Candidatus

In prokaryote nomenclature, Candidatus (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured.[1] Contemporary sequencing approaches, such as 16S 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 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 requirements are met:

"(a) Genomic information [...] to determine the phylogenetic position of the organism

(b) All information so far available on:

i.) structure and morphology ii) physiology and metabolism iii) reproductive features iv) the natural environment in which the organism can be identified and v) any other available and suitable information".[4]

The species name of an organism in the status of Candidatus consists of the word Candidatus, followed by a 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 is kept by the Judicial Commisssion 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.

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.[7] 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.

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.[8] 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.[8]

See also

References
  1. Stackebrandt, E. (2002-05-01). "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.
  2. Murray, R. G. E.; Schleifer, K. H. (1994-01-01). "Taxonomic Notes: A Proposal for Recording the Properties of Putative Taxa of Procaryotes". 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 (2006-11-01). "Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice". International Journal of Systematic and Evolutionary Microbiology. 56 (11): 2715–2720. doi:10.1099/ijs.0.64780-0. ISSN 1466-5026. PMID 17082418.
  4. "International Code of Nomenclature of Prokaryotes: Prokaryotic Code (2008 Revision)". International Journal of Systematic and Evolutionary Microbiology. 69 (1A): S1–S111. 2019-01-01. doi:10.1099/ijsem.0.000778. ISSN 1466-5026. OSTI 1254416. 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 (2019-07-01). "Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names". International Journal of Systematic and Evolutionary Microbiology. 69 (7): 2174–2175. doi:10.1099/ijsem.0.003419. ISSN 1466-5026. PMID 31066658.
  7. 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". Applied and Environmental Microbiology. 71 (12): 7819–7830. doi:10.1128/AEM.71.12.7819-7830.2005. ISSN 0099-2240. PMC 1317335. PMID 16332756.
  8. Moya, Andrés; Peretó, Juli; Gil, Rosario; Latorre, Amparo (March 2008). "Learning how to live together: genomic insights into prokaryote–animal symbioses". Nature Reviews Genetics. 9 (3): 218–229. doi:10.1038/nrg2319. ISSN 1471-0056. PMID 18268509. S2CID 2866611.

Further reading
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