Bacteria and archaea

Basic Features of Bacteria – Structure

Bacteria have a simple cell structure:

• Cell wall: Composed of peptidoglycan (except in Archaea).

• Plasma membrane: Selectively permeable, lipid bilayer.

• Cytoplasm: Contains enzymes, ribosomes, and genetic material.

• Ribosomes: 70S, unique to prokaryotes.

• DNA: Single, circular chromosome; often plasmids.

• Flagella: Used for motility.

• Pili/Fimbriae: For adhesion and genetic exchange.

• Endospores: Produced by some species for survival under extreme conditions (e.g., Bacillus, Clostridium).

Basic Features of Bacteria – Metabolism

Bacteria display metabolic diversity:

• Energy sources: Phototrophs (light) or chemotrophs (chemical compounds).

• Carbon sources: Autotrophs (CO2) or heterotrophs (organic compounds).

• Respiration types: Aerobic, anaerobic, or facultative.

• Examples:

  • Nitrogen fixation (e.g., Rhizobium spp.).

  • Sulfate reduction (e.g., Deltaproteobacteria).

  • Ammonia oxidation (e.g., Nitrosomonas).

Basic Features of Bacteria – Structure

Bacteria have a simple cell structure:

• Cell wall: Composed of peptidoglycan (except in Archaea).

• Plasma membrane: Selectively permeable, lipid bilayer.

• Cytoplasm: Contains enzymes, ribosomes, and genetic material.

• Ribosomes: 70S, unique to prokaryotes.

• DNA: Single, circular chromosome; often plasmids.

• Flagella: Used for motility.

• Pili/Fimbriae: For adhesion and genetic exchange.

• Endospores: Produced by some species for survival under extreme conditions (e.g., Bacillus, Clostridium).

Basic Features of Bacteria – Metabolism

Bacteria display metabolic diversity:

• Energy sources: Phototrophs (light) or chemotrophs (chemical compounds).

• Carbon sources: Autotrophs (CO2) or heterotrophs (organic compounds).

• Respiration types: Aerobic, anaerobic, or facultative.

• Examples:

  • Nitrogen fixation (e.g., Rhizobium spp.).

  • Sulfate reduction (e.g., Deltaproteobacteria).

  • Ammonia oxidation (e.g., Nitrosomonas).

Classification of Bacteria – Phenotypic Methods

Classical bacterial taxonomy relies on observable traits:

• Cell morphology: Shape (cocci, bacilli, spirilla).

• Staining: Gram-positive or Gram-negative.

• Pathogenicity: Resistance to antibiotics/toxins.

• Metabolic activity: Nutritional and environmental requirements.

Classification of Bacteria – Genotypic Methods

Molecular methods allow deeper insights:

• 16S rRNA sequencing: Gold standard for prokaryotes.

• G-C content analysis: DNA composition comparison.

• Whole genome sequencing: Comprehensive genetic data.

• Metagenomics: Studies complex microbiomes without culturing.

Importance of Studying Microbial Diversity

Studying microbial diversity helps to:

• Organize organisms into meaningful groups.

• Facilitate accurate identification for treatment.

• Enable predictions and hypothesis formulation.

• Improve communication between scientists about related species.

Phylogenetic Study of Microbial Diversity

Phylogenetic methods trace evolutionary relationships:

• 16S rRNA sequencing for lineage identification.

• Multi-locus sequence typing (MLST): Analysis of housekeeping genes.

• Whole genome sequencing provides the most comprehensive data.

Functional Study of Microbial Diversity

Focuses on gene presence/absence linked to function:

• Examples: Resistance genes, metabolic pathways, virulence factors.

• Correlation with phylogeny: Not always consistent due to gene loss, horizontal gene transfer, or convergent evolution.

Functional Diversity in Bacteria

• Physiological: Metabolism and biochemical processes.

• Morphological: Structural variations (e.g., filamentous, helical).

• Ecological: Interactions with the environment and other organisms.

Bacteria vs. Archaea – Key Differences

• Cell wall: Bacteria have peptidoglycan; Archaea have pseudopeptidoglycan.

• Membrane lipids: Bacteria have ester-linked; Archaea have ether-linked.

• RNA polymerase: Archaea’s is more similar to eukaryotes.

• Methanogenesis: Unique to Archaea.

• Pathogenicity: None observed in Archaea.

Molecular Tools for Classifying Microbes

• 16S rRNA sequencing: Prokaryotes (bacteria and archaea).

• 18S rRNA sequencing: Eukaryotes.

• Metagenomics: Studies entire microbial communities.

Thermophilic Bacterial Phyla – Aquificae and Thermotogae

• Aquificae: Hyperthermophiles (up to 95°C), sulphur oxidizers, found in hot springs and thermal vents.

• Thermotogae: Hyperthermophiles with horizontal gene transfer from Archaea; found in hot springs and oil reservoirs.

Cyanobacteria – Key Features

• Photosynthesis: Photoautotrophs producing free oxygen.

• Chlorophylls: Blue-green, brown-green, or red pigments.

• Nitrogen fixation: Capable in specialized cells.

• Ecology: Found in aquatic and terrestrial habitats.

Bacterial Extremophiles and Their Adaptations

• Thermophiles: Survive high temperatures (e.g., Aquificae, Deinococcus-Thermus).

• Halophiles: Require high salinity (e.g., Halobacterium).

• Acidophiles/Alkaliphiles: Adapt to extreme pH.

• Barophiles: Thrive under high pressure.

Symbiotic Relationships of Bacteria

• Mutualism: Rhizobium spp. fix nitrogen for plants.

• Parasitism: Rickettsia spp. cause typhus, spotted fever.

• Commensalism: Bacteroides in human intestines aid digestion.

Ecological Roles of Bacteria

• Nutrient cycling: Nitrogen fixation (e.g., Rhizobium), decomposition.

• Carbon cycle: Methane production by methanogens.

• Sulfur cycle: Sulfate reduction by Deltaproteobacteria.

• Oxygen production: Cyanobacteria's photosynthesis.

Bacteria in Aquatic and Terrestrial Environments

• Freshwater: Oxygen gradients, flow rates affect species.

• Marine: Light, pressure, salinity variations influence bacteria.

• Soil: pH, organic matter drive diversity (e.g., Actinobacteria).