UP microbiologists discover rich diversity of life in Antarctica’s cold, dry soils

The ice-free areas of Antarctica were initially thought to be devoid of life, but with the advent of modern genetic technologies, scientists now know that microorganisms have adapted to living in this extreme environment.

Researchers at the University of Pretoria (UP) have taken this knowledge further with their discovery that the cold, dry soils of Antarctica is home to several million microorganisms. 

The Dry Valleys of East Antarctica are the most extreme example of polar soils; these valleys are arguably the coldest and driest deserts on Earth. About 50 years ago, it was thought that these cold desert soils contained only a limited diversity of specialised species of microorganisms. In fact, initial analyses, done about four decades ago, estimated that there were only a few to a thousand microbial cells per gram of Antarctic soil.

However, Professor Don Cowan, Director of the Centre for Microbial Ecology and Genomics at UP, and his research team have shown that these cold, dry soils harbour much greater populations of microorganisms: perhaps 1 to 10 million cells per gram of soil. As a comparison, temperate, nutrient-rich agricultural soils typically contain about 100 million cells per gram.

“The use of modern environmental genetics, using eDNA – which is all the DNA that can be extracted from an environmental sample, and which provides access to all the organisms in that sample – has painted a completely different picture of the microbial landscape,” Prof Cowan explains. His lab was one of the first to use eDNA methods on Antarctic soils, and to demonstrate that these cold, dry soils contained a high diversity of bacterial fungal and viral species, very few of which have ever been isolated as pure cultures.

Prof Cowan’s work demonstrates that the microorganisms found in the 1970s were those that were easy to grow on simple culture plates. “The eDNA studies showed that these fast-growing ‘microbial weeds’ were not the dominant microorganisms, but were mostly rare members of the microbial community,” Prof Cowan says. “The use of eDNA, together with phylogenetic marker analyses, allows us to identify all the microorganisms in the soils, whether they are common or rare. This is where big data and bioinformatics become really critical.”

Microbial life can be found in a wide variety of niches of Antarctic deserts. The really interesting ones are the “lithic” niches, where microbial communities are associated with rocks. Hypolithic communities – microbial communities living on the undersides of translucent quartz or marble pebbles embedded in desert pavement – are common. This is a specialised niche habitat with a favourable micro-environment, where the overlying rock protects the microorganisms on the underside from damaging ultra-violet light, buffers extreme temperature changes – particularly by limiting freeze-thaw cycles, which are damaging to cells – and increases the water available to the microbial community.

How do cold desert microbes get water?

Although about 97% of Antarctica is covered with glacial ice, the remaining 3% is mostly ice-free. The largest ice-free area is the McMurdo Dry Valleys, an area of about 150km x 30km of mountains and valleys that consist mainly of exposed gravel, sand and rock.

This area is much warmer than the icy interior, with summer temperatures ranging from -15°C to around 0°C. Winter temperatures drop to about -60° C. This area is a true cold desert and the soils, the home of the microorganisms, are extremely dry.

The soil water content in these areas is very low – typically, less than 1%. There is often water in the permafrost, between 30cm to 90cm below the surface, but this water is frozen and unavailable to surface microbes. Occasional snowfall moistens the surface soils, but only down to a centimetre or so. “It never rains in the Dry Valleys,” Prof Cowan says.

Some Antarctic soil microorganisms were recently discovered to use atmospheric hydrogen (a “trace” gas) as an energy source. The oxidation of hydrogen produces water, raising the exciting possibility that hydrogen-using Antarctic soil microorganisms “make” their own water. “The importance of hydrogen oxidation in supplying water to soil microbial communities is not yet known, but it is an intriguing and interesting question,” Prof Cowan says.

What about climate change?

“There is powerful evidence that the continent is warming, with associated loss of glacial ice mass,” Prof Cowan explains. “Local conditions will change. How the Dry Valleys will change is not completely known, but temperature rise will increase glacial ice melt and liquid water flows, though increasing cloud cover and snowfall may have the effect of decreasing mean summer temperatures. Nevertheless, change is happening, and the issue of the resilience of microbial and other biological communities is a current focus. Whether microbial communities will adapt, change, die out or be replaced by others is still an open question.”

Despite its remote location, Antarctica remains a vitally important continent. Its ice mass is enormous, and melting continental ice will have dramatic effects on oceanic flow patterns and global seal levels. Antarctica is also the last “pristine” continent in that it remains largely unaffected by human activity, which is why conservation is imperative.

“In order to conserve, you must understand what you are conserving,” Prof Cowan says. “Further studies on the indigenous biology of the continent and its surrounding oceans are therefore critically important. Such studies are even more urgent in light of the current impacts of climate change, as both the continent and its ‘inhabitants’ are forced to change with changing global temperatures.”

The organisms in Antarctic soils have to survive extreme conditions, and the molecular adaptations that allow them to do so can be unique and help us to understand the mechanisms of survival of life on Earth, Prof Cowan adds.

Watch the webseries in the sidebar to learn more or view the gallery to experience a day in the life of a research scientist. 

Prof Don Cowan

December 7, 2022

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  • Prof Don Cowan

    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.

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