Kyrpidia tusciae

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Kyrpidia tusciae
Systematics
Department : Firmicutes
Class : Bacilli
Order : Bacillales
Family : Alicyclobacillaceae
Genre : Kyrpidia
Type : Kyrpidia tusciae
Scientific name of the  genus
Kyrpidia
(Bonjour & Aragno 1985) Klenk et al. 2012
Scientific name of the  species
Kyrpidia tusciae
Klenk et al. 2012

Kyrpidia tusciae is the only species in the genus Kyrpidia . They are gram-positive bacteria fromthe Alicyclobacillaceae family in the order of the Bacillales . Like other representatives of the Alicyclobacillaceae, they are acidophilic (acid-loving) and thermophilic (warmth-loving). They are also ableto oxidize hydrogen in order to generate energy from it. The bacterial species was discovered in 1984 in a geothermal area in the Italian Tuscan countryside. It was classified as a Bacillus speciesby the discovererswith the scientific name Bacillus tusciae . It was only through genetic studies in 2011 that it was recognized that there was too little in common with the genus Bacillus , so that in 2012 it wastransferred to a new genusas Kyrpidia tusciae . Bacillus tusciae is the basonym .

features

Appearance

The cells of Kyrpidia tusciae are rod-shaped , with a diameter of 0.8  µm and a length of 4 to 5 µm. They are usually arranged in chains of several cells. In young cultures, the Gram stain is positive and the endospores can be seen as oval inclusions at one end of the mother cell, causing the cell to expand. The cells are actively motile by individual, laterally (i.e., laterally) arranged flagella .

Growth and metabolism

Kyrpidia tusciae is chemoorgano - heterotrophic and facultative chemolitho - autotrophic . In the context of their metabolism of substances and energy , K. tusciae can use various alcohols , amino acids and short-chain fatty acids , but not carbohydrates . Better growth occurs under autotrophic conditions, where molecular hydrogen (H 2 ) is oxidized and carbon dioxide (CO 2 ) is reduced . Oxygen is not necessary for growth, but it also has no inhibitory effect, K. tusciae is facultatively anaerobic . Catalase and oxidase tests are weakly positive.

Optimal growth takes place at pH values between pH 4.2 and pH 4.8, the species is acidophilic (acid-loving). In addition, it can be characterized as thermophilic (heat-loving), as it is only able to reproduce at relatively high temperatures. The growth takes place in a temperature range of 47 to 67 ° C, optimally at 55 ° C.

Further studies of the metabolism showed that an enzyme activity of malate dehydrogenase can be detected in the cells of K. tusciae . In aerobic organisms, this enzyme is involved in the citric acid cycle and oxidizes malate to oxaloacetate , reducing NAD + . In contrast to this, the malate dehydrogenase from K. tusciae is not able to reduce NAD + or NADP + . The activity of a hydrogenase , which catalyzes the oxidation of hydrogen, was also demonstrated. The formation of the enzyme is induced by the presence of hydrogen . Cells that are cultivated under autotrophic conditions show the Calvin cycle in their metabolism , in which CO 2 is assimilated by the enzyme ribulose-1,5-bisphosphate carboxylase ( RuBisCO ) . The cells cultivated in this way have inclusions of polyhydroxybutyric acid , which serve as storage material.

genetics

The representatives of the Firmicutes are generally characterized by a low GC content , i.e. a low proportion of the nucleobases guanine and cytosine in the bacterial DNA . Although Kyrpidia tusciae belongs to the Firmicutes division, it has a rather high GC content, at 59.1  mole percent . This peculiarity is also shown by the related genus Alicyclobacillus , whose representatives were earlier also assigned to the genus Bacillus . The genome of the bacterial strain Kyrpidia tusciae DSM 2912 was completely sequenced in 2010 . At that time the bacterium was still classified in the genus Bacillus and the sequencing should provide information about its phylogenetic position within the bacteria. This happened within the project Genomic Encyclopedia of Bacteria and Archaea (abbreviated as GEBA, translated “Genome Encyclopedia of Bacteria and Archaea ”). The genome size is 3385 kilobase pairs (kb) and thus corresponds to about 75% of the genome size of Escherichia coli . There are 3150 proteins annotated . The genome is distributed on a circular bacterial chromosome , plasmids are not available. In addition, the nucleotides of 16S rRNA, a typical representative of ribosomal RNA for prokaryotes , were determined for phylogenetic studies .

Chemotaxonomy

The main quinone is MK-7 type menaquinone . The lipids in the biomembrane are mainly branched-chain , saturated fatty acids. Typical representatives are fatty acids with the abbreviations iso -C 15: 0 ( iso - pentadecanoic acid ) and iso -C 17: 0 ( iso - heptadecanoic acid ). These fatty acids with a total of 15 or 17 carbon atoms belong to the odd-numbered fatty acids. The omega-alicyclic fatty acids typical of Alicyclobacillus are not found in Kyrpidia .

Pathogenicity

Kyrpidia tusciae is not pathogenic ("pathogenic"), the basonym Bacillus tusciae is assigned to risk group 1 by the Biological Agents Ordinance in conjunction with the TRBA ( Technical Rules for Biological Agents) 466 .

Occurrence and ecology

The habitat of Kyrpidia tusciae can be found in extreme locations. The first Kyrpidia strain was isolated in 1984 from hot water springs with solfataras in the Italian countryside of Tuscany . Due to the volcanic activity, the thermal springs contain outflows of gases such as hydrogen and carbon dioxide, the water has only a small proportion of organic compounds . K. tusciae is adapted to the habitat through the facultative chemolitho-autotrophic metabolism and thermoacidophilic growth. As a result, it is difficult to cultivate under laboratory conditions.

Systematics

External system

Kyrpidia tusciae is the only species and thus also the type species of the genus Kyrpidia and belongs to the family of the Alicyclobacillaceae in the order of the Bacillales . This order belongs to the firmicutes department.

The bacterium was originally isolated, examined and first described in 1984 by Fabienne Bonjour and Michel Aragno . Because of its morphological and biochemical similarities, it was assigned to the genus Bacillus and referred to as Bacillus tusciae . As with the Bacilli , the cells are rod-shaped and form endospores, and some thermophilic Bacillus species are also known. A phylogenetic investigation of the 16S rRNA did not take place until 1994. The scientists found that Bacillus tusciae bears more similarity with representatives of the genus Alicyclobacillus than with the genus Bacillus and advocated a new classification in the bacterial system, if phenotypic features also match the phylogenetic test results support. Another comparative study of the 16S rRNA in 2009 also showed that there are too many differences to be classified in the genus Bacillus .

But it wasn't until 2011 that an international group of scientists led by Hans-Peter Klenk was able to find sufficient evidence for this after the genome had been completely sequenced. Their investigation also confirmed the relationship to Alicyclobacillus . As with representatives of this genus, the bacterial strain examined lacks the sspE gene, which codes for acid-soluble spore proteins and is often found in representatives of the Bacillales. The comparison of the sequences of the 16S rRNA showed a similarity of 87.5 to 89.0% with the known Alicyclobacilli . These values ​​are considered to be too low to be assigned to the genus, but the differences are sufficient to establish a type species of a new genus. This is supported by phenotypic characteristics, for example the lack of the omega-alicyclic fatty acids typical of Alicyclobacillus . With publication in Validation List No. 146 in 2012, the species and genus were recognized according to the rules of the bacteriological code . Thus the genus was named Kyrpidia gen. Nov. (Latin genus novum for "new genus") and the species as Kyrpidia tusciae comb. nov. (Latin combinatio nova for "new combination"). Bacillus tusciae is considered a basonym . The relationship with Alicyclobacillus is taken into account in that both genera together with the genus Tumebacillus first described in 2008 form the family Alicyclobacillaceae.

Internal system

The bacterial strain discovered in the geothermal area and initially designated as T2 is the type strain of the species. It was deposited in the collections of microorganisms in Japan (as NBRC 15312), Belgium (as LMG 17940) and Germany (at the DSMZ as DSM 2912) .

etymology

The generic name Kyrpidia was chosen in honor of Nikolaos C. Kyrpides. He is a Greek-born American scientist and one of the co-founders of the GEBA project. The species name K. tusciae refers to the place where the bacterium was found, the Italian region of Tuscia , referred to in Italian as Tuscia . The species name was chosen by Bonjour and Aragno, who named the bacterium Bacillus tusciae . According to the rules of the bacteriological code, the species name is retained when it is assigned to a new genus.

Individual evidence

  1. ↑ a b c d e f g Fabienne Bonjour, Michel Aragno: Bacillus tusciae, a new species of thermoacidophilic, facultatively chemolithoautotrophic hydrogen oxidizing sporeformer from a geothermal area. In: Archives of Microbiology. Volume 139, No. 4, November 1984, pp. 397-401, ISSN  0302-8933 . doi : 10.1007 / BF00408386 .
  2. ↑ a b c d e f g h i j k l m Hans-Peter Klenk, Alla Lapidus u. a .: Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. In: Standards in Genomic Sciences. Volume 5, No. 1, October 2011, pp. 121-134, ISSN  1944-3277 . doi : 10.4056 / sigs.2144922 . PMID 22180816 . PMC 3236038 (free full text).
  3. ↑ GI Karavaiko, TI Bogdanova u. a .: Reclassification of 'Sulfobacillus thermosulfidooxidans subsp. thermotolerans' strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus. In: International Journal of Systematic and Evolutionary Microbiology. Volume 55, No. 2, March 2005, pp. 941-947, ISSN  1466-5026 . doi : 10.1099 / ijs.0.63300-0 . PMID 15774689 .
  4. ↑ a b c Kyrpidia tusciae. In: National Center for Biotechnology Information (NCBI) Genome website . Retrieved November 4, 2014 .
  5. ↑ D. Wu, P. Hugenholtz u. a .: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. In: Nature . Volume 462, No. 7276, December 2009, pp. 1056-1060, ISSN  1476-4687 . doi : 10.1038 / nature08656 . PMID 20033048 . PMC 3073058 (free full text).
  6. ↑ a b Kyrpidia tusciae strain DSM 2912 16S ribosomal RNA gene, complete sequence. In: Website Nucleotide of Kyrpidia tusciae of the National Center for Biotechnology Information (NCBI). Retrieved November 5, 2014 .
  7. ↑ 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. 36 , accessed November 4, 2014 .
  8. ^ A b c Jean Euzéby, Aidan C. Parte: Genus Kyrpidia. In: List of Prokaryotic names with Standing in Nomenclature ( LPSN ). Retrieved November 4, 2014 .
  9. ^ FA Rainey, D. Fritze, E. Stackebrandt: The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis. In: FEMS Microbiology Letters. Vol. 115, No. 2-3, January 1994, pp. 205-211, ISSN  0378-1097 . PMID 8138135 .
  10. ↑ MS Wei Wang: Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences. In: Brazilian Journal of Microbiology. Volume 40, No. 3, July 2009, pp. 505-521, ISSN  1517-8382 . doi : 10.1590 / S1517-838220090003000013 (currently not available) . PMID 24031394 . PMC 3768542 (free full text).
  11. ↑ unknown: List of new names and new combinations previously effectively, but not validly, published - Validation List no.146 . In: International Journal of Systematic and Evolutionary Microbiology . tape 62 , no. 7 , July 5, 2012, ISSN  1466-5026 , p. 1443-1445 , doi : 10.1099 / ijs.0.044636-0 .
  12. ↑ Taxonomy Browser Kyrpidia tusciae. In: National Center for Biotechnology Information (NCBI) website . Retrieved November 4, 2014 .