A term in aquatic microbiology: picocyanobacteria

Picocyanobacteria (plural of picocyanobacterium) are tiny cyanobacteria—less than two micrometers in size [1].  The prefix pico is derived from the Italian word piccolo for small. The size of picocyanobacteria cells is smaller than that of typical cyanobacteria cells, which ranges from one to forty micrometers [2].

Picocyanobacteria occur in freshwater and marine environments. They are photosynthetic organisms. Their diversity and distribution in dependence on light penetration through water layers and also on other factors is of great interest in ecology. For example, the abundance and composition of picocyanobacterial assemblages has been studied in many lakes of varying trophic state in relation to biomass and dissolved matter [3,4]. A two-year flow-cytometry investigation and in situ experiments in Lake Tahoe revealed seasonal patterns and clear temporal and spatial partitioning between picophytoplankton communities (picocyanobacteria and picoeukaryotes) [4].

Picocyanobacteria are the dominant microbes in the sunlit epipelagic zone of open oceans [5,6]. According to Tim Friend, “these little guys are of tremendous ecological importance” [5].  He informs that various institutions and research centers began sequencing the genomes of marine picocyanobacteria in 2003. Insight in picocyanobacterial metabolisms is critical for our understanding of global environmental and climate changes. Picocyanobacteria species—for example, those in the Synechococcaceae family—have an important role in carbon fixation and nutrient cycling in diverse marine ecosystems [7].

Keywords: marine microbiology, nanobiology, limnology, oceanography, microbial ecology, terminology.

References and more to explore
[1] Wiktionary: picocyanobacterium [en.wiktionary.org/wiki/picocyanobacterium].
[2] Cyanobacteria: huey.colorado.edu/cyanobacteria/about/cyanobacteria.php.
[3] F. R. Pick: The abundance and composition of freshwater picocyanobacteria in relation to light penetration. Limnol. Oceanogr. 1991, 36 (7), 1457-1462 [www.jstor.org/stable/2837651].
[4] Monika Winder:  Photosynthetic picoplankton dynamics in Lake Tahoe: temporal and spatial niche partitioning among prokaryotic and eukaryotic cells. J. Plankton Res. 2009, 31 (11), pp. 1307-1320 [plankton.ucdavis.edu/pdf/Winder_JPR09.pdf].
[5] Tim Friend: The Third Domain. The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press, Washington, D.C., 2007; page 143.
[6] The Darwin Project: Selective pressures on picocyanobacterial nitrogen use [darwinproject.mit.edu/?page_id=16].
[7] S. Huang, S. W. Wilhelm, H. R. Harvey, K. Taylor, N. Jiao and F. Chen: Novel lineages of Prochlorococcus and Synechococcus in the global oceans. The ISME Journal 2012, 6, pp. 285-297. DOI: 10.1038/ismej.2011.106.

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:
www.marinespecies.org/aphia.php?p=taxdetails&id=573489.
[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.

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 [microbewiki.kenyon.edu/index.php/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 [www.ncbi.nlm.nih.gov/pubmed/15995215].

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 [biowiki.kenyon.edu/index.php/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 [www.ncbi.nlm.nih.gov/pmc/articles/PMC240731].
[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 [www.ncbi.nlm.nih.gov/pubmed/16111915].
[5] Global Volcanism Program > Kolbeinsey Ridge: www.volcano.si.edu/world/volcano.cfm?vnum=1705-01=.

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 [www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=postprandial]
[2]  Medscape Education: Introduction: Clinical significance of postprandial hyperglycemia [www.medscape.org/viewarticle/491410].
[3] Home Health Handbook: postprandial hypotension [www.merckmanuals.com/home/heart_and_blood_vessel_disorders/low_blood_pressure/postprandial_hypotension.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

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 [microbewiki.kenyon.edu/index.php/Bacteroides_thetaiotaomicron].
[2] J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature   [www.bacterio.cict.fr/foreword.html].
[3] Mark Isaak: Curiosities of Biological Nomenclature [www.curioustaxonomy.net/etym/acronyms.html].
[4] Jennifer Ackerman: The Ultimate Social Network. Scientific American June 2012, 306 (6), pp. 36-43. DOI: 10.1038/scientificamerican0612-36.

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] Nobelprize.org - The Official Web Site of the Nobel Prize: The Nobel Prize in Physiology or Medicine 1959 [www.nobelprize.org/nobel_prizes/medicine/laureates/1959].
[2] Ellen Dubinsky: Severo Ochoa (1905-1993). Washington University School of Medicine, Bernard Becker Medical Library [beckerexhibits.wustl.edu/mig/bios/ochoa.html].
[3] Laurence A. Moran: Nobel Laureate: Severo Ochoa. October 1, 2008 [sandwalk.blogspot.com/2008/10/nobel-laureate-severo-ochoa.html].
[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 [http://profiles.nlm.nih.gov/ps/retrieve/Narrative/JJ/p-nid/22].