Biology:Candidatus

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Short description: Indication in bacteriological nomenclature
Candidatus Prometheoarchaeum syntrophicum cells dividing under SEM (c). Cryo-electron tomography image of a single cell (d). White arrows indicate large membrane vesicles. Scale bar = 1 μm (c) and 500 μm (d)

In prokaryote nomenclature, Candidatus (abbreviated Ca.; Latin for "candidate of Roman office") is used to name prokaryotic taxa that are well characterized but yet-uncultured.[1] Contemporary sequencing approaches, such as 16S ribosomal RNA sequencing or metagenomics, provide much information about the analyzed organisms and thus allow to identify and characterize individual species. However, the majority of prokaryotic species remain uncultivable and hence inaccessible for further characterization in in vitro study. The recent discoveries of a multitude of candidate taxa has led to candidate phyla radiation expanding the tree of life through the new insights in bacterial diversity.

Nomenclature

History

The initial International Code of Nomenclature of Prokaryotes (ICNP) as well as early revisions did not account for the possibility of identifying prokaryotes which were not yet cultivable. Therefore, the term Candidatus was proposed in the context of a conference of the International Committee on Systematics of Prokaryotes, (ICSP, formerly International Committee on Systematic Bacteriology) in 1994 to initiate code revision.[2] Owing to rising numbers of Candidatus taxa associated with ongoing advances of sequencing technologies, the ICSP adopted the International Code of Nomenclature of Prokaryotes in 1996 by adding an appendix for Candidatus taxa[3] (Appendix 11 in the most recent version[4]). However, the nomenclature of Candidatus taxa is still not covered by the general rules of the Prokaryotic Code leading to ongoing discussions and proposals for changing the current code in order to grant priority to Candidatus taxa.[5][6]

Naming

Currently, the provisional status “Candidatus” may be used if the following information is provided:[citation needed]

  1. Genomic information [...] to determine the phylogenetic position of the organism.
  2. All information so far available on:
    1. structure and morphology
    2. physiology and metabolism
    3. reproductive features
    4. the natural environment in which the organism can be identified and
    5. any other available and suitable information.[4](Appendix 11)

The species name of an organism in the status of Candidatus consists of the word Candidatus, followed by an either a genus name with a specific epithet, or only a genus name, or only a specific epithet. Examples include Candidatus Liberobacter asiaticum; Candidatus magnetobacterium; Candidatus intracellularis. A list of all Candidatus taxa (a Candidatus List) is kept by the Judicial Commission of the ICSP in cooperation with the editorial board of the IJSEM and is updated in appropriate intervals.[4] Once a Candidatus taxa has been cultivated successfully, the name has to be removed from this list and a new name has to be proposed in accordance with the International Code of Nomenclature of Prokaryotes.[citation needed]

Although the 1994 proposal and the later Code call for a Candidatus List to be maintained, work on curating names did not start until 2017, when a "No. 0" trial is published. The author found that 120 of the ~400 collected names would breach the Code should they become formally proposed. Common reasons are Latin errors, duplicate names, and non-Latin names. As a result, Candidatus Lists now also offer corrections for such names. Corrected names are given corrig. (for corrigendum) in the authority field,[7] with some sources going further to cite the correction (e.g. "Ca. Karelsulcia" corrig. Moran et al. 2005 in Ogen et al. 2020).[8] Each published list, starting from No. 1, covers all known Candidatus names proposed in a given time period, plus any addendum for previous periods.[7] (As of December 2022), the latest is Candidatus List No. 4, published November 2022, covering names proposed in 2021.[9] An unnumbered list was published in 2023 to deal with Candidatus phyla; future numbered lists will include phyla.[10]

SeqCode

The Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) of 2022 standardizes the publication of names in a system separate from the ICNP. Instead of requiring a type culture, the SeqCode requires a high-quality genome as the nomenclatural type, in effect offering a route to formalizing Candidatus names. It is produced by the International Society for Microbial Ecology (ISME), which is unrelated to the ICSP.[11] The SeqCode recognizes the priority of names, including Candidatus ones, published under ICNP before 2023.[12]

The SeqCode team initially wished to simply amend the ICNP to add such a system, but ICSP rejected the petitition, necessitating the creation of a separate code.[11]

Uncultivability

Environmental factors

There are several reasons for why many prokaryotic species do not grow in the lab many of which remain poorly understood. One of these reasons is the environment the species are recovered from which can be difficult to simulate in laboratory conditions. Many prokaryotes have highly specific growth requirements including the need for a specific nutrient composition, specific pH conditions, temperatures, atmospheric pressure or levels of oxygen.[13] Most commercially available growth media and incubation protocols poorly met these requirements making a comprehensive habitat assessment necessary in order to successfully isolate the bacteria of interest from environmental samples.[citation needed]

Species interaction

Most prokaryotic species do not live alone but rather in complex communities with other species from all kingdoms of life. As a consequence, many species depend on metabolites or signaling compounds of their neighboring species for their own cell growth. The identification of the required substances can be challenging but once identified a co-cultivation or addition of the specific compound can be used to potentially cultivate the species of interest.

Genome reduction

Many instances of species interaction are of symbiotic nature which is defined as an intimate, long-term relationship between two or more species which can be either mutualistic, neutral or harmful.[14] Depending on the location of the symbiont, the symbionts can be either ectosymbionts or endosymbionts. Drastic genome reduction through gene deletions has been observed in endosymbiotic bacteria which is thought to be owing to the fact that many genes become unnecessary in the sheltered host environment. This frequently affects genes for DNA repair and transcriptional regulation which makes it difficult to cultivate these organisms outside their host.[14]

See also

References

  1. ↑ Stackebrandt, E. (1 May 2002). "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology". International Journal of Systematic and Evolutionary Microbiology 52 (3): 1043–1047. doi:10.1099/ijs.0.02360-0. PMID 12054223. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.02360-0. [yes|permanent dead link|dead link}}]
  2. ↑ Murray, R. G. E.; Schleifer, K. H. (1 January 1994). "Taxonomic Notes: A Proposal for Recording the Properties of Putative Taxa of Procaryotes" (in en). International Journal of Systematic Bacteriology 44 (1): 174–176. doi:10.1099/00207713-44-1-174. ISSN 0020-7713. PMID 8123559. 
  3. ↑ Tindall, Brian J.; Kämpfer, Peter; Euzéby, Jean P.; Oren, Aharon (1 November 2006). "Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice" (in en). International Journal of Systematic and Evolutionary Microbiology 56 (11): 2715–2720. doi:10.1099/ijs.0.64780-0. ISSN 1466-5026. PMID 17082418. 
  4. ↑ 4.0 4.1 4.2 "International Code of Nomenclature of Prokaryotes: Prokaryotic Code (2008 Revision)" (in en). International Journal of Systematic and Evolutionary Microbiology 69 (1A): S1–S111. 1 January 2019. doi:10.1099/ijsem.0.000778. ISSN 1466-5026. PMID 26596770. 
  5. ↑ Oren, Aharon; Garrity, George M.; Parker, Charles T.; Chuvochina, Maria; Trujillo, Martha E. (2020). "Lists of names of prokaryotic Candidatus taxa". International Journal of Systematic and Evolutionary Microbiology 70 (7): 3956–4042. doi:10.1099/ijsem.0.003789. ISSN 1466-5026. PMID 32603289. 
  6. ↑ Whitman, William B.; Sutcliffe, Iain C.; Rossello-Mora, Ramon (1 July 2019). "Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names" (in en). International Journal of Systematic and Evolutionary Microbiology 69 (7): 2174–2175. doi:10.1099/ijsem.0.003419. ISSN 1466-5026. PMID 31066658. 
  7. ↑ 7.0 7.1 Oren, A (November 2021). "Nomenclature of prokaryotic 'Candidatus' taxa: establishing order in the current chaos.". New Microbes and New Infections 44: 100932. doi:10.1016/j.nmni.2021.100932. PMID 34631108. 
  8. ↑ "Taxonomy browser (Candidatus Karelsulcia)". https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=336809&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  9. ↑ Oren, Aharon (25 November 2022). "Candidatus List No. 4: Lists of names of prokaryotic Candidatus taxa". International Journal of Systematic and Evolutionary Microbiology 72 (11). doi:10.1099/ijsem.0.005545. PMID 35100104. 
  10. ↑ Oren, Aharon; Göker, Markus (9 May 2023). "Candidatus List. Lists of names of prokaryotic Candidatus phyla". International Journal of Systematic and Evolutionary Microbiology 73 (5). doi:10.1099/ijsem.0.005821. 
  11. ↑ 11.0 11.1 "SeqCode: a nomenclatural code for prokaryotes described from sequence data". Nat Microbiol 7 (10): 1702–1708. October 2022. doi:10.1038/s41564-022-01214-9. PMID 36123442. 
  12. ↑ "The SeqCode version 1.0.3". 5 January 2023. https://disc-genomics.uibk.ac.at/seqcode/page/seqcode. 
  13. ↑ Köpke, Beate; Wilms, Reinhard; Engelen, Bert; Cypionka, Heribert; Sass, Henrik (December 2005). "Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients" (in en). Applied and Environmental Microbiology 71 (12): 7819–7830. doi:10.1128/AEM.71.12.7819-7830.2005. ISSN 0099-2240. PMID 16332756. Bibcode: 2005ApEnM..71.7819K. 
  14. ↑ 14.0 14.1 Moya, Andrés; Peretó, Juli; Gil, Rosario; Latorre, Amparo (March 2008). "Learning how to live together: genomic insights into prokaryote–animal symbioses" (in en). Nature Reviews Genetics 9 (3): 218–229. doi:10.1038/nrg2319. ISSN 1471-0056. PMID 18268509. http://www.nature.com/articles/nrg2319. 

Further reading

  • Labeda, D. P. (1997). "Judicial Commission of the International Committee on Systematic Bacteriology VIIIth International Congress of Microbiology and Applied Bacteriology: Minutes of the Meetings, 17 and 22 August 1996, Jerusalem, Israel". International Journal of Systematic Bacteriology 47: 240. doi:10.1099/00207713-47-1-240. 
  • "International Committee on Systematic Bacteriology VIIth International Congress of Microbiology and Applied Bacteriology: Minutes of the Meetings, 17, 18, and 22 August 1996, Jerusalem, Israel". International Journal of Systematic Bacteriology 47 (2): 597–600. 1997. doi:10.1099/00207713-47-2-597. 
  • De Vos, P.; Trüper, H. G.; Tindall, B. J. (2005). "Judicial Commission of the International Committee on Systematics of Prokaryotes; Xth International (IUMS) Congress of Bacteriology and Applied Microbiology; Minutes of the meetings, 28, 29 and 31 July and 1 August 2002, Paris, France". International Journal of Systematic and Evolutionary Microbiology 55: 525–532. doi:10.1099/ijs.0.63585-0. 
  • Stackebrandt, E.; Frederiksen, W.; Garrity, G. M.; Grimont, P. A.; Kämpfer, P.; Maiden, M. C.; Nesme, X.; Rosselló-Mora, R. et al. (2002). "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 3): 1043–1047. doi:10.1099/ijs.0.02360-0. PMID 12054223. 



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