Valid publication of names of two domains and seven kingdoms of prokaryotes

Abstract

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, ‘Bacteria’ and ‘Archaea’, as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including ‘diderms’ vs. ‘monoderms’, Gracilicutes vs. Firmicutes , ‘Negibacteria’ vs. ‘Unibacteria’, ‘Hydrobacteria’ vs. ‘Terrabacteria’, and ‘Hydrobacterida’ vs. ‘Terrabacterida’. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into ‘ Euryarchaeota ’, ‘DPANN superphylum’ and ‘TACK superphylum’.

Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.

“…‘L. ossiferum’ each respectively remain the only isolated and only enriched representatives of the lineage ‘Asgard’ archaea/‘Asgardarchaeota’, which lacks a formal phylum name that conforms to ICNP regulations [13, 14]. Furthermore, this lineage is also distinct from other archaeal phyla/supergroups [3, 30] that comprise the three archaeal kingdoms (), i.e ., Methanobacteriati , Thermoproteati , and Nanobdellati , which have been proposed in accordance with the recent emendation of ICNP to include the category of kingdom [14].…”

“…ossiferum’ each respectively remain the only isolated and only enriched representatives of the lineage ‘Asgard’ archaea/‘Asgardarchaeota’, which lacks a formal phylum name that conforms to ICNP regulations [13, 14]. Furthermore, this lineage is also distinct from other archaeal phyla/supergroups [3, 30] that comprise the three archaeal kingdoms (), i.e ., Methanobacteriati , Thermoproteati , and Nanobdellati , which have been proposed in accordance with the recent emendation of ICNP to include the category of kingdom [14]. Supporting the hypothesis that ‘Asgard’ archaea/‘Asgardarchaeota’ represent a distinct ( i.e ., fourth) kingdom, we find that the average evolutionary distances (based on the silva r138.1 16S rRNA gene alignment) between ‘Asgard’ archaea/‘Asgardarchaeota’ and Methanobacteriati or Thermoproteati are significantly different ( P <0.05) from the distances within those kingdoms (>0.286 vs .…”

“…Here, we report the strain’s detailed physiological properties and propose the name Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate the strain, as well as the associated family, order, class, phylum, and kingdom names in accordance with the current International Code of Nomenclature of Prokaryotes (ICNP) rules [11–14].…”

Plasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column

“…As previously mentioned, identification of marine smBGC episomes is likely hindered by limitations of bioinformatic pipelines and databases, as well as by the difficulties of culturing many marine prokaryotic strains (e.g., [62][63][64]). Within Cariaco Basin's redoxcline, the majority of recovered MAGs were associated with Omnitrophota (56), Chloroflexota (49), Myxococcota (33), Planctomycetota (65), Desulfobacterota (43) (now classified as Thermodesulfobacteriota; [65,66]) that collectively comprised ~55% of the assembled bacterial MAGs (463 bacterial and 102 archaeal MAGs, 565 MAGs in total; see Supplementary Data and Figure 1a from [12]). Some of these phyla (e.g., Omnitrophota) are difficult to cultivate, and hence, information on their overall genomic organization is limited.…”