The World of Microbes

Introduction to Microbiology

Microbiology is the study of microscopic organisms, including bacteria, archaea, fungi, protozoa, algae, helminths, and viruses. These organisms are diverse, ever-evolving, and play essential roles in ecosystems, health, and disease.

• Microbes are found in nearly every environment on Earth.

• They can be unicellular or multicellular, and some (like viruses) are non-cellular.

Types of Microorganisms

Cellular and Non-Cellular Microbes

Microorganisms are classified based on their cellular structure and function.

• Bacteria – Unicellular prokaryotes

• Archaea – Unicellular prokaryotes, often found in extreme environments

• Fungi – Yeasts (unicellular) and molds (multicellular)

• Protozoa – Unicellular eukaryotes

• Unicellular algae – Photosynthetic eukaryotes

• Helminths – Multicellular animal parasites

• Viruses – Non-cellular, obligate intracellular parasites

Cell Types: Prokaryotes vs. Eukaryotes

Defining Prokaryotic and Eukaryotic Cells

Cells are the basic units of life and are classified as either prokaryotic or eukaryotic based on their structure.

• Prokaryotes – Cells without a membrane-bound nucleus or organelles. Includes Bacteria and Archaea.

• Eukaryotes – Cells with a membrane-bound nucleus and organelles. Includes Fungi, Protozoa, Algae, Plants, and Animals.

Basic Unity of All Cells

Despite differences, all cells share fundamental characteristics:

• Semi-permeable membrane – Controls movement of substances in and out of the cell.

• DNA – Genetic material encoding instructions for life.

• Genetic code – Universal code for translating DNA into proteins.

• Ribosomes – Site of protein synthesis.

• ATP – Universal energy currency.

Comparing Prokaryotes and Eukaryotes

Key differences and similarities between prokaryotic and eukaryotic cells:

Examples of Cell Types

• Coccus – Spherical bacteria

• Bacillus – Rod-shaped bacteria

• Spiral – Spiral-shaped bacteria

Unusual Microbes: Giant Bacteria

Thiomargarita namibiensis and Thiomargarita magnifica

Some bacteria, such as Thiomargarita namibiensis and Thiomargarita magnifica, challenge the typical size expectations for prokaryotes.

• Thiomargarita namibiensis – Up to 180 μm in diameter

• Thiomargarita magnifica – Average length 1 cm, width 50 μm

• These bacteria have unique features, such as DNA in membrane sacs (not a true nucleus), and large vacuoles reducing cytoplasm thickness.

Genetic evidence confirms their classification as bacteria.

Viruses: Non-Cellular Microbes

Characteristics of Viruses

Viruses are non-cellular entities that require host cells to replicate.

• Obligate intracellular parasites

• Genetic material can be DNA or RNA, single or double stranded, linear or circular

• Capsid – Protein coat protecting nucleic acid

• Envelope – Lipid membrane present in some viruses

Example: SARS-CoV-2

• Single-stranded RNA virus

• Helical capsid

• Envelope with spike proteins

Classification of Organisms: The Three-Domain System

Basis for Classification

Organisms are classified into three Domains based on genetic relatedness, particularly the sequence of small subunit ribosomal RNA (SSU rRNA):

• Bacteria – Prokaryotes

• Archaea – Prokaryotes, often extremophiles

• Eukarya – Eukaryotes (includes protists, fungi, plants, animals)

All organisms have SSU rRNA genes; in bacteria, this is the 16S rRNA gene.

Comparing Bacteria and Archaea

Selective Toxicity

Selective toxicity is the principle of targeting pathogens without harming the host. Drugs must target unique and essential features of the pathogen.

• Example: Penicillin targets peptidoglycan synthesis, which is unique to bacterial cell walls.

Endosymbiont Theory

Origin of Eukaryotic Organelles

The endosymbiont theory explains the origin of mitochondria and chloroplasts in eukaryotic cells.

1. Ancestral anaerobic prokaryote developed internal membranes, forming a nucleus and ER (pre-eukaryote).

2. Engulfment of aerobic prokaryote led to mitochondria.

3. Engulfment of photosynthetic prokaryote led to chloroplasts (in plants and algae).

Genetic evidence: Mitochondrial and chloroplast ribosomes and DNA are most similar to certain bacteria.

Scientific Nomenclature

Binomial Naming System

Each organism is given a two-part scientific name: Genus and species.

• Genus is capitalized; species is lowercase.

• Names are italicized or underlined.

• Genus may be abbreviated after first use.

• Example: Escherichia coli (E. coli) – Genus honors Theodor Escherich; species refers to colon habitat.

• Example: Staphylococcus aureus (S. aureus) – Genus describes grape-like clusters; species refers to gold-colored colonies.

Species Concept in Prokaryotes

Defining Species

Species definition in prokaryotes is based on genetic similarity, not sexual reproduction.

• Reference/type strain is designated for comparison.

• Organisms with >97% 16S rRNA gene identity are considered the same species.

• Differences between 97–100% reflect strains of the same species.

• Horizontal gene transfer can lead to significant genetic diversity within a species.

Example: E. coli reference strain vs. E. coli O157:H7 (pathogenic strain).

Key Vocabulary

• Zygote – Fertilized cell formed by fusion of gametes

• Plasmic streaming – Movement of cytoplasm within eukaryotic cells

• Peptidoglycan – Polymer forming bacterial cell walls

• Obligate intracellular parasite – Organism (e.g., virus) that must live inside a host cell

• Endoplasmic reticulum – Organelle for protein and lipid synthesis

• 16S rRNA – Gene used for bacterial identification and classification

• Endosymbiont theory – Theory explaining origin of mitochondria and chloroplasts

• Selective toxicity – Ability of a drug to target pathogens without harming host

Summary Table: Features Shared by All Cells

Additional info: Some context and definitions have been expanded for clarity and completeness.