David Arky / WIRED

Eight years ago, Dutch microbiologist Jos Raaijmakers was pursuing a line of inquiry many would deem unglamorous: inspecting the inner workings of beans. Trudging over mountainside in rural Colombia, Raaijmakers and his team would collect soil samples from wild bean roots and take snapshots of the thriving community of microbes and fungi that lived there.

What they found put them on edge. Wild beans, it turned out, had different microorganisms clustered around their roots than their domesticated descendants – even when planted in the same soil. “I think this is going to be bigger than only this project,” Raaijmakers recalls telling his colleagues over beers one evening.


Long overlooked by science, we’re just starting to understand that the teeming ecosystem contained within soil – where bacteria, fungi, nematodes and earthworms feed off each other — plays a crucial role in undergirding plant life. How exactly this system functions remains a mystery. Yet, similar to how gut microbes are now thought to influence mental health, few doubt that the health of plants is linked to microscopic life in the soil.

And Raaijmakers’ beans could be the solution to a below-ground crisis that threatens to undermine our entire system of food production.

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Arable soils are shrinking and dying. Sickly modern crops rely ever more heavily on fertilisers and pesticides in order to survive – a death knell for soil. Intensive crop farming also sucks nutrients from the soil, without fully replacing them. With the global population set to rise to 10 billion by 2050, there are fears increased food demand could tip soils into oblivion.

Ancestor crops, which still grow in the wild, may provide a way out of the dilemma. Often less greedy for nutrients, and with associated communities of microorganisms that fight disease better, Raaijmakers and his colleagues hope to find – and reintroduce – beneficial ancient plant traits lost over millennia of selective breeding.


“We’re trying to find the missing microbes and we’re trying to see if those microbes have a beneficial function for plant growth or protection,” says Raaijmakers, who is now testing wild varieties of crops such as potatoes and sorghum in field trials spanning Colombia, Ethiopia and the Netherlands.

His colleague at the Netherlands’ Institute for Ecology (NIOO), Wim van der Putten, agrees that modern food crops urgently need a reboot. “Our ecological research shows that there is sort of a system error in agriculture,” he says, explaining that humans had sown their own troubles by consistently selecting for nutrient-rich but disease-prone plants. “Soils are a thing that you can only use once.”

Hidden below our feet, soils have stayed out of mind. But scientists are beginning to worry about the multitude of threats they’re facing. Fertile soil is a finite resource, for starters. It takes a century or more to naturally form one centimetre of topsoil – the uppermost layer of soil that contains most of the nutrients needed for plant growth – yet modern farming practices such as tilling and monocropping are weakening them so much that they blow away in strong winds or wash away in downpours. Pesticides and fertilisers also hurt microbial life, which loosens the soil. Forty per cent of arable soils in England and Wales are thought to be at risk of erosion, according to a June report by Britain’s Environment Agency.

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To make matters worse, soil contains the world’s largest stores of carbon, and cracking them open could provoke huge greenhouse gas emissions. Jessica Davies, a Lancaster University sustainability professor, says that disrupting soils will accelerate climate change: “They contain more carbon than all the trees and atmosphere put together”. There are other issues besides: heavy vehicles compact earth and block the through-passage of water, while developers deaden microbial life by pouring more and more concrete on top of soil.

Add to this jumble a rocketing world population and specialists fret that stressed soils won’t be able to sustain enough enough crops in the future. Only this month, the United Nation’s Intergovernmental Panel on Climate Change released a report warning that scant attention to soil health will endanger food security.

However, a more fundamental problem than ploughs and concrete threatens soil: greedy plants. “10,000 years ago, agricultural crops were developed from species that have big seeds like barley and wheat,” says Van der Putten, the towering head of terrestrial ecology at NIOO, explaining that large seeds are easy to gather, and good to eat.

However, these types of crops can foment “negative feedback”, which means that each successive crop is less able to grow in the same soil. “These are fast-growing plants, and in nature, they just come in, grow fast, produce seeds and then they’re gone again. They are very ephemeral in their behaviour.”

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Farmers used to rotate their crops over many years to circumvent the problem – changing up the plants they farmed in order to give soil time to recover. However, far fewer now practice rotation because there’s little economic incentive to do so. Repeat cultivation of these draining crops – moulded over thousands of years of breeding – has also created a problem that now increases with each harvest, like compound interest on a payday loan.

Ancient farmers took wild plants and, over thousands of years, selected for mutations with preternaturally large, calorie-dense seeds. The drawback is that today’s crops require far more water and are far more fragile than their ancient forebears, because of a trade off between high yields and disease defence. They’re also nutrient gluttons.

Simply replacing nutrients with chemical fertilisers is a poor solution. Alongside problems such as groundwater and air pollution, applying excessive nitrogen can acidify soils, while some researchers believe phosphorus harms microbial life. Van der Putten says problems are only showing up now because we’re putting soil under more stress.

To the likes of Van der Putten and Raaijmakers, the problem must be tackled at the root. At NIOO, a futuristic wood-glass complex housing gleaming lab equipment, greenhouses and test fields, researchers are examining ways to harness the power of ancient crop varieties. The idea is that if certain plant traits require fewer pesticides and fertilisers, the soil benefits. The same goes for plant traits that produce nutritious seeds less burdensome to the soil.

One avenue, which Van der Putten is looking at, involves studying “mid-successional” species – or plants that sprout up after mosses, lichens and grasses have established themselves – in an effort to isolate the traits which make these plants less demanding when they colonise a territory.

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An alternative approach being trialed by Raaijmakers is to hunt for traits linked to beneficial microbes that live around ancient plant species, and then select for those traits in modern varieties through plant breeding. This would allow the modern crop cultivation system to continue while eliminating its biggest abuses.

With strong interest from seed companies, Raaijmakers is using recent developments in chemical analysis, such as high-throughput screening, to create accurate maps of the microbiomes associated with wild plants and isolate the bacteria or fungi that fight off disease.

The work is feasible, but logistically daunting. Researchers travel back and forth to field sites where the plant grows in native ground, in places such as the Andes, to study soils at different stages of a plant’s development. Analysis must often be performed on the spot because of soil-transport restrictions linked to international biosecurity agreements. Once they find likely microbes or fungi, they then proceed to greenhouse or laboratory experiments.

One project looking at sorghum – a major cereal crop in the developing world – is the furthest along. Funded by the Bill and Melinda Gates Foundation, Raaijmakers has sorghum field trials running in the plant’s native Ethiopia. The aim is to use feisty microbes to combat witchweed, a parasitic purple plant that decimates sorghum harvests. He’s already performing greenhouse experiments, but is cautious about the results. “It’s too early to be optimistic at this stage,” Raaijmakers says.

However, to some, the sensible solutions to the looming soil crisis are more mundane. Jennifer Dungait, a former soil researcher, left academia last year to preach to farmers the simple methods they can use to alleviate soil stress, such as refraining from tilling, leaving stalks on the ground to mulch, and planting cover crops in the winter to keep soil from washing away. “[Fungi] don’t live if they’re getting chopped up by a plough,” she says.

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Even providing for a complete reset of crop cultivation, time is against the researchers. Field trials can last up to a decade, followed by a lengthy breeding process, and then regulatory hurdles. Raaijmakers estimated it could be ten to 20 years before any new crops are sown. Van der Putten says it could take up to 40.

NIOO’s work is “exploratory,” Van der Putten admitted. However, he’s seton finding a solution to a system that is already careening towards its own destruction. Fixing agriculture, he says, will mean finding a way to keep yields high without completely destroying the soil those crops need to live. If we’re to achieve this, he says, something will have to give. “We cannot go on like mad men.”

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