Parvularcula
Parvularcula bermudensis is a marine bacterium that was discovered in the western Sargasso Sea in 2003. The species is a Gram-negative, strictly aerobic, mobile bacteria. It requires sodium chloride (table salt) for the growth and thus is halophilic. On Marine agar it forms small, yellow - brown, hard colonies. The genome of the strain P. bermudensis HTCC2503 was completely sequenced in 2010.
Parvularcula bermudensis belongs to the class of Alphaproteobacteria, but differs from the known orders, so that it forms its own order " Parvularculales " within the Alphaproteobacteria. Within the order, the family " Parvularculaceae " the only family represents, with the only genus Parvularcula, so it is with the family and order a monotypical taxon.
- 2.1 Outer systematics
- 2.2 Internal systematics
- 2.3 Etymology
- 2.4 Discovery History
- 3.1 Literature
- 3.2 Notes and references
Features
Appearance
The cells of Parvularcula bermudensis are short rods, coccoid forms also occur. They are gram- negative. The cells are 0.6-1.8 microns long and 0.4-1.3 microns wide. The species is slightly motile by monopolar flagellum, that can move independently. Endospores are not formed.
On solid media, the cells grow to very small colonies, their diameter is between 0.3 and 0.8 mm. These are yellow to brown, appear opaque and are hard. In the plan, the colonies are round in shape with a clear boundary, viewed from the side convex. The colonies appear sunken into the surface of the nutrient medium.
Growth and metabolism
The metabolism of Parvularcula bermudensis based on the breathing, the species is strictly aerobic, that requires oxygen to grow. The oxidase test is positive, catalase can not be proven. Furthermore, the metabolism is marked as chemoorganotroph and heterotrophic, P. bermudensis uses organic compounds as an energy source as well as for the construction of cellular materials. The pH for best growth is 8.0. Growth occurs at pH values from 6.0 to 9.0. The optimum temperature for growth is 30 ° C. Growth is carried out within 10 to 37 ° C where it takes about 40 days at 10 ° C. until colonies are visible. P. bermudensis halophilic and grows in nutrient media containing 0.75 to 25% of sodium chloride (table salt). Optimal for growth is a level of 3.0% sodium chloride in the culture medium. For the cultivation of simple culture media are not suitable. Instead, marine agar are used, a nutrient medium that does not contain mineral salts in addition to peptone and yeast extract, which correspond in their composition of sea water.
Biochemical characteristics, such as the existing enzymes can be used bermudensis in a "colorful series" for the identification of P.. In addition to the negative catalase and oxidase - positive test, the following features can be used: It can reduce nitrate to nitrite, in this denitrification but no gas ( molecular nitrogen ) is formed. The urease test is positive, the type having the urease enzyme, and thus is capable of degrading urea. Gelatin is recovered by hydrolysis. However, it is not capable of Äskulinhydrolyse. It does not have the enzyme arginine dihydrolase (ADH ), and therefore, can not degrade the amino acid arginine. Of the indole test is negative.
As part of the chemoorgano - heterotrophic metabolism P. bermudensis can use many organic compounds as a carbon source, including carbohydrates ( pentoses, hexoses and oligosaccharides ), sugar alcohols and amino acids. For example, glucose is used under aerobic conditions, while no acid is formed, as would be typical for fermentation. Further usable are substrates such as D -arabinose, L- rhamnose, D-mannose, sucrose, D- cellobiose, D- maltose, D- melezitose, D -mannitol, D-sorbitol and myo -inositol, further, the amino acids glutamic acid, lysine, serine, leucine and isoleucine.
Carbohydrates, which can not be used, for example, D-ribose, D -xylose, D- galactose, D-fructose, L- sorbose, β -lactose, D -trehalose, D- melibiose and D- raffinose. Other organic compounds which can not utilize P. bermudensis include, inter alia, glycerin ( glycerol), adonitol, citrate, gluconate, lactate, D-malate, pyruvate and succinate.
Chemotaxonomic features
Parvularcula bermudensis produces pigments that belong to the group of carotenoids. Bacteriochlorophyll a ( a photosynthetic pigment) does not occur. The occurring in the membrane lipids fatty acids are molecules with an even number of carbon atoms ( C12 to C18 ) and one double bond ( monounsaturated fatty acids) or no double bond (saturated fatty acids). With 73% of mainly occurring fatty acid contributes the abbreviation C18: 1ω - 7c, and is referred to as cis- 7- octadecenoic acid or omega- cis- vaccenic acid.
Genetics
The genome of the bacterial strain P. bermudensis HTCC2503 was completely sequenced in 2010 and published in 2011. This is around the trunk, which was discovered in the western Sargasso Sea in 2003. The genome has a size of 2903 kilobase pairs (kb ), which is in about 60 % of the genome size of Escherichia coli and is as a circular bacterial chromosome ago. There are 2685 proteins annotated. The genome contains, inter alia, the genes for the biosynthesis of carotenoids and beta -lactamase, an enzyme, which can destroy the bacterium the antibiotic penicillin and related compounds. The GC content (the proportion of guanine and cytosine nucleic acid ) in the bacterial DNA is 61 mol percent. Previously, the nucleotides of the 16S rRNA were determined for phylogenetic studies, a typical representative for prokaryotes the ribosomal RNA.
Pathogenicity
Parvularcula bermudensis is non-pathogenic ( " pathogenic " ), it is by the Biological Agents in connection with the TRBA (Technical Rules for Biological Agents ) assigned 466 Risk Group 1.
System
Outer systematics
Sphingomonadales
Caulobacterales
Master HTCC2503
Not cultivated clone H9
A preliminary investigation of the 16S rRNA of the isolated strain HTCC2503 of Parvularcula bermudensis first showed that the strain belongs to the class of Alphaproteobacteria. Subsequently, the 16S rRNA sequence with known sequences of typical representatives of known at the time of the investigation six orders of Alphaproteobacteria was compared. The greatest similarity was found with Aminobacter aminovorans in order Rhizobiales and Silicibacter lacuscaerulensis in order Rhodobacterales. However, the phylogenetic differences were so clear that the investigated bacterial strains ( only the parent HTCC2503 still an environmental isolate with the term "non- cultured clone H9 " ) form a monophyletic group, which is considered as a separate order in addition to the Rhizobiales and Rhodobacterales.
P. bermudensis is one of several species of the genus Parvularcula. Due to the phylogenetic studies, a new one was established ( at the time of discovery, the seventh ) order " Parvularculales " within the Alphaproteobacteria. Within the order, the family " Parvularculaceae " the only family represents, with the only genus Parvularcula, so it is with the family and order a monotypical taxon. According to the classification of bacteria, the names are enclosed in quotation marks to show that these taxa have not been published yet valid or are not covered by the International Code of Nomenclature of Bacteria ( ICNB ).
From the genus following species are known (as of 2014):
- Parvularcula bermudensis Cho & Giovannoni 2003 ( the type species )
- Parvularcula dongshanensis Yu et al. 2013
- Parvularcula lutaonensis Arun et al. 2009
Inside systematics
From Parvularcula bermudensis synonyms are not known. The discovery of the species based on the examination of two bacterial strains. The logs are as HTCC2503 and HTCC2517 called and have the same phenotypic and genotypic characteristics. The strain P. bermudensis HTCC2503 is the type strain of the type He is also performed under the number ATCC BAA -594. We do several bacterial strains of P. bermudensis in various collections of microorganisms.
Etymology
The genus name is from the Latin word Parvularcula parvulus ("very small" ) and arcula ( " Jewel Box ", " jewel box" ) composed. The species name P. bermudensis refers to the type locality of the tribe in the Sargasso Sea, near Bermuda.
Discovery history
The species was first described by Jang- Cheon Cho and Stephen J. Giovannoni, 2003. They took in August 2001 near the Bermuda Islands at a depth of 10 m samples of sea water of the Atlantic Ocean. A variety of marine microorganisms can not easily be isolated by culturing on conventional solid media. For identification or taxonomic classification but pure cultures must be available.
Therefore, a special cultivation method was developed in the 1990s, which does not work with the usual culture media in microbiology, but with liquid media, the nutrients only in very low concentrations have (english extinction culturing ). For cultivation of bacteria from the sea of sterile sea water is used, the (0.001 %) is enriched with organic compounds in trace amounts. The sea water sample contained bacterial cells is added to this medium, and it produced a dilution series. The conditions for incubation are adapted to the natural habitat, such as through a dark environment, a constant temperature of 16 ° C and an incubation period of several weeks. The cell number is then determined by flow cytometry, and only the samples in which cells are found to be further investigated. At the beginning of the 21st century, this method was optimized using microtiter plates as high-throughput culturing (English high-throughput culturing, HTC). The microtiter plates, the volume required to be reduced while increasing the number of culture vessels, since such a disc usually comprising 48 or 96 wells. In this way, with little cost of materials, many studies perform. The by this method by Cho and Giovannoni recognized as positive samples were then cultured using the marine agar and further investigated the pure cultures and determined to be new species.