Fixing the nitrogen crisis: The search for sustainable fertilisers

Bacteria capturing nitrogen

Nitrogen is essential, but its overuse in fertilisers is putting us at a tipping point for a crisis. Can bacteria solve the problem? Image credit: Allanah Booth, The Oxford Scientist.

Humans, like plants, fungi, bacteria, and any other organism we consider alive, are all carbon-based life forms. These organisms, some of which are incredibly complex forms of life, are made up of very simple but essential building blocks.

Among the various biological components found in living organisms, enzymes (specialised proteins able to catalyse chemical reactions) are crucial for nearly all basic cell functions. Enzymes, along with DNA, and other proteins, are all constructed from four fundamental elements: carbon, oxygen, hydrogen, and nitrogen. Hydrogen and oxygen are provided by molecular water, which is abundant over our predominantly water covered planet. Carbon is provided by plants, which use sunlight and water to take carbon dioxide out of the air and turn it into sugars such as glucose (chemical formula: C6H12O6), which we then eat. Nitrogen on the other hand is much trickier to get a hold of.

Plants […] use sunlight and water to take carbon dioxide out of the air and turn it into glucose, which we then eat. Nitrogen on the other hand is much trickier to get a hold of.

We again rely on plants to provide us with the nitrogen that constitutes a significant part of our diet. Crucially however, plants are incapable of generating nitrogen independently. Instead, they acquire their nitrogen from the surrounding soil in the forms of ammonium (NH4+) and nitrates (NO3) which are produced naturally though the nitrogen cycle. Through their capacity to absorb soluble nitrogen from the soil, plants tend to deplete the soil’s nitrogen reserves. Consequently, when we harvest them to eat, the nitrogen they have assimilated is permanently removed from the soil.

The only natural means of replacing nitrogen lost from the soil is through using nitrogen-rich manures, lightning strikes, and planting legumes like peas, clover, cowpea, and fava beans. Legumes are able to replenish soil nitrogen due to their ability to form specialised relationships with a group of bacteria called rhizobia. These bacteria can synthesise a unique enzyme called nitrogenase.

The power of nitrogenase

Nitrogenase is able to catalyse the reaction that takes atmospheric nitrogen, breaks the powerful triple bond between nitrogen atoms, and converts it into ammonia. This enzyme’s ability to split two nitrogen atoms apart is a remarkable feat of biology. To break a single triple bond, it would take approximately 226,000 calories of energy, roughly equivalent to an adult’s daily caloric intake for around three months.

This enzyme, however, is not widely synthesised across the kingdoms of life—only a select few bacteria, archaea and cyanobacteria, called diazotrophs (meaning nitrogen-fixing), can synthesise nitrogenase and fix nitrogen from the atmosphere. The nitrogen that legumes provide to soils has been used for centuries by farmers who routinely rotate their crops alongside legumes, replenishing nitrogen lost from the soil taken up by other non-legume crops.

Feeding the world with nitrogen

At the turn of the twentieth century, traditional methods of providing crops with nitrogen weren’t enough. The world’s population was growing rapidly, and the number of mouths that needed feeding was no longer being supported by agricultural outputs of the day.

In a speech to the British Association in 1898 by Sir William Crookes, an esteemed inventor and scientist of his day, he shocked his audience by highlighting the likelihood of wheat shortages as the population continued to grow, by saying: ‘it is the chemist who must come to the rescue of the threatened communities. It is through the laboratory that starvation may ultimately be turned into plenty‘.

Indeed, it was a chemist that seemingly solved the nitrogen problem, and the legacy of their work can be seen today in the ~8 billion people that now live on the planet because of it.

The Haber–Bosch reaction

In 1909, a German-born chemist named Fritz Haber became the first person in history to artificially take nitrogen from the atmosphere and turn it into a form that humans could use. Using extremely high temperatures and pressures, he was able to fuse nitrogen and hydrogen together to form ammonia in the reaction now called the Haber–Bosch reaction:

N2 + 3H2 ↔ 2NH3

This simple equation would go on to fuel what is now called the “Green Revolution“, an era from the 1960s–1990s characterised by the widespread adoption of chemical nitrogen fertilisers, triggering remarkable surges in crop outputs.

This breakthrough played a vital role in sustaining the exponential population growth we see today. As a result, approximately 80% of the nitrogen forming the proteins within our bodies is due to this chemical reaction.

This discovery, which won Haber the Nobel Prize in chemistry, was a double-edged sword, not just for Haber but for the world as a whole. Remembered more today for his role in the First World War and his active participation in the development and use of poison gases, Fritz Haber’s legacy is neither a happy nor simple one. Despite the increases in food production as a result of their use, chemical nitrogen fertilisers are now a serious problem.

Too much of a good thing

Because it’s difficult to know exactly how much nitrogen plants need in order to grow better, farmers tend to apply as much as they can before the cost of application outweighs returns in yield. When more fertiliser is applied than is needed by crops, heavy rains and water irrigation causes fertilisers, which sit on the surface of agricultural soils, to be washed off in a process called runoff. They are then washed into bodies of water like rivers and oceans, flooding these aquatic environments with enrichments of nitrogen.

Algae, which are ubiquitous in nearly all waters, use the increase in soluble nitrogen to fuel their rapid growth and multiplication, which causes several problems for other marine organisms. Algae tend to sit on the surface of rivers and oceans, as they photosynthesise and need lots of light to do so, which can shade riverbeds and ocean floors.

Alongside this shading, which isn’t good for the aquatic plants living there, these algae also use up a lot of oxygen to fuel their growth, which leads to hypoxic (oxygen-starved) water conditions. This causes significant damage to these complex aquatic ecosystems, killing fish and other marine life in a process called eutrophication. Excessive nitrogen application to farmland is a major problem in the Netherlands and has forced policy makers to enact stringent limits on sources of nitrogen pollution as a result of the environmental damages caused.

Microbial effects on fertilisers

A single teaspoon of relatively healthy soil can contain between 100 million and 1 billion different bacteria, many of which, as part of their innate metabolism, can process ammonium nitrate—the most common form of synthetic nitrogen—into a gas called nitrous oxide (N2O).

N2O is an extremely potent greenhouse gas, 300 times more potent than carbon dioxide, and can interact with and drain the atmosphere of its protective ozone layer. Agriculture is the greatest source of UK N2O emissions, producing ~14.5 metric tonnes of carbon dioxide equivalent (MtCO2e) or roughly 69% of the total emissions from the agricultural sector in 2020. Atmospheric N2O concentrations have risen by ~18% from pre-industrial levels and excessive application of chemical nitrogen fertilisers to soils is a key contributor to this increase.

Atmospheric N2O concentrations have risen by 18% from pre-industrial levels and excessive application of chemical nitrogen fertilisers to soils is a key contributor to this increase.

The production of nitrogen fertilisers, using the Haber–Bosch process, is also highly dependent on natural gas. As such, fluctuations in gas prices caused by political instability or conflicts in regions from where they’re obtained, affect and destabilise the price of fertilisers, making them a highly unsustainable resource. This often high and variable expense prevents the people who need fertilisers the most, such as subsistence farmers (who depend on their yields for food and as a source of income), from reasonably affording them.

Sustainable solutions to nitrogen fertilisers

The effects and influence that fertilisers have had on the world is undeniable. They helped to drive agriculture from traditional, smaller-scale farming practices to the industrial production we see today, which has helped support population growth and reduce global hunger. This advancement in crop production, however, has come at a significant environmental cost. Our over-reliance on them is no longer a sustainable means of maintaining agricultural outputs. A more sustainable alternative could lie beneath our feet, within the rich microbial communities living in our soils.

A more sustainable alternative could lie beneath our feet, within the rich microbial communities living in our soils.

It might seem like we could make use of the same bacteria that legumes use (rhizobia) and inoculate cereal crops such as wheat and barley with them to enable nitrogen fixation. But the relationship between legumes and rhizobia is highly specialised among very specific bacterial and legume species that have evolved together over many millions of years, therefore it cannot be easily replicated artificially.

Legumes are able to form root structures called nodules, which the plant makes to house the bacteria. These nodules provide rhizobial bacteria with a nutrient rich and low-oxygen environment which is vital, nitrogenase activity is significantly reduced in the presence of high oxygen concentrations. Nodules are highly complex organs that crops like wheat and barley are unable to produce themselves. The entire process of bacterial invasion into legume roots, initiation of nodule development, and the maintenance and regulation of nodules, is something that is incredibly difficult to transfer to non-legume plants, but which scientists are today attempting to do.

Engineering plants and microbes

Research is also ongoing to explore the potential of engineering the nitrogenase enzyme into plant cells so they can fix nitrogen for themselves without the need for a corresponding bacterial partner. There are several obstacles, though, making this an immense challenge to overcome. The enzyme is very large and complex and requires a lot of energy to convert diatomic nitrogen into ammonia which could have deleterious effects on plant growth.

Nitrogen fixing bacteria could be the answer to the nitrogen crisis. Image credit: Matthew Campbell, created using

An alternative approach that researchers are also currently exploring is the potential of utilising free-living nitrogen fixers. These bacteria don’t need nodules in order to survive, and can be found growing between the cells of plant roots (endophytes) or on the roots’ surface (loose associating). They are still able to fix high levels of nitrogen and have been shown to have plant growth promoting effects when inoculated onto plants. That said, they aren’t optimised to maximise the release of the nitrogen that they fix, as they are adapted to a free-living lifestyle and do not depend on nutrient exchanges with a plant partner.

Researchers are looking to target complex nitrogen assimilation pathways within these bacteria and adapt it so that they accumulate less and release more fixed nitrogen. Engineering better targeting systems, using chemical such as rhizopine, that would enable plants to “talk” to engineered bacteria, biasing their association towards these diazotrophs, could also improve plant nutrition and growth.

The future of fertilisation

Utilisation of free-living diazotrophic bacteria represents a promising avenue for addressing the challenges posed by synthetic nitrogen fertilisers. Focussing future research on fine-tuning the biology of these bacteria to maximise nitrogen release, developing communication systems between plants and microbes, and adapting this technology to a broader range of crops will help to maximise the benefits that can be gained from soil microbes.

The goal is clear: to transition to more sustainable and environmentally friendly agricultural practices, ensuring food security for a growing global population while preserving the health of our planet. In doing so, we not only take a step towards solving the nitrogen crisis but also strive to strike a balance between our agricultural needs and the delicate ecosystems upon which all life depends.