Chapter: Fungi

Fungi are actually a very diverse group of multicellular organisms. We commonly know them as mushrooms. But there are several other different types of fungi that exist. Just like animals they are chemoorganoheterotrophs. But where animals ingest their food, fungi feed by absorbing their nutrients straight from the source. They can absorb nutrients from living things, but their most important ecosystem service is when they consume dead organisms. If dead organism didn’t our forests would look a lot different. Instead of walking on soil, we would be walking on millions of years of fallen trees thousands of feet thick. Not only do decomposers provide us with clear hiking trails, perhaps more importantly the break down living things so they chemicals held within them can be utilized by the living. The dead sacrifice for the living. In terrestrial environments fungi are the dominant decomposer in the world. They recycle everything.

Mychorrhizal Associations

While their most important function is to break down tissues from dead organisms, fungi can also directly help the living. Mycorrhizas form a mutualistic relationship with the roots of most plant species. While only a small proportion of all species has been examined, 95% of those plant families are predominantly mycorrhizal. They are named after their presence in the plant's rhizosphere (root system). Myco means fungi. The study of fungi is mycology. And rhizae means root.This mutualistic association provides the fungus with relatively constant and direct access to carbohydrates, such as glucose and sucrose. The carbohydrates are translocated from their source (usually leaves) to root tissue and on to the plant's fungal partners. In return, the plant gains the benefits of the mycelium's higher absorptive capacity for water and mineral nutrients due to the comparatively large surface area of fungus thus improving the plant's mineral absorption capabilities. So in this way plants are able to extract more water from the soil.Some plant roots are incapable of taking up a very important chemical, phosphate. Phosphate is important in making nucleic acids an in ATP synthesis. The P stands for Phosphate. Without Phosphate, it would be like a baker trying to make bread without flour.The mycelium of the mycorrhizal fungus can, however, access these phosphorus sources, and make them available to the plants they colonize. So to summarize, the mechanisms of increased absorption are both physical and chemical. Mycorrhizal mycelia are much smaller in diameter than the smallest root, and thus can explore a greater volume of soil, providing a larger surface area for absorption.

 Fungi and the Carbon Cycle

The carbon cycle is simply how carbon moves through the global ecosystem. Recall from Bio 1, Carbon is captured by plants during photosynthesis. That carbon serves as the base of the food chain, and is the primary food source for all animals on earth. That carbon is also used by fungi.In their main function as decomposers fungi break down plant materials. In fact they are the only organisms really good at breaking down cellulose, the polysaccharides that make up the cell walls of plants. They are also the most dominant organisms on earth that break down wood. Wood is made of a very tough polysaccharide, lignin. In this process, fungi break down these polysaccharides into smaller organic compounds in order to obtain sugars, so that they may go through their life function. When those sugars are broken down in cellular respiration, CO2 is released into the air. That CO2 can then be reabsorbed by photosynthetic organisms, like plants. And the cycle starts all over. 

Economic Importance

You might not have realized it, but fungi are really important to humans. The first antibiotic that was ever discovered came from a fungus grown on an orange. And it is known as penicillin. You might wonder why fungi would have antibacterial properties. The answer is two fold. Just like we know bacteria can cause disease in humans, bacteria can also cause disease in fungi. A second reason is that many fungi and bacteria compete for the same resources. So if a fungus can emit a chemical that kills bacteria, it has a significant competitive advantage over them.

We use the fruiting bodies of fungi for food. You know them as mushrooms, and there are several varieties: portabello, crimini, and shitake. Fungi are essential to the fermentation process that we know and love. It weren’t for fungi, you would not be enjoying your Pinot Noir alongside that filet mignon. It would just be grape juice. Your bread would have the consistency of eating sticks. And your cheese would just be rotten milk. But to say our cuisine might be different is really an understatement. Fermentation was so important to human civilization, that without it farming as we know may have turned out a lot different. Before refrigeration, which only became common in the first world countries less than a century ago, cultivated food needed to be stored between harvests. And in most parts of the world, the harvest season only lasted once a year. So mess this process up, and you are up the creek without a paddle. And really there are only two ways to store vegetable and seed crops for a long time. First, you could dry out your crops. However, once they were dry, they had to stay dry. If any moisture came in contact with them they could be spoiled. So this method was common in dry climates. In wet climates, a more common way of preserving vegetables and seed crops was pickling.  This is the process of preserving food by anaerobic fermentation. This procedure gives the food a salty and sour taste and is very common in Asian and European cuisine. Think of kimchi in Korea, and sauerkraut in Germany. Both of these are cabbages that have been harvested and pickled which allows them to be preserved for months. The reason pickling allows vegetables to be preserved is that it drops the pH of the mixture to less than 4.6, which is sufficient to kill most bacteria.

Fungi can also wreck havoc on human crops. Corn is especially susceptible to disease caused by fungus. Here is an example of aptly named, corn smut. And when it hits a field, it can damage an entire farm full of corn. And unlike bacteria, fungi are much more difficult to kill with chemicals.

 Growth Forms

Fungi grow in two different ways: unicellular or multicellular. Unicellular fungi are called yeasts. The vegetative form of multicellular fungi are known as mycelia. They form an extensive network of a filamentous hairs that form a branching network that reach out to absorb nutrients from their food. Let’s take a closer look at a mycelium. The vegetative structure of fungi is known as its mycellium. It is the structure that obtains food. The mycelium is made up of very, very thin filaments called hyphae. Look at the picture on the right. The big L-shaped structure is actually two root hairs of a plant. The really thin strings are the hyphae of the mycelium of a particular type of fungus.

As a multicellular organism, fungal cells of an organism are able to communicate with each other using chemical messages. In this way, when a hyphae grows out and comes across a food source, it senses the food source and communicates with adjacent cells, and the organism will actually put more energy into growing toward the food source. Conversely, once a food source a fungus selectively dies back, and puts its resources into consuming another food source, or searching out its environment. Hyphae also make up the reproductive structures of fungi. We know them as mushrooms. Feeding hyphae of the mycelium are usually spaced apart, hyphae that make up the reproductive structures are very densely packed. This allows the fungus to have an upright growth form, which gives it the advantage of wind to disperse its reproductive units, spores. The cells of a hyphae are connected together end on end by structures known as septa. There are pores in the septa that allow material to flow between the cells. In this way, individual cells can share resources. This feature is what make fungi a multicellular organism and not necessarily a colonial organism. Not only are they connected together, they can share molecules between the cells.

Of all the multicellular organisms on Earth, fungi have the highest surface area to volume ratio. This means that they can reach out and touch a lot of surface area within a small volume. This makes them REALLY efficient at absorbing food from other organisms, either dead or alive. As we have seen, with any great advantage there is a trade off. And the trade off for having a really high surface area to volume ratio is that these organisms tend to dry out really, really fast.

In fungi, the one exception to this is there reproductive structures, spores. When fungi creates these reproductive structures, they encase them in a really thick and fleshy structure. This protects the offspring from drying out. This is so effective that spores can last in a dry environment for months to years. The mycelium, however, needs a constant supply of water to remain viable.

Reproductive Structures

Fungi can reproduce sexually or sexually. Asexual reproductive structures are known as spores; and sexual reproductive structures are known as gametes.

Chytrids

In a primitive group of fungi known as the chytrids, the reproductive structures can have whip-like flagella that allows them to move in water. In fact, these fungi are entirely aquatic. And they are the only example of motile fungal cells. A chytrid fungus is actually responsible for disease in amphibians: principally frogs. Discovered in 1998 in Panama, this disease is know to kill amphibians in really large numbers. In fact, this has been suggests as the principal cause for the world-wise amphibian decline. The mechanism is not completely understood, but it is thought that the fungus hardens the skins of amphibians which inhibit respiration, as amphibians breathe through their skin.

Zygomycetes

Zygomycetes are another group of fungi. They differ principally by their reproductive structures. These reproductive structures are called zygosporangia, which hold its spores. They are mostly terrestrial in habitat, living in soil or on decaying plant or animal material. The most common example of a zygomycete is bread mold. Its mycelium sends hyphae into the bread to absorb nutrients. In its asexual phase it develops bulbous black sporangia at the tips of upright hyphae. Each of the sporangia contain hundreds of spores. As in most zygomycetes, asexual reproduction is the most common form of reproduction. Sexual reproduction occurs when haploid hyphae of different organisms are in close proximity to each other. They connect and their nuclei fuse, forming a diploid zoosporangia. The spores in these structures are very resistant to environmental stress. When the conditions are right these structures germinate producing vegetative hyphae.

Basidiomycetes

Basidiomycetes are another group of fungi. They are differentiated from other fungi by their reproductive structures, known as basidia. Basidia literally translates as "little pedestals." And that is what they look like…little pedestals. They are specialized spore-producing cells that form at the end of the hyphae. In these cells, meiosis occurs making haploid cells…cells with a single set of chromosomes. Many of the commonly known fungi are basidiomycetes: mushrooms, puffballs, smuts, and rusts are basidiomycetes.

Ascomycetes

Ascomycetes are another group of fungi, with a different reproductive structure. Like the basidiomycetes reproductive structure is the basidia, the ascomycetes reproductive structure is the asci. Asci is a greek word for "sac." And that is what the reproductive structures of these fungi look like, sacs. The spores are held in sacs; on average eight spores per sac. To the layperson ascomycetes are not nearly as well known as the basidiomycetes. Perhaps the most well known (and definitely most useful), is brewer’s yeast. It is what we use to make bread rise, and to brew beer. While brewer’s yeast may be the most useful, the morel is highly coveted by mushroom hunters. But make sure you identify it correctly. Otherwise, you’ll be strapped to the toilet for a couple days.

Fungi Phylogenetics

Carl Linneaus is the father of the classification of life on Earth. He created a two branched structure used to classify all the organisms that were known of in his day. Those two branches were plants and animals. The microscope had yet to be invented. So single-celled organisms weren’t even thought about. Linneaus classified fungi as plants. The logic was that they grow from the ground just like plants. So then they must be plants. That logic held for centuries until the 20th century. Biologists started to say (hey, wait a minute) fungi are really nothing like plants. They replaced Linnaeus’ two domain system with a five kingdom system, elevating fungi from a mere subgroup to a kingdom all to its own. It was like a warrior becoming a king.

And then we could sequence DNA. Lo and behold fungi form a monophyletic group with animals. But we can’t just rely on DNA. Other bits of evidence also support this relationship. One that you may be familiar with. Fungal infections afflict humans. You may have heard of athlete’s foot. If you have ever got athlete’s foot, you know it is REALLY hard to get rid of. It is thought that the reason it is so difficult to get rid of is due to the close ancestry between humans and fungi. It is difficult to kill fungi without killing the human cells. Bacteria are a lot easier to kill because we can target specific genes that are not closely related to human DNA. Other evidence exists as well. The cell wall of fungi is made of the molecule, chitin. This is the same polysachharide that makes up insects’ exoskeletons, as well as your fingernails and hairs. Plants’ cell walls are made of cellulose. And just like animals, fungi store glucose as glycogen. Plants store them as polysachharides (like starch). 

Chytridomycota and Zygomycota

Okay, now here is where it really gets weird. You would think fungi that have distinct morphological forms of reproduction should represent morphological similarities in their ancestry. However, this is not the case with the chytrids and zygotes. Remember chytrids reproductive organs are mobile. They have flagella that are whip-like structures which allow them to move, and they have very thin coats (due to the fact that they live in an aquatic environment. Whereas sporangia in the zygomycota have very tough outer coats. This is an adaptation for reproducing in a terrestrial environment. Without it, the spores would quickly dry out and would not be viable.

However, the chytrids and zygomycetes do not form two unique monophyletic groups. They form a paraphyletic grouping that is very poorly understood. This means that the actual order of phylogenetic branching events with respect to their reproductive structures is not really known. It is though that that swimming gametes and the zygosporangium evolved more than once, or that both structures were present in an ancestor and lost in certain lineages.

 Basidiomycetes

Basidiomycetes are also known as club fungi, and they do form a monophyletic group, which all have basidia, which are pedestal on which sporangium sit. They are also dikaryotic, meaning that they have two nuclei.The interpretation of this is this group of fungi all stem from a common ancestor that must have had a basidium and two nuclei.

Ascomycetes 

The ascomycetes are also monophyletic. Remember these are known as the sac fungi. The all have a sac that are directly connected to the hyphae. These species are also dikaryotic, meaning they have two nuclei. So the interpretation of this group is that the ascus evolved once, and all the ascomycetes stemmed from that common ancestor. And you will notice that the basidiomycetes and the ascomycetes also stem from a common ancestor. This means that as a group, both the basidiomycetes and ascomycetes are monophyletic. And since both groups have two nuclei, we can infer that the common ancestor of both of these groups also must have been dikaryotic.