1887

Abstract

Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-02-07
2024-07-14
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References

  1. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes – Prokaryotic Code (2008 Revision). Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article]
    [Google Scholar]
  2. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes – Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol In press
    [Google Scholar]
  3. Oren A, Arahal DR, Rosselló-Móra R, Sutcliffe IC, Moore ERB. Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum. Int J Syst Evol Microbiol 2021; 71:4851 [View Article]
    [Google Scholar]
  4. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020; 2020:baaa062 [View Article]
    [Google Scholar]
  5. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:005056 [View Article] [PubMed]
    [Google Scholar]
  6. Lloyd KG, Tahon G. Science depends on nomenclature, but nomenclature is not science. Nat Rev Microbiol 2022; 20:123–124 [View Article] [PubMed]
    [Google Scholar]
  7. Panda A, Islam ST, Sharma G. Harmonizing prokaryotic nomenclature: fixing the fuss over phylum name flipping. mBio 2022; 13:e00970-22 [View Article]
    [Google Scholar]
  8. Sutcliffe IC, Arahal DR, Göker M, Oren A. ICSP response to ‘Science depends on nomenclature, but nomenclature is not science’. Nat Rev Microbiol 2022; 20:249–250 [View Article]
    [Google Scholar]
  9. Turland N, Wiersema J, Barrie F, Greuter W, Hawksworth D et al. International Code of Nomenclature for algae, fungi, and plants Königstein im Taunus: Koeltz Botanical Books; 2018 [View Article]
    [Google Scholar]
  10. Ride W, Cogger HG, Dupuis C, Kraus O, Minelli A et al. International Code of Zoological Nomenclature London: International Trust for Zoological Nomenclature; 1999
    [Google Scholar]
  11. Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ et al. Unusual biology across a group comprising more than 15% of domain Bacteria . Nature 2015; 523:208–211 [View Article] [PubMed]
    [Google Scholar]
  12. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219 [View Article]
    [Google Scholar]
  13. Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956–4042 [View Article] [PubMed]
    [Google Scholar]
  14. Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71:004671 [View Article]
    [Google Scholar]
  15. Oren A, Garrity GM. Candidatus List No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72:005186 [View Article]
    [Google Scholar]
  16. Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017; 541:353–358 [View Article] [PubMed]
    [Google Scholar]
  17. Oren A. A plea for linguistic accuracy - also for Candidatus taxa. Int J Syst Evol Microbiol 2017; 67:1085–1094 [View Article] [PubMed]
    [Google Scholar]
  18. Whitman WB, Sutcliffe IC, Rossello-Mora R. Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names. Int J Syst Evol Microbiol 2019; 69:2174–2175 [View Article] [PubMed]
    [Google Scholar]
  19. Stearn WT. Botanical Latin Newton Abbot: David & Charles; 1973
    [Google Scholar]
  20. Oren A. Proposal to modify the Rules of the International Code of Nomenclature of Prokaryotes to abolish the taxonomic categories Subfamily, Subtribe and Kingdom. Int J Syst Evol Microbiol 2019; 69:1524–1525 [View Article]
    [Google Scholar]
  21. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
    [Google Scholar]
  22. Weon HY, Kim BY, Yoo SH, Joa JH, Kwon SW et al. Andreprevotia chitinilytica gen. nov., sp. nov., isolated from forest soil from Halla Mountain, Jeju Island, Korea. Int J Syst Evol Microbiol 2007; 57:1572–1575
    [Google Scholar]
  23. R Core Team R: A Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing; 2022
    [Google Scholar]
  24. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya . Proc Natl Acad Sci U S A 1990; 87:4576–4579 [View Article]
    [Google Scholar]
  25. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  26. Caspari R. Gesellschaften. Bericht über die Verhandlungen der botanischen Sektion der 33. Versammlung deutscher Naturforscher und Aerzte, gehalten in Bonn vom 18. bis 24. September 1857, von Dr. Rob. Caspary. Botanische Zeitung 1857; 15:749–776
    [Google Scholar]
  27. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci U S A 1977; 74:5088–5090 [View Article]
    [Google Scholar]
  28. Woese CR, Magrum LJ, Fox GE. Archaebacteria. J Mol Evol 1978; 11:245–252 [View Article]
    [Google Scholar]
  29. Murray RGE. The higher taxa, or, a place for everything…?. In Krieg NR, Holt JG. eds Bergey’s Manual of Systematic Bacteriology, first edition. vol 1 Baltimore: The Williams & Wilkins Co; 1984 pp 31–34
    [Google Scholar]
  30. Farris JS. Phylogenetic classification of fossils with recent species. Syst Zool 1976; 25:271–282 [View Article]
    [Google Scholar]
  31. Luketa S. New views on the megaclassification of life. Protistology 2012; 7:218–237
    [Google Scholar]
  32. Moore RT. Proposal for the recognition of super ranks. Taxon 1974; 23:650–652 [View Article]
    [Google Scholar]
  33. International Committee on Taxonomy of Viruses Executive Committee The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol 2020; 5:668–674
    [Google Scholar]
  34. Wiley EO. An annotated Linnaean hierarchy, with comments on natural taxa and competing systems. Syst Zool 1979; 28:308–337 [View Article]
    [Google Scholar]
  35. Cavalier-Smith T. The origin of cells: a symbiosis between genes, catalysts, and membranes. Cold Spring Harb Symp Quant Biol 1987; 52:805–824 [View Article] [PubMed]
    [Google Scholar]
  36. Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T et al. A higher level classification of all living organisms. PLoS One 2015; 10:e0119248 [View Article]
    [Google Scholar]
  37. Haeckel EH. Systematische Phylogenie der Protisten und Planzen Berlin: I.G. Reimer; 1894 [View Article]
    [Google Scholar]
  38. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420 [View Article]
    [Google Scholar]
  39. Tindall BJ. Names above the rank of genus; the radical approach. Int J Syst Evol Microbiol 2019; 69:1833–1834 [View Article] [PubMed]
    [Google Scholar]
  40. Cavalier-Smith T. Eukaryote kingdoms: seven or nine?. Biosystems 1981; 14:461–481 [View Article] [PubMed]
    [Google Scholar]
  41. Cavalier-Smith T. The origin of eukaryotic and archaebacterial cells. Ann N Y Acad Sci 1987; 503:17–54 [View Article] [PubMed]
    [Google Scholar]
  42. Cavalier-Smith T, Chao EE-Y. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 2020; 257:621–753 [View Article] [PubMed]
    [Google Scholar]
  43. Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006; 1:19 [View Article]
    [Google Scholar]
  44. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002; 52:7–76 [View Article] [PubMed]
    [Google Scholar]
  45. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev Camb Philos Soc 1998; 73:203–266 [View Article] [PubMed]
    [Google Scholar]
  46. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 2013; 4:2120 [View Article]
    [Google Scholar]
  47. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes . Front Microbiol 2016; 7:2003 [View Article]
    [Google Scholar]
  48. Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M et al. Candidatus Thermonerobacter thiotrophicus,” a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities. Front Microbiol 2018; 9:3159 [View Article]
    [Google Scholar]
  49. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes . Front Microbiol 2019; 10:2083 [View Article]
    [Google Scholar]
  50. Del Duca S, Riccardi C, Vassallo A, Fontana G, Castronovo LM et al. The histidine biosynthetic genes in the superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: insights into the evolution of gene structure and organization. Microorganisms 2021; 9:1439 [View Article]
    [Google Scholar]
  51. Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL et al. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015; 17:4929–4941 [View Article] [PubMed]
    [Google Scholar]
  52. Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Microbial life in the deep subsurface aquifer illuminated by metagenomics. Front Microbiol 2020; 11:572252 [View Article]
    [Google Scholar]
  53. Woese CR. How we do, don’t and should look at bacteria and bacteriology. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes New York, NY: Springer New York; 2006 pp 3–23
    [Google Scholar]
  54. Arahal DR, Busse H-J, Bull CT, Christensen H, Chuvochina M et al. Judicial Opinions 112-122. Int J Syst Evol Microbiol 2022; 72:5481 [View Article] [PubMed]
    [Google Scholar]
  55. Pujalte MJ, Macián MC, Arahal DR, Ludwig W, Schleifer KH et al. Nereida ignava gen. nov., sp. nov., a novel aerobic marine alpha-proteobacterium that is closely related to uncultured Prionitis (alga) gall symbionts. Int J Syst Evol Microbiol 2005; 55:631–636 [View Article] [PubMed]
    [Google Scholar]
  56. Alarico S, Rainey FA, Empadinhas N, Schumann P, Nobre MF et al. Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria . Syst Appl Microbiol 2002; 25:198–206
    [Google Scholar]
  57. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora . Int J Syst Bacteriol 1998; 48:411–422 [View Article]
    [Google Scholar]
  58. Tindall BJ. Standardised suffixes in the nomenclature of the higher taxa of prokaryotes an aid to data mining, database administration and automatic assignment of names to taxonomic ranks. Curr Microbiol 2020; 77:1135–1138 [View Article]
    [Google Scholar]
  59. Garrity GM, Holt JG. Phylum AI. Crenarchaeota phy. nov. In Boone DR, Castenholz RW, Garrity GM. eds Bergey’s Manual of Systematic BacteriologyThe Archaea and the deeply branching and phototrophic Bacteria, second edition. vol 1 New York: Springer-Verlag; 2001 pp 169–210
    [Google Scholar]
  60. List Editor Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685–690 [View Article]
    [Google Scholar]
  61. Jung M-Y, Park S-J, Kim S-J, Kim J-G, Sinninghe Damsté JS et al. A mesophilic, autotrophic, ammonia-oxidizing archaeon of thaumarchaeal group I.1a cultivated from a deep oligotrophic soil horizon. Appl Environ Microbiol 2014; 80:3645–3655 [View Article]
    [Google Scholar]
  62. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 2011; 108:15892–15897 [View Article]
    [Google Scholar]
  63. Antoine E, Cilia V, Meunier JR, Guezennec J, Lesongeur F et al. Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the southwestern Pacific Ocean. Int J Syst Bacteriol 1997; 47:1118–1123 [View Article]
    [Google Scholar]
  64. Barns SM, Takala SL, Kuske CR. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 1999; 65:1731–1737 [View Article]
    [Google Scholar]
  65. Lepage E, Marguet E, Geslin C, Matte-Tailliez O, Zillig W et al. Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microbiol 2004; 70:1277–1286 [View Article]
    [Google Scholar]
  66. Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 2017; 11:2407–2425 [View Article] [PubMed]
    [Google Scholar]
  67. Bulzu P-A, Andrei A-Ş, Salcher MM, Mehrshad M, Inoue K et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019; 4:1129–1137 [View Article] [PubMed]
    [Google Scholar]
  68. Whitman WB, Bull CT, Busse H-J, Fournier P-E, Oren A et al. Request for revision of the Statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:584–593 [View Article] [PubMed]
    [Google Scholar]
  69. Allsopp A. Phylogenetic relationships of the Procaryota and the origin of the eucaryotic cell. New Phytol 1969; 68:591–612 [View Article]
    [Google Scholar]
  70. Margulis L, Olendzenski L, Dolan M, MacIntyre F. Diversity of eukaryotic microorganisms: computer-based resources, “The Handbook of Protoctista” and its “Glossary.”. Microbiologia 1996; 12:29–42
    [Google Scholar]
  71. Murray RGE. Microbial structure as an aid to microbial classification and taxonomy. Spisy Fac Sci Univ Purkyne 1968; 43:245–252
    [Google Scholar]
  72. Gupta RS. Life’s third domain (Archaea): an established fact or an endangered paradigm?. Theor Popul Biol 1998; 54:91–104 [View Article] [PubMed]
    [Google Scholar]
  73. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499:431–437 [View Article] [PubMed]
    [Google Scholar]
  74. Lake JA, Henderson E, Oakes M, Clark MW. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci U S A 1984; 81:3786–3790 [View Article]
    [Google Scholar]
  75. Gupta RS. The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes . Crit Rev Microbiol 2004; 30:123–143 [View Article] [PubMed]
    [Google Scholar]
  76. Battistuzzi FU, Hedges SB. A major clade of prokaryotes with ancient adaptations to life on land. Mol Biol Evol 2009; 26:335–343 [View Article] [PubMed]
    [Google Scholar]
  77. Barns SM, Delwiche CF, Palmer JD, Pace NR. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci U S A 1996; 93:9188–9193 [View Article]
    [Google Scholar]
  78. Copeland HF. The kingdoms of organisms. Quart Rev Biol 1938; 13:383–420 [View Article]
    [Google Scholar]
  79. Petitjean C, Deschamps P, López-García P, Moreira D. Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota . Genome Biol Evol 2014; 7:191–204 [View Article] [PubMed]
    [Google Scholar]
  80. Wagner M, Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 2006; 17:241–249 [View Article] [PubMed]
    [Google Scholar]
  81. Guy L, Ettema TJG. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol 2011; 19:580–587 [View Article]
    [Google Scholar]
  82. Battistuzzi FU, Feijao A, Hedges SB. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 2004; 4:44 [View Article]
    [Google Scholar]
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