Bacteria and Archaea Overview

Bacteria and Archaea

• Prokaryotes are single-celled organisms lacking a nucleus and membrane-bound organelles.
• Bacteria and Archaea are distinct domains, differing in genetics, biochemistry, and cell structure.
• Gram stain classifies bacteria based on peptidoglycan layer thickness (Gram-positive vs. Gram-negative).
• Gram-negative bacteria have an outer membrane, potentially contributing to antibiotic resistance.
• Bacteria use flagella (various structures) for motility, along with gliding and twitching.
• Irreducible complexity, a concept in intelligent design, posits that complex structures couldn't evolve incrementally. Evolutionary biology explains this by co-opting pre-existing proteins.
• The F-factor (fertility factor) is a plasmid enabling bacterial conjugation (genetic transfer between cells).
• Bacteria acquire new genes through transformation, transduction, and conjugation.
• Autotrophic bacteria synthesize their own food (e.g., photosynthesis in cyanobacteria).
• Heterotrophic bacteria obtain organic molecules from other organisms (e.g., decomposers).
• Mixotrophs can switch between autotrophy and heterotrophy.
• Oxygen requirements vary: obligate aerobes require oxygen, obligate anaerobes are harmed by oxygen, and facultative anaerobes can survive with or without it.
• Prokaryotes cooperate in biofilms and nitrogen-fixing colonies (heterocysts).
• Bacteria exhibit vast genetic and metabolic diversity.
• Key differences between Bacteria vs. Archaea: cell walls (peptidoglycan vs. diverse lipids), membrane lipids (unbranched fatty acids vs. branched hydrocarbons), and RNA polymerase (single, simple vs. more similar to eukaryotic).
• Archaea are frequently found in extreme environments, whereas bacteria are more prevalent.

Proteobacteria (5 Groups)

• Alpha: Nitrogen-fixing bacteria (e.g., Rhizobium).
• Beta: Includes Nitrosomonas (nitrogen cycle).
• Gamma: Includes pathogens like Salmonella and E. coli.
• Delta: Includes myxobacteria, forming fruiting bodies.
• Epsilon: Contains Helicobacter pylori (ulcers).

Other Bacterial Groups

• Chlamydias: Intracellular parasites.
• Spirochetes: Spiral-shaped bacteria (e.g., Lyme disease).
• Cyanobacteria: Photosynthetic, oxygen-producing bacteria.
• Gram-positive bacteria: Include Streptococcus and Staphylococcus.

Extremophiles (Archaea)

• Thermophiles: Thrive in heat.
• Halophiles: Thrive in salt.
• Methanogens: Produce methane.

Ecological Interactions

• Mutualism: Both species benefit (e.g., gut bacteria & humans).
• Commensalism: One benefits, the other is unaffected.
• Parasitism: One benefits, the other is harmed.

Protists

• Protists are mostly unicellular, eukaryotic organisms.
• Four supergroups: Excavata, SAR, Rhizaria, and Unikonta.

Excavata (Diplomonads & Parabasalids, Euglenozoans)

• Lack mitochondria, anaerobic (e.g., Giardia).
• Kinetoplastids: Single large mitochondrion; some parasitic (e.g., Trypanosoma).
• Euglenids: Mixotrophs, eye spot for light detection.

SAR Supergroup (Stramenopiles, Alveolates, Rhizarians)

• Stramenopiles:
  • Diatoms: Glass-like silica walls, major producers.
  • Golden algae: Photosynthetic, some mixotrophic.
  • Brown algae: Multicellular, kelp, alternation of generations.
• Alveolates:
  • Dinoflagellates: Red tides, bioluminescence.
  • Apicomplexans: Parasitic, including Plasmodium (malaria).
  • Ciliates: Cilia for movement and feeding (e.g., Paramecium).
• Rhizarians:
  • Radiolarians: Silica skeletons, pseudopodia.
  • Forams: Calcium carbonate shells, marine sediment.
  • Cercozoans: Amoeboid, some photosynthetic.

Nutrient Acquisition (Protists)

• Apicomplexans: Parasitic, invade host cells.
• Mixotrophs: Photosynthesis and heterotrophy.
• Dinoflagellates: Photosynthetic (some heterotrophic).
• Entamoebas: Parasitic amoebas, causing diseases.

Structural/Anatomical Components (Protists)

• Examples include silica-based walls (diatoms), calcium carbonate shells (foraminiferans), cilia coverings (ciliates), and flagella (dinoflagellates). Brown algae have holdfast, stipe, and blade components.

Red & Green Algae

• Red algae: Deep water, phycoerythrin pigment.
• Green algae: Closely related to land plants.

Unikonts

• Includes animals, fungi, amoebozoans, and slime molds. Amoebozoans have lobe-shaped pseudopodia. Slime molds have fungus-like characteristics.

Fungi

• Heterotrophic decomposers, absorbing nutrients via extracellular digestion.
• Composed of hyphae (filamentous structures) forming a mycelium.
• Reproduction: sexual (plasmogamy, karyogamy) and asexual (spore formation).
• Fungal Phyla:
  • Chytrids: Aquatic, flagellated spores.
  • Zygomycetes: Fast-growing molds.
  • Glomeromycetes: Mycorrhizal symbionts.
  • Ascomycetes: Sac fungi (e.g., yeast, truffles).
  • Basidiomycetes: Club fungi (e.g., mushrooms).

Ecological Roles (Fungi)

• Decomposers: Breakdown organic matter.
• Mutualists: Mycorrhizae (fungi + plant roots).
• Pathogens: Fungal diseases in plants and animals.