The theory of soil

As Franklin Roosevelt famously once warned: “the nation that destroys its soil, destroys itself”. And whilst the issue of ‘soil health’ has been creeping up the political agenda for many years, Roosevelt’s words are, for the most part, still not being heeded.

Whilst the potential threats to soil inherent in heavy industrial activities such as construction, mining, or oil and gas extraction have long been apparent, what we hadn’t realised until recently was just how much damage everyday farming is doing to the soil. And what we’ve also realised is that, rather than being a recent development, the trouble started way back in the 19th Century.

Picture if you will, the sort of bucolic countryside scenes so beloved of Victorian painters. Weary farmers till the soil by hand or at best, using ox-drawn ploughs. Cattle, horses, geese, and chickens are raised alongside fields of wheat, barley, and rye as – unlike most modern farms – these smallholders reared both animals and crops. Manures were used to support soil fertility.

“the nation that destroys its soil, destroys itself – Franklin Roosevelt”

Whimsical, yes, but in addition to documenting a lost (albeit heavily romanticised) way of life, these paintings also document a major turning point in soil health. It was around the mid-1800s when modern artificial fertilisers started to be commercially produced.

A rapidly growing population was leading to more and more land entering cultivation, but a real shortage of manure to fertilise it. Developments such as John Lawes superphosphate ‘artificial manure’, and the mining of Chilean saltpetre to make the nitrogen equivalent allowed high crop yields to be achieved without a concurrent increase in livestock. Today, mass produced synthetic fertilisers are ubiquitous the world over.

The Theory of Soil

People’s concerns over modern ‘industrial farming’ have generally focused on the impact of pesticides on the health of humans and wildlife, opposition to genetically modified (GM) crops, water pollution caused by fertiliser runoff, and more recently, the greenhouse gas emissions of livestock.

When it came to the older – and what were considered more benign – activities of adding synthetic fertiliser or ploughing, any cost was always thought to be minimal and far outweighed by the benefits of high yielding food crops.

What we didn’t really understand was that these common practices were causing fundamental changes that negatively impact on soil’s store of organic carbon, ability to prevent flooding, and even provide us with enough food.

Unlocking soil’s secret structure

Recently, my colleagues and I took to a radical new approach of thinking about soil – and it has solved the mystery of why adding organic material like manure improves such universal ‘ecosystem services’ that are widely recognised as being worth billions to the global economy.

Using more than 50 years’ worth of data from a unique field experiment, we demonstrated that common farming practices drain the soil of carbon, altering the structure of soils’ microscopic habitat and, remarkably, the genetics of microbes living within it.

Soil research

Our team of microbiologists and physicists considered almost 9,000 genes and used X-ray imaging to look at soil pores smaller than the width of a human hair. In concert with previous work, we have started forming what we envisage will be a universal ‘Theory of Soil’.

We found that in healthy soils, relatively low nitrogen levels limit microbes’ ability to utilise carbon compounds, so they excrete them as polymers which act as a kind of ‘glue’ creating a porous, interconnected structure in the soil which allows water, air, and nutrients to coexist and circulate.

What we revealed is that the Victorian-era switch from manure to ammonium nitrate and phosphorous based fertilisers has caused microbes to metabolise more carbon, excrete less polymers and fundamentally alter the properties of farmland soils when compared to their original grassland state.

We noticed that as carbon is lost from soil, the pores within it become smaller and less connected. This results in fundamental changes in the flow of water, nutrients and oxygen through soil and forces several significant changes to microbial behaviour and metabolism. Low carbon, poorly connected soils are much less efficient at supporting growth and recycling nutrients.

A lack of oxygen in soil results in microbes having to turn to nitrogen and sulphur compounds for their energy – inefficient processes, which result in increased emissions of the greenhouse gas nitrous oxide among other issues.

The closed soil structure also means microbes need to expend more energy on activities such as searching out and degrading less easily accessible organic matter for nutrients.

Conversely, in carbon-rich soil there is an extensive network of pores which allow for greater circulation of air, nutrients, and retention
of water.

The Theory of Soil

Manure is high in carbon and nitrogen, whereas ammonia-based fertilisers are devoid of carbon. Decades of such inputs – and soil processes typically act over decades – have changed the way soil microbes get their energy and nutrients, and how they respire. Modern arable farming also returns much less organic matter to soil than Victorian farming practices.

Finding the missing link

Whilst soil carbon was already known to drive climate and water cycles the world over, the idea to look at this link between the living and non-living components of soil came about through a discussion between myself (a microbiologist) and Professor John Crawford – now at the University of Glasgow – who studies the way complex systems behave.

Despite carbon’s critical role in soil health, the mechanisms underlying carbon dynamics and the link to soil water were poorly understood. Society struggles with the concept of what soil is and how it can be managed effectively because it is such a complex combination of biological, chemical, and physical processes.

We took inspiration from a theory proposed by evolutionary biologist Richard Dawkins in the 1980s, that many structures we encounter are in fact products of organisms’ genes, which he termed the “extended phenotype” – Dawkins used the examples of bird nests and beaver dams.  This view helped us understand soil as a product of microbial genes, incorporating organic materials from plants and other inputs as energy and nutrients to create the all-important structure.

As a result, we have shown for the first time a dynamic interaction between soil structure and microbial activity – fuelled by carbon – which regulates water storage and gaseous flow rates in soil with real consequences for how microbes respire. EPS stabilises the aggregation of soil particles in the environment adjacent to the microbe. This makes the physical structure of the environment around these microbes more stable to disruption, such as occurrences when the soil wets up and dries, or when plant roots pass nearby. Because this stabilisation is linked to the activity of microbes, microenvironments that are favourable to microbial activity are preferentially reinforced relative to other microenvironments in soil.

Lab and field experiments along with computer modelling, have shown that the outcome of this over time is to increase the volume and connectivity of the pore structures that are important for storing water, enabling the supply of oxygen to microbes, and connecting water and nutrient pools to plants. 

The Theory of Soil

However, long term addition of nitrogen and phosphorous fertilisers has caused microbes to burn more of these carbon compounds for energy, an activity that has increased emissions of CO2.

Our group, which also involved scientists from The University of Nottingham, are the first to seriously study the details of this intimate two-way relationship between the microscopic life in soil and its structure at scales relevant to microbial processes.

The results also demonstrated why soils can sometimes show great resilience to human interventions. Although years of intensive management practices have altered what compounds microbes predominantly live on and increased the frequency of genes that allow this lifestyle, very few genes are ever completely lost from the system. That crucially allows soils to respond to changes and these results can really help with any future remediation efforts.

Microbes are very good at acquiring genes from each other which is why, rather than look at different species, we looked at the abundance of different genes and what functions they are ultimately coded for.

Long-term impacts of fertilisers

The results also have implications for farmers, where the addition of nitrogen and phosphorous fertilizers – and not carbon – may in fact be leading to a degradation of the natural fertility and the efficiency with which nutrients are processed in their soils that will be detrimental to the long-term productivity of their farm. The increased leakiness of the soil system also leads to damaging nutrient loss to the atmosphere and rivers.

All this new knowledge places soils at the nexus of several environmental issues currently facing agriculture and wider society: plentiful food, clean water, and the climate crisis. More than a third of the world’s soil is already degraded, and the IPCC estimates that could rise to 90% by 2050 if nothing is done. Even moderately degraded soil produces 30% less food and stores around half the water of healthy soil. Given that many productive soils now contain substantially less organic carbon than before the advent of inorganic fertilizers – over that period Rothamsted soils alone have lost approximately 50 tonnes of organic carbon per hectare from the top 30 cm – there is potential for soil to contribute to reducing carbon losses to the atmosphere and the warming that this causes.

Fixing the biodiversity crisis

By 2050, we will need to produce up to 60% more food while nearly half the world’s population may live in ongoing drought conditions. Without action, the conflict between humans and wildlife – the root cause of the current pandemic – will only intensify. Fixing soil would go a long way to alleviating this conflict by helping secure future food supply, reducing water stress, and mitigating climate change.

The Theory of Soil

The biodiversity crisis also has implications for soil management too. We rely on soil to grow almost all our food, but perhaps surprisingly we know little about how the way we manage soils affects the microbial communities which support soil fertility, provide clean water, and regulate greenhouse gas emissions. When you look at the types of microorganism species found in the soil, common farming practices such as ploughing, fertilising, and adding pesticide to fields, results in a chaotic new (microbial) world order where nitrogen robbing archaea and killer fungi have muscled their way in at the expense of many plant beneficial fungi. We saw that when grassland is converted to arable, the richness of species doesn’t change very much. Although new species move in, they don’t necessarily fill the same ecological roles.

“fixing soil would go a long way to alleviating current conflict by helping secure future food supply, reducing water stress, and mitigating climate change”

Soil research

Compared to their original grassland state, arable soils had fewer, but more varied, species of fungi. Mycorrhizal fungi, those that form mutual beneficial associations with plants and play important roles in plant nutrition, are reduced in favour of pathogenic fungi that survive by attacking insects, plants, and lichen. We also saw a greater variety of bacteria in arable soil, whilst the total number of species of archaea –a group of single cell organisms members of which generate the greenhouse gas nitrous oxide as a by-product of ammonia oxidation – also increased in response to fertilisation.

Our research has also found the more ‘nutritionally monotonous’ arable soil environment has led many bacteria to ‘reduce their running costs’ by jettisoning more than 600 of the genes usually needed when faced with the diverse range of food sources found in grasslands or pastures.  This means that typical measures of soil biodiversity aren’t adequately explaining what is going on in soil, as farming not only changes the number and relatedness of the species present, but also the genetic complement of the community as a whole.


IPCC Climate Change and Land Special Report: