Diagnosis of Fungal Plant Pathogens Using Conventional and Molecular Approaches

Fungi are a large group of eukaryotes found as saprophytes, pathogens or endophytes, which distribute in every corner of our planet. As the main pathogens, fungi can cause 70–80% of total plant diseases, leading to huge crop yield reduction and economic loss. For identification of fungal plant pathogens, mycologists and plant pathologists have mainly gone through two stages, viz. morphological observation and morphology/phylogeny, and the next era might be utilizing DNA barcodes as the tool for rapid identification. This chapter accounts i) the brief history of development for fungal identification tools and main concepts, ii) the importance and confusion of “One fungus, one name” for pathogen identification, iii) more or fewer species that we need in agricultural practice, and iv) the foreground of fungal plant pathogen identification. These will help to solve the practical problems of identification of fungal pathogens in agricultural production.

Fungi of quarantine concern for China I: Dothideomycetes

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentro­spora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens.

Fungal species associated with apple Valsa canker in East Asia

Since its discovery more than 110 years ago, Valsa canker has emerged as a devastating disease of apple in East Asia. However, our understanding of this disease, particularly the identity of the causative agents, has been in a state of confusion. Here we provide a synopsis for the current understanding of Valsa canker and the taxonomy of its causal agents. We highlight the major changes concerning the identity of pathogens and the conflicting viewpoints in moving to “One Fungus = One Name” system for this group of fungal species. We compiled a list of 21 Cytospora species associated with Malus hosts worldwide and curated 12 of them with rDNA-ITS sequences. The inadequacy of rDNA-ITS in discriminating Cytospora species suggests that additional molecular markers, more intraspecific samples and robust methods are required to achieve reliable species recognition.

The Biology of Fungi

Fungi are found ubiquitously in the environment such as soil, water, and food. There are an estimated 1.5 million fungal species worldwide, although this number is felt to be grossly underestimated and is regularly updated. Of these vast numbers, around 500 fungi to date have been implicated in human disease. As opposed to bacteria, which are prokaryotes, fungi are eukaryotes, meaning they have a well-defined nucleus and have membrane- bound organelles in the cytoplasm, including an endoplasmic reticulum and a golgi apparatus. In 1969, the scientist R. H. Whittaker first proposed that organisms be classified into five kingdoms: Monera (Bacteria), Protista (Algae and Protozoans), Plantae (Plants), Mycetae (Fungi), and Animalia (Animals). Since then, there have been dramatic changes to the classifications of fungi, largely due to the appliance of phylogenetic molecular techniques. This has resulted in variances to the number of phylums, and the species assigned to them. Table 3.1 shows the seven phyla of the Fungi Kingdom. The majority of fungi pathogenic to humans inhabit the Ascomycota and Basidiomycota phyla. Fungi used to be dually named if they had a pleomorphic life cycle with sexual/ asexual stages (teleomorph/ anamorph, respectively), which meant that fungi often had two names and were classed differently. This practice was discontinued in January 2013 after the International Commission on the Taxonomy of Fungi decided that a ‘one fungus, one name’ approach should be followed. Fungi can be unicellular (yeast) or multicellular (fungi). Yeasts may look globose in nature when grown, whereas multicellular fungi grow as tubular, filamentous material called hyphae that can create a branching, hyphal network called a mycelium. Hyphae may have septa that cross their walls or be nonseptate, which is a method of differentiating fungi. An early hyphal outgrowth from a spore is called a germ tube. The germ tube test can be used to differentiate the yeasts Candida albicans and Candida dubliniensis from other Candida species. The fungal cell wall is composed of chitin and glucans, which are different components to the human cell wall. This means that they can be an effective target for antifungal therapy.

A critical review of producers of small lactone mycotoxins: patulin, penicillic acid and moniliformin

A very large number of filamentous fungi has been reported to produce the small lactone mycotoxins patulin, penicillic acid and moniliformin. Among the 167 reported fungal producers of patulin, only production by 29 species could be confirmed. Patulin is produced by 3 Aspergillus species, 3 Paecilomyces species, 22 Penicillium species from 7 sections of Penicillium, and one Xylaria species. Among 101 reported producers of penicillic acid, 48 species could produce this mycotoxin. Penicillic acid is produced by 23 species in section Aspergillus subgenus Circumdati section Circumdati, by Malbranchea aurantiaca and by 24 Penicillium species from 9 sections in Penicillium and one species that does not actually belong to Penicillium (P. megasporum). Among 40 reported producers of moniliformin, five species have been regarded as doubtful producers of this mycotoxin or are now regarded as taxonomic synonyms. Moniliformin is produced by 34 Fusarium species and one Penicillium species. All the accepted producers of patulin, penicillic acid and moniliformin were revised according to the new one fungus – one name nomenclatural system, and the most recently accepted taxonomy of the species.

Isaria takamizusanensis is the anamorph of Cordyceps ryogamimontana, warranting a new combination, Purpureocillium takamizusanense comb. nov.

The entomogenous anamorphic fungus Isaria takamizusanensis has not been resolved clearly in its teleomorphic state. We succeeded in inducing ascostroma formation by incubating conidiomata of I. takamizusanensis on cicada adults in a moist chamber. We observed the ascostroma and conducted a phylogenetic analysis based on ITS rDNA and EF-1α genes. The morphology of the ascostroma was identical to that of Cordyceps ryogamimontana. In the phylogenetic tree inferred from EF-1α, the isolate from the partspores grouped with nine strains derived from conidia of I. takamizusanensis, which was distinct from a clade including Purpureocillium lilacinum. Moreover, a conidial structure identical to that of I. takamizusanensis was rediscovered on the holotype specimen of C. ryogamimontana. As a result, we propose a new name, Purpureocillium takamizusanense, which is a combination of the teleomorph–anamorph connection of C. ryogamimontana–I. takamizusanensis, in accordance with the ‘one fungus, one name’ concept of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN).

Let's talk about 'One fungus One name'. Changes in the fungal taxonomy

Mycologists have recorded a few hundred thousand Latin names for fungi and these are thought to refer to 70 000 or so separate species. The use of molecular techniques in fungal taxonomy and systematics in the last 25 years has provided massive amounts of information to clarify phylogenetic relationships, encouraged grant support, and complicated the jobs of classically-trained mycologists. Taxonomists have a reputation for being traditionalists, but the community has recently embraced the modernization of the nomenclatural rules by discarding the requirement for Latin descriptions, endorsing electronic publication, and ending the dual system of nomenclature, viz. teleomorph and anamorph names, which used parallel for the sexual and asexual phases of pleomorphic species. A group of taxonomists accepted ’The Amsterdam Declaration on Fungal Nomenclature’ and its basic principle the ’One fungus – one name’ has been incorporated in the Code of Nomenclature (’Melbourne Code’) in 2011. The next, and more difficult step will be to develop community standards for sequence-based classification. As the’One fungus – One name’ theory is a brand-new issue for the Hungarian plant doctors and practical specialists, it seems reasonable to review this to promote conversations between generations in Hungarian language.

One Fungus, One Name: Defining the Genus Fusarium in a Scientifically Robust Way That Preserves Longstanding Use

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.