Immobilisation of soil nitrogen in heavy stubble loads

Page last updated: Friday, 3 November 2017 - 11:32am

Please note: This content may be out of date and is currently under review.

Soil microbes often require nitrogen (N) to breakdown organic matter in soil. A key question facing growers is how much of their fertiliser N at seeding is potentially going to be immobilised or ‘tied up’ by microbes and what impact will it have on early crop performance?

Soil nitrogen cycling

The microbial demand for N often coincides with increasing crop demand at the break of season in paddocks with high stubble loads. This means less N is potentially available to the crop to support early growth. While N supply will be dependent upon a number of factors including stubble loads, background soil N status and rainfall events prior to seeding, any potential tie up of N is likely to be relatively short lived (4-6 weeks).

Soil N supply depends on the amount of organic N that is a component of soil organic matter and biological processes that convert this to plant-available forms such as ammonium and nitrate (Figure 1). Ammonium (NH4+) is released from organic N when mineralised by soil microbes, a large proportion of which is taken up by other soil microbes (immobilised) and converted into nitrate (NO3-) via nitrification (Figure 1). The balance between N supply and ‘losses’ which can include microbial demand as well as environmental losses (e.g. leaching), determine the net amount (surplus) of soil N that becomes plant available. While plants are able to take up both ammonium and nitrate, the latter is generally the dominant form of N used by plants.

Soil nitrogen cycle showing how nitrogen is cycled through different forms in the soil
Figrue 1 Soil nitrogen (N) cycle. The cycling of N through different forms in the soil determines the quantity of N that is made available for plant uptake.

The situation for 2014

High crop yields in many areas for 2013 would have required high N inputs from the soil which would have decreased soil N stocks and also resulted in high stubble loads. Combined with a dry summer with little or no soil moisture to drive mineralisation of soil organic matter, there have been few opportunities for soil N to build up over this period.

In many paddocks, the combination of low soil N and high stubble loads with a wide carbon to nitrogen (C:N) ratio (figure 2a, b) may lead to more soil N being immobilised by microbes and less being available for the crop to take up, the end result being N deficiency during the crop’s early growth stages (figure 3). Where stubble is incorporated into soil, the potential for N immobilisation is greater.

High stubble loads on the left and graph illustrating different C:N ratios for various crop residues on the right.
Figure 2 High stubble loads (a) and residue quality, as reflected in the C:N ratio (b), can result in large changes to N supply in the soil. As the amount of N decreases in residues, microbial demand for soil N increases, resulting in less plant available N.
N deficiency on old stubble rows reflected as waves of yellow foliage in the crop
Figure 3 N deficiency along old stubble rows (harvester windrows) as a result of N immobilisation in the soil

One of the simplest ways to manage a high stubble load is through burning, which may ordinarily be used to control weed populations, decrease disease incidence or improve seeding efficiencies. However, burning results in a rapid net loss of C and nutrients to the system. Retaining stubble is generally the preferred option to help build soil organic carbon, promote nutrient cycling and prevent wind erosion. For growers who are able and/or willing to retain stubble the key question is:

How much fertiliser nitrogen at seeding will be used to breakdown the stubble instead of supplying the crop?

An air seeder seeding on stubble

The answer depends on your background soil N, how the stubble is treated (incorporated or left standing), the quality of the stubble and the timeframe between the break of the season and the sowing date.

Precisely determining the amount of soil N that may be immobilised is difficult, but a working example can provide some guidance regarding the likely impacts of different stubble loads on an N budget (see the scenario calculations below). It is important to remember that organic residues can take months or years to break down and therefore any N required to enable this is used over the same timeframe – so not all N will be immobilised at once.

Deep soil testing to determine background soil N prior to seeding is needed to determine fertiliser strategies. Additional N may also be made available if significant rainfall occurs prior to sowing due to the mineralisation of soil organic matter. Under optimal conditions (warm temperatures) in summer, N can be mineralised at 10-15 kg N/ha per day, though in autumn and winter this is more likely in the region of 1-5 kg N/ha per day.

Scenario (example only)                                           

A grower retains 5t/ha of wheat stubble (3.3t/ha grain yield at a harvest index of 0.4) and wants to estimate the likely impact of the stubble on soil N levels in the paddock. Assume a C:N (carbon:nitrogen) ratio of 120:1 in the stubble.

Step 1 Calculate the amount of C in stubble that is added to the soil:

Stubble (kg/ha) x (typical C% of stubble) = 5000 x 0.45 = 2250 kg C/ha.

Step 2 Calculate N present in the crop residues added to the soil, remembering that in this example stubble contains 2250kg C and wheat has a C:N ratio of about 120:1.

(Kg C/ha) ÷ (C:N) = 2250 ÷ 120 = 18.75 kg N/ha in the stubble.

Step 3 Allow for 30% of the C to be used by microbes for their growth and the remaining 70% to be respired as carbon dioxide. Microbes need N for growth but not for respiration. The amount of C used by the microbes is:

(Kg C/ha) x (0.3) = 2250 x 0.3 = 675 kg C/ha used by the microbes for their growth.

Step 4 Assume microbes have a C:N ratio of 12:1, as in they require 1kg of N for every 12kg of C to grow. The nitrogen required to decompose the stubble residue is:

(C used by microbes) ÷ (12) = 675 ÷ 12 = 56.25 kg N/ha is going to be used by the microbes for their growth.

Step 4 Calculate how much N has been immobilised. The organic matter from the stubble contained 18.75 kg N/ha and the microbes require 56.25 kg N/ha to grow. Thus the N balance = 18.75 - 56.25

= -37.5 kg N ha

This is a NEGATIVE N balance. Thus the nitrogen deficit (equivalent to 37.5 kg N/ha) will be sourced from the existing N reserves in the soil, N supply from soil organic matter turnover and subsequent fertiliser applications.

Note: Since stubble does not normally all break down in a year, it is more likely that this is the N required by microbes over a 12-36 month period and therefore it is likely that a lower amount of N would be required at the break of season than the total N deficit that this exmaple indicates. The highest risk period will be during the first 6-8 weeks after sowing.For growers who retain high stubble loads and are considering N fertiliser strategies, the next question is:

How do I avoid nitrogen tie up if it may lead to nitrogen deficiency in my crop?


N deficiency on an old stubble row reflected as line of yellow foliage in the crop
N deficiency on the previous seasons harvester windrow due to the accumulation of residues and immobilisation of N

Banding N at seeding could potentially decrease immobilisation by physically separating the N from the C residues in order to slow turnover rates and ensure that the majority of fertiliser applied N is plant-available during crop establishment. Increasing fertiliser rates and split applications could be considered options to maintain sufficient N for crop requirements, particularly in high rainfall areas where yield potential (and subsequently N demand) are likely to be high.

Quantity, quality and handling of stubble also influence N supply. For example, legume residues generally contain more N, and as a consequence require less soil derived N and breakdown more quickly than cereal stubbles. Poor quality cereal stubbles (C:N greater than 80:1) immobilise N during their initial decomposition - largely in the first 8 weeks.

In this case, there is a risk of N deficiency in the crop's early growth stages as microbes will utilise background soil N and any residue N to breakdown organic matter. This is particularly the case when high residue loads are incorporated into soil and the microbial demand for N can quickly outweigh the supply in the soil. This is often visually reflected in the crop through poor early growth or other N deficiency symptoms, but may not be as evident in low disturbance systems where stubble remains on or above the soil surface.

Smaller stubble pieces and greater soil incorporation will potentially result in more rapid but shorter lived immobilisation due to more rapid breakdown of organic matter and release of N.

Knowing the current soil N status, stubble loads, stubble quality and soil moisture content can help you manage fertiliser applications and rates appropriately to ensure adequate N supply to the crop.

Further information on N supply from organic matter can be found in the GRDC publication Managing Soil Organic Matter: A Practical Guide authored by Dr Frances Hoyle of the Department of Agriculture and Food Western Australia. Further information on N deficiency symptoms can be found in the interactive decision support tool MyCrop.

This work is led by the Department of Agriculture and Food Western Australia and is supported by funding from the Australian Government and the Grains Research and Development Corporation.


Hoyle FC and Murphy DV (2011); Influence of organic residues and soil incorporation on temporal measures of microbial biomass and plant available nitrogen; Plant and Soil 347; pp. 53-64

Contact information

Craig Scanlan
+61 (0)8 9690 2174