Fungi - Organismal Diversity - Lecture Slides, Slides of Biology

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Fungi

Fungus Classification

• Linnaeus classified fungi as plants, part of his basic division of the world into the Plant Kingdom and the Animal Kingdom. If is wasn’t obviously an animal, it must be a plant. - Linnaeus invented the Genus species binomial naming system and the basic classification scheme we still use. - He didn’t draw phylogenetic trees: the first one was done by Darwin.
• The “Five Kingdom” model of Whitaker (1969) put the fungi into its own separate kingdom.
• Modern DNA-based techniques show that the fungi are a monophyletic group that is clearly different from plants or animals. - fungi are closer to animals than to plants. - However, oomycetes and slime molds are no longer considered fungi: only distantly related.

Fossil Fungi

• Fungi don't fossilize very well : no hard parts.
• Estimated divergence time from animals based on DNA: 1.6 billion years. Proterozoic - Earliest fossils with fungal features: about 1.4 billion years ago
• Fungus fossils become common starting in the Devonian epoch (in the Paleozoic Era, 400 million years ago.
• It is thought that fungi invaded the land during the Cambrian period, at the same time as animals, and well before land plants got past the bryophyte (moss) stage. Fungi may have been the dominant stationary organism on land in the early Paleozoic Era.
• There seems to have been a large spike in fungal spores just after the Permian extinction event. (It's controversial, and we don't know what caused the Permian Extinction.)

Rhynie chert, showing fungal hyphae invading plant cells. Tissues are very well preserved. A sudden rise in highly mineralized hot springs waters fossilized a plant community almost instantaneously.

How Many Species of Fungus?

• Most fungi don't look very different from each other, or very much like

anything at all. Thus, our estimates of species number could be way low.

• Most fungi live on land. The chytrids are the only major group that lives

primarily in the sea.

• But there are a lot of microorganisms in the sea that we know nothing about.
• After all that hedging: let's say there about 100,000 known species, with

estimates of 1.5 million species total.

Yeasts, Molds, Mushrooms

• These are all “classifications of convenience”. They

are not monophyletic groups and don’t have much

use as scientific terms.

• A yeast is a single-celled fungus. By far the most

important yeast for humans in Saccharomyces

cerevesiae , which is used to make most of our

alcoholic beverages as well as to make bread rise.

But, there are many other species that can be

called yeasts.

• A mold is a fungus growing as a mass of hyphae (a

mycellium), generally someplace we don’t want it.

• A mushroom is the fruiting body of a fungus that is

mostly living underground. Mushrooms are

produced by two of the major fungal groups, the

Ascomycetes and the Basidomycetes.

Hyphae

• Multicellular fungi are composed of filaments called hyphae (sing. = hypha) that form a mat called a mycellium. Hyphae are just 1 or 2 cells thick, so very thin compared to a plant root (5-10 μm in diameter). - A mushroom is composed of hyphae whose growth has been regulated to produce the characteristic shape.
• The hyphae grow from the tip, branching frequently. They can thoroughly explore a volume of space and find all available resources in it. - http://www.youtube.com/watch?v=X77ae6xhK3s
• Cell nuclei in the hyphae are sometimes divided into separate cells, or they can be all together in one big mass of cytoplasm with no divisions between cells. - Septate fungi have separate cells. The dividers are called septa, and they still allow a lot of material flow between them. - Coenocytic (or aseptate) fungi have all the nuclei in an undivided mass.

Hydrostatic Pressure and Fungal Growth

• Because of the cell wall, hydrostatic

pressure can build up inside the

hyphae. This allows them to exert

force, which is how they penetrate

living tissues.

• A special part of a hypha forms, called

as appresorium. It has a thick cell wall

(to resist pressure) around all but the

side facing the host. Hydrostatic

pressure builds up, and an outgrowth

of the appresorium penetrates the

host’s surface layer.

• The fungus can then grow inside and

feed on the host.

From Bastmeyer et al., 2002. Ann Rev. Biophys. Biomol. Struct. 31: 321-341.

Chitin

• Chitin is a polysaccharide: a large molecule

composed of many sugar subunits. It is similar

to cellulose, and to the peptidoglycan cell wall

of bacteria.

• The sugars are rings containing 6 carbon atoms.
• Chitin cells walls are a major defining characteristic of the monophyletic Fungi kingdom. Water molds (oomycetes) and slime molds have cellulose cell walls and are considered protists instead.
• Chitin is also used for the exoskeleton of

insects and other arthropods.

• Cell walls are rigid and not easily digested.

Peptidoglycan (without the connecting peptides). Two different sugars alternating

Cellulose. Each sugar is a glucose.

Chitin. Each sugar is a glucose derivative called N-acetyl glucosamine

• Sequencing of the Aspergillus niger

genome showed that it secretes over

200 different enzymes into the

environment.

• A. niger is used to produce industrial enzymes
• From Wikipedia: “In the heyday of the opium trade, chandoo opium, which was meant to be smoked, was made by long term fermentation of A. niger and other molds on raw opium.”
• Types of enzyme:
• carbohydrate (=polysaccharide);
• pectin, cellulose, and lignin (components of the plant cell wall);
• Proteins (proteases)
• Lipids (lipases)
• other complex compounds.

Genomics of Fungal Secretion

From Braaksma et al. (2010) BMC Genomics 11:584.

Reproduction

• Reproduction can be either sexual or asexual.
• Asexual reproduction produces offspring that are genetically identical to

the parents. The offspring are produced by the cell division mechanism of

mitosis.

• Asexual reproduction can be as simple as breaking off a piece of the parent organism and moving it to a new location.
• More frequently, the parent forms spores , which are single cells packaged in a tough coat. Spores are dispersed to new locations. They are able to survive harsh conditions, and then germinate (sprout) when they find favorable conditions.
• Sexual reproduction produces offspring that are genetically different from

their parents and each other. Sexual reproduction uses the cell division of

meiosis and the joining of cells from two parents ( fertilization ).

• The basic idea is that by mixing genes from two different parents, better combinations are formed. That is, some of the offspring are more fit, better adapted to their environment, than the parents. This is the process of natural selection.

Reproduction in Fungi

• Fungi spend most of their life cycle as

haploids. Fertilization is followed immediately

by meiosis, so the diploid stage is just one cell.

• This is the opposite of animals like humans: we are diploid most of our life cycle, and are only haploid for the 1 cell gamete stage.
• Most plants are similar to us; diploid except for a very short haploid phase.
• All fungi produce asexual spores : this is the main way fungi reproduce. There can be more than one type of asexual spore produced at different stages of the life cycle, especially in the rusts.
• Like all eukaryotes, sexual reproduction is

common in the fungi , but not all do it.

• Some species have never been seen to reproduce sexually. They are called imperfect fungi.

Plasmogamy and Karyogamy

• When they mate, one cell from each individual

merges together to make a single cell. This is

called plasmogamy , and the result is a dikaryon :

two cells in the same nucleus. That is, the

cytoplasm of the cells fuse together, but the

nuclei remain separate.

• This mean the cells are not diploid, which means having 1 nucleus with two copies of each chromosome.
• In human fertilization, the sperm and egg nuclei fuse almost immediately to form a diploid nucleus.
• The fungus can live and grow for a long time as a

dikaryon. Eventually, something triggers the

process of karyogamy : the nuceli fuse into a

diploid cell. This cell then undergoes meiosis to

produce offspring.

Nuclei in a dikaryon fuse to form a diploid nucleus, which then undergoes meiosis to form 4 haploid nuclei.

Imperfect Fungi

• Some fungi have r been seen to reproduce sexually.

These have been classed as “imperfect fungi”, and even

been put into their own phylum. However, the imperfect

fungi are not monophyletic, and aren’t recognized as a

distinct phylum.

• They don’t have the reproductive structures used to classify other fungi.
• Some examples: the athlete’s foot fungus and the

Penicillium species that produce penicllin and also are

used to make cheese

• DNA sequencing can be used to determine their close

relatives among the sexual fungi. However, this hasn’t

been done with many of them.

• In some cases, sexual reproduction hasn’t been seen

because no one had looked hard enough. In several

cases, two different imperfect fungi were found to be the

same species in different stages.

• Asperigillus and Emericella = same species

Secondary Metabolites

• All living cells contain the same four basic groups of chemical

compounds :

• 1. Nucleic acids (DNA and RNA). Genetic information
• 2. Lipids. (fatty acids) Cell membranes and food storage
• 3. Carbohydrates (sugars, polysaccharides). Structure (like cellulose and chitin) and food storage (starch)
• 4. Proteins. (made of amino acids). Act as enzymes to convert chemical compounds and generate energy. Also structure, transport, and almost anything else that needs doing in the cell.
• Secondary metabolites are compounds other than the four basics that are not involved in the primary processes of growth and reproduction. They are made by specific groups of organisms, with lots of variation between species and larger groups. Many are for defense (poisonous) or attracting mates or pollinators (as in flowers).
• Especially in the fungi and plants: they can't move out of the way of a predator.
• Source of antibiotics, food flavors, medicinal (and recreational) drugs, etc.