Yellowstone Acid Pools

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A mud pool at the Moose Pool in Yellowstone National Park. (29)


Yellowstone National Park located in the states of Wyoming, Montana, and Idaho is known for its great wildlife diversity as well as its unique geothermal features. One of the most prominent and interesting sites within the park are the acid pools. Their high acid levels and their great number of bacteria and microorganism diversity characterize these pools. Recently, the study of microorganisms within these pools have come into interest due to their unique biochemistry of coping with harsh conditions. These extremophiles have many useful applications to society and are especially important to other microbes inhabiting the same environment. Undoubtedly, the acid pools in Yellowstone National Park have become excellent tourist attractions and of scientific interest not only due to their bright and vivid colors, but also for the great diversity of microorganisms that inhabit this extreme environment.

Description of Niche


Most of these highly acidic geothermal pools can be found in areas near Norris Geyser Basin, including the superheated metal-rich Roaring Mountain Springs, as well as in the Mud Volcano and sulfur cauldron areas. Similar niches can also be found in the pyrite-rich (iron sulfides) acid mine drainages around the world, with one notable example located in the Iron Mountain Mine, California.

Physical Conditions

Norris Geyser Basin

Norris Geyser Basin comprises of three main areas: Porcelain Basin, Black Basin, and One Hundred Springs Plain. It is one of the most dynamic places in Yellowstone National Park because some of the pools here are some of the oldest, hottest and most acidic around. This thermoacidophilic niche is typically located in aquatic environments with high moisture content, including various geothermal hot springs and volcanic mud pools. The niche is adapted to highly acidic environments, generally with a pH of less than 4. Due to active volcanic activities in the area, the springs and pools in which the acidophilic niche is found are typically of fairly high temperature, usually ranging from 65 to 90 degrees Celsius. The niche is typically immersed in pools with high sulfur contents, either as hydrogen sulfide (H2S(g)) emitted as a volcanic gas, or as elemental sulfur crystals. Some niches are also found in pools rich with other metals, typically iron (1).

Green Dragon Springs
Green Dragon Springs, located in the general area of Norris Geyser Basin, is a highly acidic sulfate-chloride spring. Its spring water contains high amount of both organic carbon and inorganic molecules including hydrogen sulfide, ferrous (II) ions and arsenic (III) ions. The outflow channel of the spring also contains large amount of solid phase elemental sulfur. The temperature of the spring ranges from 66 – 73 degrees Celcius, and the pH is typically around 3 (31).
Roaring Mountain
North of Norris Geyser Basin, Roaring Mountain is a large acidic hydrothermal area with many fumaroles, or steam vents. Similar to all other acid pools, high levels of reduced inorganic molecules can be found in this area. It has an elevation of 2260 meters or 740 feet. With magma closest (1.6 to 2.2 km below surface) to the surface in this part of the park, it is the hottest part of Yellowstone National Park. The pH is typically below 2 and the temperature is around 40 degrees Celsius (16).

Mud Volcano and Sulfur Caldron

Mud volcano at Yellowstone National Park, Wyoming. The mud volcano is about 40 cm tall.(20)

The mud volcano and sulfur caldron areas, north of Yellowstone Lake, comprise the most acidic section of Yellowstone National Park. Mud pots are high-temperature geothermal hot springs or fumaroles of bubbling mud. The temperature of these areas, such as the Black Dragon Cauldron, can exceed 192 degrees Fahrenheit due to volcanic activities. The pH of these areas, such as in the case of sulfur caldron, can also be as low as 1.2, nearly identical to the pH of battery acid. The springs in the mud volcano and sulfur caldron area are generally sulfur and iron-rich: it contains suspended precipitates of FeS, which contribute to the distinct cloudy and gray color of the water. In addition, the area also has a distinct “rotten egg” smell that stems from the microbial metabolic byproduct of hydrogen sulfide gas (28).

Adjacent Communities

In the geothermal area of Yellowstone National Park, organisms can be observed along a horizontal temperature gradient from the hot, acidic waters through the cooler run off streams. At the run-off stream or periphery of pools, a range of dark green to orange communities seems to exist due to lower temperatures. These areas contain an array of brightly colored microbial mat communities. Typically, these are photosynthetic microbes and eukaryotic algae that thrive on varying conditions of light intensities giving rise to the characteristic colors of the pool. Adjacent geothermal springs, which contribute to warm temperature of the area, lead to occupation of a variety of species such as grasses, mosses, insects, and flowering plants (32).

Natural Changes on the Environment

The geothermal springs and pools of Yellowstone National Park, which is located in an active volcano, are dynamic areas with high degrees of environmental changes. The mud volcano and sulfur caldron areas are especially prone to such natural changes. One specific area of the mud pot region, the Churning Caldron, was initially a cool spring in which various microorganisms thrived. However, earthquakes in 1978 led to superheating of the area to a temperature of 164 degrees Fahrenheit, which also led to the death of most microbes living in the area (19). In addition, certain springs in the Norris Geyser Basin area carry out continuous dissolving and redepositing of rock, which lead to sealing off of the springs and later release of heated, pressurized water that can change nearby environments (30).

Who lives there?

Presence of Microbes


Thermoacidophiles are found at Yellowstone National Park, Wyoming.(23)

Thermoacidophiles are unique group of bacteria that are a combination of acidophiles and thermophiles. They belong to the kingdom of Archaebacteria and some of their features even resemble that of eukaryotes. Some notable thermoacidophiles include Sulfolobus and Acidithiobacillales ferrooxidans. Thermoacidophiles are characterized by their exclusive ability to live in both highly acidic environments and also high temperatures. The typical conditions these thermoacidophiles live under include pH at around 2 with temperatures ranging from 80 to 90 degrees Celsius. Most notably, these fascinating bacteria tend to live in some of the most extreme environments and they provide distinctive metabolism that is beneficial to both their own species and other microorganisms. Typically, thermoacidophiles tend to be anaerobic and chemolithotrophs. However, some of these extremophiles are aerobic and can obtain energy from organic sources. The combination of their unique metabolism such as sulfur oxidation coupled with their resistance to extreme conditions make thermoacidophiles a fascinating area of study in Yellowstone National Park.

Norris Geyser Basin

The eruption of Steamboat geyser in Norris Geyser Basin. (27)

Mycobacterium parascrofulaceum

This particular mycobacterium is found in the Norris Geyser Basin of Yellowstone Park. Temperatures within this environment range from 48 to 40 degrees Celsius. In addition, the pH levels (pH = 3.0) indicate that this environment is extremely acidic. The combination of both extreme temperatures and pH levels suggest that this particular mycobacterium is unique in their structure and adaptations. Normal mycobacterium can be fairly neutral and normal environments such as in drinking water and other water ecosystems. However, it long known that mycobacterium are able to survive in dire starvation leading to the notion that can adapt and flourish in extreme conditions and environments. Furthermore, tests have proved that mycobacterium parascrofulaceum possesses temperature resistance, as it was able to grow normally at temperatures reaching upward toward 56 degrees Celsius. Like other bacteria who reside in acidic and high temperature environments, mycobacterium parascrofulaceum can be classified as a thermoacidophile. (17)

Arsenite-Oxidizing Hydrogenobaculum

In the Norris Geyser Basin of Yellowstone National Park, an arsenite-oxidizing Hydrogenobaculum was isolated. This specific bacterium is categorized as a chemolithoautotroph meaning it uses inorganic material to synthesize essential reducing equivalents for biosynthesis. Indeed, the Hydrogenobaculum uses hydrogen gas as its sole energy source. Furthermore, the environment that this bacterium lives in can be categorized as both extreme temperature (55 to 60 degrees Celsius) and pH (pH = 3.0). It is interesting to note that the primary function for the arsenite oxidation capability of this bacterium is not fully understood yet. The ability to oxidize arsenic could be a detoxification mechanism that the bacterium employs or a mechanism for harvesting energy. An interesting result upon studying this particular bacterium reveals that addition of aqueous sulfide inhibits its ability to oxidize arsenite. This should be noted considering that Hydrogenobaculum live in a very acidic environment that contains aqueous sulfide. Another interesting metabolic mechanism found is the use of arsenite-oxizidizing Hydrogenbaculum. This unique redox reaction changes the aresenite levels in geothermic scource waters. The levels of arsenite (both As(III) and As(V)) change frequently when waters are mixed with each other. This Hydrogenbaculum also influence this change of arsenite levels with differing results. As(V) redox has been frequently observed when As(V) has been utilized as an electron acceptor for anaerobic or microaerobic respiration or as a part of a detoxification strategy. Another type of As(III) oxidation occurs which uses As(III) as a detoxification mechanism or as a source of energy to support growth. This type of detoxification mechanism is not yet fully understood. Another unique aspect was that the redox reactions were inhibited by H2S.(9)

Green Dragon Spring
Caldisphaera draconis and Acidilobus sulfurireducens
This highly acidic geothermal region, which is classified as a sulfate-chloride spring, is home to two novel chemoorganotrophic Crenarchaeal species that utilize anaearobic respiration: Caldisphaera draconis, which thrives at 70 – 72 degrees Celcius and pH 2.5 – 3.0, and Acidilobus sulfurireducen, which thrives at 81 degrees Celcius and pH 3.0. Both species carry out fermentation of simple and complex peptide-containing carbon, and are also capable of sulfur reduction. Metabolism via organic carbon fermentation coupled with sulfur reduction results in optimum growth of these organisms. The sulfur-reducing ability of these microbes is essential to the cycling of sulfur in the sulfur-rich geothermal springs.
Roaring Mountain
Sulfolobus acidocaldarius DSM639 project at Danish Archaea Centre by D.Janckovik and W.Zillig.(25)
Sulfolobus acidocaldarius
The extremely hot temperature and acidic conditions make this area a favorable environment for Sulfolobus acidocaldarius, a chemotropic archaea. It is considered a hyperthermophile because it likes temperatures as high as 90 degrees Celsius. These are colorless and spherical microorganisms with sulfur reducing capabilites(16). Since most extremely acidic pools contain relatively low concentrations of organic compounds and high concentrations of reduced inorganic compounds, such as hydrogen, sulfur, elemental sulfur, thiosulfate, or ferrous iron. The high inorganic compound content is essential as iron and sulfur oxidation are the primary energy source for chemotrophic microorganisms comprising this niche. Metabolism via oxidation of organic materials coupled with presence of sulfur results in optimum growth for many microbes. The ability of such bacteria to utilize sulfur is important for other microorganism cohabiting in the same environment. The reduced forms of sulfur from aqueous hydrogen sulfide provide essential electron donors and acceptors for the other microorganisms in their biosynthesis. In this sense, the byproducts of these sulfur-reducing bacteria provide important intermediates for the biochemistry of other microorganism that inhabit the same environment (8).

Mud Volcano and Sulfur Caldron

The acidic and sulfur-rich mud volcano and sulfur caldron area houses the thermoacidophile Sulfolobus acidocaldarius, which are also cohabiting the Norris Geyser Basin area.

The Effect of Metabolism on the Environment

Due to the unique formation of Yellowstone Park, elemental sulfur is abundant. Heterotrophic microorganisms take advantage of this elemental sulfur and as a result the oxidation of sulfur generates sulfuric acid. This is the primary mechanism that dramatically lowers the pH level in microsites or on the macro level which generates acid pools. (8) Also, the pools and springs are often converted into "mud" gradually due to the sulfur-oxidizing capability of the niche's microorganism: as hydrogen sulfide gas and atmospheric oxygen are oxidizied, the resulted sulfuric acid is incorporated into the spring water, and the highly acidic water, in addition to contributing to the low pH of the niche's environment, is capable of dissolving nearby rocks into mud. (10)

Presence of Non-microbes

Due to the high acidity of the pools at Yellowstone, very few non-microbes can survive using the methods of more simpler microbes. Although some insects can be found at some extreme environments, usually any environment with pH 4 or lower will support very few or none non-microbes. But there are a few non-microbes surviving in these environments possibly having a strong hydrogen pump or a low hydrogen permeable membrane. Acontium cylatium, Cephalosporium sp., and Trichosporon cerebriae, are three fungi that live near pH level of 0. Also, the characteristic colors of acid pools of red and green are from Cyanidium caldarium and Dunaliella acidophila which are also acidophiles that can live below pH 1. These acid-loving algae can be found at the base of Roaring Mountain where the acidic water reaches a cooler temperature.(12)

Microbial Interaction

A facultative intercellar gram-negative bacteria of the Legionella species, a known agent that causes a sometimes fatal type of pneumonia called Legionnarrie's disease , has been found at the acidic geothermal streams and pools which is uncommon. This bacteria has a parasitic relationship with phagocytic amoebae such as Naegleria, Acanthamoeba, and Hartmanella. These amoebae ingest the gram-negative bacteria while grazing. The Legionella survive the acidic conditions of the pools due to the protective environment of the host amoebae cells. The Legionella avoid the amoebae defense systems while multiplying within the vacuoles of the host cell. They eventually kill the host cell and return to the environment. But, in microbial biofilm communities, Legionella can survive as free-living organisms. (11)

Another microbial interaction between lysogenic viruses and bacteria is found from a bacteria species called Sulfolobus. This species is unique due to its ability to reduce sulfur and use it for energy and tolerate highly acidic environment. The lysogenic viruses infect and are able to survive the extreme environments using the protective bacteria. The natural ability of surviving in high acidic conditions of Sulfolobus makes it the perfect host for lysogenic viruses. (13)

Image above: A small mountain stream impacted by acid mine drainage, Prospect Gulch, Upper Animas River Watershed, Colo.(21)

Acid Mine Drainages

Acid mine drains located in various parts of the world are another environment that have come into interest in recent years. Acid mine drains can be found in many parts of the world including France, China, and North America. Primarily, scientists are concerned with the microbial diversity within these areas and their role in bioremediation and bioleaching. Acid mines are formed when abandoned mines, metal and coalmines in particular, are flooded with water creating a pool that becomes rich with minerals and metals. Upon the outflow from these the mines, the waters have become greatly acidic. As a result, many microorganisms and acidophiles, in specific, are attracted by the low pH of these waters and make their homes within these drains. Furthermore, the low concentration of oxygen within the mines lends to the proliferation of bacteria that are capable of surviving in anaerobic environments and also possessing the ability to oxidize metals such as iron. One particular important bacterium involved in bioleaching within acid mine drains is Acidithiobacillus ferrooxidans. Found in Carnoulès of southeastern France, this unique acidophile is been used as way of removing arsenic from the mine drains through bioleaching. Bioleaching is a novel and often-effective way of removing metals from the mines via bacteria. It is often used in acid mine drains as a way of removing certain metals from the area thus removing contaminants from the highly acidic water. However, in the process, the bacteria may produce toxic chemicals as a byproduct. Acidithiobacillus ferrooxidans utilizes iron oxidation as it’s primary source of energy and metabolism. Upon growing it on ferrous iron within the mine, Acidithiobacillus ferrooxidans is able to coprecipitate out arsenite from the mines. This significant ability now allows scientists and researchers to safely and easily removes arsenic from the acid water within the drains. Coupled with the ability to recycle bacteria easily, Acidithiobacillus ferrooxidans has become a microbe of great interest and importance. (15)


Yellowstone National Park is the largest natural geothermal area in the world with many colorful hot springs, acid pools, and microscopic life that are able to survive the extreme conditions. Due to the extreme heat and acidity in the Norris Geyser Basin and Mud Volcano area, few thermoacidophilic microoganisms have emerged with a specialized metabolism of using reduced inorganic molecules to adapt to their environment. Due to these specialized metabolism and natural causes, Yellowstone National Park is known for being the most changeable thermal area in the world. In addition, there are also acidophilic microbes being discovered in acid mine drainages in other parts of the world with the same capability of oxidizing metals. The overall survival capability of these extraordinary thermoacidophiles found in Yellowstone acid pools and acid mine drainages are of current scientific interest.

Current Research

Viral Phage as Mobile Genetic Material

The diversity of Sulfolobus spindled-shaped viruses (SSVs) and Sulfolobus islandicus rod-shaped viruses (SIRVs), which are virus types that are genus-specific for Yellowstone-dwelling Sulfolobus species, was monitored over a 2-year period of time. Comparison of amplified viral DNA sequences indicated that viral movement and immigration, rather than mutation, contributes to the high local population diversity even though the viral host sulfolobus is confined within specific geographic barriers (different thermoacidic pools). This result is significant as SSVs and SIRVs exhibit physical structures similar to that of bacteriophages and human viral pathogens. Researching of this rapid viral movement can provide significant information regarding virus circulation as well as the potential use of the viruses as mobile genetic material (4).

Image above: Virus Found within Boiling Acid Pool in Yellowstone National Park. (20)

Role of Viruses in Microbe Populations

The acid pools located in Yellowstone National Park are noted and distinctive due to their geothermal features. In specific, their high acidity and temperature give rise to a diverse and varied microbe population who possess unique capabilities. Recently, scientists have hypothesized that the virus population in these acid pools are actually responsible for controlling the microbe population. Most viruses would perish under the extreme environmental conditions that these acid pools present, however they find refuge within common bacteria such as Sulfolobus who are able to withstand the high acidity and temperature. By living within these host bacteria, viruses are able to continue to replicate and thrive under the harshest conditions. Furthermore, scientists have discovered that while microbe populations stay relatively constant between different acid pools, the population of viruses fluctuates tremendously. This observation suggest that the viruses somehow control the population of certain microbes within these acid pools. The next question scientists inquired concerned about how these viruses are able to relocate and migrate to different acid pools, which sometimes covered long distances. It has been recently proposed that the viruses travel through the steam that these pools produce as a result of extremely high temperatures. Right now, scientists have been committed to obtaining and unlocking the genomes of the many microorganisms that live within the acid pools in hopes of uncovering and understanding how they all interact with each other. (5)

Sulfur Levels Used to Predict Volcanic Activity

The Cinder Pool located in Yellowstone National Park is an acid-sulfate-chloride boiling spring in the Norris Geyser Basin. The Cinder Pool is unique in that it contains a molten layer of sulfur on the bottom of the pool. In addition, it has been discovered that the highest concentrations of thiosulfate and polythionate are found in the Cinder Pool compared to the other acid pools located in Yellowstone National Park. Moreover, scientists and researches are currently evaluating changes in the depth of the acid pool as well as the presence and significance of sulfur spherules. Researches have employed techniques including ion chromatography and colorimetric techniques in order to measure and observe the levels of sulfur spherules. Furthermore, researchers are investigating the use of sulfur and role of sulfur spherules such as polythionate and thiosulfate in the pathways of sulfur redox reactions. Studying these unique sulfur spherules are of great importance in helping monitor volcanic activity. More importantly, measuring the variation of polythionate can predict volcanic activity thus potentially helping warn residents who live near active volcanic sites. The different and variation of polythionate concentrations in the Cinder Pool may be applied to other acid crater lakes as well. (6)

Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridue and other thermoacidophilic archaea

Thermoacidophilic microorganisms, members of the Kingdom Archaea, have the extraordinary ability to survive and replicate at hot, acidic conditions. Researchers are pondering upon the mechanism utilize by these organisms to tolerate an extreme lifestyle. The experiment was based upon comparing known sequences of thermoacidophilic genera Picrophilus, Thermoplasma and Sulfolobus. After a series of comparison of genome sequences between transport proteins, energy metabolism, and genetic input via lateral gene transfer. The results revealed a high frequency of shared genes among thermoacidophiles, suggesting a high rate of lateral gene transfer. This further demonstrates that microorganisms that live in close proximity often exchange genes at a higher frequency, which contribute to the high ratio of secondary transport systems and high metabolic rates. These are important for the overall survival capabilities of thermoacidophilic microorganisms. More importantly, with the genome sequence of P. torridus known, more comparative and functional genome studies can be performed to help further understand the features that allow these organism to withstand very acidic conditions (7).

A ubiquitous obligate thermoacidophilic archaeon from deep-sea hydrothermal vents

The evolution of life that may exist on other planets can be best understood by examining how life evolves and survives in harsh environments. In the past, microbes found in hydrothermal vents lived in pH-neutral environments, but the findings have found that these microbes can also be tolerable to acidic conditions. Their findings confirmed that acidophile can flourish rapidly in the acidic condition, such as in hot springs and acid pools in Yellowstone National Park. The microbes discovered are named Aciduliprofundum boonei, which belongs to a special group of microbes called Archaea. They grow at a pH range of 3.3 to 5.8 and at temperatures of 55-75°C. These strains of microbes may be useful into many fields other than science. For example, in bio-mining, these microbes may help to extract metals from mine tailings. However, many uses of these microbes still await being studied (14).

Discovery of new photosynthetic antennae in bacteria.

A new genus and species of Cholorphyll-producing bacterium has been found in the hot springs of Yellowstone National Park in July of 2007. The new bacterium called Candidatus chloracidobacterium thermophilum found in the microbial mats in three hot springs of Yellowstone, is catagorized as a new genus and species. It is also in the family of Acidobacteria phylum, a poorly characterized phylum that were previous not known to have contained photosyntheic bacteria. This discovery marks as the first bacterium in Acidobacteria phylum to undergo photosynthesis. Although half of the earth's photosynthesis is performed by bacteria, only 5 of the major phyla of bacteria were known to contain members that photosynthesize. Candidatus choloracidobacterium thermophilum grows near cyanobacteria where there is light and oxygen near the surface of the microbiol mats. Possibly the most important find in Candidatus choloracidobacterium thermophilum is the presense of special light-harvesting antennae called chlorosomes which contain about 250,000 chlorophylls. No member of this group of bacteria or any other aerobic microbe has been found to have this structure. Strangely enough, acidophiles are usually found in environment with pH of less than 3, but this bacterium found in Yellowstone live in more alkaline environments with pH around 8.5. The mechanism and use of the new chlorosomes in this species are currently being researched. (24)


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16. Roaring Mountain

17. Ricardo Santos,* João Fernandes, Nuno Fernandes, Fernanda Oliveira, and Manuela Cadete. "Mycobacterium parascrofulaceum in Acidic Hot Springs in Yellowstone National Park." Applied and Environmental Microbiology, August 2007, p. 5071-5073, Vol. 73, No. 15







24. Don Bryant, David M. Ward, "Innovative Research Technique Reveals Another Natural Wonder in Yellowstone Park: A Unique, Photosynthesizing Life-Form" Science July 27, 2007.


26.Nation Master Encyclopedia



29. A mud pool of Moose pool at Yellowstone National Park.


31. S. Boyd, Robert A. Jackson, Gem Encarnacion, James A. Zahn. "Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park" Applied and Environmental Microbiology (2007)

32. National Park Service U.S.Department of the Interior

Edited by [Weiqin Fang, Ka Kong, Chasen Mock, Shin Trieu and Dae Yun Hwang], students of Rachel Larsen