Reducing Nitrogen-Based Fertilizer Emissions: Soil Microorganisms Could Hold the Key

To feed an ever-growing population, fertilizers are a necessity. Nitrogen-based fertilizers deliver essential nitrogen to the soil to help crops grow—that’s good—but also accelerate natural nitrogen cycle processes to exacerbate atmospheric and water pollution—that’s not good. This creates a dilemma: how do we produce enough food while minimizing the damaging effects of excess nitrogen? AXA Chair Professor Graeme Nicol of the Environmental Microbial Genomics Group at Ecole Centrale de Lyon has spent the last 5 years investigating how minuscule organisms found in the soil might hold the key to this puzzle. With more available nitrogen in the soil through fertilizer use, nitrogen-converting soil microorganisms go into overdrive, and this can cause an overproduction of various forms of polluting nitrogen. In uncovering the basic physiological characteristics of these microorganisms and their role in the nitrogen cycle, Prof Nicol’s work could help to drastically reduce the environmental pollution caused by nitrogen-based fertilizer use.  

What are the consequences of nitrogen-based fertilizer use, and why is this research so urgent?

Nitrogen, an essential component of all living organisms, helps crops grow. Artificial nitrogen-based fertilizer is the product of the “Haber-Bosch” process, whereby atmospheric nitrogen is “fixed” with hydrogen to produce ammonium, which farmers then add to the soil to stimulate plant growth. While an estimated 50% of the nitrogen that all humans eat is derived from fertilizers, fertilizer use also accelerates the natural processes of the nitrogen cycle, with harmful consequences. For example, putting more nitrogen in the soil by adding fertilizer means that excess nitrate—a mobile form of nitrogen produced by microbial transformation of ammonium—can get washed into waterways and the ocean, resulting in an overabundance of nutrients that causes algal blooms that kill fish or nitrate-pollution of drinking water.

Also accelerated is the conversion of nitrogen into the gas nitrous oxide, which then gets released into the atmosphere. Nitrous oxide has an atmospheric lifetime >100 years—it has 265 times the greenhouse warming potential of carbon dioxide. It will also be the primary compound responsible for ozone depletion in the 21st Century. Our reliance on fertilizers will only increase with the growing global population, as will the contribution to global warming, so the situation is as imminent as reducing carbon emissions. We need to work out how to feed a growing human population while minimizing the negative consequences of using artificial nitrogen-based fertilizers.

What has your work over the past 5 years revealed about the biogeochemical transformation of nitrogen?

We’ve focused on understanding the relative contribution of different organisms in the soil to nitrogen cycle processes. Bacteria and archaea look the same through a microscope but are separated by 3 billion years of evolution, meaning that their evolutionary paths diverged a very long time ago. Scientists only discovered archaea in the late 1970s, prior to which archaea were simply thought to be bacteria given their similar appearance. More recently, only 17 years ago, we discovered abundant “ammonia-oxidizing” archaea, which can transform ammonia into nitrite, which is then converted into polluting nitrate by other soil bacteria.

One of our major discoveries is that ammonia-oxidizing bacteria produce twice as much nitrous oxide than ammonia-oxidizing archaea, so contribute far more to atmospheric pollution. We also found that bacteria, the “bad guys,” use typical synthetic ammonium fertilizer, whereas archaea use more organic sources of nitrogen, such as decomposing material from dead plants and animals. This could potentially help to design fertilizer that pollution-producing bacteria can’t access as easily.

What are the broader implications of your research?

An overarching aim is to find a way to feed the human population with affordable, nutritious food while minimizing the production of nitrous oxide and nitrate. There are two potential ways to increase the ability of crops to take up the nitrogen fertilizer while simultaneously cutting down on fertilizer-associated pollution: by reducing the activity of ammonia-converting microbes and by using “smart” slow-release fertilizers. Slow-release fertilizers are fertilizers that are formulated to stop the fast release of ammonia in the soil but are added more slowly. This slow release reduces the ability of certain microbes to convert nitrogen into harmful forms that can leach into waterways as nitrate or be converted into nitrous oxide, and also means that plants are better able to take up nitrogen.

How have your breakthroughs impacted the scientific community?

Our work identifying principles of how microorganisms function could inform future systems-based and modeling research that tests our findings in different ecosystems and for different crops, for instance. On a methodological level, we’ve highlighted the importance of spatial scale when investigating ecological mechanisms that influence soil microbial community structures. We also demonstrated to the research community that one single test, or “assay”, shouldn’t be used to characterize very complex microbial communities because soils contain different organisms with different physiologies.

How has the AXA Chair facilitated the acquisition of new knowledge via international collaborations?

Most publications that have come out of the AXA Research Fund had an international collaborator. With colleagues in China at the Chinese Academy of Science, where there are many environmental problems, we’ve researched the nitrogen cycle in uniquely Chinese soils, such as tea soils, which are very acidic. We’ve also collaborated with the University of Vienna and the University of Aberdeen, who also study different representatives of soil ammonia oxidizers so that we can characterize and find a consensus of traits between different evolutionary groups of ammonia oxidizing archaea and bacteria. Through these collaborations, we now have a good understanding of the physiology of ammonia oxidizers from different soils.

Has your work reached the industry or decision-makers?

We haven’t moved into the industry yet, but we’re very conscious of it. What we have done is share our data on the potential of slow-release fertilizers to reduce nitrous oxide and nitrate emissions with companies that produce fertilizers. In our laboratory systems, we see a 50% reduction in nitrous oxide emissions when using slow-release fertilizers compared to traditional synthetic fertilizers. While these findings need to be validated in the field, they show the potential for huge reductions in emissions simply by understanding the physiology of organisms that transform nitrogen.

How has this 5-year funding impacted your professional development?

The AXA Chair has allowed me to relocate from the University of Aberdeen in Scotland to Lyon, allowing me to integrate my research into France and concentrate exclusively on research. I had a permanent position in Scotland and what was terrific was that I obtained a permanent position as director of research at the CNRS after coming to Lyon. Without the AXA Research Fund, I wouldn’t have been able to make that transition, so its fundamentally changed my career.

How has the AXA Chair aided the development of early-career researchers in your lab?

The Chair has enabled me to fund several postdocs and Ph.D. students, increased the exposure of my lab’s research through publications and conferences, and has benefited the careers of at least four people. Two are now postdocs in Berlin (Dr. Christoph Keuschnig) and at the University of Hanover (Dr. Linda Hink), one is now a project manager at a new biotechnology company involved in single cell analysis, and one of my Ph.D. students (Dr. Sungeun Lee) is now a post-doc in our group. Through the AXA Research Fund, I established a completely novel line of research—the work we’ve done on soil viruses—and obtained substantial pieces of equipment, such as our lab’s DNA sequencers, for performing cutting-edge genomics research.

What’s next?

Three new strands of research have come out of the research funded by AXA. First, we have recently received a €1.5 million grant with the University of Thessaly and the University of Vienna called ACTIONr, where we’re looking at the effect and safety of synthetic “nitrification inhibitors,” which are compounds that reduce nitrification activity. In the second strand of research funded by the Grantham Foundation, we’re trying to understand biological nitrification inhibitors produced by plants. Using these biological nitrification inhibitors would avoid the disadvantages of artificially synthesized nitrification inhibitors. Third, through a new ANR-funded program, we’re looking at the impact of native ammonia oxidizer viruses on nitrification in soil, which we know almost nothing about. Understanding these viruses could allow us to control nitrification activity using a natural and highly targeted approach without worrying about the impacts of chemicals on soil health.

November 2022

Learn more about Prof. Nicol's research project