Microbiology and Biotechnology

Lessons

Senior 4 · Biology

Microbiology and Biotechnology

5 lessons

Lesson 1 of 5

Viruses, archaea and Escherichia coli

25 min

A bacterium in every gut, and in the medicine cabinet

You are carrying billions of bacteria of one species right now: Escherichia coli, a normal resident of the lower intestine of people and other warm-blooded animals. The World Health Organization notes that most strains are harmless, yet a few, such as the Shiga toxin-producing strain O157:H7, cause severe food poisoning. The same species, its harmless laboratory strains given a human gene, has been used to manufacture human insulin for people with diabetes since the 1980s. One species can be a partner, a killer and a factory.

In S4 Unit 2 you classified the living world into three domains and met bacteria and viruses. This unit studies microorganisms as a microbiologist does: their structure, how they grow and how we culture them, and how biotechnology puts them to work. This first lesson looks at three very different examples: viruses, archaea and E. coli.

Definition

Microbiology: the study of microorganisms (microbes): organisms or particles too small to be seen clearly without a microscope, including bacteria, archaea, many fungi and protoctists, and viruses.

Virion: a complete virus particle outside a host cell. Its capsid is a protein coat built from repeating units called capsomeres; some viruses also have an envelope, a lipid membrane taken from the host cell.

Archaea (archaebacteria): prokaryotes that form their own domain, differing from bacteria in their cell walls, membrane lipids and the enzymes that copy and read their genes.

Extremophile: an organism that thrives in extreme conditions such as high temperature, salt or acidity. Methanogen: an archaeon that produces methane.

Model organism: a species studied in great detail because it is easy to grow and its findings apply widely; E. coli is the model bacterium.

Faecal indicator: an organism such as E. coli whose presence in water shows contamination with faeces.

The microbial world

Group	Cell type	Typical size	Examples
Viruses	Not cells: nucleic acid in a protein coat; multiply only inside host cells	20–300 nm	Influenza virus, HIV, poliovirus, bacteriophages
Bacteria	Prokaryotic; cell wall of peptidoglycan	0.5–5 µm	E. coli, Lactobacillus, Mycobacterium tuberculosis
Archaea	Prokaryotic; no peptidoglycan	0.5–5 µm	Methanogens, halophiles (salt-lovers), thermophiles (heat-lovers)
Fungi	Eukaryotic; chitin cell walls; yeasts single-celled, moulds made of hyphae	Yeast cells 3–10 µm; hyphae 2–10 µm wide	Yeast, Rhizopus, Penicillium (Lesson 2)
Protoctists	Eukaryotic; mostly single-celled	10–500 µm	Plasmodium, Amoeba, Paramecium, algae

The units step down by a thousand each time: $1\ \text{mm} = 1000\ \mu\text{m}$ and $1\ \mu\text{m} = 1000\ \text{nm}$ , so $1\ \text{mm} = 10^{6}\ \text{nm}$ . A light microscope cannot resolve objects closer together than about $0.2\ \mu\text{m}$ , so it shows bacteria but not viruses; viruses were first seen with the electron microscope.

The structure of viruses

Every virion has a genome of either DNA or RNA (never both), single- or double-stranded, inside a protein capsid. The capsid protects the genome and carries the proteins that attach the virus to its host cell. Capsids come in a few basic shapes:

Enveloped viruses such as influenza and HIV are surrounded by a piece of the host cell's membrane, collected as the new virions bud out of the cell. Their envelope carries viral glycoproteins that bind to receptors on the next host cell. Because a lipid envelope is easily damaged, enveloped viruses are destroyed by soap, alcohol and drying faster than viruses without one: this is why handwashing with soap works so well against influenza and coronaviruses.

Archaea: the third domain

Archaea look like bacteria under the microscope: small cells with no nucleus. But their chemistry places them in a separate domain, and in some ways closer to eukaryotes than to bacteria.

Feature	Bacteria	Archaea	Eukarya
Nucleus	No	No	Yes
Cell wall	Peptidoglycan	No peptidoglycan (protein or other polymers)	Cellulose or chitin, if present
Membrane lipids	Fatty acids joined to glycerol by ester links	Branched chains joined to glycerol by ether links, more stable in heat	Ester links
Histones with DNA	No	Yes, in many	Yes
Disease-causing species	Many	None known	Some

Many archaea are extremophiles. Thermophiles live in hot springs above 80 °C, halophiles in water saltier than the sea, and methanogens in places with no oxygen, such as the rumen of cattle, the guts of termites, swamp mud and biogas digesters (Lesson 5), where they turn carbon dioxide and hydrogen or acetate into methane. Their heat-stable enzymes are useful in industry.

Escherichia coli: the model bacterium

Structure: a Gram-negative rod about 2 µm long and 0.5 µm wide, with flagella all over its surface, short pili for attachment, a nucleoid of circular DNA and often plasmids.
Way of life: a facultative anaerobe, respiring aerobically when oxygen is present and fermenting when it is not; it grows at 37 °C, the temperature of the gut.
Roles in the gut: part of the normal gut flora; it competes with harmful microbes and makes vitamin K.
Indicator of faecal pollution: because it lives in the gut, finding E. coli in drinking water shows that faeces have contaminated it, and that other gut pathogens may be present too.
Pathogenic strains: Shiga toxin-producing E. coli, spread in undercooked meat, raw milk and contaminated vegetables, can cause bloody diarrhoea and kidney failure; it is destroyed by cooking food until all parts reach 70 °C or more (WHO).
Model organism and factory: it can divide every 20 minutes or so in rich medium, is easy to grow and to modify genetically, and much of what we know about DNA replication and gene control was first found in E. coli. Harmless laboratory strains carrying human genes produce insulin and other proteins.

Worked example 1: sizes from a micrograph

In a printed copy of an electron micrograph taken at $\times 15\,000$ , one E. coli cell measures 30 mm long. (a) Calculate its actual length in micrometres. (b) An influenza virus is 100 nm across. How many would fit side by side along the cell? (c) At what magnification would the virus appear 5 mm across?

(a) $\text{actual size} = \frac{\text{image size}}{\text{magnification}} = \frac{30\ \text{mm}}{15\,000} = 0.002\ \text{mm} = 2\ \mu\text{m}$
(b) $2\ \mu\text{m} = 2000\ \text{nm}$ , so $\frac{2000\ \text{nm}}{100\ \text{nm}} = 20$ viruses.
(c) $5\ \text{mm} = 5 \times 10^{6}\ \text{nm}$ , so $\text{magnification} = \frac{\text{image size}}{\text{actual size}} = \frac{5 \times 10^{6}\ \text{nm}}{100\ \text{nm}} = \times 50\,000$ Always convert both sizes to the same unit before dividing.

Worked example 2: living or not?

A student claims that viruses, archaea and E. coli are "all bacteria". Use their structure to evaluate the claim.

E. coli is a bacterium: a prokaryotic cell with a peptidoglycan wall, its own ribosomes and metabolism, which grows and divides on its own.
Archaea are also prokaryotic cells that grow and divide on their own, but they lack peptidoglycan, have ether-linked membrane lipids and histone-like proteins, so they belong to a separate domain, not to the bacteria.
Viruses are not cells at all: they have no ribosomes, no metabolism and no membrane of their own (an envelope is borrowed from the host), and they can multiply only inside a host cell. They are not bacteria, and are not placed in any of the three domains.
So the claim is wrong for two of the three; only E. coli is a bacterium.

European Food Safety Authority (EFSA): "What is E. coli? What can you do to protect yourself and others?". Watch for where E. coli normally lives, how harmful strains reach food, and the kitchen hygiene steps that prevent infection.

Warning

Biosafety and common mistakes

In a school laboratory, use only harmless laboratory strains supplied for teaching (such as E. coli K-12). Never try to culture bacteria from people, toilets, raw meat or water samples: you could grow pathogens such as STEC.
Calling a virus a cell or a microorganism that "grows". A virus has no metabolism; it is copied by the host cell.
Saying archaea are "ancient bacteria". They are a separate domain, living today all around us, not only in extreme places.
Thinking all E. coli are dangerous. Most strains are harmless gut partners; only some strains cause disease.
Dividing sizes in different units. Convert mm, µm and nm to the same unit first.

Tip

Memory hook. Sizes in microbiology go up by about ten each step: "Virus 0.1, Bacterium 1, Yeast 10, Protozoan 100" micrometres (roughly). And "Archaea have Alternative lipids (ether links) and Absent peptidoglycan."

✦

Practice: viruses, archaea and E. coli

Name the four basic shapes of virus capsid and give an example of each.
Explain why soap and alcohol destroy enveloped viruses more easily than non-enveloped ones.
Give three differences between archaea and bacteria.
State three reasons why E. coli is used as a model organism.
Explain why testing drinking water for E. coli is a good way to detect faecal contamination.
A virus is 80 nm across. In an electron micrograph it appears 12 mm across. Calculate the magnification.
An E. coli cell is 2.5 µm long and is drawn 50 mm long. Calculate the magnification of the drawing.

Show answersHide answers

Helical (tobacco mosaic virus); icosahedral (adenovirus, poliovirus); enveloped (influenza, HIV); complex (bacteriophage).
The envelope is a lipid membrane taken from the host cell. Soap and alcohol dissolve or disrupt lipids, so the envelope breaks apart and the virus loses the glycoproteins it needs to attach to cells; a protein capsid without an envelope is tougher.
Any three: archaea have no peptidoglycan in their cell walls; their membrane lipids are branched and ether-linked rather than ester-linked; many have histones associated with their DNA; no archaea are known to cause disease; many are extremophiles or methanogens.
Any three: it grows quickly (dividing about every 20 minutes in rich medium); it is cheap and easy to culture; harmless laboratory strains exist; its genome is small and well known; it is easy to modify genetically; results from it apply to many other organisms.
E. coli lives naturally in the gut of people and warm-blooded animals and is shed in very large numbers in faeces, but does not usually multiply in clean water. So its presence shows recent faecal contamination, which means gut pathogens such as Vibrio cholerae or Salmonella may also be present.
$12\ \text{mm} = 12 \times 10^{6}\ \text{nm}$ ; magnification $= \frac{12 \times 10^{6}}{80} = 150\,000$ , so $\times 150\,000$ .
$50\ \text{mm} = 50\,000\ \mu\text{m}$ ; magnification $= \frac{50\,000}{2.5} = 20\,000$ , so $\times 20\,000$ .

Quick check

Match each microbe to a typical size.

Tap one on the left, then its partner on the right.

Key points

Microbes span about five orders of magnitude in size: viruses 20–300 nm, prokaryotes about 1–5 µm, protoctists up to hundreds of µm. Actual size = image size ÷ magnification, in the same units.
Viruses: DNA or RNA in a protein capsid (helical, icosahedral or complex), sometimes inside a lipid envelope; no cells, no metabolism.
Archaea: prokaryotes with no peptidoglycan, ether-linked lipids and histones; many are extremophiles or methanogens; none known to cause disease.
E. coli: Gram-negative rod about 2 µm long, facultative anaerobe, normal gut bacterium, faecal indicator, model organism and producer of human insulin; a few strains (STEC) cause serious disease.

Sources and credits

1.3: Types of Microorganisms, 4.6: Archaea, 4.2: Proteobacteria and 6.1: Viruses, from Microbiology by OpenStax (Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister, Brian M. Forster), via LibreTexts Biology, licensed under CC BY 4.0. Adapted by Ganzaa.
World Health Organization, E. coli fact sheet (7 February 2018).
Figures 1 and 2, the tables, worked examples, practice and quick check: written by Ganzaa.
Images: CDC/Erskine L. Palmer and M. L. Martin, public domain; NIAID, public domain; both via Wikimedia Commons.
Video: "What is E. Coli? What can you do to protect yourself and others?", European Food Safety Authority, embedded from YouTube.

1A bacterium in every gut, and in the medicine cabinet

2The microbial world

3The structure of viruses

4Archaea: the third domain

5Escherichia coli: the model bacterium

A bacterium in every gut, and in the medicine cabinet

The microbial world

The structure of viruses

Archaea: the third domain

Escherichia coli: the model bacterium