In wet areas across the Prairies, this year has brought up a lot of questions.

When a crop sits in water, roots are starved of oxygen and development is restricted. As the roots struggle to grow and function, the crop has less ability to access nutrients, which can lead to stunting and uneven growth. High humidity can compound the problem. Reduced sunlight, from cloudier conditions, and higher humidity also reduces the transpiration potential of a crop meaning less water is being pulled from the soil through the plant.

This moisture map is based on data from an internal network of SWAT Water Stations and shows regional maximums of rainfall accumulation from May 1 to August 13, 2026, reaching up to 450mm in areas:

The decisions that come with uneven maturity, harvesting through wet spots, grain quality and increasing weed pressure are stressful enough. But what is happening beneath the surface?

Water is essential—but too much changes the soil

In reasonable amounts, water is critical to healthy crop growth. It supports mineralization, helps transport nutrients through the soil and provides structural support to plant cells through turgor pressure.

But when soils become saturated, many important soil processes can be disrupted.

Nitrogen

Excess water can have significant implications for nitrogen.

When soil becomes saturated and oxygen is limited, microorganisms can use nitrate as an alternative source of oxygen. This process, known as denitrification, can result in nitrogen being lost from the soil as nitrogen gas and nitrous oxide. The risk is particularly important in heavier clay loam and clay soils.

Excess water can also move nitrate below the crop's rooting zone, where it is no longer accessible to the crop. This is more likely to be a concern in lighter, sandy soils where water moves more readily through the profile.

Sulphur

Sulphur, like nitrogen, is relatively mobile in the soil and can move with water.

Prolonged saturated conditions can reduce available sulphur in the rooting zone, contributing to yellowing and poor early crop growth. Where excess water has moved nutrients through the profile, sulphur deficiencies may become more apparent as the crop develops.

Phosphorus

Phosphorus behaves differently from nitrogen and sulphur, but water still plays an important role.

The processes that influence phosphorus mineralization and immobilization are affected by temperature, moisture and aeration – much the same as nitrogen. Under saturated conditions, changes in soil chemistry can increase the solubility of phosphorus that would otherwise be bound to iron and aluminium oxides and other minerals.

Phosphorus can also be moved with soil through erosion, which can increase with excessive rainfall and runoff.

So, what does this mean for next year?

While we manage our way through this growing season, it will be important to understand what happened beneath the surface—and where it happened.

Not every part of a field will respond the same way. Nutrient losses and deficiencies will vary depending on where water collected, how long the soil remained saturated, soil type, drainage and what nutrients have been applied in previous years.

This is where SWAT MAPS and soil testing by SWAT Zone can provide a valuable report card.

Accurate testing by zone can help identify where nutrients are now low, where nutrients may still be present in excess, and where future fertilizer applications are most likely to provide a return on investment. Rather than treating the field as one uniform area, understanding the differences between zones can help us make more targeted decisions.

Subsurface water doesn't always behave the way we may expect or infer from what see it on the surface. The image below provides a conceptual illustration how excess rainfall water can create features such as a perched water table. Where and when perched water tables intersect a crop's root zone, and the soil situation implications on crop health, are very dynamic in time and space.

Wet conditions create challenges that we can see from the cab—but some of the most important impacts are happening below our feet.

Understanding where those impacts occurred this year can help us make better, more proactive decisions for the next crop. If we can collect data that actually drives decisions, it will deliver results.

Nitrogen (N) plays a critical but complex role in carbon (C) sequestration in soils, influencing both the accumulation and decomposition of soil organic matter (SOM). Depending on how it is managed it can either enhance or reduce the storage of carbon in soil. Proper management of nitrogen fertilization is essential in maximizing soil carbon sequestration while minimizing the loss of carbon as carbon dioxide (CO2) through microbial respiration.

One of the primary ways nitrogen influences carbon sequestration is by enhancing plant productivity. Nitrogen fertilization increases plant biomass production, which in turn leads to higher inputs of organic material into the soil through root exudates, fine root turnover, and crop residues. These carbon inputs provide the raw material for SOM formation, an essential process for long-term carbon storage in soil. When plants have adequate nutrition, their increased photosynthesis results in greater carbon fixation from the atmosphere, subsequently enriching the soil organic carbon pool. (Tiefenbacher et al., 2021)

Sequestration of carbon in SOM is inherently tied to nitrogen because organic matter contains both elements in varying proportions. As SOM builds up, it sequesters not only carbon but also nitrogen, effectively tying up nitrogen in forms that are less available to plants and microbes. While this is beneficial for long-term soil health and fertility, it also means that some nitrogen inputs are locked in stable organic forms and are not immediately available for plant uptake. The process of microbial immobilization is governed by the carbon-to-nitrogen (C:N) ratio, meaning that soils high in carbon but low in nitrogen will experience increased nitrogen immobilization by microbes. As a result, additional nitrogen fertilizers may be required to offset the extra nitrogen that is immobilized while SOM is increasing in soils. (Karimi et al., 2020)

However, it is crucial to avoid over-application of nitrogen, as excess fertilization can decrease carbon sequestration rather than enhance it further by accelerating microbial decomposition of SOM. A key challenge in carbon sequestration is the dynamic balance between carbon inputs and the decomposition of SOM. Microbial activity, which is influenced by nitrogen availability, plays a central role in determining whether soil gains or loses carbon over time. Nitrogen fertilization enhances microbial activity, leading to the accelerated decomposition of SOM and the release of CO2. While this process releases plant-available nutrients that support growth and further carbon input, excessive microbial breakdown of SOM can counteract sequestration efforts by increasing carbon losses from the soil system. (Khan et al., 2007)

The balance between carbon inputs and decomposition is crucial in determining changes in soil carbon content. When nitrogen fertilization is applied in appropriate amounts that match plant demand, it fosters plant growth and organic matter accumulation without significantly accelerating SOM decomposition. However, when nitrogen is supplied in excess, it stimulates microbial decomposition beyond the rate at which carbon is replenished, leading to net losses of soil carbon. Excess nitrogen can tip the balance toward decomposition rather than accumulation, thereby reducing the effectiveness of soil as a carbon sink.

To optimize carbon sequestration, nitrogen application should be carefully managed to match spatial and temporal plant requirements. Precision nitrogen management with SWAT MAPS—applying the right amount of nitrogen to each SWAT zone within a field—ensures that plant growth is not limited by nitrogen deficiencies while also preventing excessive nitrogen levels that would accelerate SOM decomposition. Areas within fields that are nitrogen deficient will experience reduced plant growth and, consequently, lower carbon inputs as well as increased immobilization as the C:N ratio of the soil rises. Conversely, areas within fields with consistently excessive nitrogen levels will exhibit heightened microbial activity, leading to SOM depletion and increased CO2 emissions. By optimizing nitrogen applications to match plant demand and soil conditions, it is possible to sustain agricultural productivity while maximizing carbon sequestration potential in soils.

The SWAT ECOSYSTEM allows for fine-tuning nitrogen application rates and distribution. It can therefore enhance soil carbon sequestration while maintaining or even improving crop yields. Technologies such as soil testing, moisture monitoring, remote sensing, yield monitoring, and variable-rate fertilization enable more precise nitrogen management, reducing the risks associated with both nitrogen shortages and surpluses. Ultimately, managing nitrogen effectively in agricultural systems requires a strategic approach that optimizes fertilization withing zones of varying capabilities for both productivity and long-term soil carbon storage. And long-term carbon storage benefits everyone.

Karimi, R., Pogue, S.J., Kröbel, R, Beauchemin, K.A., Schwinghamer, T. & Janzen, H.H. (2020) An updated nitrogen budget for Canadian agroecosystems. Agriculture, Ecosystems & Environment. 304: 107046. https://doi.org/10.1016/j.agee.2020.107046

Khan, S.A., Mulvaney, R.L., Ellsworth, T.R., & Boast, C.W. (2007) The myth of nitrogen fertilization for soil carbon sequestration. J. Environ. Qual. 36:1821–1832 (2007). doi:10.2134/jeq2007.0099

Tiefenbacher, A., Sandén, T., Haslmayr, H.-P., Miloczki, J., Wenzel, W., & Spiegel, H. (2021). Optimizing Carbon Sequestration in Croplands: A Synthesis. Agronomy, 11(5), 882. https://doi.org/10.3390/agronomy11050882

When fertilizer is applied, we want all those nutrients to be taken up by the crop, right? And the more fertilizer that gets into the crop the better? Yes… and no. That’s the paradox of nutrient use efficiency (NUE).

This starts with the complexity of how NUE is measured. There are many ways to measure NUE, explained in “Defining nutrient use efficiency in responsible plant nutrition” (The Scientific Panel on Responsible Plant Nutrition, 2023). The method used depends on what you want to learn and measurements that are available. But the end goal is largely the same: To understand how agriculture can provide nutrients to crops while minimizing their environmental impact.

While it would be outstanding to measure 90+% uptake of an applied nutrient in the year of application, it’s not very realistic for most nutrients and crops grown in soil. Crops acquire most of their nutrients from the soil. A recent example of this with phosphate uptake in corn was published, showing 78-92% of early – mid season corn phosphorus came from the soil, not fertilizer. (Chatterjee et al., 2024). Griesheim et al. (2022) measured a range of only 7% to 46% fertilizer nitrogen uptake efficiency in aboveground biomass in corn. The relative amount from soil versus fertilizer depends on the nutrient and the soils’ ability to supply the nutrient, either as “available” when we soil test or through mineralization during crop growth. The more deficient the soil is, the higher the percentage taken up must come from applied fertilizer. So, in a very deficient soil, NUE by many measures will look very good! But is this what we want?

Assuming all other 4Rs are adhered to, very little response to the applied nutrient means the soil is functioning the way we want it to and supplying enough nutrition. All we need to do is continue to monitor soil levels and ensure supply remains sufficient but not excessive. An example is the P response graphs in figure 1. Is the steeper response curve more exciting, or the flat one? Many would say the steep curve - it shows an impressive return on applied phosphate. But ideally, we want the curve to be relatively flat, since that tells us that we’ve done a good job of managing soil nutrient levels and our soil is functioning the way we want it to. This is the intersect of psychology and agronomy – the steep response curve gives us the excitement of knowing there’s an opportunity to fix something, and while that information is valuable, we’d be better off on the flat curve since yield isn’t limited by that particular nutrient.

Figure 1. Average corn response to fertilizer P on high P soil vs. low P soil (Leikam et al., 2010).

Given what we do with SWAT MAPS, we are particularly interested in responses by SWAT zone to demonstrate opportunities to use variable rate technology to improve returns on applied nutrients. What if the high yield, flat response curve above was from a well-drained depression with deep topsoil and high soil P, and the lower yielding, steep response curve from an upper landscape position with historical erosion and little topsoil? That’s incredibly valuable information and needed if the industry wants to drive precision ag adoption.

To recap, we want soils that can supply sufficient nutrients to the crop, because that means we don’t have to apply more from fertilizer. But if we achieve that it also means that a very small percentage of fertilizer that we do apply to maintain fertility levels will be taken up in that year, and that’s the paradox. The annual “efficiency” that is often chased is not actually what we want. Whether that H2PO4– molecule taken into a root hair came from a fertilizer granule applied 4 weeks ago or 4 years ago doesn’t really matter. The important thing is it’s there where the root can access it, it’s in high enough concentration to supply what the plant needs, but not so high it risks excessive environmental loss. That SO4-2 molecule that will contribute to high quality protein in your wheat? It may have cycled through many, many microbial proteins before finally entering a crop root years after it was applied as a sulfur fertilizer. The important part is it didn’t leach out of the root zone a week after it was applied. Soil is the ultimate nutrient laundering scheme. It supplies nutrients but we don’t usually know the original source, and frankly does it matter?

Before the inundation of “yeah buts...” I will say that nitrogen in some ways is an exception. Soil can’t reliably “store” nitrate-N. Because nitrate is susceptible to many forms of loss and it has numerous environmental effects in both surface water, groundwater, and the air, we need to be cautious about how much nitrate is available for loss at any given time. The way to mitigate those losses is by following 4R nutrient stewardship, nurturing a healthy, well-structured soil that has a suitable pH, and is nutritionally balanced. All these characteristics tend to reduce the need for applied N, maintain crop yields in a broad variety of climate conditions, and reduce losses.

It is obvious from recent research that healthy agricultural soils provide the majority of nutrient uptake rather than the fertilizer we apply. Which is why we need to understand the soil’s ability to supply these nutrients for a successful precision ag strategy. And no, it is not just a single nutrient value on a soil test. It requires an understanding of carbon cycling across the landscape that is influenced by many things – both chemical and biological.

At Croptimistic we are currently scoping out ways to measure yearly and long-term nutrient use efficiency using a partial balance method. While it's a data intensive process, it will be relatively easy to calculate for farms participating in the Yield Potential Program. It allows us to analyze whether we are building or depleting nutrient levels at the field and zone level or risking environmental losses. It’s a valuable measure of sustainability and helps us make better fertility recommendations.

So, remember, the next time you do a fertilizer trial on your farm and see no results, don’t be disappointed! It might mean you can pat yourself on the back and thank your soil for doing its job.

References:

Chatterjee, N., Li, C., & Margenot, A. J. (2024). 33P-isotope labelling ammonium phosphate fertilizers reveals majority of early growth maize phosphorus is soil-derived. European Journal of Soil Science, 75(5), e13578. https://doi.org/10.1111/ejss.13578

Griesheim, K. L., Mulvaney, R. L., Smith, T. J., & Hertzberger, A. J. (2023). Nitrogen-15 evaluation of fertilizer placement at planting for corn production. Soil Science Society of America Journal, 87, 309–323. https://doi.org/10.1002/saj2.20503

Leikam, D., G. Randall and A. Mallarino. (2010). Are current soil test-based phosphorus and potassium recommendations adequate? Crops & Soils. Vol. 43-6. Pp 27-32.

Scientific Panel on Responsible Plant Nutrition. (2023). Defining nutrient use efficiency in responsible plant nutrition. Issue Brief 04. Available at www.sprpn.org