Humans are leaving behind a 'frozen signature' of microbes on Mount Everest

Almost 5 miles above sea level in the Himalayan mountains, the rocky dip between Mount Everest and its sister peak, Lhotse, lies windswept, free of snow. It is here at the South Col where hundreds of adventurers pitch their final camp each year before attempting to scale the world's tallest peak from the southeastern side.

According to new University of Colorado Boulder-led research, they're also leaving behind a frozen legacy of hardy microbes, which can withstand harsh conditions at high elevations and lie dormant in the soil for decades or even centuries.

The research not only highlights an invisible impact of tourism on the world's highest mountain, but could also lead to a better understanding of environmental limits to life on Earth, as well as where life may exist on other planets or cold moons. The findings were published last month in Arctic, Antarctic, and Alpine Research, a journal published on behalf of the Institute of Arctic and Alpine Research (INSTAAR) at CU Boulder.

"There is a human signature frozen in the microbiome of Everest, even at that elevation," said Steve Schmidt, senior author on the paper and professor of ecology and evolutionary biology.

In decades past, scientists have been unable to conclusively identify human-associated microbes in samples collected above 26,000 feet. This study marks the first time that next-generation gene sequencing technology has been used to analyze soil from such a high elevation on Mount Everest, enabling researchers to gain new insight into almost everything and anything that's in them.

The researchers weren't surprised to find microorganisms left by humans. Microbes are everywhere, even in the air, and can easily blow around and land some distance away from nearby camps or trails.

"If somebody even blew their nose or coughed, that's the kind of thing that might show up," said Schmidt.

What they were impressed by, however, was that certain microbes which have evolved to thrive in warm and wet environments like our noses and mouths were resilient enough to survive in a dormant state in such harsh conditions.

Life in the cryosphere

This team of CU Boulder researchers -- including Schmidt, lead author Nicholas Dragone and Adam Solon, both graduate students in the Department of Ecology and Evolutionary Biology and the Cooperative Institute for Research in Environmental Science (CIRES) -- study the cryobiosphere: Earth's cold regions and the limits to life in them. They have sampled soils everywhere from Antarctica and the Andes to the Himalayas and the high Arctic. Usually, human-associated microbes don't show up in these places to the extent they appeared in the recent Everest samples.

Schmidt's work over the years connected him with researchers who were headed to Everest's South Col in May of 2019 to set up the planet's highest weather station, established by the National Geographic and Rolex Perpetual Planet Everest Expedition.

He asked his colleagues: Would you mind collecting some soil samples while you're already there?

So Baker Perry, co-author, professor of geography at Appalachian State University and a National Geographic Explorer, hiked as far away from the South Col camp as possible to scoop up some soil samples to send back to Schmidt.

Extremes on Earth, and elsewhere

Dragone and Solon then analyzed the soil in several labs at CU Boulder. Using next-generation gene sequencing technology and more traditional culturing techniques, they were able to identify the DNA of almost any living or dead microbes in the soils. They then carried out extensive bioinformatics analyses of the DNA sequences to determine the diversity of organisms, rather than their abundances.

Most of the microbial DNA sequences they found were similar to hardy, or "extremophilic" organisms previously detected in other high-elevation sites in the Andes and Antarctica. The most abundant organism they found using both old and new methods was a fungus in the genus Naganishia that can withstand extreme levels of cold and UV radiation.

But they also found microbial DNA for some organisms heavily associated with humans, including Staphylococcus, one of the most common skin and nose bacteria, and Streptococcus, a dominant genus in the human mouth.

At high elevation, microbes are often killed by ultraviolet light, cold temperatures and low water availability. Only the hardiest critters survive. Most -- like the microbes carried up great heights by humans -- go dormant or die, but there is a chance that organisms like Naganishia may grow briefly when water and the perfect ray of sunlight provides enough heat to help it momentarily prosper. But even for the toughest of microbes, Mount Everest is a Hotel California: "You can check out any time you like/ But you can never leave."

The researchers don't expect this microscopic impact on Everest to significantly affect the broader environment. But this work does carry implications for the potential for life far beyond Earth, if one day humans step foot on Mars or beyond.

"We might find life on other planets and cold moons," said Schmidt. "We'll have to be careful to make sure we're not contaminating them with our own."

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Reducing their natural signals: How sneaky germs hide from ants

Not only humans are social, ants are too. Group members are taking care of sick ones by providing collective hygiene measures. This presents germs with a task. They must circumvent the immunity of an individual ant and avoid the group's healthcare. A new study now published in Nature Ecology & Evolution reveals that germs develop a sneaky way to escape the ant colony's defense systems by reducing their detection cues.

Pathogens are disease-causing organisms. By natural selection, they develop evading mechanisms to outsmart the host's immune system and to get the upper hand. One way to support the immune system and fight back is medical intervention. However, this can lead to unwanted adaptions of pathogens as seen in antibiotic-resistant bacteria. Another strategy is social intervention. Some social groups like ants are trying to fight infection with "social immunity," the collective hygiene and health care measures to avoid spreading throughout the community. If and how pathogens can respond to this kind of group behavior, is still unknown.

The latest study by Professor Sylvia Cremer and her research team at the Institute of Science and Technology Austria (ISTA) shows the extraordinary effects of these kinds of host-parasite interactions. Together, with chemical ecologists at the University of Würzburg in Germany, the scientists took a close look at social ants, to see how pathogenic fungi respond to their hosts' social care intervention during infection. The results reveal that fungi reduce their chemical detection signals to outplay social immunity. The study is published today in Nature Ecology & Evolution.

More spores but less grooming

"Fungi infect the ants from the body surface and grow inside, but nestmates groom off many of the spores before they can even cause internal infection," explains Barbara Milutinović, one of the lead authors, former postdoc in the Cremer Group and now Marie Curie Sklodowska Fellow at Ruđer Bošković Institute in Croatia. The scientists set up an experiment where Argentine ants (Linepithemahumile) were infected with pathogenic Metarhizium fungi either in the absence or presence of caregiving colony members. "We found that the fungi fundamentally changed in response to the ant workers' caregiving," Milutinović continues. Over ten infection cycles, fungi which experienced grooming nestmate ants boosted their spore production compared to fungi accompanied by only individual ants. "Producing more spores will help the fungus counteract the spore-removal by helping nestmates. Yet, we were surprised to see that the ants showed less grooming against the spores," Sylvia Cremer adds. "This suggests, that the spores have become more difficult to detect by the ants."

Fungi lose their typical chemical profile

To check why ant workers had difficulties sensing fungi and to analyze possible fungal detection cues, the scientists teamed up with a chemical ecologist from the University of Würzburg. Local Professor Thomas Schmitt explains: "The fungi, that adapted to social hosts were perceived less strongly, due to a strong reduction of a fungi-specific compound called ergosterol." Ergosterol is an essential membrane compound, that all fungi have. By exposing the ants to pure fungal ergosterol or the slightly different non-fungal vertebrate equivalent, the researchers showed, that only the fungal compound induced intense grooming. Milutinović summarizes: "This demonstrates that fungal pathogens react to the presence of caregiving ants by reducing their characteristic fungal signals. They are no longer recognized as a disease threat and can escape the social immunity of the colony."

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How at risk are you of getting a virus on an airplane?

Fair or not, airplanes have a reputation for germs. However, there are ways to minimize the risks.

Historic research based on group movements of humans and animals suggest three simple rules:

• move away from those that are too close.
• move toward those that are far away.
• match the direction of the movement of their neighbors.

This research is especially used for air travel where there is an increased risk for contagious infection or disease, such as the recent worldwide outbreak of the coronavirus, which causes COVID-19 disease.

"Airlines use several zones in boarding," said Ashok Srinivasan, a professor in the Department of Computer Science University of West Florida. "When boarding a plane, people are blocked and forced to stand near the person putting luggage in the bin -- people are very close to each other. This problem is exacerbated when many zones are used. Deplaning is much smoother and quicker -- there isn't as much time to get infected."

Srinivasan is the principal investigator of new research on pedestrian dynamics models that has recently been used in the analysis of procedures to reduce the risk of disease spread in airplanes. The research was published in the journal PLOS ONE in March 2020.

For many years scientists have relied on the SPED (Self Propelled Entity Dynamics) model, a social force model that treats each individual as a point particle, analogous to an atom in molecular dynamics simulations. In such simulations, the attractive and repulsive forces between atoms govern the movement of atoms. The SPED model modifies the code and replaces atoms with humans.

"[The SPED model] changes the values of the parameters that govern interactions between atoms so that they reflect interactions between humans, while keeping the functional form the same," Srinivasan said.

Srinivasan and his colleagues used the SPED model to analyze the risk of an Ebola outbreak in 2015, which was widely covered in news outlets around the world. However, one limitation of the SPED model is that it is slow -- which makes it difficult to make timely decisions. Answers are needed fast in situations such as an outbreak like COVID-19.

The researchers decided there was a need for a model that could simulate the same applications as SPED, while being much faster. They proposed the CALM model (for constrained linear movement of individuals in a crowd). CALM produces similar results to SPED, but is not based on MD code. In other words, CALM was designed to run fast.

Like SPED, CALM was designed to simulate movement in narrow, linear passageways. The results of their research shows that CALM performs almost 60 times faster than the SPED model. Apart from the performance gain, the researchers also modeled additional pedestrian behaviors.

"The CALM model overcame the limitations of SPED where real time decisions are required," Srinivasan said.

Computational Work Using Frontera

The scientists designed the CALM model from scratch so it could run efficiently on computers, especially on GPUs (graphic processing units.

For their research, Srinivasan and colleagues used Frontera, the #5 most powerful supercomputer in the world and fastest academic supercomputer, according to the November 2019 rankings of the Top500 organization. Frontera is located at the Texas Advanced Computing Center and supported by National Science Foundation.

"Once Blue Waters started being phased out, Frontera was the natural choice, given that it was the new NSF-funded flagship machine," Srinivasan said. "One question you have is whether you have generated a sufficient number of scenarios to cover the range of possibilities. We check this by generating histograms of quantities of interest and seeing if the histogram converges. Using Frontera, we were able to perform sufficiently large simulations that we now know what a precise answer looks like."

In practice, it isn't feasible to make precise predictions due to inherent uncertainties, especially at the early stages of an epidemic -- this is what makes the computational aspect of this research challenging.

"We needed to generate a large number of possible scenarios to cover the range of possibilities. This makes it computationally intensive," Srinivasan said.

The team validated their results by examining disembarkation times on three different types of airplanes. Since a single simulation doesn't capture the variety of human movement patterns, they performed simulations with 1,000 different combinations of values and compared it to the empirical data.

Using Frontera's GPU subsystem, the researchers were able to get the computation time down to 1.5 minutes. "Using the GPUs turned out to be a fortunate choice because we were able to deploy these simulations in the COVID-19 emergency. The GPUs on Frontera are a means of generating answers fast."

But Wait -- Models Don't Capture Extreme Events? In terms of general preparation, Srinivasan wants people to understand that scientific models often don't capture extreme events accurately.

Though there have been thorough empirical studies on several flights to understand human behavior and cleanliness of the surfaces and air, a major infection outbreak is an extreme event -- data from typical situations may not capture it.

There are about 100,000 flights on an average day. A very low probability event could lead to frequent infection outbreaks just because the number of flights is so large. Although models have predicted infection transmission in planes as unlikely, there have been several known outbreaks.

Srinivasan offers an example.

"It's generally believed that infection spread in planes happens two rows in front and back of the index patient," he said. "During the SARS outbreak in 2002, on the few flights with infection spread, this was mostly true. However, a single outbreak accounted for more than half the cases, and half of the infected were seated farther than two rows away on that flight. One might be tempted to look at this outbreak as an outlier. But the 'outlier' had the most impact, and so people farther than two rows away accounted for a significant number of people infected with SARS on flights."

Currently, with regard to COVID-19, the typical infected person is believed to sicken 2.5 others. However, there have been communities were a single 'super-spreader' infected a large number of people and played the driving role in an outbreak. The impact of such extreme events, and the difficulty in modeling them accurately, makes prediction difficult, according to Srinivasan.

"In our approach, we don't aim to accurately predict the actual number of cases," Srinivasan said. "Rather, we try to identify vulnerabilities in different policy or procedural options, such as different boarding procedures on a plane. We generate a large number of possible scenarios that could occur and examine whether one option is consistently better than the other. If it is, then it can be considered more robust. In a decision-making setting, one may wish to choose the more robust option, rather than rely on expected values from predictions."

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