A team of researchers are set to uncover the secrets of microbiomes and the role it plays in South African agriculture. Microbiomes are communities of microorganisms (such as bacteria, fungi, and viruses) that inhabit soil and enable South African farmers to reduce input costs and maintaining or even increase yields.

Project leader, Prof Karin Jacobs from Stellenbosch University’s Microbial Ecology and Mycology lab, said that it is increasingly being recognized that soil microbiomes play crucial roles in nutrient cycling, soil formation, plant growth and ultimately, in the production of food.

According to recent findings, the intricacies of life in the rhizosphere has far reaching implications with regards to crop production and food security. The rhizosphere can be described as the area around a plant root that is inhabited by a unique population of microorganisms influenced by chemicals released from plant roots.

Jacobs said understanding the soil microbiome has clear and very practical applications in food production. She believes that understanding and harnessing the functional power of microbial communities will enable farmers to reduce input costs, while maintaining or even increasing yields over time. 

The project is funded by the Department of Science and Innovation (DSI) through the Foundational Biodiversity Information Programme (FBIP), which is jointly managed by the South African National Biodiversity Institute (SANBI) and the National Research Foundation (NRF).

Smart farming

According to Jacobs, the data generated will inform the identification of microbial profiles that are conducive to plant health, and farmers will be able to evaluate and adapt their practices to steer their soils towards harbouring more diverse and resilient microbial populations.

The results from the project will allow agriculturalists to understand how the natural microbiome can be harnessed to reduce and even replace chemical inputs for optimal yield and disease management. Microbiomes have also been shown to increase the heat and drought tolerance in crops, mitigating the effects of climate change.

The overall aim of the project is to characterise the rhizosphere microbiomes associated with two of the major crops (wheat and maize) under conventional and conservation agriculture in South Africa in terms of the microbial function and microbial species diversity.

“This study has a direct impact on the bio-economy as it informs management in terms of inputs and practices, and optimising yields – working towards sustainable agriculture will alleviate the effect of global environmental change,” Jacobs said.

South Africa’s Bio-Economy Strategy was launched in 2014 as a road map on how to develop the country’s natural biological resources into commercial products in health, agriculture and industry.

Soil health tool

Agriculture significantly contributes to the South African economy and has been recognized as a sector which could potentially drive economic growth. However, less than 12% of the country’s land mass is suitable for use as arable land.

Alarmingly, said Jacobs, substantial proportions of soils are subject to increased desertification, reducing the proportion of productive lands. Given South Africa’s increasing population, increasing the productivity of arable lands is crucial for sustenance.

Over the last few years, there has been a significant demand on the farming sector to alter agricultural practices, while simultaneously improving yield. According to Jacobs, the developments in analytical approaches such as high throughput sequencing and culture methods has helped reduce the knowledge deficit around microbial diversity and their specific roles.

“The power of this approach has been evident in the study of the human microbiome, which revolutionized our perception, diagnosis and treatment of diseases,” she said.

The project is novel and its successful completion will likely to result in a tool for measuring soil health.

The project, which runs from 2019 to 2021, will involve experts and students from several South African institutions including Stellenbosch University, Elsenburg College, University of Pretoria, Free State University, Rhodes University, North-West University, ARC-Plant Health and Protection Unit, and the University of the Western Cape. – Press release, SANBI