Rachel Brazil talks to the scientists trying to understand – and improve – the health of the planet’s soil

Soil is facing a crisis. While the developed world has improved its air and water quality, soil ‘is taken for granted’, says Ruben Sakrabani, a soil chemist at Cranfield University in the UK. ‘Now we have reached a point where we need to reassess how we have managed the soil so far.’ Climate change and the overuse of chemical fertilisers are leaving it vulnerable to erosion and loss of fertility, with serious implications for our ability to feed everyone on the planet in the future.

Although for some of us it comes in plastic bags from the garden centre, soil starts its life as bedrock, weathered down into particles which are colonised by microbes and plants. These decay to become part of the fertile mixture we know as soil (see box What is soil below). Sakrabani and many other researchers are now concerned with ‘soil health’ – the continuing capacity of soil to sustain plants, animals and ultimately humans. The EU has reported that 60–70% of European soils are degraded and about a billion tons of soil is washed away by erosion every year – at a cost of €1.25 billion (£1.06 billion). According to a United Nations-backed study, about a third of soils globally show declining health, with 24 billion tonnes of fertile soil being lost each a year.

‘There’s a tension with food security and the soil health,’ explains Mark Fitzsimons, an environmental chemist at the University of Plymouth in the UK. ‘Post second world war, developed countries have moved towards intensification of agriculture… the application of chemical fertiliser being managed according to yield rather than the effect on soil health and also the impact on other environmental factors.’ Fitzsimons also suggests that poor soil quality has lead to a reduction in the nutritional value of our food: ‘Necessary elements aren’t being replaced. Selenium in wheat is one example.’

What is soil?

Soil is a mixture of minerals, organic matter, air, water and micro-organisms that provides the ideal medium for plants to grow. Its mineral content comes from weathered bedrock, a process that takes tens of thousands of years, ultimately creating layers termed horizons where there is a transition from coarse stones to soil. 

Soil triangle diagram

Source: © Sheila Terry/Science Photo Library

As bedrock varies greatly, so do the soils derived from it, but most soils are constituted from the silicate minerals feldspars (aluminium silicates), mica (layered silicates) and quartz (silica).These minerals release nutrient elements into the soil solution including potassium, sodium, iron, copper and other micro-nutrients. Carbonate minerals derived from parent material serve as a source of calcium and magnesium.

The size of the mineral particles is the basis for classifications of soil textures as sand (50–2000µm), silt (2–50µm) or clay (smaller than 2µm). Combining these particles in different proportions provides mixtures, including loams – soils that are ideal for agriculture, as they retain moisture but do not get water-logged.

Soil acidity naturally reflects the parent material but in warmer, wetter regions soil pH decreases over time, due to leaching caused by rainfall. In dry climates, pHs tend to stay neutral or alkaline. High clay soils are more resistant to changes in pH than sandy soils, where water percolation is greater.

Organic material is also crucial to soil. In temperate climates, a thick organic horizon forms at the surface of the soil which maintains a high microbial community making fertile soils. Soils composed entirely of decaying plant matter are known as peats and are formed where soil is waterlogged and lacking in oxygen, slowing decomposition and producing deep organically rich layers – prized by gardeners but now in need of protection, as extracting it damages wildlife habitats and releases huge amounts of carbon dioxide

Leaching and loss

Ellen Fray, founder and executive director of the Sustainable Soils Alliance calls soil a ‘silent mammoth’ underpinning much else in the environment. But it’s now becoming a threat, particularly to water health and aquatic life, because that’s where it goes when it’s lost. Excess chemical fertilisers, designed to add nitrogen, potassium and phosphorus (NKP) back into soil, have contributed to the pollution of our waterways by feeding toxic algal blooms. There are now UK and EU regulations to limit this damage but the leaching of nitrate is also indicative of the soil’s inability to hold onto nutrients supplied from chemical fertilisers.

‘Adding nitrate to the soil in chemical form is the worst thing we could do in terms of hoping it’s retained,’ explains Fitzsimons. The problem is that nitrate ions are negatively charged, and so are many of the oxide species that make up soil particles. ‘The particles cannot easily hold on to the nitrate even if it wants to, it’s being repulsed, [so] it’s such a mobile form of nitrogen.’ He suggests that proteins, larger molecules with nitrogen, carbon, oxygen and potentially with positively charged sites, could attach to the particles and arrange themselves in the soil in a more stable way. It could be used and broken down as needed, he explains.

There has also been a gradual depletion of organic carbon from heavily farmed soils, which does not get replenished when chemical fertilisers are used. ‘I’m not saying that chemical fertilisers are bad – they have done a good job since they were created 50–60 years ago,’ says Sakrabani. ‘But there’s also [the] organic matter, which is basically what makes the soil a living system. It’s like the glue that binds the soil particles together.’

The soil was converting organic nitrogen to nitrate and getting rid of it

Over the years the replenishment of organic material has declined, particularly in hot climates. ‘Some parts of southern Spain, it’s almost a desert,’ says Sakrabani, ‘In the [hotter, drier] southern part of Europe, the carbon that’s present [in organic molecules] gets burn off as carbon dioxide… in the tropics, you’ve got a similar challenge as well, because it’s hot and humid, so the turnover will also be very quick.’

Based on his recent studies on synthetic soils, Fitzsimons has also hypothesised that this depletion in carbon could impact how soil retains it nitrogen content as well. When carbon is limited, he says microbes in the soil were extracting the carbon from organic molecules and rejecting the nitrogen. ‘The soil was converting [organic nitrogen] to nitrate and getting rid of it.’

On top of all this, degraded soils are adding to the release of greenhouse gases. ‘Soils store a lot more carbon than the atmosphere does,’ says Fray, but in some areas soil has become an emitter of both carbon dioxide and nitrous oxides. And of course producing ammonium nitrate fertilisers from the Haber–Bosch process is energy intensive, producing a total emission of 3.6kg of carbon dioxide equivalents per kilogram of nitrogen.

‘We recognise that soil is degraded, that it’s a global problem, yet there’s no collective action that’s discernible,’ says Fitzsimons. But this is starting to change. One novel suggestion recently proposed is to spread finely ground basalt rock dust onto unhealthy soil, known as ‘enhanced weathering’. ‘The theory behind that is that the carbon dioxide can also get trapped in the crystal lattices of the silicate material, making [the carbon content of the soil] more stable… this is possibly a quick win,’ says Sakrabani. A team from Belgium, Germany and the UK recently tested the approach with a potato crop and gained an increased yield.

Recycle and replenish

Other solutions have focused on recycling waste materials to replenish soils. ‘As a concept, it’s something that our forefathers have done for donkey’s years,’ says Sakrabani. He has been collaborating with chemical engineer Peter Hammond, chief technical officer at CCm Technologies near Oxford, a company developing a more sustainable fertiliser that they say will improve soil health.

Hammond starts with the products of anaerobic digesters, which use bacteria to break down organic matter such as manure, waste water and food waste, in the absence of oxygen. The process produces biogas (carbon dioxide and methane), heat and left-over organic digestate. ‘The great advantage we’ve got is that the ammonia is already present as a molecule in those sources,’ explains Hammond. It comes from fertiliser leachate or from the breakdown of urea from animal waste. CCm simply pass carbon dioxide over the digestate which reacts with the ammonia to produce a bicarbonate. They then add calcium nitrate to end up with ammonium nitrate and chalk mixed with the organic digestate. They even use the heat generated from the digester to turn the product into fertiliser pellets, with around 50% NKP content and 50% organic carbon.

CCm pellets

Source: © CCm Technologies

CCm’s sustainable fertiliser aims to release nutrients more slowly as well as increase the carbon content of the soil

Apart from an elegant and sustainable recycling process, and the ability to sequester some carbon dioxide, there are advantages to soil treated with their fertiliser. ‘With mineral fertilisers, there’s no [organic carbon] going back,’ says Hammond. Plus the ammonium nitrate returned to the soil in the pellets is less labile. ‘It’s going to break down in solution to the ammonium part and the nitrate part, both of which will be used by the plant, but the rate that it does that is slower than if it was available as either of those ions straight from the word go.’ Leaching of nutrients is reduced by 60–70% compared to both urea and other ammonium nitrate mineral fertilisers.

Even spreading manures and other organic matter can result in losses and leaching of nutrients before plants have a chance to use them. ‘Emissions are quite significant as well, direct carbon dioxide emissions from the breakdown of the organics, but also the nitrogen is still in ammonia form in the farmyard and so they tend to either be washed out of the system, or leave the system through evaporation where they’re broken down into various nitrous oxides and cause a level of harm to the environment,’ explains Hammond.

If you can trap the carbon dioxide into the pellet and make sure it actually stays trapped in the soil that will be fantastic

This occurs less with digestate fertiliser due to the type of organic material it contains. ‘What’s left behind [in the anaerobic digester] tends to be the larger, harder to break down, more robust molecules, so those go into the soil, and they will be around for a long time.’ Using a standard test the company says that it would expect roughly 20% of the organic material to stay in the soil for at least 20 years. Sakrabani has also been working with Hammond to understand just how stable the carbon returned to the soil will be. ‘If you can trap the carbon dioxide into the pellet and make sure it actually stays trapped in the soil post application that will be fantastic. I haven’t got all the evidence yet… we are doing some greenhouse gas measurements to understand that process.’

The company is forging ahead with trials of its fertiliser and has built a plant with PepsiCo at their Walkers Crisps facility in Leicester, where they are using waste from potato crops to create fertiliser. They are also working with Severn Trent Water to develop the process using sewage. CCm are not the only company trying to improve soils using waste – Norwegian company N2 Applied has developed a process using farm slurry to produce a nitrogen-enriched organic fertiliser. The first unit in the UK was purchased by Scotland’s Rural College in July. Their method uses an electric field to create a plasma which converts ammonia into nitrate, locking it into the fertiliser.

Synthetic soil

Fitzsimons is also utilising waste – but rather than improving unhealthy soil, he has been starting from scratch and he has experimented with reconstructed soil based on mining waste or even deposited sediment, perhaps itself eroded from soil. ‘By taking these inorganic materials, like for example waste clay, and combining that with appropriate forms of green waste, we actually have all the components of a living soil,’ he says. Some of this work has been in collaboration with the Eden project in Cornwall.

Once a material is a waste, it is very difficult to get it recognised as a product afterwards

In their first attempt to create the ideal soil in 2019, they found it difficult to retain the nitrogen. ‘It becomes what we call nitrogen-saturated,’ says Fitzsimons. The solution was to add carbon in the form of biochar – organic material that has been carbonised at high temperatures (300–1000°C) in a limited oxygen supply. They found adding biochar up to 10% by weight decreased dissolved nitrogen in soil leachate by up to 44%, and carbon by up to 35%. Fitzsimmon suggests that the biochar may provide increased ion exchange capacity and retention of molecules within its pores. Tests on their soils show an ability to sustain growth through climate extremes such as prolonged heat or rain, for at least three weeks.

Fitzsimons has also been working with a French team looking at creating reclaimed soils from dredged harbour sediments. They have subjected the material to electrokinetic treatment – a process in which a low-voltage direct-current electric field is applied to assist in removing contaminants as well as adding biodegradeable chelating agents such as citric acid and non-ionic surfactants. This can be done cost-effectively with batches of up to 40kg, but whether it can scaled up is still a question.

All these attempts to use waste materials to replenish or create soil are currently hampered by waste regulations. ‘The problem is, once a material is a waste, it is very difficult to get it recognised as a product afterwards,’ says Hammond. Fitzsimons agrees that policy changes are crucial. ‘Waste statistics indicated that 50% of landfill volume was the disposal of soils… I think as a society it shows that we don’t value soils,’ he says. According to Hammond the UKs Environment Agency is now in the process of examining these regulations so he is hopeful that there will be changes.

Microbes and monitoring

Understanding and improving the chemical make-up of the soil is only half the story. The other half is the soil microbiome – which has itself become disturbed by the degradation of soils. ‘Microbes are an essential part of life in the soil, that helps the plants to grow in the same way that microbes allow humans or animals to grow through colonising the digestive system – the digestive system of the plants being their roots,’ says Alberto Acedo, cofounder of Biome Makers, a company based in California, US, producing biofertilisers to improve soil health.

Just a handful of soil contains around 10 billion bacteria, fungi and archaea and their action will drive nutrient cycles for plants. Over-use of synthetic fertilisers or mono-agriculture tends to perturb microbe communities and this can diminish soils’ ability to withstand erosion and pathogens. Companies are now developing biofertilisers to combat this, by adding microbial life back into soils.

On example is Spanish company Symborg, which is producing the nitrogen-fixing bacteria methylobacterium symbioticum, which improves plant growth and seed productivity, while cutting down nitrous oxide emission. Acedo’s Biome Maker has taken a broader approach and is looking to understand the whole network of microbes colonising different soil types, and using AI to then infer how to optimise crop yields for each different soil and crop.

They have developed a global database of 10 million micro-organisms from 35,000 soil samples covering more than 122 crops in over 40 countries, from banana production in Costa Rica to corn in the US. In 2021, collaborating with Bayer Crop Science, they launched the first AI virtual assistant to help farmers and agronomists pinpoint what their soils need to boost yields in a sustainable way.

But not everyone thinks the answer to improving soil health is technology, some counsel a return to less intensive farming methods including leaving land for ‘green cover’ – green nitrogen-fixing plants to restore soil structure and build fertility. ‘There’s always this conundrum that you need to produce the same outputs, arguably, with fewer inputs. We’ve got to feed everybody,’ Hammond reiterates. He suggests the sorts of sustainable fertilisers CCm are producing offer a sustainable solution.

Our perception also has to change

One of the current problems according to Fray is that there is little monitoring of soil quality. ‘What is needed is a really consistent metric that everybody agrees upon in order to measure soil health.’ One novel high-resolution approach to monitoring the nitrogen content of soil has been developed by computational scientist Liangxiu Han at Manchester Metropolitan University in the UK, to help prevent over-application of fertiliser. This would currently require chemical analysis of plant tissue which is destructive and costly: ‘analysis may cost around £40 per sample’, says Han.

Instead, she has developed an AI robotic system that uses imaging to capture both spectral and spatial features above the crop canopy and from this accurately predict their nitrogen status across different parts of a field. The system, N2Vision, uses machine learning,with data sets of 3D crop images and their corresponding chemical analysis. ‘You can see that there are very subtle changes to the colour or the [plant] architecture [and] these are all being captured by AI,’ explains Han. Once trained, the system can bypass the chemical analysis step and provide accurate nitrogen level data based on the images alone.

A feasibility study in collaboration with Kew Gardens has achieved high accuracy and reproducibility for wheat crops so far, and Han says they plan to collect data and train the system for other crops. ‘For this project, we have focused on nitrogen, but we can also use the images [to quantify] other [properties] like pH and very important nutrients like calcium and we’re planning to do this as well.’

Part of the difficulty in dealing with soil is that, unlike any other natural resource, it is owned by individuals, ‘which is something you can’t say about water or the air, and that causes complexities’, says Fray. In the UK about 70% of soil is owned by farmers and Fray hopes that the government will now act to incentivise improvements in soil health, including monitoring. Current UK policies, including the Sustainable Farming Initiative launched in June, provide payments for some beneficial practices but ‘the cost–benefit analysis is quite opaque’, says Fray, and there is still no commitment to monitoring soil health.

The EU is also likely to further protect soil health in 2023 and has published a soil strategy which will include improving soils with cleaned waste materials and digestates. But this may be too little, too late. ‘Our perception also has to change,’ says Sakrabani. ‘We also need to change our lifestyle… we cannot be demanding strawberries all the time, we need to use seasonal crops.’ And, he suggests, we really should grow fruit and vegetables ourselves and start developing our own relationship with the soil.

Rachel Brazil is a science writer based in London, UK