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Notes on the Characterization of Prokaryote Strains for Taxonomic

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Notes on the Characterization of Prokaryote Strains for Taxonomic View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC International Journal of Systematic and Evolutionary Microbiology (2010), 60, 249–266 DOI 10.1099/ijs.0.016949-0 Taxonomic Notes on the characterization of prokaryote strains Note for taxonomic purposes B. J. Tindall,1 R. Rossello´-Mo´ra,2 H.-J. Busse,3 W. Ludwig4 and P. Ka¨mpfer5 Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Brian J. Tindall D-38124 Braunschweig, Germany [email protected] 2Grup de Microbiologia Marina, Departament d’Ecologia I Recursos Marins, IMEDEA (CSIC-UIB), C/Miquel Marque´s 21, E-07190, Esporles, Spain 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, University of Veterinary Medicine Vienna, Veterina¨rplatz 1, A-1210 Vienna, Austria 4Lehrstuhl fu¨r Mikrobiologie, Technische Universita¨t Mu¨nchen, Am Hochanger 4, D-85354 Freising-Weihenstephan, Germany 5Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, Heinrich-Buff-Ring 26- 32 (IFZ), D-35392 Giessen, Germany Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers. INTRODUCTION placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these The characterization of a strain is a key element in become defined. Although this approach may appear prokaryote systematics. Although various new methodo- novel, with much emphasis currently being placed on the logies have been developed over the past 100 years, both species, the advent of 16S rRNA gene sequencing forces us the newer methodologies and those considered to be to choose between primers that are specific for members of ‘traditional’ remain key elements in determining whether a the Archaea or for members of the Bacteria, so the first step strain belongs to a known taxon or constitutes a novel one. in that direction is already routine in many laboratories. In the case of a known taxon, a selected set of tests may be However, such a classification system is only possible if used to determine whether a strain has been identified as a strains are comprehensively and properly characterized. A member of an existing taxon. However, in the case of a further key element is the way in which datasets are strain or set of strains shown to be novel taxa, they compared and it is here too that some degree of guidance should be characterized as comprehensively as possible. and a discussion of the potential problems needs to be The goal of this characterization is to place them within provided. In the case of species, various recommendations the hierarchical framework laid down by the have been made with respect to the ways in which species Bacteriological Code (1990 revision) (Lapage et al., may be delineated and it is important to consider these 1992), as well as to provide a description of the taxa. aspects when considering how new strains are to be placed Strains should be allocated to species (and/or subspecies), in novel species. However, far too little attention has been but the nature of the ‘species name’ (a binomial or paid to the way in which taxa above the rank of species combination) dictates that it must also be assigned to a should be characterized and modern prokaryote taxonomy genus. The genus may be either an existing or a novel would benefit from paying greater attention to the ranks genus. The Bacteriological Code also recommends that the above those of species. Abbreviations: AFLP, amplified fragment-length polymorphism; DDH, The purpose of the present article is to deal with current DNA–DNA hybridization; LPS, lipopolysaccharides; MLSA, multilocus methodologies and to outline how these methods should sequence analysis; MLST, multilocus sequence typing. be best used and implemented. It does not set out to guide 016949 G 2010 IUMS Printed in Great Britain 249 B. J. Tindall and others the reader as to how the results should be interpreted, published. Data may be supplied by colleagues who do not although there are some aspects that are not widely wish to be co-authors, but have given their consent for the appreciated, where an indication of the value of the dataset results to be published, or they may be supplied as part of a may be helpful. The article is divided into genetic scientific service. In both cases, the source of the data (including protein sequence-based methods) and pheno- should be given clearly and unambiguously in order to typic methods. The latter include aspects such as cell shape, make it obvious that the data were not collected by the size, physiological and biochemical tests, as well as methods authors. Methods must be given. of chemical analysis of the cell. The importance of types Information on the strains being studied It should be remembered that in prokaryote taxonomy In a publication, the information presented on the the inclusion of types is of central importance. Although strains being studied should be as complete as possible. not laid down by the Code, since the Code deals with It should include the location from which the strains matters of nomenclature and not matters of taxonomy, it is were isolated (geographical references may also include taxonomic common sense to include all type strains that GPS or latitude/longitude data where possible), the are relevant to a study. Where members of different genera strain designations (including any culture collection are included and not all species belonging to those genera accession numbers) and any information that relates to can be taken into consideration, the inclusion of the type the environment from which the strains were isolated species of the genera under study is of utmost importance. (e.g. pH, salinity, temperature, chemical composition of Naturally, the type strain of that type species must be used. the environment, depth of the water column or soil It must be emphasized that the type species of the genus is profile). However, care should be taken in using such data the most important reference organism to which a novel to formulate conclusions regarding the ecological signifi- species has to be compared if it is considered to be a cance of the novel strain in the environment without member of the same genus. Other species of the same further studies (role of the organism in the environment, genus may be misclassified and may be subject to cell counts, etc.). Note that it is unacceptable to cite a reclassification in the future. Similarly, a species placed in culture collection number if that strain has not been a new genus must be compared with species of closely obtained directly from a collection (e.g. DSM 1234 vs related taxa, which must include the type species of the derived from strain DSM 1234 and supplied by x). This genera under study. In the case of comparisons across information may also be required by culture collections or families, the type genera must be included, and by databases such as GenBank, DDJB or EBI/EMBL and it is extension, the type strains of the type species of the type the responsibility of the author(s) to make sure that all the genera. Many papers published in the IJSEM seriously information is consistent in order to avoid the accumula- violate this elementary taxonomic principle. It should be tion of errors. Where reference is made to a strain as a borne in mind that the types of certain taxa may be type strain, this should be clearly indicated in the organisms that are pathogenic to humans, animals or publication, database entry (GenBank/DDBJ /strain5 plants. Not all researchers have access to the facilities or ‘,strain_id.’ /note5‘,type strain of.,Genus.,spe- permits for handling such organisms. This should be taken cies.’ or EMBL /strain5‘type strain: ,strain_id.’), or into consideration before research is begun and also by the the culture collection accession form. The current policy of editors of manuscripts that would normally require GenBank, DDBJ and EBI/EMBL is not to accept new comparative studies with such organisms. taxonomic names until they have appeared in print. In order for the database staff to update the names, it is important that the strain can be accurately identified by using the GENETIC-BASED METHODS associated information submitted to the database. This information will also enable the entry to be linked to the Modern prokaryote taxonomy has been strongly influenced relevant publication. by developments in genetic methods. The elucidation of the structure of DNA and the deciphering of the genetic code were major steps forward in biology. The long-term Source of the data in the publication goal of researchers in the 1950s was to be able to gain rapid The data presented in a manuscript may be derived from a access to the genome sequence data, a goal that was realized number of different sources. Original data should be based by the mid 1990s. Even prior to the elucidation of whole on results collected using the methods described in the text.
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