The current status of Pythium species in Iran: challenges in taxonomy

Document Type : Review Article

Author

Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran

Abstract

Pythium species are cosmopolitan, fungus-like oomycotes which may cause diseases in plants, animals and even human beings. Some of the species, however, are saprophytes and also well-proven biological control agents of plant pathogenic fungi. Since 1968, when the first Pythium species was reported from Iran, ca 44 species, two varieties, and five groups of this genus have been reported from different regions of Iran. Nevertheless, morphological or morphometric characters of only 35 species are more or less described. On the other hand more than 50% of these species have only been reported once. In the course of identification and classification of Pythium taxa in Iran, in addition to general obstacles, there exist some other problems. The lack of identification keys for the species; the absence of comprehensive checklists of the species, their dispersal and matrices; the lack of or the inadequacy of  the species descriptions; unillustrated descriptions; generalization about the host names; unspecific geographical locations; unknown isolation matrices; the absence of type specimens in type culture collections; and the overlooking of molecular analyses, especially in the case of phylogenetic species are some of the challenges ahead. In this review, the prospects of future studies on the taxonomy of the Pythium species in Iran and the proposed solutions for the taxonomic challenges are discussed.

Highlights

Apart from dry sandy deserts of Iran, Pythium species are isolated from a range of eco- and agroecosystems including agricultural fields, nurseries, grasslands, parks, forests, ponds, and surface water in almost all climates. This indicates the rich Pythium spp. mycoflora in Iran. However, the above mentioned challenges need to be addressed to identify and describe all existing taxa. A comprehensive Pythium spp. monograph for Iran with cross references and checklists seems to be of the priority. This monograph should include a key consisted of all of the species recorded and also their morphological descriptions and morphometric data. A step-by-step protocol would also help the newcomers to plan their identification tasks properly. Additionally, in order to have a better identification process, more experts must be trained through academic programs or retraining workshops. In these training projects, the main focus should be on both morphological and molecular identification.

Any reports of Pythium species, practically the same as other fungi and fungus-like microorganisms, must be well reviewed before any publications. This is especially more important in conferences where the time for any evaluations is limited. As a final step, setting up an internet-based database consisting morphological, morphometric and molecular data of Pythium spp. isolates from Iran could be a pragmatic approach to overcome some of the taxonomic challenges ahead.

Keywords

Main Subjects


INTRODUCTION

The genus Pythium Pringsheim 1858 includes various species of fungus-like Oomycota which are living as saprophytes or parasites in soil or fresh water niches. Some of the species, however, are among the well-proven biological control agents of plant pathogenic fungi. Pythium species are pathogenic to many plants and some aquatic and terrestrial animals and they also can parasitize some algae and fungi.

Species of Pythium are ecologically scattered all over the world and considered as cosmopolitan taxa. They can be found in tropical, temperate and even in cold regions. Tropical species can also be recovered from greenhouses in temperate regions (van der Plaats-Niterink 1981). Many of the plant pathogenic Pythium species are economically significant and cause devastating diseases on crops and ornamental plants. Therefore, in order to have a better understanding of biology, ecology and evolutionary relationships among species, identification and characterization of the species are of importance.

The earliest recorded report of a Pythium sp. inducing a plant disease in Iran returns to around 1947, when Esfandiari (1947) reported Pythium debaryanumR. Hesseas the causal agent of tobacco root rot based on his observations. Nevertheless, the first report based on laboratory tests has not been published until 21 years later about Pythium ultimum Trow on lentil (Kaiser et al. 1968) and a few years after, Fatemi (1971) published the first formal description of a Pythium sp. for Pythium aphanidermatum (Edson) Fitzp. from Iran.There has been ongoing attention to the species of this genus ever since. The objectives of this paper are to describe the current taxonomic status of Pythium species in Iran and to illustrate the obstacles existing in the way of identification and description of these species. The paper also reviews the prospects of future studies on taxonomy of the Pythium species in Iran and discusses the solutions for the taxonomic challenges ahead.

 

Pythium Genus, Species and Groups

 

There are almost 307 described Pythium species (www.mycobank.org) which are classified in the Kingdom Straminopila (Webster & Weber 2007) and the Phylum Oomycota. The genus concept of Pythium has been an ongoing controversy since the time of the description and there is still no consensus on the alternative genera (e.g. Fischer 1892; Schröter 1897; Sparrow 1931; Waterhouse 1967; van der Plaats-Niterink 1981; Dick 1990; Bala et al. 2010; Ko et al. 2010; Uzuhashiet al. 2010). Most of the authors tried to attend Pythium spp. into other genera based on the sporangial shapes, which is reviewed by Ho (2013). This state of flux forced me to adopt the classical definition of Pythium (Waterhouse 1974), i.e. all zoospore forming oomycetes which produce variable shapes of non-deciduous sporangia in water and in which zoospores form in a membranous vesicle connected to a discharge tube at the tip of the sporangium.

Pythium species are sexually homothallic (self-fertile) or need mating types in heterothallic species to produce oospores. There are some isolates which never produce some of the sexual organs. Theses isolates are categorized into some “Groups” (van der Plaats-Niterink 1981). Some isolates only form sporangia or hyphal swellings, but never produce oogonia or any other sexual organs in single or dual cultures. If these isolates only produce filamentous sporangia, they are grouped as Group “F”. Isolates with swollen, toruloid sporangia are categorized as Group “T”. If these isolates produce globose, non-proliferating sporangia, they are grouped as Group “G”. Globose, proliferating sporangia producing isolates are Group “P”, and isolates which only have hyphal swellings are categorized as Group “HS”.

 

Taxonomic Criteria for Species Identification

 

The available identification keys of Pythium species are generally based on morphological, biological and morphometric characteristics (e.g. Matthews 1931; Middleton 1943; Waterhouse 1967; van der Plaats-Niterink 1981; Dick 1990). Therefore, the recognition of these criteria and the factors influencing them will be helpful for accurate identification of the species. The main characteristics for conventional identification of Pythium species are: possessing or lacking the sexual organs (the shapes, sizes and positions of the oogonia the oogonial ornamentations and their sizes; the shapes, sizes, numbers, origins and positions of the antheridia; the sizes, numbers and configurations of the oospores (i.e. if they are plerotic or aplerotic); and the thickness of the oospore wall), as well as asexual organs (the shapes and diameters of the hyphae; the presence and absence of hyphal swellings and their configurations; the presence and absence of chlamydospores, their sizes and colors; the presence and absence of appressoria, their shapes and configurations; the shapes and prolife- rations of zoosporangia), the colony patterns on various media and the temperature relationships.  Due to the simple morphology of the species, the accurate identification of the species requires careful and precise examination of the isolates.

 

The Taxonomic Challenges of Pythium

 

Working with Pythium spp. isolates, one might encounter some obstacles during the course of species identification. Some of these complications were related to the biology of these microorganisms and some of which had something to do with the scientific tools and software availability. Most of the Pythium spp. isolates need sterols to produce sexual or asexual reproduction organs, such as zoosporangia and oospores in artificial media. It is possible to add some phytosterols in the form of sterol-rich plant materials, such as hemp seed extract or pure sterols, for instance β-Sitosterol, into media. However, for some isolates it takes a long time to produce any sexual or asexual organs and some of them never produce anything but a mycelial mat of coenocytic hyphae. Additionally, some sexual organs, such as antheridia may decline quickly soon after they appear. This makes the culture observation a time-consuming and laborious task. Some Pythium species produce more than one type of sporangia or antheridia. To avoid any confusion related to this multimorphism, the cultures must be absolutely pure. On the other hand, there is a high level of morphological overlapping among convergent species, especially phylogenetically related ones, which makes them an identification challenge. It is not that easy to find a compatible mating type for a heterothallic Pythium isolate to stimulate oospore production. Therefore, the identification must be solely based on asexual morphology, which is prone to error.

The biology of Pythium species is not the only issue in the course of identification and there are several software-based concerns which have something to do with the accessible tools for the identification. The most comprehensive Pythium species identification key available (van der Plaats-Niternk 1981) only covers 120 out of 307 reported species. Additionally, the latest identification key (Dick 1990) is almost 25 years old. On the other hand, there are also no descriptive sheets, no web-based database and no molecular barcode metadatabase for Pythium species. If a molecular identification is the approach of choice, species-specific primers are designed for only around 20 species (http://sppadbase.ipp.cnr.it/), most of which are developed for plant pathogens. There were some attempts for generating web-based interactive keys based on Lucid Builder platform (Moorman et al. 2014). Nevertheless, it is a modification of van der Plaats-Niternk (1981) identification key and not all the species in the original key are included.

 

The Current Status of Pythium spp. Identification in Iran

 

From the timewhen the first Pythium species was formally reported from Iran (Kaiser et al. 1968), 44 species, two varieties, and five groups of this genus have been reported (Table 1) from 76 plant taxa, including 55 plant species, as well as agricultural soil (data not shown). At the moment, there are 371 records of Pythium spp. incidence from various provinces of Iran, which are not evenly distributed in each province (Fig. 1). These reports, however, vary enormously in content, quality, detail, and format. Apart from Fars, Razavi Khorasan, Hamadan, Khuzestan and a few other provinces, there are few or no (e.g. Bushehr, South Khorasan, and Qom) reports in the most provinces.

 

 

 

Table 1. The list of Pythium spp. reported from Iran.

                                                                                                                      

Taxon

Matrices

Location

Reference

P. acanthicum Drechsler 1930

Prunus cerasus L. [Rosaceae];Prunus persica (L.) Batsch[Rosaceae]

Kermanshah (?)

Azizi et al. 2012

P. adhaerens Sparrow 1931

Soil [rice nursery]

Fars (Arsenjan)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. amasculinum Y.N. Yu 1973

Citrullus lanatus (Thunb.) Mansf. [Cucurbitaceae]; Cucumis melo L. [Cucurbitaceae]; Cucumis melo L. [Cucurbitaceae]; Cucumis sativus L. [Cucurbitaceae]; Lycopersicum esculentum Mill. [Solanaceae]; Solanum melongena L. [Solanaceae]; Soil

Razavi Khorasan (?)

Askari Farsangi  et al. 2011

P. aphanidermatum (Edson) Fitzp. 1923

Citrullus lanatus (Thunb.) Mansf. [Cucurbitaceae]; Cucumis melo L. [Cucurbitaceae]; Cucumis sativus L. [Cucurbitaceae]; Soil

Alborz (Karaj); Fars (Marvdasht, Moharloo); Gilan (Manjil); Golestan (Gorgan)

Banihashemi 1969

P. aquatile Höhnk 1953

Soil

Fars (Sepidan)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

P. aristosporum Vanterp. 1938

Triticum aestivum L. [Poaceae]

Fars (?)

Ravanlou & Banihashemi 2002

P. carolinianum V.D. Matthews 1931

Soil

Fars (Mamasani)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. catenulatum V.D. Matthews 1931

Turfgrass [Poaceae]

Tehran (Tehran)

Khodashenas Roudsari et al. 2010

P. coloratum Vaartaja 1965

Helichrysum bracteatum Andrews [Asteraceae]

Khuzestan (Ramin)

Ershad 1977

P. debaryanum R. Hesse 1874

 

Lens esculenta Moench [Fabaceae]

Khuzestan (Dezful)

Ershad 1977

P. deliense Meurs 1934

Beta vulgaris L. [Chenopodiaceae]

Fars (Marvdasht)

Afzali & Banihashemi 2000

P. diclinum Tokun. 1935

Soil

Fars (Bajgah, Borazjan)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

P. dissotocum Drechsler 1930

Soil

Fars (Bajgah, Kazeroon, Zarqan)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. echinulatum V.D. Matthews 1931

Soil

Fars (Darab)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

P. grandisporangium Fell & Master 1975

Soil

West Azerbaijan (?)

Badali & Abrinbana 2013

P. helicoides Drechsler 1931

Prunus persica(L.) Batsch[Rosaceae]

Kermanshah (?)

Azizi et al. 2012

P. heterothallicum W.A. Campb. & F.F. Hendrix 1968

Triticum aestivum L. [Poaceae]

Fars (?)

Ravanlou & Banihashemi 2002

P. hydnosporum (Mont.) J. Schröt. 1879

Plumbago europaea L. [Plumbaginaceae]

Hamadan (Hamadan)

Abad et al. 2013

P. inflatum V.D. Matthews 1931

Soil

Fars (Bajgah)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

 

 

Table 1. Continued

Taxon

Matrices

Location

Reference

P. intermedium de Bary 1881

Begonia semperflorens Link & Otto [Begoniaceae]

Tehran (Tehran)

Ershad 1977

P. irregulare Buisman 1927

Beta vulgaris L. [Chenopodiaceae]

Khorasan (?)

Afzali & Ershad 2006b

P. kashmirense B. Paul 2008

Soil

Fars (Lar)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. macrosporum Vaartaja & Plaäts-Nit. 1981

Rosa hybrida Vill. [Rosaceae]

Hamadan (Hamadan)

Abad et al. 2013

P. marsipium Drechsler 1941

Soil

Fars (Arsanjan, Kamfirooz)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. middletonii Sparrow 1960 

Cucumis sativus L. [Cucurbitaceae]

Kerman (Jiroft)

Hatami et al. 2010

P. minus Ali-Shtayeh 1985

Soil

West Azerbaijan (?)

Badali et al. 2014

P. myriotylum Drechsler 1930

Turfgrass [Poaceae]

?

Mirabolfathi & Ershad 2002

P. nunn Lifsh., Stangh. & R.E.D. Baker 1984 

Soil

Fars (Sormaq)

Bolboli & Mostowfizadeh-Ghalamfarsa 2015

P. okanoganense  P.E. Lipps 1981 

Beta vulgaris L. [Chenopodiaceae]

Khuzestan (?)

Zamani Noor et al. 2004

P. oligandrum Drechsler 1930

Amaryllis sp. [Amaryllidaceae]; Lantana sp. [Verbenaceae]; Pinus sp. [Pinaceae]; Turfgrass [Poaceae]

Tehran (Tehran); Mazandaran (Amol)

Ershad 1977

P. orthogonon Ahrens 1971

Soil

Fars (Bajgah)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

P. ostracodes Drechsler 1943

Soil

West Azerbaijan (Miandoab)

Babai-Ahari et al. 2004

P. paroecandrum Drechsler 1930

Papaver somniferum L. [Papaveraceae]

Kurdistan (Sanandaj)

Ershad 1977

P. periplocum Drechsler 1930

Triticum aestivum L. [Poaceae]

Fars (?)

Ravanlou & Banihashemi 2002

P. perplexum H. Kouyeas & Theoh. 1977

Rosa hybrida Vill. [Rosaceae]; Petunia sp. [Solanaceae]

Hamadan (Hamadan)

Abad et al. 2013

P. pyrilobum Vaartaja 1965

Cucumis sativus L. [Cucurbitaceae]

Kerman (Jiroft)

Hatami et al. 2010

P. rostratum E.J. Butler 1907

Soil

Fars (Bajgah)

Mostowfizadeh-Ghalamfarsa & Banihashemi 2005

P. salinum Höhnk 1953

Beta vulgaris L. [Chenopodiaceae]

Khuzestan (?)

Zamani Noor et al. 2004

P. splendens Hans Braun 1925

Papaver somniferum L. [Papaveraceae]

Fars (Marvdasht)

Banihashemi 1975

P. torulosum Coker & P. Patt. 1927

Turfgrass [Poaceae]

Fars (Shiraz)

Barzegar Marvasti & Banihashemi 2011

P. tracheiphilum Matta 1965

Beta vulgaris L. [Chenopodiaceae]

Khuzestan (?)

Zamani Noor et al. 2004

P. ultimum Trow 1901

Lens esculenta Moench [Fabaceae]

Tehran (?)

Kaiser et al. 1968

P. ultimum var. sporangiiferum Drechsler 1960

Actinidia chinensis Plunch. [Actinidiaceae]

Gilan (?); Mazanderan (?)

Taheri et al. 2008

 

Table 1. Continued

Taxon

Matrices

Location

Reference

P. ultimum var. ultimum Trow 1901

Beta vulgaris L. [Chenopodiaceae]

Hamadan (?)

Kashi et al. 2000

P. vanterpooli V. Kouyeas & H. Kouyeas 1963

Turfgrass [Poaceae]

Fars (Shiraz)

Barzegar Marvasti & Banihashemi 2011

P. vexans de Bary 1876

Pinus nigra Link [Pinaceae]

Mazandaran (Amol)                            

Ershad 1977

Pythium Group “F”

Triticum aestivum L. [Poaceae]

Fars (?)

Ravanlou & Banihashemi 2002

Pythium Group “G”

Beta vulgaris L. (Chenopodiaceae]

Khuzestan (?)

Zamani Noor et al. 2004

Pythium Group “HS”

Beta vulgaris L. (Chenopodiaceae]

Ardabil (Ardabil); West Azerbaijan (Miandoab)

Babai-Ahari et al. 2004

Pythium Group “P”

Beta vulgaris L. [Chenopodiaceae]

Khorasan (?)

Afzali & Ershad 2006a

Pythium Group “T”

Beta vulgaris L. [Chenopodiaceae]

Ardabil (Ardabil); West Azerbaijan (Khoy)

Babai-Ahari et al. 2004

? = unknown.

Matrix(ces) and location from which the taxon was reported for the first time in Iran.

 


The Taxonomic Challenges of Pythium spp. In Iran

 

In the course of identification and classification of Pythium taxa in Iran, in addition to general obstacles, there are some other problems in the way. There are almost no identification keys for the species from

 Iran. The only available key (Mostowfizadeh-Ghalamfarsa & Banihashemi 2005) just covers the isolates from Fars Province in southern Iran. Furthermore, the shortage of comprehensive checklists of the species, their dispersal and isolation matrices make the confirmation of species identification difficult for the researchers.


 


 

Fig. 1. The number of Pythium spp. reports from each province of Iran.

 

 

 


In most of the Pythium spp. reports from Iran, there are no or few morphometric data, illustrations or high resolution images. Lack of species descriptions sometimes makes it difficult or even impossible to reevaluate the identification. As a matter of fact, morphological or morphometric characters of only 35 species are more or less described. On the other hand, more than 50% of the recorded species have only been reported once. This could bring the possibility of a flowed identification procedure for these isolates.

 Another problem is about the metadata recording during recovering the Pythium spp. isolates. Data such as matrices, host names, locations, and the time of isolation could be confirmation sources for systematic identification of the species. Generalization about the host names was frequently happened in these reports. Names such as paper, turf grass, cucurbit, kitchen garden and summer crops are some of the instances which are vague and do not refer to a specific plant species. Additionally, unspecific geographical locations can be observed in some of the reports, for examplereferring to a province instead of the exact location of the isolation or geographical coordinates. The variable names of some provinces is also another source of confusion in the Pythium spp. reports. Some Iranian provinces have been recently named and were previously a part of another province (e.g. Alborz, Ardabil, Golestan, North Khorasan, Qazvin, Qom, Razavi Khorasan, and South Khorasan). Therefore, the old name of a province could easily be mistaken for the location it currently refers to. Furthermore, unknown isolation matrices is another problem in some of the records emerging due to the inadequacy of themetadata recording. While the name of a specific plant is mentioned, it is not clear that the isolate(s) was (were) recovered from roots or other plant tissues and materials, or even soil around the plants.

Our observations (Bolboli & Mostowfizadeh-Ghalamfarsa 2015) showed that Iranian agricultural soils are rich in Pythium spp. flora. Although there are some findings on the new species in Iran (e.g. Bolboli 2014; Chenari Bouket 2015; Salmaninejad & Mostowfizadeh-Ghalamfarsa, Unpub. data), no new Pythium species description has been published for Iranian mycoflora so far. On the other hand, the absence of type specimens for most Pythium spp. in Iranian type culture collections make the identification and description of new species difficult and the reevaluation of previous reports are even more complicated.

Finally, in the majority of Iranian reports, even in the recent ones, the molecular phylogenetic analyses is neglected and only few papers can be found in which morphological identification was backed up with molecular data. These kinds of molecular analyses are important, especially in the case of phylogenetic species or morphologically convergent ones.

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