Genome-based reclassification within Geomonas: Geomonas nitrogeniifigens Liu et al. 2022 as a heterotypic synonym of Geomonas diazotrophica Xu et al. 2022 and Geomonas fuzhouensis Yang et al. 2023 as a later heterotypic synonym of Geomonas subterrane

The genus <i>Geomonas</i> comprises Gram-stain-negative, diazotrophic bacteria associated with soil and plant environments, whose taxonomic classification has not yet been thoroughly investigated. Although 16S rRNA gene-based phylogeny remains a useful preliminary tool, it often lacks the resolution needed for accurate species delineation. In this study, we conducted a comprehensive comparative genomic analysis encompassing all validly published <i>Geomonas</i> species, integrating whole-genome phylogenomics, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and other genome-based metrics to refine their classification. Phylogenetic trees constructed from 16S rRNA gene sequences and core genome alignments consistently demonstrated close genomic clustering between <i>Geomonas diazotrophica</i> Red69ᵀ and <i>Geomonas nitrogeniifigens</i> RF4ᵀ, as well as between <i>Geomonas fuzhouensis</i> RG17ᵀ and <i>Geomonas subterranea</i> RG2ᵀ. ANI and dDDH values for these strain pairs exceeded species delineation thresholds (>96% ANI and >70 % dDDH), strongly supporting their taxonomic unification. Despite minor phenotypic variations, genomic coherence suggests that <i>Geomonas nitrogeniifigens</i> Liu <i>et al.</i> 2022 should be reclassified as <i>Geomonas diazotrophica</i> Xu <i>et al.</i> 2022, and <i>Geomonas fuzhouensis</i> Yang <i>et al.</i> 2023 should be recognized as a later heterotypic synonym of <i>Geomonas subterranea</i> Liu <i>et al.</i> 2022. These findings underscore the necessity of integrating whole-genome analyses into microbial taxonomy to ensure species classifications reflect true genomic relationships.