EXTREME microbiology: Extremophiles thrive in the toughest conditions on Earth...and beyond

Our planet is home to a vast array of environmental conditions, and humans can tolerate an impressive range of them. Communities make their homes in places where temperatures regularly fall below -50^oC or top 50^oC. Deep-sea divers experience pressure several times that of our ambient atmosphere. We may not enjoy spending time in the most extreme conditions, but we can survive there.

But earth is full of environments that fall well outside the bounds of human physiology. The arctic ocean, deep sea hydrothermal vents, acidic hot springs, hyper-saline marshes, and radioactive fallout sites are just some of the places that humans, and most organisms that we regularly interact with, cannot tolerate. But these ecosystems are not empty of life -- they are home to many organisms, mostly single-celled bacteria and archaea, that have adapted to the extreme conditions.

The organisms found in extreme environments can be divided into two categories. Extremophiles (-phile means "lover of something") thrive in these harsh conditions. They make their homes there, and they are so well-suited to their habitats that they cannot survive in more moderate environments. Other organisms can withstand temporary shifts in conditions to extremes, but only truly thrive with a return to moderate conditions. These are known as extremotolerant organisms.

True extremophiles are characterized by physiological adaptations to their environment. The adaptations vary by organism and by habitat, but many fall into three different categories. Adaptations can include proteins with altered structure that function better in extreme conditions, protections for DNA replication and repair under stress, and changes to the composition of the cell membrane to protect the organism from its surroundings.

Microorganisms under heat stress

Thermophiles, which thrive in temperatures above 60^oC like hot springs and hydrothermal vents, primarily face issues of stability. At high temperatures, molecules move faster and have more energy. Cellular proteins, DNA, and cell membranes all encounter significant stress from this elevated energy.

Grand Prismatic Spring in Yellowstone National Park, USA

Carefully-folded enzymes face the greatest threat. Enzyme folding is controlled by intramolecular bonds and interactions, which are easily disrupted at high temperatures. Thermophilic proteins tend to be more compact, with increased intramolecular interactions between different regions. This holds them together better and protects them from the effects of high molecular energy.

Under heat stress, double-stranded DNA is at risk of separating, rendering the two dissociated strands vulnerable to damage. This issue is partially solved by maintaining a small genome, to limit how much DNA the organisms must protect. Thermophiles may also have a higher percentage of G and C nucleic acids, which bond more strongly than A and T acids and help hold the strands together.

Heat adaptation also includes changes to the cell membrane. Thermophilic membranes have a higher fraction of non-branched phospholipids, which can pack closely together and resist the effects of elevated molecular energy. Finally, organisms in hot environments produce proteins called heat-shock proteins, which protect the cell from heat damage.

Microbes left out in the cold

Organisms that live in habitats consistently below 15^oC are known as psychrophiles. They face the opposite challenge of organisms in warm environments. At lower temperatures, everything slows down, including the metabolic functions that are essential to life. Psychrophilic habitats include polar oceans, the tundra, and the Antarctic continent.

Perito Mereno Glacier in Patagonia, Argentina

Enzymes in cold environments have adapted to increase binding efficiency by increasing flexibility. The proteins contain a higher fraction of small amino acids, such as glycine, while avoiding larger, bulkier acids like proline. This allows them to bend and twist into the best configuration for binding target molecules. Once binding occurs, the enzymes also have lower activation energy, so the slower-moving, lower-energy molecules can react more easily.

Just as DNA dissociates under hot conditions, the strands tend to stick together at lower temperatures. This makes the DNA harder to access for replication and transcription. Psychrophilic DNA has lower GC content and more of the weaker AT pairs, so it is easier to pull apart. Cold-dwelling organisms also produce more helicases, the proteins that separate DNA strands, to overcome the slowness with a greater number of molecules performing the same activity. RNA, the molecule that translates genes into proteins, also has a tendency to coil up in colder environments. Psychrophiles produce special binding proteins that keep the RNA open for translation.

Cell membranes are important not only for keeping a cell together, but also for allowing nutrients into the cell. At low temperatures, typical cell membranes may become too compact and solid for these important molecules to pass through. Psychrophile membranes contain bulky and branched lipids that keep them from packing too close together, even when moving slowly in the cold, and allow them to maintain fluidity.

Microbes under pressure

Piezophiles are pressure-loving organisms that thrive at or above 10MPa, equal to around 100 times standard atmospheric pressure. Their habitats are often multi-extreme, such as the Mariana trench, which is both deep and cold, and the continental subsurface, which is both high-pressure and nutrient limited. As a result, piezophiles are often tolerant to several stressors.

An Atlantic deep-sea hydrothermal vent

Proteins in pressure-adapted organisms are typically very streamlined. They contain fewer bulky amino acids and limited side chains sticking off the main structure, making them better suited for resisting compressive forces. New evidence suggests that ribosomes, the cellular machines that synthesize proteins, have also adapted to high pressure. They have elongated helical structure that may promote stability and function.

Many other adaptions to high pressure environments are similar to those occurring in the cold. Piezophile membranes contain bulky and branched lipids, allowing the membrane to maintain flexibility even under compressive forces. DNA is stable at high pressures, which presents similar challenges for DNA replication and transcription. Less is known about piezophile strategies for overcoming DNA compression, but the adaptations may be similar to those observed in cold environments.

Other extreme environments

Heat, cold, and pressure are some of the most well-studied extreme environments. Heat stress, in particular, has become vital to understand as the planet warms. But there are many other extreme environments on earth, each of which requires unique bacterial adaptations.

Among the most fascinating extreme environments are those with high levels of radiation. This includes places like Chernobyl, Fukushima, and other nuclear disaster sites. It can also include extraterrestrial locations like the international space station.

The primary threat from radiation is damage to DNA. Even a small number of mutations can prevent a cell from making the molecules it needs to survive and reproduce. Radiotolerant organisms often combat this stressor by ramping up their ability to repair DNA. For example, Deinococcus radiodurans, an organisms that has been isolated from nuclear disaster zones, upregulates its DNA repair mechanism (UvrABC) to fix damage as it occurs and prevent the buildup of mutations. This species has also been studied aboard the international space station, and was found to resist damage from solar radiation.

High-salt environments are also considered extreme, because they interfere with cellular water balance. When the environment around a cell has significantly more salt than its interior, water will passively flow out of the cell by osmosis in an attempt to correct the imbalance. In areas with high salinity, like salt lakes and briny marshes, organisms maintain higher interior salt concentrations to prevent water loss. Proteins in the cell compensate for the elevated salt concentration with an increased number of ion binding sites on non-active portions of the protein. This limits ion interference with binding at the active portion of the molecule.

Environments with extreme pH, either very low (below 3) or high (above 11), present challenges with ion management as well. These habitats include hot springs and hydrothermal vents, and some industrial wastes, such as acid mine drainage and coal spoils, are also highly acidic. Organisms in these environments face issues with cellular respiration, which involves moving electrons between molecules to generate energy. They have adapted by producing proteins that grab protons and electrons from the environment, giving cells more control over their proton and electron availability.

Microbes beyond our planet

Extremophiles help us understand life in Earth's harshest environments, but they also have applications beyond their unique habitats. Astrobiologists study extremophiles for their applications to the search for extraterrestrial life. The stresses faced by earthbound extremophiles are similar to those found on other planets, though extraterrestrial conditions are often turned up to the next level. Cold environments and extreme pressures are common, and radiation damage is particularly relevant, because many planets lack the protective atmosphere of Earth. Understanding how organisms survive these harsh conditions will help us predict what planets outside our solar system may contain life.

Extremophiles may also pave the way for terraforming other planets that humans might one day inhabit. The most promising candidates are the cyanobacteria. Not only can these organisms survive harsh conditions, they can also photosynthesize. Cyanobacterial colonization could lead to the same exponential increase in oxygen production that rapidly changed Earth's atmosphere billions of years ago, paving the way for the planet to eventually support humans.

Finally, understanding extremophiles is relevant for protecting our ecosystems here on Earth. Human activity has created and enhanced several extreme habitats, leading to an interest in the extremophiles that live there. Acidophiles proliferate in acid mine drainage. Metalloresistant and solvorsistant organisms can withstand high concentrations metals and industrial chemicals, respectively. Extreme oligotrophs, organisms that can live with very low nutrient concentrations, have become more prevalent as intensive agriculture depletes soil nutrients. Organisms isolated from these environments may be the key to removing the pollution found there. Whether studying ways to save the earth or possibilities of living beyond it, extremophiles are a vital component of understanding how organisms survive and adapt to the harshest environments.

Want to learn more about how extremophiles can be harnessed for industrial and remediation applications? AppliedMicrobio can help!