Fungal Diversity & Microbiome Lecture Notes

Explain what fungi have in common, to which domain they belong, and their role in ecosystems.
Describe similarities and differences between fungi and animals.
Describe the body of multicellular fungi using terms such as hyphae, mycelium, and sporangium.
Describe at least two familiar fungi with respect to body form, cellular structure, ecological niche, and metabolic adaptations.
Describe the unique reproductive adaptations of fungi.
Describe microbiomes and their positive and negative effects on multicellular organisms.

Eukaryote supergroup Opisthokonta:
- Includes certain protists, Kingdom Animalia, and Kingdom Fungi.
- Similarities with animals include storing surplus food as glycogen and being heterotrophs.
Fungi originated in aquatic habitats from protists related to Nuclearia, an amoeba that feeds by engulfing cells.
Cryptomycota: Earliest-diverging modern fungi group.

There are over 100,000 identified species of fungi.
They can be unicellular or multicellular.
Many fungi decompose dead organisms, while some are parasitic:
- They break down large molecules and absorb the resulting small molecules.

The largest individual organism in the world by area is a fungus located in Malheur National Forest, Oregon, with underground mycelium covering 2,200 acres.

Question: Are fungi a monophyletic clade?
Fungal taxonomy includes various groups:
  - Chytridiomycota (Chytrid fungi): Earliest diverging group.
  - Zygomycetes (approximately 1,000 species).
  - Glomeromycetes: 160 species, includes AM fungi.
  - Ascomycetes (approximately 65,000 species).
  - Basidiomycetes (approximately 30,000 species).
Septate hyphae are found in Ascomycetes and Basidiomycetes.
A brief overview of critical innovations includes beneficial associations with photosynthetic organisms and the loss of flagella in some fungi.

Fungal cell walls typically use chitin, a polysaccharide that provides strength.
This composition is important for the transition from feeding by phagocytosis (engulfing food) to osmotrophy (absorption of nutrients).

Fungi are absorptive heterotrophs:
- They secrete enzymes into the soil to break down organic matter and absorb hydrolyzed monomers needed for growth through osmotrophy.
Some fungi produce antibiotics like penicillin to outcompete bacteria in shared habitats.

The main body of fungi is a mycelium composed of haploid hyphae.
- Hyphae can be aseptate (lack septa) or septate (with septa).
- The structures associated with reproduction include spore-producing structures.
Mycelia can grow rapidly when food is plentiful:
- Hyphae extend their tips through substrates, maximizing the surface area for absorption.
- Importance of osmosis and cytoplasmic streaming in nutrient uptake.

Fungi can reproduce asexually through budding or spores called conidia.
Sexual reproduction involves mycelia pairing to form a zygote, which then divides via meiosis to produce spores.
Advantages of each reproduction method vary and include genetic diversity from sexual reproduction and rapid population growth from asexual reproduction.

The life cycle includes:
- Asexual reproduction: spores are produced and dispersed.
- Sexual reproduction: mycelium undergoes plasmogamy (fusion of cytoplasm) leading to a heterokaryotic stage before karyogamy (fusion of nuclei).
Examples like Rhizopus stolonifer (bread mold) illustrate complex mating types and reproduction processes, with detailed structures such as zygosporangium and gametangia.

Glomeromycetes (AM fungi) typically form symbiotic relationships with plant roots through mycorrhizal associations, essential for plant terrestrial adaptation.
More than 80% of terrestrial plants engage in mycorrhizae, where fungal hyphae extend beyond root systems, providing increased access to water and minerals while receiving photosynthetic products in return.

Many fungi have pathogenic effects on plants, animals, or insects, causing significant economic impacts (e.g., corn smut and white-nose syndrome in bats).

Definition: Microbiomes are particular assemblages of microbes and genes in defined environments, consisting of diverse species of bacteria, archaea, fungi, protists, and invertebrate animals.
They communicate chemically and electrically, presenting challenges for identification. Genetic differences are often the basis for classification.

Microbiomes affect animal health positively and negatively:
- Dental plaque is detrimental.
- Gut bacteria in infants assist in digestion.
Microbial roles include recycling plant biomass in termite guts, medical applications of gut microbes in tunicates, and the concept of fecal transplants for improving gut health.

Study hypothesis: Microbiomes from undernourished children impair the growth of mice.
Methodology includes analyzing fecal samples and introducing them into germ-free mice to assess weight changes over time post-transplant, aiming to understand how gut microbiota affects growth.

Viruses are generally not considered alive as they lack cellular structures and cannot reproduce independently.
Antibiotics are ineffective against viruses. They require a host cell to replicate, which involves several steps: attachment, entry, integration into the host's DNA, synthesis of viral components, assembly, and release.

Viruses can have simple structures comprising spikes for infection, nucleic acid (DNA or RNA), and protein coats (capsids).
For example, the lytic and lysogenic cycles of bacteriophages mark different strategies of virus propagation.

HIV infection involves interactions with helper T cells and multiple phases from entry to budding off new viruses.
Emerging viruses, such as SARS and COVID-19, can arise from existing pathogens and might become increasingly prevalent due to mutations.

Vaccination is essential for health, leveraging exposure to antigens to build immune memory.
Herd immunity refers to the phenomenon where a significant portion of a population becomes immune, thereby reducing disease spread and potentially eradicating diseases, as seen with smallpox.

Measles, a significant health threat, highlights the need for high vaccination rates (95% for herd immunity) due to rising incidence linked to decreasing vaccinations.
Other viral diseases like mumps and rubella showcase the importance of vaccination in preventing complications during pregnancy or infections.