Extremophiles in biotechnology

Last updated November 04, 2024

Extremophiles in biotechnology is the application of organisms that thrive in extreme environments to biotechnology.

Extremophiles are organisms that thrive in the most volatile environments on the planet and due to their talents, they have begun playing a large role in biotechnology. These organisms live everywhere from environments of high acidity or salinity to areas with limited or no oxygen. Scientists show keen interest in organisms with rare or strange talents and in the past 20-30 years extremophiles have been at the forefront with thousands of researchers delving into their abilities.^[1] The area in which there has been the most talk, research, and development in relation to these organisms is biotechnology.

Scientists around the globe are either extracting DNA to modify genomes or directly using extremophiles to complete tasks.^[2] Thanks to the discovery and interest in these organisms the enzymes used in polymerase chain reaction (PCR) were found, making the rapid replication of DNA in the lab possible. Since they gained the spotlight researchers have been amassing databases of genome data for the hopes that new traits and abilities can be used to further biotechnical advancements. Everything from the biodegradation of waste to the production of new fuels is on the horizon with the developments made in the field of biotechnology. There are many different kinds of extremophiles with each kind favoring a different environment. These organisms have become more and more important to biotechnology as their genomes have been uncovered, revealing a plethora of genetic potential. Currently the main uses of extremophiles lies in processes such as PCR, biofuel generation and biomining, but there are many other smaller scale operations at play. There are also labs that have identified what they wish to do with extremophiles, but haven't been able to fully achieve their goals. While these large scale goals have not yet been met the scientific community is working towards their completion in hope of creating new technologies and processes.

Overview of extremophiles

Extremophile is the term that covers a large group of organisms, most prominently Archaeans, which have evolved to fill the niches of extremely inhospitable environments. Such environments include high or low temperatures, high levels of salinity, high or low pH levels, and areas where volatile chemicals are prominent. These organisms have made some of the most undesirable locations on the planet their home. A few examples of these locations include thermal vents at the bottom of the ocean, soda lakes, runoffs from chemical factories and the trash heaps of landfills.

There are 4 major types of extremophiles:

Thermophiles

Thermophilic extremophiles live in areas of extreme heat with the best example being geothermal vents at the bottom of the ocean. The benefit of these organisms lies in the polymers and enzymes produced within them as they are highly thermostable.^[3]^[2]

Halophilies

Halophilic extremophiles live in areas of high salinity such as solar salterns and soda lakes. Their ability to consume and thrive in areas of such salinity open up possible benefits such as inoculating crops in salt rich soils to help them grow. Another use found for them lies in their production of polymers used to make biodegradable plastics.^[2]

Methanogens

Methanogenic extremophiles live just about anywhere and are the most widespread. These organisms take various simple organic compounds and use them to synthesize methane as their source of energy. There are no other known organisms that use the synthesis of methane as a form of energy production.^[2]

Psychrophiles

Psychrophilic extremophiles have the ability to maintain high growth rates and enzyme activity at temperatures even as low as 0°C. This presents the possibility of utilizing enzymes found in these organisms in parallel to how thermophilic organism enzymes are used, but at low temperatures as opposed to high temperatures.^[4]

Having the ability to live in such harsh environment comes from the organisms traits and abilities that are coded into their genomes. Changes inherited over time via DNA have allowed these organisms to build up various resistances and immunities to the volatile nature of their homes.^[2] It is these traits that have scientists so fixated on extremophiles because the genes that allow for said abilities can be taken from extremophiles and used in various biotechnical processes. A good example of this would be how Taq Polymerase was isolated from the bacteria Thermus aquaticus and was then used to make the process of PCR possible.^[5] In some cases even the entire organism can be utilized due to how it functions in nature. A good example of this would be the use of methanogenic extremophiles to assist in the decomposition of waste. While only four major types of extremophiles are listed above, there are many more types that are not mentioned in this article.

Importance

A great deal of biological and chemical processes undertaken in laboratories take great stretches of time, are extremely delicate and tend to be costly. This is due to the fact that general biological enzymes, proteins and other various organic compounds have very specific requirements for them to function properly.^[6] These are generally moderate conditions and therefore are known as mesophilic. Catalysts that involve changes in temperature, salinity, or acidity can impact the mesophilic organic compounds and products within a given process which in turn negatively affects the outcome. To deal with this, scientists in the past had to use longer experimental pathways to meet the moderate conditions. This, as stated previously, extends the time it takes to perform experiments and processes as well as increases costs.^{[ citation needed ]}

To overcome this issue scientists have turned to extremophiles due to their natural abilities to handle extreme conditions. These abilities are linked to genes which can be isolated, extracted and replicated in the lab.^[6]^[7] With this, the genetic information can then be implanted in the given enzymes, polymers, proteases and other various organic compounds to give them desired resistance.^[3] This allows for biological and chemical processes to be completed rapidly as the careful, long winded strategies can be bypassed. Extremophiles, both themselves and their DNA, are helping scientists to optimize lengthy research techniques and processes.

Applications

PCR

The polymerase chain reaction (PCR) was developed in the 1980s by Kary Mullis.^[5] Mullis would later receive the Nobel Prize for his creation of this process in 1993. PCR uses one of the heat resistant enzymes found in the thermophile T. aquaticus to rapidly and efficiently make copies of specific strands of DNA. The small sample of the target DNA is added to a test tube along with DNA primers, DNA nucleotides, Taq polymerase, and a buffer solution.^[8] Once these five key parts are combined they can be put into a PCR thermocycler. In this device the mixture is exposed to a series of temperatures over and over again cycling between 94-95°C, 50-56°C, and 72°C. These three stages are known as the denaturing, annealing and extending stages. During the denaturing stage at 94-95°C the DNA chains separate allowing for new bonds to be made. Then during the annealing stage from 50-56°C primers attach to the single strands of DNA to prepare them for replication. Finally, the extending stage at 72°C the strands of DNA replicate as they would naturally as the DNA nucleotides are added reforming the double stranded helix.^[8] These stages are cycled through multiple times until the desired amount of DNA is obtained. Without the enzyme produced by T. aquaticus, Taq polymerase, this process would not be possible as the components would normally denature at such high temperatures.

Biofuel production

Fuels play a large part in everyday life in everything from driving a car and heating homes to large scale industrial processes and heavy machinery. As natural gases and fuels are being used up scientists have focused their gaze on possible replacements for said fuels. One way in which this is being done is through the utilization of various methanogenic and thermophilic strains of bacteria. These extremophiles in large quantities are able to take in various substances such as sugars, cellulose, and various waste products to produce methane, butanol and biodiesel.^[9] While butanol in high percentages would normally inhibit the growth and function of biological organisms, some bacterial strains, primarily thermophiles, have been engineered to handle butanol even in high concentrations. One of the more recent developments in this area is the discovery of extremophile strains of algae which can be used to produce biodiesel. Cyanidium caldarium is noted as one of the most promising strains due to the high lipid content of the biodiesel products it creates.^[9] While this application has not yet widely developed to large scale utilization, scientists working in this field hope to find an efficient and sustainable solution involving extremophiles soon.

Biomining

Through work with various extremophiles the technique of biomining was developed. Also known as bioleaching, the process involves the use of acidophiles in the removal of insoluble sulfides and oxides from various metals as they are mined from the earth.^[9] The normal process of heap leaching involves mixing mined metals with highly volatile chemicals such as cyanide. The process of bioleaching is noted as a safer approach to the mining process. Along with this it is also much better for the environment. With heap leaching comes the possibility of runoff and spills that would poison the environment as it seeps into the ground. With biomining this worry is reduced as the conditions can be easily maintained using thermophilic and acidophilic strains of bacteria.^[9] Not only has this process been noted as safer and more environmentally friendly, but is also able to extract more metal. Heap leaching has about a 60% extraction rate while bioleaching has seen rates up to 90%.^[9] So far gold, silver, copper, zinc, nickel, and uranium have been mined successfully using this process.

These three examples listed above are a few of the primary applications of extremophiles in biotechnology, but they are not the only ones. Other various applications that will not be fully described here include: carotenoid production, protease/lipase production, Glycosyl hydrolase production and sugar production.^[9] These secondary applications focus on the production of biological compounds that can be used within primary applications such as those listed above.

Future developments

Thanks to the increased interest in extremophiles the revolutionary technique of PCR was pioneered and brought the field of DNA study to the next level. Following this trend scientists in both biotech and industry want to push farther and find new ways to impact the scientific community. One way that is currently being studied is the production of plastics by halophilic extremophiles so that modern day oil-based plastics can become a thing of the past.^[6] This would bring biodegradable plastics to the world market, which in the long run is proposed as a way to help fight the world's garbage problem. Another advancement that scientists hope to make using these organisms is to increase the degradation of landfills around the world using methanogenic species that thrive on the organic compounds found there.^[10]^[1] Not only would this reduce waste, but the methane produced is hoped to be collected and used as an energy source. One other interesting future development lies in the field of medicine. Some biotechnical labs are looking into using extremophiles engineered to produce portions of viruses on their surface to elicit immune system responses.^[9] This would help train immune memory and antibody response to defend the body in case said virus ever attacks. While this is just a handful of examples there are many more advancements and developments being worked on using extremophiles in hopes of creating a better future.

Related Research Articles

An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.

The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA sufficiently to enable detailed study. PCR was invented in 1983 by American biochemist Kary Mullis at Cetus Corporation. Mullis and biochemist Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993.

A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between 41 and 122 °C. Many thermophiles are archaea, though some of them are bacteria and fungi. Thermophilic eubacteria are suggested to have been among the earliest bacteria.

Thermus aquaticus is a species of bacteria that can tolerate high temperatures, one of several thermophilic bacteria that belong to the Deinococcota phylum. It is the source of the heat-resistant enzyme Taq DNA polymerase, one of the most important enzymes in molecular biology because of its use in the polymerase chain reaction (PCR) DNA amplification technique.

Taq polymerase is a thermostable DNA polymerase I named after the thermophilic eubacterial microorganism Thermus aquaticus, from which it was originally isolated by Chinese female scientist Alice Chien et al. in 1976. Its name is often abbreviated to Taq or Taq pol. It is frequently used in the polymerase chain reaction (PCR), a method for greatly amplifying the quantity of short segments of DNA.

Thermus thermophilus is a Gram-negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C (149 °F). Thermus thermophilus was originally isolated from a thermal vent within a hot spring in Izu, Japan by Tairo Oshima and Kazutomo Imahori. The organism has also been found to be important in the degradation of organic materials in the thermogenic phase of composting. T. thermophilus is classified into several strains, of which HB8 and HB27 are the most commonly used in laboratory environments. Genome analyses of these strains were independently completed in 2004. Thermus also displays the highest frequencies of natural transformation known to date.

Pyrococcus furiosus is a heterotrophic, strictly anaerobic, extremophilic, model species of archaea. It is classified as a hyperthermophile because it thrives best under extremely high temperatures, and is notable for having an optimum growth temperature of 100 °C. P. furiosus belongs to the Pyrococcus genus, most commonly found in extreme environmental conditions of hydrothermal vents. It is one of the few prokaryotic organisms that has enzymes containing tungsten, an element rarely found in biological molecules.

<span class="mw-page-title-main">Thermostability</span> Ability of a substance to resist changes in structure under high temperatures

In materials science and molecular biology, thermostability is the ability of a substance to resist irreversible change in its chemical or physical structure, often by resisting decomposition or polymerization, at a high relative temperature.

Geobacillus stearothermophilus is a rod-shaped, Gram-positive bacterium and a member of the phylum Bacillota. The bacterium is a thermophile and is widely distributed in soil, hot springs, ocean sediment, and is a cause of spoilage in food products. It will grow within a temperature range of 30–75 °C. Some strains are capable of oxidizing carbon monoxide aerobically. It is commonly used as a challenge organism for sterilization validation studies and periodic check of sterilization cycles. The biological indicator contains spores of the organism on filter paper inside a vial. After sterilizing, the cap is closed, an ampule of growth medium inside of the vial is crushed and the whole vial is incubated. A color and/or turbidity change indicates the results of the sterilization process; no change indicates that the sterilization conditions were achieved, otherwise the growth of the spores indicates that the sterilization process has not been met. Fluorescent-tagged strains, known as rapid-read BIs, are becoming more common to verify sterilization, since the visible fluorescence appears in about one-tenth the time needed for pH-indicator color change and an inexpensive light sensor can detect the growing colonies.

Biomining refers to any process that uses living organisms to extract metals from ores and other solid materials. Typically these processes involve prokaryotes, however fungi and plants may also be used. Biomining is one of several applications within biohydrometallurgy with applications in ore refinement, precious metal recovery, and bioremediation. The largest application currently being used is the treatment of mining waste containing iron, copper, zinc, and gold allowing for salvation of any discarded minerals. It may also be useful in maximizing the yields of increasingly low grade ore deposits. Biomining has been proposed as a relatively environmentally friendly alternative and/or supplementation to traditional mining. Current methods of biomining are modified leach mining processes. These aptly named bioleaching processes most commonly includes the inoculation of extracted rock with bacteria and acidic solution, with the leachate salvaged and processed for the metals of value. Biomining has many applications outside of metal recovery, most notably is bioremediation which has already been used to clean up coastlines after oil spills. There are also many promising future applications, like space biomining, fungal bioleaching and biomining with hybrid biomaterials.

In taxonomy, Thermococcus is a genus of thermophilic Archaea in the family the Thermococcaceae.

In taxonomy, Staphylothermus is a genus of the Desulfurococcaceae.

Functional cloning is a molecular cloning technique that relies on prior knowledge of the encoded protein’s sequence or function for gene identification. In this assay, a genomic or cDNA library is screened to identify the genetic sequence of a protein of interest. Expression cDNA libraries may be screened with antibodies specific for the protein of interest or may rely on selection via the protein function. Historically, the amino acid sequence of a protein was used to prepare degenerate oligonucleotides which were then probed against the library to identify the gene encoding the protein of interest. Once candidate clones carrying the gene of interest are identified, they are sequenced and their identity is confirmed. This method of cloning allows researchers to screen entire genomes without prior knowledge of the location of the gene or the genetic sequence.

<span class="mw-page-title-main">Thomas D. Brock</span> American microbiologist (1926–2021)

Thomas Dale Brock was an American microbiologist known for his discovery of hyperthermophiles living in hot springs at Yellowstone National Park. In the late 1960s, Brock discovered high-temperature bacteria living in the Great Fountain region of Yellowstone, and with his colleague Hudson Freeze, they isolated a sample which they named Thermus aquaticus. "Life at High Temperatures", a 1967 article summarizing his research, was published in the journal Science and led to the study of extremophiles, organisms that live in extreme environments. By 1976, T. aquaticus was found useful for artificially amplifying DNA segments. Brock's discoveries led to great progress in biology, contributed to new developments in medicine and agriculture, and helped create the new field of biotechnology.

Thermococcus celer is a Gram-negative, spherical-shaped archaeon of the genus Thermococcus. The discovery of T. celer played an important role in rerooting the tree of life when T. celer was found to be more closely related to methanogenic Archaea than to other phenotypically similar thermophilic species. T. celer was the first archaeon discovered to house a circularized genome. Several type strains of T. celer have been identified: Vu13, ATCC 35543, and DSM 2476.

Methanocaldococcus jannaschii is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon, and third organism, to have its complete genome sequenced. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.

Acidithiobacillus caldus formerly belonged to the genus Thiobacillus prior to 2000, when it was reclassified along with a number of other bacterial species into one of three new genera that better categorize sulfur-oxidizing acidophiles. As a member of the Gammaproteobacteria class of Pseudomonadota, A. caldus may be identified as a Gram-negative bacterium that is frequently found in pairs. Considered to be one of the most common microbes involved in biomining, it is capable of oxidizing reduced inorganic sulfur compounds (RISCs) that form during the breakdown of sulfide minerals. The meaning of the prefix acidi- in the name Acidithiobacillus comes from the Latin word acidus, signifying that members of this genus love a sour, acidic environment. Thio is derived from the Greek word thios and describes the use of sulfur as an energy source, and bacillus describes the shape of these microorganisms, which are small rods. The species name, caldus, is derived from the Latin word for warm or hot, denoting this species' love of a warm environment.

Persephonella marina is a Gram-negative, rod shaped bacteria that is a member of the Aquificota phylum. Stemming from Greek, the name Persephonella is based upon the mythological goddess Persephone. Marina stems from a Latin origin, meaning "belonging to the sea". It is a thermophile with an obligate chemolithoautotrophic metabolism. Growth of P. marina can occur in pairs or individually, but is rarely seen aggregating in large groups. The organism resides on sulfidic chimneys in the deep ocean and has never been documented as a pathogen.

<span class="mw-page-title-main">Thermostable DNA polymerase</span> DNA polymerases that originate from thermophiles

Thermostable DNA polymerases are DNA polymerases that originate from thermophiles, usually bacterial or archaeal species, and are therefore thermostable. They are used for the polymerase chain reaction and related methods for the amplification and modification of DNA.

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