General Microbiology Notes

What is a Microorganism?

Living things that are too small to be seen with the naked eye; observed with microscopes due to their small size.
Include bacteria, fungi, protozoa, microscopic algae, and viruses.
Can be unicellular (e.g., bacteria, yeast) or multicellular (e.g., molds).

Carbon cycle: Microorganisms (especially bacteria and fungi) decompose organic wastes and dead plants/animals, returning CO2 to the atmosphere, making it available again for plants and animals.
Photosynthesis & primary production: Algae and cyanobacteria use CO2 to make carbohydrates, which serve as food for animals, fungi, and bacteria.
Nitrogen cycle: Certain bacteria can naturally convert atmospheric nitrogen into a usable form (nitrogen fixation), making it available to plants and animals.
Beneficial and Ecological Roles of Microbes

Bioremediation: Using microbes to clean up pollutants.
- Certain bacteria use pollutants as energy sources or produce enzymes that break down toxins, helping clean up oil spills, chemical waste, and toxic sites.
Insect Pest Control by Microorganisms:
- Bacillus thuringiensis produces protein crystals toxic to insects, providing a safer alternative to chemical insecticides.
Symbiotic Relationships with living organisms:
- Mutualism: Gut bacteria digest food and produce vitamins; Rhizobia fix atmospheric nitrogen for plants (legumes).
- Commensalism: Skin microbes live on us without causing harm.

Sewage Treatment: Using Microbes to Recycle Water
- Microbes break down organic matter in wastewater into by-products like CO2, nitrates, and methane, making water safe for recycling.
Food Industry:
- Fermentation: bread, yogurt, cheese, beer, wine.
- Food preservation: Acids and alcohols produced from fermentation prevent food spoilage.
- Flavor & texture: Molds, yeasts, and bacteria give unique tastes (e.g., blue cheese, sourdough).

The system of naming organisms was developed by Carolus Linnaeus in $1735$.
Binomial nomenclature: Genus + species
Rules for writing these names:
1. Genus always begins with a capital letter.
2. The species name begins with a small letter.
3. The scientific names are always italicized.
4. When handwritten, the genus name and species name have to be underlined.

Cellular includes organisms and biological entities studied by microbiologists; examples include:
- Fungi
- Protists
- Bacteria
- Archaea
- Viruses (as presented in this schematic)
Acellular includes:
- Viroids
- Satellites
- Prions
- (Viruses are described as acellular in other contexts; here they are shown within cellular examples in the schematic.)
Composed of nucleic acids and proteins; viruses may have RNA or DNA and sometimes a lipid envelope.

Simple, unicellular organisms without a true nucleus → prokaryotes (from Greek “pre-nucleus”).
Cell walls made primarily of peptidoglycan.
Reproduce asexually by binary fission (cell divides into two equal cells).
Energy acquisition:
- Most use organic chemicals from living or dead matter.
- Some can photosynthesize.
- Others derive energy from inorganic substances.
Many bacteria can move using appendages called flagella.
Examples and roles:
- Beneficial: Lactobacillus helps ferment milk into yogurt and cheese.
- Engineered: Escherichia coli is used to produce insulin for diabetes treatment.
- Pathogenic: Mycobacterium tuberculosis (TB) and Salmonella (food poisoning).
- Roles: nutrient cycling, soil fertility, biotechnology.

Prokaryotic cells but lack peptidoglycan in their cell walls.
Found in extreme environments (extremophiles).
Methanogens → produce methane (biogas production).
Extreme halophiles → thrive in salty environments (e.g., Dead Sea, Great Salt Lake).
Extreme thermophiles → live in hot sulfurous water (e.g., Yellowstone hot springs).
Enzymes from thermophilic archaea (e.g., Thermus aquaticus) used in PCR (Taq polymerase).
Not known to cause human disease.

Eukaryotes with a distinct nucleus.
May be unicellular (yeasts) or multicellular (molds, mushrooms).
Cell walls mainly made of chitin.
Molds form masses called mycelia, composed of filaments called hyphae.
Obtain nutrition by absorbing organic solutions from environment or hosts.
Reproduction can be sexual or asexual.
Examples:
- Yeasts (Saccharomyces cerevisiae) used in baking and brewing (bread, beer, wine).
- Molds like Penicillium gave us penicillin (the first widely used antibiotic).
- Anaerobic gut fungi live in the digestive systems of herbivores; assist in degradation of cellulose and lignin; applications in animal health and biofuel production.
- Pathogenic fungi: Candida albicans (yeast infections); Aspergillus produces aflatoxins that contaminate crops and are highly toxic.

Unicellular eukaryotes with diverse shapes.
Motility: pseudopods (amoebae), flagella, or cilia.
Free-living protozoa regulate microbial populations in soil and water.
Parasitic examples: Plasmodium (causes malaria, carried by mosquitoes); Giardia (beaver fever) from contaminated water.
Nutrition: heterotrophic (feeds on organic compounds); some (e.g., Euglena) are photosynthetic.
Reproduction: sexually or asexually.

Photosynthetic eukaryotes; usually unicellular.
Cell walls composed of cellulose.
Found in freshwater, saltwater, soil, or in association with plants.
Use light, water, and CO2 for food production (photosynthetic).
Produce oxygen and carbohydrates that support other organisms.
Examples and uses:
- Spirulina → dietary supplement rich in protein and vitamins.
- Algae used in biofuels.
- Algal products (agar, alginate, carrageenan) used in foods and cosmetics.
- Harmful red algal blooms → release toxins that kill fish and contaminate seafood.

Acellular (not made of cells), very small → visible only by electron microscopy.
Structure: core of DNA or RNA + protein coat (sometimes with lipid envelope).
Viruses can infect a variety of living organisms, including bacteria, plants, and animals.
Causes diseases such as influenza, HIV/AIDS, and COVID-19.
Types: Reproduce only inside host cells by using host machinery.
Considered living only when inside a host; inert outside.