What is a Fungus?

Introduction

There are many different kinds of fungi (sing. = fungus) and some have been illustrated below (Figs. 1-12). There are some that are readily seen because of their large fruiting bodies that are visible to the naked eye. However, that they are visible does not mean that you have seen them. For example, Aseroe rubra (Fig. 12), is probably one of the more common species that occur in Hawai‘i. Its fruiting bodies can usually be found quite commonly from October to January and with its bright red coloration and its fetid odor, it would seem to be difficult to miss. Yet, I have shown this picture to numerous local people who have lived here all their lives that have never seen this species. Why is this? My guess is that for the very same reason I never saw a mushroom in nature until I took mycology as an undergraduate, and that reason is that we tend to not see what we are not looking for. Many fungi do not produce large fruiting bodies and are known only from their spore stages that can require the aide of a compound microscope. The spores of Glomus (Fig. 3) and Rhizopus stolonifer (Fig. 9) are two examples of these fungi. There are also pictures that show the impact that some fungi may have on our lives. Yeast is necessary for baking the soft leavened bread (Fig. 2) that we normally eat. Otherwise, bread would be heavy unleavened bread that can also be purchased for consumption. The unique flavor of blue cheese requires the presence of Penicillium roqueforti (Fig. 6) for its unique flavor. Athlete’s foot (Fig. 11), a prevalent condition, that can be caused by several species of fungi that are human pathogens.

Figure. 1: Tremella mesenterica, fruiting body of a "jelly fungus"

Figure. 2: Unleavened and leavened (requires yeast)  bread 

Figure. 3: Glomus sp., spore of an arbuscular mycorrhiza fungus

Figure. 4: Metatrichia vesparium, sporulating stage of an acellular slime mold

Figure. 5: Pseudoplectania sp., fruiting bodies of a discomycete

Figure. 6: Blue Cheese made from Penicillium roquerforti

Figure. 7: Peltigera venosa, a lichen, which represents two organisms, an alga and a fungus

Figure. 8: Cyathus, sp, fruiting bodies of a "bird's nest fungus"

Figure. 9: Rhizopus stolonifer, zygospore stage of "bread mold fungus"

Figure. 10: A. muscaria, fruiting bodies of the “fly agaric”

Figure. 11: Athlete's Foot can be caused by several different species of molds

Figure. 12: Aseroe rubra, fruiting bodies of a "stink horn"

All of the above pictures represent organisms that are/have been classified as fungi, but how many of you would have guessed that all of the pictures above are fungi or of something that requires the presence of fungi. So, one of the goals in this class is to make you aware of the fungi that are around you and perhaps appreciate what they are doing in your environment. However, before we can do this we must give you some background that will help you in understanding what a fungus is.

What is a fungus

What would seem like an easy question is not. The matter in which we have defined fungi has changed several times over the last 40 years when I first became interested in mycology.  Let me summarize some of the highlights of these changes. In the early 20th. Century, until around the 1950's, botanist used the term fungi to include all members of the "plant kingdom" that did not have stems, roots, leaves and chlorophyll (Alexopoulos, 1952). By this definition, bacteria were even included with the fungi. By 1962, Constantine Alexopoulos , the author of the popular mycology text book, Introductory Mycology, defined in the second edition of his textbook that fungi were "nucleated, achlorophyllous organisms which typically reproduce sexually and asexually, and whose usually filamentous branched somatic structures are surrounded by cell walls" (the bolded the terms are still emphasized when defining what a fungus is). This then excluded bacteria from being classified as fungi since they did not have nuclei. Still organisms, such as Metatrichia vesparium, commonly called slime molds, a group that Alexopoulos had considerable expertise, were still classified as fungi in the second edition to his textbook. The point of this story is that ideas as to what constitutes a fungus has changed a number of times since the last half of the 20th. Century and is quite different than the concept that we currently have. Currently, most mycologists define fungi as those organisms that are “nucleated, achlorophyllous, typically reproduce sexually and asexually by spores, and whose somatic structure is composed of filamentous branched or yeast, which are surrounded by cells walls composed of chitin and may or may not have a flagellated stage”. This is quite a bit more specific, but also more complex than the earlier definitions. Let us go over this definition, in detail, so that you may understand the above terms. 

Achlorophyllous

This term indicates that fungi cannot produce their own food. Such organisms are called heterotrophs. This was more important once upon a time than it is today because this characteristic was necessary for distinguishing fungi from the rest of the plant kingdom since they had chlorophyll and could photosynthesize. However, old traditions die hard and even though biologists now know that fungi are not plants, the layperson still refers to fungi as plants.

Heterotrophs can be divided into several categories:

1.      Saprobe (Also referred to as saprophyte and saprotroph): Heterotroph that derives its food from non-living organic carbon sources. Most fungi are in this category. Many old textbooks use the term saprophyte literally meaning, "rotting plant" (showing the botanical origin of this word). These types of fungi are very important as nature's recyclers. They consume dead organic material and break down into their most basic components, i.e. minerals, which can then be utilized by plants to produce more food. So even though we say that these fungi cause "rot" and "decay", that isn't necessarily a bad thing. This is a very important process in nature's effort to recycle.  The down side of decomposition is that fungi do not distinguish between fallen branches and logs, and your home and commercial wooden products. To a fungus, wood is wood, regardless of the source.

2.    Parasite: Heterotroph that derives its food from the living cells of another organism referred to as the host. Many fungi fit into this category, but not all, and not even most. This is just one of the many biases that we have of fungi, i.e., the common belief that most fungi are parasites.

3.    Facultative Parasite: Heterotroph that is primarily a saprobe, but when opportunity presents itself, can be a parasite.

4.    Facultative Saprobe: Heterotroph that is primarily a parasite, but when opportunity presents itself, can become a saprobe.

5.    Symbiont (used here in the mutualistic sense): Heterotroph that derives its food from another living organism, but the relationship is mutually beneficial to both organisms involved, e.g. lichens = fungus and alga. As you'll see later in the semester, fungi that are in this category are very important, i.e. if they did not exist, the world as we know it also would not exist

Facultative parasites and facultative saprobes are of more concern to plant pathologists than those that are obligate parasites. An obligate parasite will normally weaken its host, but not kill it since killing the host would almost certainly guarantee the death of the parasite. However, a facultative parasite or facultative saprobe, when they are in their parasitic mode is more likely to be an aggressive parasite that will kill their host since they will be able to survive as saprobes when they kill their host.

The Characteristics of Fungi

Before going over the characteristics of the fungi, I must emphasize here that there is no single characteristic that will be unique only to fungi. Instead we are going to cover a combination of characteristic that together will be unique to the fungi.

The Fungus Body: Mycelium and Yeasts

At one time or another, we have all come across food that has become contaminated in some forgotten corner of our refrigerator and observed the filamentous growth of fungi. The filamentous growth is called mycelium (pl.=mycelia) (Fig. 13) and represents the "body" of the fungus.   A fragment of mycelium is referred to as a hypha (pl.=hyphae). A less familiar fungus body, is the yeast. The yeast fungus is unicellular. Whether the fungus body is composed of mycelium or yeast, both will function in feeding and reproduction. Let us first discuss the more familiar filamentous appearance of the mycelium.

Mycelium

If we place a single fungal spore, the reproductive unit of a fungus, in the center of a petri plate, hyphae will germinate from the spore and grow radially, to form a circular growth of mycelium. The radial growth of the mycelium can be small as shown in the petri plate (Figure 14) below or may be extensive. Recall from the video "The Moldy World About Us" where a circle of mushrooms, called a "fairy ring", was formed.

Figure 13: Mycelium as seen through the microscope.

Figure 14: Mycelium with approximately circular colony.

An example of a mushroom that forms fairy rings is Chlorophyllum molybdities (Figs. 15 and 16). The grass can be seen to be greener inside the fairy ring because the mushroom mycelium, growing in the soil and not visible has decomposed the organic material, within the ring. Provided with more minerals, the grass inside the ring can be seen to be more lush and healthier in appearance. In either case, if this growth is observed under a microscope, you will be able to see that it is composed of the same type of branched, filaments that are shown in Figure 1b. Each branch will form more branches at a given interval, which will in turn branch further. Growth will occur only at the ends of the cells, not from further growth of cells below the tips of the mycelium.

Figure. 15: Chlorophyllum molybdites  mushrooms

Figure 16: Fairy ring of same species

Mycelium can be artificially divided into two broad categories. When mycelium forms a continuous tubular growth it is said to be coenocytic (Fig. 17) or it can be divided into cells that are attached end to end and is said to be septate (Fig. 18). The cell walls that divide the mycelium into cells are referred to as septa (sing.=septum):

 

Figure 17: Coenocytic hypha fragment.

Fig. 18. Septate hypha fragment.

Yeast

A less familiar fungus body is the yeast. Under the microscope, you can observe that yeast is composed of single cells that continually divide, by the process of budding or fission and in this way forms lots and lots of cells. When yeast is seen without the aide of a microscope it appears to a thick, syrupy growth (Fig. 19).

The process of fission is merely division of a yeast cell and its nucleus by mitosis, into two genetically identical cells, i.e. clones, and two nuclei, as can be seen in Fig. 20. The process of budding is a bit more complex and is illustrated in Fig. 21. Budding begins at a predetermined area of the yeast cell that becomes blown out forming the so-called bud. As the bud becomes larger, the nucleus will divide, as in the case of fission, by mitosis into two genetically identical nuclei. One of the two nuclei will migrate into the bud. The bud will in time become larger until it is approximately the same size as the parent cell. The opening that allowed the migration of the nucleus into the bud will be sealed off by the addition of cell wall material and the two yeast cells will separate to become independent cells. Both fission and budding are examples of asexual reproduction and will form clones of the parental cell. Some species have both a yeast and mycelial stage (Fig. 22) and are said to be dimorphic.

Figure 19: Yeast colony of Rhodotorula

Figure 20: Yeast cell undergoing fission.

Figure 21: Yeast cell undergoing budding.

Figure 22: Dimorphic species with mycelium and yeast phase.

 

Spores

Fungi reproduce by spores. Spores are usually composed of one to a few cells. They may be sexual or asexual and are variable in shape, size and color (Fig. 23):

Figure 23: Spores of various shapes and sizes

Spores are often borne directly on modified mycelial structures. In the colony of Penicllium notatum pictured below (Fig. 24), the green, central portion of the mycelium is where the spores are borne on the modified mycelial structures called conidiophores (Fig. 25). This type of spore is called a conidium (pl.=conidia) and is formed asexually, and is a clone of the parent spore.

Figure: 24. Colony of Penicillium notatum

Figure: 25. Conidia and conidiophores as seen under the microscope.

 

 

Asexual spores are also produced by yeast during fission and budding. In the structurally most complex fungi, the spores are borne in a large, often macroscopic, fruiting body, such as the mushroom in Fig. 15 that forms when mycelium becomes very tightly interwoven.  In the case of mushrooms, the spores are said to be sexual spores and each one is genetically different. More will be said on the subject of sexual versus asexual reproduction in the postscript at the end of the web page.

Cell Wall

The mycelium or yeast cell is surrounded by a cell wall that is typically composed of chitin, the same material that makes up an insect's exoskeleton. This material must be present in the cell wall of any organism that is classified in the Kingdom: Mycetae, i.e. Fungi. Note that this characteristic differs from an earlier definition that was given of fungi. In this older definition the presence of a cell wall, regardless of its composition, would not eliminate an organism from being classified as a fungus. For example there are a number of species of fungi that we will be studying has cell wall composed of cellulose that were once classified as fungi, but have now been reclassified elsewhere and not even thought to be closely related to the Fungi. During the early 1970's Solomon-Barnicki Garcia, a cell wall biochemist was the first to propose that only those organisms that produce chitin in their cell wall should be defined as fungi.

Eukaryotes

Fungi are eukaryotes. This term has been used to refer to organisms that have nuclei in their cells. For our purpose this definition will suffice. This characteristic separates them from bacteria, which are prokaryotes, i.e. they lack nuclei in their cells. 

Mode of Nutrition: Absorption

The mode of nutrition or the matter in which fungi "eat" is called absorption. Among eukaryotes, absorption is unique to the fungi. Fungi obtain their food by transporting it through their cell walls, but first, how does a fungus "find" its food since like plants, they are not mobile organisms and cannot seek out their food. The answer is fungi do not have to find their food. In order to eat, the spores that give rise to fungi must be dispersed to a location where there is food and after the spore germinates, the mycelium of the fungus must grow into its food. Another words, usually fungi must live in their food if they are to eat. If the food is composed of simple molecules such as glucose or sucrose, soluble food can be immediately transported through their cell walls. However, most food that a fungus might consume is composed of complex, organic compounds, e.g., cellulose, lignin, pectin, starch, etc., which is insoluble. In order for this food to be utilized by the fungus, it must be broken down into simpler molecules that can be transported through their cell walls. Another way in which you can think of this is that the cell wall is like a sieve that will allow only particles of a certain size to enter. The fungus breaks down the complex material by secreting digestive enzymes through their cell wall that will digest the complex organic compounds and convert them into simple molecules that can readily be transported through their cell walls. For example, If a fungus is growing in wood, digestive enzymes would be secreted from the fungus, into the wood, and break down the complex compounds of wood, e.g. cellulose and lignin into simpler materials, such as simple sugars, which then can be transported into the mycelium. 

Although this process may seem very different than our own means of obtaining food. It is not that different. The essential difference between fungi and animal digestive systems is that fungi digest their food first and then "eat" it, while animals eat their food before digesting it. The basic process of digestion is otherwise more or less the same. Our digestive system requires that our food is chewed by teeth, go through the esophagus, stomach, intestine and many associate organs. So there are a lot of things that can go wrong when we eat our food. The fungal digestive system is much more simplified and one which has been very successful for them.

It is important to understand here that different kinds of fungi will secrete only a specific number of different enzymes. This means that they can only "eat" certain materials. For example, a fungus that is usually found in your stored food, probably will not be able to "eat" wood because it does not have the enzymes that is needed to break down or "rot" the wood. Some fungi have a very broad range of enzymes. Species of Penicillium, for example, can be found on a number of different "food"; leather, cloth, paper, wood, manure, animal carcasses, ink, syrup, paint, glue, hair, literally thousands of products. A summary of absorption is illustrated in Fig. 26, below:

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Figure 26: Illustration of the process of absorption, the mechanism by which fungi consume their food.

Although yeasts are quite different in their appearance than mycelial fungi, their means of obtaining food is identical.

Summary of Fungal Attributes

1.      From our discussion on how fungi are able to carry out their various activities, the following attributes can be used to characterize those organisms that we classify as fungi:

a.     They are heterotrophs. That is, they cannot manufacture their own food from simple compounds as plants are able to do. So they are dependent on other organisms to produce their foods, e.g., sugars, starches, proteins, fats, etc. Fungi can be further divided into saprobes, parasites, symbionts, facultative parasites and facultative saprobes.

b.     The food gathering part of a fungus is made up of either filamentous, hollow, branched tubes called mycelium or are single cells called yeasts.

c.     Structures called spores reproduce the fungus in the form of mycelium or yeast cells.

d.     They have cell walls. This is a characteristic generally attributed to plants, but unlike plants, most fungal cell walls are composed of chitin, the same material that makes up the exoskeletons of insects. Plant cell walls are composed of cellulose.

e.     Fungi are eukaryotes as are most other organisms with which you are familiar. However, bacteria differ from fungi in that they are prokaryotes.

f.     Absorption: The process by which fungi "eat". This differs from the way in which we eat in that a fungus will digest its food before eating it. Bacteria are the only other group of organisms that eat in this fashion.

So What do the Set of Characteristics mean?

We have gone over several working definitions for "fungi" that have been accepted in mycology over the last 50 years. Each definition, at the time that they were used was thought to include closely related organisms, i.e. they were all derived from a single common ancestor. However, as time passed, and we gathered more information about these organisms, it became apparent that this notion was not correct. So, we redefined "fungi" to reflect these changes. The above set of characteristics is the most recent definition as to what we believe constitutes a fungus. However, in mycology, we continue to study those organisms that have been demonstrated to not being closely related to fungi. Thus, in mycology we have two definitions for fungi. One in which only those organisms that have the above characteristics and are closely related to one another are recognized as belonging to the fungus kingdom. These organism are referred to as “Fungi” (note upper case “F”). The second includes all the fungi that have been recognized as fungi since Alexopoulous' definition in 1962, i.e. includes slime molds and other organisms that have been excluded from the Fungi and will be referred to as “fungi” (note lower case “f”). More will be said on this subject in our lecture on "How fungi get their name and how they are classified".

Post Scripts

Sexual vs. Asexual Reproduction

Sexual reproduction is a subject that can probably be best understood if we discuss it in human terms rather than using plants or fungi. You are all aware that this type of reproduction must involve two parents, and that the children from two parents will inherit characteristics from each parent. For example, all of you have features that can be recognized as being maternally or paternally inherited. This will also be true for any siblings that you may have. However, you and your siblings are genetically unique in appearance and personality because the process of sexual reproduction is such that no two individuals will be exactly alike unless they are identical twins.

Asexual reproduction requires only a single parents and the "children" produced would be genetically identical to the parent. Genetically, identical individuals are said to be clones. Asexual reproduction is currently more easily understood due to the extensive coverage of cloning in the news media of Dolly, the cloned sheep and the mice that have been cloned right here on the University of Hawai‘i, Manoa campus. Although some animals, naturally, have this type of reproduction, there are far more examples of asexual reproduction in plants. Asexual reproduction occurs when a part of an individual regenerates itself into another individual. Since this new individual was originally part of the parent, the two are genetically identical.  Many agricultural plants are reproduced asexually because if you have a plant with all the qualities that you want, growing clones of this individual will ensure that everything you are growing will also have these qualities. Examples of such plants are illustrated in Figures. 20-22. In potatoes, each "eye" can be used to produce a new potato plant, the leafy tops of the pineapple and carrot can be grown to produce other plants.

 

potato2.GIF (17688 bytes)

pineapple2.GIF (17551 bytes)

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Figures 27: From Left to right, potatoes, pineapple, carrots and onion. These are example of plant structures that can be utilized in asexually reproducing the plant.

Both sexual and asexual reproduction has its advantages and disadvantages. For example, if a fungus is growing in an ideal environment that it is well suited for, it would be advantageous to reproduce asexually since the environment would also be ideal for clones of that individuals. However, if the environment should suddenly become unfavorable and lead to the death of that fungus, having an entire population of genetically, identical individuals will be a disadvantage since all of the individuals will be equally likely to die. In this situation, sexual reproduction will be advantageous since the individuals produced will all be genetically different. Being different, there may be one to several individuals that may be more suited for the new environment. 

A Few Misconceptions About Fungi

Temperature: Fungi grow best in warm temperatures. Some species of fungi do grow better at warm temperatures (70-90°F), but there are some that thrive in very high temperatures of 130-150°F and some that will thrive in very low temperatures below 32°F (below freezing). That is why when you refrigerate meat, it needs to be in a freezer at -20°F. Also, how many of you have found food in your refrigerator that has been contaminated with fungi?

Water: Fungi need lots of water to grow. For most fungi this is true. This is why fungi are more of a problem in the tropics than in temperate areas of the world. Personal property that is normally safe from fungi, such as clothing and shoes, can be damaged in the tropics. However, some fungi can grow in very dry conditions. Dried grains and fruits can become contaminated with fungi. Fungi contaminating grains have been a very serious health hazard. For example, when you go into a bar, it is not the beer that will kill you, but the free peanuts. At the other extreme, there are also fungi that can live under water.

Light: Fungi can only grow in the dark. For the most part, light does not play a role in how well fungi grow. There are some conditions where light is necessary for reproduction.

Mycelial Growth

Until the 1990's fairy rings were thought to be the largest examples of mycelial growth (actually rhizomorphs in this case) in fungi. In April 2, 1992 the war of the humongous fungus began. Smith, et al. (1992) published an article of what at that time was considered to be the world's largest organisms. This article reported that what genetically was determined to be an individual of Armillaria bulbosa, a species of mushroom, produced rhizomorphs that covered approximately 37 acres. It was estimated to be at least 1500 years old and weighing in at about 100 tons. This was published as a serious journal article, but captured the imagination of the news media that dubbed it the humongous fungus and a media blitz began that lasted for months. And just when things were going back to normal, on May 18, 1992, a still bigger mass of rhizomorph was discovered.  On Mt. Adams, in Washington State, rhizomorphs of Armillaria ostoyae covered 1500 acres. However, even this example does not represent the largest example of radial, mycelial growth. The most incredible growth of mycelium is one that was found in eastern Oregon, on August 1, 2000.  The mycelium was found to belong to a mushroom identified as Armillaria ostoyae. Researchers determined that the mycelium of this mushroom covered 2,200 acres and estimated it to be over 2400 years old. The full text of this story was written by Volks (2002). 

Literature Cited

Alexopoulous, C. J. 1952. Introductory Mycology. 1st Edition, John Wiley & Sons, New York.

Alexopoulous, C. J. 1962. Introductory Mycology. 2st Edition, John Wiley & Sons, New York.

Smith, M., J. Bruhn, and J. Anderson. 1992. The fungus Armillaria bulbosa is among the oldest and largest living organism. Nature 356:428-431

Volk, T. 2002. The Humongous Fungus -- Ten Years Later. Inoculum 53(2): 4-8. (Newsletter of the Mycological Society of America)

Mycological Terms

Absorption: The means by which fungi obtain their food. Process begins with the release of digestive enzymes, from the fungus, through their cell walls to digest the food that is around them. The digested food is then "absorbed" through their cell wall.

Budding: A form of asexual reproduction in which an outgrowth (="bud") developing on a parent yeast cell detaches to produce a new individual.

Cell Wall: The rigid outermost cell layer found in plants and certain algae, bacteria, and fungi but characteristically absent from animal cells.

Cellulose: A complex carbohydrate, (C6H10O5)n, that is composed of glucose units, forms the main constituent of the cell wall in most plants and some fungi.

Chitin: A complex, primarily nitrogen-containing carbohydrate, which forms the principal component of arthropod exoskeletons, ex. insects, and the cell walls of most fungi.

Clone: An organism descended asexually from a single ancestor, such as a plant produced by bulbs or fungi by asexual spores.

Conidium (plural: Conidia): Asexually produced spores produced on conidiophores.

Conidiophore: A specialized hypha on which conidia are borne.

Dimorphic: Fungi that have both a yeast and mycelial phase.

Eukaryote: Organisms whose cells contain a distinct membrane-bound nucleus.

Facultative parasite: An organism that primarily derives it nutrition as a saprobe, but may become a parasite if the opportunity presents itself.

Facultative saprobe: An organism that primarily derives its nutrition as a parasite, but may become a saprobe if the opportunity presents itself.

Fission: An asexual reproductive process in which a unicellular organism divides into two or more independently maturing daughter cells.

Fruiting body: A specialized spore producing structure found especially in fungi.

Heterotroph: An organism that cannot synthesize its own food and is dependent on complex organic substances, of other organisms, for nutrition.

Hyphae (sing: Hypha): Threadlike filamentous fragment of the mycelium of fungi.

Mitosis: The division of the nucleus, which results in the formation of two new nuclei. The two nuclei are identical and contain a complete copy of the parental chromosomes.

Mycelium: The vegetative part of the fungus that consisting of a mass of branching hyphae.

Parasite: An organism that derives its nutrition and is sheltered on or in a different organism (=host) while contributing nothing to the survival of that organism.

Rhizomorph: An aggregation of mycelial strands that forms a root-like structure formed in some fungi.

Saprobes: An organism that derives its nutrition from nonliving or decaying organic material.

Yeast: Unicellular fungi that reproduce asexually by budding (a small outgrowth, or "bud", on the cell's surface increases in size until a wall forms to separate the new individual) and fission.

Questions to Think About

1.      Why are facultative saprobes or facultative parasites more of a problem, as pathogens, than those that are obligate parasites?

2.    Even though fungi are all around us and are very common, people are generally unaware of their existence. What are some reasons that you can give for this lack of awareness? 

3.    Certain organisms are no longer considered to be fungi that were previously classified as such. Name these types of organisms and give the reasons that they have been excluded.

4.    How does sexual and asexual reproduction differ? What are the advantages and disadvantages of both?

5.    What are some common misconceptions about fungi?

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