Thursday, May 31, 2012

Ignicoccus islandicus, a species of archaea named by Karl Stetter

Ignicoccus islandicus is an archaea species living in marine hydrothermal vents such as those underwater fissures found in the Kolbeinsey Ridge north of Iceland, where this microbe was discovered (hence the epithet islandicus). Ignococci are hyperthermophiles. They are of great interest since they “play” host to even smaller archaea—some of the smallest organisms known: Nanoarchaeum equitans. These nano-sized microbes “sit”as parasites on the surface of ignicocci and also contain copies of parts of their host's genes within their own genome.

The World Register of Marine Species (WoRMS) provides data on the taxonomy of I. islandicus [1]:
Kingdom: Archaea
Phylum: Crenarchaeota
Class: Thermoprotei
Order: Desulfurococcales
Family: Desulfurococcaceae
Genus: Ignococcus
Species: I. islandicus (also in this genus: I. hospitalis, I. pacificus)

Tim Friend describes a presentation by German microbiologist Karl Otto Stetter at a conference in Yellowstone National Park (another hot spot of extremophile discoveries), during which Stetter talked about research on N. equitans, I. islandicus as well as the symbiotic (or parasitic) nanoarchaea-ignicoccus relationship:

Using the two-person research submersible Geo, samples were taken of sandy sediment and vent fluids at temperature around 90 degrees C [at the Kolbeinsey Ridge]. Black smoker samples obtained during a dive made on the submersible Alvin at a vent in in the Pacific also were analyzed. Initially, the samples from the mid-Atlantic ridge [Kolbeinsey Ridge] revealed a new genus and species of archaea, which Stetter named Ignicoccus islandicus. Electron microscopy photos taken at Stetter's lab of an additional Ignicoccus isolate revealed tiny strange spheres attached to its surface. This was shocking. No such thing had been seen on archaea. By culturing the organisms together Stetter was able to isolate Nanoarchaea then look for segments of its RNA. It does not possess the similar ribosomal RNA signature of other archaea. Tim Friend, 2007 [2].

Keywords: microbiology, nanobiology, hyperthermophile, crenarchaeon, nomenclature, taxonomy, history.

References and more to explore
[1] WoRMS taxon details: Ignicoccus islandicus Huber, Burggraf, Mayer, Wyschkony, Rachel & Stetter, 2000:
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pages 121 to 124.

Wednesday, May 30, 2012

An archaeum originally misclassified as bacterium: Sulfolobus acidocaldarius

The microbe Sulfolobus acidocaldarius was isolated from a hot spring in Yellowstone National Park in 1972 and originally misclassified as bacterium [1,2]. Thomas D. Brook and his team described the new genus Sulfolobus as sulfur-oxidizing bacteria with generally spherical cells producing frequent lobes—hence the term Sulfolobus. The isolated microbes were further characterized as acidophilic, living at an optimal pH of 2-3 and optimal temperatures of 70-75 °C—hence the epithet acidocaldarius. Microbes thriving at such temperatures are called hyperthermophiles.

About five years later the archaea domain was proposed by Carl Woese and George Fox. Following detailed genome studies, S. acidocaldarius was then taxonomically classified as belonging to the phylum or kingdom  crenarchaeota in the domain archaea. S. acidocaldarius serves now as a model organism for the Crenarchaeota and is used for many studies in archaeal biology [3,4].

Keywords: microbiology, hyperthermophile, crenarchaeon, nomenclature, taxonomy, history.

References and more to explore
[1] T. D. Brook, K. M. Brock, R. T. Belly and R. L. Weiss:  Sulfolobus: A new genus of sulfur-oxidizing bacteria living at pH and high temperature. Archives of Microbiology 1972, 84 (1), pp. 54-68. DOI: 10.1007/BF00408082.
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pages 110 and 111.
[3]  Microbe Wiki: Sulfolobus acidocaldarius [].
[4] L. Chen et al.: The genome Sulfolobus acidocaldarius, a model organism of the Crenarcheota. Journal of Bacteriology 2005, 187 (14), pp. 4992-4999 [].

Tuesday, May 29, 2012

Riding the fire sphere: Nanoarchaeum equitans

Nanoarchaeum equitans is one of the smallest living organisms known so far: a nano-sized (about 400 nm in diameter) microbe of the third domain,  named archaea [1-4]. The epithet equitans relates to the Latin nouns equus and equitatus, meaning “horse” and “horse riding,” respectively. N. equitans is too small to ride a horse: it is riding as a symbiont on other archaea in the genus Ignicoccus. Ignicocci (such as I.  islandicus and I. hospitalis) are sphere-shaped hyperthermophiles, (extremophiles, typically growing at 80 °C (176 F), but also at higher temperatures); hence the association that N. equitans is riding the fire sphere.

The symbiotic relationship between these two types of archaea has been described as N. equitans parasites attached to the surface of their Ignicoccus host. The parasites are living off the metabolism of its host. N. equitans lacks genes for its own metabolism, but possesses genes for DNA repair and reproduction. It has a highly compact genome—the smallest microbial genome sequenced to date [3,4].

N. equitans was discovered in 2002 by Karl Otto Stetter of the University of Regensburg (Bavaria, Germany), while exploring hydrothermal vents of the Kolbeinsey Ridge [1,2],  a stretch of the Mid-Atlantic Ridge named after a submarine volcano north of Iceland [5]. Stetter is responsible for the name Nanoarchaeum equitans.
Keywords: microbiology, nanobiology, archaeal kingdom Nanoarchaeota, hyperthermophile, crenarchaeon, nomenclature.

References and more to explore
[1] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007.
[2]  Microbe Wiki: Nanoarchaeum equitans [].
[3] E. Waters et al.: The genome of Nanoarchaeum rquitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA October 2003, 100 (22), pp. 12984-12988 [].
[4] K. S. Makarova and E. V. Koonin: Evolutionary and functional genomics of the Archaea. Curr. Opin. Microbiol. October 2005, 8 (5), pp. 586-594 [].
[5] Global Volcanism Program > Kolbeinsey Ridge:

Wednesday, May 23, 2012

The adjective postprandial, meaning “after eating a meal”

The adjective postprandial ist derived from the Latin noun prandium meaning “meal” or “breakfast.” Hence, postprandial means “after eating a meal” or “after having breakfast.” The adjective preprandial means the opposite—“before eating a meal.”

This adjective appears in medical terms such as postprandial hyperglycemia (high blood sugar after a meal) and postprandial hypotension (excessive decrease in blood pressure after eating) [1-3].

Your pre- and postprandial states are regulated by the two hormons ghrelin and leptin, telling your brain that you should eat and stop eating, respectively. In her review on the recent research of the bacterial network in human bodies, Jennifer Ackerman explains that the bacterium Helicobacter pylori, which thrives in the acidic stomach environment, is responsible for your ghrelin level: people with H. pylori experience a postprandial decrease in ghrelin, while those lacking the bacterium do not and continue to have appetite [4].  In other words: if you apply antibiotics to reduce H. pylori-induced ulcers, you are going to interfere with your postprandial hormon levels and your appetite and, hence, may gain weight. So, use your postprandial time wisely to plan your future eating and treating habits.

Keywords: Latin, terminology, nutritional planning, human body regulation, physiology, medicine.

References and more to explore
[1] Medical dictionary: postprandial []
[2]  Medscape Education: Introduction: Clinical significance of postprandial hyperglycemia [].
[3] Home Health Handbook: postprandial hypotension [].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

Monday, May 21, 2012

A gut bacterium named after Greek letters: Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a Gram-negative anaerobic microbe of the human intestinal tract [1].  The specific epithet of this scientific species name is derived from a combination of the three Greek letters theta, iota and omicron (see example in Names of species section in [2]). Curious about taxonomy, Mark Isaak provides amazing listings of diverse and interesting species and their sometimes odd names, but he admits he does not know why those letters were chosen to denote B. thetaiotaomicron [3].

Jennifer Ackerman writes that this term “sounds like it was named after a Greek sorority or fraternity” [4]. We still wonder why θ, ι and ο? More interesting than its name  is the role this bacterium plays in our intestinal tract. Ackerman reports the latest research results on how microbial genes benefit their human hosts and explains how B. thetaiotaomicron produces enzymes that are not encoded within the human genome. B. thetaiotaomicron “assists” us in digesting complex carbohydrates from plant foods: this bacterium “has genes that code for more than 260 enzymes capable of digesting plant matter, thus providing humans with a way to efficiently extract nutrients from oranges, apples, potatoes and wheat germ, among other food” [4]. B. thetaiotaomicron encodes more enzymes than there are Greek letters for.

Keywords: microbiology, microbial biorealm, nomenclature, terminology.

References and more to explore
[1] Microbe Wiki: Bacteroides thetaiotaomicron [].
[2] J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature   [].
[3] Mark Isaak: Curiosities of Biological Nomenclature [].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

Friday, May 18, 2012

Ochoa enzyme, named for the Spanish-American biochemist Severo Ochoa

The Ochoa enzyme is named for the Spanish-American biochemist Severo Ochoa (1905-1993), who was awarded the Nobel Prize in Physiology or Medicine 1959, jointly with Arthur Kornberg,  for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid [1-4].

Severo Ochoa was born in 1905 in Luarca, Spain, and died in Madrid in 1993. He worked, researched, taught and inspired others at various prestigious institutions in Spain, Germany and the Unites States [2].

The Ochoa enzyme, polynucleotide phosphorylase, was first isolated from the bacterium Azotobacter vinelandii [3]. The enzyme synthesizes RNA from ribonucleotide triphosphates. The Ochoa enzyme played a critical role in deciphering the genetic code: the American biochemist Marshall Nirenberg and Heinrich Matthaei (a postdoctoral researcher from the University of Bonn in Germany) used the Ochoa enzyme in the enzymatic synthesis of RNA, which they introduced into Escherichia coli [4,5]. Their work resulted  in an understanding of which three-nucleotide codon in a nucleic acid sequence specifies a particular single amino acid. Thanks to the Ochoa enzyme, they achieved the goal of the RNA Tie Club, whose members were corresponding with each other by amino-acid nicknames.

Keywords: history of science, biochemistry, enzymology, synthetic polynucleotides, mRNA sequences, proteins.

References and more to explore
[1] - The Official Web Site of the Nobel Prize: The Nobel Prize in Physiology or Medicine 1959 [].
[2] Ellen Dubinsky: Severo Ochoa (1905-1993). Washington University School of Medicine, Bernard Becker Medical Library [].
[3] Laurence A. Moran: Nobel Laureate: Severo Ochoa. October 1, 2008 [].
[4] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 69.
[5] Profiles in Science: The Marshall W. Nirenberg Papers [].

Thursday, May 17, 2012

Corresponding with an amino-acid nickname

Many of us are living and socially interacting with their nicknames. But can you image to use the name of an amino acid as your nickname—or worse, its associated three-letter code? That 's exactly what the members of the RNA Tie Club did  [1-3]: This club was founded in 1954 by the Russian physicist George Gamow, who was interested in the relationship between the molecular RNA structure and protein formation in living cells.

During the 1950s and 1960s it was “hot and hip” (in bioscience and beyond) to speculate about and gain insight into genetic information at the molecular level: the relation between the structure of the DNA strand with its four-letter code and the α-amino acids (see codes and names in different languages) that combine into proteins. Researchers started to realize that RNA, a single-stranded molecule, is playing a key role in this biomolecular translation procedure. To crack the genetic code—now known as the list of amino-acid-encoding three-letter codons of RNA (and DNA)—in a joint effort, the RNA Tie Club was formed. Its members included George Gamow, who was Ala for alanine, Sir Francis Crick (Tyr for tyrosine), James Watson (Pro for proline) and Sydney Brenner (Val for valine).

Each club member received a necktie with the double helix structure and a lapel pin showing his (no females involved) amino acid symbol (hence the club name). The club had 20 members, one for each amino acid of interest (the so-called standard amino acids) and four honorary members representing each nucleotide. Eight members won a Nobel Prize; but not for cracking the code. Ironically, Marshall Nirenberg and Heinrich Matthaei, the scientists who successfully deciphered the genetic code by clever experiments in 1961, were not members of the club. Obviously, the club gentlemen did not participate in the hands-on deciphering race as much as they enjoyed smoking, drinking, tie-binding and hypothesizing.   

 The last time I checked the Wikipedia RNA-Tie-Club page (, also see [2]) I found a table with all club members, their amino-acid designation and their training. Interestingly, only half of them were biologists or chemists, while the others came from a physics and mathematics background.

Keywords: history of science, biochemistry, molecular biology, scientific gentlemen's club, humor, anecdotes.

References and more to explore
[1] - The Official Web Site of the Nobel Prize: How the Code was Cracked. What Code? [].
[2] Power of the Gene > History of Genetics > The RNA Tie Club []. 
[3] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 68.

Wednesday, May 16, 2012

A term in microbiology: archaea, shortened from archaeabacteria to denote the third domain

In 1977, when Carl Woese and George Fox reformulated the prokaryote-eukaryote grouping as a result of their phylogenetic analysis based upon ribosomal RNA sequencing, they proposed three main branches for the tree of life: eubacteria (typical bacteria), archaebacteria (then only methanogenic bacteria) and urkaryotes that evolved into components of eukaryotic cells [1].  Now these three domains are named bacteria, archaea and eukarya, respectively. Animals, plants and fungi, for example, branch of as subdomains from the latter.

The name archaea was introduced in 1990 by Woese as a short form of the term archaeabacteria [2]. The intention further was to eliminate the bacteria connotation, since archaea significantly differ from “typical” bacteria.

Although the three-domain system finds wide acceptance today, this bacteriocentric scheme has also been critized since it fails to recognize cell symbiogenesis—a five-kingdom scheme has been suggested instead [3].

Archaea are now known to fill many places of our world (at least on Earth). They are thriving in harsh environments, but also in soils, swamps and animal colons. A peer-reviewed, open-access journal with the title Archaea exists in which research and review articles are published that cover topics in archaea biology, ecology and bioinformatics  [4].

Keywords: microbiology, three-kingdom system, phyla of life, taxonomy, nomenclature.

References and more to explore
[1] Carl Wose and George Fox: Phylogenetic structure of the prokarotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA November 1977, 74 (11), pp. 5088-5090 [].
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 60-61 and 86.
[3] Lynn Margulis and Karlene V. Schwartz: Five Kingdoms. Henry Holt and Company, New York, Third Edition 1998.
[4] Hindawi Publishing Corporation: Archaea [].

Tuesday, May 15, 2012

The word “prokaryote” in microbiology: a convenient classification term covering up knowledge gaps

The word prokaryote, sometimes spelled procaryote, is composed of the Greek roots pro and karyon for “before” and for “nut,” “seed” or “grain,” respectively. Within cytology contexts,  “grain” refers to the nucleus of a cell. Prokaryote literally means “before a nucleus,” describing a cell with no nucleus [1]. In contrast, an organisms consisting of cells with a nucleus is called eukaryote. The Greek prefix eu refers to a normal or well-composed condition.

The distinction between eukaryotic and prokaryotic cellular systems was first made in 1937 by the French biologist Edouard Chatton (1883-1947), who significantly contributed to our knowledge of single-celled protoctists such as ciliates and dinoflagellates and of mitotic cytology [2,3].

The paradigm of a simple prokaryote-eukaryote division has now been broken. In his book The Third Domain Tim Friend writes [3]: “Prokaryotes are a fabrication. They do not exist.” Friend reports that microbiologists Carl Woese and Norman Pace, known for their work on microorganism classification based on microbial RNA studies, “wish to rid microbiology entirely of the term prokaryote." This term was created as a matter of convenience and does not reflect how most current biologists depict the tree of life with its three main branches (domains) archaea, bacteria and eukarya (eucarya). Everything “non-eukarya” should not carelessly dumped into the “prokaryote basket”—and it doesn't have to with ever more sophisticated tools for molecular taxonomy becoming available.

Established terms rarely disappear completely.  The Principles of Modern Microbiology by Mark Wheelis [4], for example, surveys “procaryotic microbes” and focuses on the diversity of bacteria and archaea, introducing groups and lineages such as green-sulfur, green-nonsulfur, purple-nonsulfur, aerobic-sulfur and sulfate-reducing bacteria, deinococci, proteobacteria, gram-positive bacteria, cyanobacteria, spirochetes, chlamydia, euryarchaeotes, crenarchaeotes and nanoarchaeotes, just to name a few. Obviously, biodiversity is not a matter of having or not having a cell nucleus.  

Keywords: microbiology, prokaryote-eukaryote dichotomy, cell biology concepts, super-kingdoms, taxonomy, nomenclature.

References and more to explore
[1] wiseGEEK: What Are Prokaryotic Cells? [].
[2] Marie-Odile Soyer-Gobillard: Edouard Chatton (1883-1947) and the dinoflagellate protists: concepts and models. International Microbiology 2006, 9, pp. 173-177 [].
[3] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 60-61 and 75.
[4] Mark Wheelis:  Principles of Modern Microbiology. Jones and Bartlett Publishers, Sudbury, Massachusetts, 2008; pp.305-321.

Sunday, May 13, 2012

A term in physiology: piezolyte for an osmolyte whose cellular levels respond to hydrostatic and osmotic pressure

The term piezolyte derives from the Greek roots piezo and lytos, referring to something squeezed under pressure and something that is soluble or dissolved, respectively.  The “something”  is a special form of an osmolyte. An osmolyte, dissolved in intracellular liquid, regulates cell properties—mainly the cell's volume—in response to osmotic pressure. A piezolyte performs in response to both osmotic and hydrostatic pressure [1-3].

Piezolytes are organic molecules, which are found in organisms that live in shallow or deep water, where they experience hydrostatic pressure. Examples are the small molecule β-hydroxybutyrate (β-HB) and oligomers composed of β-HB units, identified as intracellular solutes in the deep-sea bacterium Photobacterium profundum [1].

Piezolytes have also been studied in crustaceans and sea cucumbers (down to 2,900 m) and in fish (down to 4,900 m), but it is not yet known how piezolytes perform in animals living at depths down to 10,000 m. The HADES (Hadal Ecosystem Studies) project includes expeditions into the hadal zone of the Kermadec trench near New Zealand and will examine how marine animals adapt to high pressures in the deep sea and which role piezolytes play in cells that grow and function above atmospheric pressures [3].  

Keywords:  biochemistry, microbiology, intracellular solutes, osmosis, marine science.

References and more to explore
[1] Deana Desmarais Martin, Douglas H. Bartlett and Mary F. Roberts: Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophiles 2002, 6, pp. 507-514 [].
[2] Paul H. Yancey: Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. The Journal of Experimental Biology 2005, 208, pp. 2819-2830 [].
[3] Jane J. Lee: Ocean's Deep, Dark Trenches to Get Their Moment in the Spotlight. Science April 13, 2012, 336 (6078), pages 141and 143. DOI: 10.1126/science.336.6078.141.

Saturday, May 12, 2012

A term in oceanography: “hadal zone” for deep-sea regions 6,000 meters below the surface

The hadal zone is the deepest zone of the ocean layering scheme. It is part of the abyssal zone that begins at  3,000 m below the ocean surface. The abyssal zone consists of the abyssopelagic zone (between 3,000 and 4,000 m), the hadalpelagic zone (between 4,000 and 6,000 m) and the hadal zone below 6,000 m [1,2]. Hadal ocean habitats are found, for example, in the Mariana Trench near the island of Guam (with Earth's deepest ocean-floor point almost 11,000 m below the surface) and the Kermadec Trench northeast of New Zealand.

The hadal zone is named after the Greek god Hades— the Lord of the Underworld and ruler of the dead [3]. Habitats of the hadal zone are dark and otherworldly, but not dead:  many fish and various marine invertebrate phyla are represented in this cold, high-pressure and oxygen-depleted or oxygen-devoid environment [4].

A Hadal Ecosystem Studies project, fittingly dubbed HADES, is planned for the next and the following years to explore the hadal life forms of the Kermadec Trench  [2]. Hadal high-tech tools (advanced imaging technology and a deep-driving Hybrid Remotely Operated Vehicle called Nereus) will play a major role in studying the biology and geology in the depth of the trench. HADES is an international collaboration with the goal to systematically study biodiversity and adaptions of life in deep ocean trenches [5].

Keywords:  marine science, expedition, ocean floor, Greek mythology.

References and more to explore
[1] The Hadal Zone Deep-sea Trenches, figure by Jeff Drazen, 2002 [].
[2] Jane J. Lee: Ocean's Deep, Dark Trenches to Get Their Moment in the Spotlight. Science April 13, 2012, 336 (6078), pages 141and 143. DOI: 10.1126/science.336.6078.141.
[3] N. S. Gill: Hades - Greek God of the Underworld. Guide [].
[4]  Nelson, R. 2009. "Deep Sea Biome" UntamedScience. Accessed May 13, 2012 [].
[5] Aberdeen scientists in major study of deep sea life. Communications Team, Office of External Affairs, University of Aberdeen [].

Thursday, May 10, 2012

Petri dish, named after German bacteriologist Richard Julius Petri

Petri dishes were named by German microbiologist Robert Koch (1843-1910) for his assistant Julius Richard Petri (1852-1921), who invented them [1-3]. In studying bacteria such as the one responsible for tuberculosis, Koch used Petri plates that were filled with nutritional agar developed by his wife. Petri dishes allow the growth of bacteria into colonies on solid medium under reproducible and sterile conditions.

Petri was trained as a physician, received his doctorate in medicine in 1876 and developed an interest in bacteriology under Koch's direction at the Kaiserliches Gesundsheitsamt,  the NIOSH version of  the German Empire (Deutsches Reich, 1871-1918). In addition to dish culturing, Petri developed a technique for producing copies of bacterial strains (cloning), still used today [2].

In his fascinating story of archaea and biotechnology,  Tim Friend highlights the role of petri dishes for identifying and studying microbes. The revolution of cultivating microorganisms in these culture dishes followed the invention of the microscope and preceded the more recent invention and evolution of polymerase chain reaction (PCR) technology for genetic fingerprinting [1].

Synonyms: Petri plate, cell culture dish.
French term: la boîte de Petri.
German term: die Petrischale.
Spanish term: la placa de Petri
Keywords: laboratory equipment, history of science, microbiology, bacteriology.

References and more to explore
[1] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 37.
[2] enotes: Petri, Richard Julius (1852-1921) [].
[3] science museum: Robert Koch (1843-1910) [].

Wednesday, May 9, 2012

A term in biology: hyperthermophile for an extremophile thriving above 60 °C

The noun hyperthermophile is composed of the Greek words hyperthermos and philos for “above,”    “hot” and “love,” respectively.  The corresponding adjective is hyperthermophilic. A hyperthermophile is a microbe that lives at temperatures we consider as hot or even more than hot.

The term hyperthermophile was coined in the 1980s by microbiologist Karl Stetter, who searched for organisms existing under extreme conditions, for example at or above boiling water [1]—conditions found at hot springs and deep-sea hydrothermal vents . Such organisms belong to the domains archaea and bacteria, which include diverse groups of extremophiles living in extreme environments. At the lower extreme of the liquid-water temperature scale are psychrophiles, which “love” frigid water and icy conditions.
Examples of hyperthermophiles can be found among bacteria species of the genus Aquifex such as Aquifex aeolicus (first obtained by K. Stetter and R. Huber) and Aquifex pyrophilus (obtained from the Kolbensey Ridge, north of Iceland) [2].

Hyperthermophiles build a subgroup of thermophiles. Some prokaryotes (cells that lack a nucleus) can grow at or above 60 °C (140 F): moderate thermophiles live between 50 and 60 °C, while hyperthermophiles typically grow at 80 °C (176 F), but also at higher temperatures [3]. The hyperthermophile Pyrolobus fumarii (a name packed with hot associations), living at 113 °C (235 F), had been the hot-temperature record holder for some time, but a tiny single-celled microbe was then discovered that survives a temperature of  121 °C—and, therefore, was named “Strain 121.” [4]. What a strange strain!

Keywords: microbiology, oceanography, astrobiology, biotechnology, archaea, tree of life, extraterrestrial life, upper temperature limit for life.

References and more to explore
[1] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 26-27.
[2] Aquifex:
[3] Earth science > Oceanography > Thermophiles and hyperthermophiles:
[4] Microbe from depths takes life to hottest known limit (press release, August 15, 2003, source:  National Science Foundation):

Sunday, May 6, 2012

A term in biology: psychrophile for cold-temperature microbe

The noun psychrophile refers to a cold-loving microorganism. This scientific term derives from the Greek words psychros and philos for “cold” and “love.” The corresponding adjective is psychrophilic.

The term cryophile, derived from the Greek word cryos for “cold” or “icy cold,” is often used as a synonym. Another synonym is rhigophile (for example, see page 21 in [1]). Cold conditions are those below the freezing point of water, under which organisms typically cannot access nutrients to efficiently sustain an existence such as being considered to be alive.

Psychrophiles are extremophiles, which live under extremely cold conditions (seen from a human viewpoint). Microbes that thrive in the other extreme, hot and very hot conditions, are called thermophiles and hyperthermophiles, respectively. Psychrophilic life forms include cold-adapted archaea that have been studied, for example, by the microbiologist Ricardo Cavicchioli at the School of Biotechnology and Biomolecular Sciences (University of New South Wales, Sydney, Australia), who collected species from the Antarctic [2].

Low-temperature conditions are also found in space and on celestial objects, including environments on planets and moons of the solar system. Therefore, astrobiologists are interested in cold-adapted microorganisms such as psychrophiles [3]. 

Keywords: microbiology, astrobiology, biotechnology, archaea, tree of life, extraterrestrial life, frigid temperatures.

References and more to explore
[1] M. Sc. Ahmed Abdel-Megeed: Psychrophilic degradation of long chain alkanes. Ph. D. Dissertation, Technical University Hamburg-Harburg, Germany, 2004 [].
[2] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; pp. 221-222.
[3] Teach Astronomy > Psychrophyles:

Saturday, May 5, 2012

A term in oceanography: brinicle for a salty ice stalactite

The term brinicle immediately raises associations with the words brine and icicle: a brinicle looks like an icicle and forms in cold or icy solutions of salt in water. Due to the fluid mechanics of cold, freezing seawater the overall form of a brinicle resembles more the shape of a tornado funnel than that of a straight, downward-pointing icicle.

Jeremy Berlin describes a brinicle descending about seven feet from the surface ice in antarctic waters, which was filmed by two British cameramen as it formed [1].  Ice stalactites look like they are out of a science fiction novel or computer animation, but they occur for real. American oceanographers Paul Dayton and Seelye Martin described them in 1971. Brinicles were successfully generated in a laboratory study by injecting cold, dense brine into an insulated tank of sea water held at its freezing point [2]. 

Sea water in polar regions, freezing at the ocean surface, can concentrate brine entrapments to very high salinities. Such brine pockets, which can have complex geometries, result into drainage tubes. When conditions are right, high-salinity drainage may descend as brine plume, “forming long, delicate, thin-walled hollow ice stalactites that on occasion can extend up to 6 m below the bottom of the sea ice ...” [3]

Brinicles are too slow forming to freeze anything in. There is no danger to submarines [1]. Brinicles are fragile and can be broken apart by currents as well as seals and divers. 

Keywords: fluid dynamics, frigid waters, seawater, dense brine.

References and more to explore
[1] Jeremy Berlin: In the frigid waters of Antarctica, briny tubes of ice can stretch down to the seafloor. National Geographic May 2012, 221 (5), pp. 30-31.
[2] Martin Seelye: Ice stalactites: comparison of a laminar flow theory with experiment. Journal of Fluid Mechanics 1974, 63, pp. 51-79. DOI: 10.1017/S0022112074001017.
[3] Austin Kovacs: Sea Ice. Part I. Bulk Salinity Versus Ice Floe Thickness. US Army Corps of Engineers - Cold Regions Research & Engineering Laboratory, CRREL Report 96-7, June 1996; Figure 3 [].