Genome-Resolved Delineation of Three Novel Endophytic <i>Achromobacter</i> Species from Desert Medicinal Plants

Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of <i>Achromobacter</i> sp. isolates recovered from root and foliar tissues of <i>Citrullus colocynthis</i> and <i>Peganum harmala</i>, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names <i>Achromobacter colocynthi</i> sp. nov., <i>Achromobacter maghribensis</i> sp. nov., and <i>Achromobacter semiaridum</i> sp. nov. Genome assemblies were highly complete (98.7-99.2%) with minimal contamination (<1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within <i>Achromobacter</i> sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of <i>Achromobacter</i> sp., establish <i>C. colocynthis</i> and <i>P. harmala</i> as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments.