Chapter 1: The Microbial World – Foundations of Microbiology

1.1 Microorganisms, Tiny Titans of the Earth

Definition and Diversity of Microorganisms

Microorganisms, or microbes, are life forms too small to be seen by the human eye and require a microscope for observation. They are classified into several major groups based on cellular structure and function.

• Prokaryotic cells: Cells lacking a true nucleus (e.g., Bacteria, Archaea).

• Eukaryotic cells: Cells with a true nucleus (e.g., Fungi, Protists, Animals, Plants).

• Viruses: Acellular entities requiring a host to reproduce; consist of DNA or RNA surrounded by a protein coat, sometimes with an envelope.

Examples:

• Bacteria: Streptococcus pyogenes

• Cyanobacteria: Anabaena

• Archaea: Methanocaldococcus jannaschii

• Fungi: Candida albicans (yeast), Rhizopus stolonifer (bread mold)

• Protist: Trypanosoma cruzi (causes Chagas disease)

• Animals: Trichuris vulpis (whipworms)

• Plants: Spirogyra (algae)

Bacteriology is the study of bacteria; Mycology is the study of fungi.

Microbial Communities and Impact

• Microbes form complex communities in diverse environments (e.g., lakes, sewage, human tongue).

• They are the oldest form of life and constitute a major fraction of Earth's biomass.

• Microorganisms affect human life through infectious diseases, food and water safety, soil fertility, animal health, and fuel production.

• Pathogens are organisms that cause disease.

Tools for Studying Microbes

• Microscope: Compound light and electron microscopes are essential for visualizing microbes.

• Culture media: Nutrient-rich mixtures (liquid = broth; solid = agar) used to grow microbes.

• Growth: Increase in cell number due to cell division; infection refers to microbial growth in the body.

• Colony: A visible mass of microbial cells derived from a single cell, representing a pure culture.

Examples of Culture Media

• Plated media: Trypticase Soy Agar (TSA), Mannitol Salt Agar (MSA)

• Liquid media: Trypticase Soy Broth (TSB), Glucose purple broth

• Slanted media: TSA slants, Citrate Agar Slants

1.2 Structure and Activities of Microbial Cells

Basic Cell Structure

All cells share fundamental structural features:

• Cytoplasmic (cell) membrane: Phospholipid bilayer separating the cytoplasm from the environment.

• Cytoplasm: Aqueous mixture of macromolecules, small organics, ions, and ribosomes.

• Ribosomes: Sites of protein synthesis (Bacteria: 70S; Eukaryotes: 80S).

Cell Walls

• Bacteria: Peptidoglycan (murein)

• Acid-fast bacteria: Mycolic acids (e.g., Mycobacterium)

• Archaea: Pseudopeptidoglycan (pseudomurein)

• Fungi: Chitin

• Plants: Cellulose

• Animal cells: Lack cell walls; only have membranes, making them sensitive to osmotic pressure.

• Mycoplasma: Bacteria without a cell wall; causes walking pneumonia.

Genetic Material

• Genome: Complete set of genes in a cell.

• Eukaryotic DNA: Linear chromosomes within a nucleus; large genomes (up to billions of base pairs).

• Prokaryotic DNA: Typically a single circular chromosome in the nucleoid; may contain plasmids (extrachromosomal DNA) for special properties (e.g., antibiotic resistance); small, compact genomes (0.5–10 million base pairs).

Cellular Activities

• Metabolism: Chemical transformation of nutrients (aerobic, anaerobic, facultative anaerobic).

• Enzymes: Protein catalysts for biochemical reactions.

• Transcription: DNA to RNA.

• Translation: RNA to protein.

• DNA replication: Copying the genome.

• Motility: Movement via flagella (bacteria) or cilia/flagella (eukaryotes).

• Differentiation: Formation of specialized cells (e.g., endospores in bacteria, spores in fungi, pili for conjugation in bacteria).

• Intercellular communication: Quorum sensing; both prokaryotes and eukaryotes communicate chemically.

• Evolution: Genetic changes passed to offspring over time.

1.3 Cell Size and Morphology

Cell Size and Shape

• 1 micrometer (μm) = one-millionth of a meter.

• Prokaryotes: 0.2–600+ μm in diameter (most 0.5–10 μm).

• Eukaryotes: Typically 5–100 μm in length.

Organism	Characteristics	Morphology	Size (μm)	Cell volume (μm³)	Volume compared to E. coli
Thiomargarita namibiensis	Sulfur chemolithotroph	Cocci in chains	750	200,000,000	1,000,000×
Epulopiscium fishelsoni	Chemorganotroph	Rods with tapered ends	80 × 600	3,000,000	15,000×
Achromatium oxaliferum	Cyanobacterium	Filaments	8 × 60	40,000	20,000×
Staphylothermus marinus	Hyperthermophile	Cocci in clusters	1	0.5	0.25×
Mycoplasma pneumoniae	Pleomorphic	Pleomorphic	0.2	0.005	0.0025×

Additional info: Table above summarizes the diversity in size and morphology among bacteria, from the largest (e.g., Thiomargarita namibiensis) to the smallest (e.g., Mycoplasma pneumoniae).

1.4 An Introduction to Microbial Life

Three Domains of Life

• Bacteria: Prokaryotes, usually undifferentiated single cells (0.5–10 μm), e.g., E. coli (rod-shaped), Staphylococcus aureus (cocci-shaped).

• Archaea: Prokaryotes, often extremophiles, lack known parasites/pathogens of plants and animals.

• Eukarya: Includes plants, animals, fungi, protists; first were unicellular, may have appeared two billion years ago; vary in size, shape, and physiology.

Viruses

• Obligate parasites; not cells; replicate only within host cells.

• Do not carry out metabolism independently.

• Classified by structure, genome composition, and host specificity.

1.5 Microorganisms and the Biosphere

History of Life on Earth

• Earth is approximately 4.6 billion years old.

• First cells appeared between 3.8 and 4.3 billion years ago.

• Atmosphere was anoxic (no O2) until ~2.6 billion years ago; only anaerobic metabolisms were possible.

• First anoxygenic phototrophs appeared ~3.6 billion years ago; cyanobacteria (oxygenic phototrophs) appeared ~2.6 billion years ago.

• Plants and animals appeared ~0.5 billion years ago.

Additional info: The evolution of oxygenic photosynthesis by cyanobacteria was a pivotal event in Earth's history, leading to the accumulation of atmospheric oxygen and the diversification of aerobic life forms.