Notes on the characterization of prokaryote strains for taxonomic purposes

Abstract

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. INTRODUCTIONThe characterization of a strain is a key element in prokaryote systematics. Although various new methodologies have been developed over the past 100 years, both the newer methodologies and those considered to be 'traditional' remain key elements in determining whether a strain belongs to a known taxon or constitutes a novel one. In the case of a known taxon, a selected set of tests may be used to determine whether a strain has been identified as a member of an existing taxon. However, in the case of a strain or set of strains shown to be novel taxa, they should be characterized as comprehensively as possible. The goal of this characterization is to place them within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992), as well as to provide a description of the taxa. Strains should be allocated to species (and/or subspecies), but the nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined. Although this approach may appear novel, with much emphasis currently being placed on the species, the advent of 16S rRNA gene sequencing forces us to choose between primers that are specific for members of the Archaea or for members of the Bacteria, so the first step in that direction is already routine in many laboratories. However, such a classification system is only possible if strains are comprehensively and properly characterized. A further key element is the way in which datasets are compared and it is here too that some degree of guidance and a discussion of the potential problems needs to be provided. In the case of species, various recommendations have been made with respect to the ways in which species may be delineated and it is important to consider these aspects when considering how new strains are to be placed in novel species. However, far too little attention has been paid to the way in which taxa above the rank of species should be characterized a...

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

“…Operational taxonomic units (OTUs) were assigned at 95% and 97% similarity threshold levels, representing bacterial genera and species according to Tindall et al (2010). Richness estimators, diversity indices and coverage percentage were calculated from randomly subsampled set of sequences (based on the smallest dataset) in mothur.…”

Burkholderia zhejiangensis sp. nov., a methyl-parathion-degrading bacterium isolated from a wastewater-treatment system

“…A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences was constructed and this clearly clustered strain OP-1 T with members of the genus Burkholderia (Fig. 1).When two strains share more than 97 % 16S rRNA gene sequence similarity, the use of DNA-DNA hybridization, to determine if the strains probably represent a single species or two, is recommended (Tindall et al, 2010). In the present study, only one recognized species, B. glathei ATCC 29195 T , showed such a high level of 16S rRNA gene sequence similarity with strain OP-1 T and was therefore run in reciprocal DNA-DNA hybridizations with the novel strain.…”

The 16S rRNA gene in the study of marine microbial communities

“…Durante los últimos 50 años, la hibridación ADN-ADN (DDH, por sus siglas en inglés) ha sido considerada una herramienta de oro para la comparación de procariotas, y parece ser muy útil para medir directamente el grado de similitud entre dos genomas. En la actualidad, en aquellos casos donde un taxón contiene más de una cepa, se recomienda la aplicación de esta técnica para mostrar el grado de hibridación y la similitud entre los probables miembros (Tindall et al 2010). El uso de DDH también se recomienda para demostrar cercanía cuando las cepas tienen más del 97% de similitud en sus secuencias de ARNr 16S.…”

“…It is still used to show the degree of hybridization and similarity between probable members in those cases where one taxon has more than one strain (Tindall et al 2010). The DDH technique is also recommended for determining closeness when strains have more than 97% 16S rRNA sequence similarity.…”