Microbes, Protists, and Fungi Notes

Diversity of Microbes, Protists and Fungi

  • Overview of prokaryotes, protists, eukaryote origins, and fungi.

The Three Domains of Life

  • Three Domains: Bacteria, Archaea, Eukarya.
  • Illustrates the relationships between different groups within these domains like spirochetes, proteobacteria, cyanobacteria, planctomyces, bacteroides, cytophaga, thermotoga, aquifex, green filamentous bacteria, gram positives, entamoebae, slime molds, animals, fungi, methanosarcina, methanobacterium, halophiles, methanococcus, T. celer, thermoproteus, pyrodicticum, plants, ciliates, flagellates, trichomonads, microsporidia, and diplomonads.
  • Highlights the non-sister taxa relationship.

Early Life on Earth

  • Early Conditions: High UV radiation, anoxic environment.
  • Thriving Organisms: Deep ocean vents, caves, and extremophiles.
  • Microbial Mats: Found around hydrothermal vents.
  • Stromatolites: Fossilized microbial mats.
  • Cyanobacteria: Present in hot springs.

Evolution of Atmosphere

  • Anoxic Atmosphere: Dominated Earth for the first 2 billion years.
  • Anaerobic Organisms: Supported by the anoxic conditions.
  • Phototropic Cyanobacteria: Increased oxygen ((O_2)) in the atmosphere.
  • Ozone Layer Formation: (O2) led to (O3) (ozone) which absorbs UV radiation.
  • Aerobic Cellular Respiration: Allowed for more efficient ATP production.

Prokaryote Characteristics

  • Lack of Organelles: No membrane-bound organelles.
  • Genetic Material: Circular chromosome and plasmids.
  • Cell Walls and Capsules: Provide protection and aid in attachment.
  • Shapes: Common bacterial shapes include cocci, bacilli, and spirilla.

Cell Wall Differences

  • Gram-Positive vs. Gram-Negative: Major classification based on cell wall structure.
  • Peptidoglycan: Relative position in the cell wall is key.
  • Archaeal Cell Walls: Lack peptidoglycan.

Biofilms

  • Microbial Communities: Mixture of prokaryotes and sometimes fungi.
  • Matrix: Film consists of secreted organic molecules for binding and protection.

Prokaryote Reproduction and Genetic Recombination

  • Binary Fission: Duplication of circular chromosome followed by splitting into daughter cells.
  • Transformation: Uptake of environmental DNA.
  • Transduction: Viral translocation of DNA from one prokaryote to another.
  • Conjugation: DNA (usually a plasmid) transfer via contact between prokaryotes.

Bacteria and Disease

  • Pathogenic Bacteria: Considered the exception rather than the rule.
  • Zoonotic Diseases (Zoonoses): Transmitted from non-human animals to humans.
  • Pandemic vs. Epidemic: Different scales of disease outbreak.
  • Examples: Bubonic plague (Yersinia pestis), Botulism (Clostridium botulinum), other foodborne illnesses like Salmonella, E. coli.

The Antibiotic Crisis

  • Antibiotic Target: Designed to target bacteria.
  • Overuse and Misuse: Incorrect use in humans and excessive use in agriculture.
  • Agricultural Use: 70% of antibiotic use is for enhancing production, not preventing disease.
  • MRSA: Methicillin (or multi-drug) resistant Staphylococcus aureus.

Beneficial Prokaryotes

  • Fermentation
  • Bioremediation
  • Commensalism & Mutualism
  • Digestion
  • Competition: Compete against pathogenic microbes.
  • Vitamin Production: Example includes Vitamin K.
  • Immune System Training

Eukaryotic Origins

  • Lynn Margulis: Proposed the Endosymbiotic Theory in the 1960s.
  • Theory: Mitochondria and chloroplasts originated from prokaryotes.

What’s a Protist?

  • Classification: Formerly a kingdom, now recognized as having multiple origins.
  • Cellularity: Usually unicellular, but not always (e.g., kelp).
  • Characteristics: Not plants, animals, or fungi, but include eukaryotic ancestors to these kingdoms.

Protist Characteristics

  • Habitat: Aquatic or moist environments, or parasitic.
  • Motility: Move by flagella, cilia, or pseudopodia.

Protist Feeding and Digestion

  • Feeding: Via photosynthesis and/or phagocytosis using food vacuoles.
  • Digestion: Occurs in lysosomes, waste expelled via exocytosis.

Protist Clades and Relationships

  • Clades: Divided into 6 monophyletic clades.
  • Uncertainty: Relationships among clades are still being researched.
  • Notable Relationships: Archaeplastida and Opisthokonta.

Pathogenic Protists: Humans

  • Malaria: Caused by Plasmodium falciparum.
    • Requires mosquitoes to complete its life cycle.
    • Transmission to human (injects sporozoites via bite).
    • Sporozoites enter liver and infect hepatocytes.
    • Liver cells rupture and merozoites released.
    • Intraerythrocytic cycle (asexual/symptomatic cycle).
    • Merozoites produce gametocytes instead (sexual cycle).
    • Transmission to mosquito (ingests gametocytes via bite).
    • Gametocytes mate, undergo meiosis.
    • Migrates through midgut wall, forms oocyst.
    • Sporozoites develop.

Pathogenic Protists: Humans

  • Trypanosomes (Trypanosoma sp.)
    • African sleeping sickness
    • Chagas disease

Pathogenic Protists: Plants

  • Downy and Powdery Mildew: Caused by Plasmopara viticola.
    • Devastated 19th-century French wine industry.
  • Potato Late Blight: Caused by Phytophthora infestans.
    • Led to the 19th-century Irish potato famine.

Beneficial Protists

  • Photosynthesis: Approximately 25% conducted by protists, including diatoms, dinoflagellates, and algae.
  • Zooxanthellae: Mutualistic relationship with coral.
  • Saprophytes: Decompose organic matter.

Fungi Overview

  • Classification: Eukaryotes in the Kingdom Fungi.
  • Diversity: 100,000 species formally described, likely over 1 million on Earth.

Fungi Characteristics

  • Evolutionary Relationships: More closely related to animals than plants based on modern DNA evidence.
  • Reproduction: Can reproduce asexually or sexually.
  • Spore Dispersal: Spores are wind-dispersed.
  • Decomposers: Essential for recycling nutrients in ecosystems.

Fungi Interactions

  • Mutualisms: Benefit both organisms.
    • Mycorrhiza: Mutualism between plant roots and symbiotic fungi (80-90% of all plants); aids in nutrient extraction from soil.
    • Lichen: Pioneer species that blanket large rocks and other exposed surfaces where most organisms can’t live.

Fungi and Humans: Benefits

  • Fermentation: Aspergillus, Lactobacillus, Saccharomyces
    • Soy Sauce
    • Cheese, Yogurt
    • Beer
    • Wine
    • Bread
  • Examples of food production through fermentation.

Fungi and Humans: Parasites and Pathogens

  • Mycoses: Fungal infections; typically cutaneous (on skin) but can be systemic (internal organs).
  • Examples: Ringworm (Trichophyton), Histoplasma

Fungi and Human Agriculture

  • Plant Pathogens: Many fungal pathogens attack plants and can damage human agriculture.

Fungi: Ecosystem Benefits

  • Nutrient Cycling: Critical role in nutrient cycling and the soil food web.
  • Ecosystem Base: Form base of ecosystems along with plants and other decomposers.