The Next Million Names for Archaea and Bacteria

Abstract

Microbiology has entered a golden era of discovery, with exponential growth in the identification of new species, genera, and high-level taxa through culturomics, genomics, and metagenomics.This creates an urgent unmet need for new taxonomic names for Archaea and Bacteria.Currently, creation of well-formed names relies on time-consuming nomenclatorial quality control by a dwindling pool of experts conversant with classical languages and the International Code of Nomenclature of Prokaryotes.These problems are compounded by the custom of creating names on an as-needed, just-in-time-fashion.Here, we outline a novel approach with three features: creation of names en masse before they are tied to taxa; combinatorial concatenation of roots from Latin and Greek, drawing on stocks of roots with relevant meanings; computerised automation of the creation of new names. Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come. Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come. In the 18th century, the Swedish naturalist Linnaeus proposed a hierarchical scheme of taxonomy (see Glossary) that assigned Latin binomials to biological species [1.Linnaeus C. Systema Naturae.10th edn. Laurentius Salvius, 1759Google Scholar]. Shortly afterwards, the first genus names were applied to bacteria [2.Müller O.F. Animalcula infusoria fluviatilia et marina, quae detexit, systematice descripsit et ad vivum delineari curavit. Typis Nicolai Mölleri, 1786Google Scholar]. In the 19th century, Darwin’s Origin of Species provided an evolutionary framework for taxonomy, confidently proclaiming: 'Our classifications will come to be, as far as they can be so made, genealogies' [3.Darwin C. On the Origin of Species.1st edn. John Murray, 1859Google Scholar]. In the 20th century, Hennig brought clarity to evolutionary taxonomy through the development of 'phylogenetic systematics', now commonly called cladistics, which stipulated that biological classifications must represent the phylogenies of organisms and that taxa should represent monophyletic groups [4.Hennig W. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, 1950Google Scholar]. Linnaean binomials, drawing on combinations of Latin and Ancient Greek roots, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. Efforts to codify bacterial nomenclature have culminated in the International Code of Nomenclature of Prokaryotes (ICNP or 'the Code') [5.Parker C.T. et al.International Code of Nomenclature of Prokaryotes.Int. J. Syst. Evol. Microbiol. 2019; 69: S1-S111Crossref PubMed Scopus (119) Google Scholar], which sets out the rules for naming species of Archaea and Bacteria. The enduring legacy of Linnaeus in microbiology is evident from the remarkable success of the ICNP in overseeing the valid publication of names for over 3400 bacterial and archaeal genera and over 20 000 bacterial and archaeal species. These names are superbly well documented in the List of Prokaryotic names with Standing in Nomenclature (https://www.bacterio.net) [6.Parte A.C. et al.List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ.Int. J. Syst. Evol. Microbiol. 2020; (Published online July 23, 2020. https://doi.org/10.1099/ijsem.0.004332)Crossref PubMed Scopus (170) Google Scholar]. However, there are clearly several shortcomings to the current approach to nomenclature of Archaea and Bacteria. The most obvious is a deficiency in scale. Comparable efforts for eukaryotes document hundreds of thousands of genera and millions of species (http://www.catalogueoflife.org/annual-checklist/2019/info/about) [7.Rees T. et al.All genera of the world: an overview and estimates based on the March 2020 release of the Interim Register of Marine and Nonmarine Genera (IRMNG).Megataxa. 2020; 1: 123-140Crossref Google Scholar]. Although estimates of the total number of bacterial and archaeal species vary from millions to billions [8.Dykhuizen D.E. Santa Rosalia revisited: why are there so many species of bacteria.Antonie van Leeuwenhoek. 1998; 73: 25-33Crossref PubMed Scopus (218) Google Scholar,9.Amann R. Rosselló-Móra R. After all, only millions.mBio. 2016; 7e00999-16Crossref PubMed Scopus (26) Google Scholar], even the most conservative figures amply document an unmet need for many millions of new names for genera and species of Archaea and Bacteria. Another pressing problem is that most microbiologists follow Shakespeare in possessing, at best, 'small Latin, less Greek' [10.Jonson B. To the memory of my beloved, The Author Mr William Shakespeare: And what he hath left us.in: Mr. William Shakespeares Comedies Histories & Tragedies: Published according to the True Originall Copies. Isaac Iaggard and Edward Blount, 1623Google Scholar] and so are poorly equipped for creating well-formed binomials that comply with the rules of Latin grammar and are presented with clear, plausible etymological justifications (Box 1). Despite the publication of several 'how-to' guides [11.MacAdoo T.O. Nomenclatural Literacy.in: Goodfellow M. Handbook of new bacterial systematics. Academic Press, 1993: 339-358Google Scholar, 12.Trüper H.G. How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature.FEMS Microbiol. Scholar, How to name new taxa of Archaea and Manual of of Archaea and Bacteria. John Scholar], has to of a is the species which even in the International of before to be according to the rules of Latin to of the publication of new names and new combinations the List J. Syst. Scopus Google nomenclature of J. Syst. Scopus Google Scholar]. are by the of the which many and difficult rules and on how names should be [5.Parker C.T. et al.International Code of Nomenclature of Prokaryotes.Int. J. Syst. Evol. Microbiol. 2019; 69: S1-S111Crossref PubMed Scopus (119) Google Scholar]. These that new names have to time-consuming nomenclatorial quality control by a dwindling pool of are to be conversant with classical the and microbiology et microbiologists with of Latin and Greek to our quality J. Syst. Evol. Microbiol. PubMed Scopus Google Scholar]. 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