Grains Research and Development

Date: 01.09.2014

Soil Biology Symposium

Author: Nicole Baxter

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Grain growers, advisers and researchers recently gathered in Melbourne at a one-day symposium to learn about the latest soil biology research being done around the country.


The GRDC’s Soil Biology Initiative (SBI) II symposium in May highlighted new knowledge gained from the five-year initiative in the form of presentations from key researchers and growers. A key message was a healthy soil is a productive soil.

Data presented showed that farm practices that have a positive impact on soil biology include no-till, effective crop sequencing (rotations), lime applications and building up soil carbon.

While a baseline of knowledge has been built, most researchers said more work is needed to better understand the role of soil biology in directly influencing farm profit.

More information:

Associate Professor Pauline Mele
03 9032 7083

Microbe manipulation to control nitrogen release

Soil microbiologist Dr Lori Phillips of the Victorian Department of Environment and Primary Industries (DEPI) says there are direct links between the microbes that release nitrogen from crop residues and soil sources, and the microbes that convert fertiliser nitrogen to crop-available nitrogen.

Dr Phillips told the Soil Biology Symposium that standard agronomic practices can be used to manipulate these links and harness the activities of soil microbes to improve nitrogen use efficiency.

For example, she said strategic tillage after legume crops increases the capacity of soil microbes to release nitrogen from organic sources in vertosol soils.

While no-till systems are still the best practice, she said, strategic tillage could be used to optimise the timing of plant-available nitrogen release during the current or next cropping season.

Interestingly, Dr Phillips’s research has also shown that the addition of artificial fertiliser slows the rate at which soil microbes process organic matter and release nitrogen from the soil.

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Soil microbiologist Dr Lori Phillips is working to increase nitrogen uptake in crops.

PHOTO: Brad Collis

Her research showed that:

  • microbes able to use mineral nitrogen respond quickly, and increases in their numbers may lead to the competitive exclusion of other groups of organisms;
  • in the presence of freely available nitrogen, these and other groups use this nitrogen rather than mining nitrogen from organic sources; and
  • the impact of soil microbes on the nitrogen supply is soil-dependent. In one soil tested the addition of fertiliser increased the abundance of nitrifiers (fertiliser processers), while in another soil fertiliser decreased the abundance of mineralisers (organic nitrogen processors).

The implication, she said, was that growers may consider minimising or even eliminating fertiliser applications at sowing to enhance microbial processing of soil organic nitrogen.

However, she said the optimal fertiliser application rates that facilitate biological balance without compromising yield need to be confirmed with paddock trials in a range of soils.

Another finding of the research was that there is a limit to the rate at which microbes can process soil nitrogen into crop-available nitrogen.

“We previously assumed that higher levels of organic matter also meant higher numbers of microorganisms to process organic nitrogen into plant-available forms, but that’s not the case,” Dr Phillips said.

“What has been driven home to us in the past three years is that soil microbes live in communities with different roles and bottlenecks may occur, so we need to understand how the system as a whole works.”

To investigate the influence of soil biology on soil nitrogen supply, Dr Phillips tracked the release of mineral nitrogen through the season (from sowing to harvest) and down through the profile (from zero to five centimetres, five to 10cm and 10 to 20cm) at the Victorian DEPI Sustainable Cropping Rotations in Mediterranean Environments  long-term field trials at Longerenong, Victoria, and related that mineral nitrogen release to the microbial communities.

The research showed that:

  • small changes in depth and pH had a big impact on the microbial community; and
  • in no-till soils, there was high level of connectivity between the microorganisms that process nitrogen. This means organic nitrogen may be transformed into nitrate more quickly, which can be either used by plants or, conversely, lost to the system through leaching or denitrification.

Dr Phillips said tillage breaks up the bio-pore network in the soil, which may slow down the conversion of organic nitrogen into plant-available forms.

The implications of this are that if strategic tillage is done after a legume crop, additional benefits may include:

  • increasing the number of soil microbes to process the nitrogen-rich organic material; and
  • reducing nitrogen loss by disrupting the microbial process associated with leaching and denitrification.

Dr Phillips said the level of disturbance required to achieve this effect, without losing the benefits of a no-till system, needs to be determined.

In related research, the University of Western Australia’s Professor Dan Murphy said his work had shown that organic molecules released from plant roots had more influence on the microbes that can retain (immobilise) nitrogen than soil organic carbon levels.

He said this means it may be possible to manipulate plant root architecture, planting density, row spacing and the choice of plants sown to benefit soil health and crop growth.

More information:

Dr Lori Phillips
03 9032 7141
0400 851 241

Professor Dan Murphy
08 6488 7083

Disease-suppressing paddocks

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Dr Daniel Hüberli, Department of Agriculture and Food, WA.

PHOTO: Nicole Baxter

Western Australian researchers have identified paddocks with natural disease suppression.

Dr Daniel Hüberli and fellow Department of Agriculture and Food, WA, researcher Shahajahan Miyan used the PreDicta B® test to check soils for the presence of the fungal pathogens rhizoctonia, take-all and crown rot.

Dr Hüberli said that from 331 paddocks assessed from 2010 to 2012, 15 paddocks were potentially suppressive, naturally, to rhizoctonia, six to take-all and 22 for crown rot.

Soils found to have a moderate level of disease pathogen DNA but low expression of the disease were considered to have natural suppressive potential.

Dr Hüberli said after confirming the results in pot tests that two paddocks were considered to be highly suppressive and five paddocks showed moderate suppression of rhizoctonia.

He said only two paddocks were highly suppressive of crown rot. The test for take-all failed to confirm any paddocks as suppressive of this disease.

While evidence of disease suppression had now been confirmed in some WA soils, Dr Hüberli said the numbers were low and often not repeated across different years.

For this reason, he said further research was needed to determine the management practices and physical characteristics of the soils that enabled them to suppress disease.

However, he said practices such as keeping paddocks ungrazed and maintaining stubble to increase carbon inputs had been shown to improve disease suppression in South Australian research.

Going forward, the researchers aim to look at the effect of crop rotation on disease suppression.

“Monitoring how microbiological activity changes in response to practices that improve soil suppression, compared with conventional management practices, would help determine the microbes that contribute to disease suppression in soils and the longevity of their effects,” Dr Hüberli said.

More information:

Dr Daniel Hüberli
08 9368 3836

No-till keeps family farming

South Australian grain grower Allen Buckley shifted away from conventional tillage to no-till in 1995 to improve soil productivity.

Allen, who farms at Waikerie with his wife Jenny, told the Soil Biology Symposium that it was either make the change or sell the farm. “I decided to change my farming system,” he said.

At the time, he said, his neighbours and agronomists advised him against the move. However, he continued along the no-till path and now sees it as one of the best changes he has made.

Allen attributed the move’s success to the partnerships he developed with researchers including CSIRO’s Dr Gupta Vadakattu, Dr Jeff Baldock and the late Dr David Roget, as well as research through the grower group Mallee Sustainable Farming.

“When I changed to no-till in 1995, it took me two years before I was completely sold on the concept,” he recalled.

“Working with researchers and testing what was happening in the soil was an instrumental part of my development and probably why I am standing here today.”

Since moving to no-till, Allen said soil tests had shown less nitrogen was available to plants at sowing than in conventional systems, but as the season progresses more nitrogen becomes available when it matters at flowering and grain fill.

Aside from a reduction in soil erosion, another benefit was increased disease suppression, which he noticed occurred after about five to six years of no-till.

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South Australian grain grower Allen Buckley.

PHOTO: Nicole Baxter

Over the years Allen tried disc seeders twice, but said he had not mastered them. Instead, he settled on a tyne and press-wheel system.

The seeding system has been designed to capture as much moisture as possible, something Allen viewed as a necessity in his area where growing-season rainfall is just 160 millimetres.

Allen uses a ribbon banding system with rows set on 305mm spacings. “With a ‘thatch’ of residual organic matter we are keeping the zone between the rows dry, which slows weed germination and growth,” he said.

Also, moisture runs down the thatch and into the crop row, further reducing the moisture available to weeds to germinate, he said.

Since moving to no-till, Allen has noticed stubbles break down more quickly than they did in the past, which he attributes to increased soil microbial activity.

In 2013 he decided to apply just 2.5 litres per hectare of urea ammonium nitrate. The result was surprising, with protein going from a high of 11.5 per cent in 2012 to 13.5 per cent in 2013.

“Either my system has continued to increase the microbial biomass needed to improve the nitrogen-fixing ability of my soils or that little bit of nitrogen gave my plants a kick at the right time,” he said.

More information:

Allen Buckley
0429 609 209

More microbes the key to locked-up P

Image of scientists with plants in pots

University of Western Australia Associate Professor Deirdre Gleeson (right) and Dr Pu Shen from the Chinese Academy of Agricultural Sciences preparing to harvest experimental pots.


Preliminary research at the University of Western Australia has given scientists a clearer picture of the impact of different organic matter inputs on soil microorganisms and phosphorus (P) cycling in the soil.

Associate Professor Deirdre Gleeson told the Soil Biology Symposium there was $10 billion worth of fixed phosphorus in Australian soils, some of which potentially could be unlocked by managing microorganisms in the soil.

In particular, Associate Professor Gleeson and her team have been investigating whether microbe release and plant uptake of fixed phosphorus in the soil can be increased by changing the carbon-to-nitrogen (C:N) ratio of organic matter inputs.

The team applied mixtures of simple organic compounds at different C:N ratios (50:1, 25:1 and 12.5:1) to plants in glasshouse experiments to test the hypothesis that:

  • organic matter inputs with low C:N ratios (for example, a legume or pasture) would increase the microbial biomass until it exhausted the supply of easily available phosphorus, forcing it to access fixed phosphorus in the soil; and
  • organic matter inputs with high C:N ratios (for example, wheat) would support a smaller but more diverse microbial community facilitating more strategies to access fixed phosphorus.

Associate Professor Gleeson said that, to date, analysis of the data broadly supports the view that a larger microbial population is the way to go and that plant growth was only increased in the treatments where organic compounds with a low C:N ratio were applied.

“Low C:N ratio inputs increased the microbial biomass and potentially offer a way to increase the cycling of fixed phosphorous from the soil and into the plant,” she said.

“The results show that we’re not just farming the soil, but also the microbial biomass and that its size, more so that its diversity, is important for cycling phosphorus. More microorganisms lead to more efficient cycling of phosphorus from the soil to the plant.”

Associate Professor Gleeson said the next step was to take the research into the paddock.

“There is already some evidence to suggest that including a legume crop in a cropping rotation increases the microbial biomass and the cycling of phosphorus from the soil to the plant compared to a continuous wheat rotation,” she said.

“Going forward, we hope to trace the movement of phosphorus into microbial cells and into plants, as well as identify the organisms involved and their contribution to phosphorus cycling.”

More information:

Associate Professor Deirdre Gleeson
08 6488 3593

Soil health test coming

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Dr Katherine Linsell, senior research officer with the South Australian Research and Development Institute.

PHOTO: Nicole Baxter

A South Australian soil biologist says a new test may soon be available to allow growers to check soil health.

Dr Katherine Linsell, senior research officer with the South Australian Research and Development Institute (SARDI), told the Soil Biology Symposium that free-living nematodes can be a measure of soil health.

“While some nematodes feed on plant roots and damage crops, there are also beneficial free-living nematodes that feed on the fungi and bacteria that decompose organic matter, and predatory and omnivorous nematodes that feed on other nematodes including the plant parasitic nematodes,” she said.

“Nematodes play a role in nitrogen mineralisation indirectly by feeding on other microorganisms but also directly by excreting ammonium into the soil.”

Dr Linsell said free-living nematodes are good indicators of soil health because they are found in all soils, occupy a central position in the food web and respond to physical and chemical changes to the soil.

In one example of such a response, bacterial and fungal-feeding nematodes multiply when nutrients or organic matter are added to soil, and this increases the rate of nutrient turnover.

In another example, populations of omnivorous and predatory nematodes increase when soil is no longer disturbed by tillage or is kept free from high pesticide inputs, and this results in greater levels of predation on other nematodes.

“A healthy soil is more likely to contain a diverse range of nematodes, and this increased diversity results in more nutrient cycling and more biological control activity,” Dr Linsell said.

Dr Linsell said nematodes were typically analysed under a microscope by a trained nematologist able to classify them into groups based on the shape of their mouthparts.

However, the drawback is that it is time-consuming and can only be performed by a small number of people in Australia.

An alternative under investigation is the use of DNA tests to quickly identify the presence of free-living nematodes in soils.

To determine which free-living nematodes would be good indicators of soil health, Dr Linsell said nematode communities were analysed in soils from 22 sites from across Australia’s northern, southern and western grain-growing regions.

The soils were taken from different environments (soil type and rainfall) under different management practices (tillage, rotation, fertiliser and stubble) across multiple years.

Dr Linsell said 17 families of free-living nematodes were found to be good indicators of soil health and 11 of these groups have been incorporated into nine DNA tests.

“Based on our results we predict that the tests cover at least 80 per cent of the free-living nematodes found in Australian cereal soils,” she said.

After analysis of the data across all sites, the two key drivers influencing changes within free-living nematode communities were found to be:

  • soil type, which was correlated with rainfall, particularly one to three months before sowing; and
  • the application of nutrients, particularly nitrogen, phosphorus, sulfur and calcium.

The analysis also demonstrated that:

  • sampling times (before and after sowing) significantly influenced free-living nematode communities, suggesting there is an impact of rainfall and/or carbon exudates from roots;
  • significant shifts in nematode structures were correlated with tillage regimes; and
  • rotation history influenced free-living nematode communities when canola, pasture and legumes were included in cereal rotations.

Dr Linsell said that after further regional validation it was hoped to deliver these DNA tests as part of the PreDicta B® diagnostic service. Growers would then be able to have their soils tested for both damaging plant parasitic and beneficial free-living nematodes, she said.

More information:

Dr Katherine Linsell
08 8303 9459

Bacteria’s N role measured

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Dr Gupta Vadakattu: soil microbes’ role measured.

PHOTO: Catherine Norwood

Research on a range of soils from across Australia has confirmed the amount of nitrogen fixed by soil microbes.

CSIRO scientist Dr Gupta Vadakattu said that under optimal conditions free-living bacteria fix between 0.2 and 2.5 kilograms of nitrogen per hectare per day in soils, with the number of optimal days per season varying in different agricultural regions.

Dr Vadakattu said the amount of nitrogen fixed was influenced by soil type, time of sampling (in-crop versus non-crop), previous crop, soil moisture content and mineral nitrogen levels.

He said carbon availability also influenced the amount of nitrogen fixed.

“Stubble removal by burning or grazing reduces the amount of nitrogen fixed,” he said. “Our trials showed nitrogen fixation by free-living bacteria was higher immediately after harvest and decreased as summer progressed.”

In the paddock, Dr Vadakattu said free-living nitrogen fixation was higher soon after rainfall when the water content was adequate to carry the carbon to where the bacteria reside and provide the required low-oxygen conditions.

Interestingly, he said the amount of nitrogen fixed during summer significantly increased in the presence of summer-active grasses such as Rhodes grass and Panicum species.

Where appropriate, he suggested southern Australian growers may benefit by including perennial grasses in their cropping systems.

When it came to determining the species responsible for fixing nitrogen, Dr Vadakattu said genetic profiling had indicated there was a diverse free-living bacterial community in Australian cropping soils, with differences observed according to soil, crop type and variety.

“We discovered, for example, that the bacteria responsible for fixing nitrogen in South Australia are different to those responsible for fixing nitrogen in Queensland and Western Australia,” he said.

“With such diversity we should, with further research, be able to suggest management systems that help promote nitrogen fixation.”

More information:

Dr Gupta Vadakattu
08 8303 8579


Inoculants need knowledge and tactics


Sci-fi scenario a crop protection breakthrough

GRDC Project Code DAV00106, UWA00139, DAW00201, UWA00150, DAS00111, CSP00138

Region North, South, West