Searching for new microorganisms in Antarctica

A PhD candidate from City St George’s, University of London has recently returned from an Antarctic expedition where he used bespoke, cutting-edge biosurveillance technology and helped pioneer climbing routes on one of the continent’s most hostile mountains.

Major Scott Pallett, a PhD candidate in the Institute of Infection and Immunity at City St George’s and an infectious diseases physician/microbiologist with the British Army, travelled to Antarctica earlier this year as part of a project that explored how advanced remote diagnostic tools could be deployed in some of the most challenging environments on Earth.

The trip also retraced some of the steps taken by Captain Robert Falcon Scott RN on the fated Terra Nova expedition over 100 years ago, an adventure that also included a doctor from the original St George’s Hospital Medical School before its move from Hyde Park Corner to Tooting, namely Dr Edward Wilson.

Antarctic exploration

The expedition focused on the use of wearable technology and salivary diagnostics to track human performance and recovery and portable DNA sequencing technologies to analyse environmental samples in extreme conditions. The primary goal was to identify previously unknown microorganisms and biosynthetic compounds that could aid antimicrobial research by testing environmental samples on site and in real-time – marking a shift away from traditional practices that require transporting biomaterials to central laboratories.

Major Pallett, who is completing his PhD under the supervision of Professor Derek Macallan, said the project grew out of his wider interest in remote diagnostics, biosecurity and antimicrobial resistance.

“I have a strong interest in remote diagnostics, biosecurity, and antimicrobial resistance research,” he said. “This project was borne out of a ‘turning over every stone’ approach to the antimicrobial resistance global public health challenge.”

Antimicrobial resistance (AMR) is widely recognised as one of the most serious threats to global health. Researchers are increasingly exploring extreme environments for microorganisms that may produce novel compounds with antimicrobial properties.

Working with collaborators in industry, Major Pallett and his Australian colleague Bill Kwok FRGS set out to test whether new portable sequencing technologies could help scientists conduct and communicate sophisticated bio-surveillance research in places where laboratory facilities are impractical.

The project also drew on Major Pallett’s background outside academia. In addition to his research role at City St George’s, he serves as a medical microbiology and infectious diseases doctor with the British Army, and he is also a Fellow of the Royal Geographical Society and a Scientific Exploration Society explorer.

He previously worked as a clinical doctor in the infection department at St George’s Hospital for around two and a half years, where he first met Professor Macallan and began developing the research interests that led to his PhD.

The Antarctic expedition received backing from Dr Danny Chambers MP (Liberal Democrat Member of Parliament for Winchester and Secretary for the All-Party Parliamentary Group on Antimicrobial Resistance), with key support from the Scientific Exploration Society. Bespoke technology was provided by ProtonDx, while the expedition’s complex logistics were managed by the Scenic Eclipse II Discovery Yachts. The expertise of their crew and the advanced conservation-purposed design of the ship were integral in bringing this expedition to life.

Links to the past

After sailing through pack ice into the Ross Sea in mid-January, the team landed at Cape Evans, the historic base used by Captain Robert Falcon Scott’s Terra Nova expedition of 1910–1913.

Before beginning the scientific work, Major Pallett visited Scott’s Hut, one of Antarctica’s best-preserved historic sites. The hut still contains many artefacts from the original expedition, including the work and bedspace of Dr Edward Wilson, a physician and naturalist who studied at legacy St George’s and served as the expedition’s chief scientist.

“Having a strong interest in the history of Antarctic exploration, the highlight has to have been coming through the pack ice and stepping back in time across the threshold of Scott’s Hut,” Major Pallett said. “The hut still smells strongly of burnt seal blubber and despite over 113 years since Scott’s team left, it barely seems to have changed.”

From Cape Evans, the expedition crossed the Barne glacier toward Mount Erebus, the southernmost active volcano on Earth and one of Antarctica’s most formidable peaks. Rising more than 3,700 metres above sea level, the volcano is known for its extreme conditions, rare open lava lake, and emission of noxious acidic vapours.

Since a first ascent during Shackleton’s Nimrod expedition in 1908, records of successful attempts have been rare. Following in the footsteps of these early explorers, Major Pallett and his colleague revived a century-old tradition of unsupported scientific exploration, crossing crevasse fields while sled-hauling 150kg of equipment.

The pair completed one ascent together, followed by a second solo climb by Major Pallett - an achievement rarely documented in the mountain's history. In historic fashion, they opted to record the mapped routes with a dedication to their expedition ship, the Scenic Eclipse II, and the Royal Army Medical Services.

Alongside the mountaineering achievements, the team carried out environmental sampling using portable sequencing devices designed for field-based diagnostics. The equipment allowed them to extract and analyse environmental DNA directly on site, using a pipeline adapted for the extreme cold while facing fierce Antarctic winds from the Ross Ice shelf, and upload sequencing data using satellite internet technology. Major Pallett described the successful deployment of the system as a significant milestone for remote bio-surveillance research.

“The successful use these novel technologies for real-time environmental DNA sequencing, including sample upload and processing via Starlink, is a significant milestone, meaning we were able to process and analyse results in the most extreme conditions without having to move biomaterial, an important factor in maintaining Antarctic biodiversity and biosecurity,” he said.

Analysing the results

Although the scientific analysis is still underway, the initial results are promising. Early sequencing data suggest the team may have detected novel pathogen sequence types and potentially new species of thermotolerant bacteria.

The next phase of the project will involve detailed analysis of the genetic data to identify biosynthetic gene clusters and explore whether any of the microorganisms discovered could have relevance for antimicrobial research.

“We are doing a deep analysis of our sequencing data to identify any novel biosynthetic compounds,” Major Pallett said.

The researchers will also review how the sequencing equipment performed in such extreme conditions, with the aim of improving its usability and expanding its potential applications in future field expeditions.

For Major Pallett, the expedition brought together scientific research, exploration and history, and it also continued the connection between Antarctica and City St George’s that dates back more than a century.