Microorganisms, Bacteria, Viruses, Fungi, Protists

Scrape the inside of your cheek with a cotton bud, smear it on a slide, and stain it, under a microscope the large oval shapes you see are your own cheek cells, and scattered among them are far smaller specks: bacteria living in your mouth right now. Microorganisms like these are everywhere, in the soil, in the air, in your gut, on your skin and inside almost every other living thing.

Almost all of that useful work comes from one habit. A bacterium cannot bite or swallow, so it feeds by releasing chemicals that break large molecules apart outside its body into small ones it can absorb. Nearly everything we get out of bacteria is a side effect of that breaking-down. The bacteria in your gut split apart fibres your own digestive system cannot, and you absorb what is left over. The Lactobacillus in yoghurt breaks down the sugar in milk and produces lactic acid, and it is that acid which thickens the milk and gives yoghurt its sour taste. Bacteria in soil break a dead leaf down into minerals a new plant can take up through its roots.

The jobs that matter most:

• Gut bacteria in your intestines help you digest food (you have about 1.5 kg of them inside you right now).
• Soil bacteria break down dead matter and fix nitrogen from the air so plants can use it.
• Dairy bacteria such as Lactobacillus turn milk into yoghurt and cheese, and the acid they produce also keeps spoilage bacteria out, which is why yoghurt keeps far longer than the milk it was made from.

So why is a small number of bacteria dangerous? Not because pathogens are a different kind of thing. They break molecules down in exactly the same way; the trouble is that some of them are good at breaking down you, or release waste chemicals your body reacts badly to. The clearest evidence that a bacterium is not simply "good" or "bad" is E. coli: billions of them live in your intestine right now doing useful work, and the same species on undercooked mince causes food poisoning. What changed was the strain and the place it ended up, not the kind of organism. Three are worth knowing by name.

Salmonella causes food poisoning, usually from undercooked chicken or eggs. Streptococcus causes strep throat. Mycobacterium tuberculosis causes tuberculosis, an infection of the lungs that, before antibiotics existed, killed roughly one person in seven across Europe.

Bacterial diseases can often be treated with antibiotics. Those are usually described as "medicines that kill bacteria but not human cells", which is true and does not say how. An antibiotic works by attacking a structure that bacteria have and your cells do not. Penicillin stops a bacterium building its cell wall, so when the bacterium next tries to divide it bursts. Your cells have no cell wall at all, so penicillin finds nothing to attack in them and leaves them alone. Hold on to that, because the next card needs it.

A virus is a tiny package of genetic material wrapped in a protein coat. It is not made of cells. On its own it can't move, grow, eat or respire, so most biologists say it is not alive. (You met this idea in Lesson 1.)

Because it is not built from cells, a virus is described as non-cellular, and the genetic material inside its protein coat is either DNA or RNA, depending on the virus. Influenza and SARS-CoV-2 both carry RNA.

Viruses only do one thing. A virus has to find a living cell to get into, which is called its host cell, and it then has to get its genetic material inside. How it does that depends on the virus. The ones that attack bacteria stay outside and inject their genetic material through the cell wall, like a syringe. Influenza, SARS-CoV-2 and HIV do it differently: each is wrapped in an oily coat that merges with the host cell's own membrane, so the contents are delivered inwards rather than pushed in from outside. Either way the result is the same. The virus hijacks the host cell's machinery and makes it build new viruses instead of doing its own job, so the virus can replicate itself hundreds of times over, and the cells doing the copying are usually destroyed in the process.

You have met the results of that hijacking many times. The influenza virus causes the flu and SARS-CoV-2 causes COVID-19, both by taking over cells in your airways. Varicella zoster causes chickenpox, then hides in nerve cells for decades before it can return as shingles. HIV causes AIDS, and it is the most damaging of the four because the cells it hijacks are the immune cells whose job is to fight infections.

Now use the antibiotic idea from the previous card. An antibiotic works by attacking a structure a bacterium has and you do not, such as a cell wall. A virus has no cell wall, no cytoplasm and no ribosomes, because it is not a cell at all, so there is nothing there for the antibiotic to attack. That is why antibiotics do not work on viruses, and why taking one for the flu does nothing at all. It also explains why antiviral medicines are so much harder to invent: a virus copies itself using your cell's machinery, so a drug that wrecked the machinery the virus depends on would be wrecking your own cells at the same time. Vaccines are the best defence instead, because they teach your immune system to recognise the virus before you get sick.

Fungi range from tiny single-celled yeasts to huge networks underground. They get their food by absorbing nutrients and cannot photosynthesise, which is why they are NOT plants.

That word "absorbing" is doing more work than it looks. A fungus grows fine threads out into whatever it is sitting on, releases digesting chemicals into the material around those threads, and then takes the small molecules back in. It digests its food outside its own body and absorbs the result, which is the same trick bacteria use. It also explains what you can actually see: mould spreads across a slice of bread as a growing patch rather than sitting on top of it, because the threads have to reach the food in order to feed on it at all.

The three kinds you should know:

• Yeasts single-celled fungi. The yeast in bread dough releases CO₂ that makes the dough rise. The yeast in beer turns sugar into alcohol.
• Moulds the fuzzy growth you see on old bread or fruit. Penicillium mould was used by Alexander Fleming to discover the antibiotic penicillin.
• Multi-celled fungi mushrooms, toadstools and the huge underground fungal networks that connect tree roots in a forest.

A fungus and a gum tree are easy to lump together and could hardly be more different. Both stay in one place, both grow, and neither moves. But a gum tree makes its own food out of air, water and light, so it needs sunlight and spends its energy growing upwards to reach it. A fungus makes none of its own food, so it needs something dead or living to feed on, and sunlight is no use to it, which is why mushrooms come up in the shade after rain instead of out in the open. Even the building material differs: a plant cell wall is made of cellulose, a fungal one of chitin, the same substance as an insect's exoskeleton.

Along with bacteria, fungi are the planet's main decomposers. Without them, dead leaves and dead animals would never rot. Forests would be buried in dead matter and the nutrients locked inside would never return to the soil.

Some fungi are harmful, ringworm and tinea (athlete's foot) are caused by fungi infecting human skin.

Protists are single-celled organisms with a nucleus. The nucleus is what makes them different from bacteria. Most live in water (a drop of pond water has dozens of them swimming around).

Having a nucleus sounds like a small detail, and it is the reason this group looks the way it does. A nucleus is a compartment that keeps the cell's DNA separate from the rest of the cell, and a cell that can wall off one job in its own compartment can wall off others too. That is why protists can afford working parts a bacterium has no room for: the cilia a Paramecium rows itself along with, the pseudopods an amoeba stretches out to engulf its prey, and the chloroplasts a Euglena uses to make its own food. Bacteria have none of this, and the missing nucleus is where the difference starts.

So protists range from harmless pond-water swimmers to one of the deadliest pathogens in human history (Plasmodium has killed billions over the centuries).