Fry, William E. and Niklaus J. Grünwald. 2010. Introduction to Oomycetes. The Plant Health Instructor. DOI:10.1094/PHI-I-2010-1207-01
AuthorsWilliam E. Fry and Niklaus J. Grünwald Cornell University and USDA-ARS
The oomycetes, also known as “water molds”, are a group of several hundred organisms that include some of the most devastating plant pathogens. The diseases they cause include seedling blights, damping-off, root rots, foliar blights and downy mildews. Some notable diseases are the late blight of potato, downy mildew of grape vine, sudden oak death, and root and stem rot of soybean. Because of their filamentous growth habit, nutrition by absorption, and reproduction via spores, oomycetes were long regarded by plant pathologists as lower fungi. However, as our understanding of evolutionary relationships has grown, it is now clear that this group of organisms is unrelated to the true fungi. Indeed, fungi appear more closely related to animals than to oomycetes, and oomycetes are more closely related to algae and to green plants (Figure 1).
Phylogenetic analyses using genes and intergenic regions have confirmed the assertions of earlier systematists that the oomycetes are different from fungi. The data from these molecular analyses have been particularly convincing to non-systematist plant pathologists. There are many features distinguishing oomycetes from fungi. Septa (cell walls) in the hyphae are rare, resulting in a multinucleate condition (termed coenocytic). The nuclei of vegetative cells are typically diploid. The cell wall is composed of β-1,3, and β-1,6 glucans, and not of chitin (the polymer of N-acetyl glucose amine, found in the walls of true fungi). Many species produce wall-less, biflagellated swimming spores (zoospores) in structures called sporangia.
One of the most distinguishing characteristics is the production of zoospores produced in sporangia. The anterior flagellum of a zoospore is a tinsel type, while the posterior flagellum is a whiplash type; both are typically attached in a ventral groove (Figure 2). Although wall-less, zoospores retain a consistent but flexible shape. Zoospores can swim in water films on leaf surfaces, in soil water, in hydroponic media and in natural bodies of water. Oomycetes can often be “baited” from soil water, streams or ponds, and it is thought that zoospores are attracted to the baits. After a time of free swimming the zoospores settle on a surface, retract their flagella, and secrete a mucilaginous matrix which affixes them to the surface. Sporangia of different taxa within the group are of diverse shapes and characteristics (Figures 3-8, 29). They may be terminal or intercalary (within a hyphal filament), bulbous or not, and if terminal, caducous (sporangia detach readily) or not.
In some species, the ability to produce zoospores has been lost, and sporangia are thought to have evolved into structures that germinate directly to produce germ tubes. In this case, the sporangia are sometimes termed “conidia”. In yet other species, sporangia can germinate directly to produce germ tubes or “indirectly” to produce zoospores, a trait which is often temperature dependent, with zoospores being produced at cooler temperatures.
Sexual reproduction occurs via the production of gametangia: oogonia and antheridia. Because meiosis does not occur until the formation of gametangia occurs, the vegetative nuclei are diploid. The morphology of antheridium attachment has been an important feature in morphological taxonomy of some genera. In some genera the antheridium is attached to the side of the oogonium (paragynous, Figure 8), but in other genera, the antheridium surrounds the base of the oogonium (amphigynous, Figure 9).
Typically each individual produces both antheridia and oogonia. There may be differences in “femaleness” and “maleness” and sexual preference is relative to other individuals. In some species, two distinct mating types occur and both are required for sexual reproduction (these are heterothallic as opposed to homothallic species). In heterothallic oomycetes, the gametangia are produced only in the presence of both mating types due to the fact that a hormone produced by one thallus stimulates the other to produce gametangia. In other species, sexual reproduction occurs within a single individual (these are homothallic individuals). Unlike the heterothallic species, homothallic individuals do not require distinct mating types, but can reproduce sexually by selfing. All Pythium and some Phytophthora species are homothallic.
The fertilized oogonium develops into a thick-walled oospore (Figure 10). When the oospores are produced in plant tissue, they may occupy a large portion of the tissue (Figure 11). Oospores of many species have been shown to be able to survive for years in soil.
After a period of dormancy (often of apparently diverse and undefined durations) oospores germinate to produce hyphae, which may immediately produce a sporangium (Figure 12). Oospore germination is often asynchronous; that is, some oospores germinate while others do not. Germination and survival of oospores is dependent on environmental conditions: generally, oospores are able to survive dry and cool or cold conditions, but seem sensitive to high temperatures (> 40-45° C).
Some species produce thick-walled survival structures called chlamydospores (Figure 13).
Our understanding of the relationships among oomycetes is evolving rapidly as we gather additional information, particularly from molecular analyses. The techniques have evolved rapidly and analysis of DNA sequence provides a common criterion for assessing relationships. The analysis of probable relationships among the major genera of oomycetes is depicted in Figure 14. While Pythium, Phytophthora and Peronospora appear related, the relationship of these organisms with the grass downy mildews remains problematic.
Dick (2001. Straminipilous Fungi: Systematics of the Peronosporomycetes including accounts of the marine straminipilous protists, the plasmodiophorids and similar organisms. Dordrecht, Boston, Kluwer Academic Publishers.) has reported two subclasses, with six prominent orders. The table below identifies some of the genera in the various orders:
Subclass: Peronosporomycetidae Order: Peronosporales Ex: Many genera of Downy Mildews, Albugo Order: Pythiales Ex: Pythium, Phytophthora Subclass: Saprolegniomycetidae Order: Saprolegniales Ex: Aphanomyces Order: Sclerosporales Ex: Downy Mildews of the Poaceae, such as: Sclerospora, Peronosclerospora, Sclerophthora) Order: Salilagenidiales Ex: Lagena Order: Leptomitales
Several recent discoveries and important developments have taken the oomycete research community by storm. An important development is that the genomes of several oomycete species have been sequenced (Hyaloperonospora arabidopsidis, Phytophthora sojae, P. ramorum, P. infestans and Pythium ultimum) or are being sequenced (P. capsici, P. parasitica, Saprolegnia parasitica). One discovery is of a group of proteins (effectors) that are secreted by oomycetes and delivered into host cells; these proteins specifically aid pathogenicity. These proteins were originally investigated as the products of “Avirulence” genes. (They were initially termed “Avirulence” genes because they were first detected as the recognition targets of some host R genes; recognition resulted in avirulence.) Effectors are now recognized by signature amino acid motifs (RxLR-dEER, where R, L, and E stand for the amino acids arginine, leucine and glutamic acid), and it is now demonstrated that these motifs are required for secretion and delivery into the host cell. Each of the sequenced genomes contains hundreds of predicted effectors. The availability of the genome sequence also facilitates investigations into the genes involved in basic developmental biology. Already, genes specific to sporulation and zoosporogenesis have been predicted and their function is now being tested. Finally, there are several developments at the population level. Phytophthora ramorum has emerged almost overnight as a very important pathogen causing sudden oak death and other diseases with a surprisingly large host range. Recent global migrations of P. infestans have changed the life history of that organism in many locations in Europe. Several new, naturally occurring hybrid Phytophthora “species” have been identified that include completely new pathogenic and non-pathogenic species such as for example P. alni. Of more academic interest is Hyaloperonospora arabidopsidis (previously known as Peronospora parasitica) that has become a model pathogen because it infects the model host plant Arabidopsis.
This is the pathogen that caused the Irish potato famine in the mid-19th century. It was first reported in the eastern United States just prior to reports of its presence in Europe. Prior to that time, it was not known to western science. However, its devastating impact on potatoes and the terrible misery it has caused have made it infamous. Foliage, stems and tubers are susceptible (Figure 15, 16). It is a heterothallic species, with only one mating type (the A1) historically dominating the worldwide population with the exception of populations that existed in Mexico; both mating types have existed in central Mexico for a very long time. However, in the late 20th century migrations from Mexico distributed a very complex and diverse population containing both A1 and A2 mating types to Europe: subpopulations were later distributed from Europe to other locations. As an asexual organism in nature or in agriculture, P. infestans is essentially an obligate parasite, with no long-term survival mechanism; potato tubers provide a mechanism for short-term survival if infected tubers are stored between cropping seasons. However, the relatively recent migrations of the A1 and A2 mating types increases the chances of sexual reproduction and the production of oospores that would represent a long-term survival mechanism for this devastating pathogen.
Phytophthora infestans is unusual for a Phytophthora in that it is an aerial pathogen. That is, it infects and reproduces mainly on the above ground portions of its host. Sporangia are dehiscent (detach easily when mature) and under cloudy conditions can survive transit sufficiently long to travel many kilometers in moving bodies of air. The pathogen is favored by moist, cool environments: sporulation is optimal at 12-18° C in water-saturated or nearly saturated environments, and zoospore production is favored at temperatures below 15° C. Lesion growth rates are typically optimal at a slightly warmer temperature range of 20 to 24° C. Under favorable conditions, the asexual life cycle (sporangium germination, infection, lesion growth, sporulation) can be completed within as few as four days, but symptoms may not be visible for the first 2-3 days after initial infection. The dominant influence of weather on the infection and sporulation process of P. infestans has caused investigators to develop various forecasts for late blight. These investigations have resulted in algorithms (Dutch Rules, Beaumont periods, rain favorable days, severity values, etc.), which identify weather that has been favorable for late blight and allow growers to predict conditions that are likely to encourage or enhance infection. The explosive potential of this pathogen is legendary, dramatic and real. When the disease is uncontrolled and when environmental conditions are favorable to the pathogen, fields of 10-40 acres will succumb to the disease within just a few days.
The general susceptibility of potatoes and tomatoes has stimulated much effort to develop resistant plants as well as to understand the pathogenicity of P. infestans. Single large-effect genes for resistance (R genes) have been identified and deployed. Unfortunately, because of variation in the pathogen population, the effect of these genes has not been long lasting. R genes recognize specific components of pathogen proteins (effectors) that are injected into the host cell. Mutation in these effectors can enable the pathogen to escape recognition and avoid the resistance mechanisms. There have also been efforts made to create resistant plants based on a less well-understood mechanism that may involve many genes. This mechanism has been termed “field” or “partial” resistance. However, the most popular cultivars of potatoes and tomatoes are quite susceptible, necessitating the use of fungicides to protect plants.
Effective disease suppression requires a strategy integrating several tactics. Because infected seed tubers can be a source of the pathogen, it is important to plant only healthy seed tubers. It is also important to eliminate any tubers that might have survived from one cropping season to the next, whether these tubers survived in soil after harvest or were discarded after storage. Some Solanaceous weeds can also harbor the pathogen, and any infected weeds in or near the crop need to be eliminated. Fungicides are used in connection with a good scouting (monitoring) program (to learn if the pathogen is present) and application timing and rates are often aided by an appropriate forecast.
This pathogen was introduced to Europe from North America in the late 19th century. It accompanied wild grape plants imported for their resistance to the sap-sucking insect pest Phylloxera. P. viticola is a heterothallic downy mildew with A1 and A2 mating types. Oospores germinate to produce sporangia with zoospores, which can be splash-dispersed to cause lesions. Sporangia from primary lesions (Figure 17, 18) can also be wind-dispersed. Symptoms on leaves are small yellow lesions also known as oil spots. European grape varieties are susceptible to P. viticola and fungicides are used extensively to suppress the disease. Forecast systems are used to improve the efficiency of disease suppression.
This devastating, omnivorous pathogen was first isolated in the early 20th century, and is thought by some to have originated in Papua New Guinea, but it now has a worldwide distribution. Its host range is thought to include more than 3000 species of plants. It is heterothallic with A1 and A2 mating types, but sexual recombination is not thought to have a significant role in population diversity. Often, populations consist of a single mating type. This pathogen infects fibrous roots and can also survive and grow saprophytically in soil. It produces chlamydospores so that even in the absence of sexual reproduction, it can survive for long periods in soil.
The asexual cycle can be very rapid during wet conditions and is described elegantly by Hardham (2005. Molecular Plant Pathology 6: 589-604); only a summary is presented here. Sporangia are produced on sporangiophores and the sporangia release 20-30 zoospores. Zoospore formation is triggered by a decrease in temperature, resulting in the change of expression of a large number of genes. Morphologically, the cytoplasm becomes delimited into uninucleate compartments, with membranes forming around each and with each developing flagella and a water expulsion vacuole. In P. cinnamomi, but not in all species of Phytophthora, the wall material at the apex of the sporangium expands into an extra-sporangial vesicle into which the zoospores are released. The vesicle is ephemeral and the zoospores are quickly released into the environment. The zoospores may travel distances of several centimeters and are attracted to potential infection sites where they encyst. A mucilaginous material is secreted over the surface and they become affixed to the host surface (encyst) within minutes upon arrival and quickly form a cell wall. Germination occurs rapidly after encystment and the germ tubes penetrate the root epidermis. Colonization of host tissue follows and in susceptible tissues, sporulation may occur within three days.
This pathogen is a threat to both agricultural and native plants. One of the most seriously affected areas is in Australia (Figure 19) where the pathogen was introduced in the early 20th century. The pathogen was apparently introduced with imported plants and escaped into the native eucalyptus forest, the jarrah, and the disease has thus been termed “Jarrah Dieback”. In addition to Eucalyptus, many other native species are also susceptible to this pathogen and the disease remains severe to the present time. Unfortunately, construction of logging roads has proven to be a mechanism for transport of this pathogen throughout the forest. Disease is most severe under wet and warm conditions, and disease abatement is associated with cooler drier weather. However, investigators are expecting the range of this pathogen in the northern hemisphere to extend further north in response to global climate changes. For agricultural plants, phosphonate fungicides (effective against oomycetes, but ineffective against fungi) have been particularly helpful to suppress the disease and are used extensively. Host resistance has also been investigated with some limited success.
P. ramorum is the pathogen best known for causing sudden oak death on different oak species. It also causes Ramorum blight and shoot dieback on many ornamental plants. The disease was simultaneously discovered in Europe and in California in the 1990s affecting oak and nursery crops such as rhododendron and viburnum. In the United States the sudden oak death disease gained instant notoriety because it led to extensive death in coast live oak and tan oak in California (Figure 20).
One aspect of this pathogen that differentiates it from many other oomycetes is that P. ramorum has a very large and diverse host range that includes many oaks, shade trees, conifers, and woody ornamentals. Symptoms differ on various hosts (Figures 21-23) and can be confused with diseases caused by other organisms or even environmental factors.
Although a center of origin has not been found, scientists currently believe that P. ramorum was introduced into North America and Europe from elsewhere on imported nursery plants.
In US nurseries this pathogen is currently managed through quarantine, eradication (Figure 24) and exclusion: nurseries are trying to avoid establishment of the pathogen by excluding it from their operations and the Oregon Department of Forestry is trying to eradicate P. ramorum in Curry County in Southern Oregon where it is entrenched in native tanoak and bay laurel (myrtle wood):
Like P. infestans and P. cinnamomi, this pathogen has two mating types (Table 1). To date, sexual reproduction via mating of A1 and A2 mating types has not been documented but is considered possible where both types coexist. The pathogen currently exists as three distinct clones (clonal lineages) that reproduce asexually: EU1, NA1, and NA2. Lineage EU1 was first found in Europe but has now also been found in the US and Canada in select nursery environments. NA1 was the lineage found to cause significant mortality on coast live oak and tanoak forests in California and Oregon and has been spread throughout North America. The third clone, NA2, has been found only in nurseries on the US West Coast and Canada.
Table 1. Characteristics of the three major clonal lineages of P. ramorum.
This downy mildew is so important that it is one of the few plant pathogens to be included on the USDA-APHIS select agent list. The list is composed of plant pathogens not present in the US, but deemed to be a potential bioterrorism threat to US agriculture. Sclerophthora rayssiae var. zeae was first reported in India, but has now also been reported in Myanmar, Nepal, Pakistan, and India; the disease has been most severe in areas of high rainfall (100-200 cm/yr). In India, annual losses of 20-90% have been reported. Survival of this pathogen is via oospores in infected seeds and soil or plant debris.
The disease cycle involves both sexual and asexual reproduction. Oospores germinate to produce sporangia, which then release zoospores that penetrate leaf tissue. Lesions are initially interveinal and appear as chlorotic, brownish or reddish stripes on the leaves (Figure 25). Asexual sporulation is favored by moderate temperatures (20-25° C) and periods of high moisture; sporangia are produced on non-necrotic leaf tissue and give the leaf a grayish-white appearance. Sporangia are dispersed short distances via wind or rain splash, and germinate to produce zoospores or, less commonly, to produce a germ tube to repeat the cycle. Oospores are produced in necrotic tissue and can survive for years in soil or in plant debris.
Due to its devastating nature and the fact that it is not yet present in the US, this pathogen has also been placed on the USDA-APHIS select agent list. Peronosclerospora philippinensis is endemic to the Philippines where annual losses of 40-60% have been reported. This oomycete does not produce zoospores, but rather the sporangia germinate directly and have been referred to as conidia. Initial infections of roots are thought to result from oospores in soil. Most infections are initiated by sporangia (conidia) produced from infected foliage that can be distributed to other plants where they germinate directly and initiate local lesions. Young plants and seeds may be infected systemically (Figure 26). In addition to maize, the hosts include sugar cane and other grasses, but yield losses on these other hosts are not well defined. Disease severity is highest in tropical climates and areas that receive 100-200 cm of rain annually. Epidemics occur due to the rapid secondary cycles that are driven by high moisture and warm temperatures (20-25° C). The role of the oospore in the disease cycle has not been determined.
Pythium species are best known for causing damping-off and seed rot disease that often occurs just after planting as young seedlings emerge. Pythium also causes root rots on newly emerged or more mature plants and can also cause soft rots of fleshy fruit.
Damping-off disease affects seedlings worldwide. Often, young seedlings are completely destroyed by this pathogen and a crop emerges unevenly (Figure 27, 28), leading to significant yield reductions. Older plants once emerged might not be significantly affected by Pythium, but do show symptoms of root rot.
Several species of Pythium cause damping-off.
Pythium insidiosum causes pythiosis and affects horses, cats and dogs and occasionally humans. Pythiosis is found in moist climates with mild winters. Pythiosis has been described in Australia, Asia, South, Central and North America including the US. Generally, P. insidiosum infects as zoospores through wounded skin. These zoospores then encyst and invade the animal host. The pathogen can also infect through the gastrointestinal tract. For more information visit Veterinary Clinical Pathology Clerkship Program.
Aphanomyces euteiches (Figure 30) causes seedling and root-rot diseases on many legumes (Figure 31) and is considered to be the most yield limiting pathogen of pea in some growing areas of the world. The genus Aphanomyces is particularly interesting because it includes plant and animal pathogens found in both terrestrial and aquatic habitats. A. euteiches affects a variety of legumes including alfalfa, clover, dry bean, lentil, faba bean, pea, snap bean, and several weed species. This pathogen infects the cortex of primary and lateral roots. Infected areas initially turn honey-brown; as disease progresses the cortex sloughs off and roots turn dark brown to black. Microscopic examination often reveals oospores in the cortex.
Like Pythium spp., this pathogen is able to reproduce sexually as a homothallic oomycete by producing oospores. During asexual reproduction, the pathogen produces distinct sporangia that differentiate zoospores.
Aphanomyces astaci is an oomycete pathogen that affects crayfish. Apparently, this pathogen was imported into Europe via ballast waters discharged by a ship from North America. This pathogen has wiped out large populations of the European crayfish.
Saprolegnia is the only genus of oomycete pathogens that does not contain plant pathogens but contains pathogens of different water-borne organisms such as crayfish and fish. Although Saprolegnia are considered secondary pathogens, given the appropriate circumstances they act as primary pathogens and cause mycoses. Typically, once an organism is infected the disease is fatal. Scientists believe that extensive mortality of salmon and trout in Europe have been caused by Saprolegnia infection. Saprolegnia can parasitize fins and flesh, gaining initial infection through wounds. It can also parasitize eggs and is often visible as a white cottony mass on the surface of eggs or fish in home aquaria.
Recently, Saprolegnia ferax (Figure 32) was linked to the decline in amphibian populations. Apparently, climate change induced shallower water levels, which exposed eggs to higher levels of UV radiation and facilitated infection by S. ferax:
Sporangia of Saprolegnia spp. are distinctly different from those of other oomycetes with an elongated, grainy sporangium.
Cooke, D. E. L., A. Drenth, J. M. Duncan, G. Wagels, and C. M. Brasier. 2000. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genetics and Biology 30:17-32.
Fry, W. E., N. J. Grünwald, D. E. L. Cooke, A. McLeod, G. A. Forbes, and K. Cao. 2009. Population genetics and population diversity of Phytophthora infestans. Pages 139-164 in K. Lamour and S. Kamoun, editors, Oomycete Genetics and Genomics: Diversity, Interactions and Research Tool. Wiley-Blackwell, Hoboken, NJ.
Grünwald, N. J., E. M. Goss, and C. M. Press. 2008. Phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals. Molecular Plant Pathology 9:729–740.
Lamour, K. and S. Kamoun, Eds. 2009. Oomycete Genetics and Genomics: Diversity, Interactions and Research Tools. Wiley-Blackwell, Hoboken, NJ.
Tyler, B. M. 2007. Phytophthora sojae: root rot pathogen of soybean and model oomycete. Molecular Plant Pathology 8:1-8.
Whisson, S. C., P. C. Boevink, L. Moleleki, A. O. Avrova, J. G. Morales, E. M. Gilroy, M. R. Armstrong, S. Grouffaud, P. van West, S. Chapman, I. Hein, I. K. Toth, L. Pritchard and P. R. J. Birch. 2007. A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450(7166):115-118.
Dick, M. W. 2001. Straminipilous Fungi: Systematics of the Peronosporomycetes Including Accounts of the Marine Straminipilous Protists, the Plasmodiophorids and Similar Organisms. Kluwer Academic Publishers, Dordrecht, Boston.
Levesque, C. A. and A. W. A. M. de Cock 2004. Molecular phylogeny and taxonomy of the genus Pythium. Mycological Research 108: 1363-1383.
Hardham, A. R. 2005. Phytophthora cinnamomi. Molecular Plant Pathology 6:589-604.
Fry, W. E. 2008. Phytophthora infestans, the crop (and R gene) destroyer. Molecular Plant Pathology 9:385-402.
Get ALL the Latest Updates for ICPP2018: PLANT HEALTH IN A GLOBAL ECONOMY. Follow APS!