Investigations by a University of Pretoria (UP) research team into the changes that occur in the microbiome of Namib Desert soils after rain have found that they are abundant with tiny life forms.
The study – which was led by Professor Don Cowan, Director of UP’s Centre for Microbial Ecology and Genomics – was carried out at the Gobabeb Namib Research Institute, a desert research station situated about 100km inland from the coast, roughly in the centre of the Namib Desert. It is the perfect base for desert research of all kinds, and has been used by thousands of researchers from all around the world for more than 60 years.
Desert soils contain a huge diversity and number of microorganisms; some may be dormant (but alive), while others continue to function even when water is scarce. Prof Cowan says that microorganisms are everywhere in the desert. “Per gram of soil, there are in the order of 1 million to 10 million cells.”
Microorganisms and microbiomes play key roles in any environment, including carbon capture, nitrogen acquisition, nutrient cycling, biomass degradation and degradation of toxins. Many of these functions are also performed by higher organisms such as invertebrates, insects and plants. However, in desert ecosystems, where higher organisms are only occasionally present, the role of the soil microbiome is proportionally more important, as this is the dominant organism in such an environment.
Understanding the ecology of desert soil microbiomes is therefore particularly important for understanding the role of desert ecosystems in a larger global context.
“The Namib Desert is near unique, because it receives a substantial input of water from regular coastal fog,” Prof Cowan says. “The only other desert with a similar coastal phenomenon is the Atacama in Chile. The fog zone, the area where fog regularly impacts in the Namib, extends about 60km inland from the coast. The next 60km is the hyper-arid zone – the central desert, which receives very little water – where there is next to no fog and only very occasional rainfall, perhaps a shower or two every five to 10 years. The eastern inland zone, nearer the mountains, receives more regular rainfall. These three effects create a complex water gradient across the desert, from coast to mountains.”
The Namib is a particularly hot desert, Prof Cowan adds. “Surface temperatures in summer can easily reach 60°C. Most hot desert organisms are either thermo-resistant or are moderate ‘thermophiles’ (heat lovers), and are quite capable of surviving temperatures of up to 60°C.”
The study conducted by Prof Cowan and his team involved irrigating a small area of desert soil with artificial rain (adding about 30mm of “rain” from a watering can) to determine changes that occur in the soil microbiome after rain. “Everything switched on amazingly quickly,” Prof Cowan says. “Parts of the microbiome switched on within seven minutes. Stress-related genes were turned off and mobility genes were switched on. There were all sorts of changes in response to the water as soil microorganisms took advantage of the liquid and the sudden availability of substrates.”
The researchers found that organisms within soil microbial communities interact with one another in complex ways. For example, viruses and bacteriophage (also known as a phage: a virus that infects and replicates within bacteria) infect their hosts and could kill them; bacteria and fungi compete with each other for nutrients, and may produce toxins like antibiotics to inhibit competing organisms around them; cyanobacteria and microalgae are the “primary producers”, using light energy from photosynthesis to fix carbon, some of which becomes available to other organisms; and predatory organisms like amoeba feed on other microbes.
Microorganisms may be small, but in deserts, they play a dominant role in important processes such as the capture and storage of carbon. Desert microbes also exhibit unusual metabolic processes: for example, they take trace gases such as hydrogen from the atmosphere to generate water and energy.
The Namib Desert has a unique array of plants and animals. Best known is the ancient Welwitschia plant, which grows in a narrow coastal region of the desert, from the central Namib up into southern Angola. There are many other specialised plants species, such as spear grass (Stipagrostis), which has special hairs on its spear-like leaves that trap fog water and channel it down to the roots. All these plants have associated microbes: rhizospheric microbiomes around the roots, as well as microbes inside plant cells (endophytes) and on leaf surfaces. These are collectively called the phytomicrobiome.
“Relatively little is known about the exact roles of these microbes,” Prof Cowan says. “There is recent evidence that cells in specialised mineral structures around desert plant roots (called rhizosheaths) play important roles in nutrient acquisition and transport from the soil to the plant.” These rhizosheaths have a crusting of mineral particles a few millimetres in diameter around the roots. The mineral quarts are held in place by very fine hairs. Unique populations of microorganisms associated with these sheaths may play a significant role in protecting the root and providing nutrients, he explains.
About 30% of Earth’s land surface is dryland, a term that describes all types of deserts: hot and cold, sub-humid through to hyper-arid. Climate change is tending to expand dryland areas; this is a process known as desertification. Climate models suggest that hot deserts will get hotter and drier, and that hot deserts will expand their range (desertification). This is a slow process that happens over decadal timescales, but it is happening. As deserts expand, human populations around desert margins are negatively impacted, as agricultural productivity is reduced by the reduction in rainfall. “Millions of people and their agricultural livelihoods depend on drylands,” Prof Cowan says.
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Prof Don Cowan
July 10, 2022
Professor Don A Cowan is the Director of both the Genomics Research Institute and the Centre for Microbial Ecology and Genomics at the University of Pretoria (UP), as well as a professor in the Department of Biochemistry, Genetics and Microbiology.
He holds a BSc, MSc and PhD in Biochemistry, and was educated at the University of Waikato in New Zealand. Prof Cowan completed a four-year period of postdoctoral research before taking up a lectureship at University College London in the UK in 1985. After 16 years in London, he was appointed to the Chair of Microbiology and as Head of the Department of Biotechnology at the University of the Western Cape (UWC), where he established the Institute for Microbial Ecology and Metagenomics, and is now a Professor Emeritus.
For his research in the fields of microbial ecology, microbial genomics and applied microbiology, Prof Cowan and his team use modern “omics” methods to understand the diversity and function of microorganisms in different environments. Omics refers to a set of advanced tools for characterising complex mixtures of biological molecules such as nucleic acids and proteins.
Much of his research focuses on the microbiology of extreme environments, including hot (Namib) and cold (Antarctic) desert soils. He is a firm believer in the value of basic or fundamental research, and sees great value in research that helps us to understand the world around us.
His work on the microbial ecology of Antarctic desert soils has spanned more than 20 years, and continues with ever more complex and sophisticated studies on the structure, function and adaptation of cold-adapted microbiomes. Most recently, in collaboration with a leading laboratory in Monash University, Australia, he published a major study on the bioenergetics of Antarctic soil microbiomes in leading US journal Proceedings of the National Academy of Sciences in the USA, which has an impact factor of 11.2.
Prof Cowan has an extensive collaborative network, and works with many other research laboratories in South Africa and across the world. At UP, most of his research is within the Natural and Agricultural Sciences Faculty, but he works with collaborators from the Faculty of Medicine and Faculty of Engineering, Built Environment and Information Technology (EBIT). “I am constantly starting new research initiatives,” he says. “The most recent, which is in collaboration with colleagues from the Department of Plant and Soil Sciences and EBIT, is to investigate the effects of grassland burns on the structure and function of the surface soil microbiome.”
Prof Cowan has published 404 research papers as well as review articles and book chapters; he also sits on the editorial boards of 10 international journals. He has a Scopus h-index of 51.
During his career, Prof Cowan has trained and graduated 50 PhD students and 52 MSc students. As Director of the Centre for Microbial Ecology and Genomics, he is currently supervising/co-supervising a research team of one research fellow, three postdoctoral researchers and five PhD candidates.
Prof Cowan is a former president of the Royal Society of South Africa and was elected as a fellow in 2007; he was also elected as a member of the Academy of Science of South Africa in 2008, as an honorary fellow of the Royal Society of New Zealand in 2009 and as a fellow of the African Academy of Sciences in 2017.
He was awarded UWC’s Vice-Rector’s Award for Research Excellence in 2008 and the South African Society for Microbiology’s Medal for Research Excellence in 2009. In 2014, Prof Cowan received the National Science and Technology Forum Capacity Development Award, and the following year, he was awarded UP’s highest research honour, the Chancellor’s Medal. He also received the 2019 Royal Society of South Africa’s John FW Herschel Medal and UP’s 2020 Exceptional Supervisor’s Award. He was awarded a National Research Foundation A1 rating in 2019.
As to whether a specific event or person has inspired his research efforts, Prof Cowan says that while he has interacted with many inspirational researchers throughout his career, several come to mind. His PhD supervisor, Prof Roy Daniel of the University of Waikato, did much to guide his early career development, and they worked together for nearly 20 years. His other major mentor was the late Prof Tony Atkinson, a British research leader and entrepreneur who, until his untimely death in 2011, had founded one of the UK’s most successful bioethanol development companies. “Prof Atkinson supported my work and career over more than 20 years and became a close friend as well as a valued mentor,” Prof Cowan says.
He adds that one of the most inspirational researchers he has ever met is Prof Frances Arnold of the California Institute of Technology in the US. Prof Arnold was awarded the Nobel Prize for Chemistry in 2018. “She has that rare ability to instantly see the core of a problem. Frances visited South Africa with her husband in 2005, worked in my wife’s lab at the University of Cape Town for six months, and we all travelled the Eastern Cape together.”
Prof Cowan hopes to have a few more papers published in the journal Nature, though adds that he has achieved almost all of his academic objectives over the course of his career. He adds that he hopes that his achievements in research have positively impacted those around him.
His advice to school learners or undergraduates who are interested in his field is to “get a good basic education – everything else leads from there”.
Prof Cowan is a keen cyclist and his principal hobby is birding.
Story
Nine new trapdoor spider species have been discovered in the Great Karoo by researchers at the University of Pretoria’s (UP) Department of Zoology and Entomology, and the Agricultural Research Council (ARC).
Infographic
Trapdoor spiders hide in underground burrows that are covered with a cork-like lid made of soil, silk and plants. Learn more about trapdoor spiders with this infographic.
Video
Watch carefully to see how a trapdoor spider catches its prey through its trapdoor.
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