prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...

nomenclature Nomenclature (, ) is a system of names or terms, or the rules for forming these terms in a particular field of arts or sciences. The principles of naming vary from the relatively informal conventions of everyday speech to the internationally ag ...

, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or

metagenomics Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

, 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 ''In vitro'' (meaning in glass, or ''in the glass'') studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called " test-tube experiments", these studies in biology ...

'' study. The recent discoveries of a multitude of candidate taxa has led to

candidate phyla radiation The candidate phyla radiation (also referred to as CPR group) is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as n ...

expanding the tree of life through the new insights in bacterial diversity.

Nomenclature

History

The initial

International Code of Nomenclature of Prokaryotes The International Code of Nomenclature of Prokaryotes (ICNP) formerly the International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for Bacteria and Archaea.P. H. A. Sneath, 2003. A short hist ...

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 The International Committee on Systematics of Prokaryotes (ICSP), formerly the International Committee on Systematic Bacteriology (ICSB), is the body that oversees the nomenclature of prokaryotes, determines the rules by which prokaryotes are named ...

, (ICSP, formerly International Committee on Systematic Bacteriology) in 1994 to initiate code revision. 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 (Appendix 11 in the most recent version). 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.

Naming

Currently, the provisional status “''Candidatus''” may be used if the following information is provided:

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. 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

. 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 An erratum or corrigendum (plurals: errata, corrigenda) (comes from la, errata corrige) is a correction of a published text. As a general rule, publishers issue an erratum for a production error (i.e., an error introduced during the publishing pro ...

'') in the authority field, with some sources going further to cite the correction (e.g. "''Ca.''

Karelsulcia "''Candidatus'' Karelsulcia muelleri" is an aerobic organism, aerobic, Gram-negative bacteria, gram-negative, Bacillus (shape), bacillus bacterium that is a part of the phylum Bacteroidota. "''Ca.'' K. muelleri" is an obligate and mutualism (bi ...

" corrig. Moran ''et al.'' 2005 in Ogen ''et al.'' 2020). Each published list, starting from No. 1, covers all known ''Candidatus'' names proposed in a given time period, plus any addendum for previous periods. , the latest is ''Candidatus List No. 4'', published November 2022, covering names proposed in 2021.

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. 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. Depending on the location of the symbiont, the symbionts can be either ectosymbionts or endosymbionts. Drastic

genome reduction Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms (trillionths (10−12) of a gram, abbreviated pg) or less frequently in daltons, or as the total ...

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 DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA da ...

and

transcriptional regulation In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from al ...

which makes it difficult to cultivate these organisms outside their host.