phosphatic fertilizer generally reduce AM root colonization (Harinikumar and Bagyaraj, 1989; Olsen et al., 1996; Vivekanandan and

Figure 1 The relationship between stability of 1- to 2-mm-size aggregates and immunoreactive
easily extractable glomalin (IREEG) from soils in four regions of the United States with ≤80% aggregate stability. From Wright and Upadhyaya (1998); used with permission.


12

SYLVIA AND CHELLEMI

Fixen, 1991); however, addition of phosphorus fertilizer to very low phosphorus
soils may increase root colonization (Bolan et al., 1984). Tillage has been shown
to delay AM colonization of maize roots and result in reduced early season phosphorus uptake (McGonigle et al., 1999; Vivekanandan and Fixen, 1991) as well
as reduced hyphal and spore densities near the soil surface (Kabir et al., 1998).
Crop rotations that include nonhost plants (Harinikumar and Bagyaraj, 1988) or
long-term fallow (Thompson, 1987) may also reduce AM fungal populations.
Pesticides, especially fumigants, substituted aromatic hydrocarbons, and benzimidazoles (Johnson and Pfleger, 1992), may adversely affect the activity of AM
fungi in soil. As an overall generalization one may conclude that conventional
management practices reduce AM fungal populations while sustainable, organic,
low-input systems tend to increase their activity (Table I) (Douds et al., 1993;
Kabir et al., 1998; Ryan et al., 1994).

E. ADDITIONAL NONPATHOGENIC FUNGI
1. Definition
This group comprises a diverse collection of fungi capable of invading and
occupying inter- and intracellular spaces within the root tissue without disrupting the cellular functions of root organelles. As a group, these fungi survive and
function as saprophytes within the soil microbial community and include members from many common genera, such as Fusarium, Gliocladium, Microdochium,
Penicillium, Phialophora, Trichoderma, and various poorly defined dark-septate
endophytes (Jumpponen and Trappe, 1998; Skipp and Christensen, 1989). They
differ from mycorrhizal fungi in that they form no specialized organelles or structures within the root. Also, they are generally thought to have no species-specific
relationships with the plants; however, some host specificity has been suggested
(Skipp and Christensen, 1989).
2. Abundance and Distribution
Fungi included in this group are ubiquitous and occur in large numbers wherever terrestrial plants are found. Many saprophytic fungal species are present in
the rhizosphere shortly after introduction of the plant host into the soil (English
and Mitchell, 1988). Furthermore, epidermal and outer cortical cells of roots are
ephemeral and begin to senesce within a few weeks in the zone of cortical lysis
(Foster, 1986). Deacon et al. (1987) describe this process as early root cortex death
(RCD). These tissues initially appear healthy, but nuclear staining reveals that nuclei have disappeared from the cells. A wide range of nonpathogenic fungi readily
colonize these senescing root tissues (Bowen and Rovira, 1976; Huisman, 1988).


ROOT-INHABITING FUNGI

13

Information on the abundance of nonpathogenic root-inhabiting fungi in natural systems is incomplete, partially because they are not normally investigated
for their contribution to ecosystem health. In crop production systems, documentation of their abundance usually occurs during investigations related to a
plant pathological disorder. For example, the composition of presumably nonpathogenic root-inhabiting fungi in association with replant diseases of perennial fruit trees was studied by Mazzola (1999). Difficulties in the identification
of fungal species also limit quantitative studies on their abundance and distribution as few molecular markers have been identified for nonpathogenic soil
fungi.

3. Role in Agroecosystems
The role of nonpathogenic root-inhabiting fungi in ecosystems is complex. As
saprophytes present in large numbers they occupy a vital link in the trophic food
web in soils. They participate in carbon recycling through the decomposition of
plant tissue (Waid, 1974). Their relationships to plant health have been documented in several systems. They may be involved as elicitors of induced systemic
resistance in the plant host (Benhamou et al., 1997; Larkin and Fravel, 1999).
They can also protect plants from infections by pathogens through direct competition for infection sites on the root or interference with saprophytic colonization
of soil organic matter (Couteaudier, 1992; Martin and Hancock, 1986; Schneider,
1984).

III. INTERACTIONS AMONG
ROOT-INHABITING FUNGI
A. INTERACTIONS AMONG PATHOGENS
Co-infection of root systems by more than one pathogenic fungus is most likely
the rule rather than the exception. Synergism between co-infecting pathogenic
fungi may or may not occur. For example, P. myriotylum interacted synergistically
with Fusarium solani to cause damping-off of peanut seedlings, but no synergistic
effect was observed when P. myriotylum was combined with R. solani (Garcia and
Mitchell, 1975). In the same study, P. myriotylum could not be reisolated from roots
co-infected with R. solani. Thus, although multiple infections may take place in
the root system among pathogens, the resultant level of disease will vary depending upon the specific species interactions. Elucidation of the interactions among
pathogens may be further complicated by soil edaphic factors and environmental
conditions.


14

SYLVIA AND CHELLEMI

B. INTERACTIONS OF AM FUNGI WITH PATHOGENIC

AND NONPATHOGENIC FUNGI
Mycorrhizal fungi colonize feeder roots and thereby interact with root pathogens
that parasitize this same tissue. A large body of literature exists on the interactions
among pathogens and AM fungi, and several reviews have been written on the
subject (Dehne, 1982; Linderman, 1994; Paulitz and Linderman, 1991; Schenck,
1981). In a natural ecosystem, a major role of mycorrhizal fungi may be protection
of the root system from endemic pathogens (Newsham et al., 1995a). In cropping
systems the role of AM fungi in disease protection is less clear; however, much of
the literature suggests that AM fungi reduce soilborne disease or at least ameliorate the effects of disease. Mechanisms put forward to explain disease protection
include (Azc´on-Aguilar and Barea, 1997):
r
r
r
r
r
r

improved nutrient status of the host plant
competition for host photosynthates
competition for infection sites
anatomical and morphological changes in the root system
microbial changes in the mycorrhizosphere
activation of plant defense mechanisms

Often inoculation with AM fungi prior to challenging with a pathogen is necessary to achieve disease reduction. This is because many root pathogens germinate
and grow more rapidly than AM fungi and, if co-inoculated, will attack the root before the mycorrhizae become established. An intriguing finding is that AM fungi
may actually stimulate spore germination of some pathogens (St-Arnaud et al.,
1995). A protective effect may result if germination of pathogen spores close to
the mycorrhizal mycelium, but far from the roots, results in reduced inoculum
potential of the pathogen.

Here we present several recent examples of AM fungal interactions with
pathogens that have been published since the previously cited reviews. Trotta
et al. (1996) reported that precolonization of tomato with the AM fungus,
Glomus mosseae decreased both weight reduction and root necrosis caused by
Phytophthora nicotianae. They concluded that the AM fungus activates a diseasesuppression mechanism to reduce root damage because improved phosphorus nutrition could not account for increased disease resistance. Cordier et al. (1996)
found a similar response, reporting that the number of P. nicotianae hyphae growing in the root cortex of tomato was reduced in mycorrhizal root systems and that
the pathogen hyphae never invaded arbuscule-containing cells. Both localized and
systemic resistance mechanisms have been demonstrated in this system, including
induction of plant wall defense responses (Cordier et al., 1998) and unique chitinase
isoforms (Pozo et al., 1998; Pozo et al., 1997). In contrast, Kjøller and Rosendahl