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Fungi and bacteria could play a role in ameliorating poor soil structure

Postgraduate student Joshua Vido at work with microorganisms in the laboratory.
Photo: La Trobe University

Microbiology is applied to unravel the role of fungi and bacteria in soil aggregates.

Key points

  • Role of microorganisms in improving soil structure is not well understood
  • Postgraduate training is a valuable component of large GRDC investments

The role of microorganisms in soil amelioration is poorly understood and considered by many to be the next frontier for investigation.

Previous studies have found that increased macro-aggregate formation occurs in dispersive clay subsoil layers following deep banding of organic amendments in the subsoil.

This improvement in subsoil structure and stability leads to increased plant root growth, increased uptake of water and nutrients from the subsoil and, consequently, significant improvements in grain yield. However, the processes and mechanisms that drive this increased aggregation are not fully understood.

New skill sets are being brought to this task for the grains industry. Joshua Vido grew up on the outskirts of Melbourne, where he developed a keen interest in native flora and fauna. Through university studies at La Trobe University in ecology, his passion was ignited for even smaller, more mysterious organisms in the soil.

"Earlier research has focused on quantifying the type and abundance of microorganisms such as fungi and bacteria in soil, but my research examines their functions, particularly in relation to their role in ameliorating dispersive clay subsoils and soil aggregate formation," Mr Vido says.

Mr Vido is in his first year of postgraduate study, which is a capacity-building component of a large GRDC investment focused on understanding the amelioration processes of subsoil amendments in the southern region. The project is being led by Professor Roger Armstrong from Agriculture Victoria.

"To be able to undertake fundamental scientific research in collaboration with industry-leading scientists on a significant grains productivity constraint is a real motivator," Mr Vido says.

Analytical approach

Next-generation technology, including but not limited to DNA sequencing, is being used to undertake a systematic investigation of the microbes' identities and roles in aggregate formation in dispersive clay (sodic) soils following the addition of various amendments.

Ultimately we are looking to gather scientific insights into microbial processes that can inform growers' soil amelioration decisions in the field. - PhD candidate Joshua Vido

To frame his research, Mr Vido is using new techniques to answer the following questions:

  1. Taxonomic composition of micro and macro-aggregates: what bacterial and fungal types are involved in aggregate formation? What is their response to different amendment types?
  2. Bioinformatic functional profiling and/or shotgun metagenomics:what processes are these microorganisms performing that contribute to the formation of aggregates? Do these processes differ based on amendment type?
  3. Fluorescent in situ hybridisation: where are microorganisms spatially distributed within and around micro and macro-aggregates to give them structure? Does the amendment type affect the structure and formation of aggregates?
  4. Quantitative polymerase chain reaction of nitrification and denitrification gene abundance: what is the effect of each amendment on nitrogen-cycling dynamics, which indirectly influences soil aggregation through increased root growth?

The microbial analysis within the project will be performed on soil collected from two field sites in Victoria at Tatyoon and Kiata, as well as on soil collected from a controlled-environment PVC column experiment at La Trobe University.

Two examples of the range of microbes found in soil and grown on agar plates are shown in Figure 1.

FIGURE 1 Microbial growth on agar plates following inoculation with a soil solution. PHOTOS Gene Drendel, PhD candidate at La Trobe University

Figure 1: Microbial growth on agar plates following inoculation with a soil solution. Photo Gene Drendel, PhD candidate at La Trobe University.

Each image illustrates the immense microbial diversity in soil. However, this is only an extremely small portion of diversity that exists within soil, as only one per cent of all microorganisms can be grown in the laboratory.

Innovative thinking

An aspect of the research that has brought some innovative thinking to Mr Vido's studies is understanding how soil aggregates of various sizes are constructed.

Mr Vido aims to image and visualise the spatial distribution of microorganisms within and around soil aggregates of various sizes. This should help to explain the roles of different microorganisms in developing small and large aggregates.

The methodology for this task is still under development; however, the approach involves fluorescent staining of different microorganisms that are involved in the formation of micro and macro-aggregates. The idea of imaging soil aggregates and the microorganisms contained within and around them was adapted from research in wastewater treatment plants where aggregates are similarly visualised.

To be able to undertake fundamental scientific research in collaboration with industry-leading scientists on a significant grains productivity constraint is a real motivator. - PhD candidate Joshua Vido

"Ultimately, we are looking to gather scientific insights into microbial processes that can inform growers' soil amelioration decisions in the field," Mr Vido says.

"If we can begin to understand these processes, we can potentially manipulate microbial processes to ameliorate dispersive clay soils using different combinations of organic amendments available on-farm and possibly enriching these amendments with desirable microorganisms."

GRDC Research Code DAV00149

More information: Joshua Vido, J.Vido@latrobe.edu.au, 0423 745 593

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