Candidatus Prometheoarchaeum syntrophicum SEM Cryo

prokaryote A prokaryote (; less commonly spelled procaryote) is a unicellular organism, single-celled organism whose cell (biology), cell lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Gree ...

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 theoretical field studying nomenclature is sometimes referred to as ''onymology'' or ''taxonymy'' ). The principl ...

, ''Candidatus'' (abbreviated ''Ca.''; Latin for "

candidate A candidate, or nominee, is a prospective recipient of an award or honor, or a person seeking or being considered for some kind of position. For example, one can be a candidate for membership in a group (sociology), group or election to an offic ...

of Roman office") is used to name prokaryotic

taxa In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and ...

that are well characterized but yet- uncultured. Contemporary sequencing approaches, such as

16S ribosomal RNA 16S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S ...

sequencing or

metagenomics Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the mic ...

, provide much information about the analyzed organisms and thus allow identification and characterization of 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'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...

'' study. The recent discoveries of a multitude of candidate taxa has led to candidate phyla radiation expanding the

tree of life The tree of life is a fundamental archetype in many of the world's mythology, mythological, religion, religious, and philosophy, philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The ...

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. This was in apparent conflict with the ICNP's stated scope, which was to be "prokaryotes", not just cultivated ones. 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. 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, until 2024, the nomenclature of ''Candidatus'' taxa was 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. Another way through which a prokaryotic name cannot be validly published under the ICNP, since 2001, is that it does not meet the Rule 30 requirement of "viable cultures of the type strain, in two culture collections, in different countries". This ensures the quality and accessibility of the type strain, but it can be difficult to follow in practice: for example, moving cultures across national borders requires interacting with Nagoya Protocol regulations. In addition, a few names have been found to be invalid after the fact due to violation of Rule 30. The 2024 change to the ICNP expands the scope of ''Candidatus'' to includes this kind of cases: a pro-validly published name can be typified by a live culture not meeting Rule 30 or a preserved culture.

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". 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 at appropriate intervals. Once a ''Candidatus'' taxon 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. 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, with some sources going further to cite the correction (e.g. "''Ca.'' Karelsulcia" 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. An unnumbered list was published in 2023 to deal with ''Candidatus''

phyla Phyla, the plural of ''phylum'', may refer to: * Phylum, a biological taxon between Kingdom and Class * by analogy, in linguistics, a large division of possibly related languages, or a major language family which is not subordinate to another Phy ...

; future numbered lists will include phyla.

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. The SeqCode recognizes the priority of names, including ''Candidatus'' ones, published under ICNP before 2023. The SeqCode team initially wished to simply amend the ICNP to add such a system, but ICSP rejected the petition, necessitating the creation of a separate code. The use of a genome sequence as the type material is useful not only for not-yet-cultured prokaryotes. A genome sequence is more stable than a cell culture, which can be (and has been) lost and are subject to genetic drift under the different selective pressure of the lab. In addition, the ICNP requires a type strain to be stored in two separate culture collections if a name is to be proposed (including new combinations, i.e. renames), which makes it hard to correct the name of some wrongly-categorized species.

Pro-valid publication

Bacteriologists from several different institutions wrote a new proposal for the ICNP to govern ''Candidatus'' names using genome sequences in 2024, providing a detailed analysis of the incompatibility of the Whitman proposal and SeqCode with the ICNP followed by a plan that avoids the reasons for the rejection of Whitman's proposal but satisfies his goals. The ICSP accepted the proposal in the same year. With this change, ''Candidatus'' names can be "pro-validly published" and become "pro-legitimate" and "pro-correct". This requires the name to meet most existing requirements for valid publication (and analogously for legitimacy and correctness), ''except'' the culture deposition in Rule 30 can be replaced by a living culture not meeting the requirements of Rule 30, a preserved specimen, a sequenced genome deposited on the INSDC, or a single-gene sequence deposited to the INSDC. Pro-legitimate ''Candidatus'' names compete with each other for priority, but do not compete with legitimate names.

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 Symbiosis (Ancient Greek : living with, companionship < : together; and ''bíōsis'': living) is any type of a close and long-term biolo ...

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

endosymbiont An endosymbiont or endobiont is an organism that lives within the body or cells of another organism. Typically the two organisms are in a mutualism (biology), mutualistic relationship. Examples are nitrogen-fixing bacteria (called rhizobia), whi ...

s. Drastic genome reduction through gene deletions has been observed in endosymbiotic bacteria which is thought to be because 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 (biology), cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is cons ...

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

Typography

''Candidatus'' or ''Ca.'' is italicized. The name that follows is not italicized. The whole name is wrapped in double quotation marks. Example: "''Candidatus'' Phytoplasma", "''Ca.'' Phytoplasma allocasuarinae".