What lives in a handful of soil? Earthworms, microbes and fungal networks

At the end of a dry summer the first rain falls, and suddenly that smell rises: the smell of wet earth. Most of us think of it as “the smell of rain” (scientists call it petrichor). Yet its best-known ingredient, geosmin, is a molecule made by bacteria that live in the soil. In other words, that smell is the signature of an invisible crowd beneath our feet. In this post we look inside a handful of soil: who lives there, what do they do, and why is looking after this crowd our business too?

A city in the palm of your hand

Depending on the source, a single gram of fertile soil holds somewhere between about a hundred million and several billion bacterial cells. A handful of soil weighs roughly a hundred grams, so you could be holding more bacteria in your palm than there are people on Earth. These bacteria belong to thousands of different species. Most of them have never been grown in a laboratory, and many do not even have a name yet.

The bacteria have company. Fungi build networks out of fine threads called hyphae, so thin they are hard to make out with the naked eye. A single gram of forest soil can contain metres, sometimes hundreds of metres, of hyphae. Then come single-celled organisms, microscopic worms called nematodes, tiny eight-legged mites and the acrobats of the soil, the springtails, which fling themselves into the air with a spring-like “tail”. The creatures you can see with the naked eye are earthworms, ants, insect larvae, centipedes and moles.

Most of this crowd share the same trade: decomposition. Fallen leaves, dead roots and animal remains are first broken into small pieces and then digested chemically by microbes. The nitrogen, phosphorus and other nutrients inside them are returned in a form plants can use again. Without decomposers, forests would be buried under their own fallen leaves, and nutrients would stay locked up in dead matter.

Humus: the crowd’s legacy

What is left at the end of decomposition is a dark, long-lasting organic material: humus. Humus gives soil its dark colour, holds water like a sponge and keeps nutrient ions on its surface so that rain does not wash them away. It also binds soil particles together into loose clumps, so the soil crumbles and air and water can get in easily. When you squeeze a handful of good garden soil and it breaks apart into crumbs, you are seeing this structure at work.

Textbooks often give the example of a fertile loam that is roughly 45% minerals, 5% organic matter, 25% water and 25% air by volume. The share of air may come as a surprise, but these spaces are essential: roots and soil organisms need to breathe.

Darwin’s last book: earthworms

The last book Charles Darwin published was not about evolution but about earthworms. In this book, which came out in 1881, Darwin brought together more than forty years of observations. He showed how worms swallow soil and leave it on the surface as little piles of castings, and he calculated that in some English fields tens of tonnes of soil per hectare were brought up to the surface this way every year. He also linked the slow sinking of stones and the remains of old buildings into the ground to this silent work. As Darwin saw it, the land was being regularly “ploughed” by earthworms long before humans invented the plough.

Earthworm burrows let rainwater soak deep into the ground and let roots breathe. Worms drag dead leaves down into their burrows and mix them into the soil, and their castings are nutrient-rich, well-formed crumbs of soil. Seeing plenty of earthworms in a garden is usually a sign that the soil is healthy.

Fungal networks: partnership or internet?

Most land plants form a partnership between their roots and fungi called mycorrhiza. The plant gives the fungus some of the sugar it makes by photosynthesis. In return, the fungus, whose hyphae are far finer than any root, reaches into pores the root cannot enter and carries water, and especially phosphorus, back to the plant. Fossils show that this partnership is more than 400 million years old.

In recent years these networks have become famous as the “wood wide web”: we have been told that trees feed their young through fungal networks and warn one another of danger. It is true that a single fungus can connect to the roots of more than one tree. But a wide-ranging review published in 2023 concluded that many of these popular claims go beyond the evidence from real forests, and that some results had been over-interpreted. Fungal links between trees do exist; how widespread they are, and how much they really carry and how, is still being researched and debated.

Slow to form, quick to go

Soil forms as rocks are slowly broken down by water, ice, changes in temperature, roots and living things, and mixed with organic matter. According to the UN Food and Agriculture Organization (FAO), forming 1 centimetre of topsoil can take anything from hundreds of years up to a thousand, depending on conditions. Yet on a slope left bare, a single violent downpour can wash away several millimetres of soil.

With its sloping terrain, semi-arid climate and centuries of tree felling and overgrazing, Türkiye has a serious erosion problem. Streams that turn the colour of mud after rain are in fact carrying topsoil torn from the fields. At Karapinar, in Konya province, sand dunes that wind erosion had set on the move from the 1950s were largely halted by tree planting and windbreaks begun in the early 1960s. Terraces, ploughing across the slope and plant cover that never leaves the soil bare are the most effective ways to keep topsoil where it belongs.

Safe composting at home

Composting means turning kitchen and garden scraps into a nutrient-rich material much like humus by “feeding” them to soil organisms. You can do it in a lidded bin on a balcony or in a heap in the garden. A few rules make the job both easier and safer:

• Balance greens and browns. “Greens” such as vegetable and fruit peelings, tea leaves, coffee grounds and fresh grass clippings provide nitrogen. “Browns” such as dry leaves, torn-up cardboard and straw provide carbon and keep the heap airy. Roughly one part greens to two or three parts browns is a good start.
• Keep it as damp as a wrung-out sponge. In a heap that is too dry the organisms stop working; a heap that is too wet runs out of air and starts to smell.
• Let the air in. Turn the heap every few weeks. A smell of rotten eggs or something sour is usually a sign that it is short of air; adding brown material and mixing it in is usually enough.
• What to leave out. Meat, fish, dairy products and greasy leftovers smell and attract pests and rodents. Cat and dog faeces can carry disease-causing microbes and parasites and have no place in compost. Do not add diseased plants or weeds that have set seed either.
• Hygiene. Wear gloves when you work with compost and garden soil, and wash your hands with soap afterwards. Soil is also home to germs such as the tetanus bacterium: if you have an open wound, keep it away from soil, and ask a doctor or health centre whether your vaccinations are up to date. Do not breathe in the dust when you open dry compost or a bag of potting mix; dampening the material slightly as you work keeps the dust down.
• Be patient. Depending on conditions, within a few months to a year the scraps turn into a dark, crumbly material that smells like forest soil. Then you can mix it into your pots and garden beds.

If you are composting with children, turning the heap and handling the material should be done under an adult’s supervision.

Summary

• A handful of fertile soil is home to billions of bacteria, metres of fungal threads and countless small animals; most of them break down dead matter and put nutrients back into circulation.
• Humus helps soil hold water and gives it a crumbly structure; earthworms mix and aerate the soil; mycorrhizal fungi carry water and phosphorus to roots.
• Forming 1 cm of topsoil can take hundreds of years, up to a thousand; erosion can destroy this slow build-up very quickly.
• Composting at home is an easy way to give kitchen scraps back to the soil; meat, dairy products and pet faeces stay out of the heap.

To put the layers of soil in order yourself and match soil organisms to their jobs, take a look at the Nature and farming topic.