Guideline Index

Chapter 5: Understanding and Managing Soil Biology

5.5 What regulates soil biology?

There is growing awareness of the importance of soil biology to efficient soil function. It is therefore helpful to understand what regulates soil biological populations so that favourable management practices can be used to promote biological function.

There are two levels of regulation of soil biology. The primary regulators are environmental and include air, water, temperature, and soil type. In the context of a habitat all of these features are related such that the texture and porosity of a soil determines the water and air available for growth. The secondary regulators relate to organic matter quality and quantity, the amount and frequency of soil disturbance, and the inputs used to manage production (fertilisers, herbicides, lime etc.).

5.5.1 Primary Regulators Soil air

The movement of air into and out of the soil is critical to the survival of aerobic organisms, and the functions they perform. There exists therefore, a strong relationship between soil structure and soil biological functions.

Given that most nutrient cycles are biologically-dependent, meeting the needs of microorganisms for air, water and food through management practices that support good structure, and avoid damaging compaction, will promote efficient nutrient cycling. Soil water

Aerobic microbial activity responds to soil water potential assuming soil temperature is not limiting. Figure 5.6 shows that microbial biomass is closely aligned with soil moisture content with populations rising with available moisture when food and temperature are not limiting. Above field capacity, the loss of soil oxygen due to inundation would see a reduction in microbial biomass.

Of the microorganisms, fungi are generally more tolerant of lower soil moisture than bacteria as bacteria are less mobile and rely on diffusion to obtain nutrients (NRCS, 2013b). Earthworms are generally numerous on dairy farms but populations fall off below 500-600mm annual rainfall with relatively few individuals remaining below 300mm (Mele & Carter, 1999).

Figure 5.6  Microbial biomass activity as influenced by the level of soil moisture (
Figure 5.6 Microbial biomass activity as influenced by the level of soil moisture ( Soil temperature

Plants as well as soil organisms require certain minimum temperatures in order to grow and carry out their activities. Biological activity and associated growth and development occurs more quickly at higher temperatures, as evidenced by growth rates of pastures speeding up in spring and slowing as winter approaches.

In the soil, biological functions, such as breaking down of organic matter or cycling of nutrients, are similarly affected by temperature. This is why it is generally not a good idea to soil test for nitrogen in spring because the increase in biological activity releases nitrogen from stores of organic matter resulting in an inflated account of the true quantity of N in dairy soils. Soil type

Soil type strongly influences microbial populations for a number of reasons. Clay soils have the potential to hold more water and for longer than a sandy soil. For this reason, they generally hold more organic carbon than sandy soils. Well-structured clay soils will have a higher number of micro- and macro-aggregates, thereby providing more potential habitat for soil organisms of varying sizes. A diversity of habitat will ensure maximum protection for soil organisms against predation.

Note that while clay soils have potential to support higher microbial biomass, this potential will only be realised if other regulators (primary and secondary) are not limiting. Most obviously this means that if the clay soil is poorly structured, its carbon capture potential, air-filled porosity, drainage, and numbers of micro-aggregates will be sub-optimal and production in such a soil is also likely to be below potential. So, even though clay soils have potential to support high microbial biomass, a heavy clay soil that has been used for cropping, or that was poorly managed in wet conditions may not be well structured and may have lower microbial biomass than a lighter loamy soil. Figure 5.7 shows two different soil types under two different land uses. Higher clay, and less disturbance results in higher microbial biomass. Actual microbial biomass on individual farms will be strongly influenced by management practices.


Figure 5.7  Microbial biomass carbon in soils with differing clay contents and management practices (
Figure 5.7 Microbial biomass carbon in soils with differing clay contents and management practices ( Survival strategies

Bacteria are simple organisms consisting of a single prokaryotic (no cell nucleus) cell. They are extremely responsive to changes in their environment either rapidly dying back or reproducing at a very high rate depending on conditions. Under favourable conditions bacteria may divide every 20 minutes. This could result in exponential growth where one bacterium could produce 10 million in just 10 hours (Agrios, 1988). However, this is unlikely to occur to this degree in soils due to reduction in food supply or accumulation of metabolic wastes. When conditions change to be less favourable, most bacteria can quickly develop a range of ‘resting bodies’ which can survive extended periods until such time as conditions again favour growth and development.

Fungi usually have plant-like vegetative bodies called mycelia (singular mycelium). The mycelium consists of elongated, branched, microscopic filaments termed hyphae. They are higher order eukaryotic (possessing a membrane-bound nucleus) organisms, the vast majority of which are saprophytic, that is they live on dead organic matter. Fungi reproduce primarily by means of spores. Fungi are not as responsive to environmental changes as bacteria due to their larger physical size allowing access to a wider range of soil resources. However spores may be produced as resting bodies when unfavourable conditions persist. Fungi may regrow from severed hyphae resulting from tillage but their recovery is slower than that of bacteria – food, water, air and nutrition notwithstanding.

This generally results in higher populations of bacteria in annual systems and equal or higher proportions of fungi in long-term perennial systems.

5.5.2 Secondary Regulators Organic matter quality and quantity

Organic amendments:

The carbon to nitrogen ratio (C:N) is a good measure of likely mineralisation (release of N by microbes) or immobilisation (tie-up of N in microbial biomass) in soil. A soil’s C:N should be in the order of 12:1. If the C:N is greater than 25:1, immobilisation of nutrients is likely. If the C:N is less than 25:1, mineralisation is likely. This means that if microbes (mainly bacteria and archaea) are in a high nitrogen environment (low C:N) they can use that nitrogen to breakdown organic matter in soils to access nutrients, including carbon, as a food resource, and their population will likely increase thereby turning over N for plant access. However, in low C:N soils, soil carbon is at risk of declining if sufficient carbon is not re-introduced into the system by growth (e.g. plant roots), or application (e.g. manures or compost). In low C:N soils, microbes will use available nitrogen to degrade soil carbon which is released as CO2.

Conversely, in a high C:N soil, bacteria will access all available nitrogen to breakdown excess C and as they are superior competitors for soil N compared to plant roots (Owen & Jones, 2001), the plant will be deprived of nitrogen because it is immobilised in the bodies of bacteria and other soil microorganisms. This is termed ‘nitrogen draw down’. It is usually a temporary phenomenon and is overcome when bacteria die off due to resource depletion, or another nitrogen source is introduced.

The C:N concept is important when adding organic amendments to soil. Table 5.2 shows average C:N ratios of common organic materials. As mentioned above, if an amendment has a C:N of less than 25:1 it will progressively release nutrients and should have a fertiliser effect. If the material has a C:N ratio of more than 25:1, it is likely that nitrogen will be immobilised and nitrogen draw down will occur.

Table 5.2  C:N ratios of common organic amendments (Charlesworth, 1997).
Table 5.2 C:N ratios of common organic amendments (Charlesworth, 1997).

Microbial diversity:

Microbial diversity refers to the number and variety of soil microorganisms. As a general rule, the more diverse the above-ground crop or pasture mix, the more diverse will be the micro-biological communities in the soil. Wilhelm (1973) cites the ‘Elton Principle’ which holds that the greater the complexity of a microbiological community in terms of total number and species of organisms, the greater the stability of the community. As shown in Table 5.2, organic amendments can vary considerably and their application to the soil will have different effects on the soil biological community. In the same way, crop and pasture mixes will also influence microbial composition and activity.

Plants vary in the size and structure of their root systems, in the quantity and quality of root exudates, and in the degradability of crop or pasture residues. This results in differences in microbial density and diversity in the plant rhizosphere (root zone) and near crop and pasture residues. Some plants possess chemicals that inhibit the growth of other plants, or have negative effects on soil organisms. Likewise, some microbes possess strategies that enhance their competitive advantage. This has particular relevance when we consider suppressive soils. The term ‘suppressive soil’ has been used to describe soils in which a pathogen is present but is not causing economic damage. Suppression of a pest or disease is the mechanism by which one or several organisms are antagonistic to a pathogen through the antibiotics they produce, competition for food, or through direct parasitising of the pathogen (Agrios, 1988). As an example, the production of isothiocyanates in canola has a suppressing effect on soil microorganisms. Isothiocyanates possess fungicidal, bacteriocidal, nematocidal and allelopathic properties (Fahey, 2001). Tillage

Organic matter persists in soils to the degree that it is protected from microbial attack (Schmidt et al. 2001) or because prevailing moisture and temperature conditions are unfavourable for microbial decomposition. Tillage of any kind impacts on these protective mechanisms and renders the organic matter vulnerable to degradation by soil organisms. Tillage mixes the soil bringing microbes into more intimate contact with organic matter. It also improves (however temporarily) air and water movement into the soil – elements important for the growth and development of soil biology. Tillage can also be used to incorporate and distribute plant residue into the soil profile, again bringing food resources into close contact with soil organisms.

Tillage favours bacteria in view of their superior ability to respond quickly to changes in the environment. Fungal populations tend to be negatively impacted in view of the damage to the hyphal networks – See Section

The incorporation of large quantities of organic material into soil can be a positive undertaking provided follow up actions maximise the use and sequestration potential of incorporated organic matter. For example, discing in crop residues will help to capture much of the carbon turned into the soil and will benefit the establishment and growth of perennial pasture.

The development of minimum- or no-till systems recognises the value of minimising soil disturbance. Stubble retention or surface applied organic materials will support slower decomposition and nutrient mineralisation, favour fungal growth to aerobically degrade lignocellulose compounds, promote better aggregation and soil structure, and improve the potential for SOM accumulation (Scott et al., 2010; de Boer et al., 2004) Chemical impacts on soil biology

The large number of chemicals registered for use on farms makes it difficult to discriminate between those that are benign and those that are harmful to soil biology. While some have little effect, others do negatively impact on soil biology. Bunemann et al. (2006) reviewed the impact of agricultural impacts on soil organisms and found that:

  • fertilisers generally enhanced soil biological activity due to increases in production;
  • the acidifying effects that can occur with the use of certain nitrogenous fertilisers resulted in negative impacts on soil biological activity;
  • organic amendments generally enhanced soil biological activity;
  • microbial inoculation, with the exception of nitrogen fixing microbes, appears to have little long-term effect;
  • the negative effects of pesticides and fungicides were more commonly reported;
  • negative effects of herbicides were less commonly reported.

Roget & Gupta (2004) found that the negative impact on soil biological activity of many herbicides is reversible i.e. given sufficient time, the soil biology bounces back. However, with some chemicals, repeated applications delays or removes that reversibility. They recommended that:

  • The short-term impacts of most of the herbicides tested are reversible, so it may be possible to develop management options to reduce non-target negative impacts;
  • An appropriate recovery period for soil biota should be allowed between herbicide applications;
  • Soils with a healthy biota could recover from short-term negative effects of herbicide application. Appropriate use of herbicides could be less destructive to soil biota if management practices that improve biological activity are promoted.

Grains Research and Development Council (GRDC) funded research from South Australia found specific effects of herbicides on soil N fixing bacteria with reductions in nodulation that resulted in reduced N benefit to the system (Drew et al, 2006).

Lime application and the associated increase in soil pH are strongly correlated with changes in microbial communities (Nelson & Mele, 2006). Lime has also been shown to influence functioning of the nitrogen cycle. Molecular techniques were used to target a section of the N-fixing gene in a wheat rhizosphere soil. The results suggest an increase in abundance of N-fixing rhizobacteria from which an increase in N fixation could be inferred. Research undertaken on acid soils in North-East Victoria showed an increase in ammonium N oxidisers following the application of lime.

Lime also impacts on soil structure by increasing aggregation of soil particles and the creation of a greater diversity of macro and micro pore spaces for improved habitat. Air and water movement through soil is also enhanced. In addition, biological access to food resources can be improved (Chan & Heenan, 1999).