Systematics of the bacteria

from Wikipedia, the free encyclopedia

The systematics of bacteria presented here is used as a reference in Wikipedia ; this applies in particular to entries in taxoboxes .

Staphylococcus aureus (subsequently colored SEM image)

The taxonomic division of bacteria and archaea is controversial. Initially classified only by appearance and physiology , today, due to new possibilities, the classification by means of phylogenetic analysis, as proposed by Carl Woese (1977, 1990) , is generally accepted .

The first description of bacterial genera , species and taxa of higher ranks has to follow a fixed procedure. A taxon or its name is only valid if it is first published or revised in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). The current status of which taxa or their names are recognized in this regard can be viewed in the List of Prokaryotic names with Standing in Nomenclature (LPSN), maintained by Jean P. Euzéby and continued by Aidan C. Parte since July 2013 . These names meet the requirements of the 1980 reformed International Code of Nomenclature of Bacteria (ICNB), i.e. H. each of these names designates a taxon that can be clearly identified on the basis of its deposited type material . These names are generally not put in quotation marks.

Phylogenetic tree based on rRNA genes according to Carl Woese , (1990)

In addition, the global classification (see phylogenetic tree ) within the bacteria has been reformed: The taxonomy is now also based on findings that are obtained by means of phylogenetic analysis based on comparisons of bacterial genetic material. Initially, the nucleotides of the 16S rRNA, a typical prokaryote representative of ribosomal RNA , were sequenced and compared, but now other phylogenetic marker genes are also sometimes used . The ICNB recommends a minimum standard for the description of new species, which is defined by the respective experts ( Recommendation 30b ). Such a minimum standard includes not only genetic but also phenotypic and ecological characteristics.

A current compilation of the taxa from this and numerous further publications appears in Bergey's Manual of Systematic Bacteriology . Some of these taxa are justified, but have not yet been published validly or otherwise not defined according to the requirements of the ICNB. These names, as well as all synonyms that can be clearly assigned to currently valid names, are placed in quotation marks.

This reference list of higher taxa contains the taxa from the ranks Domain to Family . There are contradicting entries for some taxa. These were checked for validity using the original literature and a phylogenetic analysis. Therefore, some variations within and from the relevant publications described above are possible. There are many reasons for this and there are reasons. A change of individual taxa should first be discussed and then only be done with indication of the source.

Basics

In contrast to larger multicellular eukaryotes, bacteria and archaea can not easily be incorporated into the classical system of taxonomy. On the one hand, there is no sexual reproduction, which is why the biological concept of species ( Ernst Mayr ) is not applicable, on the other hand they are so small that an optical description does not always provide essential knowledge, so that a phenetic / morphological concept of species is only partially applicable. A physiological description soon contributed to the classification, but due to a lack of suitable methods it could only achieve an incomplete classification. After the invention of the PCR (polymerase chain reaction) parts of the genetic information of the individual organisms were accessible. In particular, the sequence of the genes for the RNA subunits of the ubiquitous ribosomes was discovered as a useful marker for phylogenetic analyzes. Every living being needs the ribosomes, which are extremely conservative in their development, to assemble proteins. Most successful, if not perfect, was the analysis using the 16S rRNA gene , the main component of the small subunit of the ribosome. This opened up unimagined possibilities for the phylogenetic analysis of the organisms, in addition to the previous methods. The taxonomy of the microorganisms could be checked - not without consequences, of course. Many well-known terms have been questioned, but not yet completely replaced or modified by new ones, as there is usually a lot more work involved than a few sequencing. The systematics of the archaea is directly integrated into the article of the archaea.

Taxa of the bacteria domain, the use of which is recommended

Phylum " Acidobacteria "

Phylum " Actinobacteria "

Phylum " Aquificae "

Phylum " Armatimonadetes "

Phylum " Bacteroidetes "

Phylum " Balneolaeota "

Phylum " Caldiserica "

Phylum " Chlamydiae "

Phylum " Chlorobi "

Phylum " Chloroflexi "

Phylum " Chrysiogenetes "

Phylum " Cyanobacteria "

Phylum " Deferribacteres "

Phylum " Deinococcus-Thermus "

Phylum " Dictyoglomi "

Phylum " Elusimicrobia "

Phylum " Fibrobacteres "

Phylum " Firmicutes "

  • Class Bacilli (alternatively: Firmibacteria)

Phylum " Fusobacteria "

Phylum " Gemmatimonadetes "

Phylum " Kiritimatiellaeota "

Phylum " Lentisphaerae "

Phylum " Nitrospira "

Phylum " Planctobacteria "

Phylum Proteobacteria

Class Alphaproteobacteria

Class Betaproteobacteria

Class Gammaproteobacteria

  • Phytobacter (a genus not yet assigned)

Class Deltaproteobacteria

Class Epsilonproteobacteria

Class oligoflexia

Class " Zetaproteobacteria "

Class Acidithiobacillia

Phylum " Rhodothermaeota "

Family Rhodothermaceae
Family Rubricoccaceae
Salinibacteraceae family

Phylum " Spirochaetae "

Phylum " synergistic "

Phylum " Tenericutes "

Phylum " Thermodesulfobacteria "

Phylum " Thermotogae "

Phylum " Verrucomicrobia "

Taxa, the assignment of which has not yet been established or is not yet unequivocally established

The taxonomy of bacteria is the subject of numerous ongoing changes and improvements based on new discoveries that make a neutral, observational point of view impossible. Some higher taxa have not been considered above, others are expected to change in the near future. This appendix contains comments for clarification, where known:

  • Phylum Firmicutes : The position of many members of this phylum is currently difficult to clarify. Not only historical ballast plays a role, but also the limited possibilities of phylogenetic analysis. While some members were only completely wrongly classified for understandable reasons, far-reaching changes cannot be ruled out in some areas. This also affects the phylum deferribacteres. As the analysis of whole genomes progresses, further clarity may be provided.
    • Class "Bacilli"
      • Order Bacillales
        • Family Caryophanaceae: Other reasons
    • Class "Clostridia"
      • Order Clostridiales
        • Family Oscillospiraceae: The type genus is assigned to the family Ruminococcaceae.
  • Phylum Proteobacteria
    • Class Gammaproteobacteria: The position of many members of this phylum is currently difficult to clarify. Not only historical ballast plays a role, but also the limited possibilities of phylogenetic analysis.
    • Class Deltaproteobacteria: The Syntrophorhabdaceae family is assigned to this class, but has not yet been assigned to any order or subordination.
  • Phylum Tenericutes : In addition to informing the sequences of the 16S rRNA gene, this phylum was distinguished from the Firmicutes by differences in other phylogenetic markers and its special properties. The sequences of the 16S rRNA gene show a direct relationship to the class / order of the "Erysipelotrichi".
  • Phylum Verrucomicrobia
    • class
      • order
        • Family Xiphinematobacteriaceae: A type strain could not be isolated (syntrophic bacteria, parasites, endosymbionts or other reasons), therefore not defined as a species, but as a Candidatus . According to the current rules of the ICSB, there is no validated place for this in the taxonomy. No entry for the moment.
  • Phylum "Calditrichaeota" : Another classification in order and family is currently missing (December 2018).

Individual evidence

  1. ↑ CR Woese, GE Fox: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. In: Proceedings of the National Academy of Sciences of the United States of America. Volume 74, No. 11, November 1977, pp. 5088-5090, ISSN  0027-8424 . PMID 270744 . PMC 432104 (free full text).
  2. ↑ CR Woese, O. Kandler , ML Wheelis: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. In: Proceedings of the National Academy of Sciences . Volume 87, No. 12, June 1990, pp. 4576-4579, ISSN  0027-8424 . PMID 2112744 . PMC 54159 (free full text).
  3. ↑ BJ Tindall, P. K Merger, JP Euzéby, A. Oren: Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. In: International Journal of Systematic and Evolutionary Microbiology. Volume 56, No. 11, November 2006, pp. 2715-2720, ISSN  1466-5026 . doi : 10.1099 / ijs.0.64780-0 . PMID 17082418 .
  4. ↑ JP Euzéby: List of bacterial names with standing in nomenclature: a folder available on the Internet. In: International Journal of Systematic Bacteriology. Volume 47, 1997, pp. 590-592. PMID 9103655 .
  5. ^ A b S. P. Lapage, PHA Sneath, EF Lessel, VBD Skerman, HPR Seeliger, WA Clark (eds.): International Code of Nomenclature of Bacteria - Bacteriological Code, 1990 Revision . ASM Press, Washington (DC), USA 1992, ISBN 1-55581-039-X ( online ).
  6. ^ CR Woese, O. Kandler, ML Wheelis: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. In: Proceedings of the National Academy of Sciences . Volume 87, No. 12, 1990, pp. 4576-4579, doi: 10.1073 / pnas.87.12.4576 , ISSN  0027-8424 .
  7. ↑ CR Woese, E. Stackebrandt, TJ Macke, GE Fox: A phylogenetic definition of the major eubacterial taxa. In: Systematic and Applied Microbiology. Volume 6, 1985, pp. 143-151, ISSN  0723-2020 , PMID 11542017 .
  8. ↑ P. Mattarelli, W. Holzapfel a. a .: Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. In: International Journal of Systematic and Evolutionary Microbiology. Volume 64, No. 4, April 2014, pp. 1434-1451, ISSN  1466-5026 , doi : 10.1099 / ijs.0.060046-0 .
  9. ↑ Bergey's Manual Trust, Department of Microbiology, 527 Biological, Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
  10. ^ W. Ludwig and 31 other authors: ARB: a software environment for sequence data. In: Nucleic acids research . Volume 32, No. 4, 2004, pp. 1363-1371, ISSN  1362-4962 . doi : 10.1093 / nar / gkh293 . PMID 14985472 . PMC 390282 (free full text).
  11. ↑ E. Pruesse, C. Quast and a .: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. In: Nucleic acids research. Volume 35, No. 21, 2007, pp. 7188-7196, ISSN  1362-4962 . doi : 10.1093 / nar / gkm864 . PMID 17947321 . PMC 2175337 (free full text).
  12. ↑ P. Yarza, M. Richter, J. Peplies, J. Euzéby, R. Amann, KH Schleifer , W. Ludwig, FO Glöckner, R. Rosselló-Móra: The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. In: Systematic and Applied Microbiology. Volume 31, No. 4, September 2008, pp. 241-250, ISSN  0723-2020 . doi : 10.1016 / j.syapm.2008.07.001 . PMID 18692976 .
  13. ↑ M. Adeolu, S. Alnajar, S. Naushad, RS Gupta: Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. In: International Journal of Systematic and Evolutionary Microbiology. No. 66 , December 2016, p. 5575-5599 , doi : 10.1099 / ijsem.0.001485 .
  14. ↑ R. Nakai, M. Nishijima, N. Tazato, Y. Handa, F. Karray, S. Sayadi, H. Isoda, T. Naganuma: Oligoflexus tunisiensis gen. Nov., Sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov. In: International Journal of Systematic and Evolutionary Microbiology . No. 64 , October 2014, p. 3353-3359 , doi : 10.1099 / ijs.0.060798-0 .
  15. ↑ Martin W. Hahn, Johanna Schmidt, Ulrike Koll, Manfred Rohde, Susanne Verbarg, Alexandra Pitt, Ryosuke Nakai, Takeshi Naganuma, Elke Lang: Silvanigrella aquatica gen. Nov., Sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales . In: International Journal of Systematic and Evolutionary Microbiology . No. 67 , August 2017, p. 2555-2568 , doi : 10.1099 / ijsem.0.001965 .
  16. ↑ David Emerson, Jeremy A. Rentz, Timothy G. Lilburn, Richard E. Davis, Henry Aldrich, Clara Chan, Craig L. Moyer, Anna-Louise Reysenbach: A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities . In: PLoS ONE . tape 2 , no. 8 , August 2007, p. e667 , doi : 10.1371 / journal.pone.0000667 .
  17. ↑ KP Williams, DP Kelly: Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., With the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria . In: International Journal of Systematic and Evolutionary Microbiology . No. 63 , August 2013, p. 2901-2906 , doi : 10.1099 / ijs.0.049270-0 .
  18. ↑ P. De Vos, HG Trüper: Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. In: Int J Syst Evol Microbiol. 2000, Volume 50, pp. 2239-2244.

Web links