Microbes frozen in ancient rubbish heaps help reconstruct ancient Greenlanders’ farms, seal hunts, and toilets

Greenland has a long and checkered history of human settlement: several Paleo-Inuit cultures since approximately 2,500 BCE, descendants of Vikings between the tenth and fifteenth centuries, and early modern Danes since 1721. All left their traces on the landscape, for example in the form of ancient domestic rubbish heaps. Composed of waste like animal bones, excrement, mollusk shells, and human artefacts, these middens are a precious resource for archaeologists.

But what can microbiologists contribute to the study of these middens, for example revealing which diseases plagued historic populations, and which animals they kept but perhaps didn’t eat? And now that the Arctic is warming three to four times faster than the global average, could thawing middens be a source of resurgent infectious diseases?

“Here we show that the risk of release of ancient pathogens from ancient middens on Greenland is currently low,” said Dr Frank Møller Aarestrup, a professor at the National Food Institute of Denmark Technical University and corresponding author of the article in Frontiers in Microbiology. “Rather, we found that these middens in the cold Arctic acted like long-term natural experiments. Human- and animal-associated bacterial signals, including opportunistic bacteria and bacteria carrying antibiotic resistance genes, have remained detectable in them many centuries later as the legacy of human activity: for example, livestock farming by the ancient Norse.”

Studying the dustbins of history

In 2020 and 2021 in West and South Greenland, Aarestrup and colleagues collected samples from several middens frozen in time by permafrost and covering 4,500 years of human life in Greenland. These had been identified by the Greenland National Museum and Archives registry. At ancient Norse sites, for example at Kapisilit and Narsarsuaq, they also collected soil samples from historic winter enclosures and summer grazing grounds for livestock. The researchers used DNA sequencing to reconstruct entire bacterial communities. They compared their findings to those in 143 soil samples from areas of permafrost distant from any historical settlements.

The sequencing revealed between 9 and 202 bacterial species per midden, for a total of 1,207 species. Importantly, many of these species were previously undescribed and could only be assigned to broad taxonomic categories like families and orders. “This […] highlights how poorly described Arctic soils and archaeological deposits remain,” wrote the authors.

Middens had significantly richer bacterial communities than surrounding pristine soils, confirming that they preserved the biological legacy of human activity. Middens from the Paleo-Inuit had the most soil-like bacterial communities, indicating that the microbial imprint from humans and animals diminishes over time.

Groups of bacteria known to live on or within animal and human hosts predominated in most middens. These included harmless bacteria from human feces like Clostridium massilliamazoniense, Clostridium baratii which can cause botulism, and Paeniclostridium sordellii, which can cause life-threatening human diseases like toxic shock syndrome, sepsis, and gas gangrene.

Bacterial communities depended strongly on the type of waste material in each midden. For example, those from early colonial era Nuuk contained decomposing seal skins and were rich in the bacterium Clostridium perfringens, a major cause of food poisoning. Romboutsia species and Paraclostridium sordellii – which live in the gut of many animals – were abundant in middens filled with animal carcasses, while early Norse middens with decomposing bones were rich in unknown species of Proteobacteria and Clostridiaceae.

No reason to worry

The authors also found a great diversity of genes associated with antimicrobial resistance in bacterial genomes from middens. The presence of the same genes in ancient and contemporary soil layers signaled that microbes resistant to antimicrobials can linger in permafrost for centuries. However, the authors concluded from the spatial distribution of these pathogens that they don’t spread far from thawing middens. They thus appear to pose little risk to public health – at least for now.

"The microbiome in thawing permafrost appeared to be rapidly replaced by local contemporary environmental microbes once released into run-offs,” observed co-author Dr Saria Otani, an associate professor at the National Food Institute.

“However, it is not known whether the risk of release of pathogens will increase with increasing temperatures, or whether this might be greater in other Arctic regions. For this reason, it would be prudent to include microbiome characterization as a routine monitoring aspect during archaeological visits," counseled last author Dr Anders Priemé, a professor at the University of Copenhagen.