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Beneath our feet is an ecosystem so astonishing that it tests the limits of our imagination. Its as diverse as a rainforest or a coral reef. We depend on it for 99% of our food, yet we scarcely know it. Soil.

Under one square metre of undisturbed ground in the Earths mid-latitudes (which include the UK) there might live several hundred thousand small animals. Roughly 90% of the species to which they belong have yet to be named. One gram of this soil less than a teaspoonful contains around a kilometre of fungal filaments.

When I first examined a lump of soil with a powerful lens, I could scarcely believe what I was seeing. As soon as I found the focal length, it burst into life. I immediately saw springtails tiny animals similar to insects in dozens of shapes and sizes. Round, crabby mites were everywhere: in some soils there are half a million in every square metre.

Then I began to see creatures I had never encountered before. What I took to be a tiny white centipede turned out, when I looked it up, to be a different life form altogether, called a symphylid. I spotted something that might have stepped out of a Japanese anime: long and low, with two fine antennae at the front and two at the back, poised and sprung like a virile dragon or a flying horse. It was a bristletail, or dipluran.

As I worked my way through the lump, again and again I found animals whose existence, despite my degree in zoology and a lifetime immersed in natural history, had been unknown to me. After two hours examining a kilogram of soil, I realised I had seen more of the major branches of the animal kingdom than I would on a weeks safari in the Serengeti.

But even more arresting than soils diversity and abundance is the question of what it actually is. Most people see it as a dull mass of ground-up rock and dead plants. But it turns out to be a biological structure, built by living creatures to secure their survival, like a wasps nest or a beaver dam. Microbes make cements out of carbon, with which they stick mineral particles together, creating pores and passages through which water, oxygen and nutrients pass. The tiny clumps they build become the blocks the animals in the soil use to construct bigger labyrinths.

Soil is fractally scaled, which means its structure is consistent, regardless of magnification. Bacteria, fungi, plants and soil animals, working unconsciously together, build an immeasurably intricate, endlessly ramifying architecture that, like Dust in a Philip Pullman novel, organises itself spontaneously into coherent worlds. This biological structure helps to explain soils resistance to droughts and floods: if it were just a heap of matter, it would be swept away.

It also reveals why soil can break down so quickly when its farmed. Under certain conditions, when farmers apply nitrogen fertiliser, the microbes respond by burning through the carbon: in other words, the cement that holds their catacombs together. The pores cave in. The passages collapse. The soil becomes sodden, airless and compacted.

But none of the above captures the true wonder of soil. Lets start with something that flips our understanding of how we survive. Plants release into the soil between 11% and 40% of all the sugars they make through photosynthesis. They dont leak them accidentally. They deliberately pump them into the ground. Stranger still, before releasing them, they turn some of these sugars into compounds of tremendous complexity.

Making such chemicals requires energy and resources, so this looks like pouring money down the drain. Why do they do it? The answer unlocks the gate to a secret garden.

These complex chemicals are pumped into the zone immediately surrounding the plants roots, which is called the rhizosphere. They are released to create and manage its relationships.

Soil is full of bacteria. Its earthy scent is the smell of the compounds they produce. In most corners, most of the time, they wait, in suspended animation, for the messages that will wake them. These messages are the chemicals the plant releases. They are so complex because the plant seeks not to alert bacteria in general, but the particular bacteria that promote its growth. Plants use a sophisticated chemical language that only the microbes to whom they wish to speak can understand.

When a plant root pushes into a lump of soil and starts releasing its messages, it triggers an explosion of activity. The bacteria responding to its call consume the sugars the plant feeds them and proliferate to form some of the densest microbial communities on Earth. There can be a billion bacteria in a single gram of the rhizosphere; they unlock the nutrients on which the plant depends and produce growth hormones and other chemicals that help it grow. The plants vocabulary changes from place to place and time to time, depending on what it needs. If its starved of certain nutrients, or the soil is too dry or salty, it calls out to the bacteria species that can help.

Take a step back and you will see something that transforms our understanding of life on Earth. The rhizosphere lies outside the plant, but it functions as if it were part of the whole. It could be seen as the plants external gut. The similarities between the rhizosphere and the human gut, where bacteria also live in astonishing numbers, are uncanny. In both systems, microbes break down organic material into the simpler compounds the plant or person can absorb. Though there are more than 1,000 phyla (major groups) of bacteria, the same four dominate both the rhizosphere and the guts of mammals.

Just as human breast milk contains sugars called oligosaccharides, whose purpose is to feed not the baby but the bacteria in the babys gut, young plants release large quantities of sucrose into the soil, to feed and develop their new microbiomes. Just as the bacteria that live in our guts outcompete and attack invading pathogens, the friendly microbes in the rhizosphere create a defensive ring around the root. Just as bacteria in the colon educate our immune cells and send chemical messages that trigger our bodys defensive systems, the plants immune system is trained and primed by bacteria in the rhizosphere.

Soil might not be as beautiful to the eye as a rainforest or a coral reef, but once you begin to understand it, it is as beautiful to the mind. Upon this understanding our survival might hang.

We face what could be the greatest predicament humankind has ever encountered: feeding the world without devouring the planet. Already, farming is the worlds greatest cause of habitat destruction, the greatest cause of the global loss of wildlife and the greatest cause of the global extinction crisis. Its responsible for about 80% of the deforestation thats happened this century. Of 28,000 species known to be at imminent risk of extinction, 24,000 are threatened by farming. Only 29% of the weight of birds on Earth consists of wild species: the rest is poultry. Just 4% of the worlds mammals, by weight, are wild; humans account for 36%, and livestock for the remaining 60%.

Unless something changes, all this is likely to get worse much worse. In principle, there is plenty of food, even for a rising population. But roughly half the calories farmers grow are now fed to livestock, and the demand for animal products is rising fast. Without a radical change in the way we eat, by 2050 the world will need to grow around 50% more grain. How could we do it without wiping out much of the rest of life on Earth?

Just as farming is trashing crucial Earth systems, their destruction threatens our food supply. Sustaining even current levels of production might prove impossible. Climate breakdown is likely, on the whole, to make wet places wetter and dry places drier. One more degree of heating, one estimate suggests, would parch 32% of the worlds land surface. By the middle of this century, severe droughts could simultaneously affect an arc from Portugal to Pakistan. And this is before we consider the rising economic fragility of the global food system, or geopolitical pressures, such as the current war in Ukraine, that might threaten 30% of the worlds wheat exports.

Its not just the quantity of production thats at risk, but also its quality. A combination of higher temperatures and higher concentrations of CO2 reduces the level of minerals, protein and B vitamins that crops contain. Already, zinc deficiency alone afflicts more than a billion people. Though we seldom discuss it, one paper describes the falling concentrations of nutrients as existential threats.

Some crop scientists believe we can counter these trends by raising yields in places that remain productive. But their hopes rely on unrealistic assumptions. The most important of these is sufficient water. The anticipated growth in crop yields would require 146% more fresh water than is used today. Just one problem: that water doesnt exist.

Over the past 100 years, our use of water has increased six-fold. Irrigating crops consumes 70% of the water we withdraw from rivers, lakes and aquifers. Already, 4 billion people suffer from water scarcity for at least one month a year and 33 major cities, including So Paulo, Cape Town, Los Angeles and Chennai, are threatened by extreme water stress. As groundwater is depleted, farmers have begun to rely more heavily on meltwater from glaciers and snowpacks. But these, too, are shrinking.

A likely flashpoint is the valley of the Indus, whose water is used by three nuclear powers (India, Pakistan and China) and several unstable regions. Already, 95% of the rivers flow is extracted. As the economy and the population grow, by 2025 demand for water in the catchment is expected to be 44% greater than supply. But one of the reasons why farming there has been able to intensify and cities to grow is that, as a result of global heating, glaciers in the Hindu Kush and the Himalayas have been melting faster than theyve been accumulating, so more water has been flowing down the rivers. This cant last. By the end of the century, between one- and two-thirds of the ice mass is likely to have disappeared. It is hard to see this ending well.

And all this is before we come to the soil, the thin cushion between rock and air on which human life depends, which we treat like dirt. While there are international treaties on telecommunication, civil aviation, investment guarantees, intellectual property, psychotropic substances and doping in sport, there is no global treaty on soil. The notion that this complex and scarcely understood system can withstand all we throw at it and continue to support us could be the most dangerous of all our beliefs.

Soil degradation is bad enough in rich nations, where the ground is often left bare and exposed to winter rain, compacted and wrecked by overfertilisation and pesticides that rip through its foodwebs. But it tends to be even worse in poorer nations, partly because extreme rainfall, cyclones and hurricanes can tear bare earth from the land, and partly because hungry people are often driven to cultivate steep slopes. In some countries, mostly in Central America, tropical Africa and south-east Asia, more than 70% of the arable land is now suffering severe erosion, gravely threatening future production.

Climate breakdown, which will cause more intense droughts and storms, exacerbates the threat. The loss of a soils resilience can happen incrementally and subtly. We might scarcely detect it until a shock pushes the complex underground system past its tipping point. When severe drought strikes, the erosion rate of degraded soil can rise 6,000-fold. In other words, the soil collapses. Fertile lands turn to dustbowls.

Some people have responded to these threats by calling for the relocalisation and de-intensification of farming. I understand their concerns. But their vision is mathematically impossible.

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A study in the journal Nature Food found the average minimum distance at which the worlds people can be fed is 2,200km. In other words, this is the shortest possible average journey that our food must travel if we are not to starve. For those who depend on wheat and similar cereals, its 3,800km. A quarter of the global population that consumes these crops needs food grown at least 5,200km away.

Why? Because most of the worlds people live in big cities or populous valleys, whose hinterland is too small (and often too dry, hot or cold) to feed them. Much of the worlds food has to be grown in vast, lightly habited lands the Canadian prairies, the US plains, wide tracts in Russia and Ukraine, the Brazilian interior and shipped to tight, densely populated places.

As for reducing the intensity of farming, what this means is using more land to produce the same amount of food. Land use is arguably the most important of all environmental issues. The more land farming occupies, the less is available for forests and wetlands, savannahs and wild grasslands, and the greater is the loss of wildlife and the rate of extinction. All farming, however kind and careful, involves a radical simplification of natural ecosystems.

Environmental campaigners rail against urban sprawl: the profligate use of land for housing and infrastructure. But agricultural sprawl using large amounts of land to produce small amounts of food has transformed much greater areas. While 1% of the worlds land is used for buildings and infrastructure, crops occupy 12% and grazing, the most extensive kind of farming, uses 28%. Only 15% of land, by contrast, is protected for nature. Yet the meat and milk from animals that rely solely on grazing provide just 1% of the worlds protein.

One paper looked at what would happen if everyone in the US followed the advice of celebrity chefs and switched from grain-fed to pasture-fed beef. It found that, because they grow more slowly on grass, the number of cattle would have to rise by 30%, while the land area used to feed them would rise by 270%. Even if the US felled all its forests, drained its wetlands, watered its deserts and annulled its national parks, it would still need to import most of its beef.

Already, much of the beef the US buys comes from Brazil, which in 2018 became the worlds largest exporter. This meat is often promoted as pasture-fed. Many of the pastures were created by illegally clearing the rainforest. Worldwide, meat production could destroy 3m sq km of highly biodiverse places in 35 years. Thats almost the size of India.

Only when livestock are extremely sparse is animal farming compatible with rich, functional ecosystems. For example, the Knepp Wildland project in West Sussex, where small herds of cattle and pigs roam freely across a large estate, is often cited as a way to reconcile meat and wildlife. But while its an excellent example of rewilding, its a terrible example of food production.

If this system were to be rolled out across 10% of the UKs farmland and if, as its champions propose, we obtained our meat this way, it would furnish each person here with 420 grams of meat a year, enough for around three meals. We could eat a prime steak roughly once every three years. If all the farmland in the UK were to be managed this way, it would provide us with 75kcal a day (one 30th of our requirement) in meat, and nothing else.

Of course, this is not how it would be distributed. The very rich would eat meat every week, other people not at all. Those who say we should buy only meat like this, who often use the slogan less and better, present an exclusive product as if it were available to everyone.

Campaigners, chefs and food writers rail against intensive farming and the harm it does to us and the world. But the problem is not the adjective: its the noun. The destruction of Earth systems is caused not by intensive farming or extensive farming, but a disastrous combination of the two.

So what can we do? Part of the answer is to take as much food production out of farming as we can. As luck would have it, the enabling technology has arrived just as we need it. Precision fermentation, producing protein and fat in breweries from soil bacteria, fed on water, hydrogen, CO2 and minerals, has the potential to replace all livestock farming, all soya farming and plenty of vegetable oil production, while massively reducing land use and other environmental impacts.

But this remarkable good fortune is threatened by intellectual property rights: it could easily be captured by the same corporations that now monopolise the global grain and meat trade. We should fiercely resist this: patents should be weak and anti-trust laws strong. Ideally, this farm-free food should be open source.

Then we could relocalise production: the new fermentation technologies could be used by local businesses to serve local markets. As some of the worlds poorest nations are rich in sunlight, they could make good use of a technology that relies on green hydrogen. Microbial production horrifies some of those who demand food sovereignty and food justice. But it could deliver both more effectively than farming does.

Such technologies grant us, for the first time since the Neolithic period, the opportunity to transform not only our food system but our entire relationship with the living world. Vast tracts of land can be released from both intensive and extensive farming. The age of extinction could be replaced by an age of regenesis.

Of course, we would still need to produce cereals, roots, fruit and vegetables. So how do we do it safely and productively? The answer might lie in our new understanding of the soil.

On a farm in south Oxfordshire, techniques developed by a vegetable grower called Iain Tolhurst Tolly seem to have anticipated recent discoveries by soil scientists.

Tolly is a big, tough-looking man in his late 60s, with etched and weathered skin, a broad, heavy jaw, long blond hair, one gold earring, hands grained with earth and oil. He started farming without training or instruction, without land or any means to buy it. After a string of misadventures, he managed to lease seven hectares (17.3 acres) of very poor land at a reduced rent, 34 years ago.

No conventional grower would even look at this ground, he told me. Its 40% stone. Theyd call it building rubble. It isnt even classed as arable: an agronomist would say its only good for grass or trees. But over the past 12 months, we harvested 120 tonnes of vegetables and fruit.

Astonishingly, for these 34 years Tolly has been farming this rubble without pesticides, herbicides, mineral treatments, animal manure or any other kind of fertiliser. He has pioneered a way of growing that he calls stockfree organic. This means he uses no livestock or livestock products at any point in the farming cycle, yet he also uses no artificial inputs.

Until he proved the model, this was thought to be a formula for sucking the fertility out of the land. Vegetables in particular are considered hungry crops, which require plenty of extra nutrients to grow. Yet Tolly, while adding none, has raised his yields until theyve hit the lower bound of what intensive growers achieve with artificial fertilisers on good land: a feat widely considered impossible. Remarkably, the fertility of his soil has climbed steadily.

On my first visit, one June, I was struck by the great range and health of Tollys crops. One plot was a blue haze of onion plants, another a patchwork of sea greens: young cauliflower plants, several kinds of cabbage and kale. There were rows of rainbow chard with gold, green, white and crimson stems. Broad bean pods had begun to sprout from tight pillars of flower. His potatoes were in full bloom, nightshade sinister, stamens like yellow stings. Courgettes extruded rudely behind their trumpet flowers. There were carrots, tomatoes, peppers, beans of all kinds, herbs, parsnips, celeriac, cucumbers, lettuces. He raises 100 varieties of vegetables, which he sells in his farm shop and to subscribers to his veg box.

Separating the plots were untended banks, in which scientists studying his farm have found 75 species of wildflowers. These banks are an essential component of his system, harbouring the insect predators that control crop pests. Though he uses no pesticides, none of the vegetable plants I saw showed signs of significant insect damage: the leaves were dark and wide, with scarcely a hole or a spot.

Almost single-handedly, through trial and error, Tolly has developed a new and revolutionary model of horticulture. At first it looks like magic. In reality, its the result of many years of meticulous experiments.

Two of his innovations appear to be crucial. The first, as he puts it, is to make the system watertight: preventing rain from washing through the soil, taking the nutrients with it. What this means is ensuring the land is almost never left bare. Beneath his vegetables grows an understorey of green manure, plants that cover the soil. Under the leaves of his pumpkins, I could see thousands of tiny seedlings: the weeds he had deliberately sown. When the crops are harvested, the green manure fills the gap and soon becomes a thicket of colour: blue chicory flowers, crimson clover, yellow melilot and trefoil, mauve Phacelia, pink sainfoin.

Theres green manure under the green manure, Tolly told me. As soon as we cut the bigger plants, it comes into flower, and the bees go crazy.

Some of the plants in his mix put down deep roots that draw nutrients from the subsoil. Every so often, Tolly runs a mower over them, chopping them into a coarse straw. Earthworms pull this down and incorporate it into the ground. The idea is to let the plants put back at least as much carbon and minerals as we take out.

Tolly tells me that the green manure ties up nutrients, fixes nitrogen, adds carbon and enhances the diversity of the soil. The more plant species you sow, the more bacteria and fungi you encourage. Every plant has its own associations. Roots are the glue that holds and builds the soil biology.

The other crucial innovation is to scatter over the green manure an average of one millimetre a year of chipped and composted wood, produced from his own trees or delivered by a local tree surgeon. This tiny amendment appears to make a massive difference. In the five years after he started adding woodchip, his yields roughly doubled. As Tolly explains: It isnt fertiliser; its an inoculant that stimulates microbes. The carbon in the wood encourages the bacteria and fungi that bring the soil back to life. Tolly believes hes adding enough carbon to help the microbes build the soil, but not so much that they lock up nitrogen, which is what happens if you give them more than they need.

What Tolly appears to be doing is strengthening and diversifying the relationships in the rhizosphere the plants external gut. By keeping roots in the soil, raising the number of plant species and adding just the right amount of carbon, he seems to have encouraged bacteria to build their catacombs in his stony ground, improving the soils structure and helping his plants to grow.

Tollys success forces us to consider what fertility means. Its not just about the amount of nutrients the soil contains. Its also a function of whether theyre available to plants at the right moments, and safely immobilised when plants dont need them. In a healthy soil, crops can regulate their relationships with bacteria in the rhizosphere, ensuring that nutrients are unlocked only when theyre required. In other words, fertility is a property of a functioning ecosystem. Farm science has devoted plenty of attention to soil chemistry. But the more we understand, the more important the biology appears to be.

Can Tollys system be replicated? So far the results are inconclusive. But if we can discover how to mediate and enhance the relationship between crop plants and bacteria and fungi in a wide range of soils and climates, it should be possible to raise yields while reducing inputs. Our growing understanding of soil ecology could catalyse a greener revolution.

I believe we could combine this approach with another suite of innovations, by a non-profit organisation in Salina, Kansas, called the Land Institute. Its seeking to develop perennial grain crops to replace the annual plants from which we obtain the great majority of our food. Annuals are plants that die after a single growing season. Perennials survive from one year to the next.

Large areas dominated by annuals are rare in nature. They tend to colonise ground in the wake of catastrophe: a fire, flood, landslide or volcanic eruption that exposes bare rock or soil. In cultivating annuals, we must keep the land in a catastrophic state. If we grew perennial grain crops, we would be less reliant on smashing living systems apart to produce our food.

For 40 years, the Land Institute has been scouring the world for perennial species that could replace the annuals we grow. Already, working with Fengyi Hu and his team at Yunnan University in China, it has developed a perennial rice with yields that match, and in some cases exceed, those of modern annual breeds. Farmers are queueing up for seed. While annual rice farming can cause devastating erosion, the long roots of the perennial varieties bind and protect the soil. Some perennial rice crops have now been harvested six times without replanting.

Perennials are their own green manures. The longer they grow, the stronger their relationships with microbes that fix nitrogen from the air and release other minerals. One estimate suggests that perennial systems hold five times as much of the water that falls on the ground as annual crops do.

The Land Institute is developing promising lines of perennial wheat, oil crops and other grains. The deep roots and tough structures of perennial plants could help them to withstand climate chaos. The perennial sunflowers the institute is breeding have sailed through two severe droughts, one of which entirely destroyed the annual sunflowers grown alongside them.

While no solution is a panacea, I believe that some of the components of a new global food system one that is more resilient, more distributed, more diverse and more sustainable are falling into place. If it happens, it will be built on our new knowledge of the most neglected of major ecosystems: the soil. It could resolve the greatest of all dilemmas: how to feed ourselves without destroying the living systems on which we depend. The future is underground.

George Monbiot will discuss Regenesis at a Guardian Live event in London on Monday 30 May. Book tickets to join the event in person, or via the livestream here.

Regenesis: Feeding the World Without Devouring the Planet by George Monbiot is published by Penguin Books at 20 on 26 May. To support the Guardian and Observer, order your copy at guardianbookshop.com. Delivery charges may apply.

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The secret world beneath our feet is mind-blowing and the key to our planet's future - The Guardian