It is increasingly recognised that soil microbiomes play crucial roles in nutrient cycling, soil formation, plant growth and ultimately the production of food – understanding the microbiome has clear and very practical applications.

The FBIP large project on the characterisation of microbiomes of wheat and maize under conventional and conservation agriculture has been running for 18 months and is a team project with collaborators from six different institutions.

The goal of the project is to characterise the microbial communities associated with the rhizosphere of these important crops. 

The rhizosphere is the area around a plant root which plays host to a unique population of microorganisms influenced by chemicals released from plant roots.

All the samples for the project sites with wheat have been collected and the team is performing data analysis.

Rainfall recorded at the sampling sites showed that 2019 has been a very dry year.

This means that we will have the opportunity to investigate the influence of the microbial communities on plants during a dry period.

Preliminary data showed that despite the low rainfall, the yields were average to above average for sites applying conservation agriculture principles.  Yield data for the maize project is not available yet.

Soil chemistry and microbiomes

Soil chemistry data for wheat sampling sites showed increases in important crop nutrients over the season, and preliminary results from the three maize sites showed different responses to conservation agriculture treatments, with the more fertile sites showing a response in terms of enzyme activity, which is an indication of microbial function.

Conservation agriculture is a farming system that promotes minimal soil disturbance, maintenance of a permanent soil cover, and diversification of plant species.

United Nations

There has also been some interesting and unexpected microbial results. It appears that the soil communities are dominated by those contributing to plant health.

The fungal kingdom associated with the soil has proven to be surprisingly, although not unexpectedly diverse. From the samples thus far, 350 Trichoderma strains have been isolated and characterised, with some of these reported for the first time in South Africa.

Trichoderma is a genus of fungi that is present in most agricultural soils.  

In addition, almost all of the Trichoderma strains in the study have the potential to contribute to the growth of plants when comparing them with those reported in literature.

795 strains

There also appears to be a niche separation, with some of the species unique to wheat rhizosphere, and others to maize rhizospheres hinting that that a one-size-fits-all approach to biofertilizers may not be the best approach.

Fungal isolations from the sampled soils of the wheat fields have yielded 795 strains of Penicillium.

These strains so far represent 28 different species but analysis is not yet entirely complete so this number of species is expected to rise.

Of the isolated species five are from unpublished species or are rare species. Below are some images of the interesting and rare fungi thus far identified:

Phosphate solubilisation activity refers to the process whereby microorganisms are capable of breaking down insoluble phosphorous compounds to soluble forms that can be easily taken up by plants.

This is crucial to the health of the plants, and one of the key enzymes evaluated in soil health indicators.

Of the Penicillium fungal strains isolated 200 have been tested for phosphate solubilization activity. Of these, only 50 of them have thus far showed significant phosphate solubilization activity where another 100 showed very weak to nonsignificant activity, opening up the possibility of exploiting these strains as bio fertilisers.

The final few months of this project will be spent finishing up the classifications and phosphate solubilization potential of both the new species as well as other industrially relevant species as shown in literature.

For the next 18 months the groups at Stellenbosch University, Pretoria University, University of the Western Cape, Rhodes University and the ARC_PPRI will concentrate on the generation and analysis of high throughput sequence data.   

This will include whole genome data to screen for antibiotic resistance, detection of arbuscular mycorrhizal (AM) fungal species, as well as amplicon sequences to describe the microbiomes of the different cropping treatments in the project.