Nitrogen Fertilizer and Soil Organic Matter: What Does the Evidence Say?

Authors: Jordon Wade and Andrew McGuire

Does synthetic nitrogen fertilizer burn up soil organic matter? Whether you are focused on soil health, soil sequestration, or soil carbon credits, this is an important question. The persistent claim is that synthetic N fertilizer can “burn” soil carbon by supercharging the soil microbes. This claim mainly arises from a 2007 research article from researchers at the University of Illinois (Khan et al., 2007, see published responses to this at end) and has recently resurfaced in another article (Jesmin et al., 2021) and the resulting (flawed) media coverage. However, these studies are far from conclusive – so what does the broader scientific literature say? And what have we learned in the last few decades on the relationship between synthetic N and soil organic matter?

A bit of background

The term “soil organic matter” (SOM) usually refers to a large range of compounds of varying origins and complexity that come from dead plants or soil organisms. About half of that soil organic matter is carbon, or soil organic C (SOC) (Figure 1), which is the focus of soil carbon sequestration. The rest is mainly comprised of other compounds. Some of these compounds provide plants nutrients (e.g., nitrogen, phosphorus, and sulfur), while others do not (e.g., hydrogen and oxygen). The terms “soil organic matter” and “soil carbon” are often used interchangeably in everyday conversations, but the distinction is important to keep clear when discussing specific soil processes.

What we know

One thing is very clear in the scientific literature: soil microbes are usually N limited. On average, soil organic matter, the food/energy source for microbes, has a C:N ratio of approximately 10:1, but microbes have a C:N ratio of approximately 8:1.

Graphic showing proportions of soil organic matter
Figure 1. The relationship between soil organic matter, soil carbon and nitrogen, and microbial carbon and nitrogen needs.

This means microbes need more nitrogen than is found in organic matter. If we have 100 lbs of soil organic carbon, there will be ~10 lbs of soil organic N. However, 100 lbs of soil microbial biomass will need ~12.5 lbs of organic N. (Figure 1). To get this, microbes will scavenge the soil for N that isn’t readily available in the soil organic matter. Enter N fertilizer.

Synthetic N is readily available to microbes, so when fertilizer is added, it causes the size of the microbial biomass to rapidly increase (Geisseler and Scow, 2014). In the short-term, this increases the microbial activity (aka CO2 production or “respiration”) – but what about the long term?

Well, we now know that when those microbes die, they can become a persistent form of soil organic matter (the mineral-associated soil C). One recent meta-analysis, using 428 observations from 52 studies, showed that synthetic N additions increase both this persistent form of SOC (mineral-associated organic matter, MAOM) and the more microbially-available form of SOC (particulate organic matter, POM), as well as an overall increase in soil organic matter (Rocci et al., 2021). Another similar study using 803 comparisons from 98 published studies showed a similar result: N additions increased both forms of SOC (Tang et al., 2023). Importantly, both of these meta-analyses found this effect regardless of what type of system they were looking at, be it cropland, grassland, or forest. This is not a new finding, as many studies have shown that increases in soil carbon also require other nutrients, such as P, K, and molybdenum (van Groenigen et al., 2006; Van Groenigen et al., 2017).

One possible reason for the overall increase in SOM is simply that more nutrients (aka fertilizer) lead to more plant growth and therefore more residue input. However, it’s important to distinguish between simply increasing the fast-cycling carbon and retaining the slow-cycling carbon (or ideally, both!). One recent meta-analysis looked at this using isotopes, which help us determine both the age and the source of the soil carbon. They found that N fertilization can do both: it increases the amount of incoming “new” carbon in residues while also slowing the loss of the “old” carbon (at least at higher N rates) (Huang et al., 2020) (Figure 2).

Bar graph with error lines
Figure 2. Graph showing the effect of N fertilizer on new and old soil C pools (as determined by isotopes). From Huang et al. (2020) with permission from Springer/Nature.

In summary, we have multiple syntheses of field experiments (soils under long-term cropping systems) showing that synthetic N:

  1. Increases microbial biomass,
  2. Increases both the readily-decomposable and less-readily decomposable pools of soil carbon (the latter of which form from the dead microbes), and
  3. Increases “new” carbon inputs while also slowing the loss of “old” soil carbon.

Altogether, this is pretty strong evidence that synthetic N doesn’t cause organic matter to be “burned off”.

But why is this happening? Understanding the mechanism will go a long way towards explaining the results we have seen in the field.

Why would synthetic N help slow soil organic matter losses?

To investigate why synthetic N can slow (or even reverse) soil carbon loss, we need to look more closely at lab experiments. Lab experiments are often shorter-term than field experiments, but they let us look closely at specific root causes of observations made in field studies. One of the easiest ways to approximate field processes is to look at enzyme activity with the addition of fertilizer N.

Microbes produce enzymes that target specific bonds in residues in order to access their energy. Which enzymes are being produced can give us insights into which molecules are or aren’t being targeted by the soil microbes. One recent meta-analysis showed that N fertilization increased enzymes that we generally think of as degrading newly-added residue (hydrolytic activity) and decreased those we think of as degrading “native” or older soil organic matter (oxidase activity) (Jian et al., 2016). This agrees with the results of many field experiments we discussed previously: N additions make for more residue input while slowing down any breakdown of old soil C. However, these classifications of enzyme classes are very broad – can we get more specific on the why of synthetic N and the soil carbon story?

Another study sought to do just that by integrating both laboratory enzyme measures and in-field measurements of soil carbon from 40 studies around the world (Chen et al., 2018). They found that N additions decrease the activity of lignin-degrading enzymes and increase the activity of cellulose-degrading enzymes. Importantly, they linked the lab and field by showing that the increases in soil carbon storage from N additions were linked to the differences in lignin-degrading enzyme activity. They also (once again) showed that N additions increased the older soil carbon pools. Sensing a trend here?

Putting it together (aka the tl;dr)

So, back to our question, does synthetic nitrogen fertilizer burn up soil organic matter? In short: the available evidence suggests no, it does not. Instead, we see many field experiments, both in agricultural and in less-intensively managed systems (e.g., grasslands and forests) where N increases soil carbon. Those increases are because of increased residue inputs into the soil, as well as better retention of the older soil carbon. This seems to be happening because of the effects on specific soil enzymes.

It’s worthwhile to pause and stress how rare this is: we see evidence from both agricultural and non-agricultural systems, spanning both field and lab experiments, converging on the same conclusion. These are not isolated studies, but are meta-analyses (a quantitative study-of-studies) that include work from around the world. This evidence is quite robust and has stood up to extensive scrutiny from researchers the world over.

Synthetic N fertilizers have a complicated history. On one hand, synthetic N fertilizer has allowed the world’s population to double (Ritchie et al., 2022), while on the other hand there are a myriad number of environmental and public health risks that arise from excessive N applications (Keeler et al., 2016; Houlton et al., 2019). These consequences can be quite serious and merit the close attention that they receive from agricultural stakeholders. Without a doubt, there is an urgent need for better management of synthetic fertilizer N. However, it’s a potent tool in the toolbelt for maintaining (or even building!) our soil carbon, so hopefully we can give it the thoughtfulness and consideration that it deserves.

Jordon Wade is the Soil Health Assessment Lead for Syngenta Group, a global agricultural technology company. The opinions here reflect a data-driven approach to soil health, which is supported by his peer-reviewed research findings pre-dating his role at Syngenta.


Chen, J., Y. Luo, K.J. Van Groenigen, B.A. Hungate, J. Cao, et al. 2018. A keystone microbial enzyme for nitrogen control of soil carbon storage. Science advances 4(8): eaaq1689.

Geisseler, D., and K.M. Scow. 2014. Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry 75: 54–63. doi: 10.1016/j.soilbio.2014.03.023.

van Groenigen, K.-J., J. Six, B.A. Hungate, M.-A. de Graaff, N. Van Breemen, et al. 2006. Element interactions limit soil carbon storage. Proceedings of the National Academy of Sciences 103(17): 6571–6574.

Houlton, B.Z., M. Almaraz, V. Aneja, A.T. Austin, E. Bai, et al. 2019. A World of Cobenefits: Solving the Global Nitrogen Challenge. Earth’s Future 7(8): 865–872. doi: 10.1029/2019EF001222.

Huang, X., C. Terrer, F.A. Dijkstra, B.A. Hungate, W. Zhang, et al. 2020. New soil carbon sequestration with nitrogen enrichment: a meta-analysis. Plant and Soil 454: 299–310.

Jesmin, T., D.T. Mitchell, and R.L. Mulvaney. 2021. Short-term effect of nitrogen fertilization on carbon mineralization during corn residue decomposition in soil. Nitrogen 2(4): 444–460.

Jian, S., J. Li, J.I. Chen, G. Wang, M.A. Mayes, et al. 2016. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: A meta-analysis. Soil Biology and Biochemistry 101: 32–43.

Keeler, B.L., J.D. Gourevitch, S. Polasky, F. Isbell, C.W. Tessum, et al. 2016. The social costs of nitrogen. Science Advances 2(10): e1600219. doi: 10.1126/sciadv.1600219.

Khan, S.A., R.L. Mulvaney, T.R. Ellsworth, and C.W. Boast. 2007. The myth of nitrogen fertilization for soil carbon sequestration. Journal of Environmental Quality 36(6): 1821–1832.

Ritchie, H., M. Roser, and P. Rosado. 2022. Fertilizers. Our World in Data. (accessed 1 September 2023).

Rocci, K.S., J.M. Lavallee, C.E. Stewart, and M.F. Cotrufo. 2021. Soil organic carbon response to global environmental change depends on its distribution between mineral-associated and particulate organic matter: A meta-analysis. Science of the Total Environment 793: 148569.

Tang, B., K.S. Rocci, A. Lehmann, and M.C. Rillig. 2023. Nitrogen increases soil organic carbon accrual and alters its functionality. Global Change Biology 29(7): 1971–1983. doi: 10.1111/gcb.16588.

Van Groenigen, J.W., C. Van Kessel, B.A. Hungate, O. Oenema, D.S. Powlson, et al. 2017. Sequestering soil organic carbon: a nitrogen dilemma. ACS Publications.


5 comments on "Nitrogen Fertilizer and Soil Organic Matter: What Does the Evidence Say?"
  1. Very valuable information. Takes the guess work out of whether or not to apply chemical N. Peer reviewed information is good.

  2. Thank you for this information. The knowledge base about soil, soil microbes, nutrients, synthetic fertilizer application, is increasing rapidly since 2015 when I first started on the journey to improving soil health and capacity. It’s nice to have this piece of the puzzle consolidated into a coherent presentation. I’m also pleased to see the academic world picking up their pace on many aspects of plant life, soil life, related chemistry, and their interaction. In 2015, those of us farming, and interested in this subject were overwhelmed with information we had little understanding about, and no expertise readily available for explanation.

  3. If more N use builds more soil organic matter, why has this been going on for decades?

    “Unfortunately, there has been considerable loss of soil organic matter (SOM) in key farming regions across the U.S. over
    the past several decades. The Northern and Southern Great Plains combined have lost almost four percent of soil organic
    carbon on a per acre basis over the last 30 years. About a third of the world’s soil has already been degraded—because
    of increasing atmospheric temperature, over-exploitation, extensive mining of soil nutrients, inappropriate tillage, poor crop
    management, indiscriminate use of fertilizer, and accelerated erosion. In the U.S., the SOM degradation trend is acute: a
    USDA/NRCS simulation of the change in soil organic carbon estimated that nearly three-fourths of the cropland acres lost
    soil organic carbon over 30 years.”

    1. Hi Tom. thanks for the comment. Sorry about my late reply but our comments were not working for the past 3+ months and were just restored.
      The SOM loss that you point out is that due to farming of annual crops. It is made worse by heavy tillage, but even occurs with no-till because of the different allocation of plant C in annual crops as compared to native perennials that they replaced. SOC is not lost because of fertilizer use, which is actually a practice to limit another of their causes, the “mining of soil nutrients.”
      So, while use of N fertilizer can add C to the soil, it is less a factor than tillage and the C allocation of annual crops, and therefore if the slow loss of SOC due to the conversion of native vegetation is ongoing, N fertilizer can only slow the decrease.

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