How Extremophiles Push the Limits of Life

March 13, 2023

Bacteria in Yellowstone caldera.
Bacterial mats, golden brown in color, seen on the outer edges of 2 different chromatic Beauty Pool’s in Upper Geyser Basin of Yellowstone caldera, Wyoming.
Source: ASM Microbe Library
Thomas Brock, a famous professor of microbial ecology, was visiting Yellowstone National Park in July 1964 when he observed distinct color patterns at the hot springs. The colors formed a unique band in the water, the result of temperature gradients that formed when hot water gradually cooled as it moved away from its source. While the vibrant colors at the hot springs were quite striking in their appearance, even more remarkable to Brock was the fact that there appeared to be distinct microbial colonies in these temperature gradients. Some microbial colonies were present in water reaching temperatures as high as 80℃.

Brock was intrigued by this observation and, together with his undergraduate student Hudson Freeze, analyzed samples from the microbial biomass at the springs. These analyses revealed the presence of proteins, but not chlorophyll, a major photosynthetic pigment in both plants and photosynthetic microbes. Brock and Hudson took this to mean that these had to be bacteria and went on to call them “hyperthermophiles” (extreme heat lovers).

Subsequently, they went on to isolate a new bacterium—Thermus aquaticus, which can survive in temperatures of 60-80℃. The discovery of such extremophiles changed scientists’ way of looking at life, as the microbes were found in environments where nobody expected life to survive, let alone thrive. Studies on extremophiles have since reshaped some of our ideas on the origin, fundamental features and limits of life. Extremophiles also help unravel how metabolism can be altered by living cells when faced with adverse conditions.

Microbes are Everywhere

The discovery of T. aquaticus prompted scientists to explore the mechanisms that enable microbes to survive in such extreme environments. Subsequently, other microbes were discovered that lived in different types of harsh environments: very cold (psychrophiles), acidic (acidophiles), alkaline (alkaliphiles), salty (halophiles), high pressure (piezophiles/barophiles), heavy metal-concentrated (metalophiles) and sunlight-deprived environments.

Some microbes are adapted to survive more than one type of extreme environment, earning them the name ‘polyextremophiles.’ Hot springs, for example, are not only incredibly warm, but can also be highly acidic or alkaline, whereas the deep sea features both extreme cold and high pressure. Microbes that have adapted to live in these environments have developed ways to thrive under multiple prominent stressors.

Some Like it Hot, Some Like it Cold

What enables life to sustain itself in such extreme conditions? Several extremophiles contain unique biomolecules that are relatively stable in extreme temperatures and enable metabolic reactions to proceed unhindered. Thermophiles have enzymes known as thermozymes, which are catalytically active at high temperatures. Surprisingly, amino acid contents, protein sequences and the structure of thermozymes are quite similar to mesophilic enzymes, which function optimally between (25 and 35 °C). Moreover, thermozymes retain their functionality when cloned into mesophiles, suggesting that the thermophilic ability is encoded in the DNA sequence. Structural features in these enzymes, such as unique salt bridges, extensive hydrogen bonding and hydrophobic interactions are thought to function as stabilizing forces that enable their thermophilicity.

Thermophilic cyanobacteria growing down the side of the geyser cone of the Yellowstone caldera.
(A) Golden brown thermophilic cyanobacterial mat, morphology was mucoid/slimy, seen in the run-off water pool surrounding one of the geyser cones (B) in Upper Geyser Basin.
Source: ASM Microbe Library

Similarly, psychrophiles have special enzymes adapted to function in cold conditions. These enzymes retain their catalytic activity by allowing extensive structural flexibility. Through crystallographic studies and proteome analyses, these proteins were found to have reduced number of ion pairs, lowered interactions within subunits, clustered glycine residues and a greater accessibility to the active site. These features significantly reduce the activational energy required to perform at low temperatures, while also allowing conformational changes that retain the catalytic activity of the enzymes. Further, antifreeze proteins that bind to ice and lower the surface temperature to permit microbial growth are another special adaptation psychrophiles possess.

Surviving it All: Salt, Pressure and Radiation-Loving Microbes

Red colonies of a Halomicrobium sp. cultured from rock salt. Colonies are approximately 1 mm in size.
Colonies of Halophilic Archaea.
Source: ASM Microbe Library
Halophiles utilize interesting strategies to negate the effects of high salt concentrations in their environment. Some halophiles accumulate sodium ions in the cytoplasm, while others accumulate potassium chloride to combat the osmotic pressure of salt stress. Halophiles are also able to tightly regulate ion-mediated homeostasis, and adjust their plasma membrane fluidity to counter oxidative stress. Gene duplications were observed for certain genes that were involved in mitigating salt stress, conferring the ability to these microbes to survive in saline environments.

Piezolytes, molecules that stabilize cell proteins against high pressure, are an important component of microbes encountering high hydrostatic pressures. Piezotolerant bacteria, like Myroides profundi, assimilate trimethylamine, a N-compound found abundantly in the ocean, and metabolize it to trimethylamine oxide. Trimethylamine oxide functions as a piezolyte and helps the cell to grow and survive in hydrostatic environments. Piezophiles produce an abundance of polyunsaturated fatty acids that help stabilize the cell membrane against pressure. The presence of antioxidant proteins is an additional mechanism for survival.

Radiophiles are yet another unique class of microbes that can survive harmful radiation. Primarily belonging to Deinococcaceae family, these microbes can survive intense doses of gamma radiation (3,000 times more than what can kill humans). Several hypotheses have been postulated to explain this unique ability, but the complete picture is still missing. Initially, researchers attributed the radiophily to highly accurate DNA repair mechanisms. However, further studies established that Deinococcaceae members can regulate their metabolism by expressing cellular detoxifying genes. Further, some radiophiles synthesize small-molecule proteome shields that prevent protein degradation under radiation. In recent years, research on Deinococcus radiodurans has revealed the synthesis of novel proteins that are intrinsically resistant to oxidative damage. Unlike thermophily, the radiophilic abilities of these microbes appear to be multivariate since the genes from Deinococcaceae, when expressed in other organisms, did not confer protection from radiation.

Fundamental and Applied Relevance of Extremophiles

Enhancing Phylogenetic Studies

Extremophiles present interesting possibilities for studying life in diverse environments. Extremophiles belong to all 3 domains in the tree of life, i.e. archaea, bacteria and eukaryotes (algae and fungi). However, a large proportion of extremophiles belong to archaea, and several extremophiles are closely related to the “universal ancestor” of life. As a result, extremophiles occupy an important position in evolutionary phylogenetic studies.

Providing Clues About Possible Life in Space

Since hyperextremophiles inhabit conditions that are inhospitable to most life, they have been considered as models for extraterrestrial life. Researchers have been investigating the microbial life of sites like the Yellowstone National Park, Antarctica and the Dead Sea to isolate them. For example, a strain of the archaeon Methanopyrus, isolated from a “black smoker” hydrothermal vent grows at temperatures of 120℃, while another microbe Picrophilus can be present in conditions where the pH is as low as 0.06, such as solfataric lakes in Japan from where it was isolated. Such microbes could hold clues to understanding how life might potentially survive in other planets. Very recently, researchers discovered traces of life in geological samples in the Atacama Desert in Chile. These samples, known as the “Red Stone,” contained hematite and were geologically analogous to Martian soil. Interestingly, none of the life forms discovered could be properly classified phylogenetically. Researchers conclude that looking at extremophiles on Earth could give a better clue for addressing whether similar life existed some time ago on Mars and other planets.

Polymerizing Chain Reactions 

Apart from imparting fundamental knowledge of life at the extremes, extremophiles are also relevant for several important biotechnological applications. For example, the polymerase chain reaction (PCR), an experimental technique that is so indispensable today in the fields of medicine, industrial biotechnology and genetics, owes itself to T.aquaticus. The Taq polymerase, so far unique to T. aquaticus, is the catalytic enzyme required for PCR reactions, which makes Brock’s discovery of T. aquaticus even more remarkable.

Applications in Industrial Biotechnology

Similarly,  the performance of enzymes in extreme conditions have made them suitable alternatives to labile mesophilic enzymes in industrial biotechnology. The enzyme proteolysin, which can help in remedying organic solid wastes is obtained from Coprothermobacter proteolyticus. This enzyme can operate in a wide pH and high temperature range in the presence of organic solvents and detergents that usually destroy enzyme activity. Enzymes like β-galactosidase, which are obtained from Halorubrum lacusprofundi, a psychrophile has a lot of value towards the production of oligosacchrarides. Several molecules have been identified in extremophiles that have antibioticanticancer and antioxidative properties, and efforts are underway to produce them commercially.

The  physiological adaptations in extremophiles are intensely diverse, and together with their applications, extremophiles are a valuable sustainable resource that have important roles to play in a bio-based economy.

What do extremophiles, space microbes and “out-of-this-world” science have in common? They’ll all take center stage, as Andy Weir, author of New York Times Bestsellers, The MartianArtemis and Project Hail Mary, joins at ASM Microbe 2023 as the inaugural Science and Society Keynote Lecturer.

Author: Kartik Aiyer, Ph.D.

Kartik Aiyer, Ph.D.
Kartik Aiyer, Ph.D., is a reseracher at Center for Electromicrobiology at Aarhus University, where he is currently investigating cable bacteria.