International Journal of Systematic and Evolutionary Microbiology (2015), 65, 4284–4287
Taxonomic Note
DOI 10.1099/ijsem.0.000664
Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes Aharon Oren,1 Milton S. da Costa,2 George M. Garrity,3 Fred A. Rainey,4 Ramon Rossello´-Mo´ra,5 Bernhard Schink,6 Iain Sutcliffe,7 Martha E. Trujillo8 and William B. Whitman9
Correspondence Aharon Oren
[email protected]
1
Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904 Jerusalem, Israel
2
Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal
3
Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
4
Department of Biological Sciences, University of Alaska Anchorage, AK 99508, USA
5
Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), 07190 Esporles, Spain
6
Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
7
Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
8
Departamento de Microbiologı´a y Gene´tica, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
9
Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA 30602-2605, USA
The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.
The International Code of Nomenclature of Prokaryotes (ICNP; Parker et al., 2016) covers the nomenclature of prokaryotes up to the rank of class only. For comparison, the International Code of Nomenclature for algae, fungi and plants (McNeill et al., 2012) also covers the ranks of kingdom (regnum), division or phylum (divisio or phylum), whereas the highest rank covered by the International Code of Zoological Nomenclature is that of family. The rank of phylum is extensively used for groups of prokaryotes, and names of more than 30 phyla are known in the literature for which there are cultured representatives in the literature (http://www.bacterio.net/-classifphyla.html; Table 1); in addition there are many deep lineages equivalent to phyla that are not yet represented by organisms available in pure culture. In spite of the wide use of the term, the rank of phylum does not have standing in the nomenclature as regulated by the ICNP.
Abbreviations: ICNP, International Code of Nomenclature of Prokaryotes; ICSB, International Committee on Systematics of Bacteria; ICSP, International Committee on Systematics of Prokaryotes.
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The need to include higher taxa above the rank of class has been raised in the past, and on several occasions proposals to regulate the nomenclature of higher taxa have been discussed. Thus, Tru¨per (1994) proposed that Eucarya, Archaea and (Eu)Bacteria should be three Imperia, and that the most deeply branching phyla in the (Eu)Bacteria will have to be considered kingdoms (Latin: regnum, plural regna), and these ideas were discussed by the International Committee on Systematics of Bacteria (ICSB) in Prague in 1994 (Goodfellow, 1995). The Judicial Commission of the ICSB at its meetings in Sydney in 1999 discussed the issue of taxa of higher rank and felt that discussion on this subject must be postponed until an ad hoc committee on this matter made its report (Tindall et al., 2000). The establishment of an ad hoc committee to discuss naming of higher taxa (above class) was proposed at the meetings of the International Committee on Systematics of Prokaryotes (ICSP) in Paris in 2002 (De Vos et al., 2005). Formation of an ad hoc committee on higher taxa was discussed again in San Francisco in 2005 (De Vos & Tru¨per, 2000), but the proposed committee never convened. The need to clarify this situation has been highlighted in
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Actinobacteria Proteobacteria
Actinobacteria Alphaproteobacteria
Aquificae
Actinobacteraeota Alphaproteobacteraeota
Aquificaeota Armatimonadaeota Bacillaeota
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Synergistetes Thermodesulfobacteria Thermomicrobia Crenarchaeota
Thermotogae Verrucomicrobia
Synergistaeota Synergistia Thermodesulfobacteraeota Thermodesulfobacteria Thermomicrobaeota Thermomicrobia Thermoproteaeota
Thermotogaeota Verrucomicrobaeota
Thermotogae Verrucomicrobiae
Spirochaetes
Tenericutes Thaumarchaeota
Spirochaetaeota
Mollicutes Nitrososphaeria
Mollicutaeota Nitrososphaeraeota
Chloroflexi Chrysiogenetes Deferribacteres Deinococcus-Thermus Dictyoglomi Elusimicrobia Fibrobacteres Fusobacteria Gemmatimonadetes Ignavibacteriae Lentisphaerae Euryarchaeota
Nitrospira Planctomycetes
Chloroflexia Chrysiogenetes Deferribacteres Deinococci Dictyoglomia Elusimicrobia Fibrobacteria Fusobacteriia Gemmatimonadetes Ignavibacteria Lentisphaeria Methanobacteria
Chloroflexaeota Chrysiogenaeota Deferribacteraeota Deinococcaeota Dictyoglomaeota Elusimicrobaeota Fibrobacteraeota Fusobacteraeota Gemmatimonadaeota Ignavibacteraeota Lentisphaeraeota Methanobacteraeota
Bacteroidetes Caldiserica Chlamydiae Chlorobi
Nitrospiraeota Planctomycetaeota
Bacteroidia Caldisericia Chlamydiae
Bacteroidaeota Caldisericaeota Chlamydaeota Chlorobaeota
Bacilli
Acidobacteria
Acidobacteraeota
Aquificae Armatimonadetes Firmicutes
Phylum name currently in common use
Proposed phylum name Nomenclatural type (class)
Thermoprotei cannot be used as the name of the class as it is on the list of nomina rejicienda (Opinion 79). Instead we propose Thermoprotea. As the name Crenarchaeota is widely used for the phylum, the Judicial Commission may consider conserving this name instead of Thermoproteaeota
As the name Euryarchaeota is widely used for the phylum, the Judicial Commission may consider conserving this name instead of Methanobacteraeota Note that no nomenclatural type has been designated for the class Mollicutes As the name Thaumarchaeota is widely used for the phylum, the Judicial Commission may consider conserving this name instead of Nitrososphaeraeota We propose establishing the class Nitrospiria as the nomenclatural type Planctomycea cannot be used as the name of the class as it is on the list of nomina rejicienda (Opinion 79). Instead we propose Planctomycetes Spirochaetes cannot be used as the name of the class as it is on the list of nomina rejicienda (Opinion 79). Instead we propose Spirochaetia
Chlorobea cannot be used as the name of the class as it is on the list of nomina rejicienda (Opinion 79). Instead we propose Chlorobia
We propose establishing the class Armatimonadia as the nomenclatural type As the name Firmicutes is widely used for the phylum, the Judicial Commission may consider conserving this name instead of Bacillaeota
Acidobacteria cannot be used as the name of the class as it is on the list of nomina rejicienda (Opinion 79). Instead we propose Acidobacteriae Note that no nomenclatural type has been designated for the class Actinobacteria As the name Proteobacteria is widely used for the phylum, the Judicial Commission may consider conserving this name (earlier used for a class) instead of Alphaproteobacteraeota
Comments
Table 1. List of names of phyla to be considered for validation after approval of the proposal to include the rank of phylum in the ICNP
Rank of phylum in the International Code
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A. Oren and others
correspondence (Gribaldo & Brochier-Armanet, 2012; Garrity & Oren, 2012). We feel that inclusion of the rank of phylum under the rules of the ICNP is long overdue, and therefore we here formally propose to modify the Code accordingly. To do so, we propose the following changes in Rules 5b, 8, 15 and 22.
synonym. The nomenclatural type is not necessarily the most typical or representative element of the taxon. The types are dealt with in Rules 16–22. Types of the various taxonomic categories can be summarized as follows:’
RULE 5B ‘The taxonomic categories above and including species which are covered by these Rules are given below in ascending taxonomic rank. Those in the left-hand column should be recognized where pertinent; those in the right-hand column are optional. The Latin equivalents are given in parentheses.’
Table 2. Taxonomic categories Taxonomic category Subspecies Species
Subgenus Genus
Species (Species) Subgenus (Subgenus) Genus (Genus)
Subtribe Tribe Subfamily Family Suborder Order
Subtribe (Subtribus) Tribe (Tribus) Subfamily (Subfamilia) Family (Familia) Suborder (Subordo) Order (Ordo)
Subclass Class
Subclass (Subclassis) Class (Classis) Phylum (Phylum)
Phylum
Type 9 > > = > > ; 9 > > > > > > = > > > > > > ;
Designated strain; in special cases the place of the type strain may be taken by a description, preserved specimen, or an illustration Designated species
Genus on whose name the name of the higher taxon is based
One of the contained orders One of the contained classes
RULE 8
THE FIRST PARAGRAPH OF RULE 22
‘The name of each taxon (covered by the Code) above the rank of order is a Latin or latinized word. The name of a class is in the neuter gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -ia to the stem of the name of the type genus of the type order of the class. The name of a subclass is in the feminine gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -idae to the stem of the name of the type genus of the type order of the subclass. The name of a phylum is in the neuter gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -aeota to the stem of the name of one of the contained classes.’
‘The type of a phylum is one of the contained classes. If there is only one class this becomes the type. If there are two or more classes the type shall be designated by the author at the time of the proposal of the name, although authors are encouraged to respect priority by considering which class was described first. The type of a class or subclass is one of the contained orders, and if there is only one order this becomes the type. If there are two or more orders the type shall be designated by the author at the time of the proposal of the name.’
RULE 15 ‘A taxon consists of one or more elements. For each named taxon of the various taxonomic categories (listed below), there shall be designated a nomenclatural type. The nomenclatural type, referred to in this Code as ‘type’, is that element of the taxon with which the name is permanently associated, whether as a correct name or as a 4286
Table 1 provides a list of proposed names of phyla that can be submitted for validation after the proposed changes in the rules of the Code have been approved. It also lists names of phyla already in common use. We are mindful that the current proposal may prove problematic as it does not include a proposal for validation of well-established names such as Proteobacteria, Firmicutes, Crenarchaeota, Euryarchaeota and Thaumarchaeota, names that respectively must be changed to Alphaproteobacteraeota, Bacillaeota, Thermoproteaeota, Methanobacteraeota and Nitrososphaeraeota, based on the new Rule 8. These matters will need to be addressed in separate proposals and/or ‘Requests for an Opinion’ to be submitted to the ICSP and its Judicial Commission.
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Rank of phylum in the International Code
Our proposal is limited to those groups for which a nomenclatural type can be designated based on a type strain or type material of a species with a validly published name. Higher taxa equivalent to the rank of phylum for which no cultured representatives exist can be provisionally described as candidate phyla, similar to other ‘Candidatus’ taxa, whose nomenclature is not regulated by the rules of the ICNP. The term ‘superphylum’ has recently also come into common usage, but this rank is considered colloquial and therefore we do not recommend integration of this rank into the ICNP.
International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 28, 29 and 31 July and 1 August 2002, Paris, France. Int J Syst Evol Microbiol 55, 525–532. Garrity, G. M. & Oren, A. (2012). Response to Simonetta Gribaldo and Ce´line Brochier-Armanet: time for order in microbial systematics. Trends Microbiol 20, 353–354. Goodfellow, M. (1995). International Committee on Systematic
Bacteriology; XVIth International Congress of Microbiology. Minutes of the meetings, 2, 3, and 5 July 1994, Prague, Czech Republic. Int J Syst Bacteriol 45, 613–615. Gribaldo, S. & Brochier-Armanet, C. (2012). Time for order in
microbial systematics. Trends Microbiol 20, 209–210.
We submit these proposals to be discussed by the ICSP and its Judicial Commission.
McNeill, J., Barrie, F. R., Buck, W. R., Demoulin, V., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Marhold, K. & other authors (editors) (2012). International Code of Nomenclature
References
for algae, fungi, and plants (Melbourne Code) adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011. Regnum Vegetabile 154. Koenigstein: Koeltz Scientific Books.
De Vos, P. & Tru¨per, H. G. (2000). 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. Int J Syst Evol Microbiol 50, 2239–2244.
Parker, C. T., Garrity, G. M. & Tindall, B. J. (editors) (2016).
De Vos, P., Tru¨per, H. G. & Tindall, B. J. (2005). Judicial Commission
and their impact on the code of nomenclature of bacteria. Int J Syst Bacteriol 44, 368–369.
of the International Committee on Systematic Bacteriology; Xth
http://ijs.microbiologyresearch.org
International Code of Nomenclature of Prokaryotes. Prokaryotic Code. 2008 Revision. Published for the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 66, in press. Tru¨per, H. G. (1994). Taxonomic notes: Names for the higher taxa
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