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 subterranea Liu et al. 2022.

Abstract

The genus Geomonas 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 Geomonas 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 Geomonas diazotrophica Red69ᵀ and Geomonas nitrogeniifigens RF4ᵀ, as well as between Geomonas fuzhouensis RG17ᵀ and Geomonas subterranea 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 Geomonas nitrogeniifigens Liu et al. 2022 should be reclassified as Geomonas diazotrophica Xu et al. 2022, and Geomonas fuzhouensis Yang et al. 2023 should be recognized as a later heterotypic synonym of Geomonas subterranea Liu et al. 2022. These findings underscore the necessity of integrating whole-genome analyses into microbial taxonomy to ensure species classifications reflect true genomic relationships.