Management of soil biology

This topic has 15 questions:

  1. What are the 10 guidelines for managing the biological fertility of soil?
  2. How do agricultural practices affect soil animals?
  3. How does soil management affect the fungal and bacterial populations in soil?
  4. What soil conditions allow plant disease to develop and what management practices can decrease disease outbreaks?

Organic farming

  1. What is organic farming?
  2. What does "certified organic" mean?
  3. What is the role of soil organisms in sustainable and organic farming?
  4. How is soil fertility managed in organic farming systems?
  5. How is nitrogen supplied to plants in organic farming systems?
  6. How is phosphorus supplied to plants in organic farming systems?
  7. Is phosphorus availability on organic farms in Australia a problem?
  8. What is a nutrient budget?
  9. What does research show about phosphorus budgets on broadacre organic farms in Australia?
  10. How do you calculate a nutrient budget?
  11. What are the key issues for managing the soil fertility of organic production systems in Western Australia?


Question 1. What are the 10 guidelines for managing the biological fertility of soil?

Each of the guidelines below relates to one of the 10 key principles of soil biological fertility.

  1. Soil erosion should be controlled to minimise loss of soil organisms.
  2. Plant organic matter should be retained to maximise nutrient cycling and soil aggregation.
  3. Some disturbance of soil is necessary to maximise soil biological diversity.
  4. Nitrogen fixing bacteria should be selected that match the host, soil characteristics (such as pH) and environmental conditions.
  5. Inputs of nitrogen fertliser should be calculated to complement biological soil nitrogen supply.
  6. Inputs of phosphorus fertiliser should be calculated to complement and enhance the activities of arbuscular mycorrhizal fungi.
  7. Any substance added to soil should be assessed in terms of its effects on soil biological processes and soil biological diversity.
  8. Crop rotations and tillage practices should be selected to avoid development of soil conditions that enhance the growth and survival of plant pathogens.
  9. The capacity of a management practice to produce a commercial product should be considered in parallel with its capacity to maintain and/or increase soil biological fertility.
  10. Sufficient time should be allowed for establishment or restoration of a level of soil biological fertility appropriate for particular soils and land management.

10 Key Principles of Soil Biological Fertility

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Question 2. How do agricultural practices affect soil animals?

Agriculture generally decreases the number of individual soil animals in the soil and decreases the diversity of soil animals compared to native vegetation. Soil animals require certain soil conditions to grow and survive. Agricultural practices alter soil conditions, making them harsher than those of native vegetation:

  • soil moisture is decreased and temperature is increased
  • wetting/drying cycles are faster
  • there is less organic matter in the soil and often only from one or two plants (not a variety of plants)
  • soil may be disturbed by erosion, vehicle traffic and tillage

The harsher environment under agriculture means that some of the original species are not able to survive. This decreases the diversity and may cause different organisms to dominate.

More on Soil Animals

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Question 3. How does soil management affect the fungal and bacterial populations in soil?

Fungi and bacteria differ in their responses to changes in agricultural management practices. Fungi are usually more sensitive to these changes. The fungal-to-bacterial ratio is therefore an indicator of environmental changes in the soil. When plant residues are applied as mulch, for example, fungi prosper because their hyphae are able to grow into the litter layer. Tilling, however, destroys large amounts of the fungal hyphae. Incorporation of plant residues into the soil also favours the bacterial population because the contact surface between the substrate and bacteria is increased. This response further depends on the soil type.

Nevertheless, the dominance of either fungi or bacteria also depends on the quality of the plant residue. Substrate structure, C:N ratio and cellulose content are important characteristics of its quality. Fungi are the predominant cellulose decomposers, even though one group of bacteria, the Actinomyces also contribute significantly to its decomposition. Cellulose has a high carbon content and a corresponding high C:N ratio, making it the ideal food source for fungi. Bacteria, which have a smaller C:N ratio than fungi, need food rich in nitrogen (e.g. green manure, legume residues). A fertiliser rich in nitrogen therefore favours the bacterial community in a soil whereas a substrate with a relatively wide C:N ratio enables growth of the fungal population.

The activity of the soil microorganisms also shows strong seasonal variation. Activity increases markedly with increasing temperature and soil moisture. Usually fungi depend on a sufficient amount of water in the soil and are expected to be less active under dry conditions. In many cases a low pH is associated with fungal dominance whereas a higher pH might be related to bacterial dominance.

More on Fungi vs. Bacteria

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Question 4. What soil conditions allow plant disease to develop and what management practices can decrease disease outbreaks?

Pathogens can exist in the soil for long periods of time without causing an outbreak of disease in plants. Disease outbreaks are either caused by an increase in the population of the pathogen or by an increase in the susceptibility of the plant. The population of the pathogen is dependent on whether the soil conditions are favourable for its growth and survival. The conditions that are favourable for the growth and survival of pathogens are different for each species of pathogen but are related to:

  • soil pH,
  • water content,
  • oxygen level,
  • nutrient levels and
  • the activities of other soil organisms.

Management practises that create soil conditions that are unfavourable to pathogen growth will decrease the likelihood of disease outbreaks. The susceptibility of the plant to disease is affected by factors such as its age and nutritional status. Outbreaks of disease are also more likely in agriculture and horticulture than they are in natural systems. In agriculture and horticulture similar species are planted together in what is called a ‘monoculture’. Monocultures can increase the probability of a disease outbreak occurring.

More on Plant Disease

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Organic farming

Question 5. What is organic farming?

Organic farming systems use practices that aim to produce food with a high nutritional value without the use of artificial fertilisers or synthetic chemicals such as pesticides. Organic farming also aims to harness natural processes that are beneficial for production and to create sustainable farming systems. A book called “The Organic Alternative” published by the Kondinin Group is a useful guide to organic farming in Australia.

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Question 6. What does "certified organic" mean?

"Certified organic" means that a certification association has guaranteed that a product has been produced in accordance with their standards. The process of certifying produce as organic involves keeping records of farm activities to show that the practices used on the farm agree with the standards of the certifying organisation. In Australia, there are several associations that certify produce as organic. 

Certification standards include the aims of organic production and contain details of the practices and inputs that are permitted on farms growing organic produce. An example of certification standards for organic produce is that applied to organic exports from Australia by the Department of Agriculture and Water Resources

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Question 7. What is the role of soil organisms in sustainable and organic farming?

Soil organisms have an important role in sustainable and organic farming as these farming systems aim to harness the benefits that soil organisms can have on production. Sustainable farming depends on establishing soil conditions that maximise nutrient cycling and take advantage of biological processes that enhance the fertility of soil and decrease the need for some chemical inputs. Organic farming relies more on soil organisms than other forms of agriculture because soil organisms make nutrients in organic matter available to plants and can improve the physical fertility of soil. 

More on Biological Processes

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Question 8. How is soil fertility managed in organic farming systems?

The management of soil fertility is different in organic farming systems to that of farming systems which allow inputs of synthetic chemical fertilisers. Organic farming emphasises increasing inputs of organic matter and often results in higher levels of soil organic matter, but this is not always the case. Increased input of organic matter is usually associated with increases in the physical and biological fertility of the soil because soil organic matter improves soil structure and provides a food and energy source for soil organisms.

The activity of soil organisms is very important in organic farming because they improve soil structure and can increase the availability of nutrients to plants through nutrient cycling. This also occurs in farms managed using chemical fertilisers, but the chemical fertility of soil on organic farms depends to a greater extent on biological activity in soil in association with a balance between nutrient inputs and outputs.

If animal manure is readily available and legume nitrogen is efficiently managed, soil nutrient levels can be maintained. However, most research on the effects of organic farming on soil fertility has taken place in Europe and North America. More research is necessary under Australian conditions.

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Question 9. How is nitrogen supplied to plants in organic farming systems?

Nitrogen in organic farms is sourced primarily from biological nitrogen fixation, with liquid nitrogen inputs available to some intensive horticultural systems. During nitrogen fixation, nitrogen from the atmosphere is converted to a plant and microbe available form. This is done either by symbiotic associations between pasture legumes and root nodule bacteria, or by free-living nitrogen fixing bacteria which occur in soil.

The amount of nitrogen fixed in association with legumes depends on the efficiency of the bacterial/legume association. The nitrogen becomes available once the legume plant dies and is decomposed by soil organisms. During this degradation process, nitrogen is released into the soil for use by plants. The amount of nitrogen fixed by free living bacteria is variable and can be increased in association with activities of organisms that decompose organic matter - the bacteria gain carbon when the organic matter is degraded, allowing them to grow more rapidly and collectively to fix more nitrogen.

More on Nitrogen Cycling

More on Nitrogen Fixation

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Question 10. How is phosphorus supplied to plants in organic farming systems?

In organic farming systems phosphorus can be supplied through inputs of organic matter such as animal manure or compost. The phosphorus in these inputs is in an organic form and must be decomposed by soil organisms before it is available for plant uptake. Rock phosphate is another source of phosphorus that is used in organic farming systems. Rock phosphate is highly insoluble in most Australian soils, but is more soluble in wet, acidic soils and under pastures. In organic farming, plants may also be supplied with phosphorus through associations with mycorrhizal fungi. These fungi can form an association with the roots of many agricultural plants that supplies the plant with some phosphorus and the fungi with carbon.

More on Phosphorus Cycling

More on Mycorrhizal Fungi

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Question 11. Is phosphorus availability on organic farms in Australia a problem?

Low phosphorus availability has become a major limiting factor for broadacre organic production in Australia. Several researchers have found that in organically farmed soils in Australia, low phosphorus availability may be limiting yield of crops and pastures. This is because animal manures are not readily available for most braodacre organic farmers in Australia. They often rely on rock phosphate as a source of phosphorus for plants. However, rock phosphate is poorly soluble in many soils and may not be able to supply plants with adequate amounts of phosphorus. 

Low phosphorus availability is likely to be less of a problem for horticulture because it is more intensive and the use of other sources of phosphorus, such as compost, is feasible. The problem will also be less severe for pasture production in some high rainfall areas because rock phosphate is more soluble in these soils.

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Question 12. What is a nutrient budget?

Nutrient budgets are a kind of accounting system that keeps track of the balance of nutrient inputs to and outputs from a farming system. A nutrient budget provides an indicator for how sustainable the management of nutrients is on the farm. Nutrients are a resource and managing them in a sustainable way means that the amount of nutrients in the soil should be maintained over time and not decreased. In sustainable farming systems, the nutrient inputs (such as fertilisers and feed) must equal or exceed the nutrient outputs (in harvested products, leaching, erosion etc.). When this occurs the nutrient budget is "positive" and sustainable in the long term. If fertiliser inputs are less than what is removed from the farm, this is a "negative" nutrient budget. In this situation crops and pastures are drawing on soil reserves of nutrients and this is not sustainable in the long term.

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Question 13. What does research show about phosphorus budgets on broadacre organic farms in Australia?

Some research on broadacre organic farms in Australia has reported negtive nutrient budgets because nutrient inputs are not always sufficient to replace nutrient losses. A study of seven organic grain-livestock farms in the Western Australian wheatbelt found all of the farms had negative P budgets. On each farm, the phosphorus output in harvested wheat was greater than the phosphorus inputs in fertilisers (poultry manure or dynamic lifter) (Deria et al., 2003). Results from the Roseworthy field experiment in South Australia showed that after five years the organic paddocks had positive phosphorus budgets but the biodynamic paddocks had phosphorus budgets of -20 kg P per hectare. The biodynamic paddocks had smaller phosphorus inputs as fertiliser and larger outputs of phosphorus due to the harvest of a hay crop (Penfold et al., 1996).

Deria et al. (2003). DIO: 10.1300/J064v21n04_04. Article summary 

Penfold et al. (1996). DIO: 10.1071/EA9950849. Article summary 

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Question 14. How do you calculate a nutrient budget?

Step 1: Define the area
Determine what area you want to calculate the nutrient budget for. There are basically two choices:
a) "Farm-gate" nutrient budgets only take into account the nutrients that move into a farm from outside and out of a farm as products. They are simple to calculate, but don't give you any information about specific areas of your farm.
b) "Soil surface" budgets are useful when information is required about a smaller area of a farm, such as a paddock, or about one stage in a rotation. In soil surface budgets nutrients that come from other areas of the farm are counted as inputs. Outputs are losses from the soil, not losses from the farm.

Step 2: Decide which nutrients to measure
Determine which nutrients you are most interested in. A nutrient budget can be performed for one nutrient or as many as you can measure.

Step 3: Record inputs and outputs
Measure all the inputs and outputs of nutrients to the area. Inputs are not limited to things that are typically considered "fertilisers". Inputs are anything brought into the area that contains the nutrient you're interested in. Therefore inputs include things such as fertilisers, stock feed and mulches. Outputs include nutrients in the harvested products, whether the product is fruit or beef. Ideally, outputs will also include measures of other losses of nutrients from the system, such as leaching or erosion, but these losses can be difficult to measure.

Step 4: Calculate the budget
Once you have measured the inputs and outputs, calculate the budget for each nutrient by subtracting all the outputs of that nutrient from the inputs of that nutrient. That is, nutrient budget = (sum of all inputs) – (sum of all outputs). 

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Question 15. What are the key issues for managing the soil fertility of organic production systems in the south west of Western Australia?

The south west of Western Australia has specific conditions of Mediterranean climate and very sandy soils, which create unique biological, chemical and physical constraints for soil fertility management. There are many soil fertility issues which may be restricting organic production in this region, especially on sandy soils, and many questions about how growers can best manage soil fertility in organic farming systems. The following list of issues and questions were identified by producers and scientists attending the Organic Agriculture Workshop and Symposium at the University of Western Australia in 2001. Most of the issues and questions are still relevant and most are fundamental problems faced in conventional as well as organic systems. 

  • The inherently low levels of organic matter in the soils mean that there is a need to identify the functional benefits of organic matter for pH, soil structure, wetability, cation exchange capacity etc. What kinds of organic matter are most beneficial and how much is needed?
  • Understand organic matter dynamics in the short- and long-term including the humification of added organic matter, forms and turnover of organic matter in soil.
  • Managing soil fertility in whole systems to increase sustainability – interactions of all management practices (soil, crop, weed control, pest and disease management), need to develop farm-specific management systems.
  • Management of crop residues such as stubble, green manures etc., for optimal nutrient cycling.
  • Interaction of tillage and the management of soil fertility.
  • Matching the timing of nutrient supply to crop demand.
  • Organic sources of nutrients do not usually contain nutrients in the optimum ratios to match crop demand – getting the balance right can be difficult.
  • Supply of micronutrients.
  • pH and cation/anion balance in soils. 
  • Nitrogen – what sources of extra nitrogen are available and how should they be managed?
  • Phosphorus and potassium – what sources of supplementary nutrients are available? How should rates and timing of application be decided?
  • Cost effectiveness of soil fertility management practices in practical application for a range of organic production systems.
  • Impact of organic farming systems on soil quality. Are there indicator measurements for soil quality that are appropriate for the south west of Western Australia?
  • Environmental impact of organic farming practices, for example what are the effects on pollution of ground and surface waters, heavy metals and biodiversity?
  • Effects of organic management practices on soil biological diversity, function and abundance. Does biological diversity affect soil fertility and/or pest and disease control?
  • Knowledge of organic systems and practices needs to be shared more widely (farmers-advisors-certifiers-researchers). Development of links and practices of knowledge sharing for learning together.
  • Development and improvement of standards to enable a sound basis for sustainable management practices – linking scientific advice into the review of standards.

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  • What are soil organisms, how do they help soil fertility?


  • Which elements are essential for plant health and which may be toxic to plants?


  • How do soil physical properties affect water movement and nutrient uptake through the plant roots?
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