Does rot make living things out of nothing? Around 1668 the Italian physician Francesco Redi tested whether living things can appear by themselves out of rotting material, covering jars so that flies could not lay eggs in them, and those covered jars stayed free of maggots, which showed that young flies come from flies' eggs, not from the rot. In 1745 John Needham boiled broth, sealed it and saw it turn cloudy with tiny creatures, and he argued that they arose spontaneously. Lazzaro Spallanzani later did many careful experiments with heated broth, and his sealed flasks stayed clear unless they were opened to air, while Needham's broth, boiled and sealed, had turned cloudy.

The argument was still going in the 1850s, when Louis Pasteur's work fought the belief that some life arises from non-living matter. His rival Felix Pouchet argued for spontaneous generation in an 1859 book, and Pasteur ran a series of experiments in the early 1860s to test his germ theory. In 1861 he heated broth in a flask with a long S-shaped (swan) neck, so that air could get in but dust was trapped in the bend, and the broth stayed clear, but when he broke the neck, the broth spoiled. Redi's jars date from about 1668, so the swan-neck flask came about 193 years after the covered jars.

Pasteur showed that yeast, a living organism, causes alcoholic fermentation, and he also showed that a living organism turns sugar into lactic acid in milk, so souring is caused by life, not just chemistry. Yeasts are fungi, and they make the bubbles in bread. In 1864 Pasteur found that heating wine to 50-60 degrees C (122-140 degrees F) killed the microorganisms that spoil it, and the process, pasteurization, was later used for milk too. It came three years after the swan-neck flask. Cold also slows down the tiny living things that spoil food, which is why we keep food in the fridge, although cold slows mould but does not stop it.

A mould is a kind of fungus, seen as fuzzy growth on old bread or cheese. Its spores are microscopic, from 2 to 100 microns across, and many are so small that they float through the air. Spores turn up indoors and outdoors, yet growth happens only where there is moisture. Mould digests whatever it grows on, and moisture is the most important factor for mould growth indoors. In 1928 Alexander Fleming saw that mould on a lab dish had a bacteria-free circle around it, and the mould made penicillin. He found that a mould culture stopped staphylococci from growing even when it was diluted 800 times, and he named the active substance penicillin.

Compost is dark, crumbly and smells like fresh soil, and decomposers make it from old leaves and food scraps, including fruit and vegetable scraps and dry leaves. A good compost pile feels like a wrung-out sponge, damp but not dripping, and healthy compost smells earthy, like fresh soil, not like rotten eggs. A pile that smells like rotten eggs is too wet or short of air, and adding dry leaves and turning it helps. In a well-kept pile, compost is ready in about three to five months, while a pile left alone can take a year or more. Cool composting uses mesophiles, microbes that work at about 40 to 110 degrees F, and it makes excellent compost but needs about a year. Compost helps soil hold water, and it feeds plants by releasing nutrients slowly.

Fruit spoils on a schedule of its own. Fruits give off a gas called ethylene that starts them ripening, and riper fruit makes more of it, which speeds up ripening. Fruits are sorted into two types: climacteric fruits, such as apples, bananas, peaches and avocados, can keep ripening after picking, while non-climacteric fruits, such as grapes, cherries and strawberries, cannot. Ethylene works in a loop in climacteric fruit, because a little ethylene makes the fruit produce more, which speeds ripening, and this is why a ripe fruit can quickly soften and spoil in storage.

Microbes are not the only things that break down dead plants, because earthworms, snails, millipedes and beetles help too. Bugs and worms chew dead plants into small bits first, and then tiny fungi and bacteria finish the job. Earthworms leave behind nutrient-rich castings that plants can use, and worm composting makes a soil booster called vermicompost. Earthworms can eat up to their own weight in a day, which keeps organic material out of landfills. When things rot, nutrients go back into the soil, and living plants use them to grow, so the animals and the microbes both feed the next plants.

Words to know

• spontaneously: by itself
• fermentation: yeast change
• pasteurization: heat treatment
• spores: tiny seeds
• penicillin: mould medicine