Life in extreme locations: Dr. Adrienne Kish

Did you know that microbes live in some surprising places like hot springs, inside of salt, and at the bottom of the ocean?

These organisms that love extreme environments are called extremophiles. Dr. Adrienne Kish is an Associate Professor of Microbiology at the National Museum of Natural History (Muséum National d’Histoire Naturelle) in Paris, France. As an extremophile microbiologist, she studies how certain organisms on our planet can live in environments that we humans can’t. And really, we usually assume there is no life in those places. I’m thrilled to share my interview with her on the Joyful Microbe podcast.

In this episode, you will learn all about extremophiles:

• What extremophiles are
• Subgroups of organisms that live in extreme environments
• Adaptations of extremophiles
• Types of microbes that are extremophiles
• How extremophiles help in the search for life on other planets
• Hands-on activity to grow extremophiles from pink rock salt and extract their DNA
• Resources to further explore extremophiles

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What is an extremophile?

The word extremophile is a term created to describe microorganisms that love to live in environments that humans don’t love. Extremophile means “extreme-loving.” Different types of extremophiles live in conditions with extreme temperatures (hot or cold), pH (acidic or alkaline), salt, pressure, or radiation. Most extremophiles are microorganisms, and many are bacteria and archaea.

Extreme from a human perspective

Our understanding of extremophiles and what constitutes “extreme” is rooted in our human perspective. For the microorganisms, these conditions are completely normal. They can live in pools of boiling acid, and for them, that environment is perfect. They love it and could not imagine living the way we do. It’s all a matter of perspective.

Subgroups of organisms that live in extreme conditions

Organisms that live in extreme environments fall into different categories based on whether they require the extreme environment or not to live and whether they experience the extreme environment or are protected from it.

Those that require the extreme environment are the true extremophiles. Extremotolerant organisms can survive in direct contact with extreme environments but don’t require it. The third category of organisms includes those found in extreme environments but are not in direct contact with them.

True extremophiles

Extremophiles absolutely must live in extreme conditions. One example is the organisms at the bottom of the ocean. They are called barophiles or piezophiles and love the high pressure from the water above them. When researchers send down submarines to collect samples and bring them up to sea level, the cells explode because they can’t withstand normal atmospheric pressure. These organisms are true extremophiles. 

Extremotolerant

Some organisms can survive under extreme conditions but don’t have to live there like extremophiles do. They are just as happy in normal conditions. An example of an extremotolerant organism that most people associate with the word extremophile is Deinococcus radiodurans. Deinococcus is well known because it can survive high levels of radiation. It was originally isolated from a can of Spam meat sterilized with x-rays that had spoiled. But Deinococcus can not only live in Spam but also under normal conditions.

Organisms in extreme environments that are not in direct contact with it

The third category of organisms found in extreme environments is those that survive in extreme conditions because they are not in direct contact with the extreme environment. One example is the stomach-dwelling bacteria that causes stomach ulcers, Helicobacter pylori. They’re not actually exposed directly to our stomach acid — they protect themselves from the acid. They create a “bubble” around themselves of a neutral pH. So they survive inside stomach acid, an acidic environment, but they are not exposed directly to the acid. These are non-extremophiles because they’re not in direct contact with extreme environments and don’t love it.

Adaptations of extremophiles

What hidden talents do extremophiles have? What allows them to thrive in these environments that we would hate?

It’s the different adaptations that make extremophiles able to survive extreme environments. But these adaptations are not super special. Extremophiles work in pretty similar ways to how non-extremophiles work with a couple of key differences. They simply take what all cells have and use it efficiently.

One way we all survive radiation is by repairing our DNA. But for organisms that survive high radiation, scientists initially assumed that they must have great systems to repair their DNA. The first studies on organisms like Deinococcus radiodurans, a radiation-resistant organism, searched “silver bullet” enzymes that would be totally different from what you’d find in E. coli. But when they started going through the genome, they couldn’t find any of these special enzymes. So, they concluded that the systems to repair the DNA in non-extremophile organisms and extremophiles were the same but that extremophiles were highly efficient. It would be like the difference between a smart car and a Ferrari. They’re both cars, but one of them works a lot better than the other.

Radiation-resistant organisms also have specific amounts of metals that allow them to survive extreme conditions. We all need certain metals inside all living cells. But the cells of radiation-resistant organisms have high concentrations of manganese and low amounts of iron, allowing them to survive high levels of radiation.

Another example used in many organisms is the production of different kinds of sugars, like glycerol or trehalose. These sugars are helpful in cells because they can recycle them in numerous ways. If the cell lacks nutrients, they can use the sugars they have around as a nutrient (carbon) source when they’re in stressful environments like high pressure or salt. They would produce these sugars anyways, but it saves them the energy to do so when in stressful environments.

Halophiles do a trick to recycle nutrients: they can eat DNA. They carry multiple copies of their DNA inside their cells and have DNA outside their cells. So, when they don’t have enough phosphorus — DNA is full of phosphorus — they can eat DNA to get it.

Ultimately, these adaptations take the processes that all cells have and make them more efficient — extremophiles are the “Ferrari version of a cell.”

Types of microbes that are extremophiles

Extremophiles fall within all three domains of life (learn about types of microbes in this previous post): eukarya, bacteria, and archaea. 

Eukarya are organisms with a nucleus, which can be plants and animals (including small animals like tardigrades, aka water bears). Bacteria are single-celled organisms lacking a nucleus. Archaea are also single-celled organisms lacking a nucleus and look superficially similar to bacteria but have key differences.

Up until the 1970s, archaea were categorized as bacteria because they look the same. But when you strip them down to the molecular level, you see that their machinery — their proteins, how they replicate their DNA, and how they repair their DNA — looks like they come from eukaryotes. So, archaea look like eukaryotes packaged into bacterial cells.

When it comes to extreme environments, they tend to have more archaea than bacteria or eukaryotes. Archaea were first identified through the sampling of hot springs in Yellowstone. So, at the beginning, archaea and extremophile were synonymous. Now we know that’s not true. Some archaea aren’t extremophiles. But when you get into extreme environments, you mostly find archaea.

Carl Woese was the first to identify the archaea and proposed their existence in the 1970s, which led to a revolution in microbiology. It was shocking that there was a whole other group of organisms that nobody realized were distinct. 

But when Thaumarchaea were discovered, everything changed. These archaea are not extreme. We can find them in dirt in the park, lakewater, and just about everywhere. But because the Thaumarchaea discovery was fairly late, archaea have a reputation of being extremophiles.

The reason why archaea were hard to discover was that they are difficult to grow in the lab. Before genome sequencing, scientists attempted to grow microbes on Petri dishes (and we still do this now) but missed a lot of what was out there. The amount of organisms scientists can culture is tiny compared to what is out there. So it took a while to discover archaea. Now with genome sequencing, scientists can find these microbes that were once undiscoverable.

Culturing extremophiles in the lab is even more difficult because you encounter problems you wouldn’t imagine for an easy-to-grow organism like E. coli. The conditions you have to recreate in the lab are extreme. For example, suppose you’re studying hyperthermophiles (organisms that live at the highest temperatures like boiling water) and trying to grow them in the usual way on a Petri dish with an agar-based growth medium. It’s simply not possible to do because the agar will melt. So, growing microbes in extreme environments in the lab is a challenge and is why many of the discoveries these days are genome sequence-based.

How extremophiles help in the search for life on other planets

Part of Adrienne’s research focuses on astrobiology and the search for life on other planets, particularly how to figure out if life can survive on other planets. The only “sample” of life we have is on our planet. We don’t know of any other life in another world. And because extremophiles live in places humans think of as impossible and horrible yet are totally happy, they provide a window into what’s possible. They let us see how life can push the boundaries of our thinking. 

The work Adrienne does looks at the molecules extremophiles use as “building blocks,” like Legos. And these molecules actually persist over time, and she can look at them as fossils. Her work relates to what is going on with the mission to Mars. The Mars Perseverance Rover will try to find fossils of microbial life on Mars to see if there was life in the past on Mars. The conditions now are likely too extreme, at least at the surface of the planet, for life. But it might have been possible in the past when there was still water. So the rover is looking for molecular fossils (those Legos mentioned above). 

Proving that you have found life on other planets is tricky. The bar is set high. Adrienne says that scientists still debate whether fossils of life on Earth are even fossils, to begin with. Many scientists, Adrienne included, have looked at how extremophiles turn into fossils. They ask what does that look like? And how would we be able to detect it? How can we be sure that we’ve found life? How could we be sure that it is actually a fossil of life and not just something that would form from geology that has nothing to do with the presence of life? Scientists go through all of these questions because finding life on another planet is a huge deal. If you were ever going to say you think you found life on Mars, you want to be sure.

Other challenges come with searching for life on other planets. Whenever a spacecraft travels to another planet, it has to go through a step called planetary protection, where it is sterilized to remove organisms from Earth, so we don’t send them to another planet. With this procedure, they have to ask, will organisms survive the cleaning process before sending the spacecraft to another planet? So it all comes back to the question of what extreme conditions organisms can survive.

Extremophiles in our daily lives

Adrienne also shared how her work with extremophiles has changed her perspective on microbes in our daily lives. She says it has challenged a lot of what she assumed about life. “The great thing about working with extremophiles is that you have to, at every step, challenge your assumptions, challenge your biases about what’s possible and what isn’t possible. You can’t assume something’s correct.” We can all think about extremophiles and reimagine what’s possible because it’s likely that what we initially thought is very limited compared to what is possible. 

The second lesson Adrienne shared is that her astrobiology work changed how she thought about extreme environments on Earth. It helped her notice more of these places on our planet because these are possible analogs for locations for life on other planets. Initially, it’s easy to think of exotic locations in the Arctic or high mountains, but we can also find extreme locations close to home. You may notice piles of salt — salt evaporation sites — in places like Saskatchewan, the Great Plains, or the Great Salt Lake, Utah. Or as you drive through the desert, you see colors in the rocks, maybe green, where cyanobacteria could live even in completely dried-out conditions. You go on vacation and sit in hot springs and see again little bits of green, or the rock you walk on is a little slimy. Those are extremophiles. And they are around us in a lot of places we wouldn’t imagine. 

Adrienne suggests that we all look for subtle colors in places that you wouldn’t expect life. It’s a beautiful way to look at the world. You’ll soon notice that there’s life in the most surprising places.

At-home microbiology activity

Imagine pink rock salt, like the kind you might have in your salt grinder at home you cook with or your Himalayan salt lamp is made from. There are two reasons why the salt can be pink: either it has a lot of iron, or the salt has microbes inside. These microbes are archaea that love salty environments (aka halophiles). And they live in tiny droplets of water inside of the salt crystals. The salt is pink because these archaea make pink pigments (colors) at their surface to protect against UV rays. So, you can think of it as their own sunscreen.

Adrienne explored growing these pink archaea in her kitchen from pink rock salt that she bought from the store because she got a little bored while living and working at home during COVID. And now you can grow pink archaea too! She even looked at them under a microscope (check out at-home microscopes here).

And don’t worry, because it’s perfectly safe to do this activity, even with kids. And don’t let this freak you out that there are microbes possibly living in your salt. These halophilic archaea aren’t dangerous to humans. They can’t infect us. Adrienne told us, “just like it says on The Hitchhiker’s Guide to the Galaxy, ‘Don’t panic.’ There’s nothing dangerous here.”

How to grow microbes from pink rock salt

See Adrienne’s Instagram post about this activity, showing the supplies and demonstrating the procedure.

Materials

• Himalayan pink rock salt
• Beef stock (preservative-free)
• Sugar
• Glass container with lid
• Measuring spoons

Procedure

• Combine ½ cup beef stock with ¾ teaspoon sugar to the beef broth.
• 1 tablespoon + 1 teaspoon Himalayan pink rock salt (you are adding enough to saturate it).
• Keep in a closed jar with some airspace at the top, and place it in a window (if possible) or on the countertop.
• Let it sit, and within 2-3 weeks, you will see it get cloudy (turbid).
• Congratulations, you have halophiles (salt-loving microbes)!
• Create a wet mount and observe them under the microscope.

Bonus: Extract DNA from your salt-loving microbes

For those interested in going a step further, you can see DNA in real life by extracting it from the salt-loving microbes you grow.

• Take a small amount of the liquid from your halophiles you grew and put it in a small container. You can also buy a home child’s centrifuge (you can sometimes find one in a child’s lab kits — Adrienne recommends a kit in her Instagram post), and use the tubes that come with it, and spin down the cells you grew.
• Drip down the side of the tube some ice-cold (put it in the freezer until it’s ice-cold) 95% ethanol or 90% isopropyl alcohol until you’ve added twice as much ethanol as you have water on the inside of the tube. 
• Eventually, you will see layers form (make sure the layers don’t mix). The top part is the ethanol, and the bottom part is the water, but right between the two layers will be a white layer — that’s the DNA!
• Take a glass stir stick and spool it around, and you’ll pull out the DNA. You may also be able to take some tweezers to pull out the DNA.

Have fun with your halophiles!

Links & Resources

• Carleton College + National Science Foundation website on extremophiles – Microbial Life Educational Resources – a great introduction to all the different kinds of extremophiles
• Yellowstone National Park website section called Life in Extreme Heat – high-temperature life, all about thermophiles
• Microbiology Society magazine Microbiology Today issue Real Superheroes – halophiles and radiation-resistant microorganisms
• What is extreme life, and where do we find it? – previous post on Joyful Microbe introducing extreme life

Connect with Dr. Adrienne Kish

Dr. Adrienne Kish is an extremophile microbiologist, which means that she is fascinated by the many ways that microbial life can survive under conditions impossible for humans. In her work, she tries to identify what different extreme microorganisms have in common — right down to their molecules — that enables them to thrive under such harsh conditions. Her work helps us better understand both the richness and the limitations of life on our planet and guides us in evaluating the potential for life on other planets and moons.
Connect with Dr. Adrienne Kish: National Museum of Natural History (Muséum national d’Histoire naturelle), ResearchGate, LinkedIn, Twitter, and Instagram.