Carbon Starvation – A Crisis Of Our Time?

Are we beginning to see carbon – the fundamental building block of all life – as a pollutant? Instead of demonising carbon as a cause of climate breakdown, we need to restore balance in the natural carbon cycle that has been disrupted by the use of artificial fertilisers. In advance of his upcoming series on farming within planetary boundaries, Stuart Meikle offers a primer on the complex role of carbon in our soils. 

Carbon is everywhere, in us humans, in all animals, birds and aquatic life, in all plant life, in the soil, be it alive or dead, and in the atmosphere. With the agenda increasingly dominated by Climate Change, we could, however, be forgiven for thinking that the only carbon that counts is in the atmosphere. We even count other greenhouse gases, which may not even contain carbon (like nitrous oxide), in terms of carbon (dioxide) equivalents.      

As a consequence, are we beginning to see carbon, the fundamental building block of all life, as a pollutant?

In recent months, building upon other published articles, some of which appeared also on the ARC2020 website, I have been researching and thinking about what sustainable food systems look like. They start with the soil. And that becomes more apparent when one considers artificial fertilizers in the context of fossil fuel availability, their physical availability, and their propensity to pollute and emit. Agriculture is beginning a whole new ball game.

When it comes to understanding the vital plant-soil-plant interactions, I would highlight the work of three soils specialists: Dr Christine Jones, Dr Elaine Ingham and Jon Stika. And there are many others. For many decades now ‘Soils’ has been the Cinderella subject of agriculture, and even then, it was more about soil’s physical and chemical properties. In a world dominated by agrochemical use, soils became no more than a footnote. We will all eventually be very grateful that a few dedicated individuals continued to look upon soil as a vital living entity.

Soils do not offer a location to bury carbon. By its very organic nature, it will always be degradable by microorganisms living within the soil. And when tillage exposes that carbon to oxygen that degradation accelerates.

Soils seen as a carbon storage unit

Soil has been reduced to an inert medium for standing crops in with those crops then being fed with nutrients that are mined or manufactured. They require resources and their efficiency of use is low. Soil has become of so little importance that we now even see soilless crop growing as an option. There has, nonetheless, been a revival or interest in soils, albeit much is driven by the idea that we can remove atmospheric carbon and store it in soil.

Our new way of thinking is now about more than growing crops for food, fibre and fuel; it is about how to bury carbon in soil in a fashion akin to the deep burial of nuclear waste – an appropriate analogy given how carbon is being demonised as the cause of climate breakdown. If such can be done without having to understand and work with the soils’ natural, biological systems, all the better. Or is such just going 180o in the wrong direction?   

Sadly, as will become increasingly evident, soils do not offer a location to bury carbon. By its very organic nature, it will always be degradable by microorganisms living within the soil. And when tillage exposes that carbon to oxygen that degradation accelerates; thus, the emphasis on minimizing tillage to protect the carbon within soils.

Soil can be a store of carbon, but it will ebb and flow. Carbon can be sequestered in soil through increasing the percentage of carbon in the soil and, often neglected, by increasing the volume of soil. The latter is a moot point but gradually the anecdotal will be supported by the evidence. It then becomes about maintaining the improved carbon levels with ‘sequestration’ only being as good as the farmer’s management of his/her soil carbon stock.

Apparently, carbon absorption is often confused with carbon sequestration. Plants absorb atmospheric carbon to create their own structures and, as will be seen later, to feed microbial life forms in a symbiotic relationship. This is, however, a cyclical activity with the majority of the carbon being returned to the atmosphere when the plant matter (or animal matter that was created from plant matter) is broken down by degradation. Where aerobic degradation occurs, CO2 is released. When anaerobic degradation occurs, CH4 results. It all, however, begins with plants absorbing atmospheric carbon. Any residual soil carbon stock building is real sequestration.

This confusion is, nonetheless, understandable given that some forms of carbon degradation are considered to lead to GHG emissions, even if the original carbon was drawn from the atmosphere by the plant. Nature operates a carbon cycle and it will keep carbon absorption and ‘emissions’ in balance, but such has been distorted by the use of fossil-fuel-derived artificial plant-growing stimulants. It is on those that we should focus, not least because some anaerobic plant life degradation is inevitable if functioning, sustainable food systems are to be operated.

As fossil fuels used for manufacturing and mining, transporting and applying artificial fertilizers become scarce there will be a paradigm shift in thinking to feeding the soil to feed the plant

Soils must be the catalyst of all life

It is an anomaly that ‘plant-based’ has now entered common parlance. For an agriculturalist, everything is plant-based, albeit plants are being grown at times with artificial stimulants. Since the Second World War, the latter has become the norm (the strangely called ‘conventional’ for what is the unnatural) with artificial nutrients being fed to plants with the soil being no more than a medium of transfer, and even that is bypassed by foliar feeding plants. As fossil fuels used for manufacturing and mining, transporting and applying artificial fertilizers become scarce there will be a paradigm shift in thinking to feeding the soil to feed the plant. It will be soils-first farming.

To cite from Jon Stika’s ‘A Soil Owner’s Manual’ (2016), “the most limiting element in the soil for agricultural crop production is carbon… Carbon is the building block for all life on Earth. Since soil is designed to function as a living system, carbon is essential to make it work”. We have released ancient carbon from fossil fuels into the atmosphere and tilled the land to lose historically built soil carbon, but all life is still founded upon soil carbon.

Numerically, does soil contain most of the life forms on Earth? It is home to a vast hidden biodiversity. And that biodiversity is the foundation of all above ground, visible biodiversity. If one wishes to understand ‘biodiversity loss’, often look to the soils. As with all biodiversity, the health of its habitat is critical and ‘soils’ is first a habitat.

To quote Dr. Elaine Ingham in the USDA’s Soil Biology Primer, “An incredible diversity of organisms make up the soil food web. They range in size from the tiniest one-celled bacteria, algae, fungi, and protozoa, to the more complex nematodes and micro-arthropods, to the visible earthworms, insects, small vertebrates, and plants… Organisms live in the microscale environments within and between soil particles. Differences over short distances in pH, moisture, pore size, and the types of food available create a broad range of habitats”.

As soil organisms need space to live, soil structure and its friability (aka good soil aggregation) is vital. Its water holding capacity is also crucial. Water needs to be held without waterlogging while allowing the soil to ‘breathe’. Too little oxygen and microbial activity slows, too much and it increases to the extent that microbial life will consume existing soil carbon stocks as a food source, thus degrading the soil and releasing CO2 into the atmosphere (it is why no-till is being seen as a vital, newish farming technique). So, what leads to aggregation?

A vital component of soil is the “biologically produced glues that hold soil aggregates together. Of these, the focus has been on a glycoprotein called glomalin. Glomalin has two primary functions, to coat and protect hyphae (and to enable them to move nutrients and water to the plant’s roots) and to aggregate soil particles around a ‘framework’ of hyphae. De facto, glomalin creates the functional environment around plant roots.

NB: Hyphae are “hair-like projections of arbuscular mycorrhizal fungi… These fungi are ancient microorganisms that evolved with plants to aid in acquiring nutrients, especially immobile nutrients like phosphorus… Hyphae can grow several centimetres beyond roots and access more soil to acquire nutrients more efficiently… Below ground the plant forms a beneficial relationship with arbuscular mycorrhizal fungi… to get the nutrients that it needs”. Glomalin coats [protects] the hyphae. The beneficial relationship is maintained by the plant exuding carbohydrates to feed the arbuscular mycorrhizal fungi. It is a relationship that breaks down when living plant roots are absent from the soil, as often happens with fallowed tillage ground. Glomalin can also be lost and those relationships broken by tilling ‘permanent’ pastures.

Glomalin stores carbon in both its protein and carbohydrate. As outlined in a 2002 article by Sara F. Wright and Kristine A. Nichols of the USDA-ARS Sustainable Agricultural Systems Laboratory, it “accounts for a large amount (about 15-20%) of the organic carbon in undisturbed soils… It is resistant to microbial decay (lasting at least 10 to 50 years)”. However, as Jon Sitka notes, it is “a practical foodstuff for smaller, simpler organisms in the soil. If bacteria are allowed to consume glomalin faster than it can be produced by mycorrhizal fungi, soil aggregates will more easily disintegrate”.

Tillage breaks down soil aggregates and it creates the conditions that facilitate soil-dwelling bacteria to consume glomalin. According to Sitka: “It is this process that has been responsible for reducing the native concentrations of organic matter in the soils to the low levels today”. With the lost glomalin goes the ability of the soil to feed and water the plant. Simply, this biological soil degradation leads to soil-structure failure. Physical degradation can then follow. Such soils are also unable to hold and store much water, thus making them more drought and erosion prone.

An understanding of glomalin’s role in creating well-structure, carbon-rich soils is a driver behind no-till arable and no-dig gardening. It is vital to the creation of functional soils that enable soil microbial life to live in the symbiotic relationship with plants that will enable agriculture to continue to produce long-after artificial fertilizer usages in agriculture is curtailed by the pollution and emissions they cause and their fossil-fuel dependency.

Further, soil scientist, “[Sara F.] Wright found that glomalin is very manageable. She is studying glomalin levels under different farming and ranching practices. Levels were maintained or raised by no-till, cover crops, reduced phosphorus inputs, and the sparing use of crops that don’t have arbuscular mycorrhizal fungi on their roots. Those include members of the Brassicaceae family… When you grow those crops, it’s like a fallow period, because glomalin production stops. You need to rotate them with crops that have glomalin-producing fungi”. Top of the non-mycorrhizal fungi list are the temperate crops, oilseed rape and sugar beet.

Farming must be about protecting the stable (humus-rich) environment within which the soil biome exists

The critical liquid carbon pathway

Glomalin accounts for only a part of the carbon in soils. Ten percent or less of the carbon in soils is within living organisms. Humus is the other major component, a highly complex carbon polymer that is about 60% carbon.

Dr Ingham defines humus (or humified organic matter) as: “Complex organic compounds that remain after many organisms have used and transformed the original material. Humus is not readily decomposed because it is either physically protected inside of aggregates or chemically too complex to be used by most organisms. Humus is important in binding tiny soil aggregates and improves water and nutrient holding capacity”. It typically constitutes a third to a half of the organic matter in soils, about equivalent to the ‘active’, decomposing organic matter fraction.

Further, as Dr Christine Jones explains in her 2008 paper Liquid carbon pathway: “Under appropriate conditions, a large proportion of the soluble carbon channelled into aggregates via the hyphae of mycorrhizal fungi undergoes humification, a process in which simple sugars are resynthesized into highly complex carbon polymers. Humus polymers are made up of carbon and nitrogen from the atmosphere, combined with a range of minerals from the soil. These organic-mineral complexes form a stable and inseparable part of the soil matrix that can remain intact for hundreds of years… Humus can form relatively deep in the soil profile, provided plants are managed in ways that encourage vigorous roots. Once atmospheric carbon dioxide is sequestered as humus it has high resistance to microbial and oxidative decomposition.”

The persistence of humus is currently being questioned within the soil science community. Gabriel Popkin writes in a recent article for Quanta magazine: “A new generation of soil studies powered by modern microscopes and imaging technologies has revealed that whatever humus is, it is not the long-lasting substance scientists believed it to be. Soil researchers have concluded that even the largest, most complex molecules can be quickly devoured by soil’s abundant and voracious microbes. The magic molecule you can just stick in the soil and expect to stay there may not exist”. However, “It may still be possible to store carbon underground long term. Indeed, radioactive dating measurements suggest that some amount of carbon can stay in the soil for centuries”. It is likely that this will depend upon how the soils are managed.

So, continues Popkin: “Yes, soil is enormously varied. And it contains a lot of carbon. But there’s no carbon in soil that can’t, in principle, be broken down by microorganisms and released into the atmosphere” if the right (actually wrong) conditions exist. Most likely such results from human activity, of which tillage is, historically, the most common. “Soils contain enormous amounts of carbon — more carbon than in Earth’s atmosphere and all its vegetation combined… [but farming] over human history, has released an estimated 133 billion metric tons of carbon into the atmosphere”. Reversing this process is, nonetheless, not as straightforward as burying organic matter.

Planting crops without tillage is seen as a solution, but when practiced alone “carbon stores grew in upper soil layers, but they disappeared from lower layers. Most experts now believe that the practice redistributes carbon within the soil rather than increases it, though it can improve other factors such as water quality and soil health”, notes Popkin. Minimum tillage can reduce soil carbon loss and, critically, avoid the breakage of the symbiotic relationships between plants and their roots and their surrounding soil biome, but, apparently, its role within carbon sequestration is under scrutiny. The impact of other factors like the lack of deep rooting plants, systemic herbicide use, and artificial nitrogen use may all be inhibiting the regeneration of soil carbon by living plants.

Thus, farming must be about protecting the stable (humus-rich) environment within which the soil biome exists. It is about protecting the well aggregated soil structure that houses the soil biome and its functionality. Thus, as Lehman et al note in a 2020 paper: “Soil management should be based on constant care rather than one-time action to lock away carbon in soils.” It has to, de facto, be a continuous process. In saying such, it is implicit that thinking has to change away from just sequestering carbon to building soil carbon stocks (as the foundations of the habitat within which a fully functional soil biome operates) and maintaining those soil carbon stocks henceforth.

If soil carbon is being depleted, especially if soils are tilled, it needs to be constantly replaced. If such can happen to excess, greater volumes of carbon-rich topsoil can be formed. This has been happening for millions of years and resulted in the deep grassland soils that have since been exploited by humans to produce their food crops.

Depletion was done by cultivation techniques dating back thousands of years but which, evidently, have not evolved to preserve and maintain soil carbon. The soil carbon lost is now in the atmosphere and the soils are now biologically and, frequently, physically degraded. We now must rapidly reverse these soil carbon losses.  

A key question with respect to soil aggregation and soil carbon stock building relates to the source of carbon. Does stable soil carbon emanate from incorporated organic matter, or does it stem from the action of mycorrhizal fungi? It is a critical differentiator in how we think about soil management. Dr Jones concludes in her article Nitrogen: the double-edged sword: “It is now recognized that plant root exudates make a greater contribution to stable forms of carbon than does the above ground biomass”. If that is the case, must we now separate what is organic matter degradation for nutrient cycling from specific soil habitat building activities?

If so, argues Dr Jones, we need to consider, for example, that “stable forms of soil carbon (such as humus) cannot form in the presence of high levels of inorganic nitrogen, due to the inhibition of the microbes essential to sequestration”. Artificial nitrogen and phosphate disrupt the plant-fungi/bacteria relationships and reduce the flow of carbohydrates (energy) to these organisms. Over time, and especially when tillage is used, this leads to gradual soil carbon loss over time as lost soil carbon is not replaced. Thus, artificial fertilizer use can deplete soil carbon and, by undermining the functionality of the soil biome, inhibit natural nutrient sourcing mechanisms and, thus create a downward spiral of artificial fertilizer dependency (with its dependency on fossil fuels and, pollution and emissions from manufacturing and transport and use, not to mention the nutrient losses during application).

The cycling of plant nutrients is an essential part of farming, but it must move beyond thinking that incorporating organic matter builds soil carbon. The efficient cycling of plant nutrients is essential if farming is to move beyond artificial fertilizers, but it needs to happen in parallel to creating the conditions that enable the growing plant to feed the soil biome to create well aggregated soils. Long term, the soil biome must provide plants with all the nutrients they need (including accessing degraded plant and animal-based organic matter) but, given the human populations need for food, fibres and fuel, these cycled ‘used’ nutrients have to be supplemented by nutrient drawdown from the atmosphere (carbon and nitrogen) and from the soil profile (a wide array of minerals).

Sheep on grassland, New Zealand: Permanent pastures and long-term rotational pastures that at least mimic natural pastures for a significant period, will be vital to the supply of nutrients to the human race. They will be the key to sustainable food systems.

The soil biome starved of carbon

Jon Stika recommends that: “Soil managers should… make the soil the best habitat possible for soil microorganisms to thrive, build soil organic matter and feed plants. This can be accomplished by disturbing the soil less, growing the greatest diversity of plants possible, keeping living roots in the soil as much as possible, and keeping the soil covered at all times”. Soil habitat management is about maintaining living roots to feed carbon to microorganisms.

NB: The soil microorganisms also include basidiomycetes fungi that live close to but are not attached to roots. They also help in the formation of soil aggregates and produce enzymes that help break down crop residues, thus making their nutrients available. In terms of bacteria, rhizobia bacteria are known for their relationship with legume plant roots and nitrogen fixation. Improved fixation occurs with better soil structure and, better gaseous exchange. Less well known are the nitrogen fixing bacteria that associate with mycorrhizal fungi (glomalin is the bacteria’s feed source). The fungi then exchange the nitrogen for root exudates, thus allowing the plant to access atmospheric nitrogen. This happens in anaerobic ‘pockets’ adjacent to the roots. Again, well-structured soil will improve the growing crops access to nitrogen.

“Excessive tillage can cause a major decline in mycorrhizal fungi populations because the fungi are very sensitive to soil disturbance that breaks up their hyphae,” explains Sitka. “In undisturbed soil mycorrhizal fungi will form extensive net like webs in the soil. If the hyphae are broken by tillage, the fungi must begin again to grow new hyphae. This is a very intensive process for them… they commit a great deal of resources to restoring themselves instead of assisting their partners, the living plants”. Some tillage is, nonetheless, almost inevitable when growing many crops, but it must happen within the context of minimizing the impact it has on the soil biome’s habitat.

To do so means maintaining the flow of carbon from the growing plant to soil organisms via roots for as much of the time as possible. It comes down to ensuring that the soil microorganisms that maintain the soil as a habitat and thus the soil biome’s ability to feed plants, are not inhibited at any time by being starved of exudated carbon.

Maintaining the subterranean soil-biome habitat is easier under permanent pasture. It is not by chance that the soils created under ancient grasslands were carbon-rich (and now often tilled and degraded of soil carbon).

It is also realistic to assume that the very diverse, natural pastures of a grassland or woodland-pasture ecosystem will be better able to source soil-profile and atmospheric nutrients than a monocultured tillage crop. The latter simply do not support the soil biome functionality capable of achieving such nutrient sourcing. With a few exception (the legumes), they are, thus, dependent on artificial fertilizers, with all that their use entails. The soil biome is highly complex and, thus, its health depends upon the very diversity of nutrition that monocrops lack.

Thus, permanent pastures and long-term rotational pastures that at least mimic natural pastures for a significant period, will be vital to the supply of nutrients to the human race. They will be the key to sustainable food systems.

Nutrient offtake is inevitable given the need to feed urban human populations and farmed animals divorced from the land that feeds them. We need to consider offtake at all times. Conceptually, that can be done by sub-dividing offtake into a) on-the-run offtake, and b) static offtake. The first is where nutrients are harvested from crops and animals that are an integral part of the symbiotic plant nutrient cycle. The second is where the plant nutrients needed to generate the harvested offtake nutrients have to be provided by using a high degree of farm management skill to make the necessary plant nutrients available to crops grown outside a natural, symbiotic system. Most direct-for-human-use crops fall within the latter category. Life without fertilizers will not be easy.

It is through the understanding of the difference in offtakes that we can progress towards identifying what are sustainable food systems. Geographic plant nutrient shipping only makes it more difficult. Without artificial fertilizer, the farmer will have to replenish (or regenerate) lost plant nutrients from the atmosphere or the soil profile. It will be a complex process, made worse by having an increasingly urbanized human race which, in turn, gains much of its animal-product-based nutrition from farm animals that are themselves often urbanized.

To quote Jon Stika again, “wherever you are in the world, there is a native plant community that existed before humans made their mark on the land by tilling the soil… it is these uncompromised native plant communities that serve as the template we need to mimic in order to restore the soil to its full capacity to function”.

It is not safe to assume that all permanent pasture functions effectively. Regular tillage for reseeding can have a negative impact. A lack of plant diversity will not provide balanced nutrition for soil organisms. The pasture may also not contain the deep rooting plants necessary to access minerals from deep within the soil profile or build soil carbon at depth. Excessive fertilizer use will negatively impact the symbiotic plant-soil microorganism relationships. Excess defoliation causes root loss and breaks down established pathways. Too little defoliation and the growing plant will move to its reproductive phase and the consequential senescence will reduce leaf area and photosynthesis and reduce the flow of carbon to the soils. Thus, it is also about grazing management.

Without living plant cover, the feeding of ‘liquid carbon’ to the soil biome ceases and carbon starvation arises

Photosynthesis, the soil biome and carbon

To summarize by quoting Dr Christine Jones, “Photosynthesis is the most important process underpinning life on earth. Non-legume bacterial nitrogen fixation is the second”. Thus, when farming is it important to maintain “year-round presence of green plants and the microbial populations they support… [as actively growing] groundcover buffers soil temperatures and reduces erosion… [and] fuels the liquid carbon pathway which in turn supports… mycorrhizal fungi, associative N-fixing bacteria and phosphorous stabilizing”.

The key is the role microorganisms have in binding microaggregates into macroaggregates using glomalin and other ‘glues’, thus giving soil its structure with its associated aeration, infiltration and water-holding capacity, and thus creating and maintaining the soil habitat required for a fully functional soil biome to underpin all life.

Further, explains Dr Jones, it is the “mycorrhiza [which] deliver sunlight energy packaged as liquid carbon to a vast array of soil microbes involved in plant nutrition and disease suppression. Organic nitrogen, phosphorus, sulphur, potassium, calcium, magnesium, iron and essential trace elements such as zinc, manganese and copper are returned to plant hosts in exchange for carbon… Unless soils are actively aggregating, they will not be fixing significant amounts of atmospheric N or sequestering stable forms of carbon. All three functions (aggregation, biological N-fixation N and stable C-Sequestration are inter-dependent”. Thus, it is all about soil management to create farming systems that are less dependent on fossil-fuel derived, polluting and emitting artificial ‘fertility’.

Central to this is maintaining soil carbon stocks as a functional continuum. Soil carbon loss is almost inevitable, so it is about ensuring that the farming system functions to regenerate and replenish soil carbon. Storing carbon is not the primary goal; creating a functional ecosystem built upon a functional soil biome is. To create such an ecosystem, we will need to both restock soils with carbon and enhance and maintain a greater level of vegetation (that will also contain carbon) to maintain them securely. All will contribute to carbon drawdown. But not to be overlooked, more enhanced local ecosystems will in themselves benefit the broader planetary ecosystem.

Hence, maintaining living plant roots in the soil is essential if our food systems are to be less dependent on fossil-fuel-derived artificial fertilizers. It is the flow of carbon, as root exudates, that is critical. Future farming systems must be built around a permanence of living plants, and that is a far cry from what exists today. Living plants are absent from too many farming systems for much of the year and it brings into question their sustainability. Such action leaves the soil vulnerable to erosion, but it also inhibits the vital, symbiotic plant-soil biome interactions.

Without living plant cover, the feeding of ‘liquid carbon’ to the soil biome ceases and carbon starvation arises.

Perversely, at a time when it is all about atmospheric carbon levels, our farming systems have and continue to starve soil life of the carbon they need to recreate the very living ecosystems that we need to feed us humans.

Therefore, we must take our food systems thinking beyond accounting for carbon emissions. We must recognize that carbon is a vital plant nutrient and one that underpins soil functionality and, thus, sustainable food systems.

Ensuring that plants can deliver carbon to the soil biome is critical, as is the protection of that soil-based carbon thereafter. Our cropping will have to be chosen to ensure that this happens. And our harvesting of nutrients will have to occur in a way that does not compromise the farming system’s integrity. Thus, it is likely that we will have to look to plant permanence, not transitory cropping, and that in itself will have a major impact on what sustainable foods really are. It will be about harvesting foods from permanence first, as such will eventually be more sustainable from a plant nutrition perspective. Overall, it is only when we start with a soils-first-farming approach that we begin to understand what is needed to create genuinely sustainable agricultural systems.

Stuart Meikle’s series on farming within planetary boundaries will run from next week here on


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About Stuart Meikle 29 Articles

Stuart Meikle is an agricultural management and policy specialist, an economist, a writer and an advisor. He was brought up with agriculture and studied at the University of London. He joined the faculty on graduating and spent several years teaching, researching and consulting. His last 25 years have seen him advising governments, the World Bank and the IFC, NGOs, universities and private businesses in places as far afield as SE and Central Asia, the Caucuses, the Levant, SE Europe and the UK. Over the years he has developed a particular focus on agricultural and food sector strategy at the national and regional levels and linking rural development initiatives with the consumer through the food supply chains. He first arrived in Romania to work on a Commission project in 1997 and he lived in Transylvania for more than a decade from 2002; a location to which he was appointed as the United Kingdom's first Honorary Consul. Nowadays he and his family live in the Republic of Ireland.