Parvularcula bermudensis
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| Cho & Giovannoni , 2003 |
Parvularcula bermudensis is a marine bacterium that wasdiscovered in2003 in the western Sargasso Sea . The species is a gram-negative , strictly aerobic , motile bacterium. It needs sodium chloride (table salt) for growth and is therefore halophilic . Itforms small, yellow-brown, hard colonies on marine agar . The genome of the P. bermudensis HTCC2503strainwas 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" represents the only family with the only genus Parvularcula , so the family and the order are a monotypical taxon .
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 μm long and 0.4-1.3 μm wide. The species is weakly motile due to a monopolar flagella , so it can move independently. Endospores are not formed.
On solid culture media , the cells grow into very small colonies , their diameter is between 0.3 and 0.8 mm. These are yellow to brown in color, appear opaque and are hard. When viewed from above, the colonies are round in shape with a clear border, and when viewed from the side they are convex. The colonies appear sunken in the surface of the nutrient medium.
Growth and metabolism
The metabolism of Parvularcula bermudensis is based on breathing , the species is strictly aerobic , so it needs oxygen to grow. The oxidase test is positive, catalase cannot be detected. Furthermore, the metabolism can be characterized as chemoorganotrophic and heterotrophic , P. bermudensis uses organic compounds as an energy source and also to build up cellular substances. The pH for best growth is 8.0. Growth occurs at pH values between 6.0 and 9.0. The optimal temperature for growth is 30 ° C. Growth occurs within 10 to 37 ° C, whereby it takes about 40 days at 10 ° C before colonies are recognizable. P. bermudensis is halophilic and grows in nutrient media that contain 0.75 to 25% sodium chloride (table salt). A content of 3.0% table salt in the nutrient medium is optimal for growth. For cultivation simple culture media are not suitable. Instead, you can use marine agar, a nutrient medium that, in addition to peptone and yeast extract , also contains mineral salts with a composition similar to that of seawater .
Biochemical features, such as the enzymes present, can be used in a “colorful row” to identify P. bermudensis . In addition to the negative catalase and positive oxidase tests , the following features can be used: It can reduce nitrate to nitrite , but this denitrification does not produce any gas (molecular nitrogen ). The urease test is positive, the species has the enzyme urease and is therefore able to break down urea . Also, gelatin is hydrolysis recycled. However, it is not capable of aesculin hydrolysis . It does not have the enzyme arginine dihydrolase (ADH) and therefore can not break down the amino acid arginine . The indole test is negative.
In the context of chemoorgano-heterotrophic metabolism, P. bermudensis can use numerous 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 without the formation of acid, as would be typical for fermentation . Other usable substrates are e.g. B. D - arabinose , L - rhamnose , D - mannose , sucrose , D - cellobiose , D - maltose , D - melezitose , D - mannitol , D - sorbitol and myo-inositol , furthermore the amino acids glutamic acid , lysine , serine , leucine and isoleucine .
Carbohydrates that cannot be used are, for example, D - ribose , D - xylose , D - galactose , D - fructose , L - sorbose , β- lactose , D - trehalose , D - melibiose and D - raffinose . Other organic compounds that P. bermudensis cannot utilize include: a. 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 photosynthesis pigment) does not occur. The fatty acids found in the membrane lipids are molecules with an even number of carbon atoms (C 12 to C 18 ) and a double bond ( monounsaturated fatty acids ) or no double bond (saturated fatty acids). The fatty acid, which is mainly found at 73%, has the abbreviation C 18: 1 ω-7 c and is referred to as cis -Omega-7-octadecenoic acid or cis - vaccenoic acid .
genetics
The genome of the bacterial strain P. bermudensis HTCC2503 was completely sequenced in 2010 and published in 2011. This is the strain that was discovered in 2003 in the western Sargasso Sea. The genome has a size of 2903 kilobase pairs (kb), which is about 60% of the genome size of Escherichia coli and is present as a circular bacterial chromosome . There are 2685 proteins annotated . The genome contains u. a. Genes for the biosynthesis of the carotenoids and for a beta-lactamase , an enzyme with which the bacterium can destroy the antibiotic penicillin and related substances. The GC content (the proportion of nucleic acids guanine and cytosine ) in the bacterial DNA is 61 mol percent. Previously, the nucleotides of the 16S rRNA , a typical representative of ribosomal RNA for prokaryotes , were determined for phylogenetic studies .
Pathogenicity
Parvularcula bermudensis is not pathogenic (“pathogenic”), it is assigned to risk group 1 by the Biological Agents Ordinance in conjunction with the TRBA ( Technical Rules for Biological Agents) 466 .
Systematics
External system
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External classification of Parvularcula bermudensis according to Cho and Giovannoni 2003
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A preliminary investigation of the 16S rRNA of the isolated strain HTCC2503 from Parvularcula bermudensis initially showed that the bacterial strain belongs to the class of Alphaproteobacteria . The 16S rRNA sequence was then compared with known sequences from typical representatives of the six orders of Alphaproteobacteria known at the time of the investigation . The greatest similarity was found with Aminobacter aminovorans in the order Rhizobiales and with Silicibacter lacuscaerulensis in the order Rhodobacterales . However, the phylogenetic differences were so clear that the bacterial strains examined (in addition to the strain HTCC2503 also an environmental isolate with the designation “uncultivated clone H9”) form a monophyletic group that is to be regarded as a separate order alongside the Rhizobiales and Rhodobacterales.
P. bermudensis is one of several species in the genus Parvularcula . Due to the phylogenetic investigations, a new (at the time of discovery the seventh) order “Parvularculales” was established within the Alphaproteobacteria. Within the order, the family "Parvularculaceae" represents the only family with the only genus Parvularcula , so the family and the order are a monotypical taxon . According to the bacterial systematics , the names are put in quotation marks to show that these taxa have not yet been validly published or are not recorded by the International Code of Nomenclature of Bacteria (ICNB).
The following species are known of the genus (status 2014):
- Parvularcula bermudensis Cho & Giovannoni 2003 (the type species )
- Parvularcula dongshanensis Yu et al. 2013
- Parvularcula lutaonensis Arun et al. 2009
Internal system
From parvularcula none are synonyms known. The discovery of the species is based on the study of two strains of bacteria. The strains are named HTCC2503 and HTCC2517 and share the same phenotypic and genotypic characteristics. The strain P. bermudensis HTCC2503 is the type strain of the species. It is also listed under the designation ATCC BAA-594. Several bacterial strains of P. bermudensis are deposited in different collections of microorganisms .
etymology
The generic name Parvularcula is composed of the Latin word parvulus ("very small") and arcula ("jewelry box", "jewel box"). The species name P. bermudensis refers to the location of the type strain in the Sargasso Sea, near the Bermuda Islands .
Discovery story
The species was first described in 2003 by Jang-Cheon Cho and Stephen J. Giovannoni . In August 2001, they took samples of seawater from the Atlantic Ocean near the Bermuda Islands at a depth of 10 m. A large number of marine microorganisms cannot be isolated simply by cultivation on conventional solid nutrient media. Pure cultures have to be available for identification or taxonomic classification .
Therefore, in the 1990s a special cultivation method has been developed that do not match the otherwise in microbiology works usual nutrient media, but with liquid media, the nutrients in very small concentrations have ( English extinction culturing ). To cultivate bacteria from the sea, sterile seawater is used, which is enriched in traces (0.001%) with organic compounds. The seawater sample with the contained bacterial cells is placed in this medium and a dilution series is made from it. The conditions for incubation are adapted to the natural habitat , e.g. B. through a dark environment, a constant temperature of 16 ° C and an incubation period of several weeks. The cell number is then determined with the aid of flow cytometry and only the samples in which cells are found are examined further. At the beginning of the 21st century, this method was as high throughput Plant type ( English high-throughput culturing , HTC ) using microtiter plates optimized. The microtiter plates reduce the required volumes and at the same time increase the number of cultivation vessels, since such a plate usually contains 48 or 96 wells. In this way, many examinations can be carried out with little material expenditure. The samples identified as positive by Cho and Giovannoni according to this procedure were then cultivated with the help of marine agar and the pure cultures examined further and identified as new species.
swell
literature
- Jang-Cheon Cho, Stephen J. Giovannoni: Parvularcula bermudensis gen. Nov., Sp. nov., a marine bacterium that forms a deep branch in the alpha-Proteobacteria . In: International journal of systematic and evolutionary microbiology . tape 53 , no. 4 , 2003, p. 1031-1036 , doi : 10.1099 / ijs.0.02566-0 ( PDF, 312 kB [accessed on February 16, 2014]).
Individual evidence
- ↑ a b c d e f g h i j k l m Jang-Cheon Cho, Stephen J. Giovannoni: Parvularcula bermudensis gen. Nov., Sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria . In: International journal of systematic and evolutionary microbiology. Volume 53, No. 4, July 2003, pp. 1031-1036, ISSN 1466-5026 . doi : 10.1099 / ijs.0.02566-0 . PMID 12892122 .
- ↑ Marine Agar 2216, Marine Broth 2216. In: Website Becton, Dickinson and Company (BD) . Retrieved February 18, 2014 . ( English-language instructions for use, 2nd edition; PDF; 656 kB ).
- ↑ a b c H. M. Oh, I. Kang u. a .: Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order "Parvularculales" in the class Alphaproteobacteria. In: Journal of bacteriology. Volume 193, No. 1, January 2011, pp. 305-306, ISSN 1098-5530 . doi : 10.1128 / JB.01205-10 . PMID 21037002 . PMC 3019957 (free full text).
- ↑ a b Parvularcula bermudensis HTCC2503. In: Website Genomes Online Database (GOLD) . Retrieved February 18, 2014 .
- ^ Parvularcula bermudensis. In: National Center for Biotechnology Information (NCBI) Genome website . Retrieved February 18, 2014 .
- ↑ Parvularcula bermudensis HTCC2503 strain HTCC2503 16S ribosomal RNA, complete sequence. In: Nucleotide of Parvularcula bermudensis website of the National Center for Biotechnology Information (NCBI) . Retrieved February 18, 2014 .
- ↑ TRBA (Technical Rules for Biological Agents) 466: Classification of prokaryotes (Bacteria and Archaea) into risk groups. In: Website of the Federal Institute for Occupational Safety and Health (BAuA). April 25, 2012, p. 162 , accessed January 7, 2014 .
- ^ A b Jean Euzéby, Aidan C. Part: Genus Parvularcula. In: List of Prokaryotic names with Standing in Nomenclature ( LPSN ). Retrieved February 17, 2014 .
- ^ Jean Euzéby, Aidan C. Parte: Phylum "Proteobacteria". In: List of Prokaryotic names with Standing in Nomenclature ( LPSN ). Retrieved February 17, 2014 .
- ↑ Taxonomy Browser Parvularcula bermudensis. In: National Center for Biotechnology Information (NCBI) website . Retrieved February 17, 2014 .
- ^ Strain Passport Parvularcula bermudensis. (No longer available online.) In: StrainInfo website (information collected on bacterial strains in over 60 biological resource centers (BRCs)). Archived from the original on February 27, 2014 ; Retrieved February 19, 2014 . Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice.
- ^ SA Connon, SJ Giovannoni: High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. In: Applied and environmental microbiology. Volume 68, No. 8, August 2002, pp. 3878-3885, ISSN 0099-2240 . doi : 10.1128 / AEM.68.8.3878-3885.2002 . PMID 12147485 . PMC 124033 (free full text).
