Introduction to the Fungi

In this part of the course, we will be studying the organisms that are referred to as fungi (sing.=fungus). Although you have probably now had one to several courses in which you have studied the eukaryotic organisms, the fungi are probably the least understood. Looking back at my undergraduate career, prior to taking my first mycology class, this was certainly the status of my knowledge of the fungi. My impression of fungi was that they were disease-causing organisms that were found in unsanitary conditions. That was the sum of my knowledge about fungi. Although my impression was not entirely wrong, fungi are so much more than that. Fungi, are also very beneficial organisms. We have derived a number of useful antibiotics from them, including the "wonder drug" penicillin. Without fungi, we would not have leavened bread, Roquefort and Camembert cheeses, beer, wine and other alcoholic beverages and some mushrooms, morels and truffles are considered to be delicacies among gourmands. While these aspects of fungi are of interest, they will not be the emphasis on our discussions of fungi. If you are interested in learning about these aspects of fungi, you may go to the Botany 135 home page. The emphasis here, instead, will be to study the relationships of the various groups of fungi and attempt to make sense of their phylogeny.

Classification of Fungi

Once upon a time biologist only recognized two kingdoms: Plant and Animal (this was how organisms were classified when I was an undergraduate). Fungi, as well as bacteria and algae were classified in the plant kingdom under this system and that is the reason that these organisms are traditionally studied in botany. In the case of fungi, MYCOLOGY is that part of botany that studies fungi. Although fungi are no longer classified as plants, there is still good reason to study them in botany. Fungi are most often associated with plants, commonly as decomposers, occasionally as pathogens and as their benefactors, e.g. mycorrhiza. But What is a fungus? This is an important question because you are use to categories of organisms being closely related to one another. Members of the plant kingdom, for example, are known to be derived from a single algal ancestor from the algal division: Chlorophyta, i.e. they are monophyletic. However, from Dr. Smith's part  of the course on algae, you should now realize that this is not always the case. You now know that algae are polyphyletic and each division is derived from a separate ancestor. This means that each of the algal divisions is not closely related. Thus, the term "algae" is used to include organisms that have similar habitats and characteristics rather than to indicate relationship. The same holds true for fungi. Most organisms that we refer to as fungi have a combination of characteristics in common that we will now go over:

1. Achlorophyllous: Fungi cannot make their own food like plants. They are heterotrophs and depend upon other organism for their carbon source. Heterotrophs can further be divided into the following categories:
   1. Parasites: Organisms that derives their nutrition from the protoplasm of another organism (=host).
   2. Saprobes: Organisms that obtains their carbon source (=food) from the by-products of organisms or dead organisms. However, if the opportunity arises, some saprobes may become parasitic. Such organisms are said to be facultative parasites.
   3. Symbiosis: In the strict sense, this term refers to the habitual "living together" of different species. As such, there are a number of different categories of relationships that may fit under this term. However, we will use it in its most common usage: "Intimate association of two dissimilar organisms in a mutually beneficial relationship, e.g. lichens and mycorrhizae." This type of symbiosis is specifically referred to as a mutualistic symbiosis.
2. Eukaryotic: Fungi have membrane bound organelles, i.e. nucleus, mitochondrion, E.R., etc. Once upon a time filamentous bacteria called Actinomycetes were classified with fungi, but this is no longer the case.
3. The vegetative body of the fungus (=thallus) are one of the following forms:
   1. Yeast: Unicellular fungi that reproduce, asexually, by budding or fission (terms to be defined later).
   2. Mycelium: The collective, filamentous strands that make up the fungal thallus. Strands of mycelium is referred to as hyphae (sing.=hypha). Mycelium may be of two types:
      1. Septate: Mycelium that is divided into discreet cells by cell walls that are laid down at regular intervals along the length of the mycelium. These cell walls are called septa (sing.= septum).
      2. Coenocytic: Mycelium that is not divided up by septa and forms a continuous tubular network. Septa, however, are present occasionally, especially where reproductive structures occur and where the cell wall of the mycelium has been compromised.
   3. Some species may have have thalli that are mycelium and yeast. Such fungi are said to be dimorphic (=two forms).
4. The assimilative stage of the fungal body, i.e. mycelium or yeast, has a cell wall. In the strict sense organisms classified as fungi have cell walls composed primarily of chitin. However, we will be also be covering "fungi" that do not have chitin in their cell walls.
5. Fungi have a common nutritional mode: Absorption: The transport of food from their substrate into their cell walls. The following events occur in this mode of nutrition:
   1. If the available food that the fungus is using is soluble, i.e. a simple organic compound, such as simple sugars and amino acids, the mycelium or yeast cells can transport the food directly through their cell wall.
   2. If the available food is insoluble, i.e. a large, complex, organic compound, such as lignin, cellulose and pectin, then production the food must first be digested. Digestion is carried out by the production of various enzymes that are substrate specific and will break down insoluble food material to soluble compounds that can be transported through the cell wall. Although this appears to be very different from the way in which we (animals) digest food, it differs only in the sequence of events that takes place. Where we ingest food and then digest it, fungi first digest their food before ingestion.
6. Either sexual or asexual reproduction or both may occur by spores. Spores and/or gametes can be motile or not. However, in the strict sense as fungi are currently defined, only those organisms that produce nonmotile spores and gametes are classified as fungi. Nevertheless, we will be going over organisms that have motile spores, called zoospores, and motile gametes.

In summary then, the organisms that we call fungi, as was the case in algae, represent a heterogenous group, i.e., they are polyphyletic, that are not closely related as you will soon see.

When I was an undergraduate, organisms that were defined as fungi were heterotrophs, with cell walls, that have filamentous or yeast thalli. Compare this definition with how a fungus was defined above, in the strict sense. Why the change? As with any science discipline, knowledge in mycology is dynamic and we have accumulated a great deal of knowledge about the fungi since I first took mycology 30 years ago. The additional knowledge has led us to change our concepts as to the relationship of those organisms that were classified as fungi. Much of the knowledge that led to these changes began in the early 1960’s, when a great deal of research was carried out in fungal ultrastructure. This was later followed by comparative studies on cell wall biochemistry (Barnicki-Garcia, 1970) and more recently molecular approaches, utilized in studying relationships of organisms, has led to further changes in our concepts as to how we define fungi.

Another change that occurred during this period of time that affected not only fungi, but also "plants" and "animals" as well. When I was an undergraduate, the classification for plants and animals were very broadly defined. As I mentioned, above, organisms in those days were classified as either plants or animals. Fungi, as well as bacteria and algae were classified in the plant kingdom, based mainly on the presence of a cell wall and the lack of ingestion of food material. However, *Whittaker (1969) erected the five-kingdom system which is currently still the accepted system of classification of organisms. As a result, the fungi, algae and bacteria were placed in different kingdoms. While, the concepts of the five kingdoms have changed since Whittaker (1969), the classification of organisms into five kingdoms have persisted.

Although, our definition of a fungus has changed a great deal, by tradition, mycology classes have continued to study the same organisms that have been studied since the 1960’s and earlier. While mycologists have learned a great deal about the fungi in these last 30-35 years, there is still not agreement as to how best to classify the fungi, nor will there likely be any agreement at a later time. Some examples of the more popular classification schemes are reproduced below:

Over the last ten years, there have a great deal of changes in the concepts of the relationships of the various groups of fungi. The classification below represents one of the more recent systems and is based, in part, on molecular research that has been carried out in recent years. Because of time constraints, not all of the different taxa of "fungi" will be listed below or covered in this course. 

Kingdom: Protista

Division: Myxomycota (Currently classified with protozoans)

Flagellated Fungi

• Division: Hyphochytridiomycota
• Division: Oomycota

Kingdom: Myceteae (=Fungi)

Division: Chytridiomycota

Division: Zygomycota

Division: Ascomycota

• Class: Ascomycetes
  • Order: Saccharomycetales and Schizosaccharomycetales (Yeast)
• Filamentous Ascomycetes
  • Order: Eurotiales (Fruiting body a cleistothecium)
  • Order: Sordariales and Xylariales (Fruiting body a perithecium)
  • Order: Pezizales (Fruiting body an apothecium)
  • Order: Dothideales (Fruiting body an ascostroma)

Division: Basidiomycota

• Class: Basidiomycetes
  • Order: Agaricales (Mushrooms)
  • Order: Lycoperdales, Phallales and Nidulariales (Puffballs)
  • Order: Aphyllophorales (Polypores)
  • Order: Tremellales, Dacrymycetales and Auriculariales (Jelly Fungi)
• Class: Teliomycetes (Rust)
• Class: Ustomycetes (Smuts)

Division: "Deuteromycota" (Asexual Fungi)

As we study the various groups of fungi, I will attempt to point out the problems in using a classification scheme in a course such as this one where the goal is to study the phylogeny and relationship of the various organisms that we are calling fungi.

During the final lab in this section of the course, I will bring in several dated textbooks, such as Alexoupolous (1962) and Bessey (1950), which were considered outstanding textbooks for their time. At that time, I want you to compare the concepts of fungi in these books with our present concept. Whenever I look back at these textbooks, it never ceases to amaze me as to how much we have progressed in our knowledge of the fungi. Perhaps, this will also be something that you will appreciate by the end of this section of the course.

*Whittaker, R.H. 1969. New concepts of kingdoms of organisms. Science 163: 150-161.