BIS 2C final final

Fungi and the tree of life

What group of eukaryotes does fungi belong to?

Fungi are a part of Opisthokonts, a group a eukaryotes defined by having a single, posterior flagellum.
- Fungi provably evolved from a unicellular protist with a flagellum

Defining feature of fungi

Absorptive Heterotrophy: when fungi release enzymes to environment and then bring foods in
- Humans possess a tube that releases enzymes as we ingest food but fungi do not possess such a tube

What do fungi spend most of their lives as?

Fungi spend most of their lives as active foragers; many (but not all) are saprobes that feed off of dead or decaying organic material

What are most fungi recognized by?

Fungi are most recognized by mushroom structures, but this only one stage of their life cycle, and most of them are microscopic

General biology of fungi

Mycelium is the main fungal body and is composed of a group of hyphae, which are just one cell

Types of hyphae

1. Septate hyphae: has cell wall between segments
2. Coenocytic hyphae: multiple nuclei, no cell wall between segments
3. pseudohphae (yeast cells)

Cell wall of hyphae

Contains chitin, which makes the cell wall tough and impenetrable against osmotic pressure

What does a hyphae have to do with absorptive heterotrophy?

Enzymes are secreted outside the HYPHAE and nutrients and absorbed across the CELL MEMBRANE.

What are the advantages/disadvantages of the fungal body plan?

1. Most cells are in direct contact with the environment
2. It allows for efficient absorptive nutrition
3. Susceptible to desiccation (if environment is not moist)

Yeast

A unicellular fungus that are easy to culture, grow fast, can be maintained for long period of time and inexpensive. It is not a monophyletic group.

Fungi as Decomposers

Fungi are decomposers, which break down dead organic matter essential for nutrient cycling; so, dead plant material is continuously recycled

Fungi as parasites: chytrids

- Chytrids can be parasitic
- Possess flagellated spores and gametes that allow them to spread more readily in aquatic and marine habitats
- Contributing to global decline of amphibians

Fungi as parasites

Fungal hyphae invade host tissues
1. Parasitic mildew
2. Parasitic action of haustoria infects plants
3. Toenail fungus infects toes

Fungi as predators: Nematophagous fungi

The nematophagous fungi forms rings large enough to fit nematoads. If a nematoad enters a ring, the ring constricts, trapping the nematoad then invading and digesting the body

Fungi as mutualists

- Plant provides sugars to the fungus
- Fungal partner provides water, minerals via massive increase in surface area in roots and protection

Arbuscular Mycorrhizae fungi-plant symbiosis

Mycorrhizae is a fungi associated with roots of plants
- 400 mya- an arbuscule was found inside a fossilized Devonian plant

Fungi as Mutualists: Lichen

Lichen is composed of a fungus and photosynthetic microorganisms ( algae and/or cyanobacteria) and are capable of surviving harsh environments (dry, lacking nutrients, difficult to colonize like a rock)

Lichen symbiosis

Most lichen forming fungi are obligately dependent on their photobiont (algae and/or cyanobacteria).
- Limited amount of photobiont species for lichen symbiosis
Nearly all photobionts are NOT obligately dependent on the lichen symbiosis.

Leafcutter ants

As foragers, they carry leaves to the nest, chew them into a mulch, then use it to cultivate a fungus that breaks down toxins in the leaves and allows it to swell with proteins and sugars. The ants also carry a microbe that acts an antibiotic, killing the weed fungus and allowing the right fungus to be cultivated. This is a mutual obligate relationship.
- First form of agriculture dating back 50 mya
- Monophyletic group

Fungi in food

- Fungi integral parts of food like cheese and bread
- Fermented beverages and sauces use strains of yeast
- Ales require top yeast ferments at 14-23 C
- Lager beers require bottom yeast ferments at 6-12 C
- Used as synthetic meat substitutes; mycoproteins discovered in a soil sample
- some fungi are toxic and will cause hallucinations if consumed

Fungi in Statins

Akira Endo discovered a statin produced by fungi which was then medically replicated; for instance, Lipitor is a biosynthetic statin

Climate change and fungal diseases

Climate change has increased a number of fungal diseases; for instance, a rapid increase in Criptococcus (HIV), which causes migraines, double vision, lowered neurological control and ultimately death

Mycotoxins

Mycotoxins are secreted by fungi and can impact human health through secondary infection or chronic exposure; for instance, can cause hallucinations

Aflatoxin

Aflatoxins are mycotoxins produced by Aspergillus flavus can have lethal effects on animals, especially those without a diverse diet, such as DNA damage and cancer. It is also the strongest carcinogen.

Aspergillus Phylogeny

Aspergillus is also used to produce soy sauce, sake and more. However, it is a single species "A. oryzae", different from the toxic A. parasiticus species.

Industrial use of Fungi

Fungi function as absorptive heterotrophs and so are useful "factories" for the biosynthesis of drugs, enzymes, acids and alcohols. Basically, chemicals are produced by fungal species; for instance, citric acid is produced by Aspergillus niger (black mold) fungi

Primary Metabolites

Primary metabolites are produced during active cell growth
- In the beginning, the food is inoculated with the fungal organism. As the organism consumes the food and grows, the primary metabolite is released from the cell

Secondary metabolites

Secondary metabolites are produced near the onset of stationary phase
- Sugar is consumed and cells are growing but no metabolite is being produced during the active cell growth because it is not necessary for the organism. Once cell stops growing, then the secondary metabolite is released. This is because there is competition for food so the fungus produces the secondary metabolite in order to prevent bacteria from eating the food.

Fungi in biofuels

Fermentation of sugarcane molasses produces 12% ethanol. The ethanol from corn requires a complex starch breakdown.

Cultural use of fungi

Human use lichens to create dyes; humans pee on lichen to change the color and reproduce it synthetically

Phylogeny of Fungi

The phylogeny includes microsporidia, chytridiomycota, zygomycota, glomeromycota, ascomycota, and basidiomycota. However, relationships among fungi are not well understood since, for a long time, fungi were classified according to their sexual reproduction but many fungal sexual processs remain unknown. Also, polytomies exist in chytridiomycota and zygomycota.

Microsporidia

Intracellular parasite that use a polar tube to infect hosts; eukaryote that lacks a mitochondria but have mitosomes.

Chytrids

The only group of fungi that retain swimming spores, they have gametes with flagella and are mostly aquatic. They contribute to the global amphibian decline.

Zygomycota

Coenocytic hyphae and zygospore is only diploid cell; the most common is Rhizpus which causes bread mold

Glomeromycota

A group of fungi that form arbuscular mycorrhizae with plants in which the coenocytic hyphae penetrate plant cells. They provide multiple benefits to plants, including
1) Protection from root pathogens
2) Increased longevity of fine roots
3) Protection from heavy metals in soil
4) Linkages between plants
However, NO sexual reproduction observed

Dikarya (Ascomcytoa and Basidiomycota)

A vast fungal group that includes about 98% of all described fungal species, including species that form typical mushroom fruiting bodies and in which dikaryotic cells are formed (n+n).

Ascomycota

Septate hyphae, short dikaryon stage, formation of asci (ascus with 8 spores), meiosis + mitosis, cup-like fruiting bodies which consist of both dikaryotic and haploid hyphae, largest group of fungi (2/3 species)

Basidiomycota

Septate hyphae, long dikaryon stage, formation of basidia with 4 spores on a club, meiosis, gills
- Some fruiting bodies are highly specialized like shelf fungi, coral fungi, and giant puffball fungi
- Some have no fruiting bodies like smut fungi, rusti fungi

Chytrids life cycle

The multicellular haploid chytrid (n) produces a female gametangium and a male gametangium. The gametes (n) fuse together through karyogamy to make a diploid zygote (2n) . The zygote divides mitotically to create a multicellular diploid chytrid (2n). The diploid chytrid undergoes meiosis to create spores (n) that mitotically to create the multicellular haploid chytrid.
- two multicellular adult stages
- meiosis + mitosis
- karyogamy

Innovation in Fungi

Plasmogamy precedes karyogamy starting in Zygomycota

Plasmogamy

Fusion of cells (plasma membrane) into one cell

Karyogamy

Fusion of nuclei

Coupled vs Uncoupled Plasmogamy & Karyogamy

Sexual life cycle of Zygospore fungi (conjugating fungi)

In sexual reproduction, two compatible haploid mycelia identify each other. Where the two mycelia meet, gametangia are formed, each containing haploid nuclei. The wall between the gametangia dissolves and plasmogamy occurs. The nuclei fuse to form diploid zygospores within the zygosporangium. A sporangium germinates from the zygosporanigum and produces haploid spores via meiosis. These haploid spores can germinate and grow into new mycelia

Second Innovation in Fungi

Dikaryon stage, septate hyphae; only in Dikarya

Dikaryon stage

Long period where there are two separate nuclei that combine to form a single diploid cell

Why does karyogamy occur in bad conditions?

To increase genetic diversity so that maybe one pair of genes will succeed in the harsh environment

Sexual life cycle of club fungi (Basidiomycota)

In the club fungi, the products of meiosis are borne on the surface of the gills on specialized hyphal tips called basidia. Fruiting bodies consist solely of dikaryotic hypha, and the dikaryotic phase can last a long time

Sexual life cycle of the sac fungi (Ascomycota)

An additional mitosis allows for the development of 8 spores

Similarities between Ascomycota and Basidiomycota

1) Spore formation happens by karyogamy followed by meiosis
2) Life cycle w/ 3 stages: haploid, dikaryotic, and diploid
3) Hyphae are never diploid (2n); they are either haploid (n) or dikaryotic (n+n)

Differences between Ascomycota and Basidiomycota

1) Duration spent in dikaryon stage varies: short lived in Asco, months or years in Basidio
2) Reproduction mainly asexual in Asco, reproduction mainly sexual in Basidio.

Key to understanding generalized fungal life cycle

1) Haploid phase
2) No gametes
3) Spors

Fruiting body diversity of Ascomycota

Includes edible fungi like morels and truffles, brewer's yeast ( yeast do not have fruiting bodies)

Molds as Ascomycetes

Molds are ascomycetes that rarely undergo sexual reproduction in their life cycle since they create tons of spores that will eventually grow in a suitable environemnt

White-nose syndrome

Known as pseudogymnoASCUS destructans, it grows around mouth, nose and wings of hibernating bats. When the bats are hibernating, both body temperature and immune system is depressed, making them susceptible to fungal infection. This severe decline of bats corresponds to a severe increase of insects.

White-nose syndrome on phylogenies

Pseudogymnoascus destructans has no close relatives in North America and populations have little genetic variation (clonal). P. destructans does occur in Europe though but does not cause bat mortality due to built-up resistance from the past.

Ascomycota vs Basidiomycota

Enclosed fruiting bodies in Dikarya

Enclosed fruiting bodies (truffles, puffballs) have evolved multiple times within Basidiomycota and Ascomycota
- On the surface, fruiting bodies thrive in moist, humid environment
- In dry environments, the fruiting bodies become subterranean to prevent desiccation

Subterranean fruiting bodies

Largely dispersed by animals. Examples include:
1) Flying squirrel consumes the Rhizopogon (Basidiomycota), poops it out and is used as fertilizer to disperse spores
2) Pigs detect the Tuber (Ascomycota) that are buried within the ground since the truffles release a pheromone (Adrostenol) that female pigs scent, the same pheromone male pigs release to attract female pigs

Bird's Nest Fungi

Dispersed by a combination of water (splash cups) and animals; rain drop releases spores

Pilobolus cannonball fungi

At the tip of the hyphae, light is on the sporangium and the water pressure inside the sporangium grows, ultimately building up until the water explodes, releasing spores at a high pressure.

Metabolism

Fungal metabolism is diverse, most can degrade and recycle carbon and easy substrates while only a few species can degrade sugars and other more complex nutrients like hemicellulose cellulose (nutrient recycling)

Easy Substrates: Metabolism

Easy substrates fungi can degrade include fruit, flesh, leaves, cotton and paper

Complex Substrates: Metabolism

Some fungi can degrade wood, which is made up of:
1) cellulose: requires one enzyme to separate molecule
2) hemicellulose: requires few enzymes to break apart glyosidic bonds in the linear structure
3) lignin: requires specific chemical compounds capable of wiping out polymer

Brown rot fungi

Basidiomycete, capable of breaking down cellulose (and hemicellulose) but not lignin so the resulting organism is just brown-colored sructure

White rot fungi

Breaks down cellulose, hemicellulose, AND lignin via the enzyme laccase oxidase to degrade aromatic ring. Common in all types of trees

Basidiomycota Phylogeny

Evolution of a lignin-degrading peroxidase was one of the main determinants of diversification
- white rot fungi evolved during the permian period

Carboniferous period (300-360mya)

Lycophytes and early conifers abundant and coal deposits were formed from these taxa

What is the life cycle of animals?

Animals have a diplontic life cycle, meaning eggs and sperm are produced via meiosis and these gametes are the only haploid phase.

What taxa is sister to animals?

The choanoflagellates are sister to animals, meaning that they are each other's closest relatives in the major group Opisthokonts. They are characterized by their flagellum that is single and posterior, if present. Their common ancestor is the protist.

Choanoflagellates

1) small group of aquatic protists, unicellular or colonial
- not multicellular because there's no specialization of the cells or interdependency between the cells
2) collar cell: ovoid in shape, with a collar of microvilli (tentacles) surrounding the single flagellum
3) movement of flagellum leads to locomotion and feeding (bacteria trapped on collar)

Evidence that choanoflagellates are sister to Metazoa

1. Collar cells: similarity in morphology between sponges (choanocytes) and in metazoans
2. Choanoflagellates have homologues of metazoan cell signaling and adhesion genes, and these genes are not found in other eukaryotes
3. DNA sequence data support choanoflagellate + metazoan clade

Characteristic features of Metazoa

1. Multicellular organism with specialization, communication, and interdependency
2. Heterotrophs
3. Food ingested, followed by extracellular digestion in gut
4. Diplontic life cycle
5. Distinctive male gametes: spermatoza
6. Distinctive development: zygote --\> blastula --\> gastrula
8. Distinctive cell junctions unique to metazoans
9. Collagen and proteoglycans in the extracellular matrix

Four Unique Synapomorphies of Metazoa

The four unique synapomorphies include spermatoza, blastula, septate junctions, and collagen

Non-unique synapomorphies of Metazoa

Diplontic life cycle and multicellularity

Ancestral condition of Metazoa

Heterotrophy

Ambiguous synapomorphies of Metazoa

Extracellular digestion in a gut first evolved in Ctenophores and evolved a second time in Cnidarians

What is bilateral symmetry?

A single plane divides the animal into left and right mirror-image halves

Characteristics of bilaterally symmetrical animals

1. Distinct anterior (front) and posterior (back) ends
2. Cephalization
3. Segmentation

Cephalization

Differentiation of anterior end into a head, with concentration of sensory organs

Segmentation

Serial repetition of body parts in well-defined segments

Animal development

The zygote undergoes cleavage and forms a hallow ball with liquid inside known as the blastula, which is a characteristic of all animals. The blastula then undergoes invagination to form cell layers known as the gastrula.
(Zygote-\>Blastula-\>Gastrula)

Gastrulation

The formation of cell layers by invagination (in-pocketing) of blastula to form gastrula. Certain animals form two cell layers or three cell layers.

Diploblastic animals

Two cell layers formed, ectoderm and endoderm separated by gel-like mesoglea; found in the Cnidarians and Ctenophores

Triploblastic animals

Three cell layers formed, including the ectoderm, endoderm, and mesoderm; found in protostomes and deuterostomes

Sponges (Porifera)

Including demosponge, glass sponge, and calcareous sponge

Sponge features

- Asymmetrical gutless animals
- Aquiferous system: branched water canals
- Differentiated cell types but no true tissues or organs
- Cells arranged in gelatinous matrix (mesohyl) with collagen and usually spicules (skeletal elements)

Aquiferous System

Water flows into numerous incurrent pores known as ostia, goes through internal chambers, and exits out of one or more excurrent pores known as oscula; the system is propelled by movement of flagella of many choanocytes

Aquiferous System Variations

The aquiferous system varies in complexity among different kinds of sponges; for instance, the asconoid sponge has a simple aquiferous sytem system while the leuconoid sponge has a complex aquiferous sytem

Spicules of Sponges

The glass sponges and demosponges have siliceous spicules. The calcareous sponges have spicules of calcium carbonate.

What clade of sponges is most diverse?

The demonsponges are the main group of sponges with the most diversity

Spongin

A complex network of collagen that make up the skeleton of some demosponges that do not have spicules. They are used as bath sponges.

Sponge features: biology

- All aquatic, mostly marine
- 8000 species (7000 species of demosponges)
- Adults sessile, larvae motile
- Mostly filter feeders on microscopic particles (bacteria, organic detritus, etc.), captured on microvilli, digested intracellularly which is in contrast to most animals that involve extracellular digestion

Reproduction in sponges

Asexual: through "budding" or fragmentation
Sexual: most sponges are hermaphrodites (single sponge produces both gametes) but does not self-fertilize due to possibility of inbreeding

Sexual reproduction in sponges

Most sponges are hermaphrodites but do not self-fertilize, their sperm and eggs are produced at different times from choanocytes or other cells in the sponge body. The sperm is released into the environment via the aquiferous sytem and then enter neighboring egg-containing sponges. The embryo is retained on the parent sponge (parental investment) then released as swimming (ciliated) larva, which then settles and develops into its sessile adult form

How does sponge sperm reach the egg?

The sperm crosses the cellular barrier of choanocytes, enters the mesohyl, locates the egg and fertilizes it

Differentiated cell types in sponges

Including choanocytes, pinacocytes, and amoebocytes but no trust issues or organs
- Choanocytes are most important because they resemble what we see in Choanoflagellates

Origin of guts, nerves, muscles

Ambiguous origin in Ctenophores and evolves a second time in Cnidarians but is absent from sponges

Sponge Dominance

Sponges are often dominant organisms in marine environments and do not suffer from predation