A variety of soil organisms live in the soil, such as bacteria, fungi, archaea, nematodes, protozoa, earthworms, ants and termites. These soil biota support resilient cropping systems. Although some soil pests and diseases can negatively impact plant health, the majority of soil organisms are neutral or beneficial for the crop. Benefits to the crop are associated with:
- Cycling of carbon and nutrients;
- Improving soil structure and pore connectivity, leading to better water infiltration;
- Disease suppression;
- Degrading or immobilising contaminants; and
- Promoting plant root growth.
One critical function soil organisms perform is breaking up and decomposing soil organic matter (SOM), which primarily consists of dead and decaying plant and animal residues, as well as the by-products of living soil biota. This SOM turnover can benefit crops by improving in-season nitrogen availability and building soil carbon (given sufficient rates and time), but can have mixed results on water infiltration and the capacity of the soil to store water.
Nitrogen cycling
Mineralisation
Soil mineralisable nitrogen can be a significant source of non-fertiliser nitrogen for grain crops, with this becoming increasingly important as fertiliser prices rise. When soil organisms decompose SOM, they convert unavailable organic forms of nitrogen into plant-available mineral forms (mineralisation), using a component of the nitrogen themselves. Any surplus nitrogen not required by the soil biota is released to be taken up by other microorganisms or plants. Only a few per cent of the organic nitrogen is released as plant-available ammonium-nitrogen and nitrate-nitrogen each year.
Soil organic matter turns over at a rate of about two per cent each year, although this varies considerably with seasonal and management conditions. The total amount of organic nitrogen in the top zero to 10cm of soil in Western Australia is in the range of 150 to 10,000 kilograms of nitrogen per hectare.
In WA, microbes can cycle 100 to 300kg of nitrogen/ha annually, of which about 40 per cent is released into the soil and becomes plant available, translating to 40 to 120kg nitrogen/ha each year, depending on the rotation.
Annual pasture can provide upwards of $200/ha of nitrogen at current prices (roughly, 122kg nitrogen requires about 265kg urea, which is 46 per cent nitrogen. At $1000/t this is $265).
Up to 40 per cent of the total net nitrogen mineralised is estimated to be due to soil fauna. Protozoa and beneficial nematodes provide the greatest contribution. These soil biota feed on soil bacteria and release surplus nitrogen into the soil. The mechanism of nitrogen release or immobilisation is linked to the amount of carbon relative to the amount of nitrogen (the carbon:nitrogen ratio) the soil biota need to grow and the type of organic matter being consumed.
Bacteria-feeding nematodes have a carbon:nitrogen ratio of 6:1 and protozoa 10:1. The bacteria they consume have a ratio of 4:1. So as nematodes eat the bacteria, they ingest more nitrogen per unit of carbon than they need – releasing the excess nitrogen for uptake by other microorganisms or plants.
How much nitrogen is mineralised depends on a variety of factors including starting soil organic nitrogen stocks, soil moisture and temperature, as well as the carbon:nitrogen ratio of the decomposing organic matter. Ameliorating acidic soil can increase the speed of mineralisation, as can cultivation – but any short-term benefit of managing for these purposes should be weighed up against longer-term costs to soil structure, continued acidification and SOM stocks.
Soil texture also plays a role. Soils with more clay can physically and chemically stabilise organic matter, protecting it from decomposition. Sandy soils provide less protection and SOM is more readily available, so SOM is more likely to decompose.
The rate and timing of mineralisation can be tricky to predict. Microbes require moisture to be active and increase their activity as temperature increases (rates double for every 10°C increase in temperature).
This means that in WA, mineralisation slows during winter when it is cold, and increases in spring where moisture is available under warming conditions. However, there is also rapid mineralisation when the crops are not able to use the nitrogen – particularly in summer and early autumn after rain and when temperatures are high. Heavy rains following mineralisation can leach some of this mineralised nitrogen, particularly on lighter soils beyond the rooting zone – essentially reversing the “free kick” of nitrogen that the summer/autumn rain awarded.
Incorporating residues into soil through cultivation can increase the rate of decomposition and conversion of organic nitrogen to mineral nitrogen. However, research in WA found incorporation had little influence on the timing of the nitrogen release, which was more closely linked to climate.
Residue type and rate of decomposition will determine if there is a release of nitrogen. Where the carbon:nitrogen ratio of the residue is above about approximately 24:1, soil microbes will use available nitrogen from the soil (immobilise nitrogen) to break down the residue, making it unavailable to crops. This immobilisation is generally short-lived but may influence nitrogen availability for up to 6-8 weeks during key growth stages.
Carbon, microbes and soil pH
Soil organic carbon (SOC) is the carbon component of SOM, making up about 58 per cent of it. Fresh organic matter is about 48 per cent carbon. As carbon content increases in SOM, it is associated with a loss of nutrients. Soil organic carbon builds when organic inputs are greater than any losses. Losses can include soil erosion, cultivation, as well as natural decomposition of SOM by soil organisms. Inputs and losses fluctuate within and across seasons/years, requiring long-term considerations of changes in SOC through time.
Soil pH plays a big role in whether microbes are adding to or taking from the soil carbon pool.
As a soil becomes more acidic (less than pH 5.5 in CaCl2), microbes become less efficient at turning over the carbon in SOM (building the soil carbon pool) and a greater portion of what they turnover is lost as CO2. Maintaining topsoil at a pH more than 5.5, maximises microbial energy efficiency and as a result, there is more SOM turnover but proportionally lower CO2 release per unit of SOM. Improving soil pH supports better plant growth and therefore more SOM additions which may lead to a slow accumulation of carbon long-term, or at least minimise further losses.
Soil water holding capacity
Soil organic matter is often lauded for its ability to hold several times its own weight in water. While true, given its low concentration in the soil (often less than two per cent), this often only translates to a few millimetres of increased water holding capacity (WHC).
For surface soil layers in southern Australia, estimates are that for each one per cent increase in SOC (i.e. from one per cent to two per cent SOC), the increase in WHC is between two and five millimetres depending on clay content.
In low-rainfall regions, or in seasons with few rainfall events, this additional storage could be a reasonable source of plant available water. Each additional millimetre of rainfall (where water is limited) can produce an additional 15 to 20kg/ha of wheat grain (Hoyle and Murphy, 2018).
However, the ability to increase SOC by one per cent in low-rainfall regions is very limited.
Indirect benefits of increased SOM on plant available water may result from improvements to soil structure and aggregate stability, leading to increased pore size and volume supporting better infiltration and water retention. Both macrofauna and microorganisms are important. For example, during SOM decomposition, complex sugars are released that glue particles together. Fungi extend a network of hyphae that enmesh soil particles to form aggregates.
A good example of these indirect benefits include tunnelling soil biota such as ants that help fragment and redistribute SOM at depth. A WA study (Evans et al. 2011) found that macrofauna (ants and termites) in a deep sand, through their influence on soil porosity, could increase soil moisture and grain yield (the latter by up to 36 per cent) compared to sites where biota was excluded.
Water repellence
One downside of SOM turnover is that it can adversely impact water infiltration. As microbes break down plant residues, hydrophobic molecules can form and make the soil water repellent. Sand is more prone to water repellence as it takes less hydrophobic material to coat individual particles, compared to silt or clay which have a higher surface area.
Some microbes, such as wax-degrading actinomycete bacteria can degrade these coatings. Making conditions favourable for these microbes reduces water repellence. Liming acidic sands and retaining crop residues as a pathway for water infiltration can also help reduce water repellence.
Other practices, such as soil mixing, inversion or spading, can bring more wettable soil to the surface and bury the coated particles in contact with moisture and in better conditions for microbes to break them down.
The complex and evolving interactions of soil biota and organic matter highlight the challenges in managing soil, where changes in chemical composition, physical structure and variable climate often impact biota activity. However, the functional aspects of soil driven by these biological processes should be considered when optimising farming systems to develop more resilient and resource efficient practices. The WA Department of Primary Industries and Regional Development has advice on managing SOC on Western Australian farms. Notable increases in SOC, if they are possible, will take decades.
This content was derived from the free eBooks Soil Quality: 3 Soil Organic Matter and Soil Quality: 5 Soil Biology
References and further reading
Evans T, Dawes T, Ward P, et al. 2011. Ants and termites increase crop yield in a dry climate. Nat Commun 2, 262. https://doi.org/10.1038/ncomms1257
Hoyle F & Murphy D. Soil Quality: 3 Soil Organic Matter. SoilsWest, Perth, 2018. Apple Books.
Hoyle F & Murphy D 2011. Influence of organic residues and soil incorporation on temporal measures of microbial biomass and plant available nitrogen. Plant Soil, 347:53–64.
Murphy D, Hoyle F, Collins S, Hüberli D, Gleeson D. Soil Quality: 5 Soil Biology. SoilsWest, Perth, 2021. Apple Books. https://books.apple.com/au/book/soil-quality-5-soil-biology/id1554057153