Register list for 16 new names including Pantoea alvi sp. nov.

This species consists of the genomes of strain WMus005, isolated from the oral cavity of a wild house mouse (Mus musculus) in the United Kingdom, and the metagenome-assembled genome (MAG) UBA5707 recovered from a metagenomic sample taken from the New York City subway system. Pairwise ANI of the two genomes is over 99% and they thus clearly belong to the same species, with all comparisons to other species below species delineation guidelines. The nomenclatural type for the species is the genome UBA5707^Ts, available under the assembly accession number GCA_002419935.1.

This species consists of a single MAG, UBA6564, which was assembled from a metal surface in New York City. P. conspicua is the most closely related known species, and the ANI between P. astica UBA6564 and the P. conspicua type strain is below 95% confirming that this genome represents a separate species.

At least four genomes are available for this species. One genome is of the strain Russ isolated from an indoor trash can in Stillwater, Oklahoma, USA. The other three genomes are MAGs derived from environmental samples of metallic or plastic surfaces on the New York City subway. Pairwise ANI among the 4 genomes is over 99.25% revealing that they belong to a single clonal lineage. The P. borealis clade shares an most recent common ancestor with P. eucrina, and the ANI between genomes of the P. eucrina and this species is approximately 93%. One publication on a representative genome of this species cluster is available and discusses its potential for being an opportunistic human pathogen (Moghadam et al. 2016), however, evidence for pathogenicity isn't available. The nomenclatural type for the species is the MAG UBA6694^Ts, available under the GenBank assembly accession number GCA_002454735.1.

This species includes the genome of a single strain, RIT388, isolated from an Ayan tree (Distemonanthus benthamianus) known for its antifungal and antibacterial properties (Soutar and Stavrinides 2019), (Gan et al. 2020). This genome is located on the branch splitting off at the most basal node of the clade that includes P. septica, P. alvi, P. piersonii, and "P. latae".

This species consists of the genomes of two strains: OV426, isolated during characterization of Populus root and rhizosphere microbial communities in Tennessee, USA, and AF015A5, isolated from an indoor dust sample in Oregon, USA (GCF_004798195.1). The two genomes have a pairwise ANI of approximately 97% and thus clearly belong to the same species. The genome of strain OV426 does not contain the enterobactin biosynthesis cluster, while it does contain the pagRI genes encoding the autoinducer system (Sulja et al. 2022). This strain also contains a Hrp-2a T3SS, but its functionality has not been examined (Moretti et al. 2021). The nomenclatural type for the species is the genome of OV426^Ts, available under the NCBI assembly accession number GCF_900115075.1.

This species includes nine genomes that belong to P. symbiotica sp. nov. The clade corresponding to this group is a sister clade of the "P. endophytica" clade. Pairwise ANI between the eight genomes is over 97%, while ANI between them and "P. endophytica" genomes, which represent the most closely related known species, is approximately 93%, showing that these strains do in fact represent a separate species. The strains were isolated from poplar (Populus deltoides) roots along the Caney Fork River in Tennessee, USA; Eastern cottonwood poplar roots on the Yadkin River in North Carolina, USA (Brown et al. 2012); from fungi in New York State, USA (Wong et al. 2020); and as endophytes of grapevine. Based on these isolation sources, this species appears to be adapted to the rhizosphere. The nomenclatural type for the species is the genome of strain YR512^Ts, available under the GenBank assembly accession number GCF_900114175.1.

The species consists of the genome of a single strain, JKS000234. Its source of isolation is a fungus-farming ant garden in Wekiwa Springs State Park, Apopka, Florida. This species shares an most recent common ancestor with P. variicola sp. nov. The ANI between the genomes of the two species is below 90%.

This species comprises two genomes, PSNIH6 and UMGS54. The corresponding clade is a sister-clade of P. septica. PSNIH6, the strain whose genome serves as nomenclatural type, was isolated from hospital plumbing in the USA, while MAG UMGS54 was assembled from the metagenome of a human gut sample. The two genomes have a pairwise ANI of over 99.75%. Therefore, P. alvi sp. nov. may occupy a similar ecological niche to its sister species P. septica. The genome of PSNIH6^Ts is the nomenclatural type for the species.

Based on the BioSample metadata available for genomes in this group, all strains of this species were recovered as epiphytes from diseased cotton leaves (Gossypium hirsutum), from the Punjab province of Pakistan. This species is supported as distinct and exclusive through phylogenomics and is supported by the GTDB. The minimum pairwise ANI of genomes within this species is 99.25% and the ANI to the most similar genomes outside of the species is approximately 94%. Three clonal lineages can be distinguished based on phylogeny and ANI. However, based on reverse ecology analysis using PopCOGenT, all strains of the species cluster belong to the same population suggesting that the clonal lineages have not adapted to separate ecological niches. The nomeclatural type for the species is the genome of strain B-8^Ts, available under the GenBank assembly accession number GCA_008632075.1.

This species consists of seven genome-sequenced strains. The genomes are monophyletic with phylogenomic analyses. This clade shares an ancestor with the genomes of the GTDB species "Pantoea rwandensis_B". The minimal pairwise ANI among the seven genomes is as low as 97%. ANI between the seven genomes and and the closest relative is approximately 94%, showing that the two clades represent two different, but closely related, species. Isolation sources include insects, like stink bugs (Plautia stali, Sibaria englemani, Taurocerus sp.), and an ant (Atta laevigata) fungus garden, as well as plants (Garcinia morella) and other environmental sources. Overall, this species shares plants and insects as isolation sources with many other Pantoea species, and no adaptation to any specific environment is evident.

This species is represented by the genome of a single strain, Acro-805, isolated from the fungal garden of an ant belonging to the genus Acromyrmex, in Brazil. It shares an MRCA with the type strain of P. rwandensis LMG 26275^T. The pairwise ANI between the two strains is approximately 92% supporting the designation of this species as distinct and novel.

This species consists of the genomes of two strains, A4 and Acro-835, which have a pairwise ANI of approximately 96%, likely indicating higher genomic diversity within this species. Strain A4 was isolated from a decaying flower bud in Malaysia while strain Acro-835 was isolated from an ant (Acromyrmex) fungus garden in Brazil. This species splits off at a basal node within the Pantoea phylogeny, with lower than 80% ANI to the genomes of the closest known relatives. The nomenclatural type for the species is the genome of Acro-835^Ts, available under the GenBank assembly accession number GCF_011752615.1.

This species currently consists of the genome of a single strain, EnvH, which was isolated from asphalt in Haifa, Israel. The pairwise ANI values between this species and the two closest relatives, GCF_018842675.1 and GCF_014946725.1, are below 80% confirming that this species is distinct from those with which it shares a most recent common ancestor.

This species currently consists of the genome of a single strain, EnvD, which was isolated from asphalt in Jerusalem, Israel. The most closely related species, named Pantoea mediterraneensis_A in GTDB (GCF_014946725.1) share an ANI value with EnvD below species delineation guidelines, revealing that the two genomes represent two distinct species.

The genome of a single strain, DSM 32899 was isolated from soil in Singapore. It splits off at a node that is basal to the P. eucrina/P. borealis group. The ANI between the genome of DSM 32899 and the P. eucrina/P. borealis genomes is below 85%, indicating that this represents a distinct species.