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? [www.wisegeek.com/what-are-prokaryotic-cells.htm].
[2] Marie-Odile Soyer-Gobillard: Edouard Chatton (1883-1947) and the dinoflagellate protists: concepts and models. International Microbiology 2006, 9, pp. 173-177 [www.im.microbios.org/0903/0903173.pdf].
[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.

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 [bartlettlab.ucsd.edu/Publications_files/Martin2002.pdf].
[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 [jeb.biologists.org/content/208/15/2819.full].
[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.

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 [cmbc.ucsd.edu/Students/Current_Students/SIO277/Trenches.pdf].
[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. About.com Guide [ancienthistory.about.com/cs/grecoromanmyth1/p/Hades.htm].
[4]  Nelson, R. 2009. "Deep Sea Biome" UntamedScience. Accessed May 13, 2012 [www.untamedscience.com/biology/world-biomes/deep-sea-biome].
[5] Aberdeen scientists in major study of deep sea life. Communications Team, Office of External Affairs, University of Aberdeen [www.abdn.ac.uk/news/archive-details-11844.php].

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) [www.enotes.com/richard-julius-petri-reference/richard-julius-petri].
[3] science museum: Robert Koch (1843-1910) [www.sciencemuseum.org.uk/broughttolife/people/robertkoch.aspx].

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

The noun hyperthermophile is composed of the Greek words hyper,  thermos 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: microbewiki.kenyon.edu/index.php/Aquifex.
[3] Earth science > Oceanography > Thermophiles and hyperthermophiles: accessscience.com/content/Thermophiles-and-hyperthermophiles/YB990490.
[4] Microbe from depths takes life to hottest known limit (press release, August 15, 2003, source:  National Science Foundation): www.astrobiology.com/news/viewpr.html?pid=12337.

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 [faculty.ksu.edu.sa/75164/Ph%20D%20Thesis/Thesis.pdf].
[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: www.teachastronomy.com/astropedia/article/Psychrophiles.

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 [www.dtic.mil/cgi-bin/GetTRDoc?Location=U2&doc=GetTRDoc.pdf&AD=ADA312027].