Why are Phytophthora and Other Oomycota not True Fungi?
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ABSTRACT: Invasive fungi and other non-indigenous plant pathogens have had a significant effect on American agriculture for hundreds of years. At present crop loss due to invasive plant pathogens, especially fungi, is estimated at $21 billion per year in the United States, greater than the loss caused by non-indigenous insects. Plant pathogenic fungi are difficult to detect and identify. Thus knowledge of which fungi pose a threat is essential to prevent their entry by means others than inspection. In this paper, examples are presented of invasive fungi on agricultural commodities introduced into the United States. In all cases two factors have been crucial: first, the pathway through which these fungi have entered, and second, systematic knowledge to prevent and respond to the new invasive species. Historically important plant pathogens such as black stem rust of wheat still cause considerable damage while others such as late blight of potato appear to be having a resurgence. Known previously in Australia, then moving to Africa and South America, the virulent species of soybean rust appeared in the U.S. in 2004 but has not been as devastating as anticipated. Plant pathogenic fungi on specialty crops such as daylily, gladiola and chrysanthemum are threatened by rust fungi recently found in the U.S. apparently brought in on infected germplasm. A crisis in the export of U.S. wheat occurred in the late 1990's when the molecular diagnostic test for Karnal bunt gave a false positive response to a closely related but previously unknown species. Many potentially dangerous plant pathogens of crop plants have not yet been introduced into the U.S. It is critical that meticulous surveillance be conducted as plant material enters the country as well as where crops are grown prior to shipment. In addition, the scientific infrastructure is needed to be able to respond quickly to new invasive fungi. This requires sound systematic knowledge of plant pathogenic fungi both in the U.S. and around the world and a cadre of systematic experts who can characterize invasive fungi.Biological Invasions 01/2009; · 2.51 Impact Factor
Outlooks on Pest Management – October 2006 217
© 2006. Research Information Ltd. All rights reserved
Plant diseases result in billions of dollars in damage to
agricultural crops each year. One of the groups of organisms
that cause many serious plant diseases has long been known
as the Oomycota or oomycetes, traditionally classified in the
phycomycetes or “lower fungi.” The phycomycetes are an
informal group that, in addition to the Oomycota, have
historically included such diverse fungi as the slime molds,
chytrids, zygomycetes or bread molds, and arbuscular
mycorrhizae.The “higher fungi” have included the
ascomycetes or sac fungi such as the discomycetes, (e.g.
morels), pyrenomycetes, (including the cause of chestnut
blight), deuteromycetes or imperfect fungi, and yeasts; and
the basidiomycetes with the rust fungi, smut fungi,
mushrooms, gasteromycetes, polypores, and jelly fungi.
Over the past three decades knowledge about relationships
among groups of fungi has increased greatly such that these
traditional groupings based on gross morphology no longer
reflect genetic relationships among them.
The Oomycota or Peronosporomycetes consist of more
than 800 species that may be saprobic or parasitic on
terrestrial or aquatic plants and animals. One member of the
Oomycotahas greatly influenced
Phytophthora infestans, the cause of late blight of potatoes.
As a result of the famine in Ireland caused by this disease,
about 1 million people died and another 1.5 million
emigrated (Alexopoulos, et al. 1997).
diseases are caused by species of Phytophthora including
sudden oak death and ramorum blight caused by P.
ramorum, and cacao black pod caused by P. megakarya.
Other members of the group include species in the genus
Pythium, such as Pythium aphanidermatum, cause of
cottony blight of turf grasses, and downy mildews in the
Peronosporales such as Peronospora tabacina, tobacco blue
mold, Plasmopara viticola, downy mildew of grape, and P.
halstedii, cause of sunflower downy mildew, and many
others. Finally, a group traditionally placed in the oomycetes
is the Saprolegniales or water moulds that cause diseases of
fish and other aquatic vertebrates.
A number of other
Characteristics of the Oomycota
The Oomycota have long been considered fungi because they
obtain their nutrients via absorption and many of them
produce the filamentous threads known as mycelium
characteristic of many fungi.
classified as a distinct group allied with the lower fungi based
on a number of unique characteristics (Table 1).
members of the Oomycota undergo oogamous reproduction,
meaning they produce oospores as a result of fertilization.
These oospores may be large and solitary or smaller and
numerous inside the oogonium (Fig. 1). None of the true
Fungi produce oospores. Another distinction is the cell wall
composition. In the Oomycota, the cell walls are composed
of beta glucans and cellulose rather than chitin as in the true
Fungi. In addition the Oomycota produce motile zoospores
with two kinds of flagellae, one of which is a whiplash
flagellum oriented posteriorly while the other has a fibrous,
ciliated structure and is oriented anteriorly. The occurrence
of two kinds of flagellae is referred to as being heterokont.
Although some true Fungi, namely the Chytridiomycota,
The Oomycota have been
WHY ARE PHYTOPHTHORA AND OTHER OOMYCOTA NOTTRUE
Amy Y. Rossman, USDA Agricultural Research Service and Mary E. Palm, USDA Animal and Plant Health
Inspection Service, Systematic Botany & Mycology Laboratory, Beltsville, Maryland 20705, USA explain why
the pathogens that cause diseases such as downy mildews are not fungi
PHYTOPHTHORA AND OTHER OOMYCOTA
Keywords: Classification, Chromista, oomycetes, Peronosporomycetes,
Table 1. Major distinctions between the Oomycota in the
Chromista and the true Fungi (Chytridiomycota,
Glomeromycota, Zygomycota,Ascomycota, Basidiomycota)
Product of sexual
Nuclear state of
Type of flagellae
on zoospores, if
Heterokont, of two
types, one whiplash
the other fibrous,
With tubular cristae
If flagellae produced,
usually of only one
218Outlooks on Pest Management – October 2006
produce stages with motile zoospores, their flagellae are only
of one kind, the posterior whiplash type. A fourth major
difference between the Oomycota and the true Fungi is that
the vegetative cells and most of the reproductive structures of
the Oomycota are composed of cells in the diploid state.
This is unlike the true Fungi in which most of the mycelium
or thallus is composed of haploid or dikaryotic cells in which
the nuclei have only one set of chromosomes.
dikaryotic state two or more kinds of nuclei may be present
in the cells. In addition, most members of the Oomycota
produce either hyphae without septa, called coenocytic
mycelium, or unicellular thalli, although this is the case for
some kinds of true Fungi as well. Most true Fungi with the
exception of the Zygomycota produce septate hyphae and
With the development of the transmission electron
ultrastructural characteristics were noted between the
Oomycota and true Fungi.Some of these include having
mitochondria with tubular cristae and protoplasmic- and
nuclear-associated microtubules in the Oomycota while the
true Fungi have flattened mitochondrial cristae.
groups of organisms were examined using the TEM a
relationship was hypothesized between the Oomycota and
the heterokont algae (Table 1). This was the first modern
evidence that the Oomycota should be regarded as
“colorless” algae rather than true Fungi.
noted in Alexopoulos et al., 1997, about 150 years ago
Saprolegniales [water moulds], that the oomycetes “were
allied with certain algae.”
late‘70s, differences in
in reference to the
Relationships of the Oomycota based on
As new tools for determining phylogenetic relationships were
developed, especially those using molecular sequence data,
they have been applied to questions such as whether the
Oomycota are more closely related to the heterokont algae or
the true Fungi.
Determining relationships using DNA sequence data is
based on comparing sequence similarities in gene regions
such as small or large subunits of the nuclear ribosomal
DNA.Each base pair is regarded as a character and the
sequence of base pairs is aligned such that homologous
characters are compared. Mathematical algorithms running
on powerful computers are used to analyze changes among
the thousands of base pairs of gene regions. By determining
how many changes have occurred between different groups
of organisms, it is possible to estimate relative distance
among groups and to develop an evolutionary tree that
reflects those relationships.
Results from a number of studies using molecular
sequencedatacombined with the ultrastructural
similarities confirm unequivocally that the Oomycota share a
common ancestor with the other members of the heterokont
algae or Chromista.In addition to the Oomycota, two
smaller groups, theHyphochytridiomycota
Labyrinthulomycota appear to be most closely related to the
Chromista. The Chromista include several kinds of algae,
namely the Phaeophyta or brown algae, Xanthophyta or
yellow-green algae, Chrysophyta or golden algae, and
Bacillariophyta or diatoms as well as several smaller groups.
The heterokont algae are distinctive among the algae in
having the same two kinds of flagellae as occur in the
Oomycota, tubular mitochondrial
ultrastructural similarities. The photosynthetic members of
the Chromista possess chlorophyll c and other pigments that
are not found in any other group. Some controversy still
remains about exactly what to call this group of organisms.
Most authors refer them to the kingdom Chromista, phylum
Heterokonta, while others place them in the kingdom
Straminopila (Patterson & Sogin, 1992).
True Fungi or Eumycota
The true Fungi or Eumycota are now restricted to five major
groups, each of which is regarded as a phylum in the
Kingdom Fungi. One of these groups is the Chytridiomycota
or chytrids.In some ways the chytrids are similar to the
Saprolegniales in the Oomycota in that they are regarded as
water moulds.They attack small-celled organisms and
debris in aquatic environments. Another group of true Fungi
is the Zygomycota or zygomycetes that include the bread
moulds, Mucorales. The arbuscular mycorrhizae were once
regarded as part of the Zygomycota because they produce
what appear to be zygospores. Molecular data have shown
that these root-associated fungi are quite distinct and should
be regarded as their own phylum, the Glomeromycota.
These fungi are ancient in origin known from the fossil
record to be associated with primitive land plants from the
Devonian (Remy et al., 1994). The largest and most well
Fig. 1. Oogonium with a solitary oospore of Phytophthora
PHYTOPHTHORA AND OTHER OOMYCOTA
Outlooks on Pest Management – October 2006 219
known of the true Fungi are the Ascomycota or ascomycetes
and the Basidiomycota or basidiomycetes. The Ascomycota
include most of the lichenized fungi, yeast fungi, morels, cup
fungi, and many kinds of microfungi such as pyrenomycetes
and their asexual states. The asexual or mitotic fungi are
also referred to as the imperfect fungi, asexual fungi,
deuteromycetes or fungi imperfecti. Many plant pathogenic
fungi are these asexually reproducing ascomycetes that
include thehyphomycetes and
deuteromycetes. Many of the asexually reproducing fungi do
not have any known sexual state but using molecular
sequence data analyses it is possible to determine the species
of Ascomycota to which they are most closely related. The
Basidiomycota or basidiomycetes include the rust and smut
fungi most of which are obligate plant pathogens.
Mushrooms, gasteromycetes, jelly fungi and polypores are
also members of the Basidiomycota.
coelomycetes in the
The Remaining non-Fungi
A few other groups of organisms previously regarded as
fungi are now known to belong outside the true Fungi. The
Plasmodiophorales including Plasmodiophora brassicae,
cause of cabbage club root, have proven difficult to place in
the tree of life but they are not related to the true Fungi.
Some evidence suggests that they too share a common
ancestor with the Chromista but this is not conclusive. For
some years it has been known that the Myxomycetes or slime
molds and Acrasiales or cellular slime molds are not related
to the true Fungi.Recent studies suggest that the
Myxomycetes represent an independent evolutionary lineage
that diverged prior to the “crown” groups of organisms that
includes the Fungi, Animalia, Plantae, Chromista and
discovery is that the true Fungi are more closely related to
animals than to plants (Baldauf & Palmer, 1993; Wainright
et al., 1993), thus explaining why it is so difficult to
develop antibiotics that are effective against human fungal
Finally, a recent noteworthy
Most mycologists have not abandoned the study of the
Oomycota and still define the organisms they study “as
eukaryotic heterotrophic osmotrophs in which assimilation
takes place through a cell wall” (Dick, 1997). Adaptions of
these organisms to obtaining their nutrients by absorption
has resulted in considerable morphological convergence
among them as exemplified by the similarity of oomycetous
white rusts with true rust fungi.
evolutionary relationships among these groups of organisms
contributes greatly to our ability to develop strategies to
control the diseases these organisms cause.
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Remy, W., Taylor, T.N., Hass, H., & Kerp, H. 1994. Four hundred-
million-year-old vesicular arbuscular mycorrhizae. Proc. Natl.
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Wainright, P. O., G. Hinkle, M. L. Sogin, & S. K. Stickel. 1993.
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PHYTOPHTHORA AND OTHER OOMYCOTA
Dr.Amy Y. Rossman is the Research Leader of the Systematic Botany &
Mycology Laboratory and Director of the U.S. National Fungus
Collections, the largest collection of fungal reference specimens in the
world. She conducts research on fungi with emphasis on plant pathogenic
ascomycetes and their asexual states. She has authored or co-authored
more than 120 research papers including the much-used Fungi on Plants
and Plant Products in the United States.
Dr. Mary E. Palm is the National Mycologist for the Animal and Plant
Health Inspection Service. As such she identifies plant-associated fungi
from around the world and deals with the consequences of the
introduction of invasive fungi especially those that influence trade of
agricultural commodities. She has published over 60 research papers on
agriculturally important fungi.
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