Validation Request: Proposal to Grant an Exception under Rule 18a in Order to Validate the name ‘Paceibacter normanii’

[tvtv195]

Validation request: proposal to grant an exception under Rule 18a in order to validate the name ‘Omnitrophus fodinae’

Author/s of the original request: Chris Rinke (1)

 1. University of Innsbruck, 6020 Innsbruck, Tirol, Austria 

Reason for request: type material does not meet the quality standards, but abundant evidence of the species existence and novelty has been accumulated in the literature.

Effective publication: Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). https://doi.org/10.1038/nature12352

Proposed type genome
Single-Cell Amplified Genome GCA_000398025.1; Completeness: 78.23%, Contamination: 0.79% (CheckM2); Contains 16S rRNA and 23S rRNA genes phylogenetically concordant with other marker genes.

Evidence for taxon and its novelty
In the original publication (Rinke et al., 2013), nine SAGs were identified based on a Small Sub-Unit (SSU) ribosomal RNA (rRNA) gene phylogeny as belonging to the candidate grouping OD1, previously identified from rRNA gene sequences (Harris et al. 2004; 10.1128/AEM.70.2.845-849.2004). Phylogenetic reconstruction based on 38 marker sequences also supported delineation of these four genomes as distinct from other phyla (Rinke et al., 2013), and the highest estimated quality SAG (SAK, MDM ID 138, SCGC AAA255-P19) was selected to serve as type for a novel phylum. Since the initial proposal, the novelty and monophyly of this taxon has been supported by several studies, including a phylogenetic analysis based on non-redundant marker set, consisting of 16 ribosomal proteins and 2 RNA polymerase subunits (Jaffe et al. 2020; https://doi.org/10.1186/s12915-020-00804-5).
Subsequently, names for the associated higher ranks (Paceibacteraceae, Paceibacterales, Paceibacteria), formed by the addition of the appropriate suffix to the stem of the type genus name, were proposed (Chuvochina et al. 2023)

(i) The species can be unambiguously identified using genomic metrics and phylogenetic analyses; (ii) the proposed type genome is a representative genome of the species cluster bearing this name in GTDB; (iii) the publication that introduce this species and its associated phylum name has been cited over thousand times and these names have been used in literature for a decade; (iv) it is the first genomic representative of this lineage, which has been assigned the rank of class (Paceibacteria) in the phylum Patescibacteriota (former Patescibateria) in GTDB.

Classification:
p__Patescibacteria; c__Paceibacteria; o__Paceibacterales; f__Paceibacteraceae; g__Paceibacter; s___Paceibacter normanii_

Submitter comments: “This genome has lower completeness than suggested by standards, but we request lowering of the requirement here, because this is a historical name and allows us to keep the nomenclature for the entire class. Despite several attempts at recovering a higher completeness genome from metagenomic data, no other genomes with the required completeness >90% has been recovered for the genus, thus in order to retain the historical genus through class names with the least amount of confusion, we request special consideration for validation with this genome as type.”

Taxon description: “This species is the type of the genus g__Paceibacter. No data on cell size in the species is available. This species is represented by only one medium-quality genome, however, for historical significance, this genome serves as the nomenclatural type for the species. The %GC content of the genome is 39.03%. The available genome is estimated to be 78 % complete. This organism originated from brackish water sampled in 120 m depth in Sakinaw Lake (49°40'30"N, 124°2'2.4"W). F. The nomenclatural type for the species is the genome GCA_000398025.1.”

Historical significance
The effective publication (Rinke et al., 2013) has accrued 2,400 citations at the time of writing, and the derived class name “Pacubacteria” (= now updated to “Paceibacteria”) is found in the title or the abstract of 95 journal articles (pubmed).

Relevant SeqCode Rules and Recommendations
Rule 18a
“The type of a species or subspecies is a designated DNA sequence that is compliant with the
minimum standards designated by the SeqCode Committee for genome, metagenome-assembled
genome, or single-amplified genome sequences […] Upon recommendations of the SeqCode Committee or subcommittees on the taxonomy of specific groups, the SeqCode Committee may approve other minimal standards as suitable types for specific groups.”

Appendix I, Data quality necessary for completion of SeqCode Registry*
Required
-Type genome assembly quality for MAGs and SAGs: >90% complete and <5% contaminated (modified from Bowers et al., 2017). For isolates, read coverage ≥10x (Field et al., 2008).
-Agreement between genome and 16S rRNA taxonomic assignments

Recommended
16S rRNA genes >75% complete and passes chimera checks >80% of tRNAs present (modified from Bowers et al., 2017).
High genome integrity (contig # <100; N50 >25 kb; max. contig >100 kb).
MAG/SAG read coverage ≥10x.

• Data quality will be assessed by automated pipelines or other approaches. Exceptions for lower data quality should be justified by authors in the effective publication.

Reconciliation considerations
We request opinions from the SeqCode community on whether this taxon name can be validated based on the proposed genome sequence so that the genus name can serve as a nomenclatural type for higher taxonomic ranks including the rank of class, thus preserving the historical name for this taxon. Any additional attempts to recover a better quality genome for this species failed (personal communication).

Potential outcomes
A. Reject the proposal to validate the name “Paceibacter normanii” because there is not enough evidence to support the taxon description.
B. Accept the proposal to validate the name “Paceibacter normanii” based on the medium-quality draft genome.

[tpriest0]

Dear submitter,

The Reconciliation Commission (RC) assessed your request and concluded that there is currently no need to request an exception to validate the species name Paceibacter normanii and its corresponding genus and higher taxa names. These names fall under the recently amended Rule 23d (related to the Rule 23b), as the genus name was published before 1 January 2022 and there is no competing ICNP genus name validated before that date. Rule 23d protects Candidatus higher taxon names and also genus names until 1 January 2027, allowing time to obtain a higher-quality genome sequence to validate the corresponding taxon names. This means that even if a synonym is published under the ICNP after January 1, 2022, the Candidatus name will take priority if it can be validated before 2027.

Additionally, the RC does not see a need to validate this name at present, as it can only serve as a nomenclatural type for the family, while the order and class names already have validly published names under the ICNP (Minisyncoccales and Minisyncoccia). The phylum name has been also recently validated under the SeqCode (Patescibacteriota). The RC agreed that there is also no need for a public discussion at this stage and hopes that future sequencing efforts will yield a better-quality genome for the species Paceibacter normanii.

If you have any further questions, please do not hesitate to reach out to myself or another member of the Reconciliation Commission.