Prokaryotes (Bacteria & Archaea)

TOPIC 3: PROKARYOTES (BACTERIA & ARCHAEA)

HISTORY OF CLASSIFICATION

  • Key figures and dates in the history of biological classification:

    • Linnaeus (1735): Developed the binomial nomenclature system, classifying organisms into two kingdoms: Plantae and Animalia.

    • Haeckel (1866): Introduced a third kingdom, Protista.

    • Chatton (1925): Proposed the distinction of prokaryotes vs. eukaryotes.

    • Copeland (1938): Suggested a classification system with two empires and four kingdoms.

    • Whittaker (1969): Introduced five kingdoms: Monera, Protista, Fungi, Plantae, Animalia.

    • Woese et al. (1990): Established three domains: Bacteria, Archaea, and Eukarya.

    • Cavalier-Smith (1998): Proposed the six-kingdom system and further classification schemes.

THREE-DOMAIN HYPOTHESIS

  • Current Understanding of the Tree of Life:

    • Divided into three domains:

    • Bacteria: Prokaryotic organisms characterized by a lack of membrane-bound organelles.

    • Archaea: Also prokaryotic but genetically and biochemically distinct from bacteria.

    • Eukarya: Organisms with eukaryotic cells, including plants, animals, fungi, and protists.

    • Estimated Diversity:

    • Bacteria: Approximately 1.4 million described species, estimated at around 8 million total species.

    • Archaea: Number of species is likely in the billions, but specific numbers are unknown.

DEFINING FEATURES OF PROKARYOTES

  • What are Prokaryotes?

    • Lack of membrane-bound nucleus and organelles.

    • Possess a cell wall (typically composed of peptidoglycan in bacteria).

    • All contain a single, haploid, circular chromosome.

  • Evolutionary Timeline:

    • Formation of Earth: 4.6 billion years ago (BYA).

    • Life on Earth: 3.5 BYA.

    • Bacteria in fossil records: 3.5 BYA.

    • Eukaryotes appear: 2 BYA.

    • Multicellular life: 1 BYA.

    • Cambrian Explosion: 542 MYA.

PHYLOGENIES OF PROKARYOTES

  • Bacterial Classification:

    • Bacteria are monophyletic with at least 29 major lineages (phyla), defined by distinctive morphology or genetic sequences.

  • Archaea Classification:

    • Also considered monophyletic but discoveries of new lineages are ongoing.

DOMAIN BACTERIA

  • Key lineages include:

    • Mycoplasma

    • Firmicutes

    • Cyanobacteria

    • Actinobacteria

    • Spirochaetes

    • Chlamydiae

    • Bacteriodetes

    • Various classes of Proteobacteria ( ext{α, β, γ, δ, ε} )

DOMAIN ARCHAEA

  • Key lineages include:

    • Thaumarchaeota

    • Crenarchaeota

    • Korarchaeota

    • Euryarchaeota

CELL SHAPES AND STRUCTURES IN PROKARYOTES

  • Shapes vary significantly:

    • Spherical (cocci)

    • Rod (bacilli)

    • Spiral (spirilla)

    • Pleomorphic (varied shapes)

  • Motility:

    • Non-motile, swimming, and gliding mechanisms observed in bacteria.

    • Examples of swimming species include Salmonella.

CELL WALL STRUCTURE

  • Gram-Positive vs. Gram-Negative Bacteria:

    • Gram-Positive:

    • Thicker peptidoglycan layer, lacks outer membrane.

    • Stains purple under Gram stain.

    • Gram-Negative:

    • Thinner peptidoglycan layer, has outer membrane with lipopolysaccharides.

    • Stains pink under Gram stain.

METABOLISM TYPES IN PROKARYOTES

  • Fundamental metabolic processes utilized by prokaryotes include:

    • Catabolism: Breaking down larger molecules to release energy.

    • Anabolism: Building larger molecules from smaller units.

  • Organisms classified by energy and carbon sources:

    • Heterotrophs: Organic compounds for energy and carbon.

    • Autotrophs: Use carbon dioxide (CO2) for carbon, organic or inorganic sources for energy.

REPRODUCTION IN PROKARYOTES

  • Binary Fission:

    • Asexual reproduction where a single cell divides into two identical daughter cells.

LATERAL GENE TRANSFER (LGT)

  • Occurs when genetic material is transferred between organisms other than by vertical transmission (parents to offspring).

  • Mechanisms of LGT:

    1. Transformation: Uptake of free DNA from the environment.

    2. Transduction: Transfer of DNA via a bacteriophage.

    3. Conjugation: Direct transfer of DNA between bacterial cells through physical connection.

  • Critical for understanding phylogenetics as it complicates lineage tracing.

INTERACTIONS WITH EUKARYOTES

  • Human Microbiome:

    • Microbial communities that reside in or on the human body, essential for digestion, immunity, etc.

    • Contains more microbial cells than human cells (approx. 39 trillion microbes in a body).

  • Bioremediation:

    • Use of bacteria to clean up environmental pollutants.

EXAMPLES OF PATHOGENIC PROKARYOTES

  • Actinobacteria: Causes diseases like leprosy and tuberculosis.

  • Chlamydiaceae: Causes sexually transmitted infections.

  • Proteobacteria: Includes E. coli, responsible for foodborne illnesses.

  • Spirochaetes: Includes Lyme disease and syphilis.

UNIQUE ADAPTATIONS

  • Cyanobacteria: Essential for oxygen production in Earth's history, have capabilities for nitrogen fixation.

  • Firmicutes: Provide antibiotics and play roles in food production (e.g., yogurt).

  • Wolbachia: Alters sex ratios in insect populations.

CONCLUSION

Prokaryotes like bacteria and archaea represent a vast diversity of life forms with crucial roles in ecosystems, human health, and potential applications in biotechnology.