The phytomicrobiome can be described as the microbial community (bacteria, fungi, yeasts, algae) associated with a plant that constitutes the whole root as well as the shoot parts and which play significant roles in plant health, development and productivity. This analysis requires a holistic study involving the complimentary techniques of genomics, culturomics, transcriptomics, proteomics and metabolomics to determine the relationship between the plant and its associated microbial community. These advanced omics studies are a useful tool in the management of agro-ecosystems.

Ensuring food security in an environmentally sustainable way is a global challenge. The use of beneficial phytomicrobiome is considered one of the viable solutions to meet the challenges of food security and environmental sustainability. Within the AgriPhytomicrobiome research group we contribute to improving the quality and quantity of food production as well as informing on increased productivity via efficient resource use and resilience to biotic and abiotic stresses.

Through this research, we are able to identify pathogenic organisms causing plant and human disease, synergetic relationships between microbiota and environmental factors associated with the plant developmental stages, thus significantly contributing towards the sustainable increase in agriculture productivity and food security. Because these same microbes can contribute to restoring soil health and productivity, they have a bright future in low-input, sustainable agriculture that extends beyond more classically defined plant-microbe symbioses.


Current projects in AgriMicrobiomes
From South to North: Comparative microbiomes of export produce and indigenous foods

The focus of this study is on the phytomicrobiomes of indigenous natural fruit (marula, baobab and wild berries), vegetables (marogo, maringa and wild herbs). The comparative difference between the commercial and natural products will be studied and the impact of production systems on the unique microbiomes explored. This is done with the view of exploring the potential of biodynamics to provide a crop protective solution for safe food production, to move away from pesticides and shift towards waste and loss reduction. It is a Austria-Africa collaborative project with Technical University Graz, and is funded via various bodies including OeAD Africa-UniNet and the Universty of Pretoria. 

Distinguishing the pre and postharvest microbiomes for safe consumption and reduction of food loss and waste

Fruit surfaces harbor both beneficial and pathogenic microorganisms fostered in the field and onto the packhouse and stores for consumers. Recent advances in DNA sequencing and “omics” technologies have promoted the characterization and potential function of the microbial communities (microbiome) present in and on plant tissues. With collaborations from industry partners, including ZZ2, Roussow Boerdery, and small-holder farmers, our research into the microbiome of pre and post harvested commodities (bluberries, citrus, tomato, leafy greens, mushroom) plays an essential role in the health and physiology of produce. This is monitored regularly through the value chain to the point of consumption and is supported by the use of complementary technologies i.e. drone surveillance, smart irrigation systems and smart fruit. This has the potential of providing fundamental information that can lead to a paradigm shift in the way we think about postharvest biology, food loss and waste, biocontrol strategies, biocontrol products, as well as the health attributes of plants and their produce.

From crops to food waste, how animal feed and the environment affect the gut microbiome and health of pigs

This project is in collaboration with the Produce Quality ad Safety research group and the South African Pork Producers Organisation, and aims to develop a “fit-for-purpose” industry staggered framework that reflects the current environment and animal health and safety status of the commercial pig industry in South Africa. Within this framework, we are characterising the “feed-to-faeces” microbiomes in the food production environment, followed by a comparative assessment of the small-scale farmer biosecurity and food safety risks.  


-- Updated March 2022 --


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