soilquality.org.au | Soil Quality and Soil Health Information for Australia

Making Sense of Biological Indicators

Biological indicators give information on living organisms in soil. Biological indicators of soil quality therefore measure dynamic soil properties, i.e. properties that change over time and/or with management. It is important to monitor biological indicators as they respond more quickly to changes in management or environment than physical and chemical indicators.

For most biological indicators, there is little evidence currently available which directly links the value of the indicators to productivity or, in some cases, the risk of adverse environmental impact. However, there is good evidence from field trials carried out on a range of soils in Australia of links between biological indicators and soil processes. These have been used to create guideline ranges for the biological indicators, similar to those used for the dynamic physical and chemical indicators.

Making Sense of Biological Indicators - Qld

Soil Biological Fertility

Soil microorganisms are responsible for most of the nutrient release from organic matter. When microorganisms decompose organic matter, they use the carbon and nutrients in the organic matter for their own growth. They release excess nutrients into the soil where they can be taken up by plants. If the organic matter has a low nutrient content, micro-organisms will take nutrients from the soil to meet their requirements.
For example, applying organic matter with carbon to nitrogen ratios lower than 22:1 to soil generally increases mineral nitrogen in soil. In contrast, applying organic matter with carbon to nitrogen ratios higher than 22:1, generally results in microorganisms taking up mineral nitrogen from soil.

How Much Carbon Can Soil Store

Recent interest in carbon sequestration has raised questions about how much organic carbon (OC) can be stored in soil. Increasing the amount of OC stored in soil may be one option for decreasing the atmospheric concentration of carbon dioxide, a greenhouse gas.

Increasing the amount of OC stored in soil may also improve soil quality as OC contributes to many beneficial physical, chemical and biological processes in the soil ecosystem.

How Much Carbon Can Soil Store - NSW

Recent interest in carbon sequestration has raised questions about how much organic carbon (OC) can be stored in soil. Organic carbon in the soil includes the carbon in the materials related to living organisms or derived from them. In Australian soils, total OC is usually less than 8% of total soil weight and under rainfed farming it is typically 0.74%. Increasing the amount of carbon stored in soil may be one option for decreasing the atmospheric concentration of carbon dioxide, a greenhouse gas.

Increasing the amount of OC stored in soil may also improve soil quality as OC enhances many beneficial physical, chemical and biological processes in the soil ecosystem. When OC in soil is below 1%, soil health may be constrained and yield potential (based on rainfall) may not be achieved.

Total Organic Carbon

The term organic is used to describe materials relating to or derived from living organisms. The amount of organic matter in a soil is often used as an indicator of the potential sustainability of a system. Soil organic matter plays a key role in nutrient cycling and can help improve soil structure.

Carbon makes up approximately 50 % and nitrogen 0.5 to 10% (dependent on residue type) of the molecules in organic matter; some of which turns over rapidly (labile fraction) and is available to plants, whilst other more recalcitrant forms contribute to the stable (passive, slow turnover fractions) organic pools. Soil micro-organisms mineralise organic matter to obtain carbon, nitrogen and other nutrients for their own metabolism and growth.

Total Organic Carbon - NSW

The term organic is used to describe materials relating to or derived from living organisms. Management practices and plant inputs influence both the quantity and quality of soil organic matter, which directly impacts on soil productivity, soil resilience and soil sustainability. Soil organic matter plays a key role in nutrient cycling and can help improve soil structure.

Organic Carbon Storage - WA

Sustainable management of soil, in particular organic carbon, is essential for the continued viability of Australian agriculture. Increasing the organic carbon retained in soil (also known as sequestration) improves soil quality and can also help to reduce atmospheric carbon dioxide. The Soil Carbon Research Program (20092012) identified land uses and management practices that growers can use to increase soil organic carbon storage and improve production in a changing climate.

This fact sheet provides an overview of methods, results and outcomes from the Western Australian arm of the SCaRP program.

Organic Carbon Pools - Qld

Soil organic matter is made up of four major pools – plant residues, particulate organic carbon, humus carbon and recalcitrant organic carbon. These pools vary in their chemical composition, stage of decomposition and role in soil functioning and health. Management is capable of altering not only total organic carbon stocks, but the proportion of carbon present in these different pools. Knowledge of how carbon pools change in response to management provides valuable information on likely soil functioning and health.

Carbon Storage - Albany Sand Plain

Sustainable management of soil, in particular carbon, is essential for the continued viability of Australian agriculture. Increasing the carbon retained in soil (also known as sequestration) improves soil quality and can also help to reduce atmospheric carbon dioxide. The Soil Carbon Research Program is working to identify land uses and management practices that growers can use to increase soil carbon storage and improve production in a changing climate.

Actual carbon storage in the 0 – 30 cm layer was less than attainable carbon storage predicted by modelling (figure 3, example for deep sand). Within the lower rainfall cropping zone the actual carbon storage on the deep sand was 29 t C/ha under continuous cropping (40 % of attainable carbon) and 39 t C/ha under mixed cropping (50 % of attainable carbon). In the higher rainfall zone actual carbon storage on the deep sand was 61 t C/ha under annual pasture (55 % of attainable carbon) compared to 93 t C/ha under perennial pasture (77 % of attainable carbon).

Carbon Storage - Esperance Sand Plain

Soils on the Esperance sand plain in Western Australia range from deep sands to shallow duplexes. Close to the coast, beef production dominates and some producers use perennial pasture (often kikuyu) to combat the ‘autumn feed gap’. Perennial pastures have longer survival, deeper rooting and greater plant biomass during summer months. As a result, it has been proposed that they may store more soil carbon than annual pastures.

Soil carbon storage under perennial pastures was not greater than under annual pastures. Changing from annual pasture to perennial pasture has not increased soil carbon storage on these soils, and is likely due to the sandy nature of the soils. Soils with coarse texture have lower potential to store carbon than soils with more clay.

Soil Organic Carbon Storage in the Western Avon Basin - WA

This part of the project incorporated 24 farms (161 sites) in an area approximately 40 km by 115 km in the west of the Avon River basin, at the western margin of the Western Australian (WA) wheatbelt (figure 1). The soils in this region are generally sandy at the surface (more than 50 % of the area) but are highly variable at depth, with continuous cropping, mixed cropping in rotation with annual pasture, and permanent annual pasture the main landuses. Soil acidity is a significant problem in much of the area sampled.

The sampling program was designed to (1) provide a snap shot (2011) of organic carbon storage values across typical soil and agricultural production systems in the western Avon basin and (2) evaluate whether across this large region there is a consistent pattern between soil pH and organic carbon storage.

Labile Carbon

Although significant amounts of organic carbon are present in soils, some of this is relatively inert. Soil organic matter is made up of different pools which vary in their turnover time or rate of decomposition. The labile pool which turns over relatively rapidly (< 5 years), results from the addition of fresh residues such as plant roots and living organisms, whilst resistant residues which are physically or chemically protected are slower to turn over (20 – 40 years). The protected humus and charcoal components make up the stable soil organic matter pool which can take hundreds to thousands of years to turnover

Labile Organic Carbon - NSW

Soil organic carbon is made up from different types of organic materials with different chemical and physical properties. Soil organic carbon is frequently divided into relatively labile and stable organic fractions (also referred to as pools) that vary in their vulnerability to decomposition.

Microbial Biomass

Microbial biomass is an important indicator of soil health because it is closely related to nutrient release from crop residues. The microbial biomass consists mostly of bacteria and fungi, which decompose crop residues and organic matter in soil. This process releases nutrients, such as nitrogen (N), into the soil for plant uptake. About half the microbial biomass is located in the surface 10 cm of soil and most of the nutrient release also occurs here.

Microbial Biomass - Qld

The soil microbial biomass consists mostly of bacteria and fungi, which decompose crop residues and organic matter in soil. The microbial biomass typically makes up less than 5 % of total soil organic matter, but it plays a very large role in a number of key soil functions, including nutrient release, the maintenance of good soil structure and the suppression of plant pathogens. Changes to the microbial biomass can also be an early indicator of changes in total soil organic carbon. Unlike total organic carbon, microbial biomass carbon responds quickly to management changes, and can often be measured before changes in total organic carbon are detected.

Biological activity in Queensland cropping soils is generally low compared to other land uses, such as pasture or native vegetation, due to the low amount of labile carbon present. Adopting management practices that increase soil carbon and thus soil microbial biomass increases nutrient cycling important for crop growth.

Microbial Biomass Carbon - NSW

The microbial biomass consists mostly of bacteria and fungi, which decompose crop residues and organic matter in soil. This process releases nutrients, such as nitrogen (N), into the soil that are available for plant uptake. About half the microbial biomass is located in the surface 10 cm of soil and most of the nutrient release also occurs here. Generally, up to 5% of the total organic C and organic N in soil exists in the microbial biomass component of soil organic matter. When microorganisms die, these nutrients are released in forms that can be taken up by plants. The microbial biomass can be a significant source of N, in some cases holding more than 60 kg N/ha.

Interpreting Microbial Biomass Carbon

Microbial biomass is a measure of the weight of microorganisms in soil, which mostly consists of bacteria, fungi and other microbes called archaea. Measures of microbial biomass usually measure either the weight of carbon or nitrogen in soil microorganisms.

A challenge in interpreting values of microbial biomass is the difficulty of knowing the attainable microbial biomass for a given land use and what level of microbial biomass may constrain production.

The best way to use microbial biomass values in soil quality monitoring is to measure microbial biomass regularly over time using soil collected during the summer months.

An estimate of the attainable microbial biomass carbon is 5 % of the organic carbon in soil.

Tillage, Microbial Biomass and Soil Biological Fertility

Microbial biomass is increased by management practices that increase inputs of organic carbon to soil and improve the chemical and physical conditions experienced by microorganisms in soil.

An experiment tested the observation by farmers that low disturbance tillage increases total organic carbon in soil.

Soil Nitrogen Supply

Plants require more nitrogen (N) than any other nutrient but only a small portion of the nitrogen in soil is available to plants; 98 % of the nitrogen in soil is in organic forms. Most forms of organic nitrogen cannot be taken up by plants, with the exception of some small organic molecules.

In contrast, plants can readily take up mineral forms of nitrogen, including nitrate and ammonia. However, mineral nitrogen in soil accounts for only 2 % of the nitrogen in soil. Soil microorganisms convert organic forms of nitrogen to mineral forms when they decompose organic matter and fresh plant residues. This process is called mineralisation.

Soil nitrogen supply is a laboratory test that reflects the release of mineral nitrogen from organic matter by soil microorganisms. It is measured in milligrams of nitrogen per kilogram of soil (mg/kg) and is also known as potentially mineralisable nitrogen.

Legumes and Nitrogen Fixation - SA

All plants are able to take up nitrogen from the soil in the form of ammonium (NH₄⁺) or nitrate (NO₃^-); together these are known as available N.

In addition to taking up available N from the soil, legumes (clovers, medics, peas and beans) are also able to acquire N from the abundant supply in the atmosphere via special soil bacteria (rhizobia) which are housed in nodules on their roots.

Legumes can fix substantial quantities of nitrogen (N) and this can be maximised by ensuring low plant available N in the soil at sowing and inoculating the seed if a paddock has not had a host legume nodulated by the same rhizobia in the last four years.

Biological Inputs - Western Grain-Growing Region

There are a wide range of biological inputs on the market including inocula, various biostimulants, composts, manures and biochar. It can be difficult to evaluate their potential effectiveness and return on investment for broadacre grain production for a number of reasons.

First, the properties of biological inputs are highly variable, even within a single type of input. This makes it difficult to evaluate whether one particular product is likely to be effective. Second, few previous scientific studies have been field experiments in broadacre grain cropping. Instead many were laboratory or glasshouse experiments with horticultural crops and farming systems. Finally, many of the mechanisms claimed by manufacturers have not been assessed by scientific investigations yet.

When considering using a biological input in broadacre grain production, it may be helpful to first consider what constrains yield on your property. A biological input is unlikely to improve crop growth or yield unless it alleviates a yield constraint. Previous scientific investigations can help determine which biological inputs have the most potential to alleviate particular yield constraints.

Biological Inputs - Southern Grain-Growing Region

Biological Farming Inputs A practical guide to on-farm testing

Biological inputs include a wide range of products aimed at supporting soil fertility, biological activity, and plant growth. They include microbial inocula, biostimulants that promote favourable microbial populations and plant growth, composts and compost teas, manures, and biochars. These inputs are often used with the broad aim of reducing the use of traditional chemical fertilisers and agro-chemicals, but they may also form the back-bone of organic farming systems.

Biological Inputs - Northern Grain-Growing Region

Optimising Crop Root Systems - NSW

Soil conditions affect the development of crop root systems. One way to optimise plant uptake of nutrient reserves in soil is to maximise the area crop roots can contact in the soil and ensure they can follow nutrients and water down the profile. This is especially important for leachable nutrients such as nitrogen and sulphur, and nutrients with significant reserves in the subsoil. The abundance and depth of crop roots can be increased by recognising and improving conditions that inhibit root development or performance.

Benefits of Retaining Stubble - WA

Historically, stubble has been burnt because it improves weed control and creates easier passage for seeding equipment. However, the practice of burning stubble has recently declined due to concerns about soil erosion and loss of soil organic matter. Instead of being burnt, stubble is increasingly being retained which has several advantages for soil fertility and productivity.

Benefits of Retaining Stubble - Tas

Historically, stubble has been burnt because it improves weed control and creates easier passage for seeding equipment. However, the practice of burning stubble has recently declined due to concerns about soil erosion and loss of soil organic matter. Instead of being burnt, stubble is increasingly being retained, which has several advantages for soil fertility and productivity.

Benefits of Retaining Stubble - Qld

Historically, stubble has been burnt because it improves weed control and creates easier passage for seeding equipment. However, the practice of burning stubble has declined throughout Queensland cropping regions due to concerns about soil erosion and loss of soil organic matter. Instead of being burnt, stubble is now more commonly retained, which has several advantages for soil fertility and productivity. Some of these include a reduction in erosion risk, increased soil water content and improved biological functioning of the soil.

Benefits of Retaining Stubble - NSW

Historically, stubble has been burnt in southern and central New South Wales because it creates easier passage for seeding equipment, enhances seedling establishment of crops, and improves control of some soil-borne diseases and herbicide resistant weeds. However, the practice of burning stubble has recently declined due to concerns about soil erosion, loss of soil organic matter and air pollution. However, stubble is increasingly being retained which has several advantages of soil fertility and productivity.

Biochar for Agronomic Improvement

CSIRO is leading collaborative research across Australia to analyse the properties and potential of a variety of biochars to improve soil health and sequester carbon. Two major projects, including one funded by the Grains Research and Development Corporation (GRDC) and another by the Australian Department of Agriculture, Fisheries and Forestry (DAFF), are helping to answer some of the key questions about the potential of biochar.

The use of mulch and compost in vineyards

Mulch and compost what is the difference?
There is some confusion about the terms mulch and compost which are often used interchangeably even though they are quite different products with different uses and potential benefits.

Soil Bacteria and Fungi - NSW

Bacteria are the most abundant microbes in the soil. They are single celled organisms, and there can be billions of bacteria in a single gram of soil. Populations of bacteria can boom or bust in the space of a few days in response to changes in soil moisture, soil temperature or carbon substrate. Some bacteria species are very fragile and may be killed by slight changes in the soil environment. Others are extremely tough, able to withstand severe heat, cold or drying. Some bacteria are dependent on specific plant species.

Arbuscular Mycorrhizas - SA

Arbuscular mycorrhizas (AM) are generally beneficial associations (symbioses) between plant roots and specialised soil fungi. The chances are that all the AM fungi in any particular soil will be able to colonise all the plants that are grown there. Only a few plants do not form AM symbioses. These include canola and other brassicas (cabbage family), lupins (all other crop and pasture legumes are AM), beet and spinach, otherwise virtually all crop species form these associations. High AM colonisation is an important indication of good soil health, although this is not always recognised.

Root Lesion Nematode

Root lesion nematodes (RLN) are microscopic worm-like animals that use a syringe-like ’stylet’ to extract nutrients from the roots of plant. Pratylenchus neglectus and P. thornei are the most common RLN species in Australia, although populations of P. teres and P. penetrans are also found in Western Australian soils where they have been found to cause significant yield losses. Overall, RLN’s affect all cropping regions of southern Australia, and are an increased risk in areas where minimum tillage has been adopted.

Nematodes - NSW

Nematodes are the most abundant multicellular animals on earth. They are small, non-segmented worm-like animals about 0.35 mm long, sometimes called eelworms. Most nematode species have a beneficial role in the soil, but a few are pest species that feed on plant roots, and damage roots directly or make them more susceptible to fungal diseases. Beneficial nematodes are important in controlling the pest species and improving the soil health.

Root Lesion Nematode - SA

Root lesion nematodes emerged as potential problems in cereals (and other crops) after management strategies were implemented to control cereal cyst nematode and take-all. Yield losses in the southern region are variable and currently under investigation, but present estimates for intolerant varieties indicate a 1 % yield loss per 2 nematodes per gram soil. Pratylenchus thornei occurs throughout the root zone and is often more damaging than P. Neglectus, which tends to be concentrated in the top 15 cm of the soil.

Root Lesion Nematode - Qld

Root lesion nematodes (RLN) are microscopic worm-like animals that use a syringe-like ‘stylet’ to extract nutrients from the roots of plants (figure 1). Plant roots are damaged as RLN feed and reproduce inside plant roots. Pratylenchus thornei and P. neglectus are the most common RLN species in Australia. In the northern grain region P. thornei is the predominant RLN but P. neglectus is also present. These nematodes can be found deep in the soil profile (to 90 cm depth) and are found in a broad range of soil types – from heavy clays to sandy soils.

Root Lesion Nematode - NSW

Root lesion nematodes (RLN) are microscopic worm-like animals that use a syringe-like stylet to extract nutrients from the roots of plants, such as wheat and canola. Pratylenchus neglectus and P. thornei are the most common RLN species in Australia, where they have been shown to cause significant yield losses.

Cereal Cyst Nematode

Cereal Cyst Nematode (CCN, Heterodera avenae) is a pest of graminaceous crops worldwide. This nematode is a significant problem across eastern Australia, and is detected in the Northern and Central regions of Western Australia. CCN becomes more problematic in areas where intensive cereal cropping occurs. CCN will only infect, feed and develop on cereals and other grasses (particularly wild oat). Non-cereal crops will not host the nematode, so are useful in rotations to limit damage caused to cereals.

Rhizoctonia

Rhizoctonia is a disease affecting a wide range of crops and has become more prevalent throughout Western Australia in recent years following the introduction of minimum tillage practices. The previous practice of tillage prior to seeding encouraged the breakdown of the fungus (Rhizoctonia solani) in the soil prior to emergence. Minimum tillage practices decrease the rate of organic matter breakdown, thereby providing a habitat for Rhizoctonia over summer. The disease affects most major crops to varying degrees, with barley being most susceptible and oat crops are least susceptible. Bare patch and root rot of cereals, and damping off and hypocotyl rot of oilseed and legumes are all caused by differing strains of R. solani.

Rhizoctonia - NSW

Rhizoctonia is a fungal disease affecting a wide range of crops and has become more prevalent in light soils in recent years following the introduction of minimum tillage practices. The previous practice of tillage prior to seeding encouraged the breakdown of the fungus (Rhizoctonia solani Kuhn) in the soil prior to emergence. Minimum tillage practices decrease the rate of organic matter breakdown, thereby providing a habitat for Rhizoctonia over summer. The disease affects most major crops to varying degrees, with barley being most susceptible and oat crops are least susceptible. Bare patch and root rot of cereals, and damping off and hypocotyl rot of oilseed and legumes are all caused by differing strains of R. solani.

Cereal Cyst Nematode - SA

Cereal Cyst Nematode, Heterodera avenae, (CCN) infects cereal roots and can cause serious yield losses in wheat and oat crops in the southern region.

Field symptoms of CCN infection can resemble symptoms of other diseases or soil constraints, so examination of roots is important.

Take-All Disease

Take-all is a soil borne disease of cereal crops and is most severe on wheat crops throughout southern Australia. In Western Australia the disease is caused by two variations of the Gaeumannomyces graminis fungus; G. graminis var. tritici (Ggt) and G. graminis var. avenae (Gga) and is most severe in the high rainfall areas of the agricultural region (ie. southern cropping regions and areas closer to the coast). Control of take-all is predominantly cultural and relies on practices which minimise carry-over of the disease from one cereal crop to the next.

Take-All SA

Ggt is the main cause of take-all, and its hosts include wheat, barley, Bevy rye and the grassy weeds, barley grass and broom grass. Gga hosts include all Ggt hosts plus oat. Both fungi survive over summer on roots and crowns of infected plants. Gga and Ggt levels are reduced by significant summer rainfall, but high available nitrogen in soil over summer encourages inoculum survival.

Take-all can cause large yield losses, especially in wheat crops in seasons with above average winter/early spring rainfall followed by moisture stress around anthesis. The risk increases with consecutive above average rainfall seasons in intensive cereal and cereal/grass pasture rotations. Losses in barley are generally about 50% of those in wheat. Take-all is rarely a problem in highly acid soils (pH < 5.5 in water; pH < 4.7 in CaCl₂).

Take-All Disease - NSW

Take-all is a soil borne disease of cereal crops and is most severe on wheat crops throughout southern Australia. In New South Wales the disease is caused by two variations of the Gaeumannomyces graminis fungus; G. graminisvar. tritici (Ggt) and G. graminis var. avenae (Gga) and is most severe in the high rainfall areas of the agricultural region (ie. southern cropping regions and areas closer to the coast). Control of take-all is predominantly cultural and relies on practices which minimise carry-over of the disease from one cereal crop to the next.

Crown Rot - Queensland

Crown rot is a disease caused by the fungus Fusarium pseudograminearum, and can attack all winter cereals and many grassy weeds. The presence of the pathogen within the plant stem limits water movement, which can result in premature death of the tiller and the presence of white (dead) heads. Crown rot survives from one season to the next on infected stubble, from where it is passed onto the following crop.
The effects of crown rot on yield tend to be most severe when there are good crop conditions in the first part of the season followed by a dry finish. This is because the moist conditions at the beginning of the season enable the fungus to grow from infected stubble to an adjacent seedling, while the dry conditions during flowering and grain filling cause moisture stress, allowing rapid growth of the pathogen within the plant. A wet finish to the season can reduce the damage caused by crown rot, but will not prevent yield loss in all cases.

Fusarium - NSW

There are two types of fusarium disease that affect NSW crops, Fusarium head blight (FHB) and crown rot (CR). Durum wheats are all highly susceptible to both diseases.

FHB is usually caused by the fungus Fusarium graminearum but the crown rot fungus Fusarium pseudograminearum may cause the disease in wet years as rainsplash distributes the fungus from lower stem nodes into grain heads.

A Practical Test To Assess The Biological Status Of Australian Grain-Growing Soils

Agricultural soils contain a wide array of small animals and microbes that have many important functions. Some damage root systems and cause disease while others help maintain soil structure, fix nitrogen, store and cycle nutrients, and protect plants from soilborne pathogens. Growers wishing to maintain or improve productivity need to know something about the biological status of their soils. One way of obtaining that information is to collect a soil sample and subject it to nematode community analysis.

The Fact Sheets The Nematode Community in Australian Grain-Growing Soils and Nematodes as a Biological Indicator explain why the composition of the soil nematode community provides a good indication of a soils the biological status. However, information on the nematodes present in soil is difficult to obtain because the methods available to extract these animals are laborious, and few people have the expertise required to identify nematodes. Therefore, manual nematode community analysis is not something that can be done on a routine basis.

Nematodes as a Biological Indicator

Since bacteria and fungi are the dominant component of microbial biomass, it is often considered they provide the best indication of the soils biological status. However, they are difficult to measure as there are thousands of different species and they occur in enormous numbers. Also, their life cycles are relatively short (hours or days), and so populations change rapidly in response to changes in environmental conditions such as moisture and temperature. Soil animals, particularly nematodes, are generally considered to be better biological indicators.

The Nematode Community In Australian Grain-Growing Soils

Nematodes are microscopic worms that are sometimes known as roundworms or eelworms. Those living in soil are generally small (less than 1 mm long and only 1520 µm wide) and can only be seen with a microscope.

Most grain growers are aware that nematodes cause hundreds of millions of dollars in crop losses every year. What is usually not recognised is that these pest nematodes are only one component of the soil nematode community. A diverse range of beneficial free-living nematodes also occur in soil, and they play a vital role in many important soil processes.

Fact Sheets Biological Indicators