The history, fungal biodiversity, conservation, and future perspectives for mycology in Egypt.

Records of Egyptian fungi, including lichenized fungi, are scattered through a wide array of journals, books, and dissertations, but preliminary annotated checklists and compilations are not all readily available. This review documents the known available sources and compiles data for more than 197 years of Egyptian mycology. Species richness is analysed numerically with respect to the systematic position and ecology. Values of relative species richness of different systematic and ecological groups in Egypt compared to values of the same groups worldwide, show that our knowledge of Egyptian fungi is fragmentary, especially for certain systematic and ecological groups such as Agaricales, Glomeromycota, and lichenized, nematode-trapping, entomopathogenic, marine, aquatic and coprophilous fungi, and also yeasts. Certain groups have never been studied in Egypt, such as Trichomycetes and black yeasts. By screening available sources of information, it was possible to delineate 2281 taxa belonging to 755 genera of fungi, including 57 myxomycete species as known from Egypt. Only 105 taxa new to science have been described from Egypt, one belonging to Chytridiomycota, 47 to Ascomycota, 55 to anamorphic fungi and one to Basidiomycota.

INTRODUCTION

Biological diversity (biodiversity) encompasses the variety of life forms occurring in nature, from the ecosystem to the genetic level, as a result of evolutionary history (Wilson 1992). The idea that fungi form a kingdom distinct from plants and animals gradually became accepted only after Whittaker (1969). Presently, the “fungi” as a mega-diverse group span three kingdoms, most belonging to the Fungi (Eumycota), while others are classified in the Protozoa and Chromista (Straminipila) (Cavalier-Smith 1998, James ). The word “fungi”, lower case and not in italics, is commonly used as a collective term for organisms traditionally studied by mycologists from all three kingdoms (Hawksworth 1991). The myxomycetes have also been traditionally studied by mycologists (Everhart & Keller 2008, Rojas & Stephenson 2008), and are included here.

Estimates for the number of fungi in the world range up to ca. 13.5 M species (McNeely , Hawksworth 1991, 2001, Hawksworth & Kalin-Arroyo 1995, Hyde 1996, Hyde , Tangley 1997, Groombridge & Jenkins 2002, Brusca & Brusca 2003, Rossman 2003, Crous , Adl , Kirk ). It might be expected that the predicted numbers of fungi on Earth would have been considerably greater than the 1.5 M suggested by Hawksworth (1991), which is currently accepted as a working figure although recognized as conservative (Hawksworth 2001).

The 10th edition of Ainsworth & Bisby’s Dictionary of the Fungi (Kirk ) provided a total of 98 998 for the number of fungal species accepted to date (excluding taxa treated under Chromista and Protozoa). Kirk reported 1 039 species chromistan fungal analogues and 1 165 as protozoan in which 1 038 are regarded as protozoan fungal analogues: Percolozoa (Acrasida), Amoebozoa (Dictyostelia, Myxogastria, Protostelia), Cercozoa (Plasmodiophorida) which were previously treated as Myxomycota and Plasmodiophoromycota.

Egypt’s geographical position at the junction between two large continents (Africa and Asia), and its inclusion as part of the Mediterranean basin, has indelibly influenced both the people and the biota of the country socially, economically and biologically. Egypt is part of the Sahara of North Africa, it has an area of about 1 M km2, divided by the River Nile into a western part including the Libyan Desert (681 000 km2) and an eastern part comprising the Eastern Desert (223 000 km2), and the Sinai Peninsula (61 000 km2). The Nile basin, comprising the valley in the south (Upper Egypt) and Nile delta in the north (Lower Egypt), forms a riparian oasis (40 000 km2) that constitutes the densely inhabited farmlands of Egypt.

Kassas (2002) mentioned four gaps related to biodiversity knowledge: the number of species on Earth; the diversity of the less conspicuous organisms such as fungi, bacteria, algae, and protozoa; the role played by each species among biotic elements of ecosystems; and the human ability to assess and forecast bio-ecological degradation.

Documentation of the Egyptian fungi may be dated back to 4500 B.C., when ancient Egyptians produced a number of hieroglyphic depictions of plants (many of which are psychedelic) on walls and within texts throughout Egypt. Temples with countless pillars are shaped like huge mushrooms with tall stems, umbrella caps, and mushroom engravings distributed all over the country (Fig. 1). These are shaped like Amanita sporophores, and some like Psilocybe. Others look like bracket fungi and are decorated with pictures of an incredible variety of plants (Arthur 2000). In the Egyptian Book of the Dead, the Papyrus of Ani (Budge 1967), mushrooms are called “the food of the gods,” or “celestial food” and “the flesh of the gods.”

Fig. 1.

A. Giant mushroom-like pillars (upper part), which are common in Egyptian temples. B. Description of Phallus roseus by Delile (1813a).

Studies on fungi in Egypt started at the beginning of the 19th century on lichens (e.g. Delile 1813a, b, Nylander 1864, 1876, Müller 1880a–c, 1884, Stizenberger 1890, 1891). In the early 20th century, Sickenberger (1901) and Steiner (1893, 1916) provided information for collections of lichens from Egypt in the 19th and early 20th Century. In the Flore d’Egypte, Delile (1813a) presented a scientific study of Egyptian fungi into the early19th century (Mouchacca 2008), in which he described the gastromycete now known as Itajahya rosea (syn. Phallus roseus; Fig. 1) which he had collected in Damietta and Assiut in 1798 and 1799, respectively. It should be noted that some early works repeat previous records, sometimes ambiguously as a result of the misinterpretation of synonyms and erratic use of infraspecific ranks; further, in the case of Sickenberger, misspellings of scientific names (Seaward & Sipman 2006).

By the beginning of the 20th century, special attention was being given to phytopathogenic fungi on wild and domesticated plants of economic importance (e.g. Fletcher 1902, Reichert 1921, Fahmy 1923, Shearer 1924, Briton-Jones 1922, 1923, 1925, Bishara 1928, Melchers 1931, Sirag El-Din 1931, Abdel-Salam 1933).

Both Reichert and Melchers are considered the pioneer scientists in the documentation of Egyptian fungi. Israel Reichert (1891–1975) went to study in Germany. Here he obtained his doctorate on Die Pilzflora Ägypten in which 237 species were recognized, of which 42 were new to science. Unfortunately, none of his specimens were retained in Egypt, or if they were, there is no record of their whereabouts today. However, earlier material collected before 1914 was present in the Botanisches Museum in Berlin-Dahlem, which Reichert used when compiling his list of 1921, but it is not known if these specimens survived World War II.

In 1927 Leo E. Melchers went to Egypt at the invitation of the Egyptian Minister of Agriculture as chief mycologist for 18 months. He met a series of difficulties such as there being no records available on the occurrence, distribution, or dates of any mycological observations conducted previously by any investigator in Egypt, and no mycological reference collection existing in the country. His checklist, however, included 345 species of fungi, especially those causing plant diseases (Melchers 1931).

No studies were carried out on the soil fungi until the 1930s, yet it was to be expected that, in such a country with rich agricultural traditions, knowledge of these fungi should have attracted considerable interest. Research on Egyptian soil fungi was probably commenced by Younis Salem Sabet (1898–1977). Sabet graduated in 1921 from the High School of Agriculture (now the Faculty of Agriculture of Cairo University), and soon after was sent to England to study botany at the University of London, where he obtained a BSc (Hons) in 1925. After his return, he joined the Ministry of Agriculture in the Plant Breeding Section. In 1927 he was appointed lecturer in Botany in the faculty of Science of the newly established Egyptian University, and in 1935 published his pioneering study, which was followed by many other publications (Sabet 1936, 1938, 1939a). His exploration led to the discovery of three taxa which were described later as new to science.

Sabet took the initiative in the establishment of some scientific organisations, and served as a member and president for several years in some others. Particularly of note were the Egyptian Academy of Sciences, Egyptian Botanical Society, Egyptian Science Union, Egyptian Association for Scientific Culture, Society of Applied Microbiology, Egyptian Phytopathological Society, Society for the History of Science, and Society of Atomic Energy.

Near the end of the 1930s, new aspects of mycological research were introduced into Egypt by several investigators such as mycorrhizal fungi (Mostafa 1938, Sabet 1939b, 1940, 1945, Yousef 1946); biocontrol (Mostafa & Gayed 1953), rhizosphere (Montasir , Naim ), air (Saad 1958, Zaki 1960), and stored seeds and grains (Assawah & El-Arosi 1960).

In 1956 late Magdy A. Ragab (Department of Botany, Faculty of Agriculture, University of Cairo) isolated 16 new species for the first time from soil, water and some plant hosts (Ragab 1956).

However, the credit for initiating real research concerned with Egyptian fungi must be given to Abdel-Al H. Moubasher (Botany Department, Faculty of Science, Assiut University; Fig. 2). In the early 1960s, with colleagues and students, he broadened the scope of mycological research in Egypt by conducting many studies on fungi. These included aspects such as: cellulose-decomposition, thermophily, osmophily, seed and grain mycobiota, phylloplane fungi, mycotoxins, and aquatic fungi. Moubasher, with his colleagues and students, have published more than 150 scientific papers to date, and in 1993 he published his major contribution to mycology in the Arabic World, the lavishly illustrated Soil fungi of Qatar and other Arab Countries (Moubasher 1993). He also invited outside specialists to run courses from the 1980s and trained many PhDs students. Specialists included Colin Booth and David Hawksworth in the 1980s.

Fig. 2.

A selection of prominent mycologists who have contributed greatly to our knowledge of mycology in Egypt. A. Abdel-Al H. Moubasher. B. Samy M. El-Abyad. C. Jean Mouchacca. D. Abdul-Wahid F. Moustafa. E. Farida T. El-Hissy. F. Younis S. Sabet. G. Israel Reichert. H. Youssef A. Youssef.

El-Abyad & Abu-Taleb (1993) summarized the habitat diversity of Egyptian fungi, and in 1997 the late Samy M. El-Abyad (Botany Department, Faculty of Science, Cairo University; Fig. 2) presented his pioneering attempt to update the checklist of Egyptian fungi: 1 246 species were recorded of which 173 were referred to Mastigomycotina, 41 to Zygomycotina, 222 to Ascomycotina, 143 to Basidiomycotina, and 667 to Deuteromycotina. Different ecological and taxonomic groups were not separated cited in the checklist, such as protozoan fungal analogues (Myxomycota, Plasmodiophoromycota), lichens, yeasts, aquatic and marine fungi, entomopathogenic fungi, nematophagous fungi, and mycorrhizal fungi. A large numbers of taxa, either reported in routine isolations or as novel taxa, are completely absent from this list. This may be due to his inability to trace the majority of references, which is actually the main reason why updated information documenting the fungi of Egypt was needed today. Amongst records lacking in the El-Abyad (1997) checklist are seven Podaxis species (Melchers 1931), Chaetomium gelasinosporum and C. uniporum (Aue & Müller 1967), C. mareoticum (Besada & Yusef 1969), Zygopleurage faiyumensis (Lundqvist 1969), Podospora aegyptiaca (Lundqvist 1970), Thermoascus aegyptiacus (Udagawa & Ueda 1983), and Gelasinospora hippopotama (Krug ).

In addition to the previous efforts of Reichert (1921), Melchers (1931), El-Abyad & Abu-Taleb (1993), and El-Abyad (1997), several other studies have added to the documentation of Egyptian fungi: Moubasher (1993), Lado (1994), Mouchacca (1995, 1999, 2001a, b, 2003a, b, 2004, 2005, 2008, 2009a, b; Fig. 2), Moustafa & Abdel-Azeem (2005a, b, 2006, 2010), Moustafa (2006), and Seaward & Sipman (2006).

The late Abdel Razak Abo-Sedah organized the Second African Regional Mycological Congress, in Cairo in 1992, under the auspices of the IMA Committee for the Development of Mycology in Africa. Then in 1993 he founded the Regional Center for Mycology and Biotechnology (RCMB) in Al-Azhar University, Cairo. The major tasks of this centre were the establishment of a fungal culture collection, the application of fungi in public health, agriculture, environment and industry, and supporting researchers as well as research projects. The centre actively participated in organizing further African regional and international conferences and meetings in Cairo in 1994, Vancouver in 1994, Zimbabwe in 1995, Cairo in 1996 on “Regulations of fungal activities”, and again in Cairo in 1999 on “Fungi and the Environment”. The center had collaborative agreements with the former International Mycological Institute (IMI) in the UK, and collaborative activities with Egyptian universities as well as with others in the UK, South Africa, Mauritius, Zimbabwe and Austria. The centre also initiated and published The African Journal of Mycology and Biotechnology from 1993 to 2001, which contained numerous contributions by Egyptian authors, and also a mycological newsletter in Arabic.

From the beginning of 2005 to the end of 2007, the Biodiversity Monitoring and Assessment Project (BioMap) had as its primary objective to develop and strengthen biodiversity research, monitoring and assessment across Egypt. In this project an extensive e-database was established to map the distribution of species across Egypt, and document up to 50 % of the Egyptian fungi ().

As mentioned above, the information concerning the fungi of Egypt is still incomplete and cannot be fully documented without an updated checklist of all taxa reported for the country. The present contribution assesses the diversity of fungi in Egypt. In addition, major groups of fungi are discussed briefly to highlight the extent of their diversity, followed by examples of habitats that are unique and deserve greater attention. These data show that the present contribution is a preliminary one concerning the diversity of Egyptian fungi, and therefore this summation is intended to enhance our knowledge of, and stimulate research into, the fungi of Egypt.

MATERIALS AND METHODS

The present contribution is based on an exhaustive revision of the available literature and sources of the Egyptian fungi reported from the 19th century to the present, including dissertations, published papers, compilations and checklists. Name corrections, authorities, and taxonomic assignments of all taxa reported in this article were checked against the Index Fungorum database (). In addition, websites of international mycological centres such as the ATCC (USA) (), CABI (UK) (<194.203.77.76/grc/index.htm>), CBS (The Netherlands) (), MUCL (Belgium) () and the catalogue of the culture collection of the Assiut University Mycological Center (AUMC 2010) were also consulted. The systematic arrangement in the present article follows Kirk.

This study extended to more than eight years in documenting and updating the information on Egyptian fungi. All results of the present study can be checked against the last updated checklist (El-Abyad 1997).

RESULTS

General features of Egyptian fungi

The number of fungi recorded in Egypt is 2 281 species, out of which 105 taxa have been described from Egypt as new to science: one in Chytridiomycota, 47 in Ascomycota, 56 in anamorphic fungi, and one in Basidiomycota. Reichert introduced 24 of the new taxa, representing 24.7 % of the novel taxa, followed by Jean Mouchacca and his colleagues (Laboratoire de Cryptogamie, Muséum National d’Histoire Naturelle, Paris), who described 18 new species (17.1 % of the total), and Abdul-Wahid F. Moustafa (Fig. 2) and his colleagues and students at the Suez Canal University who contributed 11 new taxa.

Protozoan fungal analogues

The kingdom Protozoa contains 115 000 known species. They are extremely diverse in their cell structure, patterns of nutrition, metabolic needs, reproduction, and habitat. This kingdom contains a grab-bag of organisms that do not fit into the other kingdoms. Protozoa are extremely difficult to classify so for the purpose of this survey, they are grouped by their nutritional patterns. Protozoan fungal analogues are heterotrophic and most are decomposers that feed on dead plants and animals by endocytosis (Kendrick 2000). According to Kirk there are about 1 165 fungal protozoan analogues described. Slime moulds are a small and relatively homogenous group of eukaryotic organisms, and these are referred to as Myxomycota (Mycetozoa). In Egypt the slime moulds have never been the target of any widescale study (Lado 1994, Stephenson & Stempen 1994), except for the pioneer study of Abdel-Raheem (2002) on those of Upper Egypt (Ndiritu ).

Abdel-Raheem (2002) reported 20 species belonging to 17 genera in his first inventory of the protozoan fungal analogues (Myxomycota) of Upper Egypt from wood, bark of living and dead trees and leaf litter. Exhaustive examination of all available literature concerning protozoan fungal analogues in Egypt led to the discovery of reports of Protostelium irregulare (as “irregularis”; Olive & Stoianovitch 1969) and Eidamella spinosa (Kowalik & Sadurska 1973). The protozoan fungal analogues occurring on decaying wood, bark, leaf litter and papyrus papers presently amount to 57 species belonging to 25 genera. For more details refer to the PBI: Global Biodiversity of Eumycetozoans () and Farghaly (2008). In addition, three species representing three genera of Cercozoa (previously Plasmodiophoromycota) have been recorded: Plasmodiophora, Spongospora, and Woronina. No dictyostelid cellular slime moulds are so far known from Egypt (Cavender ).

Chromistan fungal analogues

The kingdom Chromista (Straminipila) is a collection of eukaryotic, walled microorganisms that produce heterokont, wall-less cells in their life-cycles, including some fungal-like groups that are not considered to be ancestors of any members of the Fungi (Lutzoni ). Kirk estimated the Chromistan fungal analogues as 1 039 known species and included the phyla Hyphochytriomycota, Labyrinthista, and Oomycota along with some taxa of uncertain position (incertae sedis).

The late Farida T. El-Hissy (Botany Department, Faculty of Science, Assiut University; Fig. 2) was the founder of aquatic mycology research in Egypt. El-Hissy and her students published more than 60 papers on this topic. However, the plant pathogenic Oomycota have been the target of many research investigations since 1921, and in the present study, 186 taxa of chromistan fungal analogues were recorded, of which 172 belong to 40 genera of Oomycota. Four species and two genera of Labyrinthista were recorded, while Hyphochytriomycota are represented by six species within three genera. For more details refer to El-Helaly , 1966), Ali Hassanein , Khallil , and El-Hissy , 1992, 1997, 2004)

Fungi (Eumycota)

Blastocladiomycota

This phylum was once considered part of the chytrids. However, most of the true chytrids (Chytridiomycota) produce a limited mycelium while Blastocladiomycota usually make extensive mycelia. Thus, they superficially resemble the water moulds to which they were thought to have been affiliated. Like the chytrids, Blastocladiomycota and Neocallimastigomycota are the only members of the fungi in which motility has been retained. In overall growth habit, the blastocladiomycetes tend to be eucarpic, in which there is an extensive vegetative growth habit in which some part of the organism participates in reproduction (asexual and sexual). Members of this phylum do exhibit a complete alternation of generation between a haploid gametophyte and a diploid sporophyte (Barr 1990, James ). Kirk give a world total for Blastocladiomycota of 179 species. In Egypt, 27 species and one variety belonging to seven genera of Blastocladiomycota were found in this study. For more details see Ragab (1956), Yusef (1964), Gad , Gad & Sadek (1968), El-Hissy (1974), El-Hissy , El-Abyad (1997), Shoulkamy , and Abdel-Moneim (2010).

Chytridiomycota

Chytridiomycota are a phylum of fungi that reproduce through the production of motile spores (zoospores), typically propelled by a single, posteriorly directed flagellum. These organisms, often referred to as chytrid fungi or chytrids, have a global total of approximately 1 000 described species (James ). Based on biochemical characteristics, including chitin in cell walls, the α-aminoadipic acid lysine synthetic pathway, and storage carbohydrates (i.e. glycogen), Bartnicki-Garcia (1970) classified Chytridiomycota as true fungi and this is supported by current molecular studies (Hibbett ). In the past some authors considered the chytrids as a transitional group between protists and fungi because of their production of motile zoospores (Barr 1990). Kirk give the number known Chytridiomycota as 706.

The study of Gaertner (1954) on Chytridiomycota of Africa is considered one of the pioneer mycological studies in Egypt. However, the real start of research on chytrids in Egypt must be credited to Samy Kamel Mohamed Hassan (Minia University) who obtained his PhD from the University of Warsaw for work on chytrids and aquatic fungi in 1982. Later, Hassan and Mohamed Abdel-Wahab El-Naghy (Minia University) made a series of studies on chytrids in Egypt.

Intensive revision of the nomenclature showed that 84 species belonging to 32 genera of Chytridiomycota were recorded in Egypt. For more details see El-Naghy , 1987), Hassan (1991a-d, 1993), Hassan & Fadl-Allah (1991), Hassan & Shoulkamy (1991), and Hassan & Shaban (1991).

Zygomycota

Zygomycota are a particularly ecologically diverse group of fungi, occurring as saprobes (Mucorales), harmless inhabitants of arthropod guts (Harpellales), plant mutualists forming ectomycorrhizas (Endogonales), and pathogens of animals, plants, amoebae, and especially other fungi (all Dimargaritales and some Zoopagales are mycoparasites) (James & O’Donnell 2007). Conversely, some Mucorales have a negative economic impact as they cause storage rots or plant diseases, while others can cause life-threatening opportunistic infections in diabetic, immuno-suppressed, and immuno-compromised patients. In addition, several species of Microsporidia cause serious human infections (de Hoog , James & O’Donnell 2007).

According to Kirk the total world number of Zygomycota is 1 065 species. Data collected from previous studies show the Zygomycota in Egypt to be fragmentary because members belonging to this group either have long been overlooked or simply reported as rare taxa during routine isolations.

Abdel-Kader (1973) carried out a pioneering study in which he was able to isolate 11 species from a range of soils collected from various Egyptian localities. The second most relevant study is probably that of Al-Alfy (1995) who reported 21 species from various substrates, including soil, dung, stored seeds and grains, and the phyllosphere. In his recent contribution on Zygomycetes in Egypt, Moustafa (2006) reported 33 species, out of which nine were considered new Egyptian records.

Revision of all available data showed that Zygomycota in Egypt comprises 70 taxa including eight varieties and seven special forms within 35 genera. In addition, Absidia aegyptiaca (Sartory ) is omitted from the list, as no living or other type of authentic material is apparently preserved; furthermore the name was not validly published as it lacked a Latin diagnosis (Mouchacca 1995). For more information on Egyptian Zygomycota refer to Kharboush (1969a, b), Besada & Yusef (1968), Abdel-Rahman , Moubasher (1993), El-Abyad & Abu-Taleb (1993), Swelim , Mouchacca (1995), El-Abyad (1997), Abdel-Azeem (2003), Moustafa (2006), Ali & Ibrahim (2008), Afify, and Moubasher .

Glomeromycota

The Glomeromycota currently comprises 169 described species (Kirk ). The phylum is not as diverse as other phyla of fungi with only three families and such a modest number of species. However, they make up for this uniformity by being among the most abundant and widespread of all fungi. As far as we know, all species of Glomeromycota are mutualistic with plants, forming endomycorrhizas. Although there are various types of mycorrhizas, involving different fungal and plant symbionts, the arbuscular mycorrhiza type is the most widespread occurring in around 80 % of plant species (Redecker & Raab 2006).

The pioneering work of Mostafa (1938) and Sabet (1939b, 1940, 1945; Fig. 2) is now accepted as the starting point of research on Egyptian Glomeromycota (Kelley 1950, Abdel-Moneim & Abdel-Azeem 2009). These studies were followed by many other investigations concerned mainly with the ecology and physiology of endomycorrhizas in Egypt, viz. Fares (1986), Ishac, Abdel-Fattah (1991), Aboulkhair & El-Sokkary (1994), Mankarios & Abdel-Fattah (1994), Abdel-Fattah & Mankarios (1995), Abdel-Fattah & Rabie (1995), Abdel-Fattah , Abdalla & Abdel-Fattah (2000), Abdel-Fattah (2001), and Abdel-Azeem .

However, surveys of Egyptian Glomeromycota are limited, and had never been the sole target of any study until Fares (1986) conducted a survey of vesicular arbuscular mycorrhizas, followed by Agwa (1990) on mycorrhizas and nodulation in some Egyptian plants. After 10 years, Agwa (2000) studied the arbuscular mycorrhizal fungi associated with medicinal plants as Glomales in Egypt (I)”. Agwa & Abdel-Fattah (2002) followed up their work “Glomales in Egypt (II)” as an ecological view of some saline affected plants in the delta of the Mediterranean coast. A study of the distribution of Glomales in the Egyptian Protectorates was published by Agwa & Al-Sodany (2003) as “Glomales in Egypt (III)”, which surveyed the distribution and ecology in some plants in the El-Omayed Biosphere Reserve. Later, other relevant studies were carried out by several investigators such as El-Zayat and Abdel-Moneim & Abdel-Azeem (2009) on the Wadi Allaqi and Saint Katherine Protectorate, respectively. Recently, Mansour (2010) screened 71 soil and root samples for endomycorrhizas in North Sinai and adopted some of them as biocontrol agents against fusarium-wilt of tomato.

Eight genera and 19 species have been recorded in Egypt since 1938: Acaulospora, Entrophospora, Gigaspora, Glomus, Paraglomus, Sclerocysti, Scutellospora and Rhizophagus. Both Paraglomus occultum and Rhizophagus were recorded and never cited in any publication related to Egyptian Glomeromycota. For more details see Sabet (1939b) and Morton & Redecker (2001).

Lichen-forming fungi

Lichens are unique associations composed of two to three different organisms living together in a mutualistic relationship in which the fungal partner forms the external structure. The name used is that of the fungal parter, and the photosynthetic partner or partners have independent scientific names. Estimates for the number of lichen fungi worldwide vary, but a draft global checklist has 18 882 names of lichen-forming and allied fungi (Feuerer & Hawksworth 2007).

Egyptian lichens have received the attention of many researchers since the early 1800s (Delile 1813a, b, Nylander 1864, 1876, Müller 1880a–c, 1884, Stizenberger 1890, 1891, Sickenberger 1901, Steiner 1893, 1916, Werner 1966, Galun & Garty 1972, Temina , 2005, Seaward & Sipman 2006). Egyptian investigators have participated in a few studies of lichens, namely in North Sinai (Khalil 1995) and on trees (Koriem 2003), and there have also been some physiological studies on the bionts (Koriem 2006). Khalil (1995) recorded 43 species belonging to 18 genera, all of which are ascolichens without any basidiolichens at all, and only one of these had a perithecioid ascoma (Gonohymenia sinaica).

Seaward & Sipman (2006) reported 157 taxa of lichenized fungi (149 species and 8 infraspecific taxa) and six lichenicolous fungi (fungi obligately growing on lichens). Foliose lichens are very scarce, only being represented by the genera Xanthoria (7 species) and Physcia (1 species). The fruticose growth form is better represented, with members of the genera Ramalina, Roccella, Seirophora and Tornabea. At the family level, Teloschistaceae accommodated the most taxa (39), followed by Roccellaceae (16), and Physciaceae (12). For more information concerning Egyptian lichens please see: check-lists of Lichens and Lichenicolous Fungi (), the Tel Aviv University Herbarium (TELA) (), Galun & Garty (1972), Khalil (1995), Koriem (2003, 2006), Temina , 2005), and Seaward & Sipman 2006).

Ascomycota (non-lichenized)

Numerically Ascomycota constitute by far the largest group of fungi so far known, accommodating a relatively large assemblage of taxa estimated to be 65 % of all described fungi (Kirk ) occurring in various habitats; aquatic or terrestrial, under moderate or stress conditions (Kodsueb , b, Kruys & Ericson 2008, Thongkantha ). A large number of Ascomycota species are economically important (e.g. Fusarium spp., Kvas ; Colletotrichum spp., Damm , Hyde ; Mycosphaerella spp., Crous 2009), while few are edible (morels and truffles), and some are used also in the production of food (including bread), drinks, organic acids, mycofungicides, fungal biofertilizers, cosmetics and hormones (Kaewchai , Hyde ).

This phylum encompasses biologically diverse forms. Many are free-living saprobes including species which may be cellulose decomposers, chitinolytic, keratinolytic, or coprophilous, others are parasitic forms including species which cause very serious plant diseases like powdery-mildew, wood-canker, ergot, rot, blight, scab, leaf curl, and leaf-spots (e.g. Alves , Aveskamp , Simonis , Wulandari ). Others that are considered symbiotic forms contain species which live in association with insects or algae (lichens) or roots of plants (mycorrhizas).

Ascomycota characteristically, when reproducing sexually, produce non-motile spores (ascospores) in a distinctive “ascus”. However, some members of the Ascomycota do not reproduce sexually and do not form asci or ascospores (anamorphic Ascomycota). These asexual members are assigned to Ascomycota based upon morphological and/or physiological similarities to ascus-bearing taxa, and in particular by phylogenetic comparisons of DNA sequences. In old classification systems these were often placed in a separate artificial phylum, the deuteromycota (or “fungi imperfecti”). Molecular analyses can now place these genera and species among ascus-bearing taxa, or more rarely in other phyla such as Basidiomycota.

The first reports of mutualistic non-lichenized ascus-forming fungi from Egypt were those of Terfezia, Tirmania, and Morchella by Reichert (1921), and then Melchers (1931) who recorded six species. Later, Sabet (1935) recorded some saprobic Chaetomium species. The saprobic Ascomycota did not receive attention, and therefore information remained limited until the early 1970s, when some research on the group was initiated by Moubasher and his co-workers during their studies on soil fungi. Since then, fragmentary information has been accumulating, but these fungi had never been the main objective of any Egyptian study focusing on their ecology, distribution, and substrate preferences, untill the study of Abdel-Azeem (2003).

Three hundred and three species of teleomorphic saprobic Ascomycota (including ascosporic yeasts) have been recorded from all terricolous substrates of Egypt (Moustafa & Abdel-Azeem 2010, and unpubl.). In their studies, 10 species of edible Ascomycota were recorded from Egypt within the genera Morchella, Terfezia, and Tirmania. In total, 328 taxa were recorded in this survey, of which only 32 species are ascosporic yeasts. Binyamini (1973) reported Peziza vesiculosa as a coprophilous fungus from occupied Palestine, and some samples were even collected from north Sinai during the occupation in 1967, but never cited as an Egyptian record in any checklist. In addition, Byssonectria tetraspora was recorded for the first time in Egypt by El-Saadawi & Shabbara (1999) as an association between a fungus and a moss.

For more details see Sabet (1936, 1939a), Binyamini (1973), El-Saadawi & Shabbara (1999), Abdel-Hafez , Ibrahim (1995), El-Abyad (1997), Zaki , Moustafa & Abdel-Azeem (2005a, b, 2006, 2008, 2010), and Abdel-Azeem (2009).

Records of phytopathogenic fungi in Egypt were scattered through the literature until 1921, when Israel Reichert (Fig. 2) carried out his pioneer study of Egyptian fungi. This was followed by a comprehensive checklist of plant diseases and fungi occurring in Egypt by Melchers (1931). Records concerning aspects of plant pathology in Egypt continued to be accumulated during many decades until El-Helaly , 1966) started to update the information, and another updated bibliography of agricultural studies conducted in Egypt between the period 1900 to 1970 appeared (Ali Hassanein ). This revealed records of 82 species of teleomorphic plant pathogenic Ascomycota. For more details please check, Natrass (1933), Abou El-Seood (1968), Ghoniem (1985), El-Desouky & El-Wakil (2003), Phillips , and Hafez (2008).

Anamorphic genera are gradually disappearing into the overall ascomycete system, though it will take many years before anamorph genera have fully integrated.

A school of medical mycology in Egypt was formed at the beginning of 1967, when the late Youssef A. Youssef (Ain Shams University, Faculty of Science; Fig. 2) published two papers on fungus infection of the human ear. Youssef and his students and colleagues became interested in medical mycology, serology and fungi affecting human health. For more details see Youssef & Abdou (1967a, b), Hassan –e, 1981), Youssef & Karam El-Din (1988a, b), Karam El-Din –c, 1995, 1996), and Youssef , 1992, 1993).

In 1979 Ismail Abdel-Razak M. El-Kady received credit as the Egyptian mycologist working on mycotoxin producing fungi in Egypt. El-Kady and his coworkers studied the majority of aspects related to toxinogenic fungi, e.g. factors affecting mycotoxin production, toxinogenic taxa in food and feed, and mutagenic effects of fungal toxins. For more details see El-Kady & Moubasher (1982 a, b), and El-Kady , 1994).

In 1987, Mamdouh S. Haridy (Minia University, Faculty of Science) became the pioneer Egyptian mycologist in yeast identification and taxonomy, having completed his PhD thesis on the taxonomy of yeasts (“Taxonomie milchwirtschaftlich wichtiger Hefen”, Technical University, Munich). He conducted a series of extensive studies on the Egyptian saprobic yeasts from different ecological habitats and sources (Haridy 1992a, b, 1993a, b, 1994a, b, 2002).

Recently, other areas of Egyptian mycology have been established, such as on the identification of human and plant pathogens by molecular techniques. Youssuf A. Gherbawy (Botany Department, Faculty of Science, South Valley University) focused on the identification of plant pathogens and saprobic fungi of food by means of molecular techniques (Gherbawy 2004, Gherbawy & Abdelzaher 2002, Gherbawy & Farghaly 2002, Gherbawy & Voigt 2010), and Sherif M. Zaki (Microbiology Department, Faculty of Science, Ain Shams University) extended the research of Youssef A. Youssef using the molecular techniques in species identification of human pathogens (Zaki , 2009, Zaki 2008).

About 905 filamentous or yeast-like anamorphic fungi have been reported from Egypt. These taxa colonize, survive and multiply in air, litter, soil, plant surfaces, the human body and other substrates. Of these, only 28 are species of anamorphic ascomycetous yeasts, which belong to three genera. Furthermore, five genera of basidiomycetous yeasts and 18 species are recorded from all habitats in Egypt.

For more information consult Al-Doory (1968), Abdel-Fattah (1985), Sherief (1985), Bagy & Abdel-Hafez (1985), Khater (1989), Shalouf (1989), Shindia (1990), Abdel-Mallek , Abdul Wahid , Hamdi & Hassanein (1996), El-Tanash (1997), Shalaby (1999), Mahmoud (1999), Ismail & Sabreen (2001), Teramoto , Abdel-Wahab (2002), Farghaly , Nofal & Haggag (2006), Haggag , Abdel-Hamed (2008), and Kottb (2008).

Aquatic and marine fungi

Marine fungi form an ecological, and not a taxonomic group (Raghukumar 2008, Jones , Hyde ). Among these, the obligate marine fungi grow and sporulate exclusively in seawater, and their spores are capable of germinating in seawater (Hyde ). On the other hand, facultative marine fungi are those obtained from freshwater or a terrestrial milieu, and have undergone physiological adaptations that allow them to grow and possibly also sporulate in the marine environment (Kohlmeyer & Kohlmeyer 1979). These fungi belong mostly to ascomycetes, their anamorphs, and a few basidiomycetes. Among the straminipilan fungi, those belonging to Labyrinthulomycetes, comprising the thraustochytrids, aplanochytrids, and labyrinthulids are obligate marine fungi (Raghukumar 2002), and those belonging to the oomycetes are also fairly widespread in the marine environment.

About 3000 fungi (exclusive of yeasts) have been reported from aquatic habitats of which Ascomycota (1 527 spp.) and anamorphic taxa (785 spp.) are the most diverse groups, followed by Chytridiomycota (576 spp.) with Basidiomycota (21 spp.) as the least diverse group (Vijaykrishna , Shearer ).

Anwar Abdel Aleem (Faculty of Science, University of Alexandria), or Peripatetic Aleem as he was known among his colleagues, is one of the most brilliant Arab marine botanists and oceanographer extraordinaire. He is considered one of the pioneer marine Egyptian mycologists, with studies on marine fungi dating back to 1950 (Aleem 1950a–c, 1952a–c, 1953, 1962, 1974, 1975, 1978, 1980a, b, Aleem & Mailbari 1981).

In Egypt, obligate and facultative marine fungi are considered as forgotten fungi (Jones 2001) because they never featured in research topics until 1993, which is considered the starting point of marine mycology research in Egypt. This provided Mohamed Abdel-Wahab (Botany Department, Faculty of Science, South Valley University, Sohag, Egypt) the possibility to publish his pioneering study on the Egyptian obligate mangrove-inhabiting fungi of the Red Sea in 1996. Three contributions of El-Sharouny , 1999) and Abd-Elaah (1998) shed light on the ecology and taxonomy of mangrovicolous, algicolous and aquatic fungi of the Red Sea in Upper Egypt. Abdel-Wahab (2000) obtained his PhD on the biodiversity of fungi in subtropical mangroves; he recorded 25 fungi on intertidal wood of Avicennia marina collected from three mangrove stands of the Red Sea coast of Egypt. Abdel-Wahab , b) published three new species, Halosarpheia unicellularis, Swampomyces aegyptiacus and S. clavatispora, from Red Sea mangroves. Pang erected Jahnulales as a new lignicolous freshwater ascomycete order with the new species Patescospora separans from Egypt. Abdel-Raheem (2004) studied the effect of different techniques on diversity of freshwater hyphomycetes in the River Nile (Upper Egypt). Abdel-Wahab (2005) examined the diversity of marine fungi on intertidal decayed wood of A. marina and on decayed prop roots of Rhizophora mucronata in mangrove stands in the southern part of the Egyptian Red Sea coast; 39 species were identified on decayed wood of A. marina, of which 19 were new records for Egypt and the Red Sea. Freshwater fungi are those relying on freshwater for at least part of their life-cycle (Wong , Raja ). Abdel-Aziz (2008) studied the diversity of aquatic fungi in Lake Manzala, which was the first report of aquatic fungi from the lake. Sixty taxa including 26 ascomycetes and 34 anamorphic fungi were recorded, of which 19 species were new records for Egypt. El-Sharouny studied the fungal diversity in brackish and saline lakes in Egypt; 97 fungi (40 ascomycetes, 55 anamorphic fungi and 2 basidiomycetes) were identified from 764 collections, obtained from 545 samples, of which 70 were new records for Egypt.

The revision of all available data sources reveals that the total number of marine and aquatic fungi known in Egypt is 207 taxa (87 Ascomycota, 117 anamorphic taxa, and 3 Basidiomycota). There is no checklist of aquatic Egyptian fungi so far. For more details on these fungi see the website (), search mangrove fungi (), and check relevant studies (Khallil 2001, Abdel-Aziz 2004, Abdel-Wahab , 2010).

Entomopathogenic fungi

The taxonomy of the entomopathogenic fungi has received much attention since the 1970s. More than 700 species of fungi are associated with insects, spiders, and mites (Samson , Hajek & St. Leger 1994, Sung , Aung ).

The invertebrate pathogenic fungi can be classified in the Mastigomycota, Zygomycota, Ascomycota, and allied anamorphic fungi; no truly entomopathogenic basidiomycetes have been documented (Samson ). Entomopathogenic fungi range from commensals or mutualists, through ectoparasites which do not seriously affect their hosts, to pathogens which are lethal and include representatives of all the groups of fungi (Hawksworth ).

Few records appeared reporting the occurrence of entomogenous fungi in Egypt until Natrass (1932) published preliminary notes on some of these fungi in Egypt. He recorded five species: Empusa grylli (= Entomophaga grylli), Beauveria bassiana, Aspergillus flavus, Mucor racemosum, and Metarhizium anisopliae. In the beginning of the 1960s, Egypt started to apply biocontrol methods to insects by entomopathogenic fungi, and Gad studied the occurrence of Coelomomyces indicus in Egypt.

There are several studies on this ecological group of fungi in Egypt, such as Badran & Aly (1995), Shoulkamy , Shoulkamy & Lucarotti (1998), Hafez , Sewify (1997), Abdel-Baky (2000), Sewify <3.interscience.wiley.com/journal/119022140/abstract?CRETRY=1&SRETRY=0 - fn1#fn1&> Hashem (2001), Abdel-Sater & Eraky (2002), Ali (2003), <3.interscience.wiley.com/journal/119022140/abstract?CRETRY=1&SRETRY=0 - fn1#fn1> Abdel-Mallek , b), El-Hady (2004), Mourad , Abdel-Mallek & Abdel-Rahman (2006), El-Maraghy , and Moubasher . As a result of these only 18 species belonging to 13 genera were recorded as entomopathogenic fungi of Egypt. For more details please refer to this site ().

Nematophagous fungi

In Egypt, the study of nematophagous fungi dated back to 1963 when Hamdy Aboul-Eid (Department of Plant Pathology, Nematology Laboratory, National Research Centre, Dokki, Cairo) isolated and illustrated four species belonging to two genera. Various studies on the biocontrol of nematodes by fungi have been the target of many studies in Egypt; the most relevant are: Ali (1994, 1995), Ali & Barakat (1994), Aboul-Eid , b, 2006), Ashour & Moustafa (1999), and Amin & Moustafa (2000). Out of these various data and information only 10 species belonging to seven genera were recorded as nematophagous fungi of Egypt.

Basidiomycota

The Basidiomycota contains about 31 503 described species, which represents 31.8 % of the known species of true Fungi (Kirk ). This group includes mushrooms, puffballs, bracket fungi and some yeasts (Petersen , Wannathes ). Many Basidiomycota decay dead organic matter, including wood and leaf litter symbiotic lifestyles (intimate mutually beneficial or harmful associations with other living organisms) are well developed in the Basidiomycota. They include major plant pathogens, such as “rusts” (Uredinales) and “smuts” (Ustilaginales), which attack wheat and other crops, and some human and animal pathogens. Not all symbiotic Basidiomycota cause harm to their partners. Indeed, some form ectomycorrhizas with the roots of plants, principally forest trees such as oaks, pines, dipterocarps, and eucalypts (Smith & Read 1997, Rinaldi ). Other symbiotic Basidiomycota form associations with insects, including leaf-cutter ants, termites, scale insects, wood wasps, and bark beetles (Wheeler & Blackwell 1984, Mueller ).

Macro-Basidiomycota

The first information on hyphenate macro-basidiomycota (phytopathogenic or saprobic) in Egypt dates back to Delile (1813a), Melchers (1931), and Morse (1933). In her study on the genus Podaxis, Morse referred to some samples collected from Egypt. After six decades more information about macro-basidiomycota came to light through a series of studies carried out by several investigators, such as Mouchacca (1977), Zakhary (1979), Salem & Michail (1980), Zakhary , MalenÇon (1984), Assawah (1991), Chen (1999), Abu El-Souod , El-Fallal (2003), El-Fallal & Khedr (n. dat.), El-Fallal & El-Diasty (2006), Kim , and Abdel-Azeem (2009).

An exhaustive revision of all the available literature and sources mentioned since 1931 shows that 108 taxa belonging to 65 genera, 104 species, and 4 varieties of Egyptian macro-basidiomycotese had been recorded up to the present time.

Plant pathogenic Basidiomycota

Though many basidiomycetes are saprobes or wood-rotters, the Basidiomycota contains two common and destructive groups of plant pathogens: rusts and smuts. Rust fungi are the largest group of fungal plant pathogens, containing 7 000 species that possess the most complex life-cycles in the kingdom fungi (Sert 2009). They are obligate biotrophs and cause disease on most crops, ornamentals, and many other plants (Hawksworth ). In addition to basidia and basidiospores, rusts produce other types of spores such as teliospores spermatia, aeciospores, and uredospores. Rusts that produce all five types of spores are referred to as macrocyclic, while rusts that lack one or more spore type are referred to as microcyclic. Unlike rusts, smuts produce only basidiospores and teliospores which can survive in the soil away from a host plant. Smuts commonly infect the ovaries of grains and are easily recognized by the formation of galls which contain masses of black spores (Agrios 2005).

The initial research and documentation of rust and smut diseases in Egypt was by Reichert (1921), Briton-Jones (1922), Philp & Selim (1941), Abdel-Hak & Abdel-Rehim (1950), Ragab & Mahdi (1966), and Assawah (1969). Later, in-depth research was carried out by Egyptian and other investigators, with different targets such as taxonomy, pathogenicity, biocontrol and serology. The most relevant studies are: Sherif , El-Shamy (1996), Baka & Gjaerum (1996), Mennicken , Abd El Fattah , Abd EL-Ghany (2009) and Ismail . Baka & Gjaerum (1996) gave the first serious modern taxonomic treatment of local rusts, reporting 23 rust species on various monocotyledonous and dicotyledonous plants in the Nile Valley (see Mouchacca 2003b). As a result of these studies, 112 species of plant pathogenic Basidiomycota belonging to 21 genera were recorded from Egypt.

Total recorded species

After the omission of duplicate names, name correction, allowance for synonyms and taxonomic assignments of all reported taxa from Egypt, the number of the Egyptian fungi recorded is 2 281 taxa belonging to 755 genera (Table 1). At the generic level, some genera exhibit an extraordinary high species richness such as Aspergillus (100 spp.) and Penicillium (83). Other genera show moderate richness such as Chaetomium (53 spp.), Fusarium (49), Puccinia (41), Pythium (30) and Alternaria (27).

Table 1. Numbers of recorded Egyptian fungi.

Groups and Phyla		El-Abyad (1997)	Present survey
Protozoan fungal analogues	Amoebozoa	0	25
	Cercozoa	0	3
Chromistan fungal analogues	Hyphochytriomycota	1	3
	Labyrinthista	0	2
	Oomycota	25	40
	Incertae sedis	0	1
Blastocladiomycota		3	7
Chytridiomycota		21	32
Zygomycota		17	35
Glomeromycota		0	8
Ascomycota	Teleomorphic genera	80	251
	Anamorphic genera	181	261
Basidiomycota		32	87
Total no. of genera recorded in Egypt		360	755
Total no. of species recorded in Egypt		1246	2281

DISCUSSION

It is generally accepted that only about 7 % of all fungi have so far been discovered, and about 93 % still wait to be discovered. Fungi are neglected organisms and they are not well protected, but like animals and plants, they are endangered by human activities. Although the 1992 Convention on Biological Diversity extends protection to all groups of organisms, it is worded in terms of “animals, plants and microorganisms” and fungi do not fit well into these categories. In Egypt and up to now fungal biodiversity and conservation topics have been overlooked. As a result, countries which signed the Convention have almost universally overlooked fungi in preparing their biodiversity conservation plans: fungi are truly the orphans of Rio (Minter 2010).

Threats to fungi throughout the globe are of concern since they are not only beautiful but also play a significant role in human welfare. Three steps were suggested by Moore for fungal conservation: (1) conservation of habitats; (2) in situ conservation of non-mycological reserves/ecological niches; and (3) ex situ conservation especially for saprobic species growing in culture. To help collections of fungal cultures to maintain appropriate standards, the World Federation for Culture Collections (WFCC) has formulated guidelines which outline the necessary requirements (Hawksworth 1991, Smith , Smith 2003). There are 573 microbial culture collections in 68 countries registered in the World Directory of Collections of Microorganisms (DCM) (). In Egypt only two centers are recorded: EMCC (WDCM583) Egypt Microbial Culture Collection, Cairo Microbiological Resources Centre (Cairo MIRCEN), Ain Shams University, and NODCAR WDCM822 Marwa Mokhtar Abd Rabo, National Organization of Drug Control and research. However, Moubasher and his colleagues founded the Assiut University Mycological Centre (AUMC) in 1999 where more than 6 000 fungal isolates belonging to more than 500 species are being preserved under low temperature (5 °C), deep-freezed (-80 °C), and lyophilized; this is the biggest reference culture collection in the Arab countries. The centre also has a collection of dried specimens (i.e. a fungarium) which is rare in Arab countries. In spite of this the AUMC is not yet registered with the WFCC.

The number of habitats that potentially support specialized fungi is enormous. The fungi described as new to science during 1981 to 1990 were associated with 1 982 host genera or substrata (Hawksworth & Rossman 1997). Some unexplored substrata and habitats from which these fungi were found include the rumens of herbivorous mammals, algae, lichens, mosses, marine plants, including mangroves and driftwood, rocks and insect scales.

The Egyptian fungi are presently represented by 2 281 taxa (1 035 species and 395 genera) out of the 101 202 world estimate. In comparing the fungal diversity recorded in Egypt with other countries, it is important to mention that some ecological groups of fungi are completely ignored or have never been studied in a comprehensive way in Egypt, such as Trichomycetes (a group of enigmatic fungi occurring in the hindguts of insects and other invertebrates; Lichtwardt 2002), in addition to hypersaline and black yeasts. Other groups needing more exploration such as algicolous fungi, invertebrate associated fungi, mycorrhizas, endophytic fungi, lichens, wood deteriorating, and coprophilous fungi. The potential fungal resources of Egypt are globally important and there are vast areas that are still unexplored. At present, Egypt needs more investigators and funds to explore and develop this research field and, therefore, the extensive collection of fungi in unexplored areas remains a priority.

This review will be followed by an updated checklist of all recorded Egyptian fungi up to the present, a bibliographic study of Egyptian mycological research, and a book on the fungi of Egypt, supplemented with provisional keys to all species listed.