Thulani Makhalanyane, Associate Professor in the University of Pretoria’s Department of Biochemistry, Genetics and Microbiology, believes that the invisible, tiny microbes that are found in ecosystems can provide clues to solving several global challenges. These include finding sustainable solutions to mitigate climate change, which ultimately impacts on food security on the continent.

“Microbial diversity affects all aspects of life,” he says, “from the carbon cycle that affects climate change, to the cycling of nitrogen that is important for agriculture, and human gut microbes that affect our health”. Despite the fact that microbiologists have been working on identifying microbes for many decades, the vast majority are unknown to science. In this respect, scientists from UP are looking specifically at the more than 99% uncharacterised microbes that are found in arid terrestrial zones, and coastal and marine environments.

Dr Thulani Makhalanyane

Using the latest innovations in microbiome science, they are combining cutting-edge technologies in bioinformatics and artificial intelligence (AI) to characterise unknown microbes and to pinpoint new and potentially valuable enzymes from different locations. “These methods allow us to directly extract DNA from any environment. We then essentially put together the equivalent of a 50 000-piece puzzle, using bioinformatics and AI, to get an idea of what is out there and what these microorganisms do.”

According to Prof Makhalanyane, microorganisms that live comfortably in extreme environments can help scientists develop crops that can cope better in unpredictable climates. “The nature of microbial ecosystems means that researchers can see the effects of climate change much faster on a small scale, compared to observing the changes on macro-fauna.” By setting up experimental systems, known as microcosms, scientists can study the effects of climate change on microbial communities in places such as the South Atlantic Ocean, providing fundamental data that can be fed into climatic models predicting ecosystem change.

This research is relevant and applicable across various ecosystems. For example, in another project, Prof Makhalanyane has joined an international team of scientists to map the microbiomes that are found in public parks worldwide. This project includes the identification of microorganisms in three parks in Pretoria, Johannesburg and Cape Town. This investigation unearthed a similar profile of park microbes across the world, as well as worrying levels of pathogens that indicate potential threats to human health.

“Although the study only provides some of the very first glimpses into the algae, amoeba and bacteria found in the world’s public parks, the results are already contributing to the development of better management strategies for parks to reduce potentially harmful microbes present in the soil,” he says.

Prof Makhalanyane assures city dwellers frequenting urban parks that they do not need to be concerned for their health. “Public parks are still a very safe way to spend time outdoors, and the risk of exposure is extremely low; it is just something we would like to raise for park managers to keep an eye on.”

While soil microbes form diverse ecosystems that are unseen beneath our feet, many of these organisms are beneficial to the environment. The study of Prof Makhalanyane and his co-workers not only found genes belonging to soil mycobacteria known to cause respiratory infections in humans, but also found large quantities of genes associated with listeria, diphtheria and antibiotic resistance.

The study compared the findings in these urban parks to pristine (unmanaged) natural areas away from the city. The data that was obtained at the undeveloped sites indicated that the fertilizers that are used at the developed sites allow these disease-causing microbes to thrive much better than they would in natural environments.

This study, which recorded the microbiomes of 56 urban green spaces in 17 countries is just one of the many similar projects on which the University’s researchers are working to map the earth’s “microverse” in an effort to solve many of the world’s pertinent challenges.