Unveiling <i>Acinetobacter endophylla</i> sp. nov.: A Specialist Endophyte from <i>Peganum harmala</i> with Distinct Genomic and Metabolic Traits

<i>Peganum harmala</i> (L.) Schrad., a perennial medicinal plant thriving in arid Moroccan soils, represents a natural reservoir of unexplored bacterial diversity. To uncover its hidden foliar endosphere microbiota, we isolated and characterized two <i>Acinetobacter</i> strains: a novel endophytic bacterium, AGC35, and another strain, AGC59, newly reported from this host. Both are non-halophilic, aerobic, Gram-negative bacteria exhibiting optimal growth at 30-35 °C, pH5, and with 1% NaCl. An integrative genomic, phylogenetic, functional, and phenotypic characterization classified both strains within the genus <i>Acinetobacter</i> (class Gamma-pseudomonadota). However, Average Nucleotide Identity (<96%) and digital DNA-DNA Hybridization (<70%) values distinguished the AGC35 strain as a novel species, for which the name <i>Acinetobacter endophylla</i> sp. nov. is proposed. A comparative genomic and phenotypic analysis with the co-isolated <i>Acinetobacter pittii</i> strain AGC59 revealed extensive genome rearrangements, reflecting distinct evolutionary lineage and ecological strategies. While both genomes share core metabolic pathways, <i>A. endophylla</i> harbors specialized genes for the degradation of plant-derived aromatic compounds (e.g., catechol) but shows reduced capacities in carbohydrate metabolism and osmotic stress tolerance, traits indicative of a metabolic specialist with plant-growth-promotion potential, including phosphorus, potassium, and silicon solubilization and indole-3-acetic acid production. In contrast, <i>A. pittii</i> exhibits a more generalist genome enriched in stress functions. Analysis using the Antibiotics and Secondary Metabolite Analysis Shell revealed multiple biosynthetic gene clusters in both strains, showing ≤26% similarity to known references, suggesting the potential for novel antimicrobial secondary metabolite biosynthesis, including antifungal lipopeptides and thiopeptide antibiotics. Altogether, functional specialization and ecological coherence of these findings support the recognition of <i>A. endophylla</i> sp. nov. as a genomically and functionally distinct species, highlighting niche partitioning and adaptive metabolism within the <i>P. harmala</i> holobiont. These results underscore the plant's value as a reservoir of untapped microbial diversity with significant ecological and biotechnological relevance. Finally, future work will focus on elucidating the novel metabolites encoded by the biosynthetic gene clusters in both isolates and exploring their applications in crop-improvement strategies and natural-product discovery.