Guideline Index

Chapter 5: Understanding and Managing Soil Biology

5.4 Why is soil biology important to dairy farmers?

Soil biology mediate critical soil functions by:

5.4.1 Nutrient cycling

Given that dairy farms have a high nutrient requirement and that all nutrient transformations in soils are biologically-mediated, diverse biological populations are required to support optimum nutrient cycling from both organic and inorganic sources. The Carbon Cycle

The breaking down of organic materials and the release of bound nutrients for plant uptake are important parts of the carbon cycle (Figure 5.4).

Figure 5.4  The Carbon Cycle (Mele, from
Figure 5.4 The Carbon Cycle (Mele, from

In photosynthesis, sunlight drives a biochemical process in plants that splits atoms of carbon dioxide and water and re-combines them as carbohydrates to form the basic units of the terrestrial (land-dwelling) food chain. A large proportion of these carbohydrates are then available to the carbon decomposing soil biota as plant litter or in the form of root exudates. Some of this carbon cycles quickly through the soil (particulate or labile carbon) while a usually larger component becomes sequestered as microbial biomass carbon, or humified carbon and will have a longer residence time. Charcoal can be a significant component of soil carbon if the land had a previous history of fire. This form of carbon can have very long residence times in soils, but ultimately all organic carbon will become mineralised and will be returned to the atmosphere as carbon dioxide.

One aspect of the carbon cycle that is of current concern involves the large return of carbon dioxide (CO2) to the atmosphere. CO2 is a potent greenhouse gas and is produced through cellular respiration – the metabolic process that takes place within cells through which organisms obtain energy from organic molecules. The Nitrogen Cycle

Another important cycle is significant in dairy systems, not only because it drives production, but because it is also implicated in the production of greenhouse gases. This is the nitrogen cycle (Figure 5.5).

Figure 5.5  The Soil Nitrogen Cycle (Adapted by Mele in from E.Paul, 2007)
Figure 5.5 The Soil Nitrogen Cycle (Adapted by Mele in from E.Paul, 2007)

Depending on the phase of the nitrogen cycle, nitrogen can exist in the atmospheric dinitrogen (N2) form, the ammonia (NH3) form, the ammonium (NH4) form, as nitrite (NO2-), as nitrate (NO3-), or as nitrous oxide (N2O). It can also exist as mono-nitrogen oxides (NOx) produced from the reaction of nitrogen and oxygen gases in the air during fires.

As the different forms of nitrogen move from one phase to the next, their conversion is mediated by biological processes either in the body of a plant or animal, or via microbial action in the nitrogen fixing, mineralising, immobilising, nitrifying or de-nitrifying stages in the soil (red arrows in Figure 5.5). Plants can only take up N as inorganic N forms (nitrate or ammonium), so organic forms of N need to be mineralised by soil microbes before they can be taken up by pasture. Conversely, ammonium and nitrate can also be immobilised back to the organic form when the nitrogen is taken up by plant or microbe. The relative speed of the nitrogen cycle in the soil is dependent on temperature and moisture. This means that warm, moist conditions favour the release of nitrous oxide (a potent greenhouse gas) from soil so care is required with regard to the form of nitrogen fertiliser used and its application rate – Refer Chapter 12.1.2.

Pasture legumes, such as subterranean clover, provide high quality feed for grazing animals and can contribute substantial quantities of nitrogen to dairy systems. This nitrogen is essentially provided at no cost. Atmospheric nitrogen is biologically ‘fixed’ by rhizobia bacteria living in association with legume roots and the availability of this fixed or reactive nitrogen can make the legume independent of soil/fertiliser nitrogen – See Chapter Rhizobia cannot form survival structures (‘resting bodies’) like spores and this makes all rhizobia very sensitive to environmental stresses. They can easily be killed by exposure to stresses such as heat, extreme pH, and chemicals such as some fertilisers or fungicides (Drew et al, 2012). Rhizobia are aerobic organisms and need oxygen for respiration, moderate temperatures, moisture and food (Table 5.1).

Table 5.1  Rhizobia needs for growth and survival (from Drew et al, 2012)
Table 5.1 Rhizobia needs for growth and survival (from Drew et al, 2012)

Popular legume varieties for dairying in southern Australia include lucerne, red clover and white clover. All require soils with good fertility, and for lucerne in particular, good drainage. A 2012 review found that annual N2 fixation rates in Australian dairy pastures are generally low – usually less than 50kg/ha. This is due to low pasture legume content with typical legume contents of grazed pastures less than 30% of total pasture biomass production – See Chapter 12.2.1. Other factors that could positively influence N2 fixation input (i.e. nutrition, acidity or moisture) were found to have little impact until the proportion of legume in the pasture increased. Potential (maximum) N2 fixation is governed by legume total dry matter production which is dependent on mineral N availability, soil fertility, and the quality and quantity of the rhizobia (Unkovich, 2012).

Over application of inorganic nitrogen fertiliser can reduce the contribution of organic nitrogen from legumes to a low level, representing a potentially unnecessary cost to the farmer (Unkovich, 2012). At low soil nitrate levels (below 50kg N/ha.) legume reliance on N fixation is high. As soil nitrate levels increase, biological N2 fixation becomes more suppressed to a point above 200kg N/ha when nodulation and nitrogen fixation will be close to zero (Drew et al, 2012). Maintaining legume levels in mixed pasture swards requires a combination of appropriate grazing management, and attention to the factors discussed above for maximum N2 fixation – See Chapter 12.6.3 for more information.

Free-living nitrogen fixing bacteria can contribute additional nitrogen per hectare per year. These bacteria, typically species of the Azospirillum and Azotobacter genera, are found in many Australian soils. Their proliferation is dependent on availability of soil C and relatively low nitrogen levels (Gupta et al., 2011; Gupta & Paterson, 2006). Their contribution to dairy soil nutrient budgets is therefore not likely to be large in dairy systems. Phosphorus cycle

Like the nitrogen cycle, the P cycle is very complex, involving many interactions and chemical reactions in the soil. The rate by which organic phosphorus becomes inorganic and plant available in the soil solution will depend on the mineralisation process driven by soil microorganisms and their enzymes. As with nitrogen, whilst in the soil solution in this soluble form, phosphorus is also subject to being immobilised by soil microorganisms back into an organic form.

Plants and soil organisms have co-evolved symbiotic associations whereby plants can signal a range of needs (e.g. nutrients, plant defence) through the form of plant root exudates produced (Rasmann & Agrawal, 2008).

Soil organisms such as mycorrhizal fungi have developed specific attributes, such as phosphorus solubilisation and transport, to make P more available to plants.

High rate application of inorganic sources of fertilisers can interrupt this process and reduce biological nutrient cycling. Conversely, a reduction in phosphorus application rates on high P soils has not resulted in loss of production suggesting a resumption of P solubilising functions.

5.4.2 Improving soil structure

Soil biology has a particularly important role in promoting and maintaining soil structure and aggregate stability. Soil structure is influenced by the amount of clay and organic carbon in soils, and the amount and proportion of cations (particularly calcium and magnesium) – See Chapter 4. The cations help flocculate soils into microaggregates and also build bridges between the mineral fraction of the soil and the organic fraction. However, this flocculation alone is not sufficient in most cases to ensure good aggregate stability and good structure. A Cornell University soil scientist, Richard Bradfield, recognised back in 1950 that ‘aggregation is flocculation – plus!’ The ‘plus’ refers to what he called ‘cementation’ – the physical enmeshment of soil aggregates by plant roots and fungal hyphae, and the ‘gluing’ of soil particles by bacterial and fungal exudates (Hillel, 1998). An example of this is the secretions of glomalin from arbuscular mycorrhizal fungi.

5.4.3 Degrading pesticides and herbicides

Soil organisms have the capacity to degrade applied biocides including pesticides, fungicides and herbicides. The concern over the persistence of organochlorines (e.g. DDT, dieldrin, chlordane) in agricultural and horticultural soils relates to their toxic effect on microorganisms (Lal & Saxena, 1982). Modern biocides are, in general, of lower persistence in soils due to the ability of organisms to degrade the chemicals into harmless compounds (UWA, 2013). Without this soil function, the repeated application of herbicides and pesticides would result in these compounds accumulating in soils to levels that would threaten the health of terrestrial and aquatic ecosystems.

5.4.4 Regulating water quality

Another important function of soil biology is the filtering of excess nutrients (within the limits of a given system) thereby contributing to improved groundwater quality before its passage into surface creeks and rivers.