Tag Archives: Microbes

Microbiology

Humans Are Leaving Behind a Frozen Legacy of Microbes on Mount Everest

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Located nearly 5 miles above sea level in the Himalayas, the barren, wind-swept depression between Mount Everest and its neighboring summit, Lhotse, remains devoid of snow. At the South Col, hundreds of thrill-seekers set up their final camp annually, preparing to ascend the world’s highest mountain from the southeast flank.

New research led by the University of Colorado Boulder indicates that these adventurers are inadvertently leaving behind a frozen signature of resilient microbes. These microorganisms can endure extreme conditions at high altitudes and remain dormant in the soil for decades, or potentially 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.

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.

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 elevations, 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 them 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.”

Reference: “Genetic analysis of the frozen microbiome at 7900 m a.s.l., on the South Col of Sagarmatha (Mount Everest)” by Nicholas B. Dragone, L. Baker Perry, Adam J. Solon, Anton Seimon, Tracie A. Seimon and Steven K. Schmidt, 16 February 2023, Arctic, Antarctic, and Alpine Research.
DOI: 10.1080/15230430.2023.2164999

The study was funded by the National Geographic and Rolex Perpetual Planet Everest Expedition, the Department of Ecology and Evolutionary Biology, and the University of Colorado Boulder Libraries Open Access Fund

University of Colorado at Boulder

Microbiology

Scientists Discover Unique Microbial Community on Short-Lived Former Island

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In 2015, an underwater volcano in the South Pacific erupted, giving rise to the short-lived Hunga Tonga Hunga Ha’apai island. The University of Colorado Boulder and the Cooperative Institute for Research in Environmental Sciences (CIRES) spearheaded a research team that seized the uncommon chance to investigate the initial microbial inhabitants of a recently formed landmass. Surprisingly, they detected a unique microbial population that can metabolize sulfur and atmospheric gases, akin to organisms present in deep-sea hydrothermal vents or geothermal hot springs.

“These types of volcanic eruptions happen all over the world, but they don’t usually produce islands. We had an incredibly unique opportunity,” said Nick Dragone, CIRES Ph.D. student and lead author of the study recently published in mBio. “No one had ever comprehensively studied the microorganisms on this type of island system at such an early stage before.”

“Studying the microbes that first colonize islands provides a glimpse into the earliest stage of ecosystem development – before even plants and animals arrive,” said Noah Fierer, CIRES fellow, professor of ecology and evolutionary biology at CU Boulder and corresponding author on the study.

A multi-institutional team of researchers on the ground collected soil samples from the island, then shipped them to CU Boulder’s campus. Dragone and Fierer could then extract and sequence DNA samples from the samples.

“We didn’t see what we were expecting,” said Dragone. “We thought we’d see organisms you find when a glacier retreats, or cyanobacteria, more typical early colonizer species—but instead we found a unique group of bacteria that metabolize sulfur and atmospheric gases.”

And that wasn’t the only unexpected twist in this work: On January 15, 2022, seven years after it formed, the volcano erupted again, obliterating the entire landmass in the largest volcanic explosion of the 21st century. The eruption completely wiped out the island and eliminated the option for the team to continue monitoring their site.

“We were all expecting the island to stay,” said Dragone. “In fact, the week before the island exploded we were starting to plan a return trip.”

However, the same fickle nature of the Hunga Tonga Hunga Ha’apai (HTHH) that made it explode also explains why the team found such a unique set of microbes on the island. Hunga Tonga was volcanically formed, like Hawaii.

“One of the reasons why we think we see these unique microbes is because of the properties associated with volcanic eruptions: lots of sulfur and hydrogen sulfide gas, which are likely fueling the unique taxa we found,” Dragone said. “The microbes were most similar to those found in hydrothermal vents, hot springs like Yellowstone, and other volcanic systems. Our best guess is the microbes came from those types of sources.”

The expedition to HTHH required close collaboration with members of the government of the Kingdom of Tonga, who were willing to work with researchers to collect samples from land normally not visited by international guests. Coordination took years of work by collaborators at the Sea Education Association and NASA: a Tongan observer must approve and oversee any sample collection that takes place within the Kingdom.

“This work brought in so many people from around the world, and we learned so much. We are of course disappointed that the island is gone, but now we have a lot of predictions about what happens when islands form,” said Dragone. “So if something formed again, we would love to go there and collect more data. We would have a game plan of how to study it.”

Reference: “The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga” by Nicholas B. Dragone, Kerry Whittaker, Olivia M. Lord, Emily A. Burke, Helen Dufel, Emily Hite, Farley Miller, Gabrielle Page, Dan Slayback and Noah Fierer, 11 January 2023, mBio.
DOI: 10.1128/mbio.03313-22

University of Colorado at Boulder

Microbiology

Were viruses around on Earth before living cells emerged? A microbiologist explains

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Curious Kids is a series for children of all ages. If you have a question you’d like an expert to answer, send it to curiouskidsus@theconversation.com.

How life on Earth started has puzzled scientists for a long time. And it still does.

Fossils provide very important evidence about the evolution of plants and animals. Unfortunately, there are very few fossils of ancient microbes available, so scientists rely on modern microbes to devise theories about how life started. I studied bacteria and another type of microbe called archaea from hot environments for many years to learn how they might have evolved on early Earth, but I still have so many unanswered questions.

Based on the fossil evidence we have, single-celled microbes appeared on Earth before larger cellular life like plants and animals. But which kinds of microbes were the very first kind of life?

Microbes are living, single-celled creatures surrounded by a membrane. They consume and convert nutrients into biological molecules or energy and are too small to be seen without a microscope.

By this definition, bacteria, archaea and single-celled eukaryotes are microbes. Bacteria and archaea are single-celled creatures that lack internal membrane-enclosed structures, like a nucleus to hold their genetic material. Single-celled eukaryotes have a nucleus and may have other membrane-enclosed structures.

Some scientists consider viruses to be microbes made of genetic material enclosed in a protein coat. They are unable to replicate on their own and hijack the machinery of other cells to make copies of themselves. Because they don’t have many features of living cells, they are not technically alive.

Fossils can provide scientists with clues as to when life started, but they best record hard things like bones and teeth. Microbes are made of soft materials that do not fossilize well. However, some live together in very large groups of cells that can accumulate minerals and leave behind quite large fossils.

For example, cyanobacteria formed large structures called stromatolites in the oceans of early Earth. Scientists have found fossil stromatolites that date back to 3.48 billion years ago.

Other scientists found what they believe are fossilized archaea in rocks from a 3.4 billion-year-old hot seafloor. The Earth became habitable about 4 billion years ago, so bacteria and archaea must have appeared between 3.5 billion and 4 billion years ago.

Looking at the chemical reactions that cells carry out can also provide clues. The reactions that make biological molecules and generate energy make up what’s called the cell’s metabolism. Scientists have found evidence that some metabolic reactions were occurring at least 4.1 billion years ago. These reactions may have been occurring on their own before cells had evolved, perhaps on the surfaces of clays or minerals.

Cells copy their genetic material, made of DNA and RNA, to pass it on to new generations. Although DNA is the form of genetic material most living organisms use today, some scientists believe that RNA was the first information storage molecule on early Earth because it can make copies of itself.

Because some modern viruses use RNA to store genetic information, some scientists believe that viruses could have evolved from self-replicating RNAs. This possibility would mean that viruses may have appeared before bacteria. But because viruses don’t leave fossils behind, there isn’t available evidence to support this idea.

At some point, metabolic reactions and replication processes had to come together inside a membrane to make an early form of a cell: a pre-cell. Perhaps this happened when a viruslike structure infected a collection of metabolic reactions enclosed within a membrane. The pre-cell could then duplicate itself, leading to the evolution of the first living cell. This cell would have been like today’s bacteria and archaea.

Maybe viruslike structures did form before cells. However, those simple viruslike structures might have been just pieces of DNA or RNA, so could they really be considered “viruses”?

Another popular theory states that viruses evolved from degenerated bacteria or archaea that lost most of the genetic instructions for carrying out metabolism and forming cells. There are many examples of similar smaller degenerations that have occurred in the bacterial world today.

The surface of the Earth today is very different from what it was 4 billion years ago. Some have speculated that deep under the Earth’s surface, where it is too hot for modern life, these early conditions might still be present, allowing some protolife forms to continue to exist where they are protected from being consumed by other microbes.

When people can explore other planets or moons, perhaps we will find processes similar to those that were at work on early Earth. This kind of discovery could help us solve the puzzle of life’s origin here.

Hello, curious kids! Do you have a question you’d like an expert to answer? Ask an adult to send your question to CuriousKidsUS@theconversation.com. Please tell us your name, age and the city where you live.

And since curiosity has no age limit – adults, let us know what you’re wondering, too. We won’t be able to answer every question, but we will do our best.


Kenneth Noll

The Conversation

Microbiology

Scientists Discover Enzyme That Can Turn Poison Into Food

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Researchers at the Max Planck Institute for Marine Microbiology have uncovered how a methane-producing microbe thrives on toxic sulfite without becoming poisoned.

Methanogens are tiny organisms that generate methane in an oxygen-deprived environment. Their production of methane, such as in the digestive system of ruminants, plays a significant role in the global carbon cycle as methane is a highly potent greenhouse gas. However, methane can also serve as an energy source for heating homes.

The object of the study now published in Nature Chemical Biology are two marine heat-loving methanogens: Methanothermococcus thermolithotrophicus (lives in geothermally heated sediments at around 65 °C) and Methanocaldococcus jannaschii (prefers deep-sea volcanos with around 85 °C).

They obtain their cellular energy by producing methane and receive sulfur for growth in form of sulfide, that is present in their environments.

While sulfide is a poison for most organisms, it is essential for methanogens and they can tolerate even high concentrations of it. However, their Achilles’ heel is the toxic and reactive sulfur compound sulfite, which destroys the enzyme needed to make methane.

In their environments, both investigated organisms are occasionally exposed to sulfite, for example, when oxygen enters and reacts with the reduced sulfide. Its partial oxidation results in the formation of sulfite, and thus the methanogens need to protect themselves. But how can they do this?

Marion Jespersen and Tristan Wagner from the Max Planck Institute for Marine Microbiology in Bremen, Germany, together with Antonio Pierik from the University of Kaiserslautern, now provide a snapshot of the enzyme detoxifying the sulfite. This butterfly-shaped enzyme is known as the F420-dependent sulfite reductase or Fsr. It is capable of turning sulfite into sulfide – a safe source of sulfur that the methanogens require for growth.

In the current study, Jespersen and her colleagues describe how the enzyme works. “The enzyme traps the sulfite and directly reduces it to sulfide, which can be incorporated, for example, into amino acids”, Jespersen explains, “As a result, the methanogen doesn’t get poisoned and even uses the product as its sulfur source. They turn poison into food!”

It sounds simple. But in fact, Jespersen and her colleagues found that they were dealing with a fascinating and complicated overlap. “There are two ways of sulfite reduction: dissimilatory and assimilatory”, Jespersen explains. “The organism under study uses an enzyme that is built like a dissimilatory one, but it uses an assimilatory mechanism. It combines the best of both worlds, one could say, at least for its living conditions.”

It is assumed that the enzymes from both the dissimilatory and the assimilatory pathways have evolved from one common ancestor. “Sulfite reductases are ancient enzymes that have a major impact on the global sulfur and carbon cycles”, adds Tristan Wagner, head of the Max Planck Research Group Microbial Metabolism at the Max Planck Institute in Bremen. “Our enzyme, the Fsr, is probably a snapshot of this ancient primordial enzyme, an exciting look back in evolution.”

The Fsr not only opens up evolutionary implications but also allows us to better understand the fascinating world of marine microbes. Methanogens that can grow only on sulfite circumvent the need to use the dangerous sulfide, their usual sulfur substrate.

“This opens opportunities for safer biotechnological applications to study these important microorganisms. An optimal solution would be to find a methanogen that reduces sulfate, which is cheap, abundant, and a completely safe sulfur source”, says Wagner.

In fact, this methanogen already exists, it is Methanothermococcus thermolithotrophicus. The researchers hypothesized that Fsr orchestrates the last reaction of this sulfate reduction pathway because one of its intermediates would be sulfite.

“Our next challenge is to understand how it can transform sulfate to sulfite, to get a complete picture of the capabilities of these miracle microbes.”

Reference: “Structures of the sulfite detoxifying F420-dependent enzyme from Methanococcales” by Marion Jespersen, Antonio J. Pierik and Tristan Wagner, 19 January 2023, Nature Chemical Biology.
DOI: 10.1038/s41589-022-01232-y

Max Planck Institute for Marine Microbiology

Microbiology

A New Ancient Branch on the Tree of Life: The “Lions of the Microbial World”

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A new branch has been discovered on the tree of life, and it is composed of predators that nibble their prey to death.

These microbial predators are divided into two groups, one of which has been referred to as “nibblerids” due to their use of tooth-like structures to bite off pieces of their prey. The other group, known as “nebulids,” consume their prey whole. Both groups form a distinct ancient branch called “Provora,” according to a recent study published in the journal Nature.

Like lions, cheetahs, and more familiar predators, these microbes are numerically rare but important to the ecosystem, says senior author Dr. Patrick Keeling, professor at the University of British Columbia department of botany. “Imagine if you were an alien and sampled the Serengeti: you would get a lot of plants and maybe a gazelle, but no lions. But lions do matter, even if they are rare. These are lions of the microbial world.”

Using water samples from marine habitats around the world, including the coral reefs of Curaçao, sediment from the Black and Red seas, and water from the northeast Pacific and Arctic oceans, the researchers discovered new microbes. “I noticed that in some water samples, there were tiny organisms with two flagella, or tails, that convulsively spun in place or swam very quickly. Thus began my hunt for these microbes,” said first author Dr. Denis Tikhonenkov, senior researcher at the Institute for Biology of Inland Waters of the Russian Academy of Sciences.

Dr. Tikhonenkov, a long-time collaborator of the UBC co-authors, noticed that in samples where these microbes were present, almost all others disappeared after one to two days. They were being eaten. Dr. Tikhonenkov fed the voracious predators with pre-grown peaceful protozoa, cultivating the organisms in order to study their DNA.

“In the taxonomy of living organisms, we often use the gene ‘18S rRNA’ to describe genetic differences. For example, humans differ from guinea pigs in this gene by only six nucleotides. We were surprised to find that these predatory microbes differ by 170 to 180 nucleotides in the 18S rRNA gene from every other living thing on Earth. It became clear that we had discovered something completely new and amazing,” Dr. Tikhonenkov said.

On the tree of life, the animal kingdom would be a twig growing from one of the boughs called “domains,” the highest category of life. But sitting under domains, and above kingdoms, are branches of creatures that biologists have taken to calling “supergroups.” About five to seven have been found, with the most recent in 2018 – until now.

Understanding more about these potentially undiscovered branches of life helps us understand the foundations of the living world and just how evolution works.

“Ignoring microbial ecosystems, like we often do, is like having a house that needs repair and just redecorating the kitchen, but ignoring the roof or the foundations,” said Dr. Keeling. “This is an ancient branch of the tree of life that is roughly as diverse as the animal and fungi kingdoms combined, and no one knew it was there.”

The researchers plan to sequence whole genomes of the organisms, as well as build 3D reconstructions of the cells, in order to learn about their molecular organization, structure, and eating habits.

Culturing the microbial predators was no mean feat since they require a mini-ecosystem with their food and their food’s food just to survive in the lab. A difficult process in itself, the cultures were initially grown in Canada and Russia, and both COVID and Russia’s war with Ukraine prevented Russian scientists from visiting the lab in Canada in recent years, slowing down the collaboration.

Reference: “Microbial predators form a new supergroup of eukaryotes” by Denis V. Tikhonenkov, Kirill V. Mikhailov, Ryan M. R. Gawryluk, Artem O. Belyaev, Varsha Mathur, Sergey A. Karpov, Dmitry G. Zagumyonnyi, Anastasia S. Borodina, Kristina I. Prokina, Alexander P. Mylnikov, Vladimir V. Aleoshin and Patrick J. Keeling, 7 December 2022, Nature.
DOI: 10.1038/s41586-022-05511-5

University of British Columbia

Microbiology

Genetically engineered bacteria make living materials for self-repairing walls and cleaning up pollution

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With just an incubator and some broth, researchers can grow reusable filters made of bacteria to clean up polluted water, detect chemicals in the environment and protect surfaces from rust and mold.

I am a synthetic biologist who studies engineered living materials – substances made from living cells that have a variety of functions. In my recently published research, I programmed bacteria to form living materials that can not only be modified for different applications, but are also quick and easy to produce.

Like human cells, bacteria contain DNA that provides the instructions to build proteins. Bacterial DNA can be modified to instruct the cell to build new proteins, including ones that don’t exist in nature. Researchers can even control exactly where these proteins will be located within the cell.

Because engineered living materials are made of living cells, they can be genetically engineered to perform a broad variety of functions, almost like programming a cellphone with different apps. For example, researchers can turn bacteria into sensors for environmental pollutants by modifying them to change color in the presence of certain molecules. Researchers have also used bacteria to create limestone particles, the chemical used to make Styrofoam and living photovoltaics, among others.

A primary challenge for engineered living materials has been figuring out how to induce them to produce a matrix, or substances surrounding the cell, that allows researchers to control the physical properties of the final material, such as its viscosity, elasticity and stiffness. To address this, my team and I created a system to encode this matrix in the bacteria’s DNA.

We modified the DNA of the bacteria Caulobacter crescentus so that the bacterial cells would produce on their surfaces a matrix made of large amounts of elastic proteins. These elastic proteins have the ability to bind to each other and form hydrogels, a type of material that can retain large amounts of water.

When two genetically modified bacterial cells come in close proximity, these proteins come together and keep the cells attached to each other. By surrounding each cell with this sticky, elastic material, bacterial cells will cluster together to form a living slime.

Furthermore, we can modify the elastic proteins to change the properties of the final material. For example, we could turn bacteria into hard construction materials that have the ability to self-repair in the event of damage. Alternatively, we could turn bacteria into soft materials that could be used as fillers in products.

Usually, creating multifunctional materials is extremely difficult, due in part to very expensive processing costs. Like a tree growing from a seed, living materials, on the other hand, grow from cells that have minimal nutrient and energy requirements. Their biodegradability and minimal production requirements allow for sustainable and economical production.

The technology to make living materials is unsophisticated and cheap. It only takes a shaking incubator, proteins and sugars to grow a multifunctional, high-performing material from bacteria. The incubator is just a metal or plastic box that keeps the temperature at about 98.6 degrees Fahrenheit (37 Celsius), which is much lower than a conventional home oven, and shakes the cells at speeds slower than a blender.

Transforming bacteria into living materials is also a quick process. My team and I were able to grow our bacterial living materials in about 24 hours. This is pretty fast compared to the manufacturing process of other materials, including living materials like wood that can take years to produce.

Moreover, our living bacterial slime is easy to transport and store. It can survive in a jar at room temperature for up to three weeks and placed back into a fresh medium to regrow. This could lower the cost of future technology based on these materials.

Lastly, engineered living materials are an environmentally friendly technology. Because they are made of living cells, they are biocompatible, or nontoxic, and biodegradable, or naturally decomposable.

There are still some aspects of our bacterial living material that need to be clarified. For example, we don’t know exactly how the proteins on the bacterial cell surface interact with each other, or how strongly they bind to each other. We also don’t know exactly how many protein molecules are required to keep cells together.

Answering these questions will enable us to further customize living materials with desired qualities for different functions.

Next, I’m planning to explore growing different types of bacteria as living materials to expand the applications they can be used for. Some types of bacteria are better than others for different purposes. For example, some bacteria survive best in specific environments, such as the human body, soil or fresh water. Some, on the other hand, can adapt to different external conditions, like varying temperature, acidity and salinity.

By having many types of bacteria to choose from, researchers can further customize the materials they can create.


Sara Molinari

The Conversation