Prokaryotic taxonomy and nomenclature in the age of big sequence data

Abstract

The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.

Combining Imaging Flow Cytometry and Molecular Biological Methods to Reveal Presence of Potentially Toxic Algae at the Ural River in Kazakhstan

“…We choose to use a combination of optical methods (IFC) and NGS because the classical optical-based morphological methods may not provide sufficient identification resolution (Eiler et al, 2013;Xiao et al, 2014;Zimmerman et al, 2015;Dzhembekova et al, 2017;Parulekar et al, 2017). Moreover, the traditional cyanobacterial taxonomy has been based on morphological features, but this classification is revised with an accumulation of molecular sequence data (Komárek et al, 2014;Hugenholtz et al, 2021). The taxonomic classification was done with a 16S NCBI database, however, the choice of database may have an effect on the results of taxonomic identification (Park and Won, 2018;Rizal et al, 2020;Winand et al, 2020).…”

Emendation of the Coccoid Cyanobacterial Genus Gloeocapsopsis and Description of the New Species Gloeocapsopsis diffluens sp. nov. and Gloeocapsopsis dulcis sp. nov. Isolated From the Coastal Range of the Atacama Desert (Chile)

“…Some works on genome-based phylogenetics even go one step further by proposing new genus and species concepts (Walter et al, 2017;Salazar et al, 2020) without giving genus and species descriptions by ignoring morphological features of the investigated strains. Currently, these proposed taxonomic concepts have not gained acceptances among taxonomists working on cyanobacteria and, for example, the establishment of type strains solely on genome date has just recently been rejected by the International Committee on Systematics of Prokaryotes (the committee which governs the Prokaryotic Code; Sutcliffe et al, 2020;Hugenholtz et al, 2021).…”

Final Destination? Pinpointing Hyella disjuncta sp. nov. PCC 6712 (Cyanobacteria) Based on Taxonomic Aspects, Multicellularity, Nitrogen Fixation and Biosynthetic Gene Clusters

“…Moreover, this study emphasizes that ignoring morphological features and focusing only on genetic- or genome-based phylogenetics to propose new genera and species concepts [ 68 , 69 ] without giving genus and species descriptions of the investigated strains, leads to confusion and frequent revisions of the taxonomic concept. Currently, taxonomic concepts purely based on genetics have not gained acceptance among cyanobacterial taxonomists and, for example, the establishment of type strains solely on genome data has just recently been rejected by the International Committee on Systematics of Prokaryotes (the committee which governs the Prokaryotic Code) [ 70 , 71 ].…”