Introduction to Microbiology: Foundations, History, and Classification

Course Introduction and Structure

Welcome and Course Overview

This course introduces the foundational concepts of microbiology, exploring the diversity, history, and impact of microbes on human society and the environment. Students will engage in readings, assignments, group projects, and laboratory work to develop a comprehensive understanding of microbial life.

• Instructor: Dr. Mary-Anne Courtney, Ph.D. (contact: [e-mail])

• Office Hours: Wed & Fri, noon to 1 pm (in-person or Zoom)

• Assessment: Exams, weekly quizzes, signature project, essays, class participation, and lab work

Course Grading and Assignments

Lecture and Lab Grading Components

• Exams: Three exams (100 pts each), lowest dropped, max 200 pts

• Weekly Quizzes: 10 quizzes, 100 pts total

• Signature Project: Group project on a microbiological topic, including concept maps and presentations

• Essays: Two essays (one on a fungus/protist, one on immunology), peer-reviewed via Perusall

• Lab Portion: Prelab quizzes, lab book checks, results/discussion checks, individual project paper, lab practical

Introduction to Microbiology

What Is a Microbe?

Microbes are living organisms that are typically too small to be seen without a microscope. They are fundamental to life on Earth and include a wide range of organisms:

• Bacteria

• Archaea

• Fungi

• Protists

• Viruses

Example: Representative microbes include cyanobacteria, Paramecium, Amoeba, and various fungi and viruses (see textbook figures for images).

Origin and Diversity of Microbial Life

• Microbial life originated shortly after Earth formed (~4.0 billion years ago, at temperatures below 100°C).

• The oldest rocks (3.8 billion years old) show chemical evidence of microbial life.

Domains of Life

Microbes are found in all three domains of life:

Domain	Type	Examples
Bacteria	Prokaryote	Escherichia coli, cyanobacteria
Archaea	Prokaryote	Methanogens, halophiles
Eukarya	Eukaryote	Fungi, protists, algae

Additional info: Viruses are not classified within the three domains as they are acellular and require host cells for replication.

Microbes and Human History

Impact of Microbial Disease

• Microbial diseases have shaped human history, often causing more deaths in warfare than wounds themselves.

• Florence Nightingale (1820–1910) founded the science of medical statistics and used the "polar area chart" to illustrate causes of death among soldiers.

• Modern pandemics, such as COVID-19, continue to demonstrate the global impact of microbes.

Microscopy and the Microbial World

Development of Microscopy

• Robert Hooke (1635–1703): Built the first compound microscope, observed mold, and coined the term "cell."

• Antonie van Leeuwenhoek: Improved microscope design and was the first to observe single-celled microbes.

Spontaneous Generation and Experimental Refutation

Historical Belief and Experiments

• Spontaneous generation was the belief that living organisms could arise from nonliving matter.

• Experiments by Joblot and Pasteur demonstrated that microbes arise from pre-existing life, not spontaneously.

Experiment	Result
Joblot's first experiment (uncovered flasks)	Microbes appeared in both flasks
Joblot's second experiment (boiled, covered flask)	No microbes appeared in covered flask
Pasteur's swan-neck flask	Broth remained sterile until exposed to air

Medical Microbiology

Germ Theory of Disease

• Robert Koch (1843–1910): German physician, founder of the scientific method in microbiology.

• Established the germ theory of disease, which states that specific diseases are caused by specific microorganisms.

Koch's Postulates

Criteria for establishing a causative link between an infectious agent and a disease:

1. Microbe is always present in diseased host (absent in healthy).

2. Microbe is grown in pure culture (no other microbes present).

3. Introduce pure microbe into healthy host (individual becomes sick).

4. Same microbe re-isolated from now-sick individual.

Example: Koch's postulates were used to identify the causative agents of diseases such as tuberculosis and anthrax.

Microbial Ecology

Role of Microbes in Ecosystems

• Microbes cycle essential minerals (e.g., nitrogen, oxygen) and are crucial for ecosystem functioning.

• Less than 0.1% of microbial species can be cultured in the laboratory; the rest constitute the majority of Earth's biosphere.

• Complex multicellular life is supported only on the outer skin of Earth, while microbes inhabit diverse and extreme environments.

Ocean Environments

• Oceans cover 70% of the planet and contain over 50 biomes with high microbial diversity.

• Oceans absorb over 90% of heat accumulation and 25% of excess CO2.

• Marine microbes play key roles in global biogeochemical cycles.

Winogradsky Column

A Winogradsky column demonstrates the diversity of microbial metabolism in a stratified environment:

• Cyanobacteria (photosynthetic, oxygenic)

• Purple sulfur bacteria (anoxygenic photosynthesis)

• Green sulfur bacteria (anoxygenic photosynthesis)

• Sulfate-reducing bacteria (anaerobic respiration)

Classification and Challenges

Challenges in Microbial Classification

• Early taxonomists faced two main challenges:

  • Low resolution of light microscopes (overcome by advances in biochemistry and microscopy)

  • Difficulty in defining microbial species (working definition: 95% similarity of DNA sequence)

Additional info: The discovery of Archaea by Carl Woese (based on 16S rRNA analysis) led to the modern classification of life into three domains: Bacteria, Archaea, and Eukarya.