The taxonomy of the Kingdom Fungi is evolving. Formerly, fungi were named and classified by analysis of their sexual stage or, if that stage could not be observed, lumped in a category “fungi imperfecti”, now simply referred to as “mitosporic”. The sexual stage and the asexual stage each had different names but in 2011 separate names for these two stages were revised and the “one fungus-one name” concept was codified.

DNA sequence analysis and construction of phylogenetic trees makes it possible to classify fungi into the correct Order, Family, Genus, even when a sexual stage is unknown. New clinical species are being recognized in diagnostic laboratories because sterile or even nonculturable fungi can be classed by DNA-sequence analysis: “by concordance of gene genealogies.”

Higher Level Classification of Medically Important Fungi. (Going from most primitive to most advanced)

Phylum: Microsporidia
Recently placed in the Kingdom Fungi, microsporidia are a large group of intracellular parasites causing disease in animals including, especially, invertebrates. They are emerging infectious agents because they can infect patients living with HIV/AIDS or recipients of organ transplants and, rarely, immune-normal persons.
Microsporidia reproduce with walled spores and infect host cells with a structure called a polar filament. They must rely on the host to produce ATP (Smith et al., 2017).
The next two fungal taxa were formerly in a Phylum, the Zygomycota. Now that name and the term “zygomycete” have no strict taxonomic standing and are informal terms.

Sub-Phylum: Entomophthoromycotina
Most are parasites of arthropods, some are saprobes and plant pathogens. Two genera contain zoopathogens-- Basidiobolus, and Conidiobolus. Disease occurs in subcutaneous tissues, nasal mucosae, and surrounding skin occurring mainly in tropical and sub-tropical Asia, Africa, and Latin America. The causative agents, however, are environmental fungi found worldwide.

Sub-Phylum: Mucoromycotina
Mucorales are a fungal Order containing important pathogens, e.g.: Rhizopus, Rhizomucor, Mucor species among others (Figure 1). They are ubiquitous in the environment as soil saprobes, as plant pathogens, and cause postharvest rot of fruit. These opportunistic pathogens cause disease in immuno-compromised individuals, in ketoacidotic diabetics, and in burn patients. Mucormycosis includes cutaneous, mucocutaneous, and rhinocerebral disease; also renal infections, gastritis, and pulmonary infections. The infectious propagules of Mucorales are called spores and their presence in indoor environments implicates them as allergens.

  Figure 1. Structural features of a mucormycete: Rhizopus oryzae
Left: A cluster of Rhizopus oryzae illustrates the “pin mold morphology.” The sporangiophores and sporangia are up to 1.5 mm in length, visible to the unaided eye. The sporangiophores, in a cluster of 8, may be simple or branched, rising from stolons opposite rhizoids. Columellae and the swollen basal part (apophysis) together are round or oval. Credit: Dr. Robert Simmons, Director, Biological Imaging Core Facility, Department of Biology, Georgia State University, Atlanta, GA.
inset: a. sporangium, b. columella, c. collapsed columella (after release of sporangiospores), d. sporangiophore, e. rhizoids. Credit: Kendrick, 1992, Dr. Bryce Kendrick and Focus Publishing R. Pullins Co.
 

The higher fungi are in the Sub-Kingdom: Dikarya because in some part of their life cycle their cells contain two genetically different haploid nuclei (one from each parent.) The dikaryotic state is prolonged in basidiomycetes but short-lived in the ascomycetes.

Phylum: Ascomycota.
The common theme for these “sac” fungi is sexual reproduction that occurs in a sac (ascus) with the production of ascopspores (figure 2). The phylum constitutes ~75% of all yeasts and molds (Taylor et al., 2006). Asexual reproduction results in conidia which are infectious propagules, spread by air, water, and by traumatic implantation via thorny plants and splinters. The development, shape and size of conidia are important taxonomic features. Examples of important pathogens classed here are: Candida species yeasts, Aspergillus species molds, Pneumocystis; and the primary respiratory pathogens: e.g.: Coccidioides species, Histoplasma capsulatum.

Figure 2
Drawing of a perithecium of an ascomycete, Sordaria species, in longitudinal section. 1. The peridium is the perithecium wall; 2. Asci and paraphyseal hyphae are the fertile layer of the ascoma: the hymenium; 3. Periphyseal hyphae provide a channel for escape of the ascospores through the 4. Pore or ostiole. Source: E. Reiss

Phylum: Basidiomycota.
The name refers to the mode of sexual reproduction in a club-shaped basidium with production of basidiospores (figures 3, A and B). Most basidiomycetes are “mushrooms” with characteristic fruiting bodies, e.g.: hallucinogenic and toxic Amanita muscaria (fly agaric). But in medical mycology the human pathogenic basidiomycetes are, for the most part, yeasts! e.g.: Cryptococcus neoformans, Malassezia species. C. neoformans is an opportunistic agent of meningoencephalitis, notorious as one of the AIDS-defining opportunistic infections. Malassezia species, on the other hand, are common commensals on skin of mammals, including humans, causing superficial dermatomycosis.

 

A

B
Figure 3A. Example of a higher fungus that is a basidiomycete, a bracket fungus showing the basidiocarp (fruiting body).
Figure 3B. Lower surface showing generative hyphae. Reproductive spores are dispersed through pores in the surface of the brackets.
© Dr Arthur DiSalvo and © Dennis Kunkel Microscopy, Inc. Used with permission