Study Notes for Microbiology and Molecular Biology (M20003)

Introduction to Microbiology

• Course Title: Microbiology and Molecular Biology (M20003)

• Instructor: Thanos Rizoulis, University of Portsmouth

• Contact: Athanasios.Rizoulis@port.ac.uk

• Date: September 2025

PART 1: A Brief History of Microbiology

Definition of Microbiology

• Microbiology is defined as the study of microorganisms.

• Microorganism Size Scale:

  • Ranges from 1 nm (nanometer) to 1 mm (millimeter): placeholders for various structures, including:

  • Atoms

  • Small molecules

  • Proteins

  • Organelles

  • Viruses

  • Bacteria

  • Eukaryotic cells

• Most microorganisms are microscopic and visible only with a microscope.

• Typical size of microbial cells is around 1 µm (micrometer); for example, a 1 mm bacterial colony consists of approximately 1,000,000,000 cells.

Founders of Microbiology

Robert Hooke

• English natural philosopher and polymath (1635 – 1703).

• Key Contributions:

  • Published Micrographia in 1665, significant for microscopic observations.

  • Utilized an early microscope, allowing the first drawing of microorganisms (mould on leather).

Antonie van Leeuwenhoek

• Dutch scientist, referred to as the “father of microbiology” (1632 – 1723).

• Key Contributions:

  • Enhanced the design of optical lenses and microscopes.

  • Corresponded with the Royal Society, sending around 190 letters with observations.

  • First published drawings of bacteria in 1684, referred to as “animalcules.”

Key Institutions

• Microbiology Museum Amsterdam serves as a dedicated repository for microbial life.

• Graphic Highlight:

  • Archaea, Viruses, Tree of Life

Other Founders of Microbiology

Louis Pasteur

• French scientist (1822 – 1895) known for disproving the concept of “spontaneous generation.”

• Key Contributions:

  • Demonstrated that living organisms do not spontaneously emerge from non-living matter, through experiments using Pasteur's swan-necked flasks.

• Innovations:

  • Foundational work in vaccination (rabies, anthrax), microbial fermentation, and pasteurization (milk and wine).

Robert Koch

• German scientist (1843 – 1910) contributed to medical microbiology.

• Established four criteria for proving cause-and-effect relationships in infectious diseases known as Koch's postulates, though not all apply universally to all pathogens.

Contributions of Notable Women in Microbiology

• Angelina Fanny Hesse: Suggested use of agar for culturing microorganisms, leading to significant advancements in isolating Mycobacterium tuberculosis.

• Gladys Loundsbury Hobby: Worked on penicillin's fermentation processes, critical during WWII for treating soldiers.

• Emmanuelle Marie Charpentier & Jennifer Doudna: Pioneered the CRISPR/Cas gene-editing technology.

• Ester Miriam Zimmer Lederberger: Important discoveries concerning genetic inheritance in bacteria.

• Francoise Barré-Sinoussi: Major contributor to identifying the HIV virus, recipient of the Nobel Prize.

• Ruth Ella Moore: First African-American woman to earn a PhD in Natural Sciences, studied tuberculosis and gut microbiota.

• Others include: Sara Branham Matthews, Alice Catherine Evans, Beatrice H. Hahn, and Tu Youyou, each contributing significantly to overcoming diseases and insights in microbiology.

PART 2: What Are Microorganisms?

The Three Domains of Life

• Prokaryotes:

  • Comprises Bacteria and Archaea.

  • Archaea classified as a separate domain by Carl Woese (1977); single-celled, lack a nucleus, more diverse than Eukaryotes.

• Prokaryotic vs. Eukaryotic Cells:

  • Prokaryotic:

  • No nucleus, organelles; DNA exists in an amorphous nucleoid.

  • Eukaryotic:

  • Contains membrane-bound organelles, with DNA enclosed in the nucleus.

Types of Microorganisms

• Includes:

  • All prokaryotes (Bacteria & Archaea)

  • Single-celled Fungi (e.g. yeasts)

  • Other single-celled eukaryotes (protozoa, algae)

  • Study of viruses, classified as microscopic entities but not true organisms.

Properties of Microbial Cells

• Viruses are non-living as they cannot grow independently; require hosts to reproduce.

• Exhibit lack of compartmentalisation, with consistencies of nucleic acids and proteins only; lack structure typical of living organisms like motility and communication.

Naming of Microorganisms

• Binomial nomenclature:

  • Genus and species names are italicized, with genus capitalized and species in lowercase.

  • Examples:

  • Correct: Escherichia coli (italicized), E. coli (abbreviated)

• Naming often reflects organism characteristics, origins, or names of scientists; etymology commonly derives from Latin or Greek.

Study Areas in Microbiology

• Microbiologists study:

  • Bacteria

  • Archaea

  • Fungi

  • Algae

  • Protozoa

  • Viruses

• Further insights in “Biodiversity and Evolution” module.

Detailed Study of Microorganisms

Bacteria

• Prokaryotic; lack nucleus/organelles; possess peptidoglycan cell walls; reproduce by binary fission; diverse in phylogenetics/metabolism.

• Energy sources include organic compounds, inorganic chemicals, and photosynthesis.

Archaea

• Similar to bacteria (Prokaryotic) but lack peptidoglycan in cell walls; can thrive in extreme environments.

  • Types: Methanogens, extreme halophiles, extreme thermophiles.

Fungi

• Eukaryotic with chitin cell walls; utilize organic carbon; include unicellular (yeasts) and multicellular organisms (moulds, mushrooms).

Algae

• Non-plant photosynthetic entities.

  • Blue-Green Algae (Cyanobacteria): Prokaryotic without a nucleus.

  • Microalgae: Eukaryotic, single-celled, microscopic (e.g. diatoms).

  • Macroalgae: Eukaryotic, multicellular, macroscopic (e.g. kelp).

Protozoa

• Eukaryotic, diverse in morphology and phylogeny, single-celled, incapable of photosynthesis; employ motility mechanisms like pseudopods, cilia, or flagella.

Viruses

• Acellular entities lacking life status; consist of DNA/RNA core and protein coat; require a host for replication; classified based on host and characteristics, not named through binomial nomenclature.

PART 3: Microbial Habitats

Distribution of Microorganisms

• Microorganisms inhabit environments like freshwater, salt lakes, domesticated animals, and more.

• Estimated microbial cell numbers on Earth: $2.5 imes 10^{30}$.

Microbial Communities

• Microbial communities exhibit complex interdependencies; no singular microorganism occupies all habitats; competition for nutrients and space is prevalent.

• Microbial Ecology: Study of these interactions within microbial communities.

Extreme Habitats

• Extremophiles survive extreme conditions; temperate environments can host >1 billion microbial cells/g soil, representing >1000 species.

Astrobiology

• Refers to the study of life beyond Earth; NASA missions (e.g., Mars 2020) aim to find biosignatures of past life on Mars.

Human Body as a Microbial Habitat

• Human microbiota (~40 trillion microbial cells, 1.3 times the number of human cells) contributes a significant portion of body mass (1-3%).

• Microbial composition varies throughout an individual's life, with normal microflora primarily being benign.

PART 4: Beneficial Microorganisms

Pathogenic Microorganisms

• Include bacteria, fungi, and viruses; other pathogens encompass nematodes, parasites, and prions, causing diseases like tuberculosis and chickenpox.

Impact on Plants and Animals

• Pathogenic microorganisms can cause losses of crops, livestock, and lead to famines/epidemics (e.g., Phytophthora infestans caused the Great Irish Famine).

Evolution of Life on Earth

• Earth is approximately 4.6 billion years old; life began as anaerobic microorganisms 3.8 billion years ago; atmospheric oxygen produced by cyanobacteria facilitated evolution to multicellular organisms.

Contributions of Microorganisms

Phototrophic Microorganisms

• Phototrophs: Organisms that obtain their energy from light.

  • Examples include purple and green bacteria, cyanobacteria, algae, and green plants, generating oxygen through photosynthesis.

Decomposition of Organic Matter

• Microorganisms are vital in breaking down organic matter, participating in the carbon cycle by converting compounds into simpler forms and utilizing CO2

  • Implemented in practices like waste water treatment.

Biogeochemical Cycles

• Contribute to the nitrogen, sulfur, and phosphorus cycles.

  • Microorganisms like Rhizobium facilitate nitrogen fixation in legume root nodules, converting atmospheric nitrogen to usable forms for plants.

Mycorrhiza

• Symbiotic association between fungi and plant roots, allowing for nutrient transfer in both directions (nutrients from soil to plant, carbohydrates from plant to fungi).

Cellulose Digestion by Ruminants

• Many domesticated ruminants (e.g., cattle) rely on microorganisms in their rumens to digest cellulose from grasses, converting it to fatty acids.

• In humans, digestion primarily operates in an acidic stomach environment.

Fermentation

• Saccharomyces cerevisiae: Yeast utilized in alcoholic beverages and baking; fermentation process generates ethanol and CO2.

Production of Yoghurt and Cheese

• Yoghurt: Produced by fermenting lactose through Lactobacillus and Streptococcus species, producing lactic acid for preservation and flavor.

• Cheese: Involves various starter bacteria and molds; specific bacteria used to create desirable properties in cheese products.

Probiotics

• Live bacteria and yeasts with health benefits; added to foods such as yoghurt, comprising strains like Lactobacillus and Bifidobacterium.

Utilization of Clostridium botulinum in Medicine

• Produces botulinum toxin; used in BOTOX treatments at ultra-low doses to cause flaccid paralysis, benefiting cosmetic procedures.

Energy Production (Biofuels)

• Microorganisms can produce biofuels:

  • Bioethanol: Created through microbial fermentation of glucose, an important motor fuel in various countries.

  • Methane: Generated through anaerobic degradation in landfills and digesters.

Environmental Applications

• Microorganisms play a role in bioremediation, facilitating the degradation of pollutants (e.g., oil spills, pesticides) through microbial action, exemplified by case studies like Exxon Valdez and Deepwater Horizon.

Industrial Microbiology

• Microorganisms are cultivated on a large scale for producing antibiotics, enzymes, and chemicals, often utilizing biotechnology for creating commercially valuable products, including human proteins and hormones.

Microbial Enzymes and Their Applications

Contributions to Molecular Biology

• Major discoveries stem from microbiology; including DNA polymerases for PCR, with origins from E. coli and Thermus aquaticus, and CRISPR-CAS gene editing technology revolutionizing genetic engineering and therapy.

Model Organisms

• Escherichia coli: Widely used due to its ease of culture, fast growth, and manipulation in genetic modifications.

• Saccharomyces cerevisiae: Shares complex internal structure with higher eukaryotes and is valued in genetic research.

Subdisciplines of Microbiology

• Areas include human microbiome study, biofilms, extremophiles, astrobiology, and newer domains such as transcriptomics, proteomics, and metabolomics, enabled by advancements in molecular biology and analytical techniques.