Microbial Diversity: Bacteria, Archaea, Fungi, and Protozoa
Microorganisms, or microbes, are living things too small to be seen with the naked eye, and they include bacteria, archaea, fungi and protozoa, along with microscopic algae. In brief: microbes are found everywhere, in soil, water, air and the bodies of animals and plants. Most are harmless or helpful: they recycle nutrients, make food, produce medicines and help digestion. Only a small fraction cause disease. Viruses are also studied in microbiology, but they are not cells and are not usually counted as living organisms.
Microbes were the first living things on Earth and still make up a large part of its biomass and biodiversity. This guide introduces the main groups, compares them in a table, describes their beneficial roles, works through a calculation of microbial numbers and corrects common mistakes about “germs”.
What are microorganisms?
Microorganisms are living things that are visible only under a microscope. Most are single-celled, although some, such as molds, are multicellular but made of microscopic filaments. They are very diverse in structure and way of life, and they are found in all three domains of life.
The total number of bacteria on Earth is estimated at about 5 × 10³⁰. A human body carries roughly as many bacterial cells as human cells, on the order of 40 trillion, mostly in the large intestine. Their total mass is only about 0.2 kilograms.
What are bacteria?
Bacteria are prokaryotes with a typical length of 1 to 5 micrometers. They have a cell wall of peptidoglycan, no nucleus and a single circular chromosome. They are classified by shape: cocci (spheres), bacilli (rods) and spirilla (spirals). They reproduce by binary fission, which can take as little as 20 minutes in good conditions in E. coli, and they can exchange genes by conjugation (transfer through contact), transformation (uptake of DNA) and transduction (transfer by viruses).
Examples: Lactobacillus (yogurt), Rhizobium (nitrogen fixation), Streptococcus pneumoniae (pneumonia) and Vibrio cholerae (cholera). Cyanobacteria are bacteria that photosynthesize.
What are archaea?
Archaea are prokaryotes that resemble bacteria, but have a different cell chemistry. They are well known for living in extreme conditions: hot springs (thermophiles), very salty water (halophiles) and oxygen-free places (methanogens), though they are also common in oceans and soils. No archaeon is known with certainty to cause a human disease.
What are microscopic fungi?
Microscopic fungi include yeasts (single-celled) and molds (multicellular, made of hyphae). They have chitin cell walls and absorb nutrients from their surroundings. Yeasts such as Saccharomyces cerevisiae reproduce by budding. Molds grow on bread, fruit and damp walls. Some, such as Candida albicans, cause infections (thrush), and some molds produce toxins. Others are the source of antibiotics, such as penicillin from Penicillium.
What are protozoa?
Protozoa are single-celled eukaryotes that are heterotrophic and usually mobile. They are classified by the way they move: amoebae use pseudopodia, ciliates use cilia, and flagellates use flagella. Many are free-living in water and soil, and they feed on bacteria. Some are parasites.
- Plasmodium causes malaria, spread by Anopheles mosquitoes.
- Trypanosoma causes sleeping sickness, spread by tsetse flies.
- Entamoeba histolytica causes amoebic dysentery, spread by contaminated water.
- Giardia causes a diarrheal disease through contaminated water.
Groups of microbes compared
| Group | Cell type | Typical size | Cell wall | Example |
|---|---|---|---|---|
| Bacteria | Prokaryote | 1 to 5 µm | Peptidoglycan | E. coli |
| Archaea | Prokaryote | 1 to 5 µm | No peptidoglycan | Methanogens |
| Fungi | Eukaryote | 5 to 10 µm (yeast) | Chitin | Yeast, molds |
| Protozoa | Eukaryote | 10 to 200 µm | None | Amoeba |
How are microorganisms beneficial?
- Nutrient cycling: decomposers (bacteria and fungi) recycle dead matter. Nitrogen-fixing and nitrifying bacteria make nitrogen available to plants.
- Food production: yeast for bread, beer and wine; Lactobacillus for yogurt, cheese and sauerkraut.
- Medicine and biotechnology: antibiotics from fungi and bacteria, insulin made by genetically modified bacteria, and enzymes used in washing powders.
- Digestion and health: gut bacteria help to digest fiber, make vitamin K and compete with harmful microbes.
- Waste treatment: bacteria break down organic matter in sewage, and some can break down oil spills.
- Oxygen production: marine cyanobacteria and algae produce a large part of the oxygen in the atmosphere.
Worked example: counting microbes on a surface
A student presses a sterile swab on a table, rinses it in 10 mL of sterile water, dilutes 1 mL of the water into 9 mL of water (a ten-fold dilution), and spreads 0.1 mL of this dilution on an agar plate. After incubating for two days, 45 colonies grow. Estimate the number of viable bacteria in the original 10 mL rinse.
- Each colony comes from one viable cell or clump in the sample spread, so 45 colony-forming units (CFU) were in 0.1 mL of the diluted sample.
- Per mL of the diluted sample: 45 ÷ 0.1 = 450 CFU/mL.
- Correct for dilution: the dilution factor is 10, so the rinse contained 450 × 10 = 4 500 CFU/mL.
- Total in the 10 mL rinse: 4 500 × 10 = 45 000 CFU.
The result is an estimate of the number of bacteria that can grow on this medium, and it is a minimum, because many microbes will not grow on a given agar or in the temperature used. For reliable counts, plates with 30 to 300 colonies are used. The method also shows that the surface had around 45 000 viable bacteria in the sample, a normal number for a table. Aseptic technique and a control plate with sterile water are needed so that contamination does not affect the result.
How were microbes discovered?
Antonie van Leeuwenhoek was the first to see bacteria and protozoa, in the 1670s. Louis Pasteur showed in the 1860s that microbes cause fermentation and spoilage, and disproved spontaneous generation. Robert Koch developed methods to grow pure cultures and linked specific microbes to diseases in the 1870s and 1880s. Alexander Fleming discovered penicillin in 1928. Carl Woese’s work led to the recognition of Archaea in 1977.
Which mistakes are common?
Mistake 1: Treating all microbes as harmful germs
The great majority are harmless or useful. Only a small fraction cause disease.
Mistake 2: Using “bacteria” for all microorganisms
Fungi, protozoa and archaea are different groups. A virus is not a bacterium.
Mistake 3: Expecting antibiotics to work on all infections
Antibiotics act on bacteria. They do not work on viruses, and antifungal drugs are needed for fungi.
Mistake 4: Forgetting the dilution factor in counts
Multiply the colony count by the dilution factor and by the volume conversion to estimate the original concentration.